diff --git a/dev/api/Bio.SeqIO.IgIO.html b/dev/api/Bio.SeqIO.IgIO.html index ade1b97c..e81a8e45 100644 --- a/dev/api/Bio.SeqIO.IgIO.html +++ b/dev/api/Bio.SeqIO.IgIO.html @@ -156,9 +156,9 @@ new line characters in the SeqRecord’s annotations dictionary under the key ‘comment’.

Examples

-
>>> with open("IntelliGenetics/TAT_mase_nuc.txt") as handle:
-...     for record in IgIterator(handle):
-...         print("%s length %i" % (record.id, len(record)))
+
>>> with open("IntelliGenetics/TAT_mase_nuc.txt") as stream:
+...     for record in IgIterator(stream):
+...         print(f"{record.id} length {len(record)}")
 ...
 A_U455 length 303
 B_HXB2R length 306
@@ -184,12 +184,12 @@
 

 

 parse(handle)

-
Start parsing the file, and return a SeqRecord generator.

+
To be removed.

 

 
 

-

-iterate(handle)

+

+__next__()

 
Iterate over the records in the IntelliGenetics file.

 

 
diff --git a/dev/api/Bio.SeqIO.html b/dev/api/Bio.SeqIO.html
index fd7d815a..a6605fb1 100644
--- a/dev/api/Bio.SeqIO.html
+++ b/dev/api/Bio.SeqIO.html
@@ -203,7 +203,7 @@ 
SubmodulesIgIterator
diff --git a/dev/genindex.html b/dev/genindex.html
index 4623a81a..b0c21c6c 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -1947,6 +1947,8 @@ 
_

         
  • (Bio.Nexus.StandardData.StandardData method)
 
    • 
         
  • (Bio.SeqIO.AbiIO.AbiIterator method)
+
    • 
+        
  • (Bio.SeqIO.IgIO.IgIterator method)
 
    • 
         
  • (Bio.SeqIO.Interfaces.SequenceIterator method)
 
    • 
@@ -8626,8 +8628,6 @@ 
    I
    
 
       
      
         
    • (Bio.SeqIO.FastaIO.FastaTwoLineIterator method)
-
      • 
-        
    • (Bio.SeqIO.IgIO.IgIterator method)
 
      • 
         
    • (Bio.SeqIO.NibIO.NibIterator method)
 
      • 
diff --git a/dev/objects.inv b/dev/objects.inv
index 0b9adb69..53d664c3 100644
Binary files a/dev/objects.inv and b/dev/objects.inv differ
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 95ffe940..102bea26 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"3D printing protein structures": [[15, "d-printing-protein-structures"]], "A blank altloc for a disordered atom": [[15, "a-blank-altloc-for-a-disordered-atom"]], "A bottom up example": [[8, "a-bottom-up-example"]], "A nice example": [[8, "a-nice-example"]], "A note about standards and conventions": [[20, "a-note-about-standards-and-conventions"]], "A top down example": [[8, "a-top-down-example"]], "A usage example": [[19, "a-usage-example"]], "A2M": [[0, "a2m"]], "API Contents:": [[306, null]], "API documentation": [[306, "api-documentation"]], "Absolute Pearson correlation": [[4, "absolute-pearson-correlation"]], "Absolute uncentered correlation": [[4, "absolute-uncentered-correlation"]], "Accessing NCBI\u2019s Entrez databases": [[7, "accessing-ncbis-entrez-databases"]], "Accessing dihedrals, angles and bond lengths": [[15, "accessing-dihedrals-angles-and-bond-lengths"]], "Accessing interpolated data": [[16, "accessing-interpolated-data"]], "Accessing raw data": [[16, "accessing-raw-data"]], "Accessing the ExPASy server": [[25, "accessing-the-expasy-server"]], "Accessing the JASPAR database": [[11, "accessing-the-jaspar-database"]], "Accessing the Protein Data Bank": [[15, "accessing-the-protein-data-bank"]], "Accessing the all-atom AtomArray": [[15, "accessing-the-all-atom-atomarray"]], "Adding SeqRecord objects": [[21, "adding-seqrecord-objects"]], "Adding alignments": [[0, "adding-alignments"]], "Affine gap scores": [[13, "affine-gap-scores"]], "Aim of this module": [[278, "aim-of-this-module"]], "Aligned FASTA": [[0, "aligned-fasta"]], "Aligning a nucleotide sequence to an amino acid sequence": [[13, "aligning-a-nucleotide-sequence-to-an-amino-acid-sequence"]], "Aligning to the reverse strand": [[13, "aligning-to-the-reverse-strand"]], "Alignment Tools": [[12, "alignment-tools"]], "Alignment file formats": [[0, "alignment-file-formats"]], "Alignment objects": [[0, "alignment-objects"]], "Alignment shape": [[0, "alignment-shape"]], "Alignments as arrays": [[0, "alignments-as-arrays"], [12, "alignments-as-arrays"]], "Ambiguous Alignments": [[12, "ambiguous-alignments"]], "Analyzing a codon alignment": [[13, "analyzing-a-codon-alignment"]], "Analyzing structures": [[15, "analyzing-structures"]], "Annotated Chromosomes": [[8, "annotated-chromosomes"]], "Appendix: Useful stuff about Python": [[1, "appendix-useful-stuff-about-python"]], "Array objects": [[13, "array-objects"]], "Arrow sigils": [[8, "arrow-sigils"]], "Associated problems": [[15, "associated-problems"]], "Atom": [[15, "atom"]], "Automatic correction": [[15, "automatic-correction"]], "BLAST (new)": [[3, "blast-new"]], "BLAST (old)": [[3, "blast-old"]], "BLAST and other sequence search tools": [[20, "blast-and-other-sequence-search-tools"]], "BLAST arguments": [[3, "blast-arguments"]], "Base class to hold a Feature": [[237, "base-class-to-hold-a-feature"]], "Basic usage": [[13, "basic-usage"]], "Bibliography": [[2, "bibliography"]], "Bio package": [[27, "bio-package"]], "Bio.Affy package": [[28, "bio-affy-package"]], "Bio.Affy.CelFile module": [[29, "module-Bio.Affy.CelFile"]], "Bio.Align package": [[30, "bio-align-package"]], "Bio.Align.AlignInfo module": [[31, "module-Bio.Align.AlignInfo"]], "Bio.Align.Applications package": [[32, "bio-align-applications-package"]], "Bio.Align.a2m module": [[33, "module-Bio.Align.a2m"]], "Bio.Align.analysis module": [[34, "module-Bio.Align.analysis"]], "Bio.Align.bed module": [[35, "module-Bio.Align.bed"]], "Bio.Align.bigbed module": [[36, "module-Bio.Align.bigbed"]], "Bio.Align.bigmaf module": [[37, "module-Bio.Align.bigmaf"]], "Bio.Align.bigpsl module": [[38, "module-Bio.Align.bigpsl"]], "Bio.Align.chain module": [[39, "module-Bio.Align.chain"]], "Bio.Align.clustal module": [[40, "module-Bio.Align.clustal"]], "Bio.Align.emboss module": [[41, "module-Bio.Align.emboss"]], "Bio.Align.exonerate module": [[42, "module-Bio.Align.exonerate"]], "Bio.Align.fasta module": [[43, "module-Bio.Align.fasta"]], "Bio.Align.hhr module": [[44, "module-Bio.Align.hhr"]], "Bio.Align.interfaces module": [[45, "module-Bio.Align.interfaces"]], "Bio.Align.maf module": [[46, "module-Bio.Align.maf"]], "Bio.Align.mauve module": [[47, "module-Bio.Align.mauve"]], "Bio.Align.msf module": [[48, "module-Bio.Align.msf"]], "Bio.Align.nexus module": [[49, "module-Bio.Align.nexus"]], "Bio.Align.phylip module": [[50, "module-Bio.Align.phylip"]], "Bio.Align.psl module": [[51, "module-Bio.Align.psl"]], "Bio.Align.sam module": [[52, "module-Bio.Align.sam"]], "Bio.Align.stockholm module": [[53, "module-Bio.Align.stockholm"]], "Bio.Align.substitution_matrices package": [[54, "bio-align-substitution-matrices-package"]], "Bio.Align.tabular module": [[55, "module-Bio.Align.tabular"]], "Bio.AlignIO package": [[56, "bio-alignio-package"]], "Bio.AlignIO.ClustalIO module": [[57, "module-Bio.AlignIO.ClustalIO"]], "Bio.AlignIO.EmbossIO module": [[58, "module-Bio.AlignIO.EmbossIO"]], "Bio.AlignIO.FastaIO module": [[59, "module-Bio.AlignIO.FastaIO"]], "Bio.AlignIO.Interfaces module": [[60, "module-Bio.AlignIO.Interfaces"]], "Bio.AlignIO.MafIO module": [[61, "module-Bio.AlignIO.MafIO"]], "Bio.AlignIO.MauveIO module": [[62, "module-Bio.AlignIO.MauveIO"]], "Bio.AlignIO.MsfIO module": [[63, "module-Bio.AlignIO.MsfIO"]], "Bio.AlignIO.NexusIO module": [[64, "module-Bio.AlignIO.NexusIO"]], "Bio.AlignIO.PhylipIO module": [[65, "module-Bio.AlignIO.PhylipIO"]], "Bio.AlignIO.StockholmIO module": [[66, "module-Bio.AlignIO.StockholmIO"]], "Bio.Application package": [[67, "bio-application-package"]], "Bio.Blast package": [[68, "bio-blast-package"]], "Bio.Blast.Applications module": [[69, "module-Bio.Blast.Applications"]], "Bio.Blast.NCBIWWW module": [[70, "module-Bio.Blast.NCBIWWW"]], "Bio.Blast.NCBIXML module": [[71, "module-Bio.Blast.NCBIXML"]], "Bio.CAPS package": [[72, "bio-caps-package"]], "Bio.Cluster package": [[73, "bio-cluster-package"]], "Bio.Compass package": [[74, "bio-compass-package"]], "Bio.Data package": [[75, "bio-data-package"]], "Bio.Data.CodonTable module": [[76, "module-Bio.Data.CodonTable"]], "Bio.Data.IUPACData module": [[77, "module-Bio.Data.IUPACData"]], "Bio.Data.PDBData module": [[78, "module-Bio.Data.PDBData"]], "Bio.Emboss package": [[79, "bio-emboss-package"]], "Bio.Emboss.Applications module": [[80, "module-Bio.Emboss.Applications"]], "Bio.Emboss.Primer3 module": [[81, "module-Bio.Emboss.Primer3"]], "Bio.Emboss.PrimerSearch module": [[82, "module-Bio.Emboss.PrimerSearch"]], "Bio.Entrez package": [[83, "bio-entrez-package"]], "Bio.Entrez.Parser module": [[84, "module-Bio.Entrez.Parser"]], "Bio.ExPASy package": [[85, "bio-expasy-package"]], "Bio.ExPASy.Enzyme module": [[86, "module-Bio.ExPASy.Enzyme"]], "Bio.ExPASy.Prodoc module": [[87, "module-Bio.ExPASy.Prodoc"]], "Bio.ExPASy.Prosite module": [[88, "module-Bio.ExPASy.Prosite"]], "Bio.ExPASy.ScanProsite module": [[89, "module-Bio.ExPASy.ScanProsite"]], "Bio.ExPASy.cellosaurus module": [[90, "module-Bio.ExPASy.cellosaurus"]], "Bio.File module": [[91, "module-Bio.File"]], "Bio.GenBank package": [[92, "bio-genbank-package"]], "Bio.GenBank.Record module": [[93, "module-Bio.GenBank.Record"]], "Bio.GenBank.Scanner module": [[94, "module-Bio.GenBank.Scanner"]], "Bio.GenBank.utils module": [[95, "module-Bio.GenBank.utils"]], "Bio.Geo package": [[96, "bio-geo-package"]], "Bio.Geo.Record module": [[97, "module-Bio.Geo.Record"]], "Bio.Graphics package": [[98, "bio-graphics-package"]], "Bio.Graphics.BasicChromosome module": [[99, "module-Bio.Graphics.BasicChromosome"]], "Bio.Graphics.ColorSpiral module": [[100, "module-Bio.Graphics.ColorSpiral"]], "Bio.Graphics.Comparative module": [[101, "module-Bio.Graphics.Comparative"]], "Bio.Graphics.DisplayRepresentation module": [[102, "module-Bio.Graphics.DisplayRepresentation"]], "Bio.Graphics.Distribution module": [[103, "module-Bio.Graphics.Distribution"]], "Bio.Graphics.GenomeDiagram package": [[104, "bio-graphics-genomediagram-package"]], "Bio.Graphics.KGML_vis module": [[105, "module-Bio.Graphics.KGML_vis"]], "Bio.HMM package": [[106, "bio-hmm-package"]], "Bio.HMM.DynamicProgramming module": [[107, "module-Bio.HMM.DynamicProgramming"]], "Bio.HMM.MarkovModel module": [[108, "module-Bio.HMM.MarkovModel"]], "Bio.HMM.Trainer module": [[109, "module-Bio.HMM.Trainer"]], "Bio.HMM.Utilities module": [[110, "module-Bio.HMM.Utilities"]], "Bio.KEGG package": [[111, "bio-kegg-package"]], "Bio.KEGG.Compound package": [[112, "bio-kegg-compound-package"]], "Bio.KEGG.Enzyme package": [[113, "bio-kegg-enzyme-package"]], "Bio.KEGG.Gene package": [[114, "bio-kegg-gene-package"]], "Bio.KEGG.KGML package": [[115, "bio-kegg-kgml-package"]], "Bio.KEGG.KGML.KGML_parser module": [[116, "module-Bio.KEGG.KGML.KGML_parser"]], "Bio.KEGG.KGML.KGML_pathway module": [[117, "module-Bio.KEGG.KGML.KGML_pathway"]], "Bio.KEGG.Map package": [[118, "bio-kegg-map-package"]], "Bio.KEGG.REST module": [[119, "module-Bio.KEGG.REST"]], "Bio.LogisticRegression module": [[120, "module-Bio.LogisticRegression"]], "Bio.MarkovModel module": [[121, "module-Bio.MarkovModel"]], "Bio.MaxEntropy module": [[122, "module-Bio.MaxEntropy"]], "Bio.Medline package": [[123, "bio-medline-package"]], "Bio.NMR package": [[124, "bio-nmr-package"]], "Bio.NMR.NOEtools module": [[125, "module-Bio.NMR.NOEtools"]], "Bio.NMR.xpktools module": [[126, "module-Bio.NMR.xpktools"]], "Bio.NaiveBayes module": [[127, "module-Bio.NaiveBayes"]], "Bio.Nexus package": [[128, "bio-nexus-package"]], "Bio.Nexus.Nexus module": [[129, "module-Bio.Nexus.Nexus"]], "Bio.Nexus.Nodes module": [[130, "module-Bio.Nexus.Nodes"]], "Bio.Nexus.StandardData module": [[131, "module-Bio.Nexus.StandardData"]], "Bio.Nexus.Trees module": [[132, "module-Bio.Nexus.Trees"]], "Bio.PDB package": [[133, "bio-pdb-package"]], "Bio.PDB.AbstractPropertyMap module": [[134, "module-Bio.PDB.AbstractPropertyMap"]], "Bio.PDB.Atom module": [[135, "module-Bio.PDB.Atom"]], "Bio.PDB.Chain module": [[136, "module-Bio.PDB.Chain"]], "Bio.PDB.DSSP module": [[137, "module-Bio.PDB.DSSP"]], "Bio.PDB.Dice module": [[138, "module-Bio.PDB.Dice"]], "Bio.PDB.Entity module": [[139, "module-Bio.PDB.Entity"]], "Bio.PDB.FragmentMapper module": [[140, "module-Bio.PDB.FragmentMapper"]], "Bio.PDB.HSExposure module": [[141, "module-Bio.PDB.HSExposure"]], "Bio.PDB.MMCIF2Dict module": [[142, "module-Bio.PDB.MMCIF2Dict"]], "Bio.PDB.MMCIFParser module": [[143, "module-Bio.PDB.MMCIFParser"]], "Bio.PDB.Model module": [[144, "module-Bio.PDB.Model"]], "Bio.PDB.NACCESS module": [[145, "module-Bio.PDB.NACCESS"]], "Bio.PDB.NeighborSearch module": [[146, "module-Bio.PDB.NeighborSearch"]], "Bio.PDB.PDBExceptions module": [[147, "module-Bio.PDB.PDBExceptions"]], "Bio.PDB.PDBIO module": [[148, "module-Bio.PDB.PDBIO"]], "Bio.PDB.PDBList module": [[149, "module-Bio.PDB.PDBList"]], "Bio.PDB.PDBMLParser module": [[150, "module-Bio.PDB.PDBMLParser"]], "Bio.PDB.PDBParser module": [[151, "module-Bio.PDB.PDBParser"]], "Bio.PDB.PICIO module": [[152, "module-Bio.PDB.PICIO"]], "Bio.PDB.PSEA module": [[153, "module-Bio.PDB.PSEA"]], "Bio.PDB.Polypeptide module": [[154, "module-Bio.PDB.Polypeptide"]], "Bio.PDB.Residue module": [[155, "module-Bio.PDB.Residue"]], "Bio.PDB.ResidueDepth module": [[156, "module-Bio.PDB.ResidueDepth"]], "Bio.PDB.SASA module": [[157, "module-Bio.PDB.SASA"]], "Bio.PDB.SCADIO module": [[158, "module-Bio.PDB.SCADIO"]], "Bio.PDB.Selection module": [[159, "module-Bio.PDB.Selection"]], "Bio.PDB.Structure module": [[160, "module-Bio.PDB.Structure"]], "Bio.PDB.StructureAlignment module": [[161, "module-Bio.PDB.StructureAlignment"]], "Bio.PDB.StructureBuilder module": [[162, "module-Bio.PDB.StructureBuilder"]], "Bio.PDB.Superimposer module": [[163, "module-Bio.PDB.Superimposer"]], "Bio.PDB.alphafold_db module": [[164, "module-Bio.PDB.alphafold_db"]], "Bio.PDB.binary_cif module": [[165, "module-Bio.PDB.binary_cif"]], "Bio.PDB.cealign module": [[166, "module-Bio.PDB.cealign"]], "Bio.PDB.ic_data module": [[167, "module-Bio.PDB.ic_data"]], "Bio.PDB.ic_rebuild module": [[168, "module-Bio.PDB.ic_rebuild"]], "Bio.PDB.internal_coords module": [[169, "module-Bio.PDB.internal_coords"]], "Bio.PDB.mmcifio module": [[170, "module-Bio.PDB.mmcifio"]], "Bio.PDB.mmtf package": [[171, "bio-pdb-mmtf-package"]], "Bio.PDB.mmtf.DefaultParser module": [[172, "module-Bio.PDB.mmtf.DefaultParser"]], "Bio.PDB.mmtf.mmtfio module": [[173, "module-Bio.PDB.mmtf.mmtfio"]], "Bio.PDB.parse_pdb_header module": [[174, "module-Bio.PDB.parse_pdb_header"]], "Bio.PDB.qcprot module": [[175, "module-Bio.PDB.qcprot"]], "Bio.PDB.vectors module": [[176, "module-Bio.PDB.vectors"]], "Bio.Pathway package": [[177, "bio-pathway-package"]], "Bio.Pathway.Rep package": [[178, "bio-pathway-rep-package"]], "Bio.Pathway.Rep.Graph module": [[179, "module-Bio.Pathway.Rep.Graph"]], "Bio.Pathway.Rep.MultiGraph module": [[180, "module-Bio.Pathway.Rep.MultiGraph"]], "Bio.Phylo package": [[181, "bio-phylo-package"]], "Bio.Phylo.Applications package": [[182, "bio-phylo-applications-package"]], "Bio.Phylo.BaseTree module": [[183, "module-Bio.Phylo.BaseTree"]], "Bio.Phylo.CDAO module": [[184, "module-Bio.Phylo.CDAO"]], "Bio.Phylo.CDAOIO module": [[185, "module-Bio.Phylo.CDAOIO"]], "Bio.Phylo.Consensus module": [[186, "module-Bio.Phylo.Consensus"]], "Bio.Phylo.NeXML module": [[187, "module-Bio.Phylo.NeXML"]], "Bio.Phylo.NeXMLIO module": [[188, "module-Bio.Phylo.NeXMLIO"]], "Bio.Phylo.Newick module": [[189, "module-Bio.Phylo.Newick"]], "Bio.Phylo.NewickIO module": [[190, "module-Bio.Phylo.NewickIO"]], "Bio.Phylo.NexusIO module": [[191, "module-Bio.Phylo.NexusIO"]], "Bio.Phylo.PAML package": [[192, "bio-phylo-paml-package"]], "Bio.Phylo.PAML.baseml module": [[193, "module-Bio.Phylo.PAML.baseml"]], "Bio.Phylo.PAML.chi2 module": [[194, "module-Bio.Phylo.PAML.chi2"]], "Bio.Phylo.PAML.codeml module": [[195, "module-Bio.Phylo.PAML.codeml"]], "Bio.Phylo.PAML.yn00 module": [[196, "module-Bio.Phylo.PAML.yn00"]], "Bio.Phylo.PhyloXML module": [[197, "module-Bio.Phylo.PhyloXML"]], "Bio.Phylo.PhyloXMLIO module": [[198, "module-Bio.Phylo.PhyloXMLIO"]], "Bio.Phylo.TreeConstruction module": [[199, "module-Bio.Phylo.TreeConstruction"]], "Bio.PopGen package": [[200, "bio-popgen-package"]], "Bio.PopGen.GenePop package": [[201, "bio-popgen-genepop-package"]], "Bio.PopGen.GenePop.Controller module": [[202, "module-Bio.PopGen.GenePop.Controller"]], "Bio.PopGen.GenePop.EasyController module": [[203, "module-Bio.PopGen.GenePop.EasyController"]], "Bio.PopGen.GenePop.FileParser module": [[204, "module-Bio.PopGen.GenePop.FileParser"]], "Bio.PopGen.GenePop.LargeFileParser module": [[205, "module-Bio.PopGen.GenePop.LargeFileParser"]], "Bio.PopGen: Population genetics": [[18, "bio-popgen-population-genetics"]], "Bio.Restriction package": [[206, "bio-restriction-package"]], "Bio.Restriction.PrintFormat module": [[207, "module-Bio.Restriction.PrintFormat"]], "Bio.Restriction.Restriction_Dictionary module": [[208, "module-Bio.Restriction.Restriction_Dictionary"]], "Bio.SCOP package": [[209, "bio-scop-package"]], "Bio.SCOP.Cla module": [[210, "module-Bio.SCOP.Cla"]], "Bio.SCOP.Des module": [[211, "module-Bio.SCOP.Des"]], "Bio.SCOP.Dom module": [[212, "module-Bio.SCOP.Dom"]], "Bio.SCOP.Hie module": [[213, "module-Bio.SCOP.Hie"]], "Bio.SCOP.Raf module": [[214, "module-Bio.SCOP.Raf"]], "Bio.SCOP.Residues module": [[215, "module-Bio.SCOP.Residues"]], "Bio.SVDSuperimposer package": [[216, "bio-svdsuperimposer-package"]], "Bio.SearchIO package": [[217, "bio-searchio-package"]], "Bio.SearchIO.BlastIO package": [[218, "bio-searchio-blastio-package"]], "Bio.SearchIO.BlastIO.blast_tab module": [[219, "module-Bio.SearchIO.BlastIO.blast_tab"]], "Bio.SearchIO.BlastIO.blast_xml module": [[220, "module-Bio.SearchIO.BlastIO.blast_xml"]], "Bio.SearchIO.BlatIO module": [[221, "module-Bio.SearchIO.BlatIO"]], "Bio.SearchIO.ExonerateIO package": [[222, "bio-searchio-exonerateio-package"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar module": [[223, "module-Bio.SearchIO.ExonerateIO.exonerate_cigar"]], "Bio.SearchIO.ExonerateIO.exonerate_text module": [[224, "module-Bio.SearchIO.ExonerateIO.exonerate_text"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar module": [[225, "module-Bio.SearchIO.ExonerateIO.exonerate_vulgar"]], "Bio.SearchIO.FastaIO module": [[226, "module-Bio.SearchIO.FastaIO"]], "Bio.SearchIO.HHsuiteIO package": [[227, "bio-searchio-hhsuiteio-package"]], "Bio.SearchIO.HHsuiteIO.hhsuite2_text module": [[228, "module-Bio.SearchIO.HHsuiteIO.hhsuite2_text"]], "Bio.SearchIO.HmmerIO package": [[229, "bio-searchio-hmmerio-package"]], "Bio.SearchIO.HmmerIO.hmmer2_text module": [[230, "module-Bio.SearchIO.HmmerIO.hmmer2_text"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab module": [[231, "module-Bio.SearchIO.HmmerIO.hmmer3_domtab"]], "Bio.SearchIO.HmmerIO.hmmer3_tab module": [[232, "module-Bio.SearchIO.HmmerIO.hmmer3_tab"]], "Bio.SearchIO.HmmerIO.hmmer3_text module": [[233, "module-Bio.SearchIO.HmmerIO.hmmer3_text"]], "Bio.SearchIO.InterproscanIO package": [[234, "bio-searchio-interproscanio-package"]], "Bio.SearchIO.InterproscanIO.interproscan_xml module": [[235, "module-Bio.SearchIO.InterproscanIO.interproscan_xml"]], "Bio.Seq module": [[236, "module-Bio.Seq"]], "Bio.SeqFeature module": [[237, "module-Bio.SeqFeature"]], "Bio.SeqIO package": [[238, "bio-seqio-package"]], "Bio.SeqIO.AbiIO module": [[239, "module-Bio.SeqIO.AbiIO"]], "Bio.SeqIO.AceIO module": [[240, "module-Bio.SeqIO.AceIO"]], "Bio.SeqIO.FastaIO module": [[241, "module-Bio.SeqIO.FastaIO"]], "Bio.SeqIO.GckIO module": [[242, "module-Bio.SeqIO.GckIO"]], "Bio.SeqIO.GfaIO module": [[243, "module-Bio.SeqIO.GfaIO"]], "Bio.SeqIO.IgIO module": [[244, "module-Bio.SeqIO.IgIO"]], "Bio.SeqIO.InsdcIO module": [[245, "module-Bio.SeqIO.InsdcIO"]], "Bio.SeqIO.Interfaces module": [[246, "module-Bio.SeqIO.Interfaces"]], "Bio.SeqIO.NibIO module": [[247, "module-Bio.SeqIO.NibIO"]], "Bio.SeqIO.PdbIO module": [[248, "module-Bio.SeqIO.PdbIO"]], "Bio.SeqIO.PhdIO module": [[249, "module-Bio.SeqIO.PhdIO"]], "Bio.SeqIO.PirIO module": [[250, "module-Bio.SeqIO.PirIO"]], "Bio.SeqIO.QualityIO module": [[251, "module-Bio.SeqIO.QualityIO"]], "Bio.SeqIO.SeqXmlIO module": [[252, "module-Bio.SeqIO.SeqXmlIO"]], "Bio.SeqIO.SffIO module": [[253, "module-Bio.SeqIO.SffIO"]], "Bio.SeqIO.SnapGeneIO module": [[254, "module-Bio.SeqIO.SnapGeneIO"]], "Bio.SeqIO.SwissIO module": [[255, "module-Bio.SeqIO.SwissIO"]], "Bio.SeqIO.TabIO module": [[256, "module-Bio.SeqIO.TabIO"]], "Bio.SeqIO.TwoBitIO module": [[257, "module-Bio.SeqIO.TwoBitIO"]], "Bio.SeqIO.UniprotIO module": [[258, "module-Bio.SeqIO.UniprotIO"]], "Bio.SeqIO.XdnaIO module": [[259, "module-Bio.SeqIO.XdnaIO"]], "Bio.SeqRecord module": [[260, "module-Bio.SeqRecord"]], "Bio.SeqUtils package": [[261, "bio-sequtils-package"]], "Bio.SeqUtils.CheckSum module": [[262, "module-Bio.SeqUtils.CheckSum"]], "Bio.SeqUtils.IsoelectricPoint module": [[263, "module-Bio.SeqUtils.IsoelectricPoint"]], "Bio.SeqUtils.MeltingTemp module": [[264, "module-Bio.SeqUtils.MeltingTemp"]], "Bio.SeqUtils.ProtParam module": [[265, "module-Bio.SeqUtils.ProtParam"]], "Bio.SeqUtils.ProtParamData module": [[266, "module-Bio.SeqUtils.ProtParamData"]], "Bio.SeqUtils.lcc module": [[267, "module-Bio.SeqUtils.lcc"]], "Bio.Sequencing package": [[268, "bio-sequencing-package"]], "Bio.Sequencing.Ace module": [[269, "module-Bio.Sequencing.Ace"]], "Bio.Sequencing.Applications package": [[270, "bio-sequencing-applications-package"]], "Bio.Sequencing.Phd module": [[271, "module-Bio.Sequencing.Phd"]], "Bio.SwissProt package": [[272, "bio-swissprot-package"]], "Bio.SwissProt.KeyWList module": [[273, "module-Bio.SwissProt.KeyWList"]], "Bio.TogoWS package": [[274, "bio-togows-package"]], "Bio.UniGene package": [[275, "bio-unigene-package"]], "Bio.UniProt package": [[276, "bio-uniprot-package"]], "Bio.UniProt.GOA module": [[277, "module-Bio.UniProt.GOA"]], "Bio.bgzf module": [[278, "module-Bio.bgzf"]], "Bio.codonalign package": [[279, "bio-codonalign-package"]], "Bio.codonalign.codonalignment module": [[280, "module-Bio.codonalign.codonalignment"]], "Bio.codonalign.codonseq module": [[281, "module-Bio.codonalign.codonseq"]], "Bio.kNN module": [[282, "module-Bio.kNN"]], "Bio.motifs package": [[283, "bio-motifs-package"]], "Bio.motifs.alignace module": [[284, "module-Bio.motifs.alignace"]], "Bio.motifs.applications package": [[285, "bio-motifs-applications-package"]], "Bio.motifs.clusterbuster module": [[286, "module-Bio.motifs.clusterbuster"]], "Bio.motifs.jaspar package": [[287, "bio-motifs-jaspar-package"]], "Bio.motifs.jaspar.db module": [[288, "module-Bio.motifs.jaspar.db"]], "Bio.motifs.mast module": [[289, "module-Bio.motifs.mast"]], "Bio.motifs.matrix module": [[290, "module-Bio.motifs.matrix"]], "Bio.motifs.meme module": [[291, "module-Bio.motifs.meme"]], "Bio.motifs.minimal module": [[292, "module-Bio.motifs.minimal"]], "Bio.motifs.pfm module": [[293, "module-Bio.motifs.pfm"]], "Bio.motifs.thresholds module": [[294, "module-Bio.motifs.thresholds"]], "Bio.motifs.transfac module": [[295, "module-Bio.motifs.transfac"]], "Bio.motifs.xms module": [[296, "module-Bio.motifs.xms"]], "Bio.pairwise2 module": [[297, "module-Bio.pairwise2"]], "Bio.phenotype package": [[298, "bio-phenotype-package"]], "Bio.phenotype.phen_micro module": [[299, "module-Bio.phenotype.phen_micro"]], "Bio.phenotype.pm_fitting module": [[300, "module-Bio.phenotype.pm_fitting"]], "Bio.phenotype: analyze phenotypic data": [[16, "bio-phenotype-analyze-phenotypic-data"]], "BioSQL package": [[301, "biosql-package"]], "BioSQL \u2013 storing sequences in a relational database": [[6, "biosql-storing-sequences-in-a-relational-database"]], "BioSQL.BioSeq module": [[302, "module-BioSQL.BioSeq"]], "BioSQL.BioSeqDatabase module": [[303, "module-BioSQL.BioSeqDatabase"]], "BioSQL.DBUtils module": [[304, "module-BioSQL.DBUtils"]], "BioSQL.Loader module": [[305, "module-BioSQL.Loader"]], "Biopython Documentation": [[307, "biopython-documentation"]], "Biopython Tutorial & Cookbook": [[26, "biopython-tutorial-cookbook"]], "Broken chains": [[15, "broken-chains"]], "Browser Extensible Data (BED)": [[0, "browser-extensible-data-bed"]], "Bug Reports + Feature Requests": [[5, "bug-reports-feature-requests"]], "Building a structure from a distance plot": [[15, "building-a-structure-from-a-distance-plot"]], "Calculating a Self-Organizing Map": [[4, "calculating-a-self-organizing-map"]], "Calculating a quick consensus sequence": [[12, "calculating-a-quick-consensus-sequence"]], "Calculating a substitution matrix from a multiple sequence alignment": [[12, "calculating-a-substitution-matrix-from-a-multiple-sequence-alignment"], [13, "calculating-a-substitution-matrix-from-a-multiple-sequence-alignment"]], "Calculating a substitution matrix from a pairwise sequence alignment": [[13, "calculating-a-substitution-matrix-from-a-pairwise-sequence-alignment"]], "Calculating cluster properties": [[4, "calculating-cluster-properties"]], "Calculating summary information": [[12, "calculating-summary-information"]], "Calculating the Half Sphere Exposure": [[15, "calculating-the-half-sphere-exposure"]], "Calculating the cluster centroids": [[4, "calculating-the-cluster-centroids"], [4, "id13"]], "Calculating the distance between clusters": [[4, "calculating-the-distance-between-clusters"], [4, "calculating-the-distance-between-clusters-1"]], "Calculating the distance matrix": [[4, "calculating-the-distance-matrix"], [4, "id12"]], "Calculating the number of nonsynonymous and synonymous substitutions per site": [[13, "calculating-the-number-of-nonsynonymous-and-synonymous-substitutions-per-site"]], "Calculating the residue depth": [[15, "calculating-the-residue-depth"]], "Chain": [[15, "chain"]], "Changing case": [[22, "changing-case"]], "Chromosomes": [[8, "chromosomes"]], "City-block distance": [[4, "city-block-distance"]], "ClustalW": [[0, "clustalw"], [12, "clustalw"]], "Cluster analysis": [[4, "cluster-analysis"]], "Codon alignments": [[13, "codon-alignments"]], "Coloring branches within a tree": [[17, "coloring-branches-within-a-tree"]], "Common alignment attributes": [[0, "common-alignment-attributes"]], "Common case": [[15, "common-case"]], "Common problems in PDB files": [[15, "common-problems-in-pdb-files"]], "Comparing Seq objects": [[22, "comparing-seq-objects"]], "Comparing alignments": [[0, "comparing-alignments"]], "Comparing motifs": [[11, "comparing-motifs"]], "Comparison": [[21, "comparison"]], "Compatibility with Perl TFBS modules": [[11, "compatibility-with-perl-tfbs-modules"]], "CompoundLocation object": [[21, "compoundlocation-object"]], "Concatenating or adding sequences": [[22, "concatenating-or-adding-sequences"]], "Connecting with biological databases": [[19, "connecting-with-biological-databases"]], "Contributing Code": [[5, "contributing-code"]], "Contributing Documentation": [[5, "contributing-documentation"]], "Contributing Unit Tests": [[5, "contributing-unit-tests"]], "Contributing cookbook examples": [[5, "contributing-cookbook-examples"]], "Control attributes in Bio.PDB.internal_coords.": [[15, "table-ic-attribs"]], "Control well subtraction": [[16, "control-well-subtraction"]], "Conventions": [[217, "conventions"]], "Conversion": [[56, "conversion"], [217, "conversion"], [238, "conversion"]], "Converting FASTA and QUAL files into FASTQ files": [[6, "converting-fasta-and-qual-files-into-fastq-files"]], "Converting FASTQ files": [[6, "converting-fastq-files"]], "Converting SFF files": [[6, "converting-sff-files"]], "Converting a file of sequences to their reverse complements": [[23, "converting-a-file-of-sequences-to-their-reverse-complements"]], "Converting between sequence alignment file formats": [[12, "converting-between-sequence-alignment-file-formats"]], "Converting between sequence file formats": [[23, "converting-between-sequence-file-formats"]], "Converting old code": [[8, "converting-old-code"]], "Cookbook \u2013 Cool things to do with it": [[6, "cookbook-cool-things-to-do-with-it"]], "Counting identities, mismatches, and gaps": [[0, "counting-identities-mismatches-and-gaps"]], "Counting substitutions": [[12, "counting-substitutions"]], "Creating a SeqRecord": [[21, "creating-a-seqrecord"]], "Creating a handle from a string": [[1, "creating-a-handle-from-a-string"]], "Creating a motif from instances": [[11, "creating-a-motif-from-instances"]], "Creating a sequence logo": [[11, "creating-a-sequence-logo"]], "Creating an Alignment object from aligned sequences": [[0, "creating-an-alignment-object-from-aligned-sequences"]], "Creating an Alignment object from sequences and coordinates": [[0, "creating-an-alignment-object-from-sequences-and-coordinates"]], "Cross-Links between tracks": [[8, "cross-links-between-tracks"]], "DSSP codes in Bio.PDB.": [[15, "table-dssp-codes"]], "Data representation": [[4, "data-representation"]], "De novo motif finding": [[11, "de-novo-motif-finding"]], "Dealing with PSI-BLAST": [[3, "dealing-with-psi-blast"], [3, "dealing-with-psi-blast-1"]], "Dealing with RPS-BLAST": [[3, "dealing-with-rps-blast"], [3, "dealing-with-rps-blast-1"]], "Dealing with large search output files with indexing": [[20, "dealing-with-large-search-output-files-with-indexing"]], "Demo: What\u2019s in a Tree?": [[17, "demo-whats-in-a-tree"]], "Determining atom-atom contacts": [[15, "determining-atom-atom-contacts"]], "Determining the secondary structure": [[15, "determining-the-secondary-structure"]], "Diagrams, tracks, feature-sets and features": [[8, "diagrams-tracks-feature-sets-and-features"]], "Discussion": [[23, "discussion"]], "Disorder": [[15, "disorder"]], "Disordered atoms": [[15, "disordered-atoms"]], "Disordered residues": [[15, "disordered-residues"]], "Distance Plots": [[15, "distance-plots"]], "Distance functions": [[4, "distance-functions"]], "Downloading structures from the Protein Data Bank": [[15, "downloading-structures-from-the-protein-data-bank"]], "Downloading the entire PDB": [[15, "downloading-the-entire-pdb"]], "Duplicate atoms": [[15, "duplicate-atoms"], [15, "duplicate-atoms-1"]], "Duplicate residues": [[15, "duplicate-residues"], [15, "duplicate-residues-1"]], "EFetch: Downloading full records from Entrez": [[7, "efetch-downloading-full-records-from-entrez"]], "EGQuery: Global Query - counts for search terms": [[7, "egquery-global-query-counts-for-search-terms"]], "EInfo: Obtaining information about the Entrez databases": [[7, "einfo-obtaining-information-about-the-entrez-databases"]], "ELink: Searching for related items in NCBI Entrez": [[7, "elink-searching-for-related-items-in-ncbi-entrez"]], "EMBOSS": [[0, "emboss"]], "EMBOSS needle and water": [[12, "emboss-needle-and-water"]], "EPost: Uploading a list of identifiers": [[7, "epost-uploading-a-list-of-identifiers"]], "ESearch: Searching the Entrez databases": [[7, "esearch-searching-the-entrez-databases"]], "ESpell: Obtaining spelling suggestions": [[7, "espell-obtaining-spelling-suggestions"]], "ESummary: Retrieving summaries from primary IDs": [[7, "esummary-retrieving-summaries-from-primary-ids"]], "Each motif object has an associated Position-Specific Scoring Matrix": [[11, "each-motif-object-has-an-associated-position-specific-scoring-matrix"]], "Entrez Guidelines": [[7, "entrez-guidelines"]], "Euclidean distance": [[4, "euclidean-distance"]], "Example calculation": [[4, "example-calculation"]], "Examples": [[7, "examples"], [13, "examples"], [15, "examples"], [90, "examples"], [137, "examples"], [206, "examples"], [265, "examples"], [278, "examples"]], "Exonerate": [[0, "exonerate"]], "Extract hetero residue from chain (e.g. glucose (GLC) moiety with resseq 10)": [[15, "extract-hetero-residue-from-chain-e-g-glucose-glc-moiety-with-resseq-10"]], "Extracting a specific Atom/Residue/Chain/Model from a Structure": [[15, "extracting-a-specific-atom-residue-chain-model-from-a-structure"]], "Extracting data": [[23, "extracting-data"]], "Extracting polypeptides from a Structure object": [[15, "extracting-polypeptides-from-a-structure-object"]], "Fatal errors": [[15, "fatal-errors"]], "Feature captions": [[8, "feature-captions"]], "Feature sigils": [[8, "feature-sigils"]], "Feature, location and position objects": [[21, "feature-location-and-position-objects"]], "Features of PhyloXML trees": [[17, "features-of-phyloxml-trees"]], "Features without a SeqFeature": [[8, "features-without-a-seqfeature"]], "Fields commonly found in TRANSFAC files": [[11, "table-transfaccodes"]], "Fields used to store references in TRANSFAC files": [[11, "id8"]], "File Formats": [[56, "file-formats"], [238, "file-formats"], [298, "file-formats"]], "Filtering a sequence file": [[6, "filtering-a-sequence-file"]], "Finding subsequences": [[22, "finding-subsequences"]], "Finding the indices of aligned sequences": [[0, "finding-the-indices-of-aligned-sequences"]], "Finding the lineage of an organism": [[7, "finding-the-lineage-of-an-organism"]], "Frames and strand values": [[217, "frames-and-strand-values"]], "Frequently Asked Questions (FAQ)": [[9, "frequently-asked-questions-faq"]], "Further options": [[8, "further-options"]], "Future plans": [[17, "future-plans"]], "Fuzzy Positions": [[21, "fuzzy-positions"]], "GCG Multiple Sequence Format (MSF)": [[0, "gcg-multiple-sequence-format-msf"]], "GenePop": [[18, "genepop"]], "General approach": [[15, "general-approach"]], "General gap scores": [[13, "general-gap-scores"]], "General overview of what Biopython provides": [[19, "general-overview-of-what-biopython-provides"]], "General questions": [[15, "general-questions"]], "Generalized pairwise alignments": [[13, "generalized-pairwise-alignments"]], "Generalized pairwise alignments using a substitution matrix and alphabet": [[13, "generalized-pairwise-alignments-using-a-substitution-matrix-and-alphabet"]], "Generalized pairwise alignments using a substitution matrix and integer sequences": [[13, "generalized-pairwise-alignments-using-a-substitution-matrix-and-integer-sequences"]], "Generalized pairwise alignments using match/mismatch scores and an alphabet": [[13, "generalized-pairwise-alignments-using-match-mismatch-scores-and-an-alphabet"]], "Generalized pairwise alignments using match/mismatch scores and integer sequences": [[13, "generalized-pairwise-alignments-using-match-mismatch-scores-and-integer-sequences"]], "Generating a multiple sequence alignment of codon sequences": [[13, "generating-a-multiple-sequence-alignment-of-codon-sequences"]], "GenomeDiagram": [[8, "genomediagram"]], "Getting a list of the records in a sequence file": [[23, "getting-a-list-of-the-records-in-a-sequence-file"]], "Getting a new-style Alignment object": [[12, "getting-a-new-style-alignment-object"]], "Getting information about the alignment": [[0, "getting-information-about-the-alignment"]], "Getting the raw data for a record": [[23, "getting-the-raw-data-for-a-record"], [23, "id2"]], "Getting your SeqRecord objects as formatted strings": [[23, "getting-your-seqrecord-objects-as-formatted-strings"]], "Getting your alignment objects as formatted strings": [[12, "getting-your-alignment-objects-as-formatted-strings"]], "Going 3D: The PDB module": [[15, "going-3d-the-pdb-module"]], "Graphics including GenomeDiagram": [[8, "graphics-including-genomediagram"]], "HH-suite output files": [[0, "hh-suite-output-files"]], "HSP": [[20, "hsp"]], "HSPFragment": [[20, "hspfragment"]], "HTML escape characters": [[7, "html-escape-characters"]], "Handling Cluster/TreeView-type files": [[4, "handling-cluster-treeview-type-files"]], "Handling errors": [[7, "handling-errors"]], "Hetero residues": [[15, "hetero-residues"]], "Hierarchical clustering": [[4, "hierarchical-clustering"]], "Histogram of sequence lengths": [[6, "histogram-of-sequence-lengths"]], "Hit": [[20, "hit"]], "Hold information about a Reference": [[237, "hold-information-about-a-reference"]], "How fast is it?": [[15, "how-fast-is-it"]], "How well tested is Bio.PDB?": [[15, "how-well-tested-is-bio-pdb"]], "I love parsing \u2013 please don\u2019t stop talking about it!": [[19, "i-love-parsing-please-dont-stop-talking-about-it"]], "I/O functions": [[17, "i-o-functions"]], "Identifying open reading frames": [[6, "identifying-open-reading-frames"]], "Indexing a FASTQ file": [[6, "indexing-a-fastq-file"]], "Indexing a dictionary using the SEGUID checksum": [[23, "indexing-a-dictionary-using-the-seguid-checksum"]], "Indexing compressed files": [[23, "indexing-compressed-files"]], "Information Content": [[12, "information-content"]], "Information methods": [[17, "information-methods"]], "Input": [[56, "input"], [217, "input"], [238, "input"], [298, "input"]], "Input - Alignments": [[238, "input-alignments"]], "Input - Multiple Records": [[238, "input-multiple-records"]], "Input - Single Records": [[238, "input-single-records"], [298, "input-single-records"]], "Installing Biopython": [[9, "installing-biopython"]], "Internal coordinates - distances, angles, torsion angles, distance plots, etc": [[15, "internal-coordinates-distances-angles-torsion-angles-distance-plots-etc"]], "Introduction": [[3, "introduction"], [3, "introduction-1"], [8, "introduction"], [9, "introduction"]], "Is there support for molecular graphics?": [[15, "is-there-support-for-molecular-graphics"]], "Iterating over alignments": [[13, "iterating-over-alignments"]], "Iterating over all residues of a model": [[15, "iterating-over-all-residues-of-a-model"]], "Iterating over the records in a sequence file": [[23, "iterating-over-the-records-in-a-sequence-file"]], "Iterating through all atoms of a structure": [[15, "iterating-through-all-atoms-of-a-structure"]], "JASPAR": [[11, "jaspar"]], "KEGG": [[10, "kegg"]], "Keeping a local copy of the PDB up to date": [[15, "keeping-a-local-copy-of-the-pdb-up-to-date"]], "Kendall\u2019s \\tau": [[4, "kendalls-tau"]], "Letter frequencies": [[0, "letter-frequencies"]], "Loading predefined substitution matrices": [[13, "loading-predefined-substitution-matrices"]], "Location testing": [[21, "location-testing"]], "Loop over all disordered atoms, and select all atoms with altloc A (if present)": [[15, "loop-over-all-disordered-atoms-and-select-all-atoms-with-altloc-a-if-present"]], "Low level FASTA and FASTQ parsers": [[23, "low-level-fasta-and-fastq-parsers"]], "MAST": [[11, "mast"]], "MEME": [[11, "meme"], [11, "sec-meme"]], "MUSCLE": [[12, "muscle"]], "Mailing lists and helping newcomers": [[5, "mailing-lists-and-helping-newcomers"]], "Maintaining a distribution for a platform": [[5, "maintaining-a-distribution-for-a-platform"]], "Making the sequences in a FASTA file upper case": [[6, "making-the-sequences-in-a-fasta-file-upper-case"]], "Manipulating Alignments": [[12, "manipulating-alignments"]], "Manipulating Phenotype Microarray data": [[16, "manipulating-phenotype-microarray-data"]], "Mapping a multiple sequence alignment": [[0, "mapping-a-multiple-sequence-alignment"]], "Mapping a pairwise sequence alignment": [[0, "mapping-a-pairwise-sequence-alignment"]], "Mapping the residues of two related structures onto each other": [[15, "mapping-the-residues-of-two-related-structures-onto-each-other"]], "Mauve eXtended Multi-FastA (xmfa) format": [[0, "mauve-extended-multi-fasta-xmfa-format"]], "Measuring angles": [[15, "measuring-angles"]], "Measuring distances": [[15, "measuring-distances"]], "Measuring torsion angles": [[15, "measuring-torsion-angles"]], "Meta-attributes of CodonAligner objects.": [[13, "table-codonalign-meta-attributes"]], "Meta-attributes of the pairwise aligner objects.": [[13, "table-align-meta-attributes"]], "Missing values": [[4, "missing-values"]], "Model": [[15, "model"]], "Modification methods": [[17, "modification-methods"]], "Modifying and rebuilding structures": [[15, "modifying-and-rebuilding-structures"]], "Modifying data": [[23, "modifying-data"]], "Module contents": [[27, "module-Bio"], [28, "module-Bio.Affy"], [30, "module-Bio.Align"], [32, "module-Bio.Align.Applications"], [54, "module-Bio.Align.substitution_matrices"], [56, "module-Bio.AlignIO"], [67, "module-Bio.Application"], [68, "module-Bio.Blast"], [72, "module-Bio.CAPS"], [73, "module-Bio.Cluster"], [74, "module-Bio.Compass"], [75, "module-Bio.Data"], [79, "module-Bio.Emboss"], [83, "module-Bio.Entrez"], [85, "module-Bio.ExPASy"], [92, "module-Bio.GenBank"], [96, "module-Bio.Geo"], [98, "module-Bio.Graphics"], [104, "module-Bio.Graphics.GenomeDiagram"], [106, "module-Bio.HMM"], [111, "module-Bio.KEGG"], [112, "module-Bio.KEGG.Compound"], [113, "module-Bio.KEGG.Enzyme"], [114, "module-Bio.KEGG.Gene"], [115, "module-Bio.KEGG.KGML"], [118, "module-Bio.KEGG.Map"], [123, "module-Bio.Medline"], [124, "module-Bio.NMR"], [128, "module-Bio.Nexus"], [133, "module-Bio.PDB"], [171, "module-Bio.PDB.mmtf"], [177, "module-Bio.Pathway"], [178, "module-Bio.Pathway.Rep"], [181, "module-Bio.Phylo"], [182, "module-Bio.Phylo.Applications"], [192, "module-Bio.Phylo.PAML"], [200, "module-Bio.PopGen"], [201, "module-Bio.PopGen.GenePop"], [206, "module-Bio.Restriction"], [209, "module-Bio.SCOP"], [216, "module-Bio.SVDSuperimposer"], [217, "module-Bio.SearchIO"], [218, "module-Bio.SearchIO.BlastIO"], [222, "module-Bio.SearchIO.ExonerateIO"], [227, "module-Bio.SearchIO.HHsuiteIO"], [229, "module-Bio.SearchIO.HmmerIO"], [234, "module-Bio.SearchIO.InterproscanIO"], [238, "module-Bio.SeqIO"], [261, "module-Bio.SeqUtils"], [268, "module-Bio.Sequencing"], [270, "module-Bio.Sequencing.Applications"], [272, "module-Bio.SwissProt"], [274, "module-Bio.TogoWS"], [275, "module-Bio.UniGene"], [276, "module-Bio.UniProt"], [279, "module-Bio.codonalign"], [283, "module-Bio.motifs"], [285, "module-Bio.motifs.applications"], [287, "module-Bio.motifs.jaspar"], [298, "module-Bio.phenotype"], [301, "module-BioSQL"]], "Motif objects": [[11, "motif-objects"]], "Multiple Alignment Format (MAF)": [[0, "multiple-alignment-format-maf"]], "Multiple Alignments": [[12, "multiple-alignments"]], "Multiple Sequence Alignment objects": [[12, "multiple-sequence-alignment-objects"]], "Multiple tracks": [[8, "multiple-tracks"]], "MutableSeq objects": [[22, "mutableseq-objects"]], "NEXUS": [[0, "nexus"]], "Navigating through a Structure object": [[15, "navigating-through-a-structure-object"]], "Note": [[65, "note"]], "Nucleotide dot plots": [[6, "nucleotide-dot-plots"]], "Nucleotide sequences and (reverse) complements": [[22, "nucleotide-sequences-and-reverse-complements"]], "Obtaining BLAST output in other formats": [[3, "obtaining-blast-output-in-other-formats"]], "Obtaining a consensus sequence": [[11, "obtaining-a-consensus-sequence"]], "Obtaining the sequence of a structure": [[15, "obtaining-the-sequence-of-a-structure"]], "Operations on an alignment": [[0, "operations-on-an-alignment"]], "Other hetero residues": [[15, "other-hetero-residues"]], "Other versions of BLAST": [[3, "other-versions-of-blast"], [3, "id5"]], "Output": [[56, "output"], [217, "output"], [238, "output"], [298, "output"]], "Output - Advanced": [[238, "output-advanced"]], "PAML integration": [[17, "paml-integration"]], "PHYLIP output files": [[0, "phylip-output-files"]], "Pairwise alignments using pairwise2": [[14, "pairwise-alignments-using-pairwise2"]], "Pairwise sequence alignment": [[13, "pairwise-sequence-alignment"]], "Parameters extraction": [[16, "parameters-extraction"]], "Parse a PDB file, and extract some Model, Chain, Residue and Atom objects": [[15, "parse-a-pdb-file-and-extract-some-model-chain-residue-and-atom-objects"]], "Parsing BLAST output": [[3, "parsing-blast-output"], [3, "id6"]], "Parsing Enzyme records": [[25, "parsing-enzyme-records"]], "Parsing GEO records": [[7, "parsing-geo-records"]], "Parsing GenBank records from the net": [[23, "parsing-genbank-records-from-the-net"]], "Parsing KEGG records": [[10, "parsing-kegg-records"]], "Parsing Medline records": [[7, "parsing-medline-records"]], "Parsing Phenotype Microarray data": [[16, "parsing-phenotype-microarray-data"]], "Parsing Prosite documentation records": [[25, "parsing-prosite-documentation-records"]], "Parsing Prosite records": [[25, "parsing-prosite-records"]], "Parsing Swiss-Prot files": [[25, "parsing-swiss-prot-files"]], "Parsing Swiss-Prot records": [[25, "parsing-swiss-prot-records"]], "Parsing SwissProt sequences from the net": [[23, "parsing-swissprot-sequences-from-the-net"]], "Parsing UniGene records": [[7, "parsing-unigene-records"]], "Parsing huge Entrez XML files": [[7, "parsing-huge-entrez-xml-files"]], "Parsing or Reading Sequence Alignments": [[12, "parsing-or-reading-sequence-alignments"]], "Parsing or Reading Sequences": [[23, "parsing-or-reading-sequences"]], "Parsing sequence file formats": [[19, "parsing-sequence-file-formats"]], "Parsing sequences from compressed files": [[23, "parsing-sequences-from-compressed-files"]], "Parsing sequences from the net": [[23, "parsing-sequences-from-the-net"]], "Parsing the Swiss-Prot keyword and category list": [[25, "parsing-the-swiss-prot-keyword-and-category-list"]], "Partitioning algorithms": [[4, "partitioning-algorithms"]], "Pattern Space Layout (PSL)": [[0, "pattern-space-layout-psl"]], "Performing hierarchical clustering": [[4, "performing-hierarchical-clustering"], [4, "performing-hierarchical-clustering-1"]], "Performing k-means or k-medians clustering": [[4, "performing-k-means-or-k-medians-clustering"]], "Performing the McDonald-Kreitman test": [[13, "performing-the-mcdonald-kreitman-test"]], "Phenotype Microarrays": [[16, "phenotype-microarrays"]], "Phylogenetics with Bio.Phylo": [[17, "phylogenetics-with-bio-phylo"]], "Plot of sequence GC%": [[6, "plot-of-sequence-gc"]], "Plotting the quality scores of sequencing read data": [[6, "plotting-the-quality-scores-of-sequencing-read-data"]], "Point mutations": [[15, "point-mutations"]], "Position Specific Score Matrices": [[12, "position-specific-score-matrices"]], "Position-Specific Scoring Matrices": [[11, "position-specific-scoring-matrices"]], "Position-Weight Matrices": [[11, "position-weight-matrices"]], "Positions and locations": [[21, "positions-and-locations"]], "Principal Component Analysis": [[4, "principal-component-analysis"]], "Print all hetero residues in chain": [[15, "print-all-hetero-residues-in-chain"]], "Print out all the residues that contain disordered atoms": [[15, "print-out-all-the-residues-that-contain-disordered-atoms"]], "Print out coordinates of all CA atoms in structure with B factor over 50": [[15, "print-out-coordinates-of-all-ca-atoms-in-structure-with-b-factor-over-50"]], "Printing alignments": [[0, "printing-alignments"]], "Producing randomized genomes": [[6, "producing-randomized-genomes"]], "Protein Internal Coordinate (.pic) files and default values": [[15, "protein-internal-coordinate-pic-files-and-default-values"]], "PubMed and Medline": [[7, "pubmed-and-medline"]], "Python-style sequence coordinates": [[217, "python-style-sequence-coordinates"]], "QueryResult": [[20, "queryresult"]], "Querying the KEGG API": [[10, "querying-the-kegg-api"]], "Quick Start \u2013 What can you do with Biopython?": [[19, "quick-start-what-can-you-do-with-biopython"]], "Random number generator": [[4, "random-number-generator"]], "Reading Array objects from file": [[13, "reading-array-objects-from-file"]], "Reading Sequence Files": [[23, "reading-sequence-files"]], "Reading a BinaryCIF file": [[15, "reading-a-binarycif-file"]], "Reading a PDB file": [[15, "reading-a-pdb-file"]], "Reading a PDBML (PDB XML) file": [[15, "reading-a-pdbml-pdb-xml-file"]], "Reading a PQR file": [[15, "reading-a-pqr-file"]], "Reading alignments": [[0, "reading-alignments"]], "Reading an mmCIF file": [[15, "reading-an-mmcif-file"]], "Reading and writing alignments": [[0, "reading-and-writing-alignments"]], "Reading and writing crystal structure files": [[15, "reading-and-writing-crystal-structure-files"]], "Reading files in the MMTF format": [[15, "reading-files-in-the-mmtf-format"]], "Reading motifs": [[11, "reading-motifs"]], "Reading search output files": [[20, "reading-search-output-files"]], "Reference": [[166, "reference"]], "References": [[21, "references"]], "Relative entropy": [[11, "relative-entropy"]], "Representing a hierarchical clustering solution": [[4, "representing-a-hierarchical-clustering-solution"]], "Residue": [[15, "residue"]], "Retrieving Prosite and Prosite documentation records": [[25, "retrieving-prosite-and-prosite-documentation-records"]], "Retrieving a Swiss-Prot record": [[25, "retrieving-a-swiss-prot-record"]], "Reverse-complementing SeqRecord objects": [[21, "reverse-complementing-seqrecord-objects"]], "Reverse-complementing a motif": [[11, "reverse-complementing-a-motif"]], "Reverse-complementing the alignment": [[0, "reverse-complementing-the-alignment"]], "Round trips": [[23, "round-trips"]], "Running BLAST locally": [[3, "running-blast-locally"], [3, "id2"]], "Running BLAST over the Internet": [[3, "running-blast-over-the-internet"], [3, "id1"]], "Running external applications": [[17, "running-external-applications"]], "Running the tests": [[24, "running-the-tests"]], "Running the tests using Tox": [[24, "running-the-tests-using-tox"]], "Saving BLAST results": [[3, "saving-blast-results"]], "Saving the clustering result": [[4, "saving-the-clustering-result"]], "Scanning the Prosite database": [[25, "scanning-the-prosite-database"]], "Search and traversal methods": [[17, "search-and-traversal-methods"]], "Searching for and downloading abstracts using the history": [[7, "searching-for-and-downloading-abstracts-using-the-history"]], "Searching for and downloading sequences using the history": [[7, "searching-for-and-downloading-sequences-using-the-history"]], "Searching for citations": [[7, "searching-for-citations"]], "Searching for exact matches": [[11, "searching-for-exact-matches"]], "Searching for instances": [[11, "searching-for-instances"]], "Searching for matches using the PSSM score": [[11, "searching-for-matches-using-the-pssm-score"]], "Searching with UniProt": [[25, "searching-with-uniprot"]], "Searching, downloading, and parsing Entrez Nucleotide records": [[7, "searching-downloading-and-parsing-entrez-nucleotide-records"]], "Searching, downloading, and parsing GenBank records": [[7, "searching-downloading-and-parsing-genbank-records"]], "See Also": [[197, "see-also"]], "Selecting a score threshold": [[11, "selecting-a-score-threshold"]], "Self-Organizing Maps": [[4, "self-organizing-maps"]], "SeqFeature objects": [[21, "seqfeature-objects"]], "SeqRecord objects from FASTA files": [[21, "seqrecord-objects-from-fasta-files"]], "SeqRecord objects from GenBank files": [[21, "seqrecord-objects-from-genbank-files"]], "SeqRecord objects from scratch": [[21, "seqrecord-objects-from-scratch"]], "Sequence Alignment/Map (SAM)": [[0, "sequence-alignment-map-sam"]], "Sequence Input/Output": [[23, "sequence-input-output"]], "Sequence alignments": [[0, "sequence-alignments"]], "Sequence annotation objects": [[21, "sequence-annotation-objects"]], "Sequence coordinate order": [[217, "sequence-coordinate-order"]], "Sequence described by a feature or location": [[21, "sequence-described-by-a-feature-or-location"]], "Sequence files as Dictionaries": [[23, "sequence-files-as-dictionaries"]], "Sequence files as Dictionaries \u2013 Database indexed files": [[23, "sequence-files-as-dictionaries-database-indexed-files"]], "Sequence files as Dictionaries \u2013 In memory": [[23, "sequence-files-as-dictionaries-in-memory"]], "Sequence files as Dictionaries \u2013 Indexed files": [[23, "sequence-files-as-dictionaries-indexed-files"]], "Sequence motif analysis using Bio.motifs": [[11, "sequence-motif-analysis-using-bio-motifs"]], "Sequence objects": [[22, "sequence-objects"]], "Sequence parsing plus simple plots": [[6, "sequence-parsing-plus-simple-plots"]], "Sequences act like strings": [[22, "sequences-act-like-strings"]], "Sequences with partially defined sequence contents": [[22, "sequences-with-partially-defined-sequence-contents"]], "Sequences with unknown sequence contents": [[22, "sequences-with-unknown-sequence-contents"]], "Simple Chromosomes": [[8, "simple-chromosomes"]], "Simple FASTA parsing example": [[19, "simple-fasta-parsing-example"]], "Simple GenBank parsing example": [[19, "simple-genbank-parsing-example"]], "Simple quality filtering for FASTQ files": [[6, "simple-quality-filtering-for-fastq-files"]], "SimpleLocation object": [[21, "simplelocation-object"]], "Single Alignments": [[12, "single-alignments"]], "Slicing a SeqRecord": [[21, "slicing-a-seqrecord"]], "Slicing a motif": [[11, "slicing-a-motif"]], "Slicing a sequence": [[22, "slicing-a-sequence"]], "Slicing alignments": [[12, "slicing-alignments"]], "Slicing and indexing an alignment": [[0, "slicing-and-indexing-an-alignment"]], "Sorting a sequence file": [[6, "sorting-a-sequence-file"]], "Sorting an alignment": [[0, "sorting-an-alignment"]], "Sorting and filtering BLAST output": [[3, "sorting-and-filtering-blast-output"]], "Spearman rank correlation": [[4, "spearman-rank-correlation"]], "Specialized parsers": [[7, "specialized-parsers"]], "Specify locations of a feature on a Sequence": [[237, "specify-locations-of-a-feature-on-a-sequence"]], "Specifying the dictionary keys": [[23, "specifying-the-dictionary-keys"], [23, "sec-seqio-index-functionkey"]], "Standalone NCBI BLAST+": [[3, "standalone-ncbi-blast"], [3, "standalone-ncbi-blast-1"]], "Stockholm": [[0, "stockholm"]], "Structure": [[15, "structure"]], "Structure representation": [[15, "structure-representation"]], "Submodules": [[27, "submodules"], [28, "submodules"], [30, "submodules"], [56, "submodules"], [68, "submodules"], [75, "submodules"], [79, "submodules"], [83, "submodules"], [85, "submodules"], [92, "submodules"], [96, "submodules"], [98, "submodules"], [106, "submodules"], [111, "submodules"], [115, "submodules"], [124, "submodules"], [128, "submodules"], [133, "submodules"], [171, "submodules"], [178, "submodules"], [181, "submodules"], [192, "submodules"], [201, "submodules"], [206, "submodules"], [209, "submodules"], [217, "submodules"], [218, "submodules"], [222, "submodules"], [227, "submodules"], [229, "submodules"], [234, "submodules"], [238, "submodules"], [261, "submodules"], [268, "submodules"], [272, "submodules"], [276, "submodules"], [279, "submodules"], [283, "submodules"], [287, "submodules"], [298, "submodules"], [301, "submodules"]], "Subpackages": [[27, "subpackages"], [30, "subpackages"], [98, "subpackages"], [111, "subpackages"], [133, "subpackages"], [177, "subpackages"], [181, "subpackages"], [200, "subpackages"], [217, "subpackages"], [268, "subpackages"], [283, "subpackages"]], "Substitution matrices": [[13, "substitution-matrices"]], "Substitution scores": [[13, "substitution-scores"]], "Substitutions": [[0, "substitutions"]], "Superimposing residues and their neighborhoods": [[15, "superimposing-residues-and-their-neighborhoods"]], "Superimposing two structures": [[15, "superimposing-two-structures"]], "Supported Formats": [[217, "supported-formats"], [218, "supported-formats"], [221, "supported-formats"], [222, "supported-formats"], [226, "supported-formats"]], "Supported format": [[234, "supported-format"]], "Supported formats": [[229, "supported-formats"]], "Swiss-Prot and ExPASy": [[25, "swiss-prot-and-expasy"]], "TRANSFAC": [[11, "transfac"]], "Table of contents": [[307, null]], "Table of contents:": [[26, null]], "Tabular output from BLAST or FASTA": [[0, "tabular-output-from-blast-or-fasta"]], "Technical Introduction to BGZF": [[278, "technical-introduction-to-bgzf"]], "Testing structures for completeness": [[15, "testing-structures-for-completeness"]], "Text Mode": [[278, "text-mode"]], "The Alignments class": [[0, "the-alignments-class"]], "The BLAST HSP class": [[3, "the-blast-hsp-class"]], "The BLAST Hit class": [[3, "the-blast-hit-class"]], "The BLAST Record class": [[3, "the-blast-record-class"]], "The BLAST Records class": [[3, "the-blast-records-class"]], "The BLAST Records, Record, and Hit classes": [[3, "the-blast-records-record-and-hit-classes"]], "The BLAST record class": [[3, "id7"]], "The Biopython testing framework": [[24, "the-biopython-testing-framework"]], "The JASPAR format jaspar": [[11, "the-jaspar-format-jaspar"]], "The JASPAR pfm format": [[11, "the-jaspar-pfm-format"]], "The JASPAR sites format": [[11, "the-jaspar-sites-format"]], "The Pearson correlation coefficient": [[4, "the-pearson-correlation-coefficient"]], "The SearchIO object model": [[20, "the-searchio-object-model"]], "The SeqRecord object": [[21, "the-seqrecord-object"]], "The file contains an error message": [[7, "the-file-contains-an-error-message"]], "The file contains items that are missing from the associated DTD": [[7, "the-file-contains-items-that-are-missing-from-the-associated-dtd"]], "The file ends prematurely or is otherwise corrupted": [[7, "the-file-ends-prematurely-or-is-otherwise-corrupted"]], "The file is not an XML file": [[7, "the-file-is-not-an-xml-file"]], "The format method": [[21, "the-format-method"]], "The generic pfm-four-columns format": [[11, "the-generic-pfm-four-columns-format"]], "The generic pfm-four-rows format": [[11, "the-generic-pfm-four-rows-format"]], "The pairwise aligner object": [[13, "the-pairwise-aligner-object"]], "Todo": [[169, "id1"]], "Transcription": [[22, "transcription"]], "Translating a FASTA file of CDS entries": [[6, "translating-a-fasta-file-of-cds-entries"]], "Translation": [[22, "translation"]], "Translation Tables": [[22, "translation-tables"]], "Trimming off adaptor sequences": [[6, "trimming-off-adaptor-sequences"]], "Trimming off primer sequences": [[6, "trimming-off-primer-sequences"]], "Turning Seq objects into strings": [[22, "turning-seq-objects-into-strings"]], "UCSC chain file format": [[0, "ucsc-chain-file-format"]], "Uncentered correlation (cosine of the angle)": [[4, "uncentered-correlation-cosine-of-the-angle"]], "Usage": [[137, "usage"]], "Useful links": [[11, "useful-links"]], "Using Tree and Clade objects": [[17, "using-tree-and-clade-objects"]], "Using a pre-defined substitution matrix and gap scores": [[13, "using-a-pre-defined-substitution-matrix-and-gap-scores"]], "Using a proxy": [[7, "using-a-proxy"]], "Using the history and WebEnv": [[7, "using-the-history-and-webenv"]], "View and export trees": [[17, "view-and-export-trees"]], "Warning about namespaces": [[278, "warning-about-namespaces"]], "Water residues": [[15, "water-residues"]], "Weighting": [[4, "weighting"]], "What can I find in the Biopython package": [[9, "what-can-i-find-in-the-biopython-package"]], "What is Biopython?": [[9, "what-is-biopython"]], "What the heck is a handle?": [[1, "what-the-heck-is-a-handle"]], "What to do next": [[19, "what-to-do-next"]], "Where to go from here \u2013 contributing to Biopython": [[5, "where-to-go-from-here-contributing-to-biopython"]], "Who\u2019s using Bio.PDB?": [[15, "whos-using-bio-pdb"]], "Working with sequence files": [[6, "working-with-sequence-files"]], "Working with sequences": [[19, "working-with-sequences"]], "Working with strings directly": [[22, "working-with-strings-directly"]], "Writing Alignments": [[12, "writing-alignments"]], "Writing BLAST records": [[3, "writing-blast-records"]], "Writing MMTF files": [[15, "writing-mmtf-files"]], "Writing PDB files": [[15, "writing-pdb-files"]], "Writing PQR files": [[15, "writing-pqr-files"]], "Writing Phenotype Microarray data": [[16, "writing-phenotype-microarray-data"]], "Writing Sequence Files": [[23, "writing-sequence-files"]], "Writing a test using unittest": [[24, "writing-a-test-using-unittest"]], "Writing alignments": [[0, "writing-alignments"]], "Writing and converting search output files": [[20, "writing-and-converting-search-output-files"]], "Writing doctests": [[24, "writing-doctests"]], "Writing doctests in the Tutorial": [[24, "writing-doctests-in-the-tutorial"]], "Writing mmCIF files": [[15, "writing-mmcif-files"]], "Writing motifs": [[11, "writing-motifs"]], "Writing tests": [[24, "writing-tests"]], "bigBed": [[0, "bigbed"]], "bigMaf": [[0, "bigmaf"]], "bigPsl": [[0, "bigpsl"]], "blast-tab": [[218, "blast-tab"]], "blast-xml": [[218, "blast-xml"]], "exonerate-cigar": [[222, "exonerate-cigar"]], "exonerate-text": [[222, "exonerate-text"]], "exonerate-vulgar": [[222, "exonerate-vulgar"]], "fasta-m10": [[226, "fasta-m10"]], "hmmer2-text and hmmer3-text": [[229, "hmmer2-text-and-hmmer3-text"]], "hmmer3-domtab": [[229, "hmmer3-domtab"]], "hmmer3-tab": [[229, "hmmer3-tab"]], "internal_coords control attributes": [[15, "internal-coords-control-attributes"]], "interproscan-xml": [[234, "interproscan-xml"]], "k-means and k-medians": [[4, "k-means-and-k-medians"]], "k-medoids clustering": [[4, "k-medoids-clustering"]]}, "docnames": ["Tutorial/chapter_align", "Tutorial/chapter_appendix", "Tutorial/chapter_bibliography", "Tutorial/chapter_blast", "Tutorial/chapter_cluster", "Tutorial/chapter_contributing", "Tutorial/chapter_cookbook", "Tutorial/chapter_entrez", "Tutorial/chapter_graphics", "Tutorial/chapter_introduction", "Tutorial/chapter_kegg", "Tutorial/chapter_motifs", "Tutorial/chapter_msa", "Tutorial/chapter_pairwise", "Tutorial/chapter_pairwise2", "Tutorial/chapter_pdb", "Tutorial/chapter_phenotype", "Tutorial/chapter_phylo", "Tutorial/chapter_popgen", "Tutorial/chapter_quick_start", "Tutorial/chapter_searchio", "Tutorial/chapter_seq_annot", "Tutorial/chapter_seq_objects", "Tutorial/chapter_seqio", "Tutorial/chapter_testing", "Tutorial/chapter_uniprot", "Tutorial/index", "api/Bio", "api/Bio.Affy", "api/Bio.Affy.CelFile", "api/Bio.Align", "api/Bio.Align.AlignInfo", "api/Bio.Align.Applications", "api/Bio.Align.a2m", "api/Bio.Align.analysis", "api/Bio.Align.bed", "api/Bio.Align.bigbed", "api/Bio.Align.bigmaf", "api/Bio.Align.bigpsl", "api/Bio.Align.chain", "api/Bio.Align.clustal", "api/Bio.Align.emboss", "api/Bio.Align.exonerate", "api/Bio.Align.fasta", "api/Bio.Align.hhr", "api/Bio.Align.interfaces", "api/Bio.Align.maf", "api/Bio.Align.mauve", "api/Bio.Align.msf", "api/Bio.Align.nexus", "api/Bio.Align.phylip", "api/Bio.Align.psl", "api/Bio.Align.sam", "api/Bio.Align.stockholm", "api/Bio.Align.substitution_matrices", "api/Bio.Align.tabular", "api/Bio.AlignIO", "api/Bio.AlignIO.ClustalIO", "api/Bio.AlignIO.EmbossIO", "api/Bio.AlignIO.FastaIO", "api/Bio.AlignIO.Interfaces", "api/Bio.AlignIO.MafIO", "api/Bio.AlignIO.MauveIO", "api/Bio.AlignIO.MsfIO", "api/Bio.AlignIO.NexusIO", "api/Bio.AlignIO.PhylipIO", "api/Bio.AlignIO.StockholmIO", "api/Bio.Application", "api/Bio.Blast", "api/Bio.Blast.Applications", "api/Bio.Blast.NCBIWWW", "api/Bio.Blast.NCBIXML", "api/Bio.CAPS", "api/Bio.Cluster", "api/Bio.Compass", "api/Bio.Data", "api/Bio.Data.CodonTable", "api/Bio.Data.IUPACData", "api/Bio.Data.PDBData", "api/Bio.Emboss", "api/Bio.Emboss.Applications", "api/Bio.Emboss.Primer3", "api/Bio.Emboss.PrimerSearch", "api/Bio.Entrez", "api/Bio.Entrez.Parser", "api/Bio.ExPASy", "api/Bio.ExPASy.Enzyme", "api/Bio.ExPASy.Prodoc", "api/Bio.ExPASy.Prosite", "api/Bio.ExPASy.ScanProsite", "api/Bio.ExPASy.cellosaurus", "api/Bio.File", "api/Bio.GenBank", "api/Bio.GenBank.Record", "api/Bio.GenBank.Scanner", "api/Bio.GenBank.utils", "api/Bio.Geo", "api/Bio.Geo.Record", "api/Bio.Graphics", "api/Bio.Graphics.BasicChromosome", "api/Bio.Graphics.ColorSpiral", "api/Bio.Graphics.Comparative", "api/Bio.Graphics.DisplayRepresentation", "api/Bio.Graphics.Distribution", "api/Bio.Graphics.GenomeDiagram", "api/Bio.Graphics.KGML_vis", "api/Bio.HMM", "api/Bio.HMM.DynamicProgramming", "api/Bio.HMM.MarkovModel", "api/Bio.HMM.Trainer", "api/Bio.HMM.Utilities", "api/Bio.KEGG", "api/Bio.KEGG.Compound", "api/Bio.KEGG.Enzyme", "api/Bio.KEGG.Gene", "api/Bio.KEGG.KGML", "api/Bio.KEGG.KGML.KGML_parser", "api/Bio.KEGG.KGML.KGML_pathway", "api/Bio.KEGG.Map", "api/Bio.KEGG.REST", "api/Bio.LogisticRegression", "api/Bio.MarkovModel", "api/Bio.MaxEntropy", "api/Bio.Medline", "api/Bio.NMR", "api/Bio.NMR.NOEtools", "api/Bio.NMR.xpktools", "api/Bio.NaiveBayes", "api/Bio.Nexus", "api/Bio.Nexus.Nexus", "api/Bio.Nexus.Nodes", "api/Bio.Nexus.StandardData", "api/Bio.Nexus.Trees", "api/Bio.PDB", "api/Bio.PDB.AbstractPropertyMap", "api/Bio.PDB.Atom", "api/Bio.PDB.Chain", "api/Bio.PDB.DSSP", "api/Bio.PDB.Dice", "api/Bio.PDB.Entity", "api/Bio.PDB.FragmentMapper", "api/Bio.PDB.HSExposure", "api/Bio.PDB.MMCIF2Dict", "api/Bio.PDB.MMCIFParser", "api/Bio.PDB.Model", "api/Bio.PDB.NACCESS", "api/Bio.PDB.NeighborSearch", "api/Bio.PDB.PDBExceptions", "api/Bio.PDB.PDBIO", "api/Bio.PDB.PDBList", "api/Bio.PDB.PDBMLParser", "api/Bio.PDB.PDBParser", "api/Bio.PDB.PICIO", "api/Bio.PDB.PSEA", "api/Bio.PDB.Polypeptide", "api/Bio.PDB.Residue", "api/Bio.PDB.ResidueDepth", "api/Bio.PDB.SASA", "api/Bio.PDB.SCADIO", "api/Bio.PDB.Selection", "api/Bio.PDB.Structure", "api/Bio.PDB.StructureAlignment", "api/Bio.PDB.StructureBuilder", "api/Bio.PDB.Superimposer", "api/Bio.PDB.alphafold_db", "api/Bio.PDB.binary_cif", "api/Bio.PDB.cealign", "api/Bio.PDB.ic_data", "api/Bio.PDB.ic_rebuild", "api/Bio.PDB.internal_coords", "api/Bio.PDB.mmcifio", "api/Bio.PDB.mmtf", "api/Bio.PDB.mmtf.DefaultParser", "api/Bio.PDB.mmtf.mmtfio", "api/Bio.PDB.parse_pdb_header", "api/Bio.PDB.qcprot", "api/Bio.PDB.vectors", "api/Bio.Pathway", "api/Bio.Pathway.Rep", "api/Bio.Pathway.Rep.Graph", "api/Bio.Pathway.Rep.MultiGraph", "api/Bio.Phylo", "api/Bio.Phylo.Applications", "api/Bio.Phylo.BaseTree", "api/Bio.Phylo.CDAO", "api/Bio.Phylo.CDAOIO", "api/Bio.Phylo.Consensus", "api/Bio.Phylo.NeXML", "api/Bio.Phylo.NeXMLIO", "api/Bio.Phylo.Newick", "api/Bio.Phylo.NewickIO", "api/Bio.Phylo.NexusIO", "api/Bio.Phylo.PAML", "api/Bio.Phylo.PAML.baseml", "api/Bio.Phylo.PAML.chi2", "api/Bio.Phylo.PAML.codeml", "api/Bio.Phylo.PAML.yn00", "api/Bio.Phylo.PhyloXML", "api/Bio.Phylo.PhyloXMLIO", "api/Bio.Phylo.TreeConstruction", "api/Bio.PopGen", "api/Bio.PopGen.GenePop", "api/Bio.PopGen.GenePop.Controller", "api/Bio.PopGen.GenePop.EasyController", "api/Bio.PopGen.GenePop.FileParser", "api/Bio.PopGen.GenePop.LargeFileParser", "api/Bio.Restriction", "api/Bio.Restriction.PrintFormat", "api/Bio.Restriction.Restriction_Dictionary", "api/Bio.SCOP", "api/Bio.SCOP.Cla", "api/Bio.SCOP.Des", "api/Bio.SCOP.Dom", "api/Bio.SCOP.Hie", "api/Bio.SCOP.Raf", "api/Bio.SCOP.Residues", "api/Bio.SVDSuperimposer", "api/Bio.SearchIO", "api/Bio.SearchIO.BlastIO", "api/Bio.SearchIO.BlastIO.blast_tab", "api/Bio.SearchIO.BlastIO.blast_xml", "api/Bio.SearchIO.BlatIO", "api/Bio.SearchIO.ExonerateIO", "api/Bio.SearchIO.ExonerateIO.exonerate_cigar", "api/Bio.SearchIO.ExonerateIO.exonerate_text", "api/Bio.SearchIO.ExonerateIO.exonerate_vulgar", "api/Bio.SearchIO.FastaIO", "api/Bio.SearchIO.HHsuiteIO", "api/Bio.SearchIO.HHsuiteIO.hhsuite2_text", "api/Bio.SearchIO.HmmerIO", "api/Bio.SearchIO.HmmerIO.hmmer2_text", "api/Bio.SearchIO.HmmerIO.hmmer3_domtab", "api/Bio.SearchIO.HmmerIO.hmmer3_tab", "api/Bio.SearchIO.HmmerIO.hmmer3_text", "api/Bio.SearchIO.InterproscanIO", "api/Bio.SearchIO.InterproscanIO.interproscan_xml", "api/Bio.Seq", "api/Bio.SeqFeature", "api/Bio.SeqIO", "api/Bio.SeqIO.AbiIO", "api/Bio.SeqIO.AceIO", "api/Bio.SeqIO.FastaIO", "api/Bio.SeqIO.GckIO", "api/Bio.SeqIO.GfaIO", "api/Bio.SeqIO.IgIO", "api/Bio.SeqIO.InsdcIO", "api/Bio.SeqIO.Interfaces", "api/Bio.SeqIO.NibIO", "api/Bio.SeqIO.PdbIO", "api/Bio.SeqIO.PhdIO", "api/Bio.SeqIO.PirIO", "api/Bio.SeqIO.QualityIO", "api/Bio.SeqIO.SeqXmlIO", "api/Bio.SeqIO.SffIO", "api/Bio.SeqIO.SnapGeneIO", "api/Bio.SeqIO.SwissIO", "api/Bio.SeqIO.TabIO", "api/Bio.SeqIO.TwoBitIO", "api/Bio.SeqIO.UniprotIO", "api/Bio.SeqIO.XdnaIO", "api/Bio.SeqRecord", "api/Bio.SeqUtils", "api/Bio.SeqUtils.CheckSum", "api/Bio.SeqUtils.IsoelectricPoint", "api/Bio.SeqUtils.MeltingTemp", "api/Bio.SeqUtils.ProtParam", "api/Bio.SeqUtils.ProtParamData", "api/Bio.SeqUtils.lcc", "api/Bio.Sequencing", "api/Bio.Sequencing.Ace", "api/Bio.Sequencing.Applications", "api/Bio.Sequencing.Phd", "api/Bio.SwissProt", "api/Bio.SwissProt.KeyWList", "api/Bio.TogoWS", "api/Bio.UniGene", "api/Bio.UniProt", "api/Bio.UniProt.GOA", "api/Bio.bgzf", "api/Bio.codonalign", "api/Bio.codonalign.codonalignment", "api/Bio.codonalign.codonseq", "api/Bio.kNN", "api/Bio.motifs", "api/Bio.motifs.alignace", "api/Bio.motifs.applications", "api/Bio.motifs.clusterbuster", "api/Bio.motifs.jaspar", "api/Bio.motifs.jaspar.db", "api/Bio.motifs.mast", "api/Bio.motifs.matrix", "api/Bio.motifs.meme", "api/Bio.motifs.minimal", "api/Bio.motifs.pfm", "api/Bio.motifs.thresholds", "api/Bio.motifs.transfac", "api/Bio.motifs.xms", "api/Bio.pairwise2", "api/Bio.phenotype", "api/Bio.phenotype.phen_micro", "api/Bio.phenotype.pm_fitting", "api/BioSQL", "api/BioSQL.BioSeq", "api/BioSQL.BioSeqDatabase", "api/BioSQL.DBUtils", "api/BioSQL.Loader", "api/index", "index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2}, "filenames": ["Tutorial/chapter_align.rst", "Tutorial/chapter_appendix.rst", "Tutorial/chapter_bibliography.rst", "Tutorial/chapter_blast.rst", "Tutorial/chapter_cluster.rst", "Tutorial/chapter_contributing.rst", "Tutorial/chapter_cookbook.rst", "Tutorial/chapter_entrez.rst", "Tutorial/chapter_graphics.rst", "Tutorial/chapter_introduction.rst", "Tutorial/chapter_kegg.rst", "Tutorial/chapter_motifs.rst", "Tutorial/chapter_msa.rst", "Tutorial/chapter_pairwise.rst", "Tutorial/chapter_pairwise2.rst", "Tutorial/chapter_pdb.rst", "Tutorial/chapter_phenotype.rst", "Tutorial/chapter_phylo.rst", "Tutorial/chapter_popgen.rst", "Tutorial/chapter_quick_start.rst", "Tutorial/chapter_searchio.rst", "Tutorial/chapter_seq_annot.rst", "Tutorial/chapter_seq_objects.rst", "Tutorial/chapter_seqio.rst", "Tutorial/chapter_testing.rst", "Tutorial/chapter_uniprot.rst", "Tutorial/index.rst", "api/Bio.rst", "api/Bio.Affy.rst", "api/Bio.Affy.CelFile.rst", "api/Bio.Align.rst", "api/Bio.Align.AlignInfo.rst", "api/Bio.Align.Applications.rst", "api/Bio.Align.a2m.rst", "api/Bio.Align.analysis.rst", "api/Bio.Align.bed.rst", "api/Bio.Align.bigbed.rst", "api/Bio.Align.bigmaf.rst", "api/Bio.Align.bigpsl.rst", "api/Bio.Align.chain.rst", "api/Bio.Align.clustal.rst", "api/Bio.Align.emboss.rst", "api/Bio.Align.exonerate.rst", "api/Bio.Align.fasta.rst", "api/Bio.Align.hhr.rst", "api/Bio.Align.interfaces.rst", "api/Bio.Align.maf.rst", "api/Bio.Align.mauve.rst", "api/Bio.Align.msf.rst", "api/Bio.Align.nexus.rst", "api/Bio.Align.phylip.rst", "api/Bio.Align.psl.rst", "api/Bio.Align.sam.rst", "api/Bio.Align.stockholm.rst", "api/Bio.Align.substitution_matrices.rst", "api/Bio.Align.tabular.rst", "api/Bio.AlignIO.rst", "api/Bio.AlignIO.ClustalIO.rst", "api/Bio.AlignIO.EmbossIO.rst", "api/Bio.AlignIO.FastaIO.rst", "api/Bio.AlignIO.Interfaces.rst", "api/Bio.AlignIO.MafIO.rst", "api/Bio.AlignIO.MauveIO.rst", "api/Bio.AlignIO.MsfIO.rst", "api/Bio.AlignIO.NexusIO.rst", "api/Bio.AlignIO.PhylipIO.rst", "api/Bio.AlignIO.StockholmIO.rst", "api/Bio.Application.rst", "api/Bio.Blast.rst", "api/Bio.Blast.Applications.rst", "api/Bio.Blast.NCBIWWW.rst", "api/Bio.Blast.NCBIXML.rst", "api/Bio.CAPS.rst", "api/Bio.Cluster.rst", "api/Bio.Compass.rst", "api/Bio.Data.rst", "api/Bio.Data.CodonTable.rst", "api/Bio.Data.IUPACData.rst", "api/Bio.Data.PDBData.rst", "api/Bio.Emboss.rst", "api/Bio.Emboss.Applications.rst", "api/Bio.Emboss.Primer3.rst", "api/Bio.Emboss.PrimerSearch.rst", "api/Bio.Entrez.rst", "api/Bio.Entrez.Parser.rst", "api/Bio.ExPASy.rst", "api/Bio.ExPASy.Enzyme.rst", "api/Bio.ExPASy.Prodoc.rst", "api/Bio.ExPASy.Prosite.rst", "api/Bio.ExPASy.ScanProsite.rst", "api/Bio.ExPASy.cellosaurus.rst", "api/Bio.File.rst", "api/Bio.GenBank.rst", "api/Bio.GenBank.Record.rst", "api/Bio.GenBank.Scanner.rst", "api/Bio.GenBank.utils.rst", "api/Bio.Geo.rst", "api/Bio.Geo.Record.rst", "api/Bio.Graphics.rst", "api/Bio.Graphics.BasicChromosome.rst", "api/Bio.Graphics.ColorSpiral.rst", "api/Bio.Graphics.Comparative.rst", "api/Bio.Graphics.DisplayRepresentation.rst", "api/Bio.Graphics.Distribution.rst", "api/Bio.Graphics.GenomeDiagram.rst", "api/Bio.Graphics.KGML_vis.rst", "api/Bio.HMM.rst", "api/Bio.HMM.DynamicProgramming.rst", "api/Bio.HMM.MarkovModel.rst", "api/Bio.HMM.Trainer.rst", "api/Bio.HMM.Utilities.rst", "api/Bio.KEGG.rst", "api/Bio.KEGG.Compound.rst", "api/Bio.KEGG.Enzyme.rst", "api/Bio.KEGG.Gene.rst", "api/Bio.KEGG.KGML.rst", "api/Bio.KEGG.KGML.KGML_parser.rst", "api/Bio.KEGG.KGML.KGML_pathway.rst", "api/Bio.KEGG.Map.rst", "api/Bio.KEGG.REST.rst", "api/Bio.LogisticRegression.rst", "api/Bio.MarkovModel.rst", "api/Bio.MaxEntropy.rst", "api/Bio.Medline.rst", "api/Bio.NMR.rst", "api/Bio.NMR.NOEtools.rst", "api/Bio.NMR.xpktools.rst", "api/Bio.NaiveBayes.rst", "api/Bio.Nexus.rst", "api/Bio.Nexus.Nexus.rst", "api/Bio.Nexus.Nodes.rst", "api/Bio.Nexus.StandardData.rst", "api/Bio.Nexus.Trees.rst", "api/Bio.PDB.rst", "api/Bio.PDB.AbstractPropertyMap.rst", "api/Bio.PDB.Atom.rst", "api/Bio.PDB.Chain.rst", "api/Bio.PDB.DSSP.rst", "api/Bio.PDB.Dice.rst", "api/Bio.PDB.Entity.rst", "api/Bio.PDB.FragmentMapper.rst", "api/Bio.PDB.HSExposure.rst", "api/Bio.PDB.MMCIF2Dict.rst", "api/Bio.PDB.MMCIFParser.rst", "api/Bio.PDB.Model.rst", "api/Bio.PDB.NACCESS.rst", "api/Bio.PDB.NeighborSearch.rst", "api/Bio.PDB.PDBExceptions.rst", "api/Bio.PDB.PDBIO.rst", "api/Bio.PDB.PDBList.rst", "api/Bio.PDB.PDBMLParser.rst", "api/Bio.PDB.PDBParser.rst", "api/Bio.PDB.PICIO.rst", "api/Bio.PDB.PSEA.rst", "api/Bio.PDB.Polypeptide.rst", "api/Bio.PDB.Residue.rst", "api/Bio.PDB.ResidueDepth.rst", "api/Bio.PDB.SASA.rst", "api/Bio.PDB.SCADIO.rst", "api/Bio.PDB.Selection.rst", "api/Bio.PDB.Structure.rst", "api/Bio.PDB.StructureAlignment.rst", "api/Bio.PDB.StructureBuilder.rst", "api/Bio.PDB.Superimposer.rst", "api/Bio.PDB.alphafold_db.rst", "api/Bio.PDB.binary_cif.rst", "api/Bio.PDB.cealign.rst", "api/Bio.PDB.ic_data.rst", "api/Bio.PDB.ic_rebuild.rst", "api/Bio.PDB.internal_coords.rst", "api/Bio.PDB.mmcifio.rst", "api/Bio.PDB.mmtf.rst", "api/Bio.PDB.mmtf.DefaultParser.rst", "api/Bio.PDB.mmtf.mmtfio.rst", "api/Bio.PDB.parse_pdb_header.rst", "api/Bio.PDB.qcprot.rst", "api/Bio.PDB.vectors.rst", "api/Bio.Pathway.rst", "api/Bio.Pathway.Rep.rst", "api/Bio.Pathway.Rep.Graph.rst", "api/Bio.Pathway.Rep.MultiGraph.rst", "api/Bio.Phylo.rst", "api/Bio.Phylo.Applications.rst", "api/Bio.Phylo.BaseTree.rst", "api/Bio.Phylo.CDAO.rst", "api/Bio.Phylo.CDAOIO.rst", "api/Bio.Phylo.Consensus.rst", "api/Bio.Phylo.NeXML.rst", "api/Bio.Phylo.NeXMLIO.rst", "api/Bio.Phylo.Newick.rst", "api/Bio.Phylo.NewickIO.rst", "api/Bio.Phylo.NexusIO.rst", "api/Bio.Phylo.PAML.rst", "api/Bio.Phylo.PAML.baseml.rst", "api/Bio.Phylo.PAML.chi2.rst", "api/Bio.Phylo.PAML.codeml.rst", "api/Bio.Phylo.PAML.yn00.rst", "api/Bio.Phylo.PhyloXML.rst", "api/Bio.Phylo.PhyloXMLIO.rst", "api/Bio.Phylo.TreeConstruction.rst", "api/Bio.PopGen.rst", "api/Bio.PopGen.GenePop.rst", "api/Bio.PopGen.GenePop.Controller.rst", "api/Bio.PopGen.GenePop.EasyController.rst", "api/Bio.PopGen.GenePop.FileParser.rst", "api/Bio.PopGen.GenePop.LargeFileParser.rst", "api/Bio.Restriction.rst", "api/Bio.Restriction.PrintFormat.rst", "api/Bio.Restriction.Restriction_Dictionary.rst", "api/Bio.SCOP.rst", "api/Bio.SCOP.Cla.rst", "api/Bio.SCOP.Des.rst", "api/Bio.SCOP.Dom.rst", "api/Bio.SCOP.Hie.rst", "api/Bio.SCOP.Raf.rst", "api/Bio.SCOP.Residues.rst", "api/Bio.SVDSuperimposer.rst", "api/Bio.SearchIO.rst", "api/Bio.SearchIO.BlastIO.rst", "api/Bio.SearchIO.BlastIO.blast_tab.rst", "api/Bio.SearchIO.BlastIO.blast_xml.rst", "api/Bio.SearchIO.BlatIO.rst", "api/Bio.SearchIO.ExonerateIO.rst", "api/Bio.SearchIO.ExonerateIO.exonerate_cigar.rst", "api/Bio.SearchIO.ExonerateIO.exonerate_text.rst", "api/Bio.SearchIO.ExonerateIO.exonerate_vulgar.rst", "api/Bio.SearchIO.FastaIO.rst", "api/Bio.SearchIO.HHsuiteIO.rst", "api/Bio.SearchIO.HHsuiteIO.hhsuite2_text.rst", "api/Bio.SearchIO.HmmerIO.rst", "api/Bio.SearchIO.HmmerIO.hmmer2_text.rst", "api/Bio.SearchIO.HmmerIO.hmmer3_domtab.rst", "api/Bio.SearchIO.HmmerIO.hmmer3_tab.rst", "api/Bio.SearchIO.HmmerIO.hmmer3_text.rst", "api/Bio.SearchIO.InterproscanIO.rst", "api/Bio.SearchIO.InterproscanIO.interproscan_xml.rst", "api/Bio.Seq.rst", "api/Bio.SeqFeature.rst", "api/Bio.SeqIO.rst", "api/Bio.SeqIO.AbiIO.rst", "api/Bio.SeqIO.AceIO.rst", "api/Bio.SeqIO.FastaIO.rst", "api/Bio.SeqIO.GckIO.rst", "api/Bio.SeqIO.GfaIO.rst", "api/Bio.SeqIO.IgIO.rst", "api/Bio.SeqIO.InsdcIO.rst", "api/Bio.SeqIO.Interfaces.rst", "api/Bio.SeqIO.NibIO.rst", "api/Bio.SeqIO.PdbIO.rst", "api/Bio.SeqIO.PhdIO.rst", "api/Bio.SeqIO.PirIO.rst", "api/Bio.SeqIO.QualityIO.rst", "api/Bio.SeqIO.SeqXmlIO.rst", "api/Bio.SeqIO.SffIO.rst", "api/Bio.SeqIO.SnapGeneIO.rst", "api/Bio.SeqIO.SwissIO.rst", "api/Bio.SeqIO.TabIO.rst", "api/Bio.SeqIO.TwoBitIO.rst", "api/Bio.SeqIO.UniprotIO.rst", "api/Bio.SeqIO.XdnaIO.rst", "api/Bio.SeqRecord.rst", "api/Bio.SeqUtils.rst", "api/Bio.SeqUtils.CheckSum.rst", "api/Bio.SeqUtils.IsoelectricPoint.rst", "api/Bio.SeqUtils.MeltingTemp.rst", "api/Bio.SeqUtils.ProtParam.rst", "api/Bio.SeqUtils.ProtParamData.rst", "api/Bio.SeqUtils.lcc.rst", "api/Bio.Sequencing.rst", "api/Bio.Sequencing.Ace.rst", "api/Bio.Sequencing.Applications.rst", "api/Bio.Sequencing.Phd.rst", "api/Bio.SwissProt.rst", "api/Bio.SwissProt.KeyWList.rst", "api/Bio.TogoWS.rst", "api/Bio.UniGene.rst", "api/Bio.UniProt.rst", "api/Bio.UniProt.GOA.rst", "api/Bio.bgzf.rst", "api/Bio.codonalign.rst", "api/Bio.codonalign.codonalignment.rst", "api/Bio.codonalign.codonseq.rst", "api/Bio.kNN.rst", "api/Bio.motifs.rst", "api/Bio.motifs.alignace.rst", "api/Bio.motifs.applications.rst", "api/Bio.motifs.clusterbuster.rst", "api/Bio.motifs.jaspar.rst", "api/Bio.motifs.jaspar.db.rst", "api/Bio.motifs.mast.rst", "api/Bio.motifs.matrix.rst", "api/Bio.motifs.meme.rst", "api/Bio.motifs.minimal.rst", "api/Bio.motifs.pfm.rst", "api/Bio.motifs.thresholds.rst", "api/Bio.motifs.transfac.rst", "api/Bio.motifs.xms.rst", "api/Bio.pairwise2.rst", "api/Bio.phenotype.rst", "api/Bio.phenotype.phen_micro.rst", "api/Bio.phenotype.pm_fitting.rst", "api/BioSQL.rst", "api/BioSQL.BioSeq.rst", "api/BioSQL.BioSeqDatabase.rst", "api/BioSQL.DBUtils.rst", "api/BioSQL.Loader.rst", "api/index.rst", "index.rst"], "indexentries": {"__abstractmethods__ (bio.align.a2m.alignmentiterator attribute)": [[33, "Bio.Align.a2m.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.a2m.alignmentwriter attribute)": [[33, "Bio.Align.a2m.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.alignments attribute)": [[30, "Bio.Align.Alignments.__abstractmethods__", false]], "__abstractmethods__ (bio.align.alignmentsabstractbaseclass attribute)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bed.alignmentiterator attribute)": [[35, "Bio.Align.bed.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bed.alignmentwriter attribute)": [[35, "Bio.Align.bed.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigbed.alignmentiterator attribute)": [[36, "Bio.Align.bigbed.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigbed.alignmentwriter attribute)": [[36, "Bio.Align.bigbed.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigmaf.alignmentiterator attribute)": [[37, "Bio.Align.bigmaf.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigmaf.alignmentwriter attribute)": [[37, "Bio.Align.bigmaf.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigpsl.alignmentiterator attribute)": [[38, "Bio.Align.bigpsl.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigpsl.alignmentwriter attribute)": [[38, "Bio.Align.bigpsl.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.chain.alignmentiterator attribute)": [[39, "Bio.Align.chain.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.chain.alignmentwriter attribute)": [[39, "Bio.Align.chain.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.clustal.alignmentiterator attribute)": [[40, "Bio.Align.clustal.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.clustal.alignmentwriter attribute)": [[40, "Bio.Align.clustal.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.emboss.alignmentiterator attribute)": [[41, "Bio.Align.emboss.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.exonerate.alignmentiterator attribute)": [[42, "Bio.Align.exonerate.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.exonerate.alignmentwriter attribute)": [[42, "Bio.Align.exonerate.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.fasta.alignmentiterator attribute)": [[43, "Bio.Align.fasta.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.fasta.alignmentwriter attribute)": [[43, "Bio.Align.fasta.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.hhr.alignmentiterator attribute)": [[44, "Bio.Align.hhr.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.maf.alignmentwriter attribute)": [[46, "Bio.Align.maf.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.mauve.alignmentiterator attribute)": [[47, "Bio.Align.mauve.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.mauve.alignmentwriter attribute)": [[47, "Bio.Align.mauve.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.msf.alignmentiterator attribute)": [[48, "Bio.Align.msf.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.nexus.alignmentiterator attribute)": [[49, "Bio.Align.nexus.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.nexus.alignmentwriter attribute)": [[49, "Bio.Align.nexus.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.pairwisealignments attribute)": [[30, "Bio.Align.PairwiseAlignments.__abstractmethods__", false]], "__abstractmethods__ (bio.align.phylip.alignmentiterator attribute)": [[50, "Bio.Align.phylip.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.phylip.alignmentwriter attribute)": [[50, "Bio.Align.phylip.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.psl.alignmentiterator attribute)": [[51, "Bio.Align.psl.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.psl.alignmentwriter attribute)": [[51, "Bio.Align.psl.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.sam.alignmentiterator attribute)": [[52, "Bio.Align.sam.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.sam.alignmentwriter attribute)": [[52, "Bio.Align.sam.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.tabular.alignmentiterator attribute)": [[55, "Bio.Align.tabular.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.blast.hit attribute)": [[68, "Bio.Blast.Hit.__abstractmethods__", false]], "__abstractmethods__ (bio.blast.records attribute)": [[68, "Bio.Blast.Records.__abstractmethods__", false]], "__abstractmethods__ (bio.codonalign.codonseq.codonseq attribute)": [[281, "Bio.codonalign.codonseq.CodonSeq.__abstractmethods__", false]], "__abstractmethods__ (bio.motifs.meme.instance attribute)": [[291, "Bio.motifs.meme.Instance.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.blastio.blast_tab.blasttabindexer attribute)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.blatio.blatpslindexer attribute)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarindexer attribute)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarparser attribute)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_text.exoneratetextindexer attribute)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_text.exoneratetextparser attribute)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer attribute)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarparser attribute)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.fastaio.fastam10indexer attribute)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer attribute)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitindexer attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmqueryindexer attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabindexer attribute)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer attribute)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.seq.mutableseq attribute)": [[236, "Bio.Seq.MutableSeq.__abstractmethods__", false]], "__abstractmethods__ (bio.seq.seq attribute)": [[236, "Bio.Seq.Seq.__abstractmethods__", false]], "__abstractmethods__ (bio.seq.sequencedataabstractbaseclass attribute)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.afterposition attribute)": [[237, "Bio.SeqFeature.AfterPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.beforeposition attribute)": [[237, "Bio.SeqFeature.BeforePosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.betweenposition attribute)": [[237, "Bio.SeqFeature.BetweenPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.compoundlocation attribute)": [[237, "Bio.SeqFeature.CompoundLocation.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.exactposition attribute)": [[237, "Bio.SeqFeature.ExactPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.location attribute)": [[237, "Bio.SeqFeature.Location.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.oneofposition attribute)": [[237, "Bio.SeqFeature.OneOfPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.position attribute)": [[237, "Bio.SeqFeature.Position.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.simplelocation attribute)": [[237, "Bio.SeqFeature.SimpleLocation.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.uncertainposition attribute)": [[237, "Bio.SeqFeature.UncertainPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.unknownposition attribute)": [[237, "Bio.SeqFeature.UnknownPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.withinposition attribute)": [[237, "Bio.SeqFeature.WithinPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.abiio.abiiterator attribute)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.fastaio.fastaiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.fastaio.fastatwolineiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.gckio.gckiterator attribute)": [[242, "Bio.SeqIO.GckIO.GckIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.igio.igiterator attribute)": [[244, "Bio.SeqIO.IgIO.IgIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.emblcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.embliterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.genbankcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.genbankiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.imgtiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.interfaces.sequenceiterator attribute)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.nibio.nibiterator attribute)": [[247, "Bio.SeqIO.NibIO.NibIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.pdbio.pdbseqresiterator attribute)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.pirio.piriterator attribute)": [[250, "Bio.SeqIO.PirIO.PirIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.qualityio.fastqphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.qualityio.qualphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.seqxmlio.seqxmliterator attribute)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.sffio.sffiterator attribute)": [[253, "Bio.SeqIO.SffIO.SffIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.snapgeneio.snapgeneiterator attribute)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.tabio.tabiterator attribute)": [[256, "Bio.SeqIO.TabIO.TabIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.twobitio.twobititerator attribute)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.xdnaio.xdnaiterator attribute)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.__abstractmethods__", false]], "__add__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__add__", false]], "__add__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__add__", false]], "__add__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__add__", false]], "__add__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__add__", false]], "__add__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__add__", false]], "__add__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__add__", false]], "__add__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__add__", false]], "__add__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__add__", false]], "__add__() (bio.seqfeature.afterposition method)": [[237, "Bio.SeqFeature.AfterPosition.__add__", false]], "__add__() (bio.seqfeature.beforeposition method)": [[237, "Bio.SeqFeature.BeforePosition.__add__", false]], "__add__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__add__", false]], "__add__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__add__", false]], "__add__() (bio.seqfeature.exactposition method)": [[237, "Bio.SeqFeature.ExactPosition.__add__", false]], "__add__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__add__", false]], "__add__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__add__", false]], "__add__() (bio.seqfeature.unknownposition method)": [[237, "Bio.SeqFeature.UnknownPosition.__add__", false]], "__add__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__add__", false]], "__add__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__add__", false]], "__annotations__ (bio.align.bigbed.autosqltable attribute)": [[36, "Bio.Align.bigbed.AutoSQLTable.__annotations__", false]], "__annotations__ (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.__annotations__", false]], "__annotations__ (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.__annotations__", false]], "__annotations__ (bio.alignio.mauveio.mauveiterator attribute)": [[62, "Bio.AlignIO.MauveIO.MauveIterator.__annotations__", false]], "__annotations__ (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.__annotations__", false]], "__annotations__ (bio.data.codontable.ncbicodontable attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTable.__annotations__", false]], "__annotations__ (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.__annotations__", false]], "__annotations__ (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.__annotations__", false]], "__annotations__ (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.__annotations__", false]], "__annotations__ (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.__annotations__", false]], "__annotations__ (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer attribute)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.__annotations__", false]], "__annotations__ (bio.seq.seq attribute)": [[236, "Bio.Seq.Seq.__annotations__", false]], "__annotations__ (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.__annotations__", false]], "__array__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__array__", false]], "__array_finalize__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_finalize__", false]], "__array_prepare__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_prepare__", false]], "__array_ufunc__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_ufunc__", false]], "__array_wrap__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_wrap__", false]], "__bool__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__bool__", false]], "__bool__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__bool__", false]], "__bool__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__bool__", false]], "__bytes__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__bytes__", false]], "__bytes__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__bytes__", false]], "__bytes__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__bytes__", false]], "__call__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__call__", false]], "__call__() (bio.pairwise2.affine_penalty method)": [[297, "Bio.pairwise2.affine_penalty.__call__", false]], "__call__() (bio.pairwise2.dictionary_match method)": [[297, "Bio.pairwise2.dictionary_match.__call__", false]], "__call__() (bio.pairwise2.identity_match method)": [[297, "Bio.pairwise2.identity_match.__call__", false]], "__contains__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__contains__", false]], "__contains__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__contains__", false]], "__contains__() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.__contains__", false]], "__contains__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__contains__", false]], "__contains__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__contains__", false]], "__contains__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__contains__", false]], "__contains__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__contains__", false]], "__contains__() (bio.pdb.fragmentmapper.fragmentmapper method)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper.__contains__", false]], "__contains__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__contains__", false]], "__contains__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__contains__", false]], "__contains__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__contains__", false]], "__contains__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__contains__", false]], "__contains__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__contains__", false]], "__contains__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__contains__", false]], "__contains__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__contains__", false]], "__contains__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__contains__", false]], "__contains__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__contains__", false]], "__contains__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__contains__", false]], "__contains__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__contains__", false]], "__contains__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__contains__", false]], "__deepcopy__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__deepcopy__", false]], "__deepcopy__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__deepcopy__", false]], "__deepcopy__() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.__deepcopy__", false]], "__deepcopy__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__deepcopy__", false]], "__delitem__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__delitem__", false]], "__delitem__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__delitem__", false]], "__delitem__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__delitem__", false]], "__delitem__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__delitem__", false]], "__delitem__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__delitem__", false]], "__delitem__() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.__delitem__", false]], "__delitem__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__delitem__", false]], "__delitem__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__delitem__", false]], "__enter__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__enter__", false]], "__enter__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__enter__", false]], "__enter__() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.__enter__", false]], "__enter__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__enter__", false]], "__eq__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__eq__", false]], "__eq__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__eq__", false]], "__eq__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__eq__", false]], "__eq__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__eq__", false]], "__eq__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__eq__", false]], "__eq__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__eq__", false]], "__eq__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__eq__", false]], "__eq__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__eq__", false]], "__eq__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__eq__", false]], "__eq__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__eq__", false]], "__eq__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__eq__", false]], "__eq__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__eq__", false]], "__eq__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__eq__", false]], "__eq__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__eq__", false]], "__eq__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__eq__", false]], "__eq__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__eq__", false]], "__eq__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__eq__", false]], "__eq__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__eq__", false]], "__exit__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__exit__", false]], "__exit__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__exit__", false]], "__exit__() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.__exit__", false]], "__exit__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__exit__", false]], "__format__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__format__", false]], "__format__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__format__", false]], "__format__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__format__", false]], "__format__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__format__", false]], "__format__() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.__format__", false]], "__format__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__format__", false]], "__ge__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__ge__", false]], "__ge__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__ge__", false]], "__ge__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__ge__", false]], "__ge__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__ge__", false]], "__ge__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__ge__", false]], "__ge__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__ge__", false]], "__ge__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__ge__", false]], "__ge__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__ge__", false]], "__ge__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__ge__", false]], "__getattr__() (bio.data.codontable.ambiguouscodontable method)": [[76, "Bio.Data.CodonTable.AmbiguousCodonTable.__getattr__", false]], "__getattr__() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.__getattr__", false]], "__getattr__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__getattr__", false]], "__getitem__() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.__getitem__", false]], "__getitem__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__getitem__", false]], "__getitem__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__getitem__", false]], "__getitem__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__getitem__", false]], "__getitem__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__getitem__", false]], "__getitem__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__getitem__", false]], "__getitem__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__getitem__", false]], "__getitem__() (bio.blast.hit method)": [[68, "Bio.Blast.Hit.__getitem__", false]], "__getitem__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__getitem__", false]], "__getitem__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__getitem__", false]], "__getitem__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__getitem__", false]], "__getitem__() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.__getitem__", false]], "__getitem__() (bio.motifs.mast.record method)": [[289, "Bio.motifs.mast.Record.__getitem__", false]], "__getitem__() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.__getitem__", false]], "__getitem__() (bio.motifs.meme.record method)": [[291, "Bio.motifs.meme.Record.__getitem__", false]], "__getitem__() (bio.motifs.minimal.record method)": [[292, "Bio.motifs.minimal.Record.__getitem__", false]], "__getitem__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__getitem__", false]], "__getitem__() (bio.motifs.transfac.motif method)": [[295, "Bio.motifs.transfac.Motif.__getitem__", false]], "__getitem__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__getitem__", false]], "__getitem__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__", false]], "__getitem__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__getitem__", false]], "__getitem__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__getitem__", false]], "__getitem__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__getitem__", false]], "__getitem__() (bio.pdb.fragmentmapper.fragmentmapper method)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper.__getitem__", false]], "__getitem__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__getitem__", false]], "__getitem__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__getitem__", false]], "__getitem__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__getitem__", false]], "__getitem__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__getitem__", false]], "__getitem__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__getitem__", false]], "__getitem__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__getitem__", false]], "__getitem__() (bio.scop.cla.index method)": [[210, "Bio.SCOP.Cla.Index.__getitem__", false]], "__getitem__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__getitem__", false]], "__getitem__() (bio.scop.raf.seqmapindex method)": [[214, "Bio.SCOP.Raf.SeqMapIndex.__getitem__", false]], "__getitem__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__getitem__", false]], "__getitem__() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__getitem__", false]], "__getitem__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__getitem__", false]], "__getitem__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__", false]], "__getitem__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__getitem__", false]], "__getnewargs__() (bio.align.alignmentcounts method)": [[30, "Bio.Align.AlignmentCounts.__getnewargs__", false]], "__getnewargs__() (bio.align.bigbed.field method)": [[36, "Bio.Align.bigbed.Field.__getnewargs__", false]], "__getnewargs__() (bio.pairwise2.alignment method)": [[297, "Bio.pairwise2.Alignment.__getnewargs__", false]], "__getnewargs__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__getnewargs__", false]], "__getnewargs__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__getnewargs__", false]], "__getnewargs__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__getnewargs__", false]], "__getstate__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__getstate__", false]], "__gt__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__gt__", false]], "__gt__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__gt__", false]], "__gt__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__gt__", false]], "__gt__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__gt__", false]], "__gt__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__gt__", false]], "__gt__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__gt__", false]], "__gt__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__gt__", false]], "__gt__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__gt__", false]], "__gt__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__gt__", false]], "__hash__ (bio.align.alignment attribute)": [[30, "Bio.Align.Alignment.__hash__", false]], "__hash__ (bio.entrez.parser.noneelement attribute)": [[84, "Bio.Entrez.Parser.NoneElement.__hash__", false]], "__hash__ (bio.pathway.rep.graph.graph attribute)": [[179, "Bio.Pathway.Rep.Graph.Graph.__hash__", false]], "__hash__ (bio.pathway.rep.multigraph.multigraph attribute)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__hash__", false]], "__hash__ (bio.phenotype.phen_micro.platerecord attribute)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__hash__", false]], "__hash__ (bio.phenotype.phen_micro.wellrecord attribute)": [[299, "Bio.phenotype.phen_micro.WellRecord.__hash__", false]], "__hash__ (bio.seqfeature.compoundlocation attribute)": [[237, "Bio.SeqFeature.CompoundLocation.__hash__", false]], "__hash__ (bio.seqfeature.reference attribute)": [[237, "Bio.SeqFeature.Reference.__hash__", false]], "__hash__ (bio.seqfeature.seqfeature attribute)": [[237, "Bio.SeqFeature.SeqFeature.__hash__", false]], "__hash__ (bio.seqfeature.simplelocation attribute)": [[237, "Bio.SeqFeature.SimpleLocation.__hash__", false]], "__hash__ (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.__hash__", false]], "__hash__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__hash__", false]], "__hash__() (bio.pathway.interaction method)": [[177, "Bio.Pathway.Interaction.__hash__", false]], "__hash__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__hash__", false]], "__hash__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__hash__", false]], "__hash__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__hash__", false]], "__hash__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__hash__", false]], "__hash__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__hash__", false]], "__hash__() (bio.seq.seq method)": [[236, "Bio.Seq.Seq.__hash__", false]], "__hash__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__hash__", false]], "__hash__() (bio.seqfeature.unknownposition method)": [[237, "Bio.SeqFeature.UnknownPosition.__hash__", false]], "__iadd__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__iadd__", false]], "__init__() (bio.affy.celfile.parsererror method)": [[29, "Bio.Affy.CelFile.ParserError.__init__", false]], "__init__() (bio.affy.celfile.record method)": [[29, "Bio.Affy.CelFile.Record.__init__", false]], "__init__() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.__init__", false]], "__init__() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.__init__", false]], "__init__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__init__", false]], "__init__() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.__init__", false]], "__init__() (bio.align.applications.clustalomegacommandline method)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.__init__", false]], "__init__() (bio.align.applications.clustalwcommandline method)": [[32, "Bio.Align.Applications.ClustalwCommandline.__init__", false]], "__init__() (bio.align.applications.dialigncommandline method)": [[32, "Bio.Align.Applications.DialignCommandline.__init__", false]], "__init__() (bio.align.applications.mafftcommandline method)": [[32, "Bio.Align.Applications.MafftCommandline.__init__", false]], "__init__() (bio.align.applications.msaprobscommandline method)": [[32, "Bio.Align.Applications.MSAProbsCommandline.__init__", false]], "__init__() (bio.align.applications.musclecommandline method)": [[32, "Bio.Align.Applications.MuscleCommandline.__init__", false]], "__init__() (bio.align.applications.prankcommandline method)": [[32, "Bio.Align.Applications.PrankCommandline.__init__", false]], "__init__() (bio.align.applications.probconscommandline method)": [[32, "Bio.Align.Applications.ProbconsCommandline.__init__", false]], "__init__() (bio.align.applications.tcoffeecommandline method)": [[32, "Bio.Align.Applications.TCoffeeCommandline.__init__", false]], "__init__() (bio.align.bed.alignmentwriter method)": [[35, "Bio.Align.bed.AlignmentWriter.__init__", false]], "__init__() (bio.align.bigbed.alignmentwriter method)": [[36, "Bio.Align.bigbed.AlignmentWriter.__init__", false]], "__init__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__init__", false]], "__init__() (bio.align.bigmaf.alignmentiterator method)": [[37, "Bio.Align.bigmaf.AlignmentIterator.__init__", false]], "__init__() (bio.align.bigmaf.alignmentwriter method)": [[37, "Bio.Align.bigmaf.AlignmentWriter.__init__", false]], "__init__() (bio.align.bigpsl.alignmentwriter method)": [[38, "Bio.Align.bigpsl.AlignmentWriter.__init__", false]], "__init__() (bio.align.codonaligner method)": [[30, "Bio.Align.CodonAligner.__init__", false]], "__init__() (bio.align.exonerate.alignmentwriter method)": [[42, "Bio.Align.exonerate.AlignmentWriter.__init__", false]], "__init__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__init__", false]], "__init__() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.__init__", false]], "__init__() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.__init__", false]], "__init__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__init__", false]], "__init__() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.__init__", false]], "__init__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__init__", false]], "__init__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__init__", false]], "__init__() (bio.align.psl.alignmentwriter method)": [[51, "Bio.Align.psl.AlignmentWriter.__init__", false]], "__init__() (bio.align.sam.alignmentwriter method)": [[52, "Bio.Align.sam.AlignmentWriter.__init__", false]], "__init__() (bio.alignio.interfaces.alignmentiterator method)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator.__init__", false]], "__init__() (bio.alignio.interfaces.alignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter.__init__", false]], "__init__() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__", false]], "__init__() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.__init__", false]], "__init__() (bio.alignio.mauveio.mauvewriter method)": [[62, "Bio.AlignIO.MauveIO.MauveWriter.__init__", false]], "__init__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__init__", false]], "__init__() (bio.application.applicationerror method)": [[67, "Bio.Application.ApplicationError.__init__", false]], "__init__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__init__", false]], "__init__() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.__init__", false]], "__init__() (bio.blast.applications.ncbiblastformattercommandline method)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbiblastncommandline method)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbiblastpcommandline method)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbiblastxcommandline method)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbideltablastcommandline method)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbimakeblastdbcommandline method)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbipsiblastcommandline method)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbirpsblastcommandline method)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbirpstblastncommandline method)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbitblastncommandline method)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbitblastxcommandline method)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.__init__", false]], "__init__() (bio.blast.corruptedxmlerror method)": [[68, "Bio.Blast.CorruptedXMLError.__init__", false]], "__init__() (bio.blast.ncbixml.alignment method)": [[71, "Bio.Blast.NCBIXML.Alignment.__init__", false]], "__init__() (bio.blast.ncbixml.blast method)": [[71, "Bio.Blast.NCBIXML.Blast.__init__", false]], "__init__() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.__init__", false]], "__init__() (bio.blast.ncbixml.databasereport method)": [[71, "Bio.Blast.NCBIXML.DatabaseReport.__init__", false]], "__init__() (bio.blast.ncbixml.description method)": [[71, "Bio.Blast.NCBIXML.Description.__init__", false]], "__init__() (bio.blast.ncbixml.descriptionext method)": [[71, "Bio.Blast.NCBIXML.DescriptionExt.__init__", false]], "__init__() (bio.blast.ncbixml.descriptionextitem method)": [[71, "Bio.Blast.NCBIXML.DescriptionExtItem.__init__", false]], "__init__() (bio.blast.ncbixml.header method)": [[71, "Bio.Blast.NCBIXML.Header.__init__", false]], "__init__() (bio.blast.ncbixml.hsp method)": [[71, "Bio.Blast.NCBIXML.HSP.__init__", false]], "__init__() (bio.blast.ncbixml.multiplealignment method)": [[71, "Bio.Blast.NCBIXML.MultipleAlignment.__init__", false]], "__init__() (bio.blast.ncbixml.parameters method)": [[71, "Bio.Blast.NCBIXML.Parameters.__init__", false]], "__init__() (bio.blast.ncbixml.psiblast method)": [[71, "Bio.Blast.NCBIXML.PSIBlast.__init__", false]], "__init__() (bio.blast.ncbixml.round method)": [[71, "Bio.Blast.NCBIXML.Round.__init__", false]], "__init__() (bio.blast.notxmlerror method)": [[68, "Bio.Blast.NotXMLError.__init__", false]], "__init__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__init__", false]], "__init__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__init__", false]], "__init__() (bio.caps.capsmap method)": [[72, "Bio.CAPS.CAPSMap.__init__", false]], "__init__() (bio.caps.differentialcutsite method)": [[72, "Bio.CAPS.DifferentialCutsite.__init__", false]], "__init__() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.__init__", false]], "__init__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__init__", false]], "__init__() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.__init__", false]], "__init__() (bio.compass.record method)": [[74, "Bio.Compass.Record.__init__", false]], "__init__() (bio.data.codontable.ambiguouscodontable method)": [[76, "Bio.Data.CodonTable.AmbiguousCodonTable.__init__", false]], "__init__() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.__init__", false]], "__init__() (bio.data.codontable.codontable method)": [[76, "Bio.Data.CodonTable.CodonTable.__init__", false]], "__init__() (bio.data.codontable.ncbicodontable method)": [[76, "Bio.Data.CodonTable.NCBICodonTable.__init__", false]], "__init__() (bio.emboss.applications.diffseqcommandline method)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.__init__", false]], "__init__() (bio.emboss.applications.einvertedcommandline method)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.__init__", false]], "__init__() (bio.emboss.applications.est2genomecommandline method)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.__init__", false]], "__init__() (bio.emboss.applications.etandemcommandline method)": [[80, "Bio.Emboss.Applications.ETandemCommandline.__init__", false]], "__init__() (bio.emboss.applications.fconsensecommandline method)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.__init__", false]], "__init__() (bio.emboss.applications.fdnadistcommandline method)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.__init__", false]], "__init__() (bio.emboss.applications.fdnaparscommandline method)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.__init__", false]], "__init__() (bio.emboss.applications.fneighborcommandline method)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.__init__", false]], "__init__() (bio.emboss.applications.fprotdistcommandline method)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.__init__", false]], "__init__() (bio.emboss.applications.fprotparscommandline method)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.__init__", false]], "__init__() (bio.emboss.applications.fseqbootcommandline method)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.__init__", false]], "__init__() (bio.emboss.applications.ftreedistcommandline method)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.__init__", false]], "__init__() (bio.emboss.applications.fuzznuccommandline method)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.__init__", false]], "__init__() (bio.emboss.applications.fuzzprocommandline method)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.__init__", false]], "__init__() (bio.emboss.applications.iepcommandline method)": [[80, "Bio.Emboss.Applications.IepCommandline.__init__", false]], "__init__() (bio.emboss.applications.needleallcommandline method)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.__init__", false]], "__init__() (bio.emboss.applications.needlecommandline method)": [[80, "Bio.Emboss.Applications.NeedleCommandline.__init__", false]], "__init__() (bio.emboss.applications.palindromecommandline method)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.__init__", false]], "__init__() (bio.emboss.applications.primer3commandline method)": [[80, "Bio.Emboss.Applications.Primer3Commandline.__init__", false]], "__init__() (bio.emboss.applications.primersearchcommandline method)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.__init__", false]], "__init__() (bio.emboss.applications.seqmatchallcommandline method)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.__init__", false]], "__init__() (bio.emboss.applications.seqretcommandline method)": [[80, "Bio.Emboss.Applications.SeqretCommandline.__init__", false]], "__init__() (bio.emboss.applications.stretchercommandline method)": [[80, "Bio.Emboss.Applications.StretcherCommandline.__init__", false]], "__init__() (bio.emboss.applications.tranaligncommandline method)": [[80, "Bio.Emboss.Applications.TranalignCommandline.__init__", false]], "__init__() (bio.emboss.applications.watercommandline method)": [[80, "Bio.Emboss.Applications.WaterCommandline.__init__", false]], "__init__() (bio.emboss.primer3.primers method)": [[81, "Bio.Emboss.Primer3.Primers.__init__", false]], "__init__() (bio.emboss.primer3.record method)": [[81, "Bio.Emboss.Primer3.Record.__init__", false]], "__init__() (bio.emboss.primersearch.amplifier method)": [[82, "Bio.Emboss.PrimerSearch.Amplifier.__init__", false]], "__init__() (bio.emboss.primersearch.inputrecord method)": [[82, "Bio.Emboss.PrimerSearch.InputRecord.__init__", false]], "__init__() (bio.emboss.primersearch.outputrecord method)": [[82, "Bio.Emboss.PrimerSearch.OutputRecord.__init__", false]], "__init__() (bio.entrez.parser.corruptedxmlerror method)": [[84, "Bio.Entrez.Parser.CorruptedXMLError.__init__", false]], "__init__() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.__init__", false]], "__init__() (bio.entrez.parser.datahandlermeta method)": [[84, "Bio.Entrez.Parser.DataHandlerMeta.__init__", false]], "__init__() (bio.entrez.parser.dictionaryelement method)": [[84, "Bio.Entrez.Parser.DictionaryElement.__init__", false]], "__init__() (bio.entrez.parser.errorelement method)": [[84, "Bio.Entrez.Parser.ErrorElement.__init__", false]], "__init__() (bio.entrez.parser.integerelement method)": [[84, "Bio.Entrez.Parser.IntegerElement.__init__", false]], "__init__() (bio.entrez.parser.listelement method)": [[84, "Bio.Entrez.Parser.ListElement.__init__", false]], "__init__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__init__", false]], "__init__() (bio.entrez.parser.notxmlerror method)": [[84, "Bio.Entrez.Parser.NotXMLError.__init__", false]], "__init__() (bio.entrez.parser.orderedlistelement method)": [[84, "Bio.Entrez.Parser.OrderedListElement.__init__", false]], "__init__() (bio.entrez.parser.stringelement method)": [[84, "Bio.Entrez.Parser.StringElement.__init__", false]], "__init__() (bio.entrez.parser.validationerror method)": [[84, "Bio.Entrez.Parser.ValidationError.__init__", false]], "__init__() (bio.expasy.cellosaurus.record method)": [[90, "Bio.ExPASy.cellosaurus.Record.__init__", false]], "__init__() (bio.expasy.enzyme.record method)": [[86, "Bio.ExPASy.Enzyme.Record.__init__", false]], "__init__() (bio.expasy.prodoc.record method)": [[87, "Bio.ExPASy.Prodoc.Record.__init__", false]], "__init__() (bio.expasy.prodoc.reference method)": [[87, "Bio.ExPASy.Prodoc.Reference.__init__", false]], "__init__() (bio.expasy.prosite.record method)": [[88, "Bio.ExPASy.Prosite.Record.__init__", false]], "__init__() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.__init__", false]], "__init__() (bio.expasy.scanprosite.parser method)": [[89, "Bio.ExPASy.ScanProsite.Parser.__init__", false]], "__init__() (bio.expasy.scanprosite.record method)": [[89, "Bio.ExPASy.ScanProsite.Record.__init__", false]], "__init__() (bio.genbank.featureparser method)": [[92, "Bio.GenBank.FeatureParser.__init__", false]], "__init__() (bio.genbank.iterator method)": [[92, "Bio.GenBank.Iterator.__init__", false]], "__init__() (bio.genbank.record.feature method)": [[93, "Bio.GenBank.Record.Feature.__init__", false]], "__init__() (bio.genbank.record.qualifier method)": [[93, "Bio.GenBank.Record.Qualifier.__init__", false]], "__init__() (bio.genbank.record.record method)": [[93, "Bio.GenBank.Record.Record.__init__", false]], "__init__() (bio.genbank.record.reference method)": [[93, "Bio.GenBank.Record.Reference.__init__", false]], "__init__() (bio.genbank.recordparser method)": [[92, "Bio.GenBank.RecordParser.__init__", false]], "__init__() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.__init__", false]], "__init__() (bio.genbank.utils.featurevaluecleaner method)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.__init__", false]], "__init__() (bio.geo.record.record method)": [[97, "Bio.Geo.Record.Record.__init__", false]], "__init__() (bio.graphics.basicchromosome.annotatedchromosomesegment method)": [[99, "Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment.__init__", false]], "__init__() (bio.graphics.basicchromosome.chromosome method)": [[99, "Bio.Graphics.BasicChromosome.Chromosome.__init__", false]], "__init__() (bio.graphics.basicchromosome.chromosomesegment method)": [[99, "Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__", false]], "__init__() (bio.graphics.basicchromosome.organism method)": [[99, "Bio.Graphics.BasicChromosome.Organism.__init__", false]], "__init__() (bio.graphics.basicchromosome.telomeresegment method)": [[99, "Bio.Graphics.BasicChromosome.TelomereSegment.__init__", false]], "__init__() (bio.graphics.colorspiral.colorspiral method)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.__init__", false]], "__init__() (bio.graphics.comparative.comparativescatterplot method)": [[101, "Bio.Graphics.Comparative.ComparativeScatterPlot.__init__", false]], "__init__() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__", false]], "__init__() (bio.graphics.distribution.barchartdistribution method)": [[103, "Bio.Graphics.Distribution.BarChartDistribution.__init__", false]], "__init__() (bio.graphics.distribution.distributionpage method)": [[103, "Bio.Graphics.Distribution.DistributionPage.__init__", false]], "__init__() (bio.graphics.distribution.linedistribution method)": [[103, "Bio.Graphics.Distribution.LineDistribution.__init__", false]], "__init__() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.__init__", false]], "__init__() (bio.graphics.genomediagram.crosslink method)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.__init__", false]], "__init__() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.__init__", false]], "__init__() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.__init__", false]], "__init__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__init__", false]], "__init__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__init__", false]], "__init__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__init__", false]], "__init__() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.__init__", false]], "__init__() (bio.graphics.kgml_vis.kgmlcanvas method)": [[105, "Bio.Graphics.KGML_vis.KGMLCanvas.__init__", false]], "__init__() (bio.hmm.dynamicprogramming.abstractdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__", false]], "__init__() (bio.hmm.dynamicprogramming.logdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__", false]], "__init__() (bio.hmm.dynamicprogramming.scaleddpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__", false]], "__init__() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.__init__", false]], "__init__() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.__init__", false]], "__init__() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.__init__", false]], "__init__() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.__init__", false]], "__init__() (bio.hmm.trainer.knownstatetrainer method)": [[109, "Bio.HMM.Trainer.KnownStateTrainer.__init__", false]], "__init__() (bio.hmm.trainer.trainingsequence method)": [[109, "Bio.HMM.Trainer.TrainingSequence.__init__", false]], "__init__() (bio.kegg.compound.record method)": [[112, "Bio.KEGG.Compound.Record.__init__", false]], "__init__() (bio.kegg.enzyme.record method)": [[113, "Bio.KEGG.Enzyme.Record.__init__", false]], "__init__() (bio.kegg.gene.record method)": [[114, "Bio.KEGG.Gene.Record.__init__", false]], "__init__() (bio.kegg.kgml.kgml_parser.kgmlparser method)": [[116, "Bio.KEGG.KGML.KGML_parser.KGMLParser.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.component method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.graphics method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.relation method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.__init__", false]], "__init__() (bio.knn.knn method)": [[282, "Bio.kNN.kNN.__init__", false]], "__init__() (bio.logisticregression.logisticregression method)": [[120, "Bio.LogisticRegression.LogisticRegression.__init__", false]], "__init__() (bio.markovmodel.markovmodel method)": [[121, "Bio.MarkovModel.MarkovModel.__init__", false]], "__init__() (bio.maxentropy.maxentropy method)": [[122, "Bio.MaxEntropy.MaxEntropy.__init__", false]], "__init__() (bio.motifs.alignace.record method)": [[284, "Bio.motifs.alignace.Record.__init__", false]], "__init__() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.__init__", false]], "__init__() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.__init__", false]], "__init__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__init__", false]], "__init__() (bio.motifs.jaspar.record method)": [[287, "Bio.motifs.jaspar.Record.__init__", false]], "__init__() (bio.motifs.mast.record method)": [[289, "Bio.motifs.mast.Record.__init__", false]], "__init__() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.__init__", false]], "__init__() (bio.motifs.matrix.positionweightmatrix method)": [[290, "Bio.motifs.matrix.PositionWeightMatrix.__init__", false]], "__init__() (bio.motifs.meme.instance method)": [[291, "Bio.motifs.meme.Instance.__init__", false]], "__init__() (bio.motifs.meme.motif method)": [[291, "Bio.motifs.meme.Motif.__init__", false]], "__init__() (bio.motifs.meme.record method)": [[291, "Bio.motifs.meme.Record.__init__", false]], "__init__() (bio.motifs.minimal.record method)": [[292, "Bio.motifs.minimal.Record.__init__", false]], "__init__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__init__", false]], "__init__() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.__init__", false]], "__init__() (bio.motifs.transfac.record method)": [[295, "Bio.motifs.transfac.Record.__init__", false]], "__init__() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.__init__", false]], "__init__() (bio.naivebayes.naivebayes method)": [[127, "Bio.NaiveBayes.NaiveBayes.__init__", false]], "__init__() (bio.nexus.nexus.block method)": [[129, "Bio.Nexus.Nexus.Block.__init__", false]], "__init__() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.__init__", false]], "__init__() (bio.nexus.nexus.commandline method)": [[129, "Bio.Nexus.Nexus.Commandline.__init__", false]], "__init__() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.__init__", false]], "__init__() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.__init__", false]], "__init__() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.__init__", false]], "__init__() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.__init__", false]], "__init__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__init__", false]], "__init__() (bio.nexus.trees.nodedata method)": [[132, "Bio.Nexus.Trees.NodeData.__init__", false]], "__init__() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.__init__", false]], "__init__() (bio.nmr.xpktools.peaklist method)": [[126, "Bio.NMR.xpktools.Peaklist.__init__", false]], "__init__() (bio.nmr.xpktools.xpkentry method)": [[126, "Bio.NMR.xpktools.XpkEntry.__init__", false]], "__init__() (bio.pairwise2.affine_penalty method)": [[297, "Bio.pairwise2.affine_penalty.__init__", false]], "__init__() (bio.pairwise2.dictionary_match method)": [[297, "Bio.pairwise2.dictionary_match.__init__", false]], "__init__() (bio.pairwise2.identity_match method)": [[297, "Bio.pairwise2.identity_match.__init__", false]], "__init__() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.__init__", false]], "__init__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__init__", false]], "__init__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__init__", false]], "__init__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__", false]], "__init__() (bio.pathway.system method)": [[177, "Bio.Pathway.System.__init__", false]], "__init__() (bio.pdb.abstractpropertymap.abstractatompropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__", false]], "__init__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__", false]], "__init__() (bio.pdb.abstractpropertymap.abstractresiduepropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__", false]], "__init__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__init__", false]], "__init__() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.__init__", false]], "__init__() (bio.pdb.binary_cif.binarycifparser method)": [[165, "Bio.PDB.binary_cif.BinaryCIFParser.__init__", false]], "__init__() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.__init__", false]], "__init__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__init__", false]], "__init__() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.__init__", false]], "__init__() (bio.pdb.dssp.dssp method)": [[137, "Bio.PDB.DSSP.DSSP.__init__", false]], "__init__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__init__", false]], "__init__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__init__", false]], "__init__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__init__", false]], "__init__() (bio.pdb.fragmentmapper.fragmentmapper method)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper.__init__", false]], "__init__() (bio.pdb.hsexposure.exposurecn method)": [[141, "Bio.PDB.HSExposure.ExposureCN.__init__", false]], "__init__() (bio.pdb.hsexposure.hsexposureca method)": [[141, "Bio.PDB.HSExposure.HSExposureCA.__init__", false]], "__init__() (bio.pdb.hsexposure.hsexposurecb method)": [[141, "Bio.PDB.HSExposure.HSExposureCB.__init__", false]], "__init__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__init__", false]], "__init__() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.__init__", false]], "__init__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__init__", false]], "__init__() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.__init__", false]], "__init__() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.__init__", false]], "__init__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__init__", false]], "__init__() (bio.pdb.mmcif2dict.mmcif2dict method)": [[142, "Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__", false]], "__init__() (bio.pdb.mmcifio.mmcifio method)": [[170, "Bio.PDB.mmcifio.MMCIFIO.__init__", false]], "__init__() (bio.pdb.mmcifparser.fastmmcifparser method)": [[143, "Bio.PDB.MMCIFParser.FastMMCIFParser.__init__", false]], "__init__() (bio.pdb.mmcifparser.mmcifparser method)": [[143, "Bio.PDB.MMCIFParser.MMCIFParser.__init__", false]], "__init__() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.__init__", false]], "__init__() (bio.pdb.mmtf.mmtfio.mmtfio method)": [[173, "Bio.PDB.mmtf.mmtfio.MMTFIO.__init__", false]], "__init__() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.__init__", false]], "__init__() (bio.pdb.naccess.naccess method)": [[145, "Bio.PDB.NACCESS.NACCESS.__init__", false]], "__init__() (bio.pdb.naccess.naccess_atomic method)": [[145, "Bio.PDB.NACCESS.NACCESS_atomic.__init__", false]], "__init__() (bio.pdb.neighborsearch.neighborsearch method)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch.__init__", false]], "__init__() (bio.pdb.pdbio.pdbio method)": [[148, "Bio.PDB.PDBIO.PDBIO.__init__", false]], "__init__() (bio.pdb.pdbio.structureio method)": [[148, "Bio.PDB.PDBIO.StructureIO.__init__", false]], "__init__() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.__init__", false]], "__init__() (bio.pdb.pdbmlparser.pdbmlparser method)": [[150, "Bio.PDB.PDBMLParser.PDBMLParser.__init__", false]], "__init__() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.__init__", false]], "__init__() (bio.pdb.polypeptide.cappbuilder method)": [[154, "Bio.PDB.Polypeptide.CaPPBuilder.__init__", false]], "__init__() (bio.pdb.polypeptide.ppbuilder method)": [[154, "Bio.PDB.Polypeptide.PPBuilder.__init__", false]], "__init__() (bio.pdb.psea.psea method)": [[153, "Bio.PDB.PSEA.PSEA.__init__", false]], "__init__() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.__init__", false]], "__init__() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.__init__", false]], "__init__() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.__init__", false]], "__init__() (bio.pdb.residuedepth.residuedepth method)": [[156, "Bio.PDB.ResidueDepth.ResidueDepth.__init__", false]], "__init__() (bio.pdb.sasa.shrakerupley method)": [[157, "Bio.PDB.SASA.ShrakeRupley.__init__", false]], "__init__() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.__init__", false]], "__init__() (bio.pdb.structurealignment.structurealignment method)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment.__init__", false]], "__init__() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.__init__", false]], "__init__() (bio.pdb.superimposer.superimposer method)": [[163, "Bio.PDB.Superimposer.Superimposer.__init__", false]], "__init__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__init__", false]], "__init__() (bio.phenotype.phen_micro.jsonwriter method)": [[299, "Bio.phenotype.phen_micro.JsonWriter.__init__", false]], "__init__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__init__", false]], "__init__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__init__", false]], "__init__() (bio.phylo.applications.fasttreecommandline method)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.__init__", false]], "__init__() (bio.phylo.applications.phymlcommandline method)": [[182, "Bio.Phylo.Applications.PhymlCommandline.__init__", false]], "__init__() (bio.phylo.applications.raxmlcommandline method)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.__init__", false]], "__init__() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.__init__", false]], "__init__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__init__", false]], "__init__() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.__init__", false]], "__init__() (bio.phylo.cdao.clade method)": [[184, "Bio.Phylo.CDAO.Clade.__init__", false]], "__init__() (bio.phylo.cdao.tree method)": [[184, "Bio.Phylo.CDAO.Tree.__init__", false]], "__init__() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.__init__", false]], "__init__() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.__init__", false]], "__init__() (bio.phylo.newick.clade method)": [[189, "Bio.Phylo.Newick.Clade.__init__", false]], "__init__() (bio.phylo.newick.tree method)": [[189, "Bio.Phylo.Newick.Tree.__init__", false]], "__init__() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.__init__", false]], "__init__() (bio.phylo.newickio.writer method)": [[190, "Bio.Phylo.NewickIO.Writer.__init__", false]], "__init__() (bio.phylo.nexml.clade method)": [[187, "Bio.Phylo.NeXML.Clade.__init__", false]], "__init__() (bio.phylo.nexml.tree method)": [[187, "Bio.Phylo.NeXML.Tree.__init__", false]], "__init__() (bio.phylo.nexmlio.parser method)": [[188, "Bio.Phylo.NeXMLIO.Parser.__init__", false]], "__init__() (bio.phylo.nexmlio.writer method)": [[188, "Bio.Phylo.NeXMLIO.Writer.__init__", false]], "__init__() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.__init__", false]], "__init__() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.__init__", false]], "__init__() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.__init__", false]], "__init__() (bio.phylo.phyloxml.accession method)": [[197, "Bio.Phylo.PhyloXML.Accession.__init__", false]], "__init__() (bio.phylo.phyloxml.annotation method)": [[197, "Bio.Phylo.PhyloXML.Annotation.__init__", false]], "__init__() (bio.phylo.phyloxml.binarycharacters method)": [[197, "Bio.Phylo.PhyloXML.BinaryCharacters.__init__", false]], "__init__() (bio.phylo.phyloxml.branchcolor method)": [[197, "Bio.Phylo.PhyloXML.BranchColor.__init__", false]], "__init__() (bio.phylo.phyloxml.clade method)": [[197, "Bio.Phylo.PhyloXML.Clade.__init__", false]], "__init__() (bio.phylo.phyloxml.claderelation method)": [[197, "Bio.Phylo.PhyloXML.CladeRelation.__init__", false]], "__init__() (bio.phylo.phyloxml.date method)": [[197, "Bio.Phylo.PhyloXML.Date.__init__", false]], "__init__() (bio.phylo.phyloxml.distribution method)": [[197, "Bio.Phylo.PhyloXML.Distribution.__init__", false]], "__init__() (bio.phylo.phyloxml.domainarchitecture method)": [[197, "Bio.Phylo.PhyloXML.DomainArchitecture.__init__", false]], "__init__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__init__", false]], "__init__() (bio.phylo.phyloxml.id method)": [[197, "Bio.Phylo.PhyloXML.Id.__init__", false]], "__init__() (bio.phylo.phyloxml.molseq method)": [[197, "Bio.Phylo.PhyloXML.MolSeq.__init__", false]], "__init__() (bio.phylo.phyloxml.other method)": [[197, "Bio.Phylo.PhyloXML.Other.__init__", false]], "__init__() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.__init__", false]], "__init__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__init__", false]], "__init__() (bio.phylo.phyloxml.point method)": [[197, "Bio.Phylo.PhyloXML.Point.__init__", false]], "__init__() (bio.phylo.phyloxml.polygon method)": [[197, "Bio.Phylo.PhyloXML.Polygon.__init__", false]], "__init__() (bio.phylo.phyloxml.property method)": [[197, "Bio.Phylo.PhyloXML.Property.__init__", false]], "__init__() (bio.phylo.phyloxml.proteindomain method)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain.__init__", false]], "__init__() (bio.phylo.phyloxml.reference method)": [[197, "Bio.Phylo.PhyloXML.Reference.__init__", false]], "__init__() (bio.phylo.phyloxml.sequence method)": [[197, "Bio.Phylo.PhyloXML.Sequence.__init__", false]], "__init__() (bio.phylo.phyloxml.sequencerelation method)": [[197, "Bio.Phylo.PhyloXML.SequenceRelation.__init__", false]], "__init__() (bio.phylo.phyloxml.taxonomy method)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.__init__", false]], "__init__() (bio.phylo.phyloxml.uri method)": [[197, "Bio.Phylo.PhyloXML.Uri.__init__", false]], "__init__() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.__init__", false]], "__init__() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.__init__", false]], "__init__() (bio.phylo.treeconstruction.distancecalculator method)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.__init__", false]], "__init__() (bio.phylo.treeconstruction.distancematrix method)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix.__init__", false]], "__init__() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.__init__", false]], "__init__() (bio.phylo.treeconstruction.nnitreesearcher method)": [[199, "Bio.Phylo.TreeConstruction.NNITreeSearcher.__init__", false]], "__init__() (bio.phylo.treeconstruction.parsimonyscorer method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyScorer.__init__", false]], "__init__() (bio.phylo.treeconstruction.parsimonytreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor.__init__", false]], "__init__() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.__init__", false]], "__init__() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.__init__", false]], "__init__() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.__init__", false]], "__init__() (bio.popgen.genepop.largefileparser.record method)": [[205, "Bio.PopGen.GenePop.LargeFileParser.Record.__init__", false]], "__init__() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.__init__", false]], "__init__() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.__init__", false]], "__init__() (bio.scop.cla.index method)": [[210, "Bio.SCOP.Cla.Index.__init__", false]], "__init__() (bio.scop.cla.record method)": [[210, "Bio.SCOP.Cla.Record.__init__", false]], "__init__() (bio.scop.des.record method)": [[211, "Bio.SCOP.Des.Record.__init__", false]], "__init__() (bio.scop.dom.record method)": [[212, "Bio.SCOP.Dom.Record.__init__", false]], "__init__() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.__init__", false]], "__init__() (bio.scop.hie.record method)": [[213, "Bio.SCOP.Hie.Record.__init__", false]], "__init__() (bio.scop.node method)": [[209, "Bio.SCOP.Node.__init__", false]], "__init__() (bio.scop.raf.res method)": [[214, "Bio.SCOP.Raf.Res.__init__", false]], "__init__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__init__", false]], "__init__() (bio.scop.raf.seqmapindex method)": [[214, "Bio.SCOP.Raf.SeqMapIndex.__init__", false]], "__init__() (bio.scop.residues.residues method)": [[215, "Bio.SCOP.Residues.Residues.__init__", false]], "__init__() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.__init__", false]], "__init__() (bio.searchio.blastio.blast_tab.blasttabindexer method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__init__", false]], "__init__() (bio.searchio.blastio.blast_tab.blasttabparser method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser.__init__", false]], "__init__() (bio.searchio.blastio.blast_tab.blasttabwriter method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter.__init__", false]], "__init__() (bio.searchio.blastio.blast_xml.blastxmlindexer method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.__init__", false]], "__init__() (bio.searchio.blastio.blast_xml.blastxmlparser method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser.__init__", false]], "__init__() (bio.searchio.blastio.blast_xml.blastxmlwriter method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter.__init__", false]], "__init__() (bio.searchio.blatio.blatpslindexer method)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.__init__", false]], "__init__() (bio.searchio.blatio.blatpslparser method)": [[221, "Bio.SearchIO.BlatIO.BlatPslParser.__init__", false]], "__init__() (bio.searchio.blatio.blatpslwriter method)": [[221, "Bio.SearchIO.BlatIO.BlatPslWriter.__init__", false]], "__init__() (bio.searchio.fastaio.fastam10indexer method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.__init__", false]], "__init__() (bio.searchio.fastaio.fastam10parser method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Parser.__init__", false]], "__init__() (bio.searchio.hhsuiteio.hhsuite2_text.hhsuite2textparser method)": [[228, "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitwriter method)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabparser method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabwriter method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_text.hmmer3textparser method)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser.__init__", false]], "__init__() (bio.searchio.interproscanio.interproscan_xml.interproscanxmlparser method)": [[235, "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser.__init__", false]], "__init__() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.__init__", false]], "__init__() (bio.seq.seq method)": [[236, "Bio.Seq.Seq.__init__", false]], "__init__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__init__", false]], "__init__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__init__", false]], "__init__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__init__", false]], "__init__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__init__", false]], "__init__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__init__", false]], "__init__() (bio.seqio.abiio.abiiterator method)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__init__", false]], "__init__() (bio.seqio.fastaio.fastaiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.__init__", false]], "__init__() (bio.seqio.fastaio.fastatwolineiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.__init__", false]], "__init__() (bio.seqio.fastaio.fastatwolinewriter method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineWriter.__init__", false]], "__init__() (bio.seqio.fastaio.fastawriter method)": [[241, "Bio.SeqIO.FastaIO.FastaWriter.__init__", false]], "__init__() (bio.seqio.gckio.gckiterator method)": [[242, "Bio.SeqIO.GckIO.GckIterator.__init__", false]], "__init__() (bio.seqio.igio.igiterator method)": [[244, "Bio.SeqIO.IgIO.IgIterator.__init__", false]], "__init__() (bio.seqio.insdcio.emblcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.__init__", false]], "__init__() (bio.seqio.insdcio.embliterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.__init__", false]], "__init__() (bio.seqio.insdcio.genbankcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.__init__", false]], "__init__() (bio.seqio.insdcio.genbankiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.__init__", false]], "__init__() (bio.seqio.insdcio.imgtiterator method)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.__init__", false]], "__init__() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__init__", false]], "__init__() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.__init__", false]], "__init__() (bio.seqio.nibio.nibiterator method)": [[247, "Bio.SeqIO.NibIO.NibIterator.__init__", false]], "__init__() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.__init__", false]], "__init__() (bio.seqio.pdbio.pdbseqresiterator method)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__init__", false]], "__init__() (bio.seqio.phdio.phdwriter method)": [[249, "Bio.SeqIO.PhdIO.PhdWriter.__init__", false]], "__init__() (bio.seqio.pirio.piriterator method)": [[250, "Bio.SeqIO.PirIO.PirIterator.__init__", false]], "__init__() (bio.seqio.pirio.pirwriter method)": [[250, "Bio.SeqIO.PirIO.PirWriter.__init__", false]], "__init__() (bio.seqio.qualityio.fastqphrediterator method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__init__", false]], "__init__() (bio.seqio.qualityio.qualphrediterator method)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.__init__", false]], "__init__() (bio.seqio.qualityio.qualphredwriter method)": [[251, "Bio.SeqIO.QualityIO.QualPhredWriter.__init__", false]], "__init__() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.__init__", false]], "__init__() (bio.seqio.seqxmlio.seqxmliterator method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__", false]], "__init__() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__", false]], "__init__() (bio.seqio.sffio.sffiterator method)": [[253, "Bio.SeqIO.SffIO.SffIterator.__init__", false]], "__init__() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.__init__", false]], "__init__() (bio.seqio.snapgeneio.snapgeneiterator method)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__init__", false]], "__init__() (bio.seqio.tabio.tabiterator method)": [[256, "Bio.SeqIO.TabIO.TabIterator.__init__", false]], "__init__() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__init__", false]], "__init__() (bio.seqio.uniprotio.parser method)": [[258, "Bio.SeqIO.UniprotIO.Parser.__init__", false]], "__init__() (bio.seqio.xdnaio.xdnaiterator method)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.__init__", false]], "__init__() (bio.seqio.xdnaio.xdnawriter method)": [[259, "Bio.SeqIO.XdnaIO.XdnaWriter.__init__", false]], "__init__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__init__", false]], "__init__() (bio.sequencing.ace.acefilerecord method)": [[269, "Bio.Sequencing.Ace.ACEFileRecord.__init__", false]], "__init__() (bio.sequencing.ace.af method)": [[269, "Bio.Sequencing.Ace.af.__init__", false]], "__init__() (bio.sequencing.ace.bs method)": [[269, "Bio.Sequencing.Ace.bs.__init__", false]], "__init__() (bio.sequencing.ace.contig method)": [[269, "Bio.Sequencing.Ace.Contig.__init__", false]], "__init__() (bio.sequencing.ace.ct method)": [[269, "Bio.Sequencing.Ace.ct.__init__", false]], "__init__() (bio.sequencing.ace.ds method)": [[269, "Bio.Sequencing.Ace.ds.__init__", false]], "__init__() (bio.sequencing.ace.qa method)": [[269, "Bio.Sequencing.Ace.qa.__init__", false]], "__init__() (bio.sequencing.ace.rd method)": [[269, "Bio.Sequencing.Ace.rd.__init__", false]], "__init__() (bio.sequencing.ace.reads method)": [[269, "Bio.Sequencing.Ace.Reads.__init__", false]], "__init__() (bio.sequencing.ace.rt method)": [[269, "Bio.Sequencing.Ace.rt.__init__", false]], "__init__() (bio.sequencing.ace.wa method)": [[269, "Bio.Sequencing.Ace.wa.__init__", false]], "__init__() (bio.sequencing.ace.wr method)": [[269, "Bio.Sequencing.Ace.wr.__init__", false]], "__init__() (bio.sequencing.applications.bwaaligncommandline method)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwabwaswcommandline method)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwaindexcommandline method)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwamemcommandline method)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwasampecommandline method)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwasamsecommandline method)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.__init__", false]], "__init__() (bio.sequencing.applications.novoaligncommandline method)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolscalmdcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolscatcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsfaidxcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsFaidxCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsfixmatecommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsidxstatscommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsindexcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsIndexCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsmergecommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsmpileupcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsphasecommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsreheadercommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsrmdupcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolstargetcutcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsversion0xsortcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsversion1xsortcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsviewcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.__init__", false]], "__init__() (bio.sequencing.phd.record method)": [[271, "Bio.Sequencing.Phd.Record.__init__", false]], "__init__() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.__init__", false]], "__init__() (bio.sequtils.isoelectricpoint.isoelectricpoint method)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__", false]], "__init__() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__", false]], "__init__() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.__init__", false]], "__init__() (bio.swissprot.keywlist.record method)": [[273, "Bio.SwissProt.KeyWList.Record.__init__", false]], "__init__() (bio.swissprot.record method)": [[272, "Bio.SwissProt.Record.__init__", false]], "__init__() (bio.swissprot.reference method)": [[272, "Bio.SwissProt.Reference.__init__", false]], "__init__() (bio.swissprot.swissprotparsererror method)": [[272, "Bio.SwissProt.SwissProtParserError.__init__", false]], "__init__() (bio.unigene.protsimline method)": [[275, "Bio.UniGene.ProtsimLine.__init__", false]], "__init__() (bio.unigene.record method)": [[275, "Bio.UniGene.Record.__init__", false]], "__init__() (bio.unigene.sequenceline method)": [[275, "Bio.UniGene.SequenceLine.__init__", false]], "__init__() (bio.unigene.stsline method)": [[275, "Bio.UniGene.STSLine.__init__", false]], "__init__() (biosql.bioseq.dbseqrecord method)": [[302, "BioSQL.BioSeq.DBSeqRecord.__init__", false]], "__init__() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.__init__", false]], "__init__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__init__", false]], "__init__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__init__", false]], "__init__() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.__init__", false]], "__init__() (biosql.loader.databaseloader method)": [[305, "BioSQL.Loader.DatabaseLoader.__init__", false]], "__init__() (biosql.loader.databaseremover method)": [[305, "BioSQL.Loader.DatabaseRemover.__init__", false]], "__iter__() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__iter__", false]], "__iter__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__iter__", false]], "__iter__() (bio.alignio.interfaces.alignmentiterator method)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator.__iter__", false]], "__iter__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__iter__", false]], "__iter__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__iter__", false]], "__iter__() (bio.genbank.iterator method)": [[92, "Bio.GenBank.Iterator.__iter__", false]], "__iter__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__iter__", false]], "__iter__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__iter__", false]], "__iter__() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.__iter__", false]], "__iter__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__iter__", false]], "__iter__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__iter__", false]], "__iter__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__iter__", false]], "__iter__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__iter__", false]], "__iter__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__iter__", false]], "__iter__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__iter__", false]], "__iter__() (bio.phylo.phyloxml.other method)": [[197, "Bio.Phylo.PhyloXML.Other.__iter__", false]], "__iter__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_tab.blasttabindexer method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_tab.blasttabparser method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_xml.blastxmlindexer method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_xml.blastxmlparser method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser.__iter__", false]], "__iter__() (bio.searchio.blatio.blatpslindexer method)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.__iter__", false]], "__iter__() (bio.searchio.blatio.blatpslparser method)": [[221, "Bio.SearchIO.BlatIO.BlatPslParser.__iter__", false]], "__iter__() (bio.searchio.fastaio.fastam10indexer method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.__iter__", false]], "__iter__() (bio.searchio.fastaio.fastam10parser method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Parser.__iter__", false]], "__iter__() (bio.searchio.hhsuiteio.hhsuite2_text.hhsuite2textparser method)": [[228, "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabindexer method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabparser method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer method)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_text.hmmer3textparser method)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser.__iter__", false]], "__iter__() (bio.searchio.interproscanio.interproscan_xml.interproscanxmlparser method)": [[235, "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser.__iter__", false]], "__iter__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__iter__", false]], "__iter__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__iter__", false]], "__iter__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__iter__", false]], "__iter__() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__iter__", false]], "__iter__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__iter__", false]], "__iter__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__iter__", false]], "__iter__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__iter__", false]], "__le__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__le__", false]], "__le__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__le__", false]], "__le__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__le__", false]], "__le__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__le__", false]], "__le__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__le__", false]], "__le__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__le__", false]], "__le__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__le__", false]], "__le__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__le__", false]], "__le__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__le__", false]], "__len__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__len__", false]], "__len__() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.__len__", false]], "__len__() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__len__", false]], "__len__() (bio.align.bigbed.alignmentiterator method)": [[36, "Bio.Align.bigbed.AlignmentIterator.__len__", false]], "__len__() (bio.align.hhr.alignmentiterator method)": [[44, "Bio.Align.hhr.AlignmentIterator.__len__", false]], "__len__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__len__", false]], "__len__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__len__", false]], "__len__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__len__", false]], "__len__() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.__len__", false]], "__len__() (bio.emboss.primer3.primers method)": [[81, "Bio.Emboss.Primer3.Primers.__len__", false]], "__len__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__len__", false]], "__len__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__len__", false]], "__len__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__len__", false]], "__len__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__len__", false]], "__len__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__len__", false]], "__len__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__len__", false]], "__len__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__len__", false]], "__len__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__len__", false]], "__len__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__len__", false]], "__len__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__len__", false]], "__len__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__len__", false]], "__len__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__len__", false]], "__len__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__len__", false]], "__len__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__len__", false]], "__len__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__len__", false]], "__len__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__len__", false]], "__len__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__len__", false]], "__len__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__len__", false]], "__len__() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__len__", false]], "__len__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__len__", false]], "__len__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__len__", false]], "__len__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__len__", false]], "__lt__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__lt__", false]], "__lt__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__lt__", false]], "__lt__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__lt__", false]], "__lt__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__lt__", false]], "__lt__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__lt__", false]], "__lt__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__lt__", false]], "__lt__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__lt__", false]], "__lt__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__lt__", false]], "__lt__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__lt__", false]], "__mul__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__mul__", false]], "__mul__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__mul__", false]], "__ne__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__ne__", false]], "__ne__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__ne__", false]], "__ne__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__ne__", false]], "__ne__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__ne__", false]], "__ne__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__ne__", false]], "__ne__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__ne__", false]], "__ne__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__ne__", false]], "__neg__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__neg__", false]], "__new__() (bio.align.alignmentcounts static method)": [[30, "Bio.Align.AlignmentCounts.__new__", false]], "__new__() (bio.align.bigbed.field static method)": [[36, "Bio.Align.bigbed.Field.__new__", false]], "__new__() (bio.align.substitution_matrices.array static method)": [[54, "Bio.Align.substitution_matrices.Array.__new__", false]], "__new__() (bio.entrez.parser.errorelement static method)": [[84, "Bio.Entrez.Parser.ErrorElement.__new__", false]], "__new__() (bio.entrez.parser.integerelement static method)": [[84, "Bio.Entrez.Parser.IntegerElement.__new__", false]], "__new__() (bio.entrez.parser.stringelement static method)": [[84, "Bio.Entrez.Parser.StringElement.__new__", false]], "__new__() (bio.pairwise2.alignment static method)": [[297, "Bio.pairwise2.Alignment.__new__", false]], "__new__() (bio.phylo.phyloxml.confidence static method)": [[197, "Bio.Phylo.PhyloXML.Confidence.__new__", false]], "__new__() (bio.seqfeature.afterposition static method)": [[237, "Bio.SeqFeature.AfterPosition.__new__", false]], "__new__() (bio.seqfeature.beforeposition static method)": [[237, "Bio.SeqFeature.BeforePosition.__new__", false]], "__new__() (bio.seqfeature.betweenposition static method)": [[237, "Bio.SeqFeature.BetweenPosition.__new__", false]], "__new__() (bio.seqfeature.exactposition static method)": [[237, "Bio.SeqFeature.ExactPosition.__new__", false]], "__new__() (bio.seqfeature.oneofposition static method)": [[237, "Bio.SeqFeature.OneOfPosition.__new__", false]], "__new__() (bio.seqfeature.withinposition static method)": [[237, "Bio.SeqFeature.WithinPosition.__new__", false]], "__next__() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.__next__", false]], "__next__() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__next__", false]], "__next__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__next__", false]], "__next__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__next__", false]], "__next__() (bio.alignio.clustalio.clustaliterator method)": [[57, "Bio.AlignIO.ClustalIO.ClustalIterator.__next__", false]], "__next__() (bio.alignio.embossio.embossiterator method)": [[58, "Bio.AlignIO.EmbossIO.EmbossIterator.__next__", false]], "__next__() (bio.alignio.interfaces.alignmentiterator method)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator.__next__", false]], "__next__() (bio.alignio.mauveio.mauveiterator method)": [[62, "Bio.AlignIO.MauveIO.MauveIterator.__next__", false]], "__next__() (bio.alignio.msfio.msfiterator method)": [[63, "Bio.AlignIO.MsfIO.MsfIterator.__next__", false]], "__next__() (bio.alignio.phylipio.phylipiterator method)": [[65, "Bio.AlignIO.PhylipIO.PhylipIterator.__next__", false]], "__next__() (bio.alignio.phylipio.sequentialphylipiterator method)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipIterator.__next__", false]], "__next__() (bio.alignio.stockholmio.stockholmiterator method)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.__next__", false]], "__next__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__next__", false]], "__next__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__next__", false]], "__next__() (bio.genbank.iterator method)": [[92, "Bio.GenBank.Iterator.__next__", false]], "__next__() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.__next__", false]], "__next__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__next__", false]], "__next__() (bio.seqio.abiio.abiiterator method)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__next__", false]], "__next__() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__next__", false]], "__next__() (bio.seqio.pdbio.pdbseqresiterator method)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__next__", false]], "__next__() (bio.seqio.pirio.piriterator method)": [[250, "Bio.SeqIO.PirIO.PirIterator.__next__", false]], "__next__() (bio.seqio.seqxmlio.seqxmliterator method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__next__", false]], "__nonzero__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__nonzero__", false]], "__nonzero__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__nonzero__", false]], "__orig_bases__ (bio.pdb.chain.chain attribute)": [[136, "Bio.PDB.Chain.Chain.__orig_bases__", false]], "__orig_bases__ (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.__orig_bases__", false]], "__orig_bases__ (bio.pdb.model.model attribute)": [[144, "Bio.PDB.Model.Model.__orig_bases__", false]], "__orig_bases__ (bio.pdb.residue.residue attribute)": [[155, "Bio.PDB.Residue.Residue.__orig_bases__", false]], "__orig_bases__ (bio.pdb.structure.structure attribute)": [[160, "Bio.PDB.Structure.Structure.__orig_bases__", false]], "__orig_bases__ (bio.seqio.interfaces.sequenceiterator attribute)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__orig_bases__", false]], "__orig_bases__ (bio.seqio.qualityio.fastqphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__orig_bases__", false]], "__parameters__ (bio.pdb.chain.chain attribute)": [[136, "Bio.PDB.Chain.Chain.__parameters__", false]], "__parameters__ (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.__parameters__", false]], "__parameters__ (bio.pdb.model.model attribute)": [[144, "Bio.PDB.Model.Model.__parameters__", false]], "__parameters__ (bio.pdb.residue.residue attribute)": [[155, "Bio.PDB.Residue.Residue.__parameters__", false]], "__parameters__ (bio.pdb.structure.structure attribute)": [[160, "Bio.PDB.Structure.Structure.__parameters__", false]], "__parameters__ (bio.seqio.abiio.abiiterator attribute)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__parameters__", false]], "__parameters__ (bio.seqio.fastaio.fastaiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.__parameters__", false]], "__parameters__ (bio.seqio.fastaio.fastatwolineiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.__parameters__", false]], "__parameters__ (bio.seqio.gckio.gckiterator attribute)": [[242, "Bio.SeqIO.GckIO.GckIterator.__parameters__", false]], "__parameters__ (bio.seqio.igio.igiterator attribute)": [[244, "Bio.SeqIO.IgIO.IgIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.emblcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.embliterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.genbankcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.genbankiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.imgtiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.__parameters__", false]], "__parameters__ (bio.seqio.interfaces.sequenceiterator attribute)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__parameters__", false]], "__parameters__ (bio.seqio.nibio.nibiterator attribute)": [[247, "Bio.SeqIO.NibIO.NibIterator.__parameters__", false]], "__parameters__ (bio.seqio.pdbio.pdbseqresiterator attribute)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__parameters__", false]], "__parameters__ (bio.seqio.pirio.piriterator attribute)": [[250, "Bio.SeqIO.PirIO.PirIterator.__parameters__", false]], "__parameters__ (bio.seqio.qualityio.fastqphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__parameters__", false]], "__parameters__ (bio.seqio.qualityio.qualphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.__parameters__", false]], "__parameters__ (bio.seqio.seqxmlio.seqxmliterator attribute)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__parameters__", false]], "__parameters__ (bio.seqio.sffio.sffiterator attribute)": [[253, "Bio.SeqIO.SffIO.SffIterator.__parameters__", false]], "__parameters__ (bio.seqio.snapgeneio.snapgeneiterator attribute)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__parameters__", false]], "__parameters__ (bio.seqio.tabio.tabiterator attribute)": [[256, "Bio.SeqIO.TabIO.TabIterator.__parameters__", false]], "__parameters__ (bio.seqio.twobitio.twobititerator attribute)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__parameters__", false]], "__parameters__ (bio.seqio.xdnaio.xdnaiterator attribute)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.__parameters__", false]], "__pow__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__pow__", false]], "__radd__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__radd__", false]], "__radd__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__radd__", false]], "__radd__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__radd__", false]], "__radd__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__radd__", false]], "__reduce__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__reduce__", false]], "__repr__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__repr__", false]], "__repr__() (bio.align.alignmentcounts method)": [[30, "Bio.Align.AlignmentCounts.__repr__", false]], "__repr__() (bio.align.bigbed.field method)": [[36, "Bio.Align.bigbed.Field.__repr__", false]], "__repr__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__repr__", false]], "__repr__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__repr__", false]], "__repr__() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.__repr__", false]], "__repr__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__repr__", false]], "__repr__() (bio.application.applicationerror method)": [[67, "Bio.Application.ApplicationError.__repr__", false]], "__repr__() (bio.blast.hit method)": [[68, "Bio.Blast.Hit.__repr__", false]], "__repr__() (bio.blast.hsp method)": [[68, "Bio.Blast.HSP.__repr__", false]], "__repr__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__repr__", false]], "__repr__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__repr__", false]], "__repr__() (bio.data.codontable.ncbicodontable method)": [[76, "Bio.Data.CodonTable.NCBICodonTable.__repr__", false]], "__repr__() (bio.entrez.parser.dictionaryelement method)": [[84, "Bio.Entrez.Parser.DictionaryElement.__repr__", false]], "__repr__() (bio.entrez.parser.errorelement method)": [[84, "Bio.Entrez.Parser.ErrorElement.__repr__", false]], "__repr__() (bio.entrez.parser.integerelement method)": [[84, "Bio.Entrez.Parser.IntegerElement.__repr__", false]], "__repr__() (bio.entrez.parser.listelement method)": [[84, "Bio.Entrez.Parser.ListElement.__repr__", false]], "__repr__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__repr__", false]], "__repr__() (bio.entrez.parser.orderedlistelement method)": [[84, "Bio.Entrez.Parser.OrderedListElement.__repr__", false]], "__repr__() (bio.entrez.parser.stringelement method)": [[84, "Bio.Entrez.Parser.StringElement.__repr__", false]], "__repr__() (bio.expasy.cellosaurus.record method)": [[90, "Bio.ExPASy.cellosaurus.Record.__repr__", false]], "__repr__() (bio.expasy.enzyme.record method)": [[86, "Bio.ExPASy.Enzyme.Record.__repr__", false]], "__repr__() (bio.genbank.record.feature method)": [[93, "Bio.GenBank.Record.Feature.__repr__", false]], "__repr__() (bio.genbank.record.qualifier method)": [[93, "Bio.GenBank.Record.Qualifier.__repr__", false]], "__repr__() (bio.genbank.utils.featurevaluecleaner method)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.__repr__", false]], "__repr__() (bio.pairwise2.alignment method)": [[297, "Bio.pairwise2.Alignment.__repr__", false]], "__repr__() (bio.pathway.interaction method)": [[177, "Bio.Pathway.Interaction.__repr__", false]], "__repr__() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.__repr__", false]], "__repr__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__repr__", false]], "__repr__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__repr__", false]], "__repr__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__repr__", false]], "__repr__() (bio.pathway.system method)": [[177, "Bio.Pathway.System.__repr__", false]], "__repr__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__repr__", false]], "__repr__() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.__repr__", false]], "__repr__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__repr__", false]], "__repr__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__repr__", false]], "__repr__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__repr__", false]], "__repr__() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.__repr__", false]], "__repr__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__repr__", false]], "__repr__() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.__repr__", false]], "__repr__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__repr__", false]], "__repr__() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.__repr__", false]], "__repr__() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.__repr__", false]], "__repr__() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.__repr__", false]], "__repr__() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.__repr__", false]], "__repr__() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.__repr__", false]], "__repr__() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.__repr__", false]], "__repr__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__repr__", false]], "__repr__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__repr__", false]], "__repr__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__repr__", false]], "__repr__() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.__repr__", false]], "__repr__() (bio.phylo.basetree.treeelement method)": [[183, "Bio.Phylo.BaseTree.TreeElement.__repr__", false]], "__repr__() (bio.seqfeature.afterposition method)": [[237, "Bio.SeqFeature.AfterPosition.__repr__", false]], "__repr__() (bio.seqfeature.beforeposition method)": [[237, "Bio.SeqFeature.BeforePosition.__repr__", false]], "__repr__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__repr__", false]], "__repr__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__repr__", false]], "__repr__() (bio.seqfeature.exactposition method)": [[237, "Bio.SeqFeature.ExactPosition.__repr__", false]], "__repr__() (bio.seqfeature.location method)": [[237, "Bio.SeqFeature.Location.__repr__", false]], "__repr__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__repr__", false]], "__repr__() (bio.seqfeature.position method)": [[237, "Bio.SeqFeature.Position.__repr__", false]], "__repr__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__repr__", false]], "__repr__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__repr__", false]], "__repr__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__repr__", false]], "__repr__() (bio.seqfeature.unknownposition method)": [[237, "Bio.SeqFeature.UnknownPosition.__repr__", false]], "__repr__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__repr__", false]], "__repr__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__repr__", false]], "__repr__() (bio.unigene.protsimline method)": [[275, "Bio.UniGene.ProtsimLine.__repr__", false]], "__repr__() (bio.unigene.record method)": [[275, "Bio.UniGene.Record.__repr__", false]], "__repr__() (bio.unigene.sequenceline method)": [[275, "Bio.UniGene.SequenceLine.__repr__", false]], "__repr__() (bio.unigene.stsline method)": [[275, "Bio.UniGene.STSLine.__repr__", false]], "__repr__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__repr__", false]], "__repr__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__repr__", false]], "__setattr__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__setattr__", false]], "__setattr__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__setattr__", false]], "__setitem__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__setitem__", false]], "__setitem__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__", false]], "__setitem__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__setitem__", false]], "__setitem__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__setitem__", false]], "__setitem__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__setitem__", false]], "__setitem__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__setitem__", false]], "__setitem__() (bio.phylo.treeconstruction.distancematrix method)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix.__setitem__", false]], "__setitem__() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.__setitem__", false]], "__setstate__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__setstate__", false]], "__setstate__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__setstate__", false]], "__slots__ (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.__slots__", false]], "__slots__ (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.__slots__", false]], "__slots__ (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.__slots__", false]], "__slots__ (bio.seq.sequencedataabstractbaseclass attribute)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__slots__", false]], "__str__() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.__str__", false]], "__str__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__str__", false]], "__str__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__str__", false]], "__str__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__str__", false]], "__str__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__str__", false]], "__str__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__str__", false]], "__str__() (bio.application.applicationerror method)": [[67, "Bio.Application.ApplicationError.__str__", false]], "__str__() (bio.blast.corruptedxmlerror method)": [[68, "Bio.Blast.CorruptedXMLError.__str__", false]], "__str__() (bio.blast.hit method)": [[68, "Bio.Blast.Hit.__str__", false]], "__str__() (bio.blast.hsp method)": [[68, "Bio.Blast.HSP.__str__", false]], "__str__() (bio.blast.ncbixml.alignment method)": [[71, "Bio.Blast.NCBIXML.Alignment.__str__", false]], "__str__() (bio.blast.ncbixml.description method)": [[71, "Bio.Blast.NCBIXML.Description.__str__", false]], "__str__() (bio.blast.ncbixml.descriptionextitem method)": [[71, "Bio.Blast.NCBIXML.DescriptionExtItem.__str__", false]], "__str__() (bio.blast.ncbixml.hsp method)": [[71, "Bio.Blast.NCBIXML.HSP.__str__", false]], "__str__() (bio.blast.notxmlerror method)": [[68, "Bio.Blast.NotXMLError.__str__", false]], "__str__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__str__", false]], "__str__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__str__", false]], "__str__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__str__", false]], "__str__() (bio.data.codontable.codontable method)": [[76, "Bio.Data.CodonTable.CodonTable.__str__", false]], "__str__() (bio.emboss.primersearch.inputrecord method)": [[82, "Bio.Emboss.PrimerSearch.InputRecord.__str__", false]], "__str__() (bio.entrez.parser.corruptedxmlerror method)": [[84, "Bio.Entrez.Parser.CorruptedXMLError.__str__", false]], "__str__() (bio.entrez.parser.notxmlerror method)": [[84, "Bio.Entrez.Parser.NotXMLError.__str__", false]], "__str__() (bio.entrez.parser.validationerror method)": [[84, "Bio.Entrez.Parser.ValidationError.__str__", false]], "__str__() (bio.expasy.cellosaurus.record method)": [[90, "Bio.ExPASy.cellosaurus.Record.__str__", false]], "__str__() (bio.expasy.enzyme.record method)": [[86, "Bio.ExPASy.Enzyme.Record.__str__", false]], "__str__() (bio.genbank.record.feature method)": [[93, "Bio.GenBank.Record.Feature.__str__", false]], "__str__() (bio.genbank.record.qualifier method)": [[93, "Bio.GenBank.Record.Qualifier.__str__", false]], "__str__() (bio.genbank.record.record method)": [[93, "Bio.GenBank.Record.Record.__str__", false]], "__str__() (bio.genbank.record.reference method)": [[93, "Bio.GenBank.Record.Reference.__str__", false]], "__str__() (bio.geo.record.record method)": [[97, "Bio.Geo.Record.Record.__str__", false]], "__str__() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.__str__", false]], "__str__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__str__", false]], "__str__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__str__", false]], "__str__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__str__", false]], "__str__() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.__str__", false]], "__str__() (bio.kegg.compound.record method)": [[112, "Bio.KEGG.Compound.Record.__str__", false]], "__str__() (bio.kegg.enzyme.record method)": [[113, "Bio.KEGG.Enzyme.Record.__str__", false]], "__str__() (bio.kegg.gene.record method)": [[114, "Bio.KEGG.Gene.Record.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.relation method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.__str__", false]], "__str__() (bio.markovmodel.markovmodel method)": [[121, "Bio.MarkovModel.MarkovModel.__str__", false]], "__str__() (bio.motifs.clusterbuster.record method)": [[286, "Bio.motifs.clusterbuster.Record.__str__", false]], "__str__() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.__str__", false]], "__str__() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.__str__", false]], "__str__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__str__", false]], "__str__() (bio.motifs.jaspar.record method)": [[287, "Bio.motifs.jaspar.Record.__str__", false]], "__str__() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.__str__", false]], "__str__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__str__", false]], "__str__() (bio.motifs.pfm.record method)": [[293, "Bio.motifs.pfm.Record.__str__", false]], "__str__() (bio.motifs.transfac.record method)": [[295, "Bio.motifs.transfac.Record.__str__", false]], "__str__() (bio.motifs.xms.record method)": [[296, "Bio.motifs.xms.Record.__str__", false]], "__str__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__str__", false]], "__str__() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.__str__", false]], "__str__() (bio.pathway.interaction method)": [[177, "Bio.Pathway.Interaction.__str__", false]], "__str__() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.__str__", false]], "__str__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__str__", false]], "__str__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__str__", false]], "__str__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__str__", false]], "__str__() (bio.pathway.system method)": [[177, "Bio.Pathway.System.__str__", false]], "__str__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__str__", false]], "__str__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__str__", false]], "__str__() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.__str__", false]], "__str__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__str__", false]], "__str__() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.__str__", false]], "__str__() (bio.phylo.basetree.treeelement method)": [[183, "Bio.Phylo.BaseTree.TreeElement.__str__", false]], "__str__() (bio.phylo.phyloxml.accession method)": [[197, "Bio.Phylo.PhyloXML.Accession.__str__", false]], "__str__() (bio.phylo.phyloxml.date method)": [[197, "Bio.Phylo.PhyloXML.Date.__str__", false]], "__str__() (bio.phylo.phyloxml.id method)": [[197, "Bio.Phylo.PhyloXML.Id.__str__", false]], "__str__() (bio.phylo.phyloxml.molseq method)": [[197, "Bio.Phylo.PhyloXML.MolSeq.__str__", false]], "__str__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__str__", false]], "__str__() (bio.phylo.phyloxml.polygon method)": [[197, "Bio.Phylo.PhyloXML.Polygon.__str__", false]], "__str__() (bio.phylo.phyloxml.taxonomy method)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.__str__", false]], "__str__() (bio.phylo.phyloxml.uri method)": [[197, "Bio.Phylo.PhyloXML.Uri.__str__", false]], "__str__() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.__str__", false]], "__str__() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.__str__", false]], "__str__() (bio.scop.cla.record method)": [[210, "Bio.SCOP.Cla.Record.__str__", false]], "__str__() (bio.scop.des.record method)": [[211, "Bio.SCOP.Des.Record.__str__", false]], "__str__() (bio.scop.dom.record method)": [[212, "Bio.SCOP.Dom.Record.__str__", false]], "__str__() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.__str__", false]], "__str__() (bio.scop.hie.record method)": [[213, "Bio.SCOP.Hie.Record.__str__", false]], "__str__() (bio.scop.node method)": [[209, "Bio.SCOP.Node.__str__", false]], "__str__() (bio.scop.residues.residues method)": [[215, "Bio.SCOP.Residues.Residues.__str__", false]], "__str__() (bio.seqfeature.afterposition method)": [[237, "Bio.SeqFeature.AfterPosition.__str__", false]], "__str__() (bio.seqfeature.beforeposition method)": [[237, "Bio.SeqFeature.BeforePosition.__str__", false]], "__str__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__str__", false]], "__str__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__str__", false]], "__str__() (bio.seqfeature.exactposition method)": [[237, "Bio.SeqFeature.ExactPosition.__str__", false]], "__str__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__str__", false]], "__str__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__str__", false]], "__str__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__str__", false]], "__str__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__str__", false]], "__str__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__str__", false]], "__str__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__str__", false]], "__str__() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.__str__", false]], "__sub__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__sub__", false]], "__sub__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__sub__", false]], "__sub__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__sub__", false]], "__sub__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__sub__", false]], "__sub__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__sub__", false]], "__sub__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__sub__", false]], "__sub__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__sub__", false]], "__truediv__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__truediv__", false]], "a (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.a", false]], "a (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.a", false]], "a (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.a", false]], "a (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.A", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.a", false]], "a (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.a", false]], "a (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.A", false]], "a (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.A", false]], "a (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.A", false]], "aacateg (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.aacateg", false]], "aamatrix (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.aamatrix", false]], "aasiz (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.AAsiz", false]], "abiiterator (class in bio.seqio.abiio)": [[239, "Bio.SeqIO.AbiIO.AbiIterator", false]], "abstractatompropertymap (class in bio.pdb.abstractpropertymap)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap", false]], "abstractcommandline (class in bio.application)": [[67, "Bio.Application.AbstractCommandline", false]], "abstractdpalgorithms (class in bio.hmm.dynamicprogramming)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms", false]], "abstractpropertymap (class in bio.pdb.abstractpropertymap)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap", false]], "abstractresiduepropertymap (class in bio.pdb.abstractpropertymap)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap", false]], "abstracttrainer (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.AbstractTrainer", false]], "accept_atom() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_atom", false]], "accept_atom() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_atom", false]], "accept_atoms (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_atoms", false]], "accept_backbone (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_backbone", false]], "accept_chain() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_chain", false]], "accept_chain() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_chain", false]], "accept_deuteriums (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_deuteriums", false]], "accept_hydrogens (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_hydrogens", false]], "accept_mainchain (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_mainchain", false]], "accept_model() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_model", false]], "accept_model() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_model", false]], "accept_residue() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_residue", false]], "accept_residue() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_residue", false]], "accept_resnames (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_resnames", false]], "accept_sidechain (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_sidechain", false]], "accession (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Accession", false]], "accession() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.accession", false]], "accession() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.accession", false]], "acefilerecord (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.ACEFileRecord", false]], "aceiterator() (in module bio.seqio.aceio)": [[240, "Bio.SeqIO.AceIO.AceIterator", false]], "adam_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.adam_consensus", false]], "adapter3 (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.adapter3", false]], "adapter5 (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.adapter5", false]], "adaptor (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.Adaptor", false]], "add() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.add", false]], "add() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.add", false]], "add() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.add", false]], "add() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.add", false]], "add() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.add", false]], "add_annotation() (bio.phylo.nexmlio.parser method)": [[188, "Bio.Phylo.NeXMLIO.Parser.add_annotation", false]], "add_component() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.add_component", false]], "add_count() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.add_count", false]], "add_edge() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.add_edge", false]], "add_edge() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.add_edge", false]], "add_entry() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.add_entry", false]], "add_feature() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.add_feature", false]], "add_graphics() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.add_graphics", false]], "add_interaction() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.add_interaction", false]], "add_label() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.add_label", false]], "add_node() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.add_node", false]], "add_node() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.add_node", false]], "add_point() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.add_point", false]], "add_primer_set() (bio.emboss.primersearch.inputrecord method)": [[82, "Bio.Emboss.PrimerSearch.InputRecord.add_primer_set", false]], "add_product() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.add_product", false]], "add_reaction() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.add_reaction", false]], "add_reaction() (bio.pathway.system method)": [[177, "Bio.Pathway.System.add_reaction", false]], "add_relation() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.add_relation", false]], "add_residue() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.add_residue", false]], "add_sequence() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.add_sequence", false]], "add_set() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.add_set", false]], "add_species() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.add_species", false]], "add_stmt_to_handle() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.add_stmt_to_handle", false]], "add_substrate() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.add_substrate", false]], "add_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.add_succ", false]], "add_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.add_track", false]], "adjustdirection (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.adjustdirection", false]], "adjustdirectionaccurately (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.adjustdirectionaccurately", false]], "af (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.af", false]], "afc (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.afc", false]], "afc_v (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.afc_v", false]], "affine_penalty (class in bio.pairwise2)": [[297, "Bio.pairwise2.affine_penalty", false]], "aformat (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.aformat", false]], "aformat (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.aformat", false]], "aformat (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.aformat", false]], "aformat (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.aformat", false]], "aformat (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.aformat", false]], "afterposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.AfterPosition", false]], "algorithm (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.algorithm", false]], "algorithm (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.algorithm", false]], "align (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.align", false]], "align (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.align", false]], "align() (bio.align.codonaligner method)": [[30, "Bio.Align.CodonAligner.align", false]], "align() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.align", false]], "align() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.align", false]], "aligned (bio.align.alignment property)": [[30, "Bio.Align.Alignment.aligned", false]], "alignment (bio.align.multipleseqalignment property)": [[30, "Bio.Align.MultipleSeqAlignment.alignment", false]], "alignment (bio.phylo.phyloxml.phylogeny property)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.alignment", false]], "alignment (class in bio.align)": [[30, "Bio.Align.Alignment", false]], "alignment (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Alignment", false]], "alignment (class in bio.pairwise2)": [[297, "Bio.pairwise2.Alignment", false]], "alignment_order (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.alignment_order", false]], "alignmentcounts (class in bio.align)": [[30, "Bio.Align.AlignmentCounts", false]], "alignmenthasdifferentlengthserror": [[72, "Bio.CAPS.AlignmentHasDifferentLengthsError", false]], "alignmentiterator (class in bio.align.a2m)": [[33, "Bio.Align.a2m.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bed)": [[35, "Bio.Align.bed.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bigmaf)": [[37, "Bio.Align.bigmaf.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bigpsl)": [[38, "Bio.Align.bigpsl.AlignmentIterator", false]], "alignmentiterator (class in bio.align.chain)": [[39, "Bio.Align.chain.AlignmentIterator", false]], "alignmentiterator (class in bio.align.clustal)": [[40, "Bio.Align.clustal.AlignmentIterator", false]], "alignmentiterator (class in bio.align.emboss)": [[41, "Bio.Align.emboss.AlignmentIterator", false]], "alignmentiterator (class in bio.align.exonerate)": [[42, "Bio.Align.exonerate.AlignmentIterator", false]], "alignmentiterator (class in bio.align.fasta)": [[43, "Bio.Align.fasta.AlignmentIterator", false]], "alignmentiterator (class in bio.align.hhr)": [[44, "Bio.Align.hhr.AlignmentIterator", false]], "alignmentiterator (class in bio.align.interfaces)": [[45, "Bio.Align.interfaces.AlignmentIterator", false]], "alignmentiterator (class in bio.align.maf)": [[46, "Bio.Align.maf.AlignmentIterator", false]], "alignmentiterator (class in bio.align.mauve)": [[47, "Bio.Align.mauve.AlignmentIterator", false]], "alignmentiterator (class in bio.align.msf)": [[48, "Bio.Align.msf.AlignmentIterator", false]], "alignmentiterator (class in bio.align.nexus)": [[49, "Bio.Align.nexus.AlignmentIterator", false]], "alignmentiterator (class in bio.align.phylip)": [[50, "Bio.Align.phylip.AlignmentIterator", false]], "alignmentiterator (class in bio.align.psl)": [[51, "Bio.Align.psl.AlignmentIterator", false]], "alignmentiterator (class in bio.align.sam)": [[52, "Bio.Align.sam.AlignmentIterator", false]], "alignmentiterator (class in bio.align.stockholm)": [[53, "Bio.Align.stockholm.AlignmentIterator", false]], "alignmentiterator (class in bio.align.tabular)": [[55, "Bio.Align.tabular.AlignmentIterator", false]], "alignmentiterator (class in bio.alignio.interfaces)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator", false]], "alignments (class in bio.align)": [[30, "Bio.Align.Alignments", false]], "alignmentsabstractbaseclass (class in bio.align)": [[30, "Bio.Align.AlignmentsAbstractBaseClass", false]], "alignmentwriter (class in bio.align.a2m)": [[33, "Bio.Align.a2m.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bed)": [[35, "Bio.Align.bed.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bigmaf)": [[37, "Bio.Align.bigmaf.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bigpsl)": [[38, "Bio.Align.bigpsl.AlignmentWriter", false]], "alignmentwriter (class in bio.align.chain)": [[39, "Bio.Align.chain.AlignmentWriter", false]], "alignmentwriter (class in bio.align.clustal)": [[40, "Bio.Align.clustal.AlignmentWriter", false]], "alignmentwriter (class in bio.align.exonerate)": [[42, "Bio.Align.exonerate.AlignmentWriter", false]], "alignmentwriter (class in bio.align.fasta)": [[43, "Bio.Align.fasta.AlignmentWriter", false]], "alignmentwriter (class in bio.align.interfaces)": [[45, "Bio.Align.interfaces.AlignmentWriter", false]], "alignmentwriter (class in bio.align.maf)": [[46, "Bio.Align.maf.AlignmentWriter", false]], "alignmentwriter (class in bio.align.mauve)": [[47, "Bio.Align.mauve.AlignmentWriter", false]], "alignmentwriter (class in bio.align.nexus)": [[49, "Bio.Align.nexus.AlignmentWriter", false]], "alignmentwriter (class in bio.align.phylip)": [[50, "Bio.Align.phylip.AlignmentWriter", false]], "alignmentwriter (class in bio.align.psl)": [[51, "Bio.Align.psl.AlignmentWriter", false]], "alignmentwriter (class in bio.align.sam)": [[52, "Bio.Align.sam.AlignmentWriter", false]], "alignmentwriter (class in bio.align.stockholm)": [[53, "Bio.Align.stockholm.AlignmentWriter", false]], "alignmentwriter (class in bio.alignio.interfaces)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter", false]], "all_ids() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.all_ids", false]], "allow_all_transitions() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.allow_all_transitions", false]], "allow_transition() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.allow_transition", false]], "alpha (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.alpha", false]], "alphabet (bio.align.substitution_matrices.array property)": [[54, "Bio.Align.substitution_matrices.Array.alphabet", false]], "alt() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.alt", false]], "altloc_match() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.altloc_match", false]], "ambiguouscodontable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.AmbiguousCodonTable", false]], "ambiguousforwardtable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable", false]], "amino (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.amino", false]], "amino (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.amino", false]], "amino_acids_percent (bio.sequtils.protparam.proteinanalysis property)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.amino_acids_percent", false]], "amplifier (class in bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.Amplifier", false]], "anc (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.anc", false]], "anchors (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.anchors", false]], "anchorspacing (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.anchorspacing", false]], "angle (bio.pdb.internal_coords.dihedron property)": [[169, "Bio.PDB.internal_coords.Dihedron.angle", false]], "angle (bio.pdb.internal_coords.hedron property)": [[169, "Bio.PDB.internal_coords.Hedron.angle", false]], "angle() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.angle", false]], "angle_avg() (bio.pdb.internal_coords.dihedron static method)": [[169, "Bio.PDB.internal_coords.Dihedron.angle_avg", false]], "angle_dif() (bio.pdb.internal_coords.dihedron static method)": [[169, "Bio.PDB.internal_coords.Dihedron.angle_dif", false]], "angle_pop_sd() (bio.pdb.internal_coords.dihedron static method)": [[169, "Bio.PDB.internal_coords.Dihedron.angle_pop_sd", false]], "annot (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.annot", false]], "annot (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.annot", false]], "annotate() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.annotate", false]], "annotatedchromosomesegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment", false]], "annotation (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Annotation", false]], "annotation() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.annotation", false]], "annotation() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.annotation", false]], "annotations (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.annotations", false]], "annotations (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.annotations", false]], "anticonsensus (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.anticonsensus", false]], "anticonsensus (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.anticonsensus", false]], "aoutfeat (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.aoutfeat", false]], "append() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.append", false]], "append() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.append", false]], "append() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.append", false]], "append_item() (bio.blast.ncbixml.descriptionext method)": [[71, "Bio.Blast.NCBIXML.DescriptionExt.append_item", false]], "append_sets() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.append_sets", false]], "applicationerror": [[67, "Bio.Application.ApplicationError", false]], "apply() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.apply", false]], "apply() (bio.pdb.superimposer.superimposer method)": [[163, "Bio.PDB.Superimposer.Superimposer.apply", false]], "applymtx() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.applyMtx", false]], "archive (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.archive", false]], "aromaticity() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.aromaticity", false]], "array (class in bio.align.substitution_matrices)": [[54, "Bio.Align.substitution_matrices.Array", false]], "artemis_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.artemis_color", false]], "as_fasta() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.as_fasta", false]], "as_fasta_2line() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.as_fasta_2line", false]], "as_fastq() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_fastq", false]], "as_fastq_illumina() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_fastq_illumina", false]], "as_fastq_solexa() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_fastq_solexa", false]], "as_handle() (in module bio.file)": [[91, "Bio.File.as_handle", false]], "as_phyloxml() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.as_phyloxml", false]], "as_phyloxml() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.as_phyloxml", false]], "as_qual() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_qual", false]], "as_tab() (in module bio.seqio.tabio)": [[256, "Bio.SeqIO.TabIO.as_tab", false]], "as_type (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.as_type", false]], "asequence (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.asequence", false]], "asequence (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.asequence", false]], "asequence (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.asequence", false]], "asequence (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.asequence", false]], "asequence (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.asequence", false]], "asequence (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.asequence", false]], "assemble() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.assemble", false]], "assemble_residues() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.assemble_residues", false]], "assemble_residues_ser() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.assemble_residues_ser", false]], "astral (class in bio.scop)": [[209, "Bio.SCOP.Astral", false]], "atm() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.atm", false]], "atom (class in bio.pdb.atom)": [[135, "Bio.PDB.Atom.Atom", false]], "atom_chain (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.atom_chain", false]], "atom_re (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.atom_re", false]], "atom_sernum (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.atom_sernum", false]], "atom_to_internal_coordinates() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.atom_to_internal_coordinates", false]], "atom_to_internal_coordinates() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.atom_to_internal_coordinates", false]], "atom_to_internal_coordinates() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.atom_to_internal_coordinates", false]], "atom_to_internal_coordinates() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.atom_to_internal_coordinates", false]], "atomarray (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.atomArray", false]], "atomiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.AtomIterator", false]], "atomkey (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.AtomKey", false]], "auto (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.auto", false]], "auto (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.auto", false]], "auto (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.auto", false]], "auto (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.auto", false]], "auto (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.auto", false]], "auto (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.auto", false]], "auto (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.auto", false]], "auto (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.auto", false]], "auto (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.auto", false]], "auto (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.auto", false]], "auto (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.auto", false]], "auto (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.auto", false]], "auto (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.auto", false]], "auto (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.auto", false]], "auto (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.auto", false]], "auto (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.auto", false]], "auto (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.auto", false]], "auto (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.auto", false]], "auto (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.auto", false]], "auto (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.auto", false]], "auto (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.auto", false]], "auto (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.auto", false]], "auto (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.auto", false]], "auto (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.auto", false]], "auto (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.auto", false]], "auto (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.auto", false]], "auto (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.auto", false]], "autocommit() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.autocommit", false]], "autocommit() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.autocommit", false]], "autocommit() (biosql.dbutils.pgdb_dbutils method)": [[304, "BioSQL.DBUtils.Pgdb_dbutils.autocommit", false]], "autocommit() (biosql.dbutils.psycopg2_dbutils method)": [[304, "BioSQL.DBUtils.Psycopg2_dbutils.autocommit", false]], "autosqltable (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.AutoSQLTable", false]], "b (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.b", false]], "b (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.B", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.b", false]], "b (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.b", false]], "b (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.B", false]], "b (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.b", false]], "b (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.B", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.b", false]], "b (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.b", false]], "b (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.b", false]], "b1 (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.b1", false]], "b2 (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.b2", false]], "back_table (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.back_table", false]], "back_transcribe() (in module bio.seq)": [[236, "Bio.Seq.back_transcribe", false]], "background (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.background", false]], "backward_algorithm() (bio.hmm.dynamicprogramming.abstractdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.backward_algorithm", false]], "bam (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.bam", false]], "bam_file (bio.sequencing.applications.samtoolsreheadercommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline.bam_file", false]], "bams (bio.sequencing.applications.samtoolscatcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.bams", false]], "barchartdistribution (class in bio.graphics.distribution)": [[103, "Bio.Graphics.Distribution.BarChartDistribution", false]], "base_feature_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.BASE_FEATURE_FORMAT", false]], "base_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.BASE_FORMAT", false]], "base_id (bio.motifs.jaspar.motif property)": [[287, "Bio.motifs.jaspar.Motif.base_id", false]], "basefreq (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.basefreq", false]], "basefreq (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.basefreq", false]], "baseml (class in bio.phylo.paml.baseml)": [[193, "Bio.Phylo.PAML.baseml.Baseml", false]], "basemlerror": [[193, "Bio.Phylo.PAML.baseml.BasemlError", false]], "baumwelchtrainer (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer", false]], "bc() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.bc", false]], "beforeposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.BeforePosition", false]], "best (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.best", false]], "best_hit_overhang (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.best_hit_overhang", false]], "best_hit_score_edge (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.best_hit_score_edge", false]], "betweenposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.BetweenPosition", false]], "bf_search() (in module bio.pathway.rep.multigraph)": [[180, "Bio.Pathway.Rep.MultiGraph.bf_search", false]], "bgcolor (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.bgcolor", false]], "bgzfblocks() (in module bio.bgzf)": [[278, "Bio.bgzf.BgzfBlocks", false]], "bgzfreader (class in bio.bgzf)": [[278, "Bio.bgzf.BgzfReader", false]], "bgzfwriter (class in bio.bgzf)": [[278, "Bio.bgzf.BgzfWriter", false]], "binary_characters() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.binary_characters", false]], "binary_characters() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.binary_characters", false]], "binary_constraint (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.binary_constraint", false]], "binarycharacters (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.BinaryCharacters", false]], "binarycifparser (class in bio.pdb.binary_cif)": [[165, "Bio.PDB.binary_cif.BinaryCIFParser", false]], "bio": [[27, "module-Bio", false]], "bio.affy": [[28, "module-Bio.Affy", false]], "bio.affy.celfile": [[29, "module-Bio.Affy.CelFile", false]], "bio.align": [[30, "module-Bio.Align", false]], "bio.align.a2m": [[33, "module-Bio.Align.a2m", false]], "bio.align.aligninfo": [[31, "module-Bio.Align.AlignInfo", false]], "bio.align.analysis": [[34, "module-Bio.Align.analysis", false]], "bio.align.applications": [[32, "module-Bio.Align.Applications", false]], "bio.align.bed": [[35, "module-Bio.Align.bed", false]], "bio.align.bigbed": [[36, "module-Bio.Align.bigbed", false]], "bio.align.bigmaf": [[37, "module-Bio.Align.bigmaf", false]], "bio.align.bigpsl": [[38, "module-Bio.Align.bigpsl", false]], "bio.align.chain": [[39, "module-Bio.Align.chain", false]], "bio.align.clustal": [[40, "module-Bio.Align.clustal", false]], "bio.align.emboss": [[41, "module-Bio.Align.emboss", false]], "bio.align.exonerate": [[42, "module-Bio.Align.exonerate", false]], "bio.align.fasta": [[43, "module-Bio.Align.fasta", false]], "bio.align.hhr": [[44, "module-Bio.Align.hhr", false]], "bio.align.interfaces": [[45, "module-Bio.Align.interfaces", false]], "bio.align.maf": [[46, "module-Bio.Align.maf", false]], "bio.align.mauve": [[47, "module-Bio.Align.mauve", false]], "bio.align.msf": [[48, "module-Bio.Align.msf", false]], "bio.align.nexus": [[49, "module-Bio.Align.nexus", false]], "bio.align.phylip": [[50, "module-Bio.Align.phylip", false]], "bio.align.psl": [[51, "module-Bio.Align.psl", false]], "bio.align.sam": [[52, "module-Bio.Align.sam", false]], "bio.align.stockholm": [[53, "module-Bio.Align.stockholm", false]], "bio.align.substitution_matrices": [[54, "module-Bio.Align.substitution_matrices", false]], "bio.align.tabular": [[55, "module-Bio.Align.tabular", false]], "bio.alignio": [[56, "module-Bio.AlignIO", false]], "bio.alignio.clustalio": [[57, "module-Bio.AlignIO.ClustalIO", false]], "bio.alignio.embossio": [[58, "module-Bio.AlignIO.EmbossIO", false]], "bio.alignio.fastaio": [[59, "module-Bio.AlignIO.FastaIO", false]], "bio.alignio.interfaces": [[60, "module-Bio.AlignIO.Interfaces", false]], "bio.alignio.mafio": [[61, "module-Bio.AlignIO.MafIO", false]], "bio.alignio.mauveio": [[62, "module-Bio.AlignIO.MauveIO", false]], "bio.alignio.msfio": [[63, "module-Bio.AlignIO.MsfIO", false]], "bio.alignio.nexusio": [[64, "module-Bio.AlignIO.NexusIO", false]], "bio.alignio.phylipio": [[65, "module-Bio.AlignIO.PhylipIO", false]], "bio.alignio.stockholmio": [[66, "module-Bio.AlignIO.StockholmIO", false]], "bio.application": [[67, "module-Bio.Application", false]], "bio.bgzf": [[278, "module-Bio.bgzf", false]], "bio.blast": [[68, "module-Bio.Blast", false]], "bio.blast.applications": [[69, "module-Bio.Blast.Applications", false]], "bio.blast.ncbiwww": [[70, "module-Bio.Blast.NCBIWWW", false]], "bio.blast.ncbixml": [[71, "module-Bio.Blast.NCBIXML", false]], "bio.caps": [[72, "module-Bio.CAPS", false]], "bio.cluster": [[73, "module-Bio.Cluster", false]], "bio.codonalign": [[279, "module-Bio.codonalign", false]], "bio.codonalign.codonalignment": [[280, "module-Bio.codonalign.codonalignment", false]], "bio.codonalign.codonseq": [[281, "module-Bio.codonalign.codonseq", false]], "bio.compass": [[74, "module-Bio.Compass", false]], "bio.data": [[75, "module-Bio.Data", false]], "bio.data.codontable": [[76, "module-Bio.Data.CodonTable", false]], "bio.data.iupacdata": [[77, "module-Bio.Data.IUPACData", false]], "bio.data.pdbdata": [[78, "module-Bio.Data.PDBData", false]], "bio.emboss": [[79, "module-Bio.Emboss", false]], "bio.emboss.applications": [[80, "module-Bio.Emboss.Applications", false]], "bio.emboss.primer3": [[81, "module-Bio.Emboss.Primer3", false]], "bio.emboss.primersearch": [[82, "module-Bio.Emboss.PrimerSearch", false]], "bio.entrez": [[83, "module-Bio.Entrez", false]], "bio.entrez.parser": [[84, "module-Bio.Entrez.Parser", false]], "bio.expasy": [[85, "module-Bio.ExPASy", false]], "bio.expasy.cellosaurus": [[90, "module-Bio.ExPASy.cellosaurus", false]], "bio.expasy.enzyme": [[86, "module-Bio.ExPASy.Enzyme", false]], "bio.expasy.prodoc": [[87, "module-Bio.ExPASy.Prodoc", false]], "bio.expasy.prosite": [[88, "module-Bio.ExPASy.Prosite", false]], "bio.expasy.scanprosite": [[89, "module-Bio.ExPASy.ScanProsite", false]], "bio.file": [[91, "module-Bio.File", false]], "bio.genbank": [[92, "module-Bio.GenBank", false]], "bio.genbank.record": [[93, "module-Bio.GenBank.Record", false]], "bio.genbank.scanner": [[94, "module-Bio.GenBank.Scanner", false]], "bio.genbank.utils": [[95, "module-Bio.GenBank.utils", false]], "bio.geo": [[96, "module-Bio.Geo", false]], "bio.geo.record": [[97, "module-Bio.Geo.Record", false]], "bio.graphics": [[98, "module-Bio.Graphics", false]], "bio.graphics.basicchromosome": [[99, "module-Bio.Graphics.BasicChromosome", false]], "bio.graphics.colorspiral": [[100, "module-Bio.Graphics.ColorSpiral", false]], "bio.graphics.comparative": [[101, "module-Bio.Graphics.Comparative", false]], "bio.graphics.displayrepresentation": [[102, "module-Bio.Graphics.DisplayRepresentation", false]], "bio.graphics.distribution": [[103, "module-Bio.Graphics.Distribution", false]], "bio.graphics.genomediagram": [[104, "module-Bio.Graphics.GenomeDiagram", false]], "bio.graphics.kgml_vis": [[105, "module-Bio.Graphics.KGML_vis", false]], "bio.hmm": [[106, "module-Bio.HMM", false]], "bio.hmm.dynamicprogramming": [[107, "module-Bio.HMM.DynamicProgramming", false]], "bio.hmm.markovmodel": [[108, "module-Bio.HMM.MarkovModel", false]], "bio.hmm.trainer": [[109, "module-Bio.HMM.Trainer", false]], "bio.hmm.utilities": [[110, "module-Bio.HMM.Utilities", false]], "bio.kegg": [[111, "module-Bio.KEGG", false]], "bio.kegg.compound": [[112, "module-Bio.KEGG.Compound", false]], "bio.kegg.enzyme": [[113, "module-Bio.KEGG.Enzyme", false]], "bio.kegg.gene": [[114, "module-Bio.KEGG.Gene", false]], "bio.kegg.kgml": [[115, "module-Bio.KEGG.KGML", false]], "bio.kegg.kgml.kgml_parser": [[116, "module-Bio.KEGG.KGML.KGML_parser", false]], "bio.kegg.kgml.kgml_pathway": [[117, "module-Bio.KEGG.KGML.KGML_pathway", false]], "bio.kegg.map": [[118, "module-Bio.KEGG.Map", false]], "bio.kegg.rest": [[119, "module-Bio.KEGG.REST", false]], "bio.knn": [[282, "module-Bio.kNN", false]], "bio.logisticregression": [[120, "module-Bio.LogisticRegression", false]], "bio.markovmodel": [[121, "module-Bio.MarkovModel", false]], "bio.maxentropy": [[122, "module-Bio.MaxEntropy", false]], "bio.medline": [[123, "module-Bio.Medline", false]], "bio.motifs": [[283, "module-Bio.motifs", false]], "bio.motifs.alignace": [[284, "module-Bio.motifs.alignace", false]], "bio.motifs.applications": [[285, "module-Bio.motifs.applications", false]], "bio.motifs.clusterbuster": [[286, "module-Bio.motifs.clusterbuster", false]], "bio.motifs.jaspar": [[287, "module-Bio.motifs.jaspar", false]], "bio.motifs.jaspar.db": [[288, "module-Bio.motifs.jaspar.db", false]], "bio.motifs.mast": [[289, "module-Bio.motifs.mast", false]], "bio.motifs.matrix": [[290, "module-Bio.motifs.matrix", false]], "bio.motifs.meme": [[291, "module-Bio.motifs.meme", false]], "bio.motifs.minimal": [[292, "module-Bio.motifs.minimal", false]], "bio.motifs.pfm": [[293, "module-Bio.motifs.pfm", false]], "bio.motifs.thresholds": [[294, "module-Bio.motifs.thresholds", false]], "bio.motifs.transfac": [[295, "module-Bio.motifs.transfac", false]], "bio.motifs.xms": [[296, "module-Bio.motifs.xms", false]], "bio.naivebayes": [[127, "module-Bio.NaiveBayes", false]], "bio.nexus": [[128, "module-Bio.Nexus", false]], "bio.nexus.nexus": [[129, "module-Bio.Nexus.Nexus", false]], "bio.nexus.nodes": [[130, "module-Bio.Nexus.Nodes", false]], "bio.nexus.standarddata": [[131, "module-Bio.Nexus.StandardData", false]], "bio.nexus.trees": [[132, "module-Bio.Nexus.Trees", false]], "bio.nmr": [[124, "module-Bio.NMR", false]], "bio.nmr.noetools": [[125, "module-Bio.NMR.NOEtools", false]], "bio.nmr.xpktools": [[126, "module-Bio.NMR.xpktools", false]], "bio.pairwise2": [[297, "module-Bio.pairwise2", false]], "bio.pathway": [[177, "module-Bio.Pathway", false]], "bio.pathway.rep": [[178, "module-Bio.Pathway.Rep", false]], "bio.pathway.rep.graph": [[179, "module-Bio.Pathway.Rep.Graph", false]], "bio.pathway.rep.multigraph": [[180, "module-Bio.Pathway.Rep.MultiGraph", false]], "bio.pdb": [[133, "module-Bio.PDB", false]], "bio.pdb.abstractpropertymap": [[134, "module-Bio.PDB.AbstractPropertyMap", false]], "bio.pdb.alphafold_db": [[164, "module-Bio.PDB.alphafold_db", false]], "bio.pdb.atom": [[135, "module-Bio.PDB.Atom", false]], "bio.pdb.binary_cif": [[165, "module-Bio.PDB.binary_cif", false]], "bio.pdb.cealign": [[166, "module-Bio.PDB.cealign", false]], "bio.pdb.chain": [[136, "module-Bio.PDB.Chain", false]], "bio.pdb.dice": [[138, "module-Bio.PDB.Dice", false]], "bio.pdb.dssp": [[137, "module-Bio.PDB.DSSP", false]], "bio.pdb.entity": [[139, "module-Bio.PDB.Entity", false]], "bio.pdb.fragmentmapper": [[140, "module-Bio.PDB.FragmentMapper", false]], "bio.pdb.hsexposure": [[141, "module-Bio.PDB.HSExposure", false]], "bio.pdb.ic_data": [[167, "module-Bio.PDB.ic_data", false]], "bio.pdb.ic_rebuild": [[168, "module-Bio.PDB.ic_rebuild", false]], "bio.pdb.internal_coords": [[169, "module-Bio.PDB.internal_coords", false]], "bio.pdb.mmcif2dict": [[142, "module-Bio.PDB.MMCIF2Dict", false]], "bio.pdb.mmcifio": [[170, "module-Bio.PDB.mmcifio", false]], "bio.pdb.mmcifparser": [[143, "module-Bio.PDB.MMCIFParser", false]], "bio.pdb.mmtf": [[171, "module-Bio.PDB.mmtf", false]], "bio.pdb.mmtf.defaultparser": [[172, "module-Bio.PDB.mmtf.DefaultParser", false]], "bio.pdb.mmtf.mmtfio": [[173, "module-Bio.PDB.mmtf.mmtfio", false]], "bio.pdb.model": [[144, "module-Bio.PDB.Model", false]], "bio.pdb.naccess": [[145, "module-Bio.PDB.NACCESS", false]], "bio.pdb.neighborsearch": [[146, "module-Bio.PDB.NeighborSearch", false]], "bio.pdb.parse_pdb_header": [[174, "module-Bio.PDB.parse_pdb_header", false]], "bio.pdb.pdbexceptions": [[147, "module-Bio.PDB.PDBExceptions", false]], "bio.pdb.pdbio": [[148, "module-Bio.PDB.PDBIO", false]], "bio.pdb.pdblist": [[149, "module-Bio.PDB.PDBList", false]], "bio.pdb.pdbmlparser": [[150, "module-Bio.PDB.PDBMLParser", false]], "bio.pdb.pdbparser": [[151, "module-Bio.PDB.PDBParser", false]], "bio.pdb.picio": [[152, "module-Bio.PDB.PICIO", false]], "bio.pdb.polypeptide": [[154, "module-Bio.PDB.Polypeptide", false]], "bio.pdb.psea": [[153, "module-Bio.PDB.PSEA", false]], "bio.pdb.qcprot": [[175, "module-Bio.PDB.qcprot", false]], "bio.pdb.residue": [[155, "module-Bio.PDB.Residue", false]], "bio.pdb.residuedepth": [[156, "module-Bio.PDB.ResidueDepth", false]], "bio.pdb.sasa": [[157, "module-Bio.PDB.SASA", false]], "bio.pdb.scadio": [[158, "module-Bio.PDB.SCADIO", false]], "bio.pdb.selection": [[159, "module-Bio.PDB.Selection", false]], "bio.pdb.structure": [[160, "module-Bio.PDB.Structure", false]], "bio.pdb.structurealignment": [[161, "module-Bio.PDB.StructureAlignment", false]], "bio.pdb.structurebuilder": [[162, "module-Bio.PDB.StructureBuilder", false]], "bio.pdb.superimposer": [[163, "module-Bio.PDB.Superimposer", false]], "bio.pdb.vectors": [[176, "module-Bio.PDB.vectors", false]], "bio.phenotype": [[298, "module-Bio.phenotype", false]], "bio.phenotype.phen_micro": [[299, "module-Bio.phenotype.phen_micro", false]], "bio.phenotype.pm_fitting": [[300, "module-Bio.phenotype.pm_fitting", false]], "bio.phylo": [[181, "module-Bio.Phylo", false]], "bio.phylo.applications": [[182, "module-Bio.Phylo.Applications", false]], "bio.phylo.basetree": [[183, "module-Bio.Phylo.BaseTree", false]], "bio.phylo.cdao": [[184, "module-Bio.Phylo.CDAO", false]], "bio.phylo.cdaoio": [[185, "module-Bio.Phylo.CDAOIO", false]], "bio.phylo.consensus": [[186, "module-Bio.Phylo.Consensus", false]], "bio.phylo.newick": [[189, "module-Bio.Phylo.Newick", false]], "bio.phylo.newickio": [[190, "module-Bio.Phylo.NewickIO", false]], "bio.phylo.nexml": [[187, "module-Bio.Phylo.NeXML", false]], "bio.phylo.nexmlio": [[188, "module-Bio.Phylo.NeXMLIO", false]], "bio.phylo.nexusio": [[191, "module-Bio.Phylo.NexusIO", false]], "bio.phylo.paml": [[192, "module-Bio.Phylo.PAML", false]], "bio.phylo.paml.baseml": [[193, "module-Bio.Phylo.PAML.baseml", false]], "bio.phylo.paml.chi2": [[194, "module-Bio.Phylo.PAML.chi2", false]], "bio.phylo.paml.codeml": [[195, "module-Bio.Phylo.PAML.codeml", false]], "bio.phylo.paml.yn00": [[196, "module-Bio.Phylo.PAML.yn00", false]], "bio.phylo.phyloxml": [[197, "module-Bio.Phylo.PhyloXML", false]], "bio.phylo.phyloxmlio": [[198, "module-Bio.Phylo.PhyloXMLIO", false]], "bio.phylo.treeconstruction": [[199, "module-Bio.Phylo.TreeConstruction", false]], "bio.popgen": [[200, "module-Bio.PopGen", false]], "bio.popgen.genepop": [[201, "module-Bio.PopGen.GenePop", false]], "bio.popgen.genepop.controller": [[202, "module-Bio.PopGen.GenePop.Controller", false]], "bio.popgen.genepop.easycontroller": [[203, "module-Bio.PopGen.GenePop.EasyController", false]], "bio.popgen.genepop.fileparser": [[204, "module-Bio.PopGen.GenePop.FileParser", false]], "bio.popgen.genepop.largefileparser": [[205, "module-Bio.PopGen.GenePop.LargeFileParser", false]], "bio.restriction": [[206, "module-Bio.Restriction", false]], "bio.restriction.printformat": [[207, "module-Bio.Restriction.PrintFormat", false]], "bio.restriction.restriction_dictionary": [[208, "module-Bio.Restriction.Restriction_Dictionary", false]], "bio.scop": [[209, "module-Bio.SCOP", false]], "bio.scop.cla": [[210, "module-Bio.SCOP.Cla", false]], "bio.scop.des": [[211, "module-Bio.SCOP.Des", false]], "bio.scop.dom": [[212, "module-Bio.SCOP.Dom", false]], "bio.scop.hie": [[213, "module-Bio.SCOP.Hie", false]], "bio.scop.raf": [[214, "module-Bio.SCOP.Raf", false]], "bio.scop.residues": [[215, "module-Bio.SCOP.Residues", false]], "bio.searchio": [[217, "module-Bio.SearchIO", false]], "bio.searchio.blastio": [[218, "module-Bio.SearchIO.BlastIO", false]], "bio.searchio.blastio.blast_tab": [[219, "module-Bio.SearchIO.BlastIO.blast_tab", false]], "bio.searchio.blastio.blast_xml": [[220, "module-Bio.SearchIO.BlastIO.blast_xml", false]], "bio.searchio.blatio": [[221, "module-Bio.SearchIO.BlatIO", false]], "bio.searchio.exonerateio": [[222, "module-Bio.SearchIO.ExonerateIO", false]], "bio.searchio.exonerateio.exonerate_cigar": [[223, "module-Bio.SearchIO.ExonerateIO.exonerate_cigar", false]], "bio.searchio.exonerateio.exonerate_text": [[224, "module-Bio.SearchIO.ExonerateIO.exonerate_text", false]], "bio.searchio.exonerateio.exonerate_vulgar": [[225, "module-Bio.SearchIO.ExonerateIO.exonerate_vulgar", false]], "bio.searchio.fastaio": [[226, "module-Bio.SearchIO.FastaIO", false]], "bio.searchio.hhsuiteio": [[227, "module-Bio.SearchIO.HHsuiteIO", false]], "bio.searchio.hhsuiteio.hhsuite2_text": [[228, "module-Bio.SearchIO.HHsuiteIO.hhsuite2_text", false]], "bio.searchio.hmmerio": [[229, "module-Bio.SearchIO.HmmerIO", false]], "bio.searchio.hmmerio.hmmer2_text": [[230, "module-Bio.SearchIO.HmmerIO.hmmer2_text", false]], "bio.searchio.hmmerio.hmmer3_domtab": [[231, "module-Bio.SearchIO.HmmerIO.hmmer3_domtab", false]], "bio.searchio.hmmerio.hmmer3_tab": [[232, "module-Bio.SearchIO.HmmerIO.hmmer3_tab", false]], "bio.searchio.hmmerio.hmmer3_text": [[233, "module-Bio.SearchIO.HmmerIO.hmmer3_text", false]], "bio.searchio.interproscanio": [[234, "module-Bio.SearchIO.InterproscanIO", false]], "bio.searchio.interproscanio.interproscan_xml": [[235, "module-Bio.SearchIO.InterproscanIO.interproscan_xml", false]], "bio.seq": [[236, "module-Bio.Seq", false]], "bio.seqfeature": [[237, "module-Bio.SeqFeature", false]], "bio.seqio": [[238, "module-Bio.SeqIO", false]], "bio.seqio.abiio": [[239, "module-Bio.SeqIO.AbiIO", false]], "bio.seqio.aceio": [[240, "module-Bio.SeqIO.AceIO", false]], "bio.seqio.fastaio": [[241, "module-Bio.SeqIO.FastaIO", false]], "bio.seqio.gckio": [[242, "module-Bio.SeqIO.GckIO", false]], "bio.seqio.gfaio": [[243, "module-Bio.SeqIO.GfaIO", false]], "bio.seqio.igio": [[244, "module-Bio.SeqIO.IgIO", false]], "bio.seqio.insdcio": [[245, "module-Bio.SeqIO.InsdcIO", false]], "bio.seqio.interfaces": [[246, "module-Bio.SeqIO.Interfaces", false]], "bio.seqio.nibio": [[247, "module-Bio.SeqIO.NibIO", false]], "bio.seqio.pdbio": [[248, "module-Bio.SeqIO.PdbIO", false]], "bio.seqio.phdio": [[249, "module-Bio.SeqIO.PhdIO", false]], "bio.seqio.pirio": [[250, "module-Bio.SeqIO.PirIO", false]], "bio.seqio.qualityio": [[251, "module-Bio.SeqIO.QualityIO", false]], "bio.seqio.seqxmlio": [[252, "module-Bio.SeqIO.SeqXmlIO", false]], "bio.seqio.sffio": [[253, "module-Bio.SeqIO.SffIO", false]], "bio.seqio.snapgeneio": [[254, "module-Bio.SeqIO.SnapGeneIO", false]], "bio.seqio.swissio": [[255, "module-Bio.SeqIO.SwissIO", false]], "bio.seqio.tabio": [[256, "module-Bio.SeqIO.TabIO", false]], "bio.seqio.twobitio": [[257, "module-Bio.SeqIO.TwoBitIO", false]], "bio.seqio.uniprotio": [[258, "module-Bio.SeqIO.UniprotIO", false]], "bio.seqio.xdnaio": [[259, "module-Bio.SeqIO.XdnaIO", false]], "bio.seqrecord": [[260, "module-Bio.SeqRecord", false]], "bio.sequencing": [[268, "module-Bio.Sequencing", false]], "bio.sequencing.ace": [[269, "module-Bio.Sequencing.Ace", false]], "bio.sequencing.applications": [[270, "module-Bio.Sequencing.Applications", false]], "bio.sequencing.phd": [[271, "module-Bio.Sequencing.Phd", false]], "bio.sequtils": [[261, "module-Bio.SeqUtils", false]], "bio.sequtils.checksum": [[262, "module-Bio.SeqUtils.CheckSum", false]], "bio.sequtils.isoelectricpoint": [[263, "module-Bio.SeqUtils.IsoelectricPoint", false]], "bio.sequtils.lcc": [[267, "module-Bio.SeqUtils.lcc", false]], "bio.sequtils.meltingtemp": [[264, "module-Bio.SeqUtils.MeltingTemp", false]], "bio.sequtils.protparam": [[265, "module-Bio.SeqUtils.ProtParam", false]], "bio.sequtils.protparamdata": [[266, "module-Bio.SeqUtils.ProtParamData", false]], "bio.svdsuperimposer": [[216, "module-Bio.SVDSuperimposer", false]], "bio.swissprot": [[272, "module-Bio.SwissProt", false]], "bio.swissprot.keywlist": [[273, "module-Bio.SwissProt.KeyWList", false]], "bio.togows": [[274, "module-Bio.TogoWS", false]], "bio.unigene": [[275, "module-Bio.UniGene", false]], "bio.uniprot": [[276, "module-Bio.UniProt", false]], "bio.uniprot.goa": [[277, "module-Bio.UniProt.GOA", false]], "bionj (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.bionj", false]], "biopythondeprecationwarning": [[27, "Bio.BiopythonDeprecationWarning", false]], "biopythonexperimentalwarning": [[27, "Bio.BiopythonExperimentalWarning", false]], "biopythonparserwarning": [[27, "Bio.BiopythonParserWarning", false]], "biopythonwarning": [[27, "Bio.BiopythonWarning", false]], "bioseqdatabase (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase", false]], "biosql": [[301, "module-BioSQL", false]], "biosql.bioseq": [[302, "module-BioSQL.BioSeq", false]], "biosql.bioseqdatabase": [[303, "module-BioSQL.BioSeqDatabase", false]], "biosql.dbutils": [[304, "module-BioSQL.DBUtils", false]], "biosql.loader": [[305, "module-BioSQL.Loader", false]], "bipartition_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.bipartition_filename", false]], "bits() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.bits", false]], "bl (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.bl", false]], "blast (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Blast", false]], "blastdb_version (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.blastdb_version", false]], "blastparser (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.BlastParser", false]], "blasttabindexer (class in bio.searchio.blastio.blast_tab)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer", false]], "blasttabparser (class in bio.searchio.blastio.blast_tab)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser", false]], "blasttabwriter (class in bio.searchio.blastio.blast_tab)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter", false]], "blastxmlindexer (class in bio.searchio.blastio.blast_xml)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer", false]], "blastxmlparser (class in bio.searchio.blastio.blast_xml)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser", false]], "blastxmlwriter (class in bio.searchio.blastio.blast_xml)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter", false]], "blatpslindexer (class in bio.searchio.blatio)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer", false]], "blatpslparser (class in bio.searchio.blatio)": [[221, "Bio.SearchIO.BlatIO.BlatPslParser", false]], "blatpslwriter (class in bio.searchio.blatio)": [[221, "Bio.SearchIO.BlatIO.BlatPslWriter", false]], "block (bio.seqio.seqxmlio.seqxmliterator attribute)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.BLOCK", false]], "block (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.Block", false]], "block_size (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.block_size", false]], "blocks_per_line (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.BLOCKS_PER_LINE", false]], "blocksize (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.blocksize", false]], "blue() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.blue", false]], "bond_rotate() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.bond_rotate", false]], "bond_set() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.bond_set", false]], "boot (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.boot", false]], "bootlabels (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.bootlabels", false]], "bootstrap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.bootstrap", false]], "bootstrap (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.bootstrap", false]], "bootstrap() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.bootstrap", false]], "bootstrap() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.bootstrap", false]], "bootstrap_branch_lengths (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.bootstrap_branch_lengths", false]], "bootstrap_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.bootstrap_consensus", false]], "bootstrap_seed (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.bootstrap_seed", false]], "bootstrap_trees() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.bootstrap_trees", false]], "bounds (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.bounds", false]], "bounds (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.bounds", false]], "bounds (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.bounds", false]], "boutfeat (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.boutfeat", false]], "branch_length() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.branch_length", false]], "branchcolor (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.BranchColor", false]], "branchcolor (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.BranchColor", false]], "branchlength2support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.branchlength2support", false]], "brenner (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.brenner", false]], "brief (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.brief", false]], "brief (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.brief", false]], "brief (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.brief", false]], "bs (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.bs", false]], "bsequence (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.bsequence", false]], "bsequence (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.bsequence", false]], "bsequence (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.bsequence", false]], "bsequence (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.bsequence", false]], "bsequence (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.bsequence", false]], "bsequence (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.bsequence", false]], "build() (in module bio.codonalign)": [[279, "Bio.codonalign.build", false]], "build_atomarray() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.build_atomArray", false]], "build_edraarrays() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.build_edraArrays", false]], "build_tree() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.build_tree", false]], "build_tree() (bio.phylo.treeconstruction.parsimonytreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor.build_tree", false]], "build_tree() (bio.phylo.treeconstruction.treeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.TreeConstructor.build_tree", false]], "bwaaligncommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline", false]], "bwabwaswcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline", false]], "bwaindexcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline", false]], "bwamemcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline", false]], "bwasampecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline", false]], "bwasamsecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline", false]], "c (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.c", false]], "c (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.c", false]], "c (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.c", false]], "c (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.C", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.c", false]], "c (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.C", false]], "c (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.C", false]], "c (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.c", false]], "ca_depth() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.ca_depth", false]], "cal_dn_ds() (in module bio.codonalign.codonseq)": [[281, "Bio.codonalign.codonseq.cal_dn_ds", false]], "calc_affine_penalty() (in module bio.pairwise2)": [[297, "Bio.pairwise2.calc_affine_penalty", false]], "calc_allele_genotype_freqs() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_allele_genotype_freqs", false]], "calc_angle() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.calc_angle", false]], "calc_dihedral() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.calc_dihedral", false]], "calc_diversities_fis_with_identity() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_diversities_fis_with_identity", false]], "calc_diversities_fis_with_size() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_diversities_fis_with_size", false]], "calc_fst_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_fst_all", false]], "calc_fst_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_fst_pair", false]], "calc_ibd() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.calc_ibd", false]], "calc_ibd_diplo() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_ibd_diplo", false]], "calc_ibd_haplo() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_ibd_haplo", false]], "calc_rho_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_rho_all", false]], "calc_rho_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_rho_pair", false]], "calculate() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.calculate", false]], "calculate() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.calculate", false]], "calculate() (in module bio.knn)": [[282, "Bio.kNN.calculate", false]], "calculate() (in module bio.logisticregression)": [[120, "Bio.LogisticRegression.calculate", false]], "calculate() (in module bio.maxentropy)": [[122, "Bio.MaxEntropy.calculate", false]], "calculate() (in module bio.naivebayes)": [[127, "Bio.NaiveBayes.calculate", false]], "calculate_consensus() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.calculate_consensus", false]], "calculate_dn_ds() (in module bio.align.analysis)": [[34, "Bio.Align.analysis.calculate_dn_ds", false]], "calculate_dn_ds_matrix() (in module bio.align.analysis)": [[34, "Bio.Align.analysis.calculate_dn_ds_matrix", false]], "calculate_pseudocounts() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.calculate_pseudocounts", false]], "cappbuilder (class in bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.CaPPBuilder", false]], "capsmap (class in bio.caps)": [[72, "Bio.CAPS.CAPSMap", false]], "carboxyl (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.carboxyl", false]], "case (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.case", false]], "cat (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.cat", false]], "categories (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.categories", false]], "catergories (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.catergories", false]], "catergories (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.catergories", false]], "cdao_to_obo() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.cdao_to_obo", false]], "cdf_chi2() (in module bio.phylo.paml.chi2)": [[194, "Bio.Phylo.PAML.chi2.cdf_chi2", false]], "cealigner (class in bio.pdb.cealign)": [[166, "Bio.PDB.cealign.CEAligner", false]], "center (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.center", false]], "center_of_mass() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.center_of_mass", false]], "center_of_mass() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.center_of_mass", false]], "centre (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.centre", false]], "chain (class in bio.nexus.nodes)": [[130, "Bio.Nexus.Nodes.Chain", false]], "chain (class in bio.pdb.chain)": [[136, "Bio.PDB.Chain.Chain", false]], "chainexception": [[130, "Bio.Nexus.Nodes.ChainException", false]], "chainselector (class in bio.pdb.dice)": [[138, "Bio.PDB.Dice.ChainSelector", false]], "characterdatahandlerescape() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.characterDataHandlerEscape", false]], "characterdatahandlerraw() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.characterDataHandlerRaw", false]], "characters() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.characters", false]], "characters() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.characters", false]], "charbuffer (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.CharBuffer", false]], "charge_at_ph() (bio.sequtils.isoelectricpoint.isoelectricpoint method)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.charge_at_pH", false]], "charge_at_ph() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.charge_at_pH", false]], "check (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.check", false]], "checkpoints (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.checkpoints", false]], "chem_correction() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.chem_correction", false]], "child_dict (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.child_dict", false]], "child_edges() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.child_edges", false]], "child_edges() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.child_edges", false]], "child_list (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.child_list", false]], "children() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.children", false]], "children() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.children", false]], "chromosome (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.Chromosome", false]], "chromosomecounts (class in bio.graphics.displayrepresentation)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts", false]], "chromosomesegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.ChromosomeSegment", false]], "cifatomiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.CifAtomIterator", false]], "cifseqresiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.CifSeqresIterator", false]], "clade (bio.phylo.basetree.tree property)": [[183, "Bio.Phylo.BaseTree.Tree.clade", false]], "clade (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.Clade", false]], "clade (class in bio.phylo.cdao)": [[184, "Bio.Phylo.CDAO.Clade", false]], "clade (class in bio.phylo.newick)": [[189, "Bio.Phylo.Newick.Clade", false]], "clade (class in bio.phylo.nexml)": [[187, "Bio.Phylo.NeXML.Clade", false]], "clade (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Clade", false]], "clade() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.clade", false]], "clade_relation() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.clade_relation", false]], "clade_relation() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.clade_relation", false]], "claderelation (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.CladeRelation", false]], "classify() (in module bio.knn)": [[282, "Bio.kNN.classify", false]], "classify() (in module bio.logisticregression)": [[120, "Bio.LogisticRegression.classify", false]], "classify() (in module bio.maxentropy)": [[122, "Bio.MaxEntropy.classify", false]], "classify() (in module bio.naivebayes)": [[127, "Bio.NaiveBayes.classify", false]], "clean() (bio.alignio.interfaces.alignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter.clean", false]], "clean() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.clean", false]], "clean_value() (bio.genbank.utils.featurevaluecleaner method)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.clean_value", false]], "clear_ic() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.clear_ic", false]], "clear_transforms() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.clear_transforms", false]], "close (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.close", false]], "close() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.close", false]], "close() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.close", false]], "close() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.close", false]], "close() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.close", false]], "close() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.close", false]], "clustaliterator (class in bio.alignio.clustalio)": [[57, "Bio.AlignIO.ClustalIO.ClustalIterator", false]], "clustalomegacommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline", false]], "clustalout (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.clustalout", false]], "clustalw (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.clustalw", false]], "clustalw (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.clustalw", false]], "clustalwcommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.ClustalwCommandline", false]], "clustalwriter (class in bio.alignio.clustalio)": [[57, "Bio.AlignIO.ClustalIO.ClustalWriter", false]], "cluster (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.cluster", false]], "cluster1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.cluster1", false]], "cluster2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.cluster2", false]], "cluster_threshold (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.cluster_threshold", false]], "cluster_threshold_fast (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.cluster_threshold_fast", false]], "clustercentroids() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.clustercentroids", false]], "clustercentroids() (in module bio.cluster)": [[73, "Bio.Cluster.clustercentroids", false]], "clusterdistance() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.clusterdistance", false]], "clusterdistance() (in module bio.cluster)": [[73, "Bio.Cluster.clusterdistance", false]], "clustering (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.clustering", false]], "clusteringout (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.clusteringout", false]], "clustersize (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.clustersize", false]], "clw (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clw", false]], "clwout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clwout", false]], "clwstrict (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clwstrict", false]], "clwstrictout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clwstrictout", false]], "cmodulo (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.Cmodulo", false]], "cmp_sccs() (in module bio.scop)": [[209, "Bio.SCOP.cmp_sccs", false]], "code() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.code", false]], "codeml (class in bio.phylo.paml.codeml)": [[195, "Bio.Phylo.PAML.codeml.Codeml", false]], "codemlerror": [[195, "Bio.Phylo.PAML.codeml.CodemlError", false]], "codon (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.codon", false]], "codonadaptationindex (class in bio.sequtils)": [[261, "Bio.SeqUtils.CodonAdaptationIndex", false]], "codonaligner (class in bio.align)": [[30, "Bio.Align.CodonAligner", false]], "codonalignment (class in bio.codonalign.codonalignment)": [[280, "Bio.codonalign.codonalignment.CodonAlignment", false]], "codonseq (class in bio.codonalign.codonseq)": [[281, "Bio.codonalign.codonseq.CodonSeq", false]], "codontable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.CodonTable", false]], "collapse() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.collapse", false]], "collapse() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.collapse", false]], "collapse_all() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.collapse_all", false]], "collapse_genera() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.collapse_genera", false]], "color (bio.phylo.basetree.clade property)": [[183, "Bio.Phylo.BaseTree.Clade.color", false]], "color() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.color", false]], "color() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.color", false]], "color_names (bio.phylo.basetree.branchcolor attribute)": [[183, "Bio.Phylo.BaseTree.BranchColor.color_names", false]], "color_to_reportlab() (in module bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.color_to_reportlab", false]], "colorspiral (class in bio.graphics.colorspiral)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral", false]], "colortranslator (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator", false]], "column_annotations (bio.align.multipleseqalignment property)": [[30, "Bio.Align.MultipleSeqAlignment.column_annotations", false]], "combine() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.combine", false]], "commandline (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.Commandline", false]], "comment (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.comment", false]], "commit() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.commit", false]], "commit() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.commit", false]], "common_ancestor() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.common_ancestor", false]], "common_ancestor() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.common_ancestor", false]], "common_name() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.common_name", false]], "comp_based_stats (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.comp_based_stats", false]], "comparativescatterplot (class in bio.graphics.comparative)": [[101, "Bio.Graphics.Comparative.ComparativeScatterPlot", false]], "compare_residues() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.compare_residues", false]], "complement (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.complement", false]], "complement() (in module bio.seq)": [[236, "Bio.Seq.complement", false]], "complement_rna() (in module bio.seq)": [[236, "Bio.Seq.complement_rna", false]], "component (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component", false]], "compoundlocation (class in bio.seqfeature)": [[237, "Bio.SeqFeature.CompoundLocation", false]], "compounds (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.compounds", false]], "compute() (bio.pdb.sasa.shrakerupley method)": [[157, "Bio.PDB.SASA.ShrakeRupley.compute", false]], "confidence (bio.phylo.phyloxml.clade property)": [[197, "Bio.Phylo.PhyloXML.Clade.confidence", false]], "confidence (bio.phylo.phyloxml.phylogeny property)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.confidence", false]], "confidence (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Confidence", false]], "confidence() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.confidence", false]], "confidence() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.confidence", false]], "consensus (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.consensus", false]], "consensus (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.consensus", false]], "consensus() (in module bio.nexus.trees)": [[132, "Bio.Nexus.Trees.consensus", false]], "consistency (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.consistency", false]], "consistency (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.consistency", false]], "consolewidth (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth", false]], "constant() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.constant", false]], "constraints (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.constraints", false]], "constraintweight (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.constraintWeight", false]], "contenthandler (class in bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler", false]], "contenthandler (class in bio.seqio.seqxmlio)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler", false]], "contig (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.Contig", false]], "convert (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.convert", false]], "convert (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.convert", false]], "convert (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.convert", false]], "convert() (in module bio.alignio)": [[56, "Bio.AlignIO.convert", false]], "convert() (in module bio.searchio)": [[217, "Bio.SearchIO.convert", false]], "convert() (in module bio.seqio)": [[238, "Bio.SeqIO.convert", false]], "convert() (in module bio.togows)": [[274, "Bio.TogoWS.convert", false]], "convert_absolute_support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.convert_absolute_support", false]], "coord_space() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.coord_space", false]], "coords (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.coords", false]], "copy() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.copy", false]], "copy() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.copy", false]], "copy() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.copy", false]], "copy() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.copy", false]], "copy() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.copy", false]], "copy_initncacs() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.copy_initNCaCs", false]], "core (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.core", false]], "cores (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.cores", false]], "corruptedxmlerror": [[68, "Bio.Blast.CorruptedXMLError", false], [84, "Bio.Entrez.Parser.CorruptedXMLError", false]], "count() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.count", false]], "count() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.count", false]], "count() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.count", false]], "count_amino_acids() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.count_amino_acids", false]], "count_terminals() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.count_terminals", false]], "count_terminals() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.count_terminals", false]], "counts() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.counts", false]], "cr_class() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.cr_class", false]], "crc32() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.crc32", false]], "crc64() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.crc64", false]], "create() (in module bio.motifs)": [[283, "Bio.motifs.create", false]], "create_contingency_tables() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.create_contingency_tables", false]], "crop_matrix() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.crop_matrix", false]], "crosslink (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink", false]], "cs (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.cs", false]], "cstatus() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.cstatus", false]], "csviterator() (in module bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.CsvIterator", false]], "ct (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.ct", false]], "culling_limit (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.culling_limit", false]], "cut() (bio.cluster.tree method)": [[73, "Bio.Cluster.Tree.cut", false]], "cw (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.cw", false]], "d (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.d", false]], "d (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.d", false]], "d (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.d", false]], "d (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.D", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.d", false]], "d2h (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.d2h", false]], "darken() (in module bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.darken", false]], "data (bio.blast.records property)": [[68, "Bio.Blast.Records.data", false]], "data_generator() (bio.popgen.genepop.largefileparser.record method)": [[205, "Bio.PopGen.GenePop.LargeFileParser.Record.data_generator", false]], "data_quartiles() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.data_quartiles", false]], "data_table() (in module bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.data_table", false]], "database (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.database", false]], "databaseloader (class in biosql.loader)": [[305, "BioSQL.Loader.DatabaseLoader", false]], "databaseremover (class in biosql.loader)": [[305, "BioSQL.Loader.DatabaseRemover", false]], "databasereport (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.DatabaseReport", false]], "datafile (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.datafile", false]], "datafile (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.datafile", false]], "datafile (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.datafile", false]], "datafile (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.datafile", false]], "datafile (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.datafile", false]], "datahandler (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.DataHandler", false]], "datahandlermeta (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.DataHandlerMeta", false]], "datatype (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.datatype", false]], "date (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Date", false]], "date() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.date", false]], "date() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.date", false]], "db (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.db", false]], "db (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.db", false]], "db (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.db", false]], "db (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.db", false]], "db (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.db", false]], "db (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.db", false]], "db (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.db", false]], "db (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db", false]], "db (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db", false]], "db_gencode (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db_gencode", false]], "db_gencode (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db_gencode", false]], "db_hard_mask (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db_hard_mask", false]], "db_soft_mask (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db_soft_mask", false]], "dbseqrecord (class in biosql.bioseq)": [[302, "BioSQL.BioSeq.DBSeqRecord", false]], "dbserver (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.DBServer", false]], "dbsize (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.dbsize", false]], "dbtype (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.dbtype", false]], "dbxrefs (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.dbxrefs", false]], "dbxrefs (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.dbxrefs", false]], "dcoordspace (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.dCoordSpace", false]], "dcsvalid (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.dcsValid", false]], "dealign (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.dealign", false]], "debug (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.debug", false]], "debug (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.debug", false]], "debug (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.debug", false]], "debug (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.debug", false]], "debug (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.debug", false]], "debug (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.debug", false]], "debug (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.debug", false]], "debug (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.debug", false]], "debug (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.debug", false]], "debug (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.debug", false]], "debug (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.debug", false]], "debug (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.debug", false]], "debug (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.debug", false]], "debug (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.debug", false]], "debug (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.debug", false]], "debug (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.debug", false]], "debug (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.debug", false]], "debug (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.debug", false]], "debug (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.debug", false]], "debug (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.debug", false]], "debug (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.debug", false]], "debug (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.debug", false]], "debug (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.debug", false]], "debug (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.debug", false]], "debug (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.debug", false]], "decode() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.decode", false]], "default (bio.align.bigbed.autosqltable attribute)": [[36, "Bio.Align.bigbed.AutoSQLTable.default", false]], "default_pseudo (bio.hmm.markovmodel.markovmodelbuilder attribute)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.DEFAULT_PSEUDO", false]], "defined (bio.seq.sequencedataabstractbaseclass property)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.defined", false]], "defined_ranges (bio.seq.sequencedataabstractbaseclass property)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.defined_ranges", false]], "degenerate_consensus (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.degenerate_consensus", false]], "degenerate_consensus (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.degenerate_consensus", false]], "del_feature() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.del_feature", false]], "del_graph() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.del_graph", false]], "del_set() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.del_set", false]], "del_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.del_track", false]], "depths() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.depths", false]], "desc() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.desc", false]], "description (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Description", false]], "description() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.description", false]], "descriptionext (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.DescriptionExt", false]], "descriptionextitem (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.DescriptionExtItem", false]], "destroy_transition() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.destroy_transition", false]], "detach_child() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.detach_child", false]], "detach_parent() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.detach_parent", false]], "detach_parent() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.detach_parent", false]], "detach_parent() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.detach_parent", false]], "df_search() (in module bio.pathway.rep.multigraph)": [[180, "Bio.Pathway.Rep.MultiGraph.df_search", false]], "diagbreak (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diagbreak", false]], "diaglength (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diaglength", false]], "diagmargin (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diagmargin", false]], "diagram (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.Diagram", false]], "diags (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diags", false]], "dialigncommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.DialignCommandline", false]], "dictionary_match (class in bio.pairwise2)": [[297, "Bio.pairwise2.dictionary_match", false]], "dictionaryelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.DictionaryElement", false]], "die (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.die", false]], "die (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.die", false]], "die (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.die", false]], "die (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.die", false]], "die (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.die", false]], "die (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.die", false]], "die (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.die", false]], "die (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.die", false]], "die (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.die", false]], "die (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.die", false]], "die (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.die", false]], "die (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.die", false]], "die (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.die", false]], "die (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.die", false]], "die (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.die", false]], "die (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.die", false]], "die (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.die", false]], "die (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.die", false]], "die (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.die", false]], "die (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.die", false]], "die (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.die", false]], "die (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.die", false]], "die (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.die", false]], "die (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.die", false]], "die (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.die", false]], "difference() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.difference", false]], "differentialcutsite (class in bio.caps)": [[72, "Bio.CAPS.DifferentialCutsite", false]], "diffseqcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.DiffseqCommandline", false]], "dihedral_signs() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.dihedral_signs", false]], "dihedron (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.Dihedron", false]], "dimer (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.dimer", false]], "directory (bio.entrez.parser.datahandlermeta property)": [[84, "Bio.Entrez.Parser.DataHandlerMeta.directory", false]], "disordered_add() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.disordered_add", false]], "disordered_add() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add", false]], "disordered_add() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.disordered_add", false]], "disordered_get() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get", false]], "disordered_get_id_list() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_id_list", false]], "disordered_get_list() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.disordered_get_list", false]], "disordered_get_list() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list", false]], "disordered_has_id() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_has_id", false]], "disordered_remove() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.disordered_remove", false]], "disordered_remove() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_remove", false]], "disordered_remove() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.disordered_remove", false]], "disordered_select() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select", false]], "disorderedatom (class in bio.pdb.atom)": [[135, "Bio.PDB.Atom.DisorderedAtom", false]], "disorderedentitywrapper (class in bio.pdb.entity)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper", false]], "disorderedresidue (class in bio.pdb.residue)": [[155, "Bio.PDB.Residue.DisorderedResidue", false]], "display() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.display", false]], "dist_pearson() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.dist_pearson", false]], "dist_pearson_at() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.dist_pearson_at", false]], "distance() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.distance", false]], "distance() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.distance", false]], "distance1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.distance1", false]], "distance2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.distance2", false]], "distance_plot() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.distance_plot", false]], "distance_to_internal_coordinates() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.distance_to_internal_coordinates", false]], "distancecalculator (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator", false]], "distancematrix (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix", false]], "distancematrix() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.distancematrix", false]], "distancematrix() (in module bio.cluster)": [[73, "Bio.Cluster.distancematrix", false]], "distancetreeconstructor (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor", false]], "distmat_full (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_full", false]], "distmat_full_iter (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_full_iter", false]], "distmat_in (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_in", false]], "distmat_out (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_out", false]], "distplot_to_dh_arrays() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.distplot_to_dh_arrays", false]], "distribution (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Distribution", false]], "distribution() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.distribution", false]], "distribution() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.distribution", false]], "distribution() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.distribution", false]], "distributionpage (class in bio.graphics.distribution)": [[103, "Bio.Graphics.Distribution.DistributionPage", false]], "disulphides (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.disulphides", false]], "dna_models (bio.phylo.treeconstruction.distancecalculator attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.dna_models", false]], "dnaconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.dnaconc", false]], "dnafreqs (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.dnafreqs", false]], "dnamatrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.dnamatrix", false]], "domain (class in bio.scop)": [[209, "Bio.SCOP.Domain", false]], "domain() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.domain", false]], "domain() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.domain", false]], "domain_architecture() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.domain_architecture", false]], "domain_architecture() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.domain_architecture", false]], "domain_inclusion_ethresh (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.domain_inclusion_ethresh", false]], "domainarchitecture (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.DomainArchitecture", false]], "domainsclusteredbyev() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.domainsClusteredByEv", false]], "domainsclusteredbyid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.domainsClusteredById", false]], "dotdiff (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.dotdiff", false]], "dotdiff (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.dotdiff", false]], "dotdiff (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.dotdiff", false]], "dots (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.dots", false]], "download_all_assemblies() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_all_assemblies", false]], "download_cif_for() (in module bio.pdb.alphafold_db)": [[164, "Bio.PDB.alphafold_db.download_cif_for", false]], "download_entire_pdb() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_entire_pdb", false]], "download_obsolete_entries() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_obsolete_entries", false]], "download_pdb_files() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_pdb_files", false]], "dpparttree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.dpparttree", false]], "draw() (bio.graphics.basicchromosome.chromosome method)": [[99, "Bio.Graphics.BasicChromosome.Chromosome.draw", false]], "draw() (bio.graphics.basicchromosome.chromosomesegment method)": [[99, "Bio.Graphics.BasicChromosome.ChromosomeSegment.draw", false]], "draw() (bio.graphics.basicchromosome.organism method)": [[99, "Bio.Graphics.BasicChromosome.Organism.draw", false]], "draw() (bio.graphics.basicchromosome.spacersegment method)": [[99, "Bio.Graphics.BasicChromosome.SpacerSegment.draw", false]], "draw() (bio.graphics.distribution.barchartdistribution method)": [[103, "Bio.Graphics.Distribution.BarChartDistribution.draw", false]], "draw() (bio.graphics.distribution.distributionpage method)": [[103, "Bio.Graphics.Distribution.DistributionPage.draw", false]], "draw() (bio.graphics.distribution.linedistribution method)": [[103, "Bio.Graphics.Distribution.LineDistribution.draw", false]], "draw() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.draw", false]], "draw() (bio.graphics.kgml_vis.kgmlcanvas method)": [[105, "Bio.Graphics.KGML_vis.KGMLCanvas.draw", false]], "draw_to_file() (bio.graphics.comparative.comparativescatterplot method)": [[101, "Bio.Graphics.Comparative.ComparativeScatterPlot.draw_to_file", false]], "ds (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ds", false]], "ds (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.ds", false]], "dssp (class in bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.DSSP", false]], "dssp_dict_from_pdb_file() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.dssp_dict_from_pdb_file", false]], "dtype (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.dtype", false]], "dumb_consensus() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.dumb_consensus", false]], "duplications() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.duplications", false]], "dust (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.dust", false]], "e (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.E", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.e", false]], "e (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.E", false]], "e (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.E", false], [270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.e", false]], "e (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.E", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.e", false]], "ease (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.ease", false]], "easycontroller (class in bio.popgen.genepop.easycontroller)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController", false]], "ecitmatch() (in module bio.entrez)": [[83, "Bio.Entrez.ecitmatch", false]], "edges() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.edges", false]], "edges() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.edges", false]], "edron (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.Edron", false]], "edron_re (bio.pdb.internal_coords.edron attribute)": [[169, "Bio.PDB.internal_coords.Edron.edron_re", false]], "efetch() (in module bio.entrez)": [[83, "Bio.Entrez.efetch", false]], "egquery() (in module bio.entrez)": [[83, "Bio.Entrez.egquery", false]], "einfo() (in module bio.entrez)": [[83, "Bio.Entrez.einfo", false]], "einvertedcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.EInvertedCommandline", false]], "element (bio.kegg.kgml.kgml_pathway.component property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component.element", false]], "element (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.element", false]], "element (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.element", false]], "element (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.element", false]], "element (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.element", false]], "element (bio.kegg.kgml.kgml_pathway.relation property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.element", false]], "elementdecl() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.elementDecl", false]], "elink() (in module bio.entrez)": [[83, "Bio.Entrez.elink", false]], "em0 (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.em0", false]], "em1 (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.em1", false]], "em2 (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.em2", false]], "embl_indent (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.EMBL_INDENT", false]], "embl_spacer (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.EMBL_SPACER", false]], "emblcdsfeatureiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator", false]], "embliterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator", false]], "emblscanner (class in bio.genbank.scanner)": [[94, "Bio.GenBank.Scanner.EmblScanner", false]], "emblwriter (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter", false]], "embossiterator (class in bio.alignio.embossio)": [[58, "Bio.AlignIO.EmbossIO.EmbossIterator", false]], "emissions (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.emissions", false]], "empty_status_characters (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.empty_status_characters", false]], "end (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.end", false]], "end (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.end", false]], "end (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.end", false]], "enda (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.endA", false]], "endb (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.endB", false]], "enddbrefelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endDBRefElement", false]], "enddescriptionelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endDescriptionElement", false]], "endelement() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.endElement", false]], "endelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endElementHandler", false]], "endentryelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endEntryElement", false]], "enderrorelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endErrorElementHandler", false]], "endextend (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.endextend", false]], "endextend (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.endextend", false]], "endgaps (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.endgaps", false]], "endintegerelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endIntegerElementHandler", false]], "endnamespacedeclhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endNamespaceDeclHandler", false]], "endopen (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.endopen", false]], "endopen (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.endopen", false]], "endpropertyelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endPropertyElement", false]], "endrawelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endRawElementHandler", false]], "endsequenceelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endSequenceElement", false]], "endseqxmlelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endSeqXMLElement", false]], "endskipelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endSkipElementHandler", false]], "endspecieselement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endSpeciesElement", false]], "endstringelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endStringElementHandler", false]], "endswith() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.endswith", false]], "endweight (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.endweight", false]], "endweight (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.endweight", false]], "entity (class in bio.pdb.entity)": [[139, "Bio.PDB.Entity.Entity", false]], "entrez_query (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.entrez_query", false]], "entry (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.entry", false]], "entry (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry", false]], "entry() (in module bio.togows)": [[274, "Bio.TogoWS.entry", false]], "entry1 (bio.kegg.kgml.kgml_pathway.relation property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.entry1", false]], "entry2 (bio.kegg.kgml.kgml_pathway.relation property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.entry2", false]], "enumerate_atoms() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.enumerate_atoms", false]], "ep (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.ep", false]], "epost() (in module bio.entrez)": [[83, "Bio.Entrez.epost", false]], "epsilon (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.epsilon", false]], "equal_weight() (in module bio.knn)": [[282, "Bio.kNN.equal_weight", false]], "error (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.error", false]], "error (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.error", false]], "error (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.error", false]], "error (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.error", false]], "error (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.error", false]], "error (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.error", false]], "error (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.error", false]], "error (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.error", false]], "error (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.error", false]], "error (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.error", false]], "error (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.error", false]], "error (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.error", false]], "error (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.error", false]], "error (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.error", false]], "error (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.error", false]], "error (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.error", false]], "error (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.error", false]], "error (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.error", false]], "error (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.error", false]], "error (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.error", false]], "error (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.error", false]], "error (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.error", false]], "error (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.error", false]], "error (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.error", false]], "error (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.error", false]], "errorelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.ErrorElement", false]], "errorfile (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.errorfile", false]], "esearch() (in module bio.entrez)": [[83, "Bio.Entrez.esearch", false]], "espell() (in module bio.entrez)": [[83, "Bio.Entrez.espell", false]], "est (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.est", false]], "est2genomecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline", false]], "estimate_nm() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.estimate_nm", false]], "estimate_nm() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.estimate_nm", false]], "estimate_params() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.estimate_params", false]], "esummary() (in module bio.entrez)": [[83, "Bio.Entrez.esummary", false]], "etandemcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.ETandemCommandline", false]], "evalue (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.evalue", false]], "evalue (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.evalue", false]], "evalue (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.evalue", false]], "evalue (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.evalue", false]], "evalue (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.evalue", false]], "evalue (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.evalue", false]], "evalue (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.evalue", false]], "evalue (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.evalue", false]], "evalue (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.evalue", false]], "events (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Events", false]], "events() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.events", false]], "events() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.events", false]], "exactposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.ExactPosition", false]], "exclude_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.exclude_filename", false]], "excludedregion (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.excludedregion", false]], "execute() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute", false]], "execute() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.execute", false]], "execute() (biosql.dbutils.sqlite_dbutils method)": [[304, "BioSQL.DBUtils.Sqlite_dbutils.execute", false]], "execute_and_fetch_col0() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0", false]], "execute_and_fetch_col0() (biosql.bioseqdatabase.mysqlconnectoradaptor method)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor.execute_and_fetch_col0", false]], "execute_and_fetchall() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall", false]], "execute_and_fetchall() (biosql.bioseqdatabase.mysqlconnectoradaptor method)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor.execute_and_fetchall", false]], "execute_one() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute_one", false]], "execute_one() (biosql.bioseqdatabase.mysqlconnectoradaptor method)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor.execute_one", false]], "executemany() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.executemany", false]], "executemany() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.executemany", false]], "executemany() (biosql.dbutils.sqlite_dbutils method)": [[304, "BioSQL.DBUtils.Sqlite_dbutils.executemany", false]], "exoneratecigarindexer (class in bio.searchio.exonerateio.exonerate_cigar)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer", false]], "exoneratecigarparser (class in bio.searchio.exonerateio.exonerate_cigar)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser", false]], "exoneratetextindexer (class in bio.searchio.exonerateio.exonerate_text)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer", false]], "exoneratetextparser (class in bio.searchio.exonerateio.exonerate_text)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser", false]], "exoneratevulgarindexer (class in bio.searchio.exonerateio.exonerate_vulgar)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer", false]], "exoneratevulgarparser (class in bio.searchio.exonerateio.exonerate_vulgar)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser", false]], "expert (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.expert", false]], "explainflag (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.explainflag", false]], "export_fasta() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.export_fasta", false]], "export_phylip() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.export_phylip", false]], "export_search_strategy (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.export_search_strategy", false]], "exposurecn (class in bio.pdb.hsexposure)": [[141, "Bio.PDB.HSExposure.ExposureCN", false]], "extend() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.extend", false]], "extend() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.extend", false]], "extend() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.extend", false]], "externalentityrefhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.externalEntityRefHandler", false]], "extract() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.extract", false]], "extract() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.extract", false]], "extract() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.extract", false]], "extract() (in module bio.pdb.dice)": [[138, "Bio.PDB.Dice.extract", false]], "f (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.F", false], [32, "Bio.Align.Applications.PrankCommandline.f", false]], "f (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.f", false]], "f (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.f", false]], "f (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.F", false]], "f (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.f", false]], "f (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.F", false], [270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.f", false]], "fa (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fa", false]], "fast_bam (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.fast_bam", false]], "fast_bam (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.fast_bam", false]], "fasta (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.fasta", false]], "fastaiterator (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaIterator", false]], "fastam10indexer (class in bio.searchio.fastaio)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer", false]], "fastam10iterator() (in module bio.alignio.fastaio)": [[59, "Bio.AlignIO.FastaIO.FastaM10Iterator", false]], "fastam10parser (class in bio.searchio.fastaio)": [[226, "Bio.SearchIO.FastaIO.FastaM10Parser", false]], "fastaout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.fastaout", false]], "fastapair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fastapair", false]], "fastaparttree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fastaparttree", false]], "fastatwolineiterator (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator", false]], "fastatwolineparser() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineParser", false]], "fastatwolinewriter (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineWriter", false]], "fastawriter (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaWriter", false]], "fastest (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.fastest", false]], "fastmmcifparser (class in bio.pdb.mmcifparser)": [[143, "Bio.PDB.MMCIFParser.FastMMCIFParser", false]], "fastqgeneraliterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqGeneralIterator", false]], "fastqilluminaiterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqIlluminaIterator", false]], "fastqilluminawriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqIlluminaWriter", false]], "fastqphrediterator (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator", false]], "fastqphredwriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqPhredWriter", false]], "fastqsolexaiterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqSolexaIterator", false]], "fastqsolexawriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqSolexaWriter", false]], "fasttreecommandline (class in bio.phylo.applications)": [[182, "Bio.Phylo.Applications.FastTreeCommandline", false]], "fconsensecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FConsenseCommandline", false]], "fdnadistcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FDNADistCommandline", false]], "fdnaparscommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline", false]], "feature (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Feature", false]], "feature (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.Feature", false]], "feature_end_markers (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_END_MARKERS", false]], "feature_end_markers (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_END_MARKERS", false]], "feature_end_markers (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_END_MARKERS", false]], "feature_header (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.FEATURE_HEADER", false]], "feature_header (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.FEATURE_HEADER", false]], "feature_qualifier_indent (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_QUALIFIER_INDENT", false]], "feature_qualifier_indent (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_QUALIFIER_INDENT", false]], "feature_qualifier_indent (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_QUALIFIER_INDENT", false]], "feature_qualifier_spacer (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_QUALIFIER_SPACER", false]], "feature_qualifier_spacer (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_QUALIFIER_SPACER", false]], "feature_qualifier_spacer (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_QUALIFIER_SPACER", false]], "feature_start_markers (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_START_MARKERS", false]], "feature_start_markers (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_START_MARKERS", false]], "feature_start_markers (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_START_MARKERS", false]], "featurelocation (in module bio.seqfeature)": [[237, "Bio.SeqFeature.FeatureLocation", false]], "featureparser (class in bio.genbank)": [[92, "Bio.GenBank.FeatureParser", false]], "features (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.features", false]], "featureset (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet", false]], "featuretable (class in bio.swissprot)": [[272, "Bio.SwissProt.FeatureTable", false]], "featurevaluecleaner (class in bio.genbank.utils)": [[95, "Bio.GenBank.utils.FeatureValueCleaner", false]], "feed() (bio.expasy.scanprosite.parser method)": [[89, "Bio.ExPASy.ScanProsite.Parser.feed", false]], "feed() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.feed", false]], "fetch_dbid_by_dbname() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_dbid_by_dbname", false]], "fetch_motif_by_id() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.fetch_motif_by_id", false]], "fetch_motifs() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.fetch_motifs", false]], "fetch_motifs_by_name() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.fetch_motifs_by_name", false]], "fetch_seqid_by_accession() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_accession", false]], "fetch_seqid_by_display_id() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_display_id", false]], "fetch_seqid_by_identifier() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_identifier", false]], "fetch_seqid_by_version() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_version", false]], "fetch_seqids_by_accession() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqids_by_accession", false]], "ff (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ff", false]], "fft (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fft", false]], "fgcolor (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.fgcolor", false]], "field (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.Field", false]], "fieldnames (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.fieldNames", false]], "fields (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.fields", false]], "fileno() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.fileno", false]], "fileno() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.fileno", false]], "filerecord (class in bio.popgen.genepop.fileparser)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord", false]], "fill_chromosome() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.fill_chromosome", false]], "filter (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.filter", false]], "filter (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.filter", false]], "filter (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.filter", false]], "filter (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.filter", false]], "filter (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.filter", false]], "filter (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.filter", false]], "filter (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.filter", false]], "filter (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.filter", false]], "filter (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.filter", false]], "filter (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.filter", false]], "filter (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.filter", false]], "filter (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.filter", false]], "filter (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.filter", false]], "filter (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.filter", false]], "filter (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.filter", false]], "filter (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.filter", false]], "filter (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.filter", false]], "filter (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.filter", false]], "filter (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.filter", false]], "filter (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.filter", false]], "filter (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.filter", false]], "filter (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.filter", false]], "filter (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.filter", false]], "filter (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.filter", false]], "filter (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.filter", false]], "filtering_db (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.filtering_db", false]], "finalize_structure() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.finalize_structure", false]], "find() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.find", false]], "find_any() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.find_any", false]], "find_clades() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.find_clades", false]], "find_elements() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.find_elements", false]], "find_start() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.find_start", false]], "find_states() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.find_states", false]], "fit() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.fit", false]], "fit() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.fit", false]], "fixedbranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.fixedbranches", false]], "flag_disorder() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.flag_disorder", false]], "flag_disordered() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.flag_disordered", false]], "flexibility() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.flexibility", false]], "float1_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.float1_color", false]], "flush() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.flush", false]], "fmodel (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fmodel", false]], "fmt (bio.align.a2m.alignmentiterator attribute)": [[33, "Bio.Align.a2m.AlignmentIterator.fmt", false]], "fmt (bio.align.a2m.alignmentwriter attribute)": [[33, "Bio.Align.a2m.AlignmentWriter.fmt", false]], "fmt (bio.align.bed.alignmentiterator attribute)": [[35, "Bio.Align.bed.AlignmentIterator.fmt", false]], "fmt (bio.align.bigbed.alignmentiterator attribute)": [[36, "Bio.Align.bigbed.AlignmentIterator.fmt", false]], "fmt (bio.align.bigbed.alignmentwriter attribute)": [[36, "Bio.Align.bigbed.AlignmentWriter.fmt", false]], "fmt (bio.align.bigmaf.alignmentiterator attribute)": [[37, "Bio.Align.bigmaf.AlignmentIterator.fmt", false]], "fmt (bio.align.bigmaf.alignmentwriter attribute)": [[37, "Bio.Align.bigmaf.AlignmentWriter.fmt", false]], "fmt (bio.align.bigpsl.alignmentiterator attribute)": [[38, "Bio.Align.bigpsl.AlignmentIterator.fmt", false]], "fmt (bio.align.bigpsl.alignmentwriter attribute)": [[38, "Bio.Align.bigpsl.AlignmentWriter.fmt", false]], "fmt (bio.align.chain.alignmentiterator attribute)": [[39, "Bio.Align.chain.AlignmentIterator.fmt", false]], "fmt (bio.align.chain.alignmentwriter attribute)": [[39, "Bio.Align.chain.AlignmentWriter.fmt", false]], "fmt (bio.align.clustal.alignmentiterator attribute)": [[40, "Bio.Align.clustal.AlignmentIterator.fmt", false]], "fmt (bio.align.clustal.alignmentwriter attribute)": [[40, "Bio.Align.clustal.AlignmentWriter.fmt", false]], "fmt (bio.align.emboss.alignmentiterator attribute)": [[41, "Bio.Align.emboss.AlignmentIterator.fmt", false]], "fmt (bio.align.exonerate.alignmentiterator attribute)": [[42, "Bio.Align.exonerate.AlignmentIterator.fmt", false]], "fmt (bio.align.exonerate.alignmentwriter attribute)": [[42, "Bio.Align.exonerate.AlignmentWriter.fmt", false]], "fmt (bio.align.fasta.alignmentiterator attribute)": [[43, "Bio.Align.fasta.AlignmentIterator.fmt", false]], "fmt (bio.align.fasta.alignmentwriter attribute)": [[43, "Bio.Align.fasta.AlignmentWriter.fmt", false]], "fmt (bio.align.hhr.alignmentiterator attribute)": [[44, "Bio.Align.hhr.AlignmentIterator.fmt", false]], "fmt (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.fmt", false]], "fmt (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.fmt", false]], "fmt (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.fmt", false]], "fmt (bio.align.maf.alignmentwriter attribute)": [[46, "Bio.Align.maf.AlignmentWriter.fmt", false]], "fmt (bio.align.mauve.alignmentiterator attribute)": [[47, "Bio.Align.mauve.AlignmentIterator.fmt", false]], "fmt (bio.align.mauve.alignmentwriter attribute)": [[47, "Bio.Align.mauve.AlignmentWriter.fmt", false]], "fmt (bio.align.msf.alignmentiterator attribute)": [[48, "Bio.Align.msf.AlignmentIterator.fmt", false]], "fmt (bio.align.nexus.alignmentiterator attribute)": [[49, "Bio.Align.nexus.AlignmentIterator.fmt", false]], "fmt (bio.align.nexus.alignmentwriter attribute)": [[49, "Bio.Align.nexus.AlignmentWriter.fmt", false]], "fmt (bio.align.phylip.alignmentiterator attribute)": [[50, "Bio.Align.phylip.AlignmentIterator.fmt", false]], "fmt (bio.align.phylip.alignmentwriter attribute)": [[50, "Bio.Align.phylip.AlignmentWriter.fmt", false]], "fmt (bio.align.psl.alignmentiterator attribute)": [[51, "Bio.Align.psl.AlignmentIterator.fmt", false]], "fmt (bio.align.psl.alignmentwriter attribute)": [[51, "Bio.Align.psl.AlignmentWriter.fmt", false]], "fmt (bio.align.sam.alignmentiterator attribute)": [[52, "Bio.Align.sam.AlignmentIterator.fmt", false]], "fmt (bio.align.sam.alignmentwriter attribute)": [[52, "Bio.Align.sam.AlignmentWriter.fmt", false]], "fmt (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.fmt", false]], "fmt (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.fmt", false]], "fmt (bio.align.tabular.alignmentiterator attribute)": [[55, "Bio.Align.tabular.AlignmentIterator.fmt", false]], "fmt_() (in module bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.fmt_", false]], "fn (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fn", false]], "fneighborcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FNeighborCommandline", false]], "fop (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fop", false]], "force (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.force", false]], "format (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.format", false]], "format() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.format", false]], "format() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.format", false]], "format() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.format", false]], "format() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.format", false]], "format() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.format", false]], "format_alignment() (bio.align.a2m.alignmentwriter method)": [[33, "Bio.Align.a2m.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.bed.alignmentwriter method)": [[35, "Bio.Align.bed.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.chain.alignmentwriter method)": [[39, "Bio.Align.chain.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.clustal.alignmentwriter method)": [[40, "Bio.Align.clustal.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.fasta.alignmentwriter method)": [[43, "Bio.Align.fasta.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.maf.alignmentwriter method)": [[46, "Bio.Align.maf.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.phylip.alignmentwriter method)": [[50, "Bio.Align.phylip.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.psl.alignmentwriter method)": [[51, "Bio.Align.psl.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.sam.alignmentwriter method)": [[52, "Bio.Align.sam.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.stockholm.alignmentwriter method)": [[53, "Bio.Align.stockholm.AlignmentWriter.format_alignment", false]], "format_alignment() (in module bio.pairwise2)": [[297, "Bio.pairwise2.format_alignment", false]], "format_label() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.format_label", false]], "format_output() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.format_output", false]], "format_phylip() (bio.phylo.treeconstruction.distancematrix method)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix.format_phylip", false]], "forward_algorithm() (bio.hmm.dynamicprogramming.abstractdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.forward_algorithm", false]], "forward_table (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.forward_table", false]], "forwardinput (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.forwardinput", false]], "fprotdistcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FProtDistCommandline", false]], "fprotparscommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FProtParsCommandline", false]], "fracsample (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.fracsample", false]], "fragment (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.fragment", false]], "fragment (class in bio.pdb.fragmentmapper)": [[140, "Bio.PDB.FragmentMapper.Fragment", false]], "fragmentmapper (class in bio.pdb.fragmentmapper)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper", false]], "frame_shift_penalty (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.frame_shift_penalty", false]], "frame_shift_penalty (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.frame_shift_penalty", false]], "freqsfrom (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.freqsfrom", false]], "frequencies (bio.align.alignment property)": [[30, "Bio.Align.Alignment.frequencies", false]], "frequencies (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.frequencies", false]], "frequencypositionmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.FrequencyPositionMatrix", false]], "from_bytes() (bio.align.bigbed.autosqltable class method)": [[36, "Bio.Align.bigbed.AutoSQLTable.from_bytes", false]], "from_clade() (bio.phylo.basetree.tree class method)": [[183, "Bio.Phylo.BaseTree.Tree.from_clade", false]], "from_clade() (bio.phylo.phyloxml.clade class method)": [[197, "Bio.Phylo.PhyloXML.Clade.from_clade", false]], "from_clade() (bio.phylo.phyloxml.phylogeny class method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.from_clade", false]], "from_hex() (bio.phylo.basetree.branchcolor class method)": [[183, "Bio.Phylo.BaseTree.BranchColor.from_hex", false]], "from_msa() (bio.codonalign.codonalignment.codonalignment class method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.from_msa", false]], "from_name() (bio.phylo.basetree.branchcolor class method)": [[183, "Bio.Phylo.BaseTree.BranchColor.from_name", false]], "from_seq() (bio.codonalign.codonseq.codonseq class method)": [[281, "Bio.codonalign.codonseq.CodonSeq.from_seq", false]], "from_seqfeature() (bio.phylo.phyloxml.proteindomain class method)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain.from_seqfeature", false]], "from_seqrecord() (bio.phylo.phyloxml.sequence class method)": [[197, "Bio.Phylo.PhyloXML.Sequence.from_seqrecord", false]], "from_string() (bio.align.bigbed.autosqltable class method)": [[36, "Bio.Align.bigbed.AutoSQLTable.from_string", false]], "from_string() (bio.phylo.cdaoio.parser class method)": [[185, "Bio.Phylo.CDAOIO.Parser.from_string", false]], "from_string() (bio.phylo.newickio.parser class method)": [[190, "Bio.Phylo.NewickIO.Parser.from_string", false]], "from_string() (bio.phylo.nexmlio.parser class method)": [[188, "Bio.Phylo.NeXMLIO.Parser.from_string", false]], "from_tree() (bio.phylo.phyloxml.phylogeny class method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.from_tree", false]], "fromstring() (bio.seqfeature.location method)": [[237, "Bio.SeqFeature.Location.fromstring", false]], "fromstring() (bio.seqfeature.position static method)": [[237, "Bio.SeqFeature.Position.fromstring", false]], "fromstring() (bio.seqfeature.simplelocation static method)": [[237, "Bio.SeqFeature.SimpleLocation.fromstring", false]], "fseqbootcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline", false]], "fsm (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fsm", false]], "ftreedistcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline", false]], "full_translate() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.full_translate", false]], "fullhelp (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.fullhelp", false]], "fuzznuccommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FuzznucCommandline", false]], "fuzzprocommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FuzzproCommandline", false]], "g (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.g", false]], "gafbyproteiniterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gafbyproteiniterator", false]], "gafiterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gafiterator", false]], "gamma (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.gamma", false]], "gamma (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.gamma", false]], "gamma (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gamma", false]], "gammacoefficient (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.gammacoefficient", false]], "gammacoefficient (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.gammacoefficient", false]], "gap (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.gap", false]], "gap_consensus() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.gap_consensus", false]], "gap_extend (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.gap_extend", false]], "gap_open (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.gap_open", false]], "gap_trigger (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gap_trigger", false]], "gap_trigger (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gap_trigger", false]], "gapdist (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.gapdist", false]], "gapext (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.gapext", false]], "gapext (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.gapext", false]], "gapext (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.gapext", false]], "gapextend (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.gapextend", false]], "gapextend (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.gapextend", false]], "gapextend (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.gapextend", false]], "gapextend (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.gapextend", false]], "gapextend (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.gapextend", false]], "gaplimit (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.gaplimit", false]], "gaponly() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.gaponly", false]], "gapopen (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.gapopen", false]], "gapopen (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.gapopen", false]], "gapopen (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.gapopen", false]], "gapopen (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.gapopen", false]], "gapopen (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.gapopen", false]], "gapopen (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.gapopen", false]], "gapopen (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.gapopen", false]], "gappenalty (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.gappenalty", false]], "gaprate (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.gaprate", false]], "gaps (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.gaps", false]], "gb_base_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_BASE_INDENT", false]], "gb_feature_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_FEATURE_INDENT", false]], "gb_feature_internal_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_FEATURE_INTERNAL_INDENT", false]], "gb_internal_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_INTERNAL_INDENT", false]], "gb_line_length (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_LINE_LENGTH", false]], "gb_other_internal_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_OTHER_INTERNAL_INDENT", false]], "gb_sequence_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_SEQUENCE_INDENT", false]], "gc123() (in module bio.sequtils)": [[261, "Bio.SeqUtils.GC123", false]], "gc_content (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.gc_content", false]], "gc_content (bio.motifs.matrix.positionspecificscoringmatrix property)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.gc_content", false]], "gc_fraction() (in module bio.sequtils)": [[261, "Bio.SeqUtils.gc_fraction", false]], "gc_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gc_mapping", false]], "gc_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gc_mapping", false]], "gc_skew() (in module bio.sequtils)": [[261, "Bio.SeqUtils.GC_skew", false]], "gcclamp (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.gcclamp", false]], "gcg() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.gcg", false]], "gckiterator (class in bio.seqio.gckio)": [[242, "Bio.SeqIO.GckIO.GckIterator", false]], "gen_key() (bio.pdb.internal_coords.edron static method)": [[169, "Bio.PDB.internal_coords.Edron.gen_key", false]], "gen_tuple() (bio.pdb.internal_coords.edron static method)": [[169, "Bio.PDB.internal_coords.Edron.gen_tuple", false]], "genafpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.genafpair", false]], "genbank_indent (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.GENBANK_INDENT", false]], "genbank_spacer (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.GENBANK_SPACER", false]], "genbankcdsfeatureiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator", false]], "genbankiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator", false]], "genbankscanner (class in bio.genbank.scanner)": [[94, "Bio.GenBank.Scanner.GenBankScanner", false]], "genbankwriter (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter", false]], "genepopcontroller (class in bio.popgen.genepop.controller)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController", false]], "generic_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Generic_dbutils", false]], "genericpositionmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.GenericPositionMatrix", false]], "genes (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.genes", false]], "genome (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.genome", false]], "get() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.get", false]], "get() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.get", false]], "get_acgt() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.get_acgt", false]], "get_alignment_length() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.get_alignment_length", false]], "get_all_assemblies() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_all_assemblies", false]], "get_all_entries() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_all_entries", false]], "get_all_obsolete() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_all_obsolete", false]], "get_allele_frequency() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_allele_frequency", false]], "get_alleles() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_alleles", false]], "get_alleles_all_pops() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_alleles_all_pops", false]], "get_aln_length() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.get_aln_length", false]], "get_altloc() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_altloc", false]], "get_amino_acids_percent() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent", false]], "get_angle() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.get_angle", false]], "get_anisou() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_anisou", false]], "get_area() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.get_area", false]], "get_array() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.get_array", false]], "get_artemis_colorscheme() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.get_artemis_colorscheme", false]], "get_atoms() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.get_atoms", false]], "get_atoms() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.get_atoms", false]], "get_atoms() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_atoms", false]], "get_atoms() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_atoms", false]], "get_avg_fis() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_avg_fis", false]], "get_avg_fst_pair() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_avg_fst_pair", false]], "get_avg_fst_pair_locus() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_avg_fst_pair_locus", false]], "get_basic_info() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_basic_info", false]], "get_bfactor() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_bfactor", false]], "get_blank_emissions() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.get_blank_emissions", false]], "get_blank_transitions() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.get_blank_transitions", false]], "get_ca_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_ca_list", false]], "get_chains() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.get_chains", false]], "get_chains() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_chains", false]], "get_charge() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_charge", false]], "get_codon() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.get_codon", false]], "get_codon_num() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.get_codon_num", false]], "get_color_dict() (in module bio.graphics.colorspiral)": [[100, "Bio.Graphics.ColorSpiral.get_color_dict", false]], "get_colors() (bio.graphics.colorspiral.colorspiral method)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.get_colors", false]], "get_colors() (in module bio.graphics.colorspiral)": [[100, "Bio.Graphics.ColorSpiral.get_colors", false]], "get_colorscheme() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.get_colorscheme", false]], "get_column() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.get_column", false]], "get_column() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.get_column", false]], "get_coord() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_coord", false]], "get_coords() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.get_coords", false]], "get_data() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.get_data", false]], "get_data() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_data", false]], "get_dbutils() (in module biosql.dbutils)": [[304, "BioSQL.DBUtils.get_dbutils", false]], "get_distance() (bio.phylo.treeconstruction.distancecalculator method)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.get_distance", false]], "get_dn_ds_matrix() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.get_dn_ds_matrix", false]], "get_dn_ds_tree() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.get_dn_ds_tree", false]], "get_drawn_levels() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.get_drawn_levels", false]], "get_f_stats() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_f_stats", false]], "get_feature() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.get_feature", false]], "get_features() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.get_features", false]], "get_fis() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_fis", false]], "get_from_decoded() (in module bio.pdb.mmtf)": [[171, "Bio.PDB.mmtf.get_from_decoded", false]], "get_full_id() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_full_id", false]], "get_full_id() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_full_id", false]], "get_full_rf_table() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.get_full_rf_table", false]], "get_fullname() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_fullname", false]], "get_genotype_count() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_genotype_count", false]], "get_graphs() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.get_graphs", false]], "get_guide_coord_from_structure() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.get_guide_coord_from_structure", false]], "get_header() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.get_header", false]], "get_heterozygosity_info() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_heterozygosity_info", false]], "get_id() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_id", false]], "get_id() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_id", false]], "get_id() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.get_id", false]], "get_id() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_id", false]], "get_id() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.get_id", false]], "get_ids() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.get_ids", false]], "get_ids() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.get_ids", false]], "get_ids() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.get_ids", false]], "get_indiv() (in module bio.popgen.genepop)": [[201, "Bio.PopGen.GenePop.get_indiv", false]], "get_indiv() (in module bio.popgen.genepop.largefileparser)": [[205, "Bio.PopGen.GenePop.LargeFileParser.get_indiv", false]], "get_individual() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.get_individual", false]], "get_init_rms() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_init_rms", false]], "get_init_rms() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_init_rms", false]], "get_iterator() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_iterator", false]], "get_iterator() (bio.pdb.structurealignment.structurealignment method)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment.get_iterator", false]], "get_kgml() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.get_KGML", false]], "get_length() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.get_length", false]], "get_length() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.get_length", false]], "get_level() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_level", false]], "get_level() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_level", false]], "get_levels() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.get_levels", false]], "get_list() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_list", false]], "get_maps() (bio.pdb.structurealignment.structurealignment method)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment.get_maps", false]], "get_markov_model() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.get_markov_model", false]], "get_models() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_models", false]], "get_multilocus_f_stats() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_multilocus_f_stats", false]], "get_name() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_name", false]], "get_node_info() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.get_node_info", false]], "get_nonterminals() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.get_nonterminals", false]], "get_occupancy() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_occupancy", false]], "get_parent() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_parent", false]], "get_parent() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.get_parent", false]], "get_parent() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_parent", false]], "get_path() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.get_path", false]], "get_phi_psi_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_phi_psi_list", false]], "get_predictions() (in module bio.pdb.alphafold_db)": [[164, "Bio.PDB.alphafold_db.get_predictions", false]], "get_prev() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_prev", false]], "get_prodoc_entry() (in module bio.expasy)": [[85, "Bio.ExPASy.get_prodoc_entry", false]], "get_property_value() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.get_property_value", false]], "get_prosite_entry() (in module bio.expasy)": [[85, "Bio.ExPASy.get_prosite_entry", false]], "get_prosite_raw() (in module bio.expasy)": [[85, "Bio.ExPASy.get_prosite_raw", false]], "get_qresult_id() (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarindexer method)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer.get_qresult_id", false]], "get_qresult_id() (bio.searchio.exonerateio.exonerate_text.exoneratetextindexer method)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer.get_qresult_id", false]], "get_qresult_id() (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer method)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.get_qresult_id", false]], "get_radius() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_radius", false]], "get_raw() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.get_raw", false]], "get_raw() (bio.searchio.blastio.blast_tab.blasttabindexer method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.get_raw", false]], "get_raw() (bio.searchio.blastio.blast_xml.blastxmlindexer method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.get_raw", false]], "get_raw() (bio.searchio.blatio.blatpslindexer method)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.get_raw", false]], "get_raw() (bio.searchio.exonerateio.exonerate_text.exoneratetextindexer method)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer.get_raw", false]], "get_raw() (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer method)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.get_raw", false]], "get_raw() (bio.searchio.fastaio.fastam10indexer method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.get_raw", false]], "get_raw() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabindexer method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer.get_raw", false]], "get_recent_changes() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_recent_changes", false]], "get_residue() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.get_residue", false]], "get_residues() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.get_residues", false]], "get_residues() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.get_residues", false]], "get_residues() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_residues", false]], "get_resname() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_resname", false]], "get_resname_list() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.get_resname_list", false]], "get_rms() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_rms", false]], "get_rms() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_rms", false]], "get_rotran() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_rotran", false]], "get_rotran() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_rotran", false]], "get_row() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.get_row", false]], "get_score() (bio.phylo.treeconstruction.parsimonyscorer method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyScorer.get_score", false]], "get_score() (bio.phylo.treeconstruction.scorer method)": [[199, "Bio.Phylo.TreeConstruction.Scorer.get_score", false]], "get_segid() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_segid", false]], "get_segment_info() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.get_segment_info", false]], "get_seq() (bio.pdb.psea.psea method)": [[153, "Bio.PDB.PSEA.PSEA.get_seq", false]], "get_seq_by_acc() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_acc", false]], "get_seq_by_id() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_id", false]], "get_seq_by_ver() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_ver", false]], "get_seqres_file() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_seqres_file", false]], "get_seqs_by_acc() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seqs_by_acc", false]], "get_sequence() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_sequence", false]], "get_serial_number() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_serial_number", false]], "get_sets() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.get_sets", false]], "get_sigatm() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_sigatm", false]], "get_signals() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.get_signals", false]], "get_siguij() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_siguij", false]], "get_spherical_coordinates() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.get_spherical_coordinates", false]], "get_spliced() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.get_spliced", false]], "get_sprot_raw() (in module bio.expasy)": [[85, "Bio.ExPASy.get_sprot_raw", false]], "get_start_end() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.get_start_end", false]], "get_status_list() (bio.pdb.pdblist.pdblist static method)": [[149, "Bio.PDB.PDBList.PDBList.get_status_list", false]], "get_structural_models_for() (in module bio.pdb.alphafold_db)": [[164, "Bio.PDB.alphafold_db.get_structural_models_for", false]], "get_structure() (bio.pdb.binary_cif.binarycifparser method)": [[165, "Bio.PDB.binary_cif.BinaryCIFParser.get_structure", false]], "get_structure() (bio.pdb.mmcifparser.fastmmcifparser method)": [[143, "Bio.PDB.MMCIFParser.FastMMCIFParser.get_structure", false]], "get_structure() (bio.pdb.mmcifparser.mmcifparser method)": [[143, "Bio.PDB.MMCIFParser.MMCIFParser.get_structure", false]], "get_structure() (bio.pdb.mmtf.mmtfparser static method)": [[171, "Bio.PDB.mmtf.MMTFParser.get_structure", false]], "get_structure() (bio.pdb.pdbmlparser.pdbmlparser method)": [[150, "Bio.PDB.PDBMLParser.PDBMLParser.get_structure", false]], "get_structure() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.get_structure", false]], "get_structure() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.get_structure", false]], "get_structure_from_url() (bio.pdb.mmtf.mmtfparser static method)": [[171, "Bio.PDB.mmtf.MMTFParser.get_structure_from_url", false]], "get_subseq_as_string() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string", false]], "get_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_succ", false]], "get_support() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.get_support", false]], "get_surface() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.get_surface", false]], "get_tau_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_tau_list", false]], "get_taxa() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.get_taxa", false]], "get_temp_imagefilename() (in module bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.get_temp_imagefilename", false]], "get_terminals() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.get_terminals", false]], "get_terminals() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.get_terminals", false]], "get_text() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.get_text", false]], "get_theta_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_theta_list", false]], "get_times() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.get_times", false]], "get_tracks() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.get_tracks", false]], "get_trailer() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.get_trailer", false]], "get_transformed() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_transformed", false]], "get_transformed() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_transformed", false]], "get_unique_parents() (in module bio.pdb.selection)": [[159, "Bio.PDB.Selection.get_unique_parents", false]], "get_unpacked_list() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.get_unpacked_list", false]], "get_unpacked_list() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_unpacked_list", false]], "get_vector() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_vector", false]], "getascendent() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getAscendent", false]], "getascendentfromsql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getAscendentFromSQL", false]], "getastraldomainsfromfile() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getAstralDomainsFromFile", false]], "getastraldomainsfromsql() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getAstralDomainsFromSQL", false]], "getatoms() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.getAtoms", false]], "getchildren() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getChildren", false]], "getdescendents() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getDescendents", false]], "getdescendentsfromsql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDescendentsFromSQL", false]], "getdomainbysid() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDomainBySid", false]], "getdomainfromsql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDomainFromSQL", false]], "getdomains() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDomains", false]], "getnodebysunid() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getNodeBySunid", false]], "getparent() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getParent", false]], "getroot() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getRoot", false]], "getseq() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getSeq", false]], "getseqbysid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getSeqBySid", false]], "getseqmap() (bio.scop.raf.seqmapindex method)": [[214, "Bio.SCOP.Raf.SeqMapIndex.getSeqMap", false]], "gf_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gf_mapping", false]], "gf_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gf_mapping", false]], "gfa1iterator() (in module bio.seqio.gfaio)": [[243, "Bio.SeqIO.GfaIO.Gfa1Iterator", false]], "gfa2iterator() (in module bio.seqio.gfaio)": [[243, "Bio.SeqIO.GfaIO.Gfa2Iterator", false]], "gi_mask (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.gi_mask", false]], "gi_mask_name (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.gi_mask_name", false]], "gilist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.gilist", false]], "gilist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.gilist", false]], "gilist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.gilist", false]], "gilist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gilist", false]], "gilist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gilist", false]], "gilist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.gilist", false]], "gilist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.gilist", false]], "gilist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.gilist", false]], "gilist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.gilist", false]], "global_dtd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.global_dtd_dir", false]], "global_xsd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.global_xsd_dir", false]], "globalpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.globalpair", false]], "gly_cbeta (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.gly_Cbeta", false]], "gompertz() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.gompertz", false]], "good_bases (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.good_bases", false]], "gpa_iterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gpa_iterator", false]], "gpi_iterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gpi_iterator", false]], "gr_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gr_mapping", false]], "gr_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gr_mapping", false]], "graph (class in bio.pathway.rep.graph)": [[179, "Bio.Pathway.Rep.Graph.Graph", false]], "graphdata (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.GraphData", false]], "graphics (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics", false]], "graphset (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet", false]], "gravy() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.gravy", false]], "green() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.green", false]], "group (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.group", false]], "grouping_constraint (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.grouping_constraint", false]], "groupsize (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.groupsize", false]], "gs_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gs_mapping", false]], "gs_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gs_mapping", false]], "gtr (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gtr", false]], "gtrfreq (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gtrfreq", false]], "gtrrates (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gtrrates", false]], "guess_lag() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.guess_lag", false]], "guess_plateau() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.guess_plateau", false]], "guidetree_in (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.guidetree_in", false]], "guidetree_out (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.guidetree_out", false]], "h (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.h", false]], "h (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.h", false]], "h (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.h", false]], "h (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.h", false]], "h (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.h", false]], "h (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.h", false]], "h (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.h", false]], "h (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.h", false]], "h (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.h", false]], "h (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.h", false]], "h (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.h", false]], "h (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.H", false]], "h (bio.sequencing.applications.samtoolscatcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.h", false]], "h (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.h", false]], "h (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.h", false]], "h (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.H", false], [270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.h", false]], "handle_motif() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.handle_motif", false]], "handlemissingdocumentdefinition() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.handleMissingDocumentDefinition", false]], "has_id() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.has_id", false]], "has_id() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.has_id", false]], "has_support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.has_support", false]], "hash_index (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.hash_index", false]], "hasheddomainsbyev() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.hashedDomainsByEv", false]], "hasheddomainsbyid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.hashedDomainsById", false]], "header (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Header", false]], "header_width (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.HEADER_WIDTH", false]], "header_width (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.HEADER_WIDTH", false]], "header_width (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.HEADER_WIDTH", false]], "header_width (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.HEADER_WIDTH", false]], "header_width (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.HEADER_WIDTH", false]], "header_width (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.HEADER_WIDTH", false]], "hedron (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.Hedron", false]], "hedronmatcherror": [[169, "Bio.PDB.internal_coords.HedronMatchError", false]], "height (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.height", false]], "helixendin (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.helixendin", false]], "helixendout (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.helixendout", false]], "helixgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.helixgap", false]], "help (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.help", false]], "help (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.help", false]], "help (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.help", false]], "help (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.help", false]], "help (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.help", false]], "help (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.help", false]], "help (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.help", false]], "help (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.help", false]], "help (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.help", false]], "help (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.help", false]], "help (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.help", false]], "help (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.help", false]], "help (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.help", false]], "help (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.help", false]], "help (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.help", false]], "help (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.help", false]], "help (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.help", false]], "help (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.help", false]], "help (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.help", false]], "help (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.help", false]], "help (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.help", false]], "help (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.help", false]], "help (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.help", false]], "help (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.help", false]], "help (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.help", false]], "help (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.help", false]], "help (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.help", false]], "help (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.help", false]], "help (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.help", false]], "help (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.help", false]], "help (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.help", false]], "help (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.help", false]], "help (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.help", false]], "help (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.help", false]], "help (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.help", false]], "help (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.help", false]], "help (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.help", false]], "help (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.help", false]], "help (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.help", false]], "hgapresidues (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.hgapresidues", false]], "hhsuite2textparser (class in bio.searchio.hhsuiteio.hhsuite2_text)": [[228, "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser", false]], "hiddenmarkovmodel (class in bio.hmm.markovmodel)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel", false]], "hit (class in bio.blast)": [[68, "Bio.Blast.Hit", false]], "hit_coverage() (bio.compass.record method)": [[74, "Bio.Compass.Record.hit_coverage", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitparser attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser.hmm_as_hit", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitwriter attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter.hmm_as_hit", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmqueryparser attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser.hmm_as_hit", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmquerywriter attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter.hmm_as_hit", false]], "hmm_input (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.hmm_input", false]], "hmmer2textindexer (class in bio.searchio.hmmerio.hmmer2_text)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer", false]], "hmmer2textparser (class in bio.searchio.hmmerio.hmmer2_text)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser", false]], "hmmer3domtabhmmhitindexer (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer", false]], "hmmer3domtabhmmhitparser (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser", false]], "hmmer3domtabhmmhitwriter (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter", false]], "hmmer3domtabhmmqueryindexer (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer", false]], "hmmer3domtabhmmqueryparser (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser", false]], "hmmer3domtabhmmquerywriter (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter", false]], "hmmer3tabindexer (class in bio.searchio.hmmerio.hmmer3_tab)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer", false]], "hmmer3tabparser (class in bio.searchio.hmmerio.hmmer3_tab)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser", false]], "hmmer3tabwriter (class in bio.searchio.hmmerio.hmmer3_tab)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter", false]], "hmmer3textindexer (class in bio.searchio.hmmerio.hmmer3_text)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer", false]], "hmmer3textparser (class in bio.searchio.hmmerio.hmmer3_text)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser", false]], "homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.homog_rot_mtx", false]], "homog_scale_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.homog_scale_mtx", false]], "homog_trans_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.homog_trans_mtx", false]], "homopolymer (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.homopolymer", false]], "hsexposureca (class in bio.pdb.hsexposure)": [[141, "Bio.PDB.HSExposure.HSExposureCA", false]], "hsexposurecb (class in bio.pdb.hsexposure)": [[141, "Bio.PDB.HSExposure.HSExposureCB", false]], "hsp (class in bio.blast)": [[68, "Bio.Blast.HSP", false]], "hsp (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.HSP", false]], "html (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.html", false]], "html (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.html", false]], "html (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.html", false]], "html (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.html", false]], "html (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.html", false]], "html (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.html", false]], "html (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.html", false]], "html (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.html", false]], "html (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.html", false]], "html (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.html", false]], "html (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.html", false]], "htmlout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.htmlout", false]], "hybridprobe (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.hybridprobe", false]], "hydro (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.hydro", false]], "hydrofactor (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.hydrofactor", false]], "i (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.I", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.i", false]], "i (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.I", false]], "i (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.i", false]], "i (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.I", false]], "ic_chain (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.IC_Chain", false]], "ic_duplicate() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.IC_duplicate", false]], "ic_residue (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.IC_Residue", false]], "id (bio.kegg.kgml.kgml_pathway.component property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component.id", false]], "id (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.id", false]], "id (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.id", false]], "id (bio.pdb.entity.entity property)": [[139, "Bio.PDB.Entity.Entity.id", false]], "id (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Id", false]], "id() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.id", false]], "id() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.id", false]], "id_width (bio.alignio.phylipio.phylipiterator attribute)": [[65, "Bio.AlignIO.PhylipIO.PhylipIterator.id_width", false]], "identities (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.identities", false]], "identity_match (class in bio.pairwise2)": [[297, "Bio.pairwise2.identity_match", false]], "iepcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.IepCommandline", false]], "igiterator (class in bio.seqio.igio)": [[244, "Bio.SeqIO.IgIO.IgIterator", false]], "ignore_msa_master (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.ignore_msa_master", false]], "illumina_13 (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.illumina_13", false]], "imgtiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator", false]], "imgtwriter (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter", false]], "import_search_strategy (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.import_search_strategy", false]], "in1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.in1", false]], "in2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.in2", false]], "in_bam (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.in_bam", false]], "in_bam (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.in_bam", false]], "in_msa (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.in_msa", false]], "in_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.in_pssm", false]], "in_pssm (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.in_pssm", false]], "includedregion (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.includedregion", false]], "inclusion_ethresh (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.inclusion_ethresh", false]], "inclusion_ethresh (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.inclusion_ethresh", false]], "indent (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.Indent", false]], "index (class in bio.scop.cla)": [[210, "Bio.SCOP.Cla.Index", false]], "index() (bio.blast.record method)": [[68, "Bio.Blast.Record.index", false]], "index() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.index", false]], "index() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.index", false]], "index() (in module bio.searchio)": [[217, "Bio.SearchIO.index", false]], "index() (in module bio.seqio)": [[238, "Bio.SeqIO.index", false]], "index_db() (in module bio.searchio)": [[217, "Bio.SearchIO.index_db", false]], "index_db() (in module bio.seqio)": [[238, "Bio.SeqIO.index_db", false]], "index_name (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.index_name", false]], "index_to_one() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.index_to_one", false]], "index_to_three() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.index_to_three", false]], "indices (bio.align.alignment property)": [[30, "Bio.Align.Alignment.indices", false]], "infer_coordinates() (bio.align.alignment class method)": [[30, "Bio.Align.Alignment.infer_coordinates", false]], "infile (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.infile", false]], "infile (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.infile", false]], "infile (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.infile", false]], "infile (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.infile", false]], "infile (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.infile", false]], "infile (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.infile", false]], "infmt (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.infmt", false]], "information_content() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.information_content", false]], "init_atom() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_atom", false]], "init_atom_coords() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.init_atom_coords", false]], "init_chain() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_chain", false]], "init_edra() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.init_edra", false]], "init_model() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_model", false]], "init_residue() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_residue", false]], "init_seg() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_seg", false]], "init_structure() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.init_structure", false]], "init_structure() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_structure", false]], "input (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.input", false]], "input (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.input", false]], "input (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.input", false]], "input (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.input", false]], "input (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.input", false]], "input (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.input", false]], "input (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.input", false]], "input (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.input", false]], "input1 (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.input1", false]], "input_bam (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.input_bam", false]], "input_bam (bio.sequencing.applications.samtoolsidxstatscommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline.input_bam", false]], "input_bam (bio.sequencing.applications.samtoolsindexcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsIndexCommandline.input_bam", false]], "input_file (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsfixmatecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsrmdupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.input_file", false]], "input_tree (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.input_tree", false]], "input_type (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.input_type", false]], "inputorder (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.inputorder", false]], "inputrecord (class in bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.InputRecord", false]], "insdcscanner (class in bio.genbank.scanner)": [[94, "Bio.GenBank.Scanner.InsdcScanner", false]], "insert() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.insert", false]], "insert() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.insert", false]], "insert_gap() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.insert_gap", false]], "instability_index() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.instability_index", false]], "instance (class in bio.motifs.meme)": [[291, "Bio.motifs.meme.Instance", false]], "instances (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.instances", false]], "instances (class in bio.motifs)": [[283, "Bio.motifs.Instances", false]], "int255_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.int255_color", false]], "integerelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.IntegerElement", false]], "integers (bio.expasy.scanprosite.contenthandler attribute)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.integers", false]], "interaction (class in bio.pathway)": [[177, "Bio.Pathway.Interaction", false]], "interactions() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.interactions", false]], "internal_feature_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.INTERNAL_FEATURE_FORMAT", false]], "internal_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.INTERNAL_FORMAT", false]], "internal_to_atom_coordinates() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.internal_to_atom_coordinates", false]], "internal_to_atom_coordinates() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.internal_to_atom_coordinates", false]], "internal_to_atom_coordinates() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.internal_to_atom_coordinates", false]], "internal_to_atom_coordinates() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.internal_to_atom_coordinates", false]], "interproscanxmlparser (class in bio.searchio.interproscanio.interproscan_xml)": [[235, "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser", false]], "intree (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.intree", false]], "intree1 (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.intree1", false]], "intreefile (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.intreefile", false]], "intreefile (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.intreefile", false]], "intreefile (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.intreefile", false]], "intreefile (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.intreefile", false]], "intronpenalty (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.intronpenalty", false]], "invarcoefficient (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.invarcoefficient", false]], "invarfrac (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.invarfrac", false]], "inverse_indices (bio.align.alignment property)": [[30, "Bio.Align.Alignment.inverse_indices", false]], "invert() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.invert", false]], "ir (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.ir", false]], "is_aa() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.is_aa", false]], "is_backbone() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.is_backbone", false]], "is_backbone() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.is_backbone", false]], "is_bifurcating() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_bifurcating", false]], "is_bifurcating() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_bifurcating", false]], "is_compatible() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_compatible", false]], "is_disordered() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.is_disordered", false]], "is_disordered() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered", false]], "is_disordered() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.is_disordered", false]], "is_identical() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_identical", false]], "is_internal() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_internal", false]], "is_monophyletic() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_monophyletic", false]], "is_monophyletic() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_monophyletic", false]], "is_nucleic() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.is_nucleic", false]], "is_parent_of() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.is_parent_of", false]], "is_parent_of() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_parent_of", false]], "is_preterminal() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_preterminal", false]], "is_preterminal() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_preterminal", false]], "is_reactant (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.is_reactant", false]], "is_terminal() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_terminal", false]], "is_terminal() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.is_terminal", false]], "is_terminal() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.is_terminal", false]], "isatty() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.isatty", false]], "isatty() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.isatty", false]], "isdomaininev() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.isDomainInEv", false]], "isdomaininid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.isDomainInId", false]], "islower() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.islower", false]], "islower() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.islower", false]], "isoelectric_point() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.isoelectric_point", false]], "isoelectricpoint (class in bio.sequtils.isoelectricpoint)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint", false]], "isprofile (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.isprofile", false]], "isupper() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.isupper", false]], "isupper() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.isupper", false]], "itemindex() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.itemindex", false]], "items() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.items", false]], "items() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.items", false]], "items() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.items", false]], "items() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.items", false]], "iterate() (bio.seqio.fastaio.fastaiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.iterate", false]], "iterate() (bio.seqio.fastaio.fastatwolineiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.iterate", false]], "iterate() (bio.seqio.igio.igiterator method)": [[244, "Bio.SeqIO.IgIO.IgIterator.iterate", false]], "iterate() (bio.seqio.nibio.nibiterator method)": [[247, "Bio.SeqIO.NibIO.NibIterator.iterate", false]], "iterate() (bio.seqio.qualityio.fastqphrediterator method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.iterate", false]], "iterate() (bio.seqio.qualityio.qualphrediterator method)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.iterate", false]], "iterate() (bio.seqio.sffio.sffiterator method)": [[253, "Bio.SeqIO.SffIO.SffIterator.iterate", false]], "iterate() (bio.seqio.snapgeneio.snapgeneiterator method)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.iterate", false]], "iterate() (bio.seqio.tabio.tabiterator method)": [[256, "Bio.SeqIO.TabIO.TabIterator.iterate", false]], "iterate() (bio.seqio.xdnaio.xdnaiterator method)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.iterate", false]], "iteration (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.iteration", false]], "iterations (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.iterations", false]], "iterative_refinement (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.iterative_refinement", false]], "iterator (class in bio.genbank)": [[92, "Bio.GenBank.Iterator", false]], "iw (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.iw", false]], "jaspar5 (class in bio.motifs.jaspar.db)": [[288, "Bio.motifs.jaspar.db.JASPAR5", false]], "jitter (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.jitter", false]], "jsoniterator() (in module bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.JsonIterator", false]], "jsonwriter (class in bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.JsonWriter", false]], "jtt (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.jtt", false]], "jumble (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.jumble", false]], "jusweights (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.jusweights", false]], "k (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.k", false]], "k (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.k", false]], "k (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.k", false]], "kappa (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.kappa", false]], "kcluster() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.kcluster", false]], "kcluster() (in module bio.cluster)": [[73, "Bio.Cluster.kcluster", false]], "kegg_conv() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_conv", false]], "kegg_find() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_find", false]], "kegg_get() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_get", false]], "kegg_info() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_info", false]], "kegg_link() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_link", false]], "kegg_list() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_list", false]], "key (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.key", false]], "keys() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.keys", false]], "keys() (bio.blast.record method)": [[68, "Bio.Blast.Record.keys", false]], "keys() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys", false]], "keys() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.keys", false]], "keys() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.keys", false]], "keys() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.keys", false]], "keys() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.keys", false]], "keys_to_process (bio.genbank.utils.featurevaluecleaner attribute)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.keys_to_process", false]], "keyword (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.keyword", false]], "kgmlcanvas (class in bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.KGMLCanvas", false]], "kgmlparser (class in bio.kegg.kgml.kgml_parser)": [[116, "Bio.KEGG.KGML.KGML_parser.KGMLParser", false]], "kill() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.kill", false]], "kimura (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.kimura", false]], "kmedoids() (in module bio.cluster)": [[73, "Bio.Cluster.kmedoids", false]], "knn (class in bio.knn)": [[282, "Bio.kNN.kNN", false]], "knownstatetrainer (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.KnownStateTrainer", false]], "ktuple (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.ktuple", false]], "l (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.l", false]], "l (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.L", false]], "l (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.L", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.l", false]], "l (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.l", false]], "labels() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.labels", false]], "labels() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.labels", false]], "ladderize() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.ladderize", false]], "last_id() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.last_id", false]], "last_id() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.last_id", false]], "last_id() (biosql.dbutils.mysql_dbutils method)": [[304, "BioSQL.DBUtils.Mysql_dbutils.last_id", false]], "lat() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.lat", false]], "lcase_masking (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.lcase_masking", false]], "lcc_mult() (in module bio.sequtils.lcc)": [[267, "Bio.SeqUtils.lcc.lcc_mult", false]], "lcc_simp() (in module bio.sequtils.lcc)": [[267, "Bio.SeqUtils.lcc.lcc_simp", false]], "le (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.le", false]], "left_multiply() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.left_multiply", false]], "len12 (bio.pdb.internal_coords.hedron property)": [[169, "Bio.PDB.internal_coords.Hedron.len12", false]], "len23 (bio.pdb.internal_coords.hedron property)": [[169, "Bio.PDB.internal_coords.Hedron.len23", false]], "length (bio.align.alignment property)": [[30, "Bio.Align.Alignment.length", false]], "lep (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.lep", false]], "letter_annotations (bio.seqrecord.seqrecord property)": [[260, "Bio.SeqRecord.SeqRecord.letter_annotations", false]], "letters_per_block (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.LETTERS_PER_BLOCK", false]], "letters_per_line (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.LETTERS_PER_LINE", false]], "letters_per_line (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.LETTERS_PER_LINE", false]], "level (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.level", false]], "lexp (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.LEXP", false], [32, "Bio.Align.Applications.MafftCommandline.lexp", false]], "lgs (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lgs", false]], "lgs_t (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lgs_t", false]], "line_length (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.line_length", false]], "line_length (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.line_length", false]], "line_length (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.line_length", false]], "line_length (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.line_length", false]], "line_length (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.line_length", false]], "line_length (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.line_length", false]], "line_length (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.line_length", false]], "line_length (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.line_length", false]], "line_length (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.line_length", false]], "line_length (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.line_length", false]], "linedistribution (class in bio.graphics.distribution)": [[103, "Bio.Graphics.Distribution.LineDistribution", false]], "linesize (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.linesize", false]], "link() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.link", false]], "list_ambiguous_codons() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.list_ambiguous_codons", false]], "list_any_ids() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_any_ids", false]], "list_biodatabase_names() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_biodatabase_names", false]], "list_bioentry_display_ids() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_bioentry_display_ids", false]], "list_bioentry_ids() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_bioentry_ids", false]], "list_possible_proteins() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.list_possible_proteins", false]], "listelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.ListElement", false]], "lmax (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lmax", false]], "lo (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lo", false]], "load() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.load", false]], "load() (in module bio.align.substitution_matrices)": [[54, "Bio.Align.substitution_matrices.load", false]], "load() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.load", false]], "load_database_sql() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.load_database_sql", false]], "load_seqrecord() (biosql.loader.databaseloader method)": [[305, "BioSQL.Loader.DatabaseLoader.load_seqrecord", false]], "local_dtd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.local_dtd_dir", false]], "local_xsd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.local_xsd_dir", false]], "localpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.localpair", false]], "location (class in bio.seqfeature)": [[237, "Bio.SeqFeature.Location", false]], "location() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.location", false]], "locationparsererror": [[237, "Bio.SeqFeature.LocationParserError", false]], "log (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.log", false]], "log (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.log", false]], "log (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.log", false]], "log_likelihood() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.log_likelihood", false]], "log_odds() (bio.motifs.matrix.positionweightmatrix method)": [[290, "Bio.motifs.matrix.PositionWeightMatrix.log_odds", false]], "loga (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.loga", false]], "logdpalgorithms (class in bio.hmm.dynamicprogramming)": [[107, "Bio.HMM.DynamicProgramming.LogDPAlgorithms", false]], "logfile (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.logfile", false]], "logistic() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.logistic", false]], "logisticregression (class in bio.logisticregression)": [[120, "Bio.LogisticRegression.LogisticRegression", false]], "long() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.long", false]], "long_version (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.long_version", false]], "longseq (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.longseq", false]], "lookup() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.lookup", false]], "loopgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.loopgap", false]], "lop (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.LOP", false], [32, "Bio.Align.Applications.MafftCommandline.lop", false]], "losses() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.losses", false]], "lower (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.lower", false]], "lower() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.lower", false]], "lower() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.lower", false]], "lstrip() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.lstrip", false]], "lysinemodified (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.lysinemodified", false]], "m (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.m", false]], "m (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.M", false]], "m (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.M", false]], "m (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.M", false]], "m (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.m", false]], "m (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.m", false]], "m2rotaxis() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.m2rotaxis", false]], "ma (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ma", false]], "mafftcommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.MafftCommandline", false]], "mafindex (class in bio.alignio.mafio)": [[61, "Bio.AlignIO.MafIO.MafIndex", false]], "mafiterator() (in module bio.alignio.mafio)": [[61, "Bio.AlignIO.MafIO.MafIterator", false]], "mafwriter (class in bio.alignio.mafio)": [[61, "Bio.AlignIO.MafIO.MafWriter", false]], "majority_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.majority_consensus", false]], "make_back_table() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.make_back_table", false]], "make_dssp_dict() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.make_dssp_dict", false]], "make_extended() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.make_extended", false]], "make_format() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.make_format", false]], "make_table() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.make_table", false]], "make_virtual_offset() (in module bio.bgzf)": [[278, "Bio.bgzf.make_virtual_offset", false]], "makematrix (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.makematrix", false]], "map() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.map", false]], "mapall() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.mapall", false]], "maps (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.maps", false]], "markovmodel (class in bio.markovmodel)": [[121, "Bio.MarkovModel.MarkovModel", false]], "markovmodelbuilder (class in bio.hmm.markovmodel)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder", false]], "mask (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mask", false]], "mask (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.mask", false]], "mask_data (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.mask_data", false]], "mask_desc (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.mask_desc", false]], "mask_id (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.mask_id", false]], "mat (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mat", false]], "mat_thr (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mat_thr", false]], "match (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.MATCH", false]], "match (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.match", false]], "match (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.match", false]], "matches() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.matches", false]], "mate_file (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.mate_file", false]], "matinitsize (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.matinitsize", false]], "matresize (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.matresize", false]], "matrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.matrix", false]], "matrix (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.matrix", false]], "matrix (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.matrix", false]], "matrix (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.matrix", false]], "matrix (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.matrix", false]], "matrix (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.matrix", false]], "matrix (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.matrix", false]], "matrix (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.matrix", false]], "matrix (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.matrix", false]], "matrix (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.matrix", false]], "matrixtype (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.matrixtype", false]], "mauveiterator (class in bio.alignio.mauveio)": [[62, "Bio.AlignIO.MauveIO.MauveIterator", false]], "mauvewriter (class in bio.alignio.mauveio)": [[62, "Bio.AlignIO.MauveIO.MauveWriter", false]], "max (bio.motifs.matrix.positionspecificscoringmatrix property)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.max", false]], "max_file_sz (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.max_file_sz", false]], "max_guidetree_iterations (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.max_guidetree_iterations", false]], "max_hmm_iterations (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.max_hmm_iterations", false]], "max_hsps (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_hsps", false]], "max_hsps_per_subject (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_hsps_per_subject", false]], "max_intron_length (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_intron_length", false]], "max_intron_length (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_intron_length", false]], "max_intron_length (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_intron_length", false]], "max_link (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.max_link", false]], "max_target_seqs (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_target_seqs", false]], "maxbranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.maxbranches", false]], "maxdiagbreak (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxdiagbreak", false]], "maxdifftm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxdifftm", false]], "maxdiv (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.maxdiv", false]], "maxentropy (class in bio.maxentropy)": [[122, "Bio.MaxEntropy.MaxEntropy", false]], "maxgc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxgc", false]], "maxhours (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxhours", false]], "maximum() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.maximum", false]], "maxiterate (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.maxiterate", false]], "maxiters (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxiters", false]], "maxmispriming (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxmispriming", false]], "maxnumseq (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.maxnumseq", false]], "maxpallen (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.maxpallen", false]], "maxpeptidebond (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.MaxPeptideBond", false]], "maxpolyx (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxpolyx", false]], "maxrepeat (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.maxrepeat", false]], "maxrepeat (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.maxrepeat", false]], "maxseqlen (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.maxseqlen", false]], "maxseqlen (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.maxseqlen", false]], "maxsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxsize", false]], "maxsize (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.MaxSize", false]], "maxtm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxtm", false]], "maxtrees (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxtrees", false]], "maxtrees (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.maxtrees", false]], "mean() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.mean", false]], "mean() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.mean", false]], "memsave (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.memsave", false]], "merge_with_support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.merge_with_support", false]], "method (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.method", false]], "method (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.method", false]], "method (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.method", false]], "methods (bio.phylo.treeconstruction.distancetreeconstructor attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.methods", false]], "min (bio.motifs.matrix.positionspecificscoringmatrix property)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.min", false]], "min_dist() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.min_dist", false]], "min_link (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.min_link", false]], "min_raw_gapped_score (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.min_raw_gapped_score", false]], "minbestcolscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.minbestcolscore", false]], "mingc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mingc", false]], "minimum() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.minimum", false]], "minpallen (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.minpallen", false]], "minrepeat (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.minrepeat", false]], "minscore (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.minscore", false]], "minscore (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.minscore", false]], "minsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.minsize", false]], "minsmoothscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.minsmoothscore", false]], "mintm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mintm", false]], "mirna (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.miRNA", false]], "mishyblibraryfile (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mishyblibraryfile", false]], "mismatch (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.mismatch", false]], "mismatch (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.mismatch", false]], "mismatch (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.mismatch", false]], "mismatches (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.mismatches", false]], "mismatchpercent (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.mismatchpercent", false]], "mispriminglibraryfile (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mispriminglibraryfile", false]], "missingatomerror": [[169, "Bio.PDB.internal_coords.MissingAtomError", false]], "missingexternaldependencyerror": [[27, "Bio.MissingExternalDependencyError", false]], "missingpythondependencyerror": [[27, "Bio.MissingPythonDependencyError", false]], "mktest() (in module bio.align.analysis)": [[34, "Bio.Align.analysis.mktest", false]], "mktest() (in module bio.codonalign.codonalignment)": [[280, "Bio.codonalign.codonalignment.mktest", false]], "ml_estimator() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.ml_estimator", false]], "mlacc (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.mlacc", false]], "mlfrac (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.mlfrac", false]], "mllen (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.mllen", false]], "mlnni (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.mlnni", false]], "mmcif2dict (class in bio.pdb.mmcif2dict)": [[142, "Bio.PDB.MMCIF2Dict.MMCIF2Dict", false]], "mmcifio (class in bio.pdb.mmcifio)": [[170, "Bio.PDB.mmcifio.MMCIFIO", false]], "mmcifparser (class in bio.pdb.mmcifparser)": [[143, "Bio.PDB.MMCIFParser.MMCIFParser", false]], "mmtfio (class in bio.pdb.mmtf.mmtfio)": [[173, "Bio.PDB.mmtf.mmtfio.MMTFIO", false]], "mmtfparser (class in bio.pdb.mmtf)": [[171, "Bio.PDB.mmtf.MMTFParser", false]], "mode (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.mode", false]], "mode (bio.align.bigbed.alignmentiterator attribute)": [[36, "Bio.Align.bigbed.AlignmentIterator.mode", false]], "mode (bio.align.bigbed.alignmentwriter attribute)": [[36, "Bio.Align.bigbed.AlignmentWriter.mode", false]], "mode (bio.align.bigmaf.alignmentiterator attribute)": [[37, "Bio.Align.bigmaf.AlignmentIterator.mode", false]], "mode (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.mode", false]], "mode (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.mode", false]], "mode (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.mode", false]], "model (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.model", false]], "model (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.model", false]], "model (class in bio.pdb.model)": [[144, "Bio.PDB.Model.Model", false]], "models (bio.phylo.treeconstruction.distancecalculator attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.models", false]], "modify() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.modify", false]], "module": [[27, "module-Bio", false], [28, "module-Bio.Affy", false], [29, "module-Bio.Affy.CelFile", false], [30, "module-Bio.Align", false], [31, "module-Bio.Align.AlignInfo", false], [32, "module-Bio.Align.Applications", false], [33, "module-Bio.Align.a2m", false], [34, "module-Bio.Align.analysis", false], [35, "module-Bio.Align.bed", false], [36, "module-Bio.Align.bigbed", false], [37, "module-Bio.Align.bigmaf", false], [38, "module-Bio.Align.bigpsl", false], [39, "module-Bio.Align.chain", false], [40, "module-Bio.Align.clustal", false], [41, "module-Bio.Align.emboss", false], [42, "module-Bio.Align.exonerate", false], [43, "module-Bio.Align.fasta", false], [44, "module-Bio.Align.hhr", false], [45, "module-Bio.Align.interfaces", false], [46, "module-Bio.Align.maf", false], [47, "module-Bio.Align.mauve", false], [48, "module-Bio.Align.msf", false], [49, "module-Bio.Align.nexus", false], [50, "module-Bio.Align.phylip", false], [51, "module-Bio.Align.psl", false], [52, "module-Bio.Align.sam", false], [53, "module-Bio.Align.stockholm", false], [54, "module-Bio.Align.substitution_matrices", false], [55, "module-Bio.Align.tabular", false], [56, "module-Bio.AlignIO", false], [57, "module-Bio.AlignIO.ClustalIO", false], [58, "module-Bio.AlignIO.EmbossIO", false], [59, "module-Bio.AlignIO.FastaIO", false], [60, "module-Bio.AlignIO.Interfaces", false], [61, "module-Bio.AlignIO.MafIO", false], [62, "module-Bio.AlignIO.MauveIO", false], [63, "module-Bio.AlignIO.MsfIO", false], [64, "module-Bio.AlignIO.NexusIO", false], [65, "module-Bio.AlignIO.PhylipIO", false], [66, "module-Bio.AlignIO.StockholmIO", false], [67, "module-Bio.Application", false], [68, "module-Bio.Blast", false], [69, "module-Bio.Blast.Applications", false], [70, "module-Bio.Blast.NCBIWWW", false], [71, "module-Bio.Blast.NCBIXML", false], [72, "module-Bio.CAPS", false], [73, "module-Bio.Cluster", false], [74, "module-Bio.Compass", false], [75, "module-Bio.Data", false], [76, "module-Bio.Data.CodonTable", false], [77, "module-Bio.Data.IUPACData", false], [78, "module-Bio.Data.PDBData", false], [79, "module-Bio.Emboss", false], [80, "module-Bio.Emboss.Applications", false], [81, "module-Bio.Emboss.Primer3", false], [82, "module-Bio.Emboss.PrimerSearch", false], [83, "module-Bio.Entrez", false], [84, "module-Bio.Entrez.Parser", false], [85, "module-Bio.ExPASy", false], [86, "module-Bio.ExPASy.Enzyme", false], [87, "module-Bio.ExPASy.Prodoc", false], [88, "module-Bio.ExPASy.Prosite", false], [89, "module-Bio.ExPASy.ScanProsite", false], [90, "module-Bio.ExPASy.cellosaurus", false], [91, "module-Bio.File", false], [92, "module-Bio.GenBank", false], [93, "module-Bio.GenBank.Record", false], [94, "module-Bio.GenBank.Scanner", false], [95, "module-Bio.GenBank.utils", false], [96, "module-Bio.Geo", false], [97, "module-Bio.Geo.Record", false], [98, "module-Bio.Graphics", false], [99, "module-Bio.Graphics.BasicChromosome", false], [100, "module-Bio.Graphics.ColorSpiral", false], [101, "module-Bio.Graphics.Comparative", false], [102, "module-Bio.Graphics.DisplayRepresentation", false], [103, "module-Bio.Graphics.Distribution", false], [104, "module-Bio.Graphics.GenomeDiagram", false], [105, "module-Bio.Graphics.KGML_vis", false], [106, "module-Bio.HMM", false], [107, "module-Bio.HMM.DynamicProgramming", false], [108, "module-Bio.HMM.MarkovModel", false], [109, "module-Bio.HMM.Trainer", false], [110, "module-Bio.HMM.Utilities", false], [111, "module-Bio.KEGG", false], [112, "module-Bio.KEGG.Compound", false], [113, "module-Bio.KEGG.Enzyme", false], [114, "module-Bio.KEGG.Gene", false], [115, "module-Bio.KEGG.KGML", false], [116, "module-Bio.KEGG.KGML.KGML_parser", false], [117, "module-Bio.KEGG.KGML.KGML_pathway", false], [118, "module-Bio.KEGG.Map", false], [119, "module-Bio.KEGG.REST", false], [120, "module-Bio.LogisticRegression", false], [121, "module-Bio.MarkovModel", false], [122, "module-Bio.MaxEntropy", false], [123, "module-Bio.Medline", false], [124, "module-Bio.NMR", false], [125, "module-Bio.NMR.NOEtools", false], [126, "module-Bio.NMR.xpktools", false], [127, "module-Bio.NaiveBayes", false], [128, "module-Bio.Nexus", false], [129, "module-Bio.Nexus.Nexus", false], [130, "module-Bio.Nexus.Nodes", false], [131, "module-Bio.Nexus.StandardData", false], [132, "module-Bio.Nexus.Trees", false], [133, "module-Bio.PDB", false], [134, "module-Bio.PDB.AbstractPropertyMap", false], [135, "module-Bio.PDB.Atom", false], [136, "module-Bio.PDB.Chain", false], [137, "module-Bio.PDB.DSSP", false], [138, "module-Bio.PDB.Dice", false], [139, "module-Bio.PDB.Entity", false], [140, "module-Bio.PDB.FragmentMapper", false], [141, "module-Bio.PDB.HSExposure", false], [142, "module-Bio.PDB.MMCIF2Dict", false], [143, "module-Bio.PDB.MMCIFParser", false], [144, "module-Bio.PDB.Model", false], [145, "module-Bio.PDB.NACCESS", false], [146, "module-Bio.PDB.NeighborSearch", false], [147, "module-Bio.PDB.PDBExceptions", false], [148, "module-Bio.PDB.PDBIO", false], [149, "module-Bio.PDB.PDBList", false], [150, "module-Bio.PDB.PDBMLParser", false], [151, "module-Bio.PDB.PDBParser", false], [152, "module-Bio.PDB.PICIO", false], [153, "module-Bio.PDB.PSEA", false], [154, "module-Bio.PDB.Polypeptide", false], [155, "module-Bio.PDB.Residue", false], [156, "module-Bio.PDB.ResidueDepth", false], [157, "module-Bio.PDB.SASA", false], [158, "module-Bio.PDB.SCADIO", false], [159, "module-Bio.PDB.Selection", false], [160, "module-Bio.PDB.Structure", false], [161, "module-Bio.PDB.StructureAlignment", false], [162, "module-Bio.PDB.StructureBuilder", false], [163, "module-Bio.PDB.Superimposer", false], [164, "module-Bio.PDB.alphafold_db", false], [165, "module-Bio.PDB.binary_cif", false], [166, "module-Bio.PDB.cealign", false], [167, "module-Bio.PDB.ic_data", false], [168, "module-Bio.PDB.ic_rebuild", false], [169, "module-Bio.PDB.internal_coords", false], [170, "module-Bio.PDB.mmcifio", false], [171, "module-Bio.PDB.mmtf", false], [172, "module-Bio.PDB.mmtf.DefaultParser", false], [173, "module-Bio.PDB.mmtf.mmtfio", false], [174, "module-Bio.PDB.parse_pdb_header", false], [175, "module-Bio.PDB.qcprot", false], [176, "module-Bio.PDB.vectors", false], [177, "module-Bio.Pathway", false], [178, "module-Bio.Pathway.Rep", false], [179, "module-Bio.Pathway.Rep.Graph", false], [180, "module-Bio.Pathway.Rep.MultiGraph", false], [181, "module-Bio.Phylo", false], [182, "module-Bio.Phylo.Applications", false], [183, "module-Bio.Phylo.BaseTree", false], [184, "module-Bio.Phylo.CDAO", false], [185, "module-Bio.Phylo.CDAOIO", false], [186, "module-Bio.Phylo.Consensus", false], [187, "module-Bio.Phylo.NeXML", false], [188, "module-Bio.Phylo.NeXMLIO", false], [189, "module-Bio.Phylo.Newick", false], [190, "module-Bio.Phylo.NewickIO", false], [191, "module-Bio.Phylo.NexusIO", false], [192, "module-Bio.Phylo.PAML", false], [193, "module-Bio.Phylo.PAML.baseml", false], [194, "module-Bio.Phylo.PAML.chi2", false], [195, "module-Bio.Phylo.PAML.codeml", false], [196, "module-Bio.Phylo.PAML.yn00", false], [197, "module-Bio.Phylo.PhyloXML", false], [198, "module-Bio.Phylo.PhyloXMLIO", false], [199, "module-Bio.Phylo.TreeConstruction", false], [200, "module-Bio.PopGen", false], [201, "module-Bio.PopGen.GenePop", false], [202, "module-Bio.PopGen.GenePop.Controller", false], [203, "module-Bio.PopGen.GenePop.EasyController", false], [204, "module-Bio.PopGen.GenePop.FileParser", false], [205, "module-Bio.PopGen.GenePop.LargeFileParser", false], [206, "module-Bio.Restriction", false], [207, "module-Bio.Restriction.PrintFormat", false], [208, "module-Bio.Restriction.Restriction_Dictionary", false], [209, "module-Bio.SCOP", false], [210, "module-Bio.SCOP.Cla", false], [211, "module-Bio.SCOP.Des", false], [212, "module-Bio.SCOP.Dom", false], [213, "module-Bio.SCOP.Hie", false], [214, "module-Bio.SCOP.Raf", false], [215, "module-Bio.SCOP.Residues", false], [216, "module-Bio.SVDSuperimposer", false], [217, "module-Bio.SearchIO", false], [218, "module-Bio.SearchIO.BlastIO", false], [219, "module-Bio.SearchIO.BlastIO.blast_tab", false], [220, "module-Bio.SearchIO.BlastIO.blast_xml", false], [221, "module-Bio.SearchIO.BlatIO", false], [222, "module-Bio.SearchIO.ExonerateIO", false], [223, "module-Bio.SearchIO.ExonerateIO.exonerate_cigar", false], [224, "module-Bio.SearchIO.ExonerateIO.exonerate_text", false], [225, "module-Bio.SearchIO.ExonerateIO.exonerate_vulgar", false], [226, "module-Bio.SearchIO.FastaIO", false], [227, "module-Bio.SearchIO.HHsuiteIO", false], [228, "module-Bio.SearchIO.HHsuiteIO.hhsuite2_text", false], [229, "module-Bio.SearchIO.HmmerIO", false], [230, "module-Bio.SearchIO.HmmerIO.hmmer2_text", false], [231, "module-Bio.SearchIO.HmmerIO.hmmer3_domtab", false], [232, "module-Bio.SearchIO.HmmerIO.hmmer3_tab", false], [233, "module-Bio.SearchIO.HmmerIO.hmmer3_text", false], [234, "module-Bio.SearchIO.InterproscanIO", false], [235, "module-Bio.SearchIO.InterproscanIO.interproscan_xml", false], [236, "module-Bio.Seq", false], [237, "module-Bio.SeqFeature", false], [238, "module-Bio.SeqIO", false], [239, "module-Bio.SeqIO.AbiIO", false], [240, "module-Bio.SeqIO.AceIO", false], [241, "module-Bio.SeqIO.FastaIO", false], [242, "module-Bio.SeqIO.GckIO", false], [243, "module-Bio.SeqIO.GfaIO", false], [244, "module-Bio.SeqIO.IgIO", false], [245, "module-Bio.SeqIO.InsdcIO", false], [246, "module-Bio.SeqIO.Interfaces", false], [247, "module-Bio.SeqIO.NibIO", false], [248, "module-Bio.SeqIO.PdbIO", false], [249, "module-Bio.SeqIO.PhdIO", false], [250, "module-Bio.SeqIO.PirIO", false], [251, "module-Bio.SeqIO.QualityIO", false], [252, "module-Bio.SeqIO.SeqXmlIO", false], [253, "module-Bio.SeqIO.SffIO", false], [254, "module-Bio.SeqIO.SnapGeneIO", false], [255, "module-Bio.SeqIO.SwissIO", false], [256, "module-Bio.SeqIO.TabIO", false], [257, "module-Bio.SeqIO.TwoBitIO", false], [258, "module-Bio.SeqIO.UniprotIO", false], [259, "module-Bio.SeqIO.XdnaIO", false], [260, "module-Bio.SeqRecord", false], [261, "module-Bio.SeqUtils", false], [262, "module-Bio.SeqUtils.CheckSum", false], [263, "module-Bio.SeqUtils.IsoelectricPoint", false], [264, "module-Bio.SeqUtils.MeltingTemp", false], [265, "module-Bio.SeqUtils.ProtParam", false], [266, "module-Bio.SeqUtils.ProtParamData", false], [267, "module-Bio.SeqUtils.lcc", false], [268, "module-Bio.Sequencing", false], [269, "module-Bio.Sequencing.Ace", false], [270, "module-Bio.Sequencing.Applications", false], [271, "module-Bio.Sequencing.Phd", false], [272, "module-Bio.SwissProt", false], [273, "module-Bio.SwissProt.KeyWList", false], [274, "module-Bio.TogoWS", false], [275, "module-Bio.UniGene", false], [276, "module-Bio.UniProt", false], [277, "module-Bio.UniProt.GOA", false], [278, "module-Bio.bgzf", false], [279, "module-Bio.codonalign", false], [280, "module-Bio.codonalign.codonalignment", false], [281, "module-Bio.codonalign.codonseq", false], [282, "module-Bio.kNN", false], [283, "module-Bio.motifs", false], [284, "module-Bio.motifs.alignace", false], [285, "module-Bio.motifs.applications", false], [286, "module-Bio.motifs.clusterbuster", false], [287, "module-Bio.motifs.jaspar", false], [288, "module-Bio.motifs.jaspar.db", false], [289, "module-Bio.motifs.mast", false], [290, "module-Bio.motifs.matrix", false], [291, "module-Bio.motifs.meme", false], [292, "module-Bio.motifs.minimal", false], [293, "module-Bio.motifs.pfm", false], [294, "module-Bio.motifs.thresholds", false], [295, "module-Bio.motifs.transfac", false], [296, "module-Bio.motifs.xms", false], [297, "module-Bio.pairwise2", false], [298, "module-Bio.phenotype", false], [299, "module-Bio.phenotype.phen_micro", false], [300, "module-Bio.phenotype.pm_fitting", false], [301, "module-BioSQL", false], [302, "module-BioSQL.BioSeq", false], [303, "module-BioSQL.BioSeqDatabase", false], [304, "module-BioSQL.DBUtils", false], [305, "module-BioSQL.Loader", false]], "mol_seq() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.mol_seq", false]], "mol_seq() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.mol_seq", false]], "molar_extinction_coefficient() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.molar_extinction_coefficient", false]], "molecular_weight() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.molecular_weight", false]], "molecular_weight() (in module bio.sequtils)": [[261, "Bio.SeqUtils.molecular_weight", false]], "molseq (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.MolSeq", false]], "mot (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mot", false]], "motif (class in bio.motifs)": [[283, "Bio.motifs.Motif", false]], "motif (class in bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.Motif", false]], "motif (class in bio.motifs.meme)": [[291, "Bio.motifs.meme.Motif", false]], "motif (class in bio.motifs.transfac)": [[295, "Bio.motifs.transfac.Motif", false]], "move_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.move_track", false]], "msa_master_idx (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.msa_master_idx", false]], "msaprobscommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.MSAProbsCommandline", false]], "msf (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.msf", false]], "msf (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.msf", false]], "msfiterator (class in bio.alignio.msfio)": [[63, "Bio.AlignIO.MsfIO.MsfIterator", false]], "msfout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.msfout", false]], "mttranslate (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.mttranslate", false]], "multi_coord_space() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.multi_coord_space", false]], "multi_rot_y() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.multi_rot_Y", false]], "multi_rot_z() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.multi_rot_Z", false]], "multigraph (class in bio.pathway.rep.multigraph)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph", false]], "multiple (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.multiple", false]], "multiple_value_keys (bio.motifs.transfac.motif attribute)": [[295, "Bio.motifs.transfac.Motif.multiple_value_keys", false]], "multiplealignment (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.MultipleAlignment", false]], "multipleseqalignment (class in bio.align)": [[30, "Bio.Align.MultipleSeqAlignment", false]], "musclecommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.MuscleCommandline", false]], "mutableseq (class in bio.seq)": [[236, "Bio.Seq.MutableSeq", false]], "mysql_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Mysql_dbutils", false]], "mysqlconnectoradaptor (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor", false]], "n (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.n", false]], "n (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.n", false]], "n (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.N", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.n", false]], "n (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.N", false]], "n (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.N", false], [270, "Bio.Sequencing.Applications.BwaSampeCommandline.n", false]], "n (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.n", false]], "n (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.n", false]], "n (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.n", false]], "n (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.n", false]], "n_rand_starts (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.n_rand_starts", false]], "naccess (class in bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.NACCESS", false]], "naccess_atomic (class in bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.NACCESS_atomic", false]], "naivebayes (class in bio.naivebayes)": [[127, "Bio.NaiveBayes.NaiveBayes", false]], "name (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.name", false]], "name (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.name", false]], "name (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.name", false]], "name (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.name", false]], "name (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.name", false]], "name() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.name", false]], "namelength (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.namelength", false]], "namewidth (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.NameWidth", false]], "ncategories (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.ncategories", false]], "ncategories (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.ncategories", false]], "ncbiblastformattercommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline", false]], "ncbiblastncommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline", false]], "ncbiblastpcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline", false]], "ncbiblastxcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline", false]], "ncbicodontable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.NCBICodonTable", false]], "ncbicodontabledna (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.NCBICodonTableDNA", false]], "ncbicodontablerna (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.NCBICodonTableRNA", false]], "ncbideltablastcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline", false]], "ncbimakeblastdbcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline", false]], "ncbipsiblastcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline", false]], "ncbirpsblastcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline", false]], "ncbirpstblastncommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline", false]], "ncbitblastncommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline", false]], "ncbitblastxcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline", false]], "nclasses (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.nclasses", false]], "needleallcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.NeedleallCommandline", false]], "needlecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.NeedleCommandline", false]], "negative (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.negative", false]], "negative_gilist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.negative_gilist", false]], "negative_seqidlist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.negative_seqidlist", false]], "neighborsearch (class in bio.pdb.neighborsearch)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch", false]], "network (class in bio.pathway)": [[177, "Bio.Pathway.Network", false]], "new_clade() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.new_clade", false]], "new_clade() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.new_clade", false]], "new_database() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.new_database", false]], "new_graph() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.new_graph", false]], "new_label() (bio.phylo.nexmlio.writer method)": [[188, "Bio.Phylo.NeXMLIO.Writer.new_label", false]], "new_set() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.new_set", false]], "new_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.new_track", false]], "newickerror": [[190, "Bio.Phylo.NewickIO.NewickError", false]], "newtree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.newtree", false]], "newtree1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.newtree1", false]], "newtree2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.newtree2", false]], "nexmlerror": [[188, "Bio.Phylo.NeXMLIO.NeXMLError", false]], "next_nonwhitespace() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.next_nonwhitespace", false]], "next_until() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.next_until", false]], "next_word() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.next_word", false]], "nexus (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.Nexus", false]], "nexuserror": [[129, "Bio.Nexus.Nexus.NexusError", false], [131, "Bio.Nexus.StandardData.NexusError", false]], "nexusiterator() (in module bio.alignio.nexusio)": [[64, "Bio.AlignIO.NexusIO.NexusIterator", false]], "nexuswriter (class in bio.alignio.nexusio)": [[64, "Bio.AlignIO.NexusIO.NexusWriter", false]], "nibiterator (class in bio.seqio.nibio)": [[247, "Bio.SeqIO.NibIO.NibIterator", false]], "nibwriter (class in bio.seqio.nibio)": [[247, "Bio.SeqIO.NibIO.NibWriter", false]], "nj (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nj", false]], "nj() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.nj", false]], "njumble (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.njumble", false]], "njumble (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.njumble", false]], "nni (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nni", false]], "nnitreesearcher (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.NNITreeSearcher", false]], "no2nd (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.no2nd", false]], "no_altloc (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.no_altloc", false]], "no_greedy (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.no_greedy", false]], "noanchors (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.noanchors", false]], "nobrief (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.nobrief", false]], "nobrief (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.nobrief", false]], "nobrief (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.nobrief", false]], "nocat (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nocat", false]], "nocore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.nocore", false]], "node (class in bio.cluster)": [[73, "Bio.Cluster.Node", false]], "node (class in bio.nexus.nodes)": [[130, "Bio.Nexus.Nodes.Node", false]], "node (class in bio.scop)": [[209, "Bio.SCOP.Node", false]], "node() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.node", false]], "node_id() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.node_id", false]], "nodedata (class in bio.nexus.trees)": [[132, "Bio.Nexus.Trees.NodeData", false]], "nodeexception": [[130, "Bio.Nexus.Nodes.NodeException", false]], "nodes() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.nodes", false]], "nodes() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes", false]], "nofft (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.nofft", false]], "nohgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nohgap", false]], "nomatrix (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nomatrix", false]], "nome (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nome", false]], "noml (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.noml", false]], "none (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.NONE", false]], "noneelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.NoneElement", false]], "nopgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nopgap", false]], "nopost (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.nopost", false]], "nopr (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nopr", false]], "norm() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.norm", false]], "normalize() (bio.motifs.matrix.frequencypositionmatrix method)": [[290, "Bio.motifs.matrix.FrequencyPositionMatrix.normalize", false]], "normalize() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.normalize", false]], "normalize_letters() (in module bio.scop.raf)": [[214, "Bio.SCOP.Raf.normalize_letters", false]], "normalized() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.normalized", false]], "normsq() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.normsq", false]], "noroot (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.noroot", false]], "noscore (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.noscore", false]], "nosecstr1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nosecstr1", false]], "nosecstr2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nosecstr2", false]], "nosupport (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nosupport", false]], "notermini (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.notermini", false]], "notop (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.notop", false]], "notree (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.notree", false]], "notxmlerror": [[68, "Bio.Blast.NotXMLError", false], [84, "Bio.Entrez.Parser.NotXMLError", false]], "novoaligncommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline", false]], "noweights (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.noweights", false]], "noxml (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.noxml", false]], "nt (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.nt", false]], "nt (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nt", false]], "nt_search() (in module bio.sequtils)": [[261, "Bio.SeqUtils.nt_search", false]], "nta (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.nta", false]], "nuc (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.nuc", false]], "nucleotide_alphabet (bio.data.codontable.ncbicodontable attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTable.nucleotide_alphabet", false]], "nucleotide_alphabet (bio.data.codontable.ncbicodontabledna attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTableDNA.nucleotide_alphabet", false]], "nucleotide_alphabet (bio.data.codontable.ncbicodontablerna attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTableRNA.nucleotide_alphabet", false]], "num_alignments (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.num_alignments", false]], "num_bootstrap_searches (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.num_bootstrap_searches", false]], "num_categories (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.num_categories", false]], "num_descriptions (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.num_descriptions", false]], "num_iterations (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_iterations", false]], "num_iterations (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_iterations", false]], "num_replicates (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.num_replicates", false]], "num_threads (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.num_threads", false]], "number (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.number", false]], "numiter (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.numiter", false]], "nummismatches (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.nummismatches", false]], "numreturn (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.numreturn", false]], "numthreads (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.numthreads", false]], "o (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.o", false]], "o (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.o", false]], "o (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.O", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.o", false]], "o (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.O", false]], "o (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.o", false]], "o (bio.sequencing.applications.samtoolscatcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.o", false]], "o (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.o", false]], "o (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.o", false]], "o (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.O", false], [270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.o", false]], "o (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.o", false]], "oanyself (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oanyself", false]], "objscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.objscore", false]], "odnaconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.odnaconc", false]], "oendself (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oendself", false]], "oexcludedregion (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oexcludedregion", false]], "off_diagonal_range (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.off_diagonal_range", false]], "ogcmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcmax", false]], "ogcmin (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcmin", false]], "ogcopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcopt", false]], "ogcpercent (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcpercent", false]], "ok_applies_to (bio.phylo.phyloxml.property attribute)": [[197, "Bio.Phylo.PhyloXML.Property.ok_applies_to", false]], "ok_datatype (bio.phylo.phyloxml.property attribute)": [[197, "Bio.Phylo.PhyloXML.Property.ok_datatype", false]], "ok_rank (bio.phylo.phyloxml.taxonomy attribute)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.ok_rank", false]], "ok_type (bio.phylo.phyloxml.events attribute)": [[197, "Bio.Phylo.PhyloXML.Events.ok_type", false]], "ok_type (bio.phylo.phyloxml.sequencerelation attribute)": [[197, "Bio.Phylo.PhyloXML.SequenceRelation.ok_type", false]], "oligoinput (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oligoinput", false]], "omaxsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.omaxsize", false]], "ominsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ominsize", false]], "omishybmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.omishybmax", false]], "once (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.once", false]], "one_to_index() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.one_to_index", false]], "oneofposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.OneOfPosition", false]], "op (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.op", false]], "open() (in module bio.bgzf)": [[278, "Bio.bgzf.open", false]], "open_database() (in module biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.open_database", false]], "open_dtd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.open_dtd_file", false]], "open_xsd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.open_xsd_file", false]], "opolyxmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.opolyxmax", false]], "optimize (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.optimize", false]], "optimize() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.optimize", false]], "options (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.options", false]], "options (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.options", false]], "options (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.options", false]], "options (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.options", false]], "options (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.options", false]], "options (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.options", false]], "options (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.options", false]], "options (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.options", false]], "options (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.options", false]], "options (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.options", false]], "options (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.options", false]], "options (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.options", false]], "options (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.options", false]], "options (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.options", false]], "options (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.options", false]], "options (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.options", false]], "options (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.options", false]], "options (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.options", false]], "options (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.options", false]], "options (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.options", false]], "options (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.options", false]], "options (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.options", false]], "options (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.options", false]], "options (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.options", false]], "options (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.options", false]], "options (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.options", false]], "opttm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.opttm", false]], "orderedlistelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.OrderedListElement", false]], "organism (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.Organism", false]], "orthologs (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.orthologs", false]], "osaltconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.osaltconc", false]], "osformat (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.osformat", false]], "osize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.osize", false]], "osizeopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.osizeopt", false]], "other (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Other", false]], "other() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.other", false]], "other() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.other", false]], "other_internal_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.OTHER_INTERNAL_FORMAT", false]], "otm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otm", false]], "otmmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otmmax", false]], "otmmin (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otmmin", false]], "otmopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otmopt", false]], "out (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.out", false]], "out (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.out", false]], "out (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.out", false]], "out (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.out", false]], "out (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.out", false]], "out (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.out", false]], "out (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.out", false]], "out (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.out", false]], "out (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.out", false]], "out (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.out", false]], "out (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.out", false]], "out (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.out", false]], "out (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.out", false]], "out_ascii_pssm (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.out_ascii_pssm", false]], "out_ascii_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.out_ascii_pssm", false]], "out_block() (in module bio.geo.record)": [[97, "Bio.Geo.Record.out_block", false]], "out_prefix (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.out_prefix", false]], "out_pssm (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.out_pssm", false]], "out_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.out_pssm", false]], "outfile (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.outfile", false]], "outfile (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.outfile", false]], "outfile (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.outfile", false]], "outfile (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.outfile", false]], "outfile (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.outfile", false]], "outfile (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.outfile", false]], "outfile (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.outfile", false]], "outfile (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.outfile", false]], "outfile (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.outfile", false]], "outfile (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.outfile", false]], "outfile (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.outfile", false]], "outfile (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.outfile", false]], "outfile (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.outfile", false]], "outfile (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.outfile", false]], "outfile (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.outfile", false]], "outfile (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.outfile", false]], "outfile (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.outfile", false]], "outfile (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.outfile", false]], "outfile (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.outfile", false]], "outfile (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.outfile", false]], "outfile (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.outfile", false]], "outfile (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.outfile", false]], "outfile (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.outfile", false]], "outfile (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.outfile", false]], "outfile (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.outfile", false]], "outfile (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.outfile", false]], "outfile (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.outfile", false]], "outfile (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.outfile", false]], "outfmt (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.outfmt", false]], "outgrno (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.outgrno", false]], "outgrno (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.outgrno", false]], "outgrno (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.outgrno", false]], "outgrno (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.outgrno", false]], "outgrno (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.outgrno", false]], "outgroup (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.outgroup", false]], "outorder (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.outorder", false]], "outorder (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.outorder", false]], "output (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.output", false]], "output (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.output", false]], "output (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.output", false]], "output_file (bio.sequencing.applications.samtoolsfixmatecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline.output_file", false]], "output_file (bio.sequencing.applications.samtoolsrmdupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.output_file", false]], "outputorder (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.outputorder", false]], "outputrecord (class in bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.OutputRecord", false]], "outputtree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.outputtree", false]], "outseq (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.outseq", false]], "outseq (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.outseq", false]], "outtreefile (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.outtreefile", false]], "outtreefile (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.outtreefile", false]], "outtreefile (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.outtreefile", false]], "outtreefile (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.outtreefile", false]], "overlap (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.overlap", false]], "ow (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ow", false]], "p (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.P", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.p", false]], "p (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.p", false]], "pairedfastaqualiterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.PairedFastaQualIterator", false]], "pairgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pairgap", false]], "pairing (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.pairing", false]], "pairs (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.pairs", false]], "pairwisealigner (class in bio.align)": [[30, "Bio.Align.PairwiseAligner", false]], "pairwisealignments (class in bio.align)": [[30, "Bio.Align.PairwiseAlignments", false]], "palindromecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.PalindromeCommandline", false]], "parallelassembleresidues (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.ParallelAssembleResidues", false]], "parameters (bio.application.abstractcommandline attribute)": [[67, "Bio.Application.AbstractCommandline.parameters", false]], "parameters (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Parameters", false]], "paramfile (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.paramfile", false]], "parent (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.parent", false]], "parent_edges() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.parent_edges", false]], "parent_edges() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.parent_edges", false]], "parents() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.parents", false]], "parents() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.parents", false]], "pars (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.pars", false]], "parse() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.parse", false]], "parse() (bio.genbank.featureparser method)": [[92, "Bio.GenBank.FeatureParser.parse", false]], "parse() (bio.genbank.recordparser method)": [[92, "Bio.GenBank.RecordParser.parse", false]], "parse() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse", false]], "parse() (bio.kegg.kgml.kgml_parser.kgmlparser method)": [[116, "Bio.KEGG.KGML.KGML_parser.KGMLParser.parse", false]], "parse() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse", false]], "parse() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.parse", false]], "parse() (bio.phylo.nexmlio.parser method)": [[188, "Bio.Phylo.NeXMLIO.Parser.parse", false]], "parse() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.parse", false]], "parse() (bio.seqio.abiio.abiiterator method)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.parse", false]], "parse() (bio.seqio.fastaio.fastaiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.parse", false]], "parse() (bio.seqio.fastaio.fastatwolineiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.parse", false]], "parse() (bio.seqio.gckio.gckiterator method)": [[242, "Bio.SeqIO.GckIO.GckIterator.parse", false]], "parse() (bio.seqio.igio.igiterator method)": [[244, "Bio.SeqIO.IgIO.IgIterator.parse", false]], "parse() (bio.seqio.insdcio.emblcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.parse", false]], "parse() (bio.seqio.insdcio.embliterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.parse", false]], "parse() (bio.seqio.insdcio.genbankcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.parse", false]], "parse() (bio.seqio.insdcio.genbankiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.parse", false]], "parse() (bio.seqio.insdcio.imgtiterator method)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.parse", false]], "parse() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.parse", false]], "parse() (bio.seqio.nibio.nibiterator method)": [[247, "Bio.SeqIO.NibIO.NibIterator.parse", false]], "parse() (bio.seqio.pdbio.pdbseqresiterator method)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.parse", false]], "parse() (bio.seqio.pirio.piriterator method)": [[250, "Bio.SeqIO.PirIO.PirIterator.parse", false]], "parse() (bio.seqio.qualityio.fastqphrediterator method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.parse", false]], "parse() (bio.seqio.qualityio.qualphrediterator method)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.parse", false]], "parse() (bio.seqio.seqxmlio.seqxmliterator method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.parse", false]], "parse() (bio.seqio.sffio.sffiterator method)": [[253, "Bio.SeqIO.SffIO.SffIterator.parse", false]], "parse() (bio.seqio.snapgeneio.snapgeneiterator method)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.parse", false]], "parse() (bio.seqio.tabio.tabiterator method)": [[256, "Bio.SeqIO.TabIO.TabIterator.parse", false]], "parse() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.parse", false]], "parse() (bio.seqio.uniprotio.parser method)": [[258, "Bio.SeqIO.UniprotIO.Parser.parse", false]], "parse() (bio.seqio.xdnaio.xdnaiterator method)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.parse", false]], "parse() (in module bio.align)": [[30, "Bio.Align.parse", false]], "parse() (in module bio.alignio)": [[56, "Bio.AlignIO.parse", false]], "parse() (in module bio.blast)": [[68, "Bio.Blast.parse", false]], "parse() (in module bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.parse", false]], "parse() (in module bio.compass)": [[74, "Bio.Compass.parse", false]], "parse() (in module bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.parse", false]], "parse() (in module bio.entrez)": [[83, "Bio.Entrez.parse", false]], "parse() (in module bio.expasy.cellosaurus)": [[90, "Bio.ExPASy.cellosaurus.parse", false]], "parse() (in module bio.expasy.enzyme)": [[86, "Bio.ExPASy.Enzyme.parse", false]], "parse() (in module bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.parse", false]], "parse() (in module bio.expasy.prosite)": [[88, "Bio.ExPASy.Prosite.parse", false]], "parse() (in module bio.genbank)": [[92, "Bio.GenBank.parse", false]], "parse() (in module bio.geo)": [[96, "Bio.Geo.parse", false]], "parse() (in module bio.kegg.compound)": [[112, "Bio.KEGG.Compound.parse", false]], "parse() (in module bio.kegg.enzyme)": [[113, "Bio.KEGG.Enzyme.parse", false]], "parse() (in module bio.kegg.gene)": [[114, "Bio.KEGG.Gene.parse", false]], "parse() (in module bio.kegg.kgml.kgml_parser)": [[116, "Bio.KEGG.KGML.KGML_parser.parse", false]], "parse() (in module bio.kegg.map)": [[118, "Bio.KEGG.Map.parse", false]], "parse() (in module bio.medline)": [[123, "Bio.Medline.parse", false]], "parse() (in module bio.motifs)": [[283, "Bio.motifs.parse", false]], "parse() (in module bio.phenotype)": [[298, "Bio.phenotype.parse", false]], "parse() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.parse", false]], "parse() (in module bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.parse", false]], "parse() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.parse", false]], "parse() (in module bio.phylo.nexusio)": [[191, "Bio.Phylo.NexusIO.parse", false]], "parse() (in module bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.parse", false]], "parse() (in module bio.scop.cla)": [[210, "Bio.SCOP.Cla.parse", false]], "parse() (in module bio.scop.des)": [[211, "Bio.SCOP.Des.parse", false]], "parse() (in module bio.scop.dom)": [[212, "Bio.SCOP.Dom.parse", false]], "parse() (in module bio.scop.hie)": [[213, "Bio.SCOP.Hie.parse", false]], "parse() (in module bio.scop.raf)": [[214, "Bio.SCOP.Raf.parse", false]], "parse() (in module bio.searchio)": [[217, "Bio.SearchIO.parse", false]], "parse() (in module bio.seqio)": [[238, "Bio.SeqIO.parse", false]], "parse() (in module bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.parse", false]], "parse() (in module bio.sequencing.phd)": [[271, "Bio.Sequencing.Phd.parse", false]], "parse() (in module bio.swissprot)": [[272, "Bio.SwissProt.parse", false]], "parse() (in module bio.swissprot.keywlist)": [[273, "Bio.SwissProt.KeyWList.parse", false]], "parse() (in module bio.unigene)": [[275, "Bio.UniGene.parse", false]], "parse_alignment_block() (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarparser method)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser.parse_alignment_block", false]], "parse_alignment_block() (bio.searchio.exonerateio.exonerate_text.exoneratetextparser method)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser.parse_alignment_block", false]], "parse_alignment_block() (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarparser method)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser.parse_alignment_block", false]], "parse_btop() (bio.align.tabular.alignmentiterator method)": [[55, "Bio.Align.tabular.AlignmentIterator.parse_btop", false]], "parse_cds_features() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_cds_features", false]], "parse_children() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse_children", false]], "parse_cigar() (bio.align.tabular.alignmentiterator method)": [[55, "Bio.Align.tabular.AlignmentIterator.parse_cigar", false]], "parse_deflines (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.parse_deflines", false]], "parse_domain() (in module bio.scop)": [[209, "Bio.SCOP.parse_domain", false]], "parse_feature() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_feature", false]], "parse_features() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_features", false]], "parse_footer() (bio.genbank.scanner.emblscanner method)": [[94, "Bio.GenBank.Scanner.EmblScanner.parse_footer", false]], "parse_footer() (bio.genbank.scanner.genbankscanner method)": [[94, "Bio.GenBank.Scanner.GenBankScanner.parse_footer", false]], "parse_footer() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_footer", false]], "parse_graph() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse_graph", false]], "parse_handle_to_graph() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse_handle_to_graph", false]], "parse_header() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_header", false]], "parse_hits() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_hits", false]], "parse_hsp_alignments() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_hsp_alignments", false]], "parse_hsps() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_hsps", false]], "parse_key_value() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_key_value", false]], "parse_pdb_header() (in module bio.pdb.parse_pdb_header)": [[174, "Bio.PDB.parse_pdb_header.parse_pdb_header", false]], "parse_preamble() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_preamble", false]], "parse_printed_alignment() (bio.align.alignment class method)": [[30, "Bio.Align.Alignment.parse_printed_alignment", false]], "parse_qresult() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_qresult", false]], "parse_records() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_records", false]], "parse_seqids (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.parse_seqids", false]], "parse_xsd() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.parse_xsd", false]], "parser (class in bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.Parser", false]], "parser (class in bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.Parser", false]], "parser (class in bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.Parser", false]], "parser (class in bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.Parser", false]], "parser (class in bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.Parser", false]], "parser (class in bio.seqio.uniprotio)": [[258, "Bio.SeqIO.UniprotIO.Parser", false]], "parsererror": [[29, "Bio.Affy.CelFile.ParserError", false]], "parserfailureerror": [[92, "Bio.GenBank.ParserFailureError", false]], "parsimony (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.parsimony", false]], "parsimony_seed (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.parsimony_seed", false]], "parsimonyscorer (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyScorer", false]], "parsimonytreeconstructor (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor", false]], "partition_branch_lengths (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.partition_branch_lengths", false]], "partition_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.partition_filename", false]], "parts (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.parts", false]], "partsize (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.partsize", false]], "parttree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.parttree", false]], "pathway (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway", false]], "pattern (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.pattern", false]], "pattern (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.pattern", false]], "pca() (in module bio.cluster)": [[73, "Bio.Cluster.pca", false]], "pcb_vectors_pymol() (bio.pdb.hsexposure.hsexposureca method)": [[141, "Bio.PDB.HSExposure.HSExposureCA.pcb_vectors_pymol", false]], "pdb_date() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.pdb_date", false]], "pdb_ref (bio.pdb.pdblist.pdblist attribute)": [[149, "Bio.PDB.PDBList.PDBList.PDB_REF", false]], "pdb_residue_string() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pdb_residue_string", false]], "pdbatomiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.PdbAtomIterator", false]], "pdbconstructionexception": [[147, "Bio.PDB.PDBExceptions.PDBConstructionException", false]], "pdbconstructionwarning": [[147, "Bio.PDB.PDBExceptions.PDBConstructionWarning", false]], "pdbexception": [[147, "Bio.PDB.PDBExceptions.PDBException", false]], "pdbio (class in bio.pdb.pdbio)": [[148, "Bio.PDB.PDBIO.PDBIO", false]], "pdbioexception": [[147, "Bio.PDB.PDBExceptions.PDBIOException", false]], "pdblist (class in bio.pdb.pdblist)": [[149, "Bio.PDB.PDBList.PDBList", false]], "pdbmlparser (class in bio.pdb.pdbmlparser)": [[150, "Bio.PDB.PDBMLParser.PDBMLParser", false]], "pdbparser (class in bio.pdb.pdbparser)": [[151, "Bio.PDB.PDBParser.PDBParser", false]], "pdbseqresiterator (class in bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator", false]], "peaklist (class in bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.Peaklist", false]], "peek() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.peek", false]], "peek_nonwhitespace() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.peek_nonwhitespace", false]], "peek_word() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.peek_word", false]], "penalty (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.penalty", false]], "perc_identity (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.perc_identity", false]], "percentid (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.percentid", false]], "pfam_gc_mapping (bio.alignio.stockholmio.stockholmiterator attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gc_mapping", false]], "pfam_gc_mapping (bio.alignio.stockholmio.stockholmwriter attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gc_mapping", false]], "pfam_gr_mapping (bio.alignio.stockholmio.stockholmiterator attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping", false]], "pfam_gr_mapping (bio.alignio.stockholmio.stockholmwriter attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping", false]], "pfam_gs_mapping (bio.alignio.stockholmio.stockholmiterator attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping", false]], "pfam_gs_mapping (bio.alignio.stockholmio.stockholmwriter attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping", false]], "pgdb_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Pgdb_dbutils", false]], "phditerator() (in module bio.seqio.phdio)": [[249, "Bio.SeqIO.PhdIO.PhdIterator", false]], "phdwriter (class in bio.seqio.phdio)": [[249, "Bio.SeqIO.PhdIO.PhdWriter", false]], "phi_pattern (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.phi_pattern", false]], "phred_quality_from_solexa() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.phred_quality_from_solexa", false]], "phyi (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.phyi", false]], "phyiout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.phyiout", false]], "phylipiterator (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.PhylipIterator", false]], "phylipout (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.phylipout", false]], "phylipwriter (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.PhylipWriter", false]], "phyloelement (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.PhyloElement", false]], "phylogeny (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Phylogeny", false]], "phylogeny() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.phylogeny", false]], "phyloxml (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Phyloxml", false]], "phyloxml() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.phyloxml", false]], "phyloxmlerror": [[198, "Bio.Phylo.PhyloXMLIO.PhyloXMLError", false]], "phyloxmlwarning": [[197, "Bio.Phylo.PhyloXML.PhyloXMLWarning", false]], "phymlcommandline (class in bio.phylo.applications)": [[182, "Bio.Phylo.Applications.PhymlCommandline", false]], "phys (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.phys", false]], "physout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.physout", false]], "pi() (bio.sequtils.isoelectricpoint.isoelectricpoint method)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi", false]], "pic_accuracy (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.pic_accuracy", false]], "pic_flags (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.pic_flags", false]], "picflagsdefault (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.picFlagsDefault", false]], "picflagsdict (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.picFlagsDict", false]], "pick_angle() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pick_angle", false]], "pick_length() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pick_length", false]], "pim (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pim", false]], "piriterator (class in bio.seqio.pirio)": [[250, "Bio.SeqIO.PirIO.PirIterator", false]], "pirwriter (class in bio.seqio.pirio)": [[250, "Bio.SeqIO.PirIO.PirWriter", false]], "platerecord (class in bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.PlateRecord", false]], "pmismatch (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.pmismatch", false]], "pmismatch (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.pmismatch", false]], "point (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Point", false]], "point() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.point", false]], "point() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.point", false]], "polygon (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Polygon", false]], "polygon() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.polygon", false]], "polygon() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.polygon", false]], "polypeptide (class in bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.Polypeptide", false]], "pop() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.pop", false]], "pos_specific_score_matrix() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.pos_specific_score_matrix", false]], "position (class in bio.seqfeature)": [[237, "Bio.SeqFeature.Position", false]], "position_padding (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.POSITION_PADDING", false]], "positionspecificscoringmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix", false]], "positionweightmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.PositionWeightMatrix", false]], "ppbuilder (class in bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.PPBuilder", false]], "prange (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.prange", false]], "prankcommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.PrankCommandline", false]], "pre (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.pre", false]], "predictnoe() (in module bio.nmr.noetools)": [[125, "Bio.NMR.NOEtools.predictNOE", false]], "prefix (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.prefix", false]], "prefixes (bio.phylo.cdaoio.writer attribute)": [[185, "Bio.Phylo.CDAOIO.Writer.prefixes", false]], "prefwidth (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.PrefWidth", false]], "pretty_print_prediction() (in module bio.hmm.utilities)": [[110, "Bio.HMM.Utilities.pretty_print_prediction", false]], "pretty_str() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pretty_str", false]], "primer3commandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.Primer3Commandline", false]], "primers (class in bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.Primers", false]], "primersearchcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline", false]], "print_as() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.print_as", false]], "print_info_content() (in module bio.align.aligninfo)": [[31, "Bio.Align.AlignInfo.print_info_content", false]], "print_matrix() (in module bio.pairwise2)": [[297, "Bio.pairwise2.print_matrix", false]], "print_options() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.print_options", false]], "print_site_lnl (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.print_site_lnl", false]], "print_that() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.print_that", false]], "print_trace (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.print_trace", false]], "printformat (class in bio.restriction.printformat)": [[207, "Bio.Restriction.PrintFormat.PrintFormat", false]], "printnodes (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.printnodes", false]], "probconscommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.ProbconsCommandline", false]], "process_asa_data() (in module bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.process_asa_data", false]], "process_clade() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.process_clade", false]], "process_clade() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.process_clade", false]], "process_rsa_data() (in module bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.process_rsa_data", false]], "products (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.products", false]], "profile (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.profile", false]], "profile (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.profile", false]], "profile1 (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.profile1", false]], "profile1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.profile1", false]], "profile2 (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.profile2", false]], "profile2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.profile2", false]], "progress (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.progress", false]], "prop_invar (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.prop_invar", false]], "propagate_changes() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.propagate_changes", false]], "property (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Property", false]], "property() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.property", false]], "property() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.property", false]], "protein_alphabet (bio.data.codontable.ncbicodontable attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTable.protein_alphabet", false]], "protein_model (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.protein_model", false]], "protein_models (bio.phylo.treeconstruction.distancecalculator attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.protein_models", false]], "protein_scale() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.protein_scale", false]], "proteinanalysis (class in bio.sequtils.protparam)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis", false]], "proteindomain (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain", false]], "protsimline (class in bio.unigene)": [[275, "Bio.UniGene.ProtsimLine", false]], "prune() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.prune", false]], "prune() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.prune", false]], "psea (class in bio.pdb.psea)": [[153, "Bio.PDB.PSEA.PSEA", false]], "psea() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.psea", false]], "psea2hec() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.psea2HEC", false]], "pseudo (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.pseudo", false]], "pseudocount (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.pseudocount", false]], "pseudocount (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.pseudocount", false]], "pseudocounts (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.pseudocounts", false]], "psiblast (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.PSIBlast", false]], "psizeopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.psizeopt", false]], "pssm (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.pssm", false]], "pssm (class in bio.align.aligninfo)": [[31, "Bio.Align.AlignInfo.PSSM", false]], "pst (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.pst", false]], "psycopg2_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Psycopg2_dbutils", false]], "ptmmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ptmmax", false]], "ptmmin (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ptmmin", false]], "ptmopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ptmopt", false]], "push_back() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.push_back", false]], "pwdist (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.pwdist", false]], "pwdnamatrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwdnamatrix", false]], "pwgapext (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwgapext", false]], "pwgapopen (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwgapopen", false]], "pwgenomic (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.pwgenomic", false]], "pwgenomicdist (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.pwgenomicdist", false]], "pwm (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.pwm", false]], "pwmatrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwmatrix", false]], "q (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.q", false]], "q (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.q", false]], "q (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.Q", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.q", false]], "q (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.Q", false], [270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.q", false]], "q (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.Q", false]], "q (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.q", false]], "qa (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.qa", false]], "qblast() (in module bio.blast)": [[68, "Bio.Blast.qblast", false]], "qblast() (in module bio.blast.ncbiwww)": [[70, "Bio.Blast.NCBIWWW.qblast", false]], "qcov_hsp_perc (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.qcov_hsp_perc", false]], "qcp() (in module bio.pdb.qcprot)": [[175, "Bio.PDB.qcprot.qcp", false]], "qcpsuperimposer (class in bio.pdb.qcprot)": [[175, "Bio.PDB.qcprot.QCPSuperimposer", false]], "qend_mark (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.qend_mark", false]], "qresult_end (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer attribute)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.qresult_end", false]], "qresult_end (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer attribute)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.qresult_end", false]], "qresult_start (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer attribute)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.qresult_start", false]], "qresult_start (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer attribute)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.qresult_start", false]], "qstart_mark (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.qstart_mark", false]], "qual_digits (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.qual_digits", false]], "qualifier (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Qualifier", false]], "qualifier_indent (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.QUALIFIER_INDENT", false]], "qualifier_indent (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.QUALIFIER_INDENT", false]], "qualifier_indent (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.QUALIFIER_INDENT", false]], "qualifier_indent_str (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.QUALIFIER_INDENT_STR", false]], "qualifier_indent_str (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.QUALIFIER_INDENT_STR", false]], "qualifier_indent_tmp (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.QUALIFIER_INDENT_TMP", false]], "qualifier_indent_tmp (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.QUALIFIER_INDENT_TMP", false]], "quality (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.quality", false]], "qualphrediterator (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator", false]], "qualphredwriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.QualPhredWriter", false]], "quartiles() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.quartiles", false]], "query (bio.align.alignment property)": [[30, "Bio.Align.Alignment.query", false]], "query (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.query", false]], "query (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.query", false]], "query (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.query", false]], "query (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.query", false]], "query (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.query", false]], "query (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.query", false]], "query (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.query", false]], "query (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.query", false]], "query (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.query", false]], "query_coverage() (bio.compass.record method)": [[74, "Bio.Compass.Record.query_coverage", false]], "query_gap (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.QUERY_GAP", false]], "query_gencode (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.query_gencode", false]], "query_gencode (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.query_gencode", false]], "query_gencode (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.query_gencode", false]], "query_loc (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.query_loc", false]], "quicktree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.quicktree", false]], "quiet (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.quiet", false]], "quiet (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.quiet", false]], "quiet (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.quiet", false]], "quiet (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.quiet", false]], "quiet (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.quiet", false]], "quiet (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.quiet", false]], "quiet (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.quiet", false]], "quote (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.quote", false]], "quotestrip() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.quotestrip", false]], "quri() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.qUri", false]], "quri() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.qUri", false]], "r (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.R", false]], "r (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.r", false]], "r (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.R", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.r", false]], "r (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.r", false]], "r (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.r", false]], "r (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.r", false]], "r (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.R", false], [270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.r", false]], "r (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.r", false]], "r (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.R", false], [270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.r", false]], "r_method (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.r_method", false]], "r_seed (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.r_seed", false]], "rak() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.rak", false]], "rand_start (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.rand_start", false]], "random_starting_tree (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.random_starting_tree", false]], "randomize() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.randomize", false]], "randomized() (bio.phylo.basetree.tree class method)": [[183, "Bio.Phylo.BaseTree.Tree.randomized", false]], "range (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.range", false]], "range() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.range", false]], "range() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.range", false]], "range() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.range", false]], "range() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.range", false]], "range() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.range", false]], "rank() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.rank", false]], "rapid_bootstrap_seed (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.rapid_bootstrap_seed", false]], "rate (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.rate", false]], "rate (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.rate", false]], "raw() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.raw", false]], "rawdist (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.rawdist", false]], "raxmlcommandline (class in bio.phylo.applications)": [[182, "Bio.Phylo.Applications.RaxmlCommandline", false]], "rd (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.rd", false]], "re_code (bio.phylo.phyloxml.taxonomy attribute)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.re_code", false]], "re_doi (bio.phylo.phyloxml.reference attribute)": [[197, "Bio.Phylo.PhyloXML.Reference.re_doi", false]], "re_ref (bio.phylo.phyloxml.annotation attribute)": [[197, "Bio.Phylo.PhyloXML.Annotation.re_ref", false]], "re_ref (bio.phylo.phyloxml.property attribute)": [[197, "Bio.Phylo.PhyloXML.Property.re_ref", false]], "re_symbol (bio.phylo.phyloxml.sequence attribute)": [[197, "Bio.Phylo.PhyloXML.Sequence.re_symbol", false]], "re_value (bio.phylo.phyloxml.molseq attribute)": [[197, "Bio.Phylo.PhyloXML.MolSeq.re_value", false]], "reactant_ids (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.reactant_ids", false]], "reaction (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.reaction", false]], "reaction (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction", false]], "reaction (class in bio.pathway)": [[177, "Bio.Pathway.Reaction", false]], "reaction_entries (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.reaction_entries", false]], "reactions (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.reactions", false]], "reactions() (bio.pathway.system method)": [[177, "Bio.Pathway.System.reactions", false]], "read() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.read", false]], "read() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.read", false]], "read() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.read", false]], "read() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.read", false]], "read() (in module bio.affy.celfile)": [[29, "Bio.Affy.CelFile.read", false]], "read() (in module bio.align)": [[30, "Bio.Align.read", false]], "read() (in module bio.align.substitution_matrices)": [[54, "Bio.Align.substitution_matrices.read", false]], "read() (in module bio.alignio)": [[56, "Bio.AlignIO.read", false]], "read() (in module bio.blast)": [[68, "Bio.Blast.read", false]], "read() (in module bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.read", false]], "read() (in module bio.cluster)": [[73, "Bio.Cluster.read", false]], "read() (in module bio.compass)": [[74, "Bio.Compass.read", false]], "read() (in module bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.read", false]], "read() (in module bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.read", false]], "read() (in module bio.entrez)": [[83, "Bio.Entrez.read", false]], "read() (in module bio.expasy.cellosaurus)": [[90, "Bio.ExPASy.cellosaurus.read", false]], "read() (in module bio.expasy.enzyme)": [[86, "Bio.ExPASy.Enzyme.read", false]], "read() (in module bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.read", false]], "read() (in module bio.expasy.prosite)": [[88, "Bio.ExPASy.Prosite.read", false]], "read() (in module bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.read", false]], "read() (in module bio.genbank)": [[92, "Bio.GenBank.read", false]], "read() (in module bio.kegg.enzyme)": [[113, "Bio.KEGG.Enzyme.read", false]], "read() (in module bio.kegg.kgml.kgml_parser)": [[116, "Bio.KEGG.KGML.KGML_parser.read", false]], "read() (in module bio.medline)": [[123, "Bio.Medline.read", false]], "read() (in module bio.motifs)": [[283, "Bio.motifs.read", false]], "read() (in module bio.motifs.alignace)": [[284, "Bio.motifs.alignace.read", false]], "read() (in module bio.motifs.clusterbuster)": [[286, "Bio.motifs.clusterbuster.read", false]], "read() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.read", false]], "read() (in module bio.motifs.mast)": [[289, "Bio.motifs.mast.read", false]], "read() (in module bio.motifs.meme)": [[291, "Bio.motifs.meme.read", false]], "read() (in module bio.motifs.minimal)": [[292, "Bio.motifs.minimal.read", false]], "read() (in module bio.motifs.pfm)": [[293, "Bio.motifs.pfm.read", false]], "read() (in module bio.motifs.transfac)": [[295, "Bio.motifs.transfac.read", false]], "read() (in module bio.motifs.xms)": [[296, "Bio.motifs.xms.read", false]], "read() (in module bio.phenotype)": [[298, "Bio.phenotype.read", false]], "read() (in module bio.phylo.paml.baseml)": [[193, "Bio.Phylo.PAML.baseml.read", false]], "read() (in module bio.phylo.paml.codeml)": [[195, "Bio.Phylo.PAML.codeml.read", false]], "read() (in module bio.phylo.paml.yn00)": [[196, "Bio.Phylo.PAML.yn00.read", false]], "read() (in module bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.read", false]], "read() (in module bio.popgen.genepop)": [[201, "Bio.PopGen.GenePop.read", false]], "read() (in module bio.popgen.genepop.fileparser)": [[204, "Bio.PopGen.GenePop.FileParser.read", false]], "read() (in module bio.popgen.genepop.largefileparser)": [[205, "Bio.PopGen.GenePop.LargeFileParser.read", false]], "read() (in module bio.searchio)": [[217, "Bio.SearchIO.read", false]], "read() (in module bio.seqio)": [[238, "Bio.SeqIO.read", false]], "read() (in module bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.read", false]], "read() (in module bio.sequencing.phd)": [[271, "Bio.Sequencing.Phd.read", false]], "read() (in module bio.swissprot)": [[272, "Bio.SwissProt.read", false]], "read() (in module bio.unigene)": [[275, "Bio.UniGene.read", false]], "read_cal (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.read_cal", false]], "read_colorscheme() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.read_colorscheme", false]], "read_ctl_file() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.read_ctl_file", false]], "read_ctl_file() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.read_ctl_file", false]], "read_ctl_file() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.read_ctl_file", false]], "read_file (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.read_file", false]], "read_file (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.read_file", false]], "read_file (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.read_file", false]], "read_file1 (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.read_file1", false]], "read_file1 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.read_file1", false]], "read_file2 (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.read_file2", false]], "read_file2 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.read_file2", false]], "read_next() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.read_next", false]], "read_pic() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.read_PIC", false]], "read_pic_seq() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.read_PIC_seq", false]], "readfile (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.readfile", false]], "readline() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.readline", false]], "readrochexmlmanifest() (in module bio.seqio.sffio)": [[253, "Bio.SeqIO.SffIO.ReadRocheXmlManifest", false]], "reads (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.Reads", false]], "realbranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.realbranches", false]], "rearrange (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.rearrange", false]], "rearrangements (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.rearrangements", false]], "record (class in bio.affy.celfile)": [[29, "Bio.Affy.CelFile.Record", false]], "record (class in bio.blast)": [[68, "Bio.Blast.Record", false]], "record (class in bio.cluster)": [[73, "Bio.Cluster.Record", false]], "record (class in bio.compass)": [[74, "Bio.Compass.Record", false]], "record (class in bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.Record", false]], "record (class in bio.expasy.cellosaurus)": [[90, "Bio.ExPASy.cellosaurus.Record", false]], "record (class in bio.expasy.enzyme)": [[86, "Bio.ExPASy.Enzyme.Record", false]], "record (class in bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.Record", false]], "record (class in bio.expasy.prosite)": [[88, "Bio.ExPASy.Prosite.Record", false]], "record (class in bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.Record", false]], "record (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Record", false]], "record (class in bio.geo.record)": [[97, "Bio.Geo.Record.Record", false]], "record (class in bio.kegg.compound)": [[112, "Bio.KEGG.Compound.Record", false]], "record (class in bio.kegg.enzyme)": [[113, "Bio.KEGG.Enzyme.Record", false]], "record (class in bio.kegg.gene)": [[114, "Bio.KEGG.Gene.Record", false]], "record (class in bio.medline)": [[123, "Bio.Medline.Record", false]], "record (class in bio.motifs.alignace)": [[284, "Bio.motifs.alignace.Record", false]], "record (class in bio.motifs.clusterbuster)": [[286, "Bio.motifs.clusterbuster.Record", false]], "record (class in bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.Record", false]], "record (class in bio.motifs.mast)": [[289, "Bio.motifs.mast.Record", false]], "record (class in bio.motifs.meme)": [[291, "Bio.motifs.meme.Record", false]], "record (class in bio.motifs.minimal)": [[292, "Bio.motifs.minimal.Record", false]], "record (class in bio.motifs.pfm)": [[293, "Bio.motifs.pfm.Record", false]], "record (class in bio.motifs.transfac)": [[295, "Bio.motifs.transfac.Record", false]], "record (class in bio.motifs.xms)": [[296, "Bio.motifs.xms.Record", false]], "record (class in bio.popgen.genepop)": [[201, "Bio.PopGen.GenePop.Record", false]], "record (class in bio.popgen.genepop.largefileparser)": [[205, "Bio.PopGen.GenePop.LargeFileParser.Record", false]], "record (class in bio.scop.cla)": [[210, "Bio.SCOP.Cla.Record", false]], "record (class in bio.scop.des)": [[211, "Bio.SCOP.Des.Record", false]], "record (class in bio.scop.dom)": [[212, "Bio.SCOP.Dom.Record", false]], "record (class in bio.scop.hie)": [[213, "Bio.SCOP.Hie.Record", false]], "record (class in bio.sequencing.phd)": [[271, "Bio.Sequencing.Phd.Record", false]], "record (class in bio.swissprot)": [[272, "Bio.SwissProt.Record", false]], "record (class in bio.swissprot.keywlist)": [[273, "Bio.SwissProt.KeyWList.Record", false]], "record (class in bio.unigene)": [[275, "Bio.UniGene.Record", false]], "record_has() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.record_has", false]], "record_start (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.RECORD_START", false]], "record_start (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.RECORD_START", false]], "record_start (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.RECORD_START", false]], "recorded (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.recorded", false]], "recordparser (class in bio.genbank)": [[92, "Bio.GenBank.RecordParser", false]], "records (class in bio.blast)": [[68, "Bio.Blast.Records", false]], "red() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.red", false]], "ref (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.ref", false]], "ref (bio.seqfeature.seqfeature property)": [[237, "Bio.SeqFeature.SeqFeature.ref", false]], "ref (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.ref", false]], "ref (bio.sequencing.applications.samtoolsfaidxcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsFaidxCommandline.ref", false]], "ref_db (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.ref_db", false]], "ref_db (bio.seqfeature.seqfeature property)": [[237, "Bio.SeqFeature.SeqFeature.ref_db", false]], "reference (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.reference", false]], "reference (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.reference", false]], "reference (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.reference", false]], "reference (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.reference", false]], "reference (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.reference", false]], "reference (class in bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.Reference", false]], "reference (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Reference", false]], "reference (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Reference", false]], "reference (class in bio.seqfeature)": [[237, "Bio.SeqFeature.Reference", false]], "reference (class in bio.swissprot)": [[272, "Bio.SwissProt.Reference", false]], "reference() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.reference", false]], "reference() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.reference", false]], "reference_keys (bio.motifs.transfac.motif attribute)": [[295, "Bio.motifs.transfac.Motif.reference_keys", false]], "refine (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.refine", false]], "refinew (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.refinew", false]], "refinewindow (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.refinewindow", false]], "refmat() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.refmat", false]], "refresh (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.refresh", false]], "region (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.region", false]], "register_ncbi_table() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.register_ncbi_table", false]], "regular (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.regular", false]], "relation (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation", false]], "relations (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.relations", false]], "relative_entropy (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.relative_entropy", false]], "relaxedphylipiterator (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.RelaxedPhylipIterator", false]], "relaxedphylipwriter (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.RelaxedPhylipWriter", false]], "remote (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.remote", false]], "remote (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.remote", false]], "remote (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.remote", false]], "remote (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.remote", false]], "remote (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.remote", false]], "remote (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.remote", false]], "remote (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.remote", false]], "remote (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.remote", false]], "remote (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.remote", false]], "remove() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.remove", false]], "remove() (biosql.loader.databaseremover method)": [[305, "BioSQL.Loader.DatabaseRemover.remove", false]], "remove_component() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.remove_component", false]], "remove_edge() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.remove_edge", false]], "remove_edge() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.remove_edge", false]], "remove_entry() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.remove_entry", false]], "remove_graphics() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.remove_graphics", false]], "remove_loci_by_name() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_loci_by_name", false]], "remove_loci_by_position() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_loci_by_position", false]], "remove_locus_by_name() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_locus_by_name", false]], "remove_locus_by_name() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.remove_locus_by_name", false]], "remove_locus_by_position() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_locus_by_position", false]], "remove_locus_by_position() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.remove_locus_by_position", false]], "remove_node() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.remove_node", false]], "remove_node() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.remove_node", false]], "remove_population() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_population", false]], "remove_population() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.remove_population", false]], "remove_reaction() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.remove_reaction", false]], "remove_reaction() (bio.pathway.system method)": [[177, "Bio.Pathway.System.remove_reaction", false]], "remove_relation() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.remove_relation", false]], "remove_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.remove_succ", false]], "removeprefix() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.removeprefix", false]], "removesuffix() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.removesuffix", false]], "renumber_tracks() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.renumber_tracks", false]], "reorder (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.reorder", false]], "repeats (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.repeats", false]], "replace() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.replace", false]], "replace_entry() (in module bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.replace_entry", false]], "replacement_dictionary() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.replacement_dictionary", false]], "report (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.report", false]], "report_ic() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.report_IC", false]], "reps (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.reps", false]], "res (class in bio.scop.raf)": [[214, "Bio.SCOP.Raf.Res", false]], "reset() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.reset", false]], "residue (class in bio.pdb.residue)": [[155, "Bio.PDB.Residue.Residue", false]], "residue_depth() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.residue_depth", false]], "residue_dict() (bio.nmr.xpktools.peaklist method)": [[126, "Bio.NMR.xpktools.Peaklist.residue_dict", false]], "residuedepth (class in bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.ResidueDepth", false]], "residuenumber (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.residuenumber", false]], "residues (class in bio.scop.residues)": [[215, "Bio.SCOP.Residues.Residues", false]], "rest() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.rest", false]], "retree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.retree", false]], "retrieve_assembly_file() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.retrieve_assembly_file", false]], "retrieve_pdb_file() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.retrieve_pdb_file", false]], "reverse (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.reverse", false]], "reverse() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.reverse", false]], "reverse() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.reverse", false]], "reverse_complement() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.reverse_complement", false]], "reverse_complement() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.reverse_complement", false]], "reverse_complement() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.reverse_complement", false]], "reverse_complement() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.reverse_complement", false]], "reverse_complement() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.reverse_complement", false]], "reverse_complement() (in module bio.seq)": [[236, "Bio.Seq.reverse_complement", false]], "reverse_complement_rna() (in module bio.seq)": [[236, "Bio.Seq.reverse_complement_rna", false]], "reverseinput (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.reverseinput", false]], "reward (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.reward", false]], "rewind() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.rewind", false]], "rewind() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.rewind", false]], "rewind() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.rewind", false]], "rewind() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.rewind", false]], "rewriteformat (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.rewriteformat", false]], "rfind() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rfind", false]], "rformat (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.rformat", false]], "rformat (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.rformat", false]], "rformat (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.rformat", false]], "rformat (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.rformat", false]], "rho (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.rho", false]], "richards() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.richards", false]], "rid (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.rid", false]], "right_multiply() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.right_multiply", false]], "rindex() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rindex", false]], "rollback() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.rollback", false]], "rollback() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.rollback", false]], "root (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.root", false]], "root (bio.phylo.basetree.clade property)": [[183, "Bio.Phylo.BaseTree.Clade.root", false]], "root1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.root1", false]], "root2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.root2", false]], "root_at_midpoint() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.root_at_midpoint", false]], "root_with_outgroup() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.root_with_outgroup", false]], "root_with_outgroup() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.root_with_outgroup", false]], "rotaxis() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.rotaxis", false]], "rotaxis2m() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.rotaxis2m", false]], "rotmat() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.rotmat", false]], "round (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Round", false]], "rpsdb (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.rpsdb", false]], "rsplit() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rsplit", false]], "rstrip() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rstrip", false]], "rt (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.rt", false]], "run() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.run", false]], "run() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.run", false]], "run() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.run", false]], "run() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.run", false]], "run() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.run", false]], "run_id (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.run_id", false]], "run_naccess() (in module bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.run_naccess", false]], "run_psea() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.run_psea", false]], "s (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.s", false]], "s (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.S", false]], "s (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.S", false]], "s (bio.sequencing.applications.samtoolsrmdupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.S", false], [270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.s", false]], "s (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.S", false]], "safename() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.safename", false]], "sai_file (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.sai_file", false]], "sai_file1 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.sai_file1", false]], "sai_file2 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.sai_file2", false]], "salt_correction() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.salt_correction", false]], "saltconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.saltconc", false]], "sam_file (bio.sequencing.applications.samtoolsreheadercommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline.sam_file", false]], "samtoolscalmdcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline", false]], "samtoolscatcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline", false]], "samtoolsfaidxcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsFaidxCommandline", false]], "samtoolsfixmatecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline", false]], "samtoolsidxstatscommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline", false]], "samtoolsindexcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsIndexCommandline", false]], "samtoolsmergecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline", false]], "samtoolsmpileupcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline", false]], "samtoolsphasecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline", false]], "samtoolsreheadercommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline", false]], "samtoolsrmdupcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline", false]], "samtoolssortcommandline (in module bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsSortCommandline", false]], "samtoolstargetcutcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline", false]], "samtoolsversion0xsortcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline", false]], "samtoolsversion1xsortcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline", false]], "samtoolsviewcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline", false]], "sanitize_name() (in module bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.sanitize_name", false]], "save() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.save", false]], "save() (bio.pdb.mmcifio.mmcifio method)": [[170, "Bio.PDB.mmcifio.MMCIFIO.save", false]], "save() (bio.pdb.mmtf.mmtfio.mmtfio method)": [[173, "Bio.PDB.mmtf.mmtfio.MMTFIO.save", false]], "save() (bio.pdb.pdbio.pdbio method)": [[148, "Bio.PDB.PDBIO.PDBIO.save", false]], "save() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.save", false]], "save_dtd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.save_dtd_file", false]], "save_each_pssm (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.save_each_pssm", false]], "save_each_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.save_each_pssm", false]], "save_pssm_after_last_round (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.save_pssm_after_last_round", false]], "save_pssm_after_last_round (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.save_pssm_after_last_round", false]], "save_xsd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.save_xsd_file", false]], "scale_segment_value() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.scale_segment_value", false]], "scalebranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.scalebranches", false]], "scaleddpalgorithms (class in bio.hmm.dynamicprogramming)": [[107, "Bio.HMM.DynamicProgramming.ScaledDPAlgorithms", false]], "scan() (in module bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.scan", false]], "schemahandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.schemaHandler", false]], "scheme_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.scheme_color", false]], "scientific_name() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.scientific_name", false]], "scop (class in bio.scop)": [[209, "Bio.SCOP.Scop", false]], "score (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.score", false]], "score (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.score", false]], "score() (bio.align.codonaligner method)": [[30, "Bio.Align.CodonAligner.score", false]], "score() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.score", false]], "scoredistribution (class in bio.motifs.thresholds)": [[294, "Bio.motifs.thresholds.ScoreDistribution", false]], "scorefile (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.scorefile", false]], "scorer (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.Scorer", false]], "search (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.search", false]], "search() (bio.align.bigbed.alignmentiterator method)": [[36, "Bio.Align.bigbed.AlignmentIterator.search", false]], "search() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.search", false]], "search() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.search", false]], "search() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.search", false]], "search() (bio.pdb.neighborsearch.neighborsearch method)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch.search", false]], "search() (bio.phylo.treeconstruction.nnitreesearcher method)": [[199, "Bio.Phylo.TreeConstruction.NNITreeSearcher.search", false]], "search() (bio.phylo.treeconstruction.treesearcher method)": [[199, "Bio.Phylo.TreeConstruction.TreeSearcher.search", false]], "search() (in module bio.scop)": [[209, "Bio.SCOP.search", false]], "search() (in module bio.togows)": [[274, "Bio.TogoWS.search", false]], "search() (in module bio.uniprot)": [[276, "Bio.UniProt.search", false]], "search_all() (bio.pdb.neighborsearch.neighborsearch method)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch.search_all", false]], "search_count() (in module bio.togows)": [[274, "Bio.TogoWS.search_count", false]], "search_iter() (in module bio.togows)": [[274, "Bio.TogoWS.search_iter", false]], "search_taxon() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.search_taxon", false]], "searchsp (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.searchsp", false]], "second (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.second", false]], "secondary_structure_fraction() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.secondary_structure_fraction", false]], "secstrout (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.secstrout", false]], "seed (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.seed", false]], "seed (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.seed", false]], "seed (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.seed", false]], "seed (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.seed", false]], "seed (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.seed", false]], "seed (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.seed", false]], "seed (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.seed", false]], "seed (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.seed", false]], "seek() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.seek", false]], "seek_position() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.seek_position", false]], "seekable() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.seekable", false]], "seekable() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.seekable", false]], "seg (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.seg", false]], "seg (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.seg", false]], "seg (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.seg", false]], "seg (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.seg", false]], "seg (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.seg", false]], "seg (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.seg", false]], "seg (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.seg", false]], "seg (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.seg", false]], "seguid() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.seguid", false]], "select (class in bio.pdb.pdbio)": [[148, "Bio.PDB.PDBIO.Select", false]], "select() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.select", false]], "seq (bio.seqrecord.seqrecord property)": [[260, "Bio.SeqRecord.SeqRecord.seq", false]], "seq (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.seq", false]], "seq (class in bio.seq)": [[236, "Bio.Seq.Seq", false]], "seq1() (in module bio.sequtils)": [[261, "Bio.SeqUtils.seq1", false]], "seq3() (in module bio.sequtils)": [[261, "Bio.SeqUtils.seq3", false]], "seq_types (bio.align.applications.tcoffeecommandline attribute)": [[32, "Bio.Align.Applications.TCoffeeCommandline.SEQ_TYPES", false]], "seqa (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.seqA", false]], "seqall (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.seqall", false]], "seqb (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.seqB", false]], "seqfeature (class in bio.seqfeature)": [[237, "Bio.SeqFeature.SeqFeature", false]], "seqidlist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.seqidlist", false]], "seqmap (class in bio.scop.raf)": [[214, "Bio.SCOP.Raf.SeqMap", false]], "seqmapindex (class in bio.scop.raf)": [[214, "Bio.SCOP.Raf.SeqMapIndex", false]], "seqmatchallcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline", false]], "seqno_range (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.seqno_range", false]], "seqnos (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.seqnos", false]], "seqrecord (class in bio.seqrecord)": [[260, "Bio.SeqRecord.SeqRecord", false]], "seqretcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.SeqretCommandline", false]], "seqtype (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.seqtype", false]], "seqtype (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.seqtype", false]], "seqtype (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.seqtype", false]], "sequence (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.sequence", false]], "sequence (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.sequence", false]], "sequence (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.sequence", false]], "sequence (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.sequence", false]], "sequence (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.sequence", false]], "sequence (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.sequence", false]], "sequence (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.sequence", false]], "sequence (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.sequence", false]], "sequence (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.sequence", false]], "sequence (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.sequence", false]], "sequence (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.sequence", false]], "sequence (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.sequence", false]], "sequence (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.sequence", false]], "sequence (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.sequence", false]], "sequence (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Sequence", false]], "sequence() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.sequence", false]], "sequence_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.SEQUENCE_FORMAT", false]], "sequence_headers (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.SEQUENCE_HEADERS", false]], "sequence_headers (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.SEQUENCE_HEADERS", false]], "sequence_headers (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.SEQUENCE_HEADERS", false]], "sequence_indent (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.SEQUENCE_INDENT", false]], "sequence_relation() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.sequence_relation", false]], "sequence_relation() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.sequence_relation", false]], "sequencedataabstractbaseclass (class in bio.seq)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass", false]], "sequenceiterator (class in bio.seqio.interfaces)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator", false]], "sequenceline (class in bio.unigene)": [[275, "Bio.UniGene.SequenceLine", false]], "sequencerelation (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.SequenceRelation", false]], "sequences (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.sequences", false]], "sequences (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.sequences", false]], "sequencewriter (class in bio.seqio.interfaces)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter", false]], "sequential (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.sequential", false]], "sequentialalignmentwriter (class in bio.alignio.interfaces)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter", false]], "sequentialphylipiterator (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipIterator", false]], "sequentialphylipwriter (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipWriter", false]], "seqxmliterator (class in bio.seqio.seqxmlio)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator", false]], "seqxmlwriter (class in bio.seqio.seqxmlio)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter", false]], "set() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.set", false]], "set() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.set", false]], "set() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.set", false]], "set_accuracy_95() (in module bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.set_accuracy_95", false]], "set_all_features() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.set_all_features", false]], "set_all_tracks() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.set_all_tracks", false]], "set_altloc() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_altloc", false]], "set_angle() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_angle", false]], "set_anisou() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_anisou", false]], "set_anisou() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_anisou", false]], "set_atom_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_atom_info", false]], "set_atoms() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.set_atoms", false]], "set_atoms() (bio.pdb.superimposer.superimposer method)": [[163, "Bio.PDB.Superimposer.Superimposer.set_atoms", false]], "set_bfactor() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_bfactor", false]], "set_bio_assembly_trans() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_bio_assembly_trans", false]], "set_chain_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_chain_info", false]], "set_charge() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_charge", false]], "set_color() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.set_color", false]], "set_colour() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.set_colour", false]], "set_coord() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_coord", false]], "set_data() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.set_data", false]], "set_data() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_data", false]], "set_dict() (bio.pdb.mmcifio.mmcifio method)": [[170, "Bio.PDB.mmcifio.MMCIFIO.set_dict", false]], "set_emission_pseudocount() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_emission_pseudocount", false]], "set_emission_score() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_emission_score", false]], "set_entity_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_entity_info", false]], "set_equal_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_equal_probabilities", false]], "set_feature() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.set_feature", false]], "set_flexible() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_flexible", false]], "set_group_bond() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_group_bond", false]], "set_group_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_group_info", false]], "set_handle() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.set_handle", false]], "set_hbond() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_hbond", false]], "set_header() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_header", false]], "set_header_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_header_info", false]], "set_hit_accession() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_accession", false]], "set_hit_def() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_def", false]], "set_hit_id() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_id", false]], "set_hit_len() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_len", false]], "set_homog_trans_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_homog_trans_mtx", false]], "set_id() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_id", false]], "set_initial_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_initial_probabilities", false]], "set_inter_group_bond() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_inter_group_bond", false]], "set_length() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.set_length", false]], "set_length() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_length", false]], "set_line_counter() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_line_counter", false]], "set_model_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_model_info", false]], "set_occupancy() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_occupancy", false]], "set_parameter() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.set_parameter", false]], "set_parent() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_parent", false]], "set_parent() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.set_parent", false]], "set_parent() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.set_parent", false]], "set_prev() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_prev", false]], "set_radius() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_radius", false]], "set_random_emission_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_emission_probabilities", false]], "set_random_initial_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_initial_probabilities", false]], "set_random_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_probabilities", false]], "set_random_transition_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_transition_probabilities", false]], "set_reference() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.set_reference", false]], "set_scale() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.set_scale", false]], "set_serial_number() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_serial_number", false]], "set_sigatm() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_sigatm", false]], "set_sigatm() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_sigatm", false]], "set_siguij() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_siguij", false]], "set_siguij() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_siguij", false]], "set_structure() (bio.pdb.pdbio.structureio method)": [[148, "Bio.PDB.PDBIO.StructureIO.set_structure", false]], "set_subtree() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.set_subtree", false]], "set_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_succ", false]], "set_symmetry() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_symmetry", false]], "set_transition_pseudocount() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_transition_pseudocount", false]], "set_transition_score() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_transition_score", false]], "set_x_homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_X_homog_rot_mtx", false]], "set_xtal_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_xtal_info", false]], "set_y_homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_Y_homog_rot_mtx", false]], "set_z_homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_Z_homog_rot_mtx", false]], "sffiterator (class in bio.seqio.sffio)": [[253, "Bio.SeqIO.SffIO.SffIterator", false]], "sffwriter (class in bio.seqio.sffio)": [[253, "Bio.SeqIO.SffIO.SffWriter", false]], "sformat (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.sformat", false]], "shape (bio.align.alignment property)": [[30, "Bio.Align.Alignment.shape", false]], "shortnames (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.shortnames", false]], "show_domain_hits (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.show_domain_hits", false]], "show_gis (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.show_gis", false]], "showtree (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.showtree", false]], "showxml (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.showxml", false]], "shrakerupley (class in bio.pdb.sasa)": [[157, "Bio.PDB.SASA.ShrakeRupley", false]], "shuffle (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.shuffle", false]], "similarity (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.similarity", false]], "similarity (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.similarity", false]], "similarity (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.similarity", false]], "simplefastaparser() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.SimpleFastaParser", false]], "simplelocation (class in bio.seqfeature)": [[237, "Bio.SeqFeature.SimpleLocation", false]], "sink() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.sink", false]], "sink_interactions() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.sink_interactions", false]], "six_frame_translations() (in module bio.sequtils)": [[261, "Bio.SeqUtils.six_frame_translations", false]], "sixmerpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.sixmerpair", false]], "skip_header() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.skip_header", false]], "skip_population() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.skip_population", false]], "skip_whitespace() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.skip_whitespace", false]], "skipcharacterdatahandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.skipCharacterDataHandler", false]], "skipins (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.skipins", false]], "slow (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.slow", false]], "slownni (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.slownni", false]], "smin (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.smin", false]], "smoothscoreceil (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.smoothscoreceil", false]], "smoothwindow (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.smoothwindow", false]], "smprint() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.smprint", false]], "snapgeneiterator (class in bio.seqio.snapgeneio)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator", false]], "snucleotide (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.snucleotide", false]], "soft_masking (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.soft_masking", false]], "solexa_quality_from_phred() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.solexa_quality_from_phred", false]], "somcluster() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.somcluster", false]], "somcluster() (in module bio.cluster)": [[73, "Bio.Cluster.somcluster", false]], "sort() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.sort", false]], "sort() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.sort", false]], "sort() (bio.cluster.tree method)": [[73, "Bio.Cluster.Tree.sort", false]], "sort() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.sort", false]], "sort() (bio.sequencing.ace.acefilerecord method)": [[269, "Bio.Sequencing.Ace.ACEFileRecord.sort", false]], "source() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.source", false]], "source_interactions() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.source_interactions", false]], "sp (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.sp", false]], "space (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.space", false]], "spacersegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.SpacerSegment", false]], "speciations() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.speciations", false]], "species() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.species", false]], "species() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.species", false]], "species() (bio.pathway.system method)": [[177, "Bio.Pathway.System.species", false]], "splice (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.splice", false]], "splicepenalty (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.splicepenalty", false]], "split() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.split", false]], "split() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.split", false]], "split() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.split", false]], "split_akl() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.split_akl", false]], "split_in_loci() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.split_in_loci", false]], "split_in_pops() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.split_in_pops", false]], "split_jaspar_id() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.split_jaspar_id", false]], "split_virtual_offset() (in module bio.bgzf)": [[278, "Bio.bgzf.split_virtual_offset", false]], "spn (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.spn", false]], "spr (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.spr", false]], "sprlength (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.sprlength", false]], "sprotein (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.sprotein", false]], "sprotein (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.sprotein", false]], "sprotein (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.sprotein", false]], "sprotein (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.sprotein", false]], "sprotein (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.sprotein", false]], "spscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.spscore", false]], "sqlite_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Sqlite_dbutils", false]], "ss_to_index() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.ss_to_index", false]], "stable (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.stable", false]], "standarddata (class in bio.nexus.standarddata)": [[131, "Bio.Nexus.StandardData.StandardData", false]], "stars (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.stars", false]], "start (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.start", false]], "start (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.start", false]], "start (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.start", false]], "start_codons (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.start_codons", false]], "start_read() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.start_read", false]], "starta (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.startA", false]], "startb (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.startB", false]], "startdbrefelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startDBRefElement", false]], "startdescriptionelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startDescriptionElement", false]], "startdocument() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startDocument", false]], "startelement() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.startElement", false]], "startelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startElementHandler", false]], "startentryelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startEntryElement", false]], "startentryfieldelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startEntryFieldElement", false]], "startentryfieldelementversion01() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startEntryFieldElementVersion01", false]], "starting_tree (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.starting_tree", false]], "startnamespacedeclhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startNamespaceDeclHandler", false]], "startpropertyelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startPropertyElement", false]], "startrawelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startRawElementHandler", false]], "startsequenceelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startSequenceElement", false]], "startseqxmlelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startSeqXMLElement", false]], "startskipelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startSkipElementHandler", false]], "startspecieselement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startSpeciesElement", false]], "startswith() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.startswith", false]], "state (class in bio.align.tabular)": [[55, "Bio.Align.tabular.State", false]], "stats (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.stats", false]], "status_characters (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.status_characters", false]], "std() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.std", false]], "stdev() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.stdev", false]], "stdo (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.stdo", false]], "stdout (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.stdout", false]], "stdout (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.stdout", false]], "stdout (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.stdout", false]], "stdout (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.stdout", false]], "stdout (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.stdout", false]], "stdout (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.stdout", false]], "stdout (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.stdout", false]], "stdout (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.stdout", false]], "stdout (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.stdout", false]], "stdout (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.stdout", false]], "stdout (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.stdout", false]], "stdout (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.stdout", false]], "stdout (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.stdout", false]], "stdout (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.stdout", false]], "stdout (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.stdout", false]], "stdout (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.stdout", false]], "stdout (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.stdout", false]], "stdout (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.stdout", false]], "stdout (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.stdout", false]], "stdout (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.stdout", false]], "stdout (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.stdout", false]], "stdout (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.stdout", false]], "stdout (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.stdout", false]], "stdout (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.stdout", false]], "stdout (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.stdout", false]], "stepmatrix (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.StepMatrix", false]], "stochiometry() (bio.pathway.system method)": [[177, "Bio.Pathway.System.stochiometry", false]], "stockholmiterator (class in bio.alignio.stockholmio)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator", false]], "stockholmwriter (class in bio.alignio.stockholmio)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter", false]], "stop_codons (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.stop_codons", false]], "store() (bio.entrez.parser.dictionaryelement method)": [[84, "Bio.Entrez.Parser.DictionaryElement.store", false]], "store() (bio.entrez.parser.listelement method)": [[84, "Bio.Entrez.Parser.ListElement.store", false]], "store() (bio.entrez.parser.orderedlistelement method)": [[84, "Bio.Entrez.Parser.OrderedListElement.store", false]], "strand (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.strand", false]], "strand (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.strand", false]], "strand (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.strand", false]], "strand (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.strand", false]], "strand (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.strand", false]], "strand (bio.seqfeature.seqfeature property)": [[237, "Bio.SeqFeature.SeqFeature.strand", false]], "strand (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.strand", false]], "strandendin (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.strandendin", false]], "strandendout (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.strandendout", false]], "strandgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.strandgap", false]], "streammodeerror": [[27, "Bio.StreamModeError", false]], "stretchercommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.StretcherCommandline", false]], "strict_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.strict_consensus", false]], "strictly_equals() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.strictly_equals", false]], "strictly_equals() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.strictly_equals", false]], "strictly_equals() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.strictly_equals", false]], "strictly_equals() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.strictly_equals", false]], "stringelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.StringElement", false]], "strings (bio.expasy.scanprosite.contenthandler attribute)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.strings", false]], "strip() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.strip", false]], "structure (class in bio.pdb.structure)": [[160, "Bio.PDB.Structure.Structure", false]], "structure_rebuild_test() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.structure_rebuild_test", false]], "structurealignment (class in bio.pdb.structurealignment)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment", false]], "structurebuilder (class in bio.pdb.structurebuilder)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder", false]], "structured_comment_delim (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.STRUCTURED_COMMENT_DELIM", false]], "structured_comment_delim (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.STRUCTURED_COMMENT_DELIM", false]], "structured_comment_end (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.STRUCTURED_COMMENT_END", false]], "structured_comment_end (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.STRUCTURED_COMMENT_END", false]], "structured_comment_start (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.STRUCTURED_COMMENT_START", false]], "structured_comment_start (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.STRUCTURED_COMMENT_START", false]], "structuredecoder (class in bio.pdb.mmtf.defaultparser)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder", false]], "structureio (class in bio.pdb.pdbio)": [[148, "Bio.PDB.PDBIO.StructureIO", false]], "stsline (class in bio.unigene)": [[275, "Bio.UniGene.STSLine", false]], "style (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.style", false]], "subcomponent_size() (bio.graphics.basicchromosome.chromosome method)": [[99, "Bio.Graphics.BasicChromosome.Chromosome.subcomponent_size", false]], "subject (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.subject", false]], "subject (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.subject", false]], "subject (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.subject", false]], "subject (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.subject", false]], "subject (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.subject", false]], "subject (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.subject", false]], "subject (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.subject", false]], "subject_loc (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.subject_loc", false]], "substitutions (bio.align.alignment property)": [[30, "Bio.Align.Alignment.substitutions", false]], "substitutions (bio.align.multipleseqalignment property)": [[30, "Bio.Align.MultipleSeqAlignment.substitutions", false]], "substrates (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.substrates", false]], "subtract_control() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.subtract_control", false]], "sueff (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.sueff", false]], "sum() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.sum", false]], "sum_branchlength() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.sum_branchlength", false]], "sum_statistics (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.sum_statistics", false]], "sum_stats (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.sum_stats", false]], "summaryinfo (class in bio.align.aligninfo)": [[31, "Bio.Align.AlignInfo.SummaryInfo", false]], "superimposer (class in bio.pdb.superimposer)": [[163, "Bio.PDB.Superimposer.Superimposer", false]], "sv (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.sv", false]], "svdsuperimposer (class in bio.svdsuperimposer)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer", false]], "swissiterator() (in module bio.seqio.swissio)": [[255, "Bio.SeqIO.SwissIO.SwissIterator", false]], "swissprotparsererror": [[272, "Bio.SwissProt.SwissProtParserError", false]], "symbol() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.symbol", false]], "synonym() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.synonym", false]], "system (class in bio.pathway)": [[177, "Bio.Pathway.System", false]], "t (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.t", false]], "t (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.t", false]], "t (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.T", false], [270, "Bio.Sequencing.Applications.BwaBwaswCommandline.t", false]], "t (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.T", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.t", false]], "t (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.T", false]], "t (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.t", false]], "ta (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ta", false]], "tabiterator (class in bio.seqio.tabio)": [[256, "Bio.SeqIO.TabIO.TabIterator", false]], "table (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.table", false]], "tabwriter (class in bio.seqio.tabio)": [[256, "Bio.SeqIO.TabIO.TabWriter", false]], "target (bio.align.alignment property)": [[30, "Bio.Align.Alignment.target", false]], "target (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.target", false]], "target_gap (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.TARGET_GAP", false]], "task (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.task", false]], "task (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.task", false]], "task (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.task", false]], "task (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.task", false]], "task (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.task", false]], "taxid (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.taxid", false]], "taxid_map (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.taxid_map", false]], "taxonomy (bio.phylo.phyloxml.clade property)": [[197, "Bio.Phylo.PhyloXML.Clade.taxonomy", false]], "taxonomy (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Taxonomy", false]], "taxonomy() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.taxonomy", false]], "tcoffeecommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.TCoffeeCommandline", false]], "tell() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.tell", false]], "tell() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.tell", false]], "telomeresegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.TelomereSegment", false]], "template_length (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.template_length", false]], "template_type (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.template_type", false]], "termgap (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.termgap", false]], "terminal_gap_to_missing() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.terminal_gap_to_missing", false]], "terminalgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.terminalgap", false]], "test (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.test", false]], "test_genic_diff_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genic_diff_all", false]], "test_genic_diff_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genic_diff_pair", false]], "test_genotypic_diff_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genotypic_diff_all", false]], "test_genotypic_diff_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genotypic_diff_pair", false]], "test_global_hz_deficiency() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_global_hz_deficiency", false]], "test_global_hz_excess() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_global_hz_excess", false]], "test_hw_global() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.test_hw_global", false]], "test_hw_pop() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.test_hw_pop", false]], "test_ld() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_ld", false]], "test_ld_all_pair() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.test_ld_all_pair", false]], "test_pop_hz_deficiency() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_pop_hz_deficiency", false]], "test_pop_hz_excess() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_pop_hz_excess", false]], "test_pop_hz_prob() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_pop_hz_prob", false]], "thorough (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.thorough", false]], "thr (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.thr", false]], "thread (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.thread", false]], "threads (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.threads", false]], "threads (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.threads", false]], "three_to_index() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.three_to_index", false]], "thresh (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.thresh", false]], "thresh (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.thresh", false]], "threshold (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.threshold", false]], "threshold (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.threshold", false]], "threshold (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.threshold", false]], "threshold (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.threshold", false]], "threshold (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.threshold", false]], "threshold (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.threshold", false]], "threshold (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.threshold", false]], "threshold (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.threshold", false]], "threshold (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.threshold", false]], "threshold (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.threshold", false]], "threshold (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.threshold", false]], "threshold_balanced() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_balanced", false]], "threshold_fnr() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_fnr", false]], "threshold_fpr() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_fpr", false]], "threshold_patser() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_patser", false]], "title (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.title", false]], "tm (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.tm", false]], "tm_gc() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.Tm_GC", false]], "tm_nn() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.Tm_NN", false]], "tm_wallace() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.Tm_Wallace", false]], "tname() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.tname", false]], "to_alignment() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.to_alignment", false]], "to_dict() (bio.motifs.jaspar.record method)": [[287, "Bio.motifs.jaspar.Record.to_dict", false]], "to_dict() (in module bio.searchio)": [[217, "Bio.SearchIO.to_dict", false]], "to_dict() (in module bio.seqio)": [[238, "Bio.SeqIO.to_dict", false]], "to_generic() (bio.blast.ncbixml.multiplealignment method)": [[71, "Bio.Blast.NCBIXML.MultipleAlignment.to_generic", false]], "to_hex() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.to_hex", false]], "to_phylogeny() (bio.phylo.phyloxml.clade method)": [[197, "Bio.Phylo.PhyloXML.Clade.to_phylogeny", false]], "to_phyloxml_container() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.to_phyloxml_container", false]], "to_rgb() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.to_rgb", false]], "to_seqfeature() (bio.phylo.phyloxml.proteindomain method)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain.to_seqfeature", false]], "to_seqrecord() (bio.phylo.phyloxml.sequence method)": [[197, "Bio.Phylo.PhyloXML.Sequence.to_seqrecord", false]], "to_string() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.to_string", false]], "to_string() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.to_string", false]], "to_string() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.to_string", false]], "to_string() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.to_string", false]], "to_strings() (bio.phylo.newickio.writer method)": [[190, "Bio.Phylo.NewickIO.Writer.to_strings", false]], "toclarecord() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.toClaRecord", false]], "todesrecord() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.toDesRecord", false]], "todesrecord() (bio.scop.node method)": [[209, "Bio.SCOP.Node.toDesRecord", false]], "tohierecord() (bio.scop.node method)": [[209, "Bio.SCOP.Node.toHieRecord", false]], "tomultipleseqalignment() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.toMultipleSeqAlignment", false]], "top (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.top", false]], "topdiags (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.topdiags", false]], "topm (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.topm", false]], "toseq() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.toSeq", false]], "tossgaps (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.tossgaps", false]], "total_branch_length() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.total_branch_length", false]], "trace() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.trace", false]], "trace() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.trace", false]], "track (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.Track", false]], "train (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.train", false]], "train() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.train", false]], "train() (bio.hmm.trainer.knownstatetrainer method)": [[109, "Bio.HMM.Trainer.KnownStateTrainer.train", false]], "train() (in module bio.knn)": [[282, "Bio.kNN.train", false]], "train() (in module bio.logisticregression)": [[120, "Bio.LogisticRegression.train", false]], "train() (in module bio.maxentropy)": [[122, "Bio.MaxEntropy.train", false]], "train() (in module bio.naivebayes)": [[127, "Bio.NaiveBayes.train", false]], "train_bw() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.train_bw", false]], "train_visible() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.train_visible", false]], "trainingsequence (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.TrainingSequence", false]], "tranaligncommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.TranalignCommandline", false]], "transcribe() (in module bio.seq)": [[236, "Bio.Seq.transcribe", false]], "transform() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.transform", false]], "transform() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.transform", false]], "transform() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.transform", false]], "transformation() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.transformation", false]], "transitions_from() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_from", false]], "transitions_to() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_to", false]], "translate (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.translate", false]], "translate() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.translate", false]], "translate() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.translate", false]], "translate() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.translate", false]], "translate() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.translate", false]], "translate() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.translate", false]], "translate() (in module bio.seq)": [[236, "Bio.Seq.translate", false]], "translationerror": [[76, "Bio.Data.CodonTable.TranslationError", false]], "transpose() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.transpose", false]], "transversion (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.transversion", false]], "transweight (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.transweight", false]], "tree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.tree", false]], "tree (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.tree", false]], "tree (class in bio.cluster)": [[73, "Bio.Cluster.Tree", false]], "tree (class in bio.nexus.trees)": [[132, "Bio.Nexus.Trees.Tree", false]], "tree (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.Tree", false]], "tree (class in bio.phylo.cdao)": [[184, "Bio.Phylo.CDAO.Tree", false]], "tree (class in bio.phylo.newick)": [[189, "Bio.Phylo.Newick.Tree", false]], "tree (class in bio.phylo.nexml)": [[187, "Bio.Phylo.NeXML.Tree", false]], "tree1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.tree1", false]], "tree2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.tree2", false]], "treecluster() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.treecluster", false]], "treecluster() (in module bio.cluster)": [[73, "Bio.Cluster.treecluster", false]], "treeconstructor (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.TreeConstructor", false]], "treeelement (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.TreeElement", false]], "treeerror": [[132, "Bio.Nexus.Trees.TreeError", false]], "treemixin (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.TreeMixin", false]], "treeout (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.treeout", false]], "treeprint (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.treeprint", false]], "treesearcher (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.TreeSearcher", false]], "treetype (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.treetype", false]], "trimming (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.trimming", false]], "trout (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.trout", false]], "trout (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.trout", false]], "trout (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.trout", false]], "trout (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.trout", false]], "truncate (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.truncate", false]], "ts_tv_ratio (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.ts_tv_ratio", false]], "ttratio (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.ttratio", false]], "ttratio (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.ttratio", false]], "twice (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.twice", false]], "twobititerator (class in bio.seqio.twobitio)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator", false]], "type (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.type", false]], "type (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.type", false]], "type() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.type", false]], "types (bio.phylo.phyloxml.sequence attribute)": [[197, "Bio.Phylo.PhyloXML.Sequence.types", false]], "u (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.U", false]], "u (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.u", false]], "u (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.u", false]], "u (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.u", false]], "u (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.u", false]], "uncertainposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.UncertainPosition", false]], "unconverted (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.unconverted", false]], "undefinedsequenceerror": [[236, "Bio.Seq.UndefinedSequenceError", false]], "unfold_entities() (in module bio.pdb.selection)": [[159, "Bio.PDB.Selection.unfold_entities", false]], "ungap() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.ungap", false]], "ungapped (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.ungapped", false]], "uniform (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.uniform", false]], "uniprotiterator() (in module bio.seqio.uniprotio)": [[258, "Bio.SeqIO.UniprotIO.UniprotIterator", false]], "uniqueify() (in module bio.pdb.selection)": [[159, "Bio.PDB.Selection.uniqueify", false]], "unknownposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.UnknownPosition", false]], "unlink() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.unlink", false]], "unroot() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.unroot", false]], "update() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.update", false]], "update_dcoordspace() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.update_dCoordSpace", false]], "update_emissions() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.update_emissions", false]], "update_pdb() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.update_pdb", false]], "update_transitions() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.update_transitions", false]], "upgma() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.upgma", false]], "upper() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.upper", false]], "upper() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.upper", false]], "uri (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Uri", false]], "uri() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.uri", false]], "uri() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.uri", false]], "use_index (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.use_index", false]], "use_sw_tback (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.use_sw_tback", false]], "usekimura (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.usekimura", false]], "uselogs (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.uselogs", false]], "usetree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.usetree", false]], "usetree (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.usetree", false]], "usetree1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.usetree1", false]], "usetree2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.usetree2", false]], "v (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.v", false]], "v_final (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.v_final", false]], "v_init (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.v_init", false]], "validationerror": [[84, "Bio.Entrez.Parser.ValidationError", false]], "value (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.value", false]], "value (bio.phylo.phyloxml.confidence property)": [[197, "Bio.Phylo.PhyloXML.Confidence.value", false]], "value() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.value", false]], "values() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.values", false]], "values() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.values", false]], "values() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.values", false]], "values() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.values", false]], "variation (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.variation", false]], "vector (class in bio.pdb.vectors)": [[176, "Bio.PDB.vectors.Vector", false]], "vector_to_axis() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.vector_to_axis", false]], "verbose (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.verbose", false]], "verbose (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.verbose", false]], "verbose (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.verbose", false]], "verbose (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.verbose", false]], "verbose (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.verbose", false]], "verbose (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.verbose", false]], "verbose (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.verbose", false]], "verbose (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.verbose", false]], "verbose (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.verbose", false]], "verbose (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.verbose", false]], "verbose (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.verbose", false]], "verbose (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.verbose", false]], "verbose (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.verbose", false]], "verbose (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.verbose", false]], "verbose (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.verbose", false]], "verbose (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.verbose", false]], "verbose (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.verbose", false]], "verbose (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.verbose", false]], "verbose (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.verbose", false]], "verbose (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.verbose", false]], "verbose (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.verbose", false]], "verbose (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.verbose", false]], "verbose (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.verbose", false]], "verbose (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.verbose", false]], "verbose (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.verbose", false]], "verbose (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.verbose", false]], "verbose (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.verbose", false]], "verbose (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.verbose", false]], "verbose (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.verbose", false]], "version (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.version", false]], "version (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.version", false]], "version (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.version", false]], "version (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.version", false]], "version (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.version", false]], "version (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.version", false]], "version (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.version", false]], "version (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.version", false]], "version (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.version", false]], "version (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.version", false]], "version (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.version", false]], "version (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.version", false]], "version (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.version", false]], "version (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.version", false]], "version (bio.motifs.jaspar.motif property)": [[287, "Bio.motifs.jaspar.Motif.version", false]], "version (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.version", false]], "version() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.version", false]], "viterbi (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.viterbi", false]], "viterbi() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.viterbi", false]], "w (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.w", false]], "w (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.w", false]], "wa (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.wa", false]], "wag (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.wag", false]], "warning (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.warning", false]], "warning (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.warning", false]], "warning (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.warning", false]], "warning (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.warning", false]], "warning (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.warning", false]], "warning (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.warning", false]], "warning (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.warning", false]], "warning (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.warning", false]], "warning (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.warning", false]], "warning (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.warning", false]], "warning (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.warning", false]], "warning (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.warning", false]], "warning (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.warning", false]], "warning (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.warning", false]], "warning (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.warning", false]], "warning (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.warning", false]], "warning (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.warning", false]], "warning (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.warning", false]], "warning (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.warning", false]], "warning (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.warning", false]], "warning (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.warning", false]], "warning (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.warning", false]], "warning (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.warning", false]], "warning (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.warning", false]], "warning (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.warning", false]], "watercommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.WaterCommandline", false]], "weblogo() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.weblogo", false]], "weight1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.weight1", false]], "weight2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.weight2", false]], "weight_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.weight_filename", false]], "weighted_stepmatrix() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.weighted_stepmatrix", false]], "weighti (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.weighti", false]], "weighting() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.weighting", false]], "weights (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.weights", false]], "weights (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.weights", false]], "weights (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.weights", false]], "weights (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.weights", false]], "weights (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.weights", false]], "wellrecord (class in bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.WellRecord", false]], "whichcode (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.whichcode", false]], "whichcode (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.whichcode", false]], "width (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.width", false]], "width (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.width", false]], "width() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.width", false]], "window (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.window", false]], "window_masker_db (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.window_masker_db", false]], "window_masker_taxid (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.window_masker_taxid", false]], "window_size (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.window_size", false]], "window_size (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.window_size", false]], "window_size (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.window_size", false]], "window_size (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.window_size", false]], "window_size (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.window_size", false]], "window_size (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.window_size", false]], "window_size (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.window_size", false]], "window_size (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.window_size", false]], "window_size (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.window_size", false]], "withinposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.WithinPosition", false]], "word_size (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.word_size", false]], "word_size (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.word_size", false]], "word_size (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.word_size", false]], "word_size (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.word_size", false]], "word_size (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.word_size", false]], "word_size (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.word_size", false]], "word_size (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.word_size", false]], "word_size (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.word_size", false]], "word_size (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.word_size", false]], "wordsize (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.wordsize", false]], "wordsize (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.wordsize", false]], "working_dir (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.working_dir", false]], "wr (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.wr", false]], "wrap (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.wrap", false]], "write() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write", false]], "write() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.write", false]], "write() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.write", false]], "write() (bio.phenotype.phen_micro.jsonwriter method)": [[299, "Bio.phenotype.phen_micro.JsonWriter.write", false]], "write() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.write", false]], "write() (bio.phylo.newickio.writer method)": [[190, "Bio.Phylo.NewickIO.Writer.write", false]], "write() (bio.phylo.nexmlio.writer method)": [[188, "Bio.Phylo.NeXMLIO.Writer.write", false]], "write() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.write", false]], "write() (in module bio.align)": [[30, "Bio.Align.write", false]], "write() (in module bio.alignio)": [[56, "Bio.AlignIO.write", false]], "write() (in module bio.blast)": [[68, "Bio.Blast.write", false]], "write() (in module bio.motifs)": [[283, "Bio.motifs.write", false]], "write() (in module bio.motifs.clusterbuster)": [[286, "Bio.motifs.clusterbuster.write", false]], "write() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.write", false]], "write() (in module bio.motifs.pfm)": [[293, "Bio.motifs.pfm.write", false]], "write() (in module bio.motifs.transfac)": [[295, "Bio.motifs.transfac.write", false]], "write() (in module bio.phenotype)": [[298, "Bio.phenotype.write", false]], "write() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.write", false]], "write() (in module bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.write", false]], "write() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.write", false]], "write() (in module bio.phylo.nexusio)": [[191, "Bio.Phylo.NexusIO.write", false]], "write() (in module bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.write", false]], "write() (in module bio.searchio)": [[217, "Bio.SearchIO.write", false]], "write() (in module bio.seqio)": [[238, "Bio.SeqIO.write", false]], "write_alignment() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.write_alignment", false]], "write_alignment() (bio.alignio.clustalio.clustalwriter method)": [[57, "Bio.AlignIO.ClustalIO.ClustalWriter.write_alignment", false]], "write_alignment() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_alignment", false]], "write_alignment() (bio.alignio.mafio.mafwriter method)": [[61, "Bio.AlignIO.MafIO.MafWriter.write_alignment", false]], "write_alignment() (bio.alignio.mauveio.mauvewriter method)": [[62, "Bio.AlignIO.MauveIO.MauveWriter.write_alignment", false]], "write_alignment() (bio.alignio.nexusio.nexuswriter method)": [[64, "Bio.AlignIO.NexusIO.NexusWriter.write_alignment", false]], "write_alignment() (bio.alignio.phylipio.phylipwriter method)": [[65, "Bio.AlignIO.PhylipIO.PhylipWriter.write_alignment", false]], "write_alignment() (bio.alignio.phylipio.relaxedphylipwriter method)": [[65, "Bio.AlignIO.PhylipIO.RelaxedPhylipWriter.write_alignment", false]], "write_alignment() (bio.alignio.phylipio.sequentialphylipwriter method)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipWriter.write_alignment", false]], "write_alignment() (bio.alignio.stockholmio.stockholmwriter method)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.write_alignment", false]], "write_alignments() (bio.align.a2m.alignmentwriter method)": [[33, "Bio.Align.a2m.AlignmentWriter.write_alignments", false]], "write_alignments() (bio.align.bigbed.alignmentwriter method)": [[36, "Bio.Align.bigbed.AlignmentWriter.write_alignments", false]], "write_alignments() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_alignments", false]], "write_alignments() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.write_alignments", false]], "write_cal (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.write_cal", false]], "write_cla() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_cla", false]], "write_cla_sql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_cla_sql", false]], "write_ctl_file() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.write_ctl_file", false]], "write_ctl_file() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.write_ctl_file", false]], "write_ctl_file() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.write_ctl_file", false]], "write_des() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_des", false]], "write_des_sql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_des_sql", false]], "write_file() (bio.align.bigbed.alignmentwriter method)": [[36, "Bio.Align.bigbed.AlignmentWriter.write_file", false]], "write_file() (bio.align.bigmaf.alignmentwriter method)": [[37, "Bio.Align.bigmaf.AlignmentWriter.write_file", false]], "write_file() (bio.align.bigpsl.alignmentwriter method)": [[38, "Bio.Align.bigpsl.AlignmentWriter.write_file", false]], "write_file() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_file", false]], "write_file() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.write_file", false]], "write_file() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.write_file", false]], "write_file() (bio.alignio.interfaces.alignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter.write_file", false]], "write_file() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_file", false]], "write_file() (bio.alignio.nexusio.nexuswriter method)": [[64, "Bio.AlignIO.NexusIO.NexusWriter.write_file", false]], "write_file() (bio.searchio.blastio.blast_tab.blasttabwriter method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter.write_file", false]], "write_file() (bio.searchio.blastio.blast_xml.blastxmlwriter method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter.write_file", false]], "write_file() (bio.searchio.blatio.blatpslwriter method)": [[221, "Bio.SearchIO.BlatIO.BlatPslWriter.write_file", false]], "write_file() (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitwriter method)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter.write_file", false]], "write_file() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabwriter method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter.write_file", false]], "write_file() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_file", false]], "write_file() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.write_file", false]], "write_file() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.write_file", false]], "write_file() (bio.seqio.xdnaio.xdnawriter method)": [[259, "Bio.SeqIO.XdnaIO.XdnaWriter.write_file", false]], "write_footer() (bio.align.exonerate.alignmentwriter method)": [[42, "Bio.Align.exonerate.AlignmentWriter.write_footer", false]], "write_footer() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_footer", false]], "write_footer() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_footer", false]], "write_footer() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_footer", false]], "write_footer() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_footer", false]], "write_header() (bio.align.clustal.alignmentwriter method)": [[40, "Bio.Align.clustal.AlignmentWriter.write_header", false]], "write_header() (bio.align.exonerate.alignmentwriter method)": [[42, "Bio.Align.exonerate.AlignmentWriter.write_header", false]], "write_header() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_header", false]], "write_header() (bio.align.maf.alignmentwriter method)": [[46, "Bio.Align.maf.AlignmentWriter.write_header", false]], "write_header() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.write_header", false]], "write_header() (bio.align.psl.alignmentwriter method)": [[51, "Bio.Align.psl.AlignmentWriter.write_header", false]], "write_header() (bio.align.sam.alignmentwriter method)": [[52, "Bio.Align.sam.AlignmentWriter.write_header", false]], "write_header() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_header", false]], "write_header() (bio.alignio.mafio.mafwriter method)": [[61, "Bio.AlignIO.MafIO.MafWriter.write_header", false]], "write_header() (bio.nmr.xpktools.peaklist method)": [[126, "Bio.NMR.xpktools.Peaklist.write_header", false]], "write_header() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_header", false]], "write_header() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.write_header", false]], "write_header() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_header", false]], "write_header() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.write_header", false]], "write_hie() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_hie", false]], "write_hie_sql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_hie_sql", false]], "write_multiple_alignments() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_multiple_alignments", false]], "write_nexus_data() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.write_nexus_data", false]], "write_nexus_data_partitions() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.write_nexus_data_partitions", false]], "write_pdb() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.write_PDB", false]], "write_pic() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.write_PIC", false]], "write_record() (bio.seqio.fastaio.fastawriter method)": [[241, "Bio.SeqIO.FastaIO.FastaWriter.write_record", false]], "write_record() (bio.seqio.insdcio.emblwriter method)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.write_record", false]], "write_record() (bio.seqio.insdcio.genbankwriter method)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.write_record", false]], "write_record() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_record", false]], "write_record() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.write_record", false]], "write_record() (bio.seqio.phdio.phdwriter method)": [[249, "Bio.SeqIO.PhdIO.PhdWriter.write_record", false]], "write_record() (bio.seqio.pirio.pirwriter method)": [[250, "Bio.SeqIO.PirIO.PirWriter.write_record", false]], "write_record() (bio.seqio.qualityio.fastqilluminawriter method)": [[251, "Bio.SeqIO.QualityIO.FastqIlluminaWriter.write_record", false]], "write_record() (bio.seqio.qualityio.fastqphredwriter method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredWriter.write_record", false]], "write_record() (bio.seqio.qualityio.fastqsolexawriter method)": [[251, "Bio.SeqIO.QualityIO.FastqSolexaWriter.write_record", false]], "write_record() (bio.seqio.qualityio.qualphredwriter method)": [[251, "Bio.SeqIO.QualityIO.QualPhredWriter.write_record", false]], "write_record() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_record", false]], "write_record() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.write_record", false]], "write_record() (bio.seqio.tabio.tabwriter method)": [[256, "Bio.SeqIO.TabIO.TabWriter.write_record", false]], "write_records() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_records", false]], "write_scad() (in module bio.pdb.scadio)": [[158, "Bio.PDB.SCADIO.write_SCAD", false]], "write_single_alignment() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_single_alignment", false]], "write_to_string() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.write_to_string", false]], "writeanc (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.writeanc", false]], "writebyproteinrec() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.writebyproteinrec", false]], "writer (class in bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.Writer", false]], "writer (class in bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.Writer", false]], "writer (class in bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.Writer", false]], "writer (class in bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.Writer", false]], "writerec() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.writerec", false]], "writetosql() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.writeToSQL", false]], "x (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.x", false]], "xdnaiterator (class in bio.seqio.xdnaio)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator", false]], "xdnawriter (class in bio.seqio.xdnaio)": [[259, "Bio.SeqIO.XdnaIO.XdnaWriter", false]], "xdrop_gap (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.xdrop_gap", false]], "xdrop_gap_final (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.xdrop_gap_final", false]], "xdrop_ungap (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.xdrop_ungap", false]], "xfr (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.xfr", false]], "xgc_skew() (in module bio.sequtils)": [[261, "Bio.SeqUtils.xGC_skew", false]], "xmldeclhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.xmlDeclHandler", false]], "xmsscanner (class in bio.motifs.xms)": [[296, "Bio.motifs.xms.XMSScanner", false]], "xpkentry (class in bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.XpkEntry", false]], "y (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.y", false]], "yn00 (class in bio.phylo.paml.yn00)": [[196, "Bio.Phylo.PAML.yn00.Yn00", false]], "yn00error": [[196, "Bio.Phylo.PAML.yn00.Yn00Error", false]], "z (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.z", false]]}, "objects": {"": [[27, 0, 0, "-", "Bio"], [301, 0, 0, "-", "BioSQL"]], "Bio": [[28, 0, 0, "-", "Affy"], [30, 0, 0, "-", "Align"], [56, 0, 0, "-", "AlignIO"], [67, 0, 0, "-", "Application"], [27, 1, 1, "", "BiopythonDeprecationWarning"], [27, 1, 1, "", "BiopythonExperimentalWarning"], [27, 1, 1, "", "BiopythonParserWarning"], [27, 1, 1, "", "BiopythonWarning"], [68, 0, 0, "-", "Blast"], [72, 0, 0, "-", "CAPS"], [73, 0, 0, "-", "Cluster"], [74, 0, 0, "-", "Compass"], [75, 0, 0, "-", "Data"], [79, 0, 0, "-", "Emboss"], [83, 0, 0, "-", "Entrez"], [85, 0, 0, "-", "ExPASy"], [91, 0, 0, "-", "File"], [92, 0, 0, "-", "GenBank"], [96, 0, 0, "-", "Geo"], [98, 0, 0, "-", "Graphics"], [106, 0, 0, "-", "HMM"], [111, 0, 0, "-", "KEGG"], [120, 0, 0, "-", "LogisticRegression"], [121, 0, 0, "-", "MarkovModel"], [122, 0, 0, "-", "MaxEntropy"], [123, 0, 0, "-", "Medline"], [27, 1, 1, "", "MissingExternalDependencyError"], [27, 1, 1, "", "MissingPythonDependencyError"], [124, 0, 0, "-", "NMR"], [127, 0, 0, "-", "NaiveBayes"], [128, 0, 0, "-", "Nexus"], [133, 0, 0, "-", "PDB"], [177, 0, 0, "-", "Pathway"], [181, 0, 0, "-", "Phylo"], [200, 0, 0, "-", "PopGen"], [206, 0, 0, "-", "Restriction"], [209, 0, 0, "-", "SCOP"], [216, 0, 0, "-", "SVDSuperimposer"], [217, 0, 0, "-", "SearchIO"], [236, 0, 0, "-", "Seq"], [237, 0, 0, "-", "SeqFeature"], [238, 0, 0, "-", "SeqIO"], [260, 0, 0, "-", "SeqRecord"], [261, 0, 0, "-", "SeqUtils"], [268, 0, 0, "-", "Sequencing"], [27, 1, 1, "", "StreamModeError"], [272, 0, 0, "-", "SwissProt"], [274, 0, 0, "-", "TogoWS"], [275, 0, 0, "-", "UniGene"], [276, 0, 0, "-", "UniProt"], [278, 0, 0, "-", "bgzf"], [279, 0, 0, "-", "codonalign"], [282, 0, 0, "-", "kNN"], [283, 0, 0, "-", "motifs"], [297, 0, 0, "-", "pairwise2"], [298, 0, 0, "-", "phenotype"]], "Bio.Affy": [[29, 0, 0, "-", "CelFile"]], "Bio.Affy.CelFile": [[29, 1, 1, "", "ParserError"], [29, 3, 1, "", "Record"], [29, 4, 1, "", "read"]], "Bio.Affy.CelFile.ParserError": [[29, 2, 1, "", "__init__"]], "Bio.Affy.CelFile.Record": [[29, 2, 1, "", "__init__"]], "Bio.Align": [[31, 0, 0, "-", "AlignInfo"], [30, 3, 1, "", "Alignment"], [30, 3, 1, "", "AlignmentCounts"], [30, 3, 1, "", "Alignments"], [30, 3, 1, "", "AlignmentsAbstractBaseClass"], [32, 0, 0, "-", "Applications"], [30, 3, 1, "", "CodonAligner"], [30, 3, 1, "", "MultipleSeqAlignment"], [30, 3, 1, "", "PairwiseAligner"], [30, 3, 1, "", "PairwiseAlignments"], [33, 0, 0, "-", "a2m"], [34, 0, 0, "-", "analysis"], [35, 0, 0, "-", "bed"], [36, 0, 0, "-", "bigbed"], [37, 0, 0, "-", "bigmaf"], [38, 0, 0, "-", "bigpsl"], [39, 0, 0, "-", "chain"], [40, 0, 0, "-", "clustal"], [41, 0, 0, "-", "emboss"], [42, 0, 0, "-", "exonerate"], [43, 0, 0, "-", "fasta"], [44, 0, 0, "-", "hhr"], [45, 0, 0, "-", "interfaces"], [46, 0, 0, "-", "maf"], [47, 0, 0, "-", "mauve"], [48, 0, 0, "-", "msf"], [49, 0, 0, "-", "nexus"], [30, 4, 1, "", "parse"], [50, 0, 0, "-", "phylip"], [51, 0, 0, "-", "psl"], [30, 4, 1, "", "read"], [52, 0, 0, "-", "sam"], [53, 0, 0, "-", "stockholm"], [54, 0, 0, "-", "substitution_matrices"], [55, 0, 0, "-", "tabular"], [30, 4, 1, "", "write"]], "Bio.Align.AlignInfo": [[31, 3, 1, "", "PSSM"], [31, 3, 1, "", "SummaryInfo"], [31, 4, 1, "", "print_info_content"]], "Bio.Align.AlignInfo.PSSM": [[31, 2, 1, "", "__getitem__"], [31, 2, 1, "", "__init__"], [31, 2, 1, "", "__str__"], [31, 2, 1, "", "get_residue"]], "Bio.Align.AlignInfo.SummaryInfo": [[31, 2, 1, "", "__init__"], [31, 2, 1, "", "dumb_consensus"], [31, 2, 1, "", "gap_consensus"], [31, 2, 1, "", "get_column"], [31, 2, 1, "", "information_content"], [31, 2, 1, "", "pos_specific_score_matrix"], [31, 2, 1, "", "replacement_dictionary"]], "Bio.Align.Alignment": [[30, 2, 1, "", "__add__"], [30, 2, 1, "", "__array__"], [30, 2, 1, "", "__eq__"], [30, 2, 1, "", "__format__"], [30, 2, 1, "", "__ge__"], [30, 2, 1, "", "__getitem__"], [30, 2, 1, "", "__gt__"], [30, 5, 1, "", "__hash__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__le__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__lt__"], [30, 2, 1, "", "__ne__"], [30, 2, 1, "", "__repr__"], [30, 2, 1, "", "__str__"], [30, 6, 1, "", "aligned"], [30, 2, 1, "", "counts"], [30, 2, 1, "", "format"], [30, 6, 1, "", "frequencies"], [30, 6, 1, "", "indices"], [30, 2, 1, "", "infer_coordinates"], [30, 6, 1, "", "inverse_indices"], [30, 6, 1, "", "length"], [30, 2, 1, "", "map"], [30, 2, 1, "", "mapall"], [30, 2, 1, "", "parse_printed_alignment"], [30, 6, 1, "", "query"], [30, 2, 1, "", "reverse_complement"], [30, 6, 1, "", "shape"], [30, 2, 1, "", "sort"], [30, 6, 1, "", "substitutions"], [30, 6, 1, "", "target"]], "Bio.Align.AlignmentCounts": [[30, 2, 1, "", "__getnewargs__"], [30, 2, 1, "", "__new__"], [30, 2, 1, "", "__repr__"], [30, 5, 1, "", "__slots__"], [30, 5, 1, "", "gaps"], [30, 5, 1, "", "identities"], [30, 5, 1, "", "mismatches"]], "Bio.Align.Alignments": [[30, 5, 1, "", "__abstractmethods__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__next__"], [30, 2, 1, "", "rewind"]], "Bio.Align.AlignmentsAbstractBaseClass": [[30, 5, 1, "", "__abstractmethods__"], [30, 2, 1, "", "__iter__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__next__"], [30, 2, 1, "", "rewind"]], "Bio.Align.Applications": [[32, 3, 1, "", "ClustalOmegaCommandline"], [32, 3, 1, "", "ClustalwCommandline"], [32, 3, 1, "", "DialignCommandline"], [32, 3, 1, "", "MSAProbsCommandline"], [32, 3, 1, "", "MafftCommandline"], [32, 3, 1, "", "MuscleCommandline"], [32, 3, 1, "", "PrankCommandline"], [32, 3, 1, "", "ProbconsCommandline"], [32, 3, 1, "", "TCoffeeCommandline"]], "Bio.Align.Applications.ClustalOmegaCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "auto"], [32, 6, 1, "", "clusteringout"], [32, 6, 1, "", "clustersize"], [32, 6, 1, "", "dealign"], [32, 6, 1, "", "distmat_full"], [32, 6, 1, "", "distmat_full_iter"], [32, 6, 1, "", "distmat_in"], [32, 6, 1, "", "distmat_out"], [32, 6, 1, "", "force"], [32, 6, 1, "", "guidetree_in"], [32, 6, 1, "", "guidetree_out"], [32, 6, 1, "", "help"], [32, 6, 1, "", "hmm_input"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "infmt"], [32, 6, 1, "", "isprofile"], [32, 6, 1, "", "iterations"], [32, 6, 1, "", "log"], [32, 6, 1, "", "long_version"], [32, 6, 1, "", "max_guidetree_iterations"], [32, 6, 1, "", "max_hmm_iterations"], [32, 6, 1, "", "maxnumseq"], [32, 6, 1, "", "maxseqlen"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "outfmt"], [32, 6, 1, "", "outputorder"], [32, 6, 1, "", "percentid"], [32, 6, 1, "", "profile1"], [32, 6, 1, "", "profile2"], [32, 6, 1, "", "residuenumber"], [32, 6, 1, "", "seqtype"], [32, 6, 1, "", "threads"], [32, 6, 1, "", "usekimura"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "version"], [32, 6, 1, "", "wrap"]], "Bio.Align.Applications.ClustalwCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "align"], [32, 6, 1, "", "bootlabels"], [32, 6, 1, "", "bootstrap"], [32, 6, 1, "", "case"], [32, 6, 1, "", "check"], [32, 6, 1, "", "clustering"], [32, 6, 1, "", "convert"], [32, 6, 1, "", "dnamatrix"], [32, 6, 1, "", "endgaps"], [32, 6, 1, "", "fullhelp"], [32, 6, 1, "", "gapdist"], [32, 6, 1, "", "gapext"], [32, 6, 1, "", "gapopen"], [32, 6, 1, "", "helixendin"], [32, 6, 1, "", "helixendout"], [32, 6, 1, "", "helixgap"], [32, 6, 1, "", "help"], [32, 6, 1, "", "hgapresidues"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "iteration"], [32, 6, 1, "", "kimura"], [32, 6, 1, "", "ktuple"], [32, 6, 1, "", "loopgap"], [32, 6, 1, "", "matrix"], [32, 6, 1, "", "maxdiv"], [32, 6, 1, "", "maxseqlen"], [32, 6, 1, "", "negative"], [32, 6, 1, "", "newtree"], [32, 6, 1, "", "newtree1"], [32, 6, 1, "", "newtree2"], [32, 6, 1, "", "nohgap"], [32, 6, 1, "", "nopgap"], [32, 6, 1, "", "nosecstr1"], [32, 6, 1, "", "nosecstr2"], [32, 6, 1, "", "noweights"], [32, 6, 1, "", "numiter"], [32, 6, 1, "", "options"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "outorder"], [32, 6, 1, "", "output"], [32, 6, 1, "", "outputtree"], [32, 6, 1, "", "pairgap"], [32, 6, 1, "", "pim"], [32, 6, 1, "", "profile"], [32, 6, 1, "", "profile1"], [32, 6, 1, "", "profile2"], [32, 6, 1, "", "pwdnamatrix"], [32, 6, 1, "", "pwgapext"], [32, 6, 1, "", "pwgapopen"], [32, 6, 1, "", "pwmatrix"], [32, 6, 1, "", "quicktree"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "range"], [32, 6, 1, "", "score"], [32, 6, 1, "", "secstrout"], [32, 6, 1, "", "seed"], [32, 6, 1, "", "seqno_range"], [32, 6, 1, "", "seqnos"], [32, 6, 1, "", "sequences"], [32, 6, 1, "", "stats"], [32, 6, 1, "", "strandendin"], [32, 6, 1, "", "strandendout"], [32, 6, 1, "", "strandgap"], [32, 6, 1, "", "terminalgap"], [32, 6, 1, "", "topdiags"], [32, 6, 1, "", "tossgaps"], [32, 6, 1, "", "transweight"], [32, 6, 1, "", "tree"], [32, 6, 1, "", "type"], [32, 6, 1, "", "usetree"], [32, 6, 1, "", "usetree1"], [32, 6, 1, "", "usetree2"], [32, 6, 1, "", "window"]], "Bio.Align.Applications.DialignCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "afc"], [32, 6, 1, "", "afc_v"], [32, 6, 1, "", "anc"], [32, 6, 1, "", "cs"], [32, 6, 1, "", "cw"], [32, 6, 1, "", "ds"], [32, 6, 1, "", "fa"], [32, 6, 1, "", "ff"], [32, 6, 1, "", "fn"], [32, 6, 1, "", "fop"], [32, 6, 1, "", "fsm"], [32, 6, 1, "", "input"], [32, 6, 1, "", "iw"], [32, 6, 1, "", "lgs"], [32, 6, 1, "", "lgs_t"], [32, 6, 1, "", "lmax"], [32, 6, 1, "", "lo"], [32, 6, 1, "", "ma"], [32, 6, 1, "", "mask"], [32, 6, 1, "", "mat"], [32, 6, 1, "", "mat_thr"], [32, 6, 1, "", "max_link"], [32, 6, 1, "", "min_link"], [32, 6, 1, "", "mot"], [32, 6, 1, "", "msf"], [32, 6, 1, "", "n"], [32, 6, 1, "", "nt"], [32, 6, 1, "", "nta"], [32, 6, 1, "", "o"], [32, 6, 1, "", "ow"], [32, 6, 1, "", "pst"], [32, 6, 1, "", "smin"], [32, 6, 1, "", "stars"], [32, 6, 1, "", "stdo"], [32, 6, 1, "", "ta"], [32, 6, 1, "", "thr"], [32, 6, 1, "", "xfr"]], "Bio.Align.Applications.MSAProbsCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "alignment_order"], [32, 6, 1, "", "annot"], [32, 6, 1, "", "clustalw"], [32, 6, 1, "", "consistency"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "iterative_refinement"], [32, 6, 1, "", "numthreads"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "version"]], "Bio.Align.Applications.MafftCommandline": [[32, 6, 1, "", "LEXP"], [32, 6, 1, "", "LOP"], [32, 2, 1, "", "__init__"], [32, 6, 1, "", "aamatrix"], [32, 6, 1, "", "adjustdirection"], [32, 6, 1, "", "adjustdirectionaccurately"], [32, 6, 1, "", "amino"], [32, 6, 1, "", "auto"], [32, 6, 1, "", "bl"], [32, 6, 1, "", "clustalout"], [32, 6, 1, "", "dpparttree"], [32, 6, 1, "", "ep"], [32, 6, 1, "", "fastapair"], [32, 6, 1, "", "fastaparttree"], [32, 6, 1, "", "fft"], [32, 6, 1, "", "fmodel"], [32, 6, 1, "", "genafpair"], [32, 6, 1, "", "globalpair"], [32, 6, 1, "", "groupsize"], [32, 6, 1, "", "input"], [32, 6, 1, "", "input1"], [32, 6, 1, "", "inputorder"], [32, 6, 1, "", "jtt"], [32, 6, 1, "", "lep"], [32, 6, 1, "", "lexp"], [32, 6, 1, "", "localpair"], [32, 6, 1, "", "lop"], [32, 6, 1, "", "maxiterate"], [32, 6, 1, "", "memsave"], [32, 6, 1, "", "namelength"], [32, 6, 1, "", "nofft"], [32, 6, 1, "", "noscore"], [32, 6, 1, "", "nuc"], [32, 6, 1, "", "op"], [32, 6, 1, "", "partsize"], [32, 6, 1, "", "parttree"], [32, 6, 1, "", "phylipout"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "reorder"], [32, 6, 1, "", "retree"], [32, 6, 1, "", "seed"], [32, 6, 1, "", "sixmerpair"], [32, 6, 1, "", "thread"], [32, 6, 1, "", "tm"], [32, 6, 1, "", "treeout"], [32, 6, 1, "", "weighti"]], "Bio.Align.Applications.MuscleCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "anchors"], [32, 6, 1, "", "anchorspacing"], [32, 6, 1, "", "brenner"], [32, 6, 1, "", "center"], [32, 6, 1, "", "cluster"], [32, 6, 1, "", "cluster1"], [32, 6, 1, "", "cluster2"], [32, 6, 1, "", "clw"], [32, 6, 1, "", "clwout"], [32, 6, 1, "", "clwstrict"], [32, 6, 1, "", "clwstrictout"], [32, 6, 1, "", "core"], [32, 6, 1, "", "diagbreak"], [32, 6, 1, "", "diaglength"], [32, 6, 1, "", "diagmargin"], [32, 6, 1, "", "diags"], [32, 6, 1, "", "dimer"], [32, 6, 1, "", "distance1"], [32, 6, 1, "", "distance2"], [32, 6, 1, "", "fasta"], [32, 6, 1, "", "fastaout"], [32, 6, 1, "", "gapextend"], [32, 6, 1, "", "gapopen"], [32, 6, 1, "", "group"], [32, 6, 1, "", "html"], [32, 6, 1, "", "htmlout"], [32, 6, 1, "", "hydro"], [32, 6, 1, "", "hydrofactor"], [32, 6, 1, "", "in1"], [32, 6, 1, "", "in2"], [32, 6, 1, "", "input"], [32, 6, 1, "", "le"], [32, 6, 1, "", "log"], [32, 6, 1, "", "loga"], [32, 6, 1, "", "matrix"], [32, 6, 1, "", "maxdiagbreak"], [32, 6, 1, "", "maxhours"], [32, 6, 1, "", "maxiters"], [32, 6, 1, "", "maxtrees"], [32, 6, 1, "", "minbestcolscore"], [32, 6, 1, "", "minsmoothscore"], [32, 6, 1, "", "msf"], [32, 6, 1, "", "msfout"], [32, 6, 1, "", "noanchors"], [32, 6, 1, "", "nocore"], [32, 6, 1, "", "objscore"], [32, 6, 1, "", "out"], [32, 6, 1, "", "phyi"], [32, 6, 1, "", "phyiout"], [32, 6, 1, "", "phys"], [32, 6, 1, "", "physout"], [32, 6, 1, "", "profile"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "refine"], [32, 6, 1, "", "refinew"], [32, 6, 1, "", "refinewindow"], [32, 6, 1, "", "root1"], [32, 6, 1, "", "root2"], [32, 6, 1, "", "scorefile"], [32, 6, 1, "", "seqtype"], [32, 6, 1, "", "smoothscoreceil"], [32, 6, 1, "", "smoothwindow"], [32, 6, 1, "", "sp"], [32, 6, 1, "", "spn"], [32, 6, 1, "", "spscore"], [32, 6, 1, "", "stable"], [32, 6, 1, "", "sueff"], [32, 6, 1, "", "sv"], [32, 6, 1, "", "tree1"], [32, 6, 1, "", "tree2"], [32, 6, 1, "", "usetree"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "version"], [32, 6, 1, "", "weight1"], [32, 6, 1, "", "weight2"]], "Bio.Align.Applications.PrankCommandline": [[32, 6, 1, "", "F"], [32, 2, 1, "", "__init__"], [32, 6, 1, "", "codon"], [32, 6, 1, "", "convert"], [32, 6, 1, "", "d"], [32, 6, 1, "", "dnafreqs"], [32, 6, 1, "", "dots"], [32, 6, 1, "", "f"], [32, 6, 1, "", "fixedbranches"], [32, 6, 1, "", "gapext"], [32, 6, 1, "", "gaprate"], [32, 6, 1, "", "kappa"], [32, 6, 1, "", "longseq"], [32, 6, 1, "", "m"], [32, 6, 1, "", "matinitsize"], [32, 6, 1, "", "matresize"], [32, 6, 1, "", "maxbranches"], [32, 6, 1, "", "mttranslate"], [32, 6, 1, "", "nopost"], [32, 6, 1, "", "notree"], [32, 6, 1, "", "noxml"], [32, 6, 1, "", "o"], [32, 6, 1, "", "once"], [32, 6, 1, "", "printnodes"], [32, 6, 1, "", "pwdist"], [32, 6, 1, "", "pwgenomic"], [32, 6, 1, "", "pwgenomicdist"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "realbranches"], [32, 6, 1, "", "rho"], [32, 6, 1, "", "scalebranches"], [32, 6, 1, "", "shortnames"], [32, 6, 1, "", "showtree"], [32, 6, 1, "", "showxml"], [32, 6, 1, "", "skipins"], [32, 6, 1, "", "t"], [32, 6, 1, "", "termgap"], [32, 6, 1, "", "translate"], [32, 6, 1, "", "tree"], [32, 6, 1, "", "twice"], [32, 6, 1, "", "uselogs"], [32, 6, 1, "", "writeanc"]], "Bio.Align.Applications.ProbconsCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "a"], [32, 6, 1, "", "annot"], [32, 6, 1, "", "clustalw"], [32, 6, 1, "", "consistency"], [32, 6, 1, "", "emissions"], [32, 6, 1, "", "input"], [32, 6, 1, "", "ir"], [32, 6, 1, "", "pairs"], [32, 6, 1, "", "paramfile"], [32, 6, 1, "", "pre"], [32, 6, 1, "", "train"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "viterbi"]], "Bio.Align.Applications.TCoffeeCommandline": [[32, 5, 1, "", "SEQ_TYPES"], [32, 2, 1, "", "__init__"], [32, 6, 1, "", "convert"], [32, 6, 1, "", "gapext"], [32, 6, 1, "", "gapopen"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "matrix"], [32, 6, 1, "", "mode"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "outorder"], [32, 6, 1, "", "output"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "type"]], "Bio.Align.CodonAligner": [[30, 2, 1, "", "__init__"], [30, 2, 1, "", "align"], [30, 2, 1, "", "score"]], "Bio.Align.MultipleSeqAlignment": [[30, 2, 1, "", "__add__"], [30, 2, 1, "", "__delitem__"], [30, 2, 1, "", "__format__"], [30, 2, 1, "", "__getitem__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__iter__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__repr__"], [30, 2, 1, "", "__str__"], [30, 6, 1, "", "alignment"], [30, 2, 1, "", "append"], [30, 6, 1, "", "column_annotations"], [30, 2, 1, "", "extend"], [30, 2, 1, "", "get_alignment_length"], [30, 2, 1, "", "sort"], [30, 6, 1, "", "substitutions"]], "Bio.Align.PairwiseAligner": [[30, 2, 1, "", "__getstate__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__setattr__"], [30, 2, 1, "", "__setstate__"], [30, 2, 1, "", "align"], [30, 2, 1, "", "score"]], "Bio.Align.PairwiseAlignments": [[30, 5, 1, "", "__abstractmethods__"], [30, 2, 1, "", "__getitem__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__next__"], [30, 2, 1, "", "rewind"]], "Bio.Align.a2m": [[33, 3, 1, "", "AlignmentIterator"], [33, 3, 1, "", "AlignmentWriter"]], "Bio.Align.a2m.AlignmentIterator": [[33, 5, 1, "", "__abstractmethods__"], [33, 5, 1, "", "fmt"]], "Bio.Align.a2m.AlignmentWriter": [[33, 5, 1, "", "__abstractmethods__"], [33, 5, 1, "", "fmt"], [33, 2, 1, "", "format_alignment"], [33, 2, 1, "", "write_alignments"]], "Bio.Align.analysis": [[34, 4, 1, "", "calculate_dn_ds"], [34, 4, 1, "", "calculate_dn_ds_matrix"], [34, 4, 1, "", "mktest"]], "Bio.Align.bed": [[35, 3, 1, "", "AlignmentIterator"], [35, 3, 1, "", "AlignmentWriter"]], "Bio.Align.bed.AlignmentIterator": [[35, 5, 1, "", "__abstractmethods__"], [35, 5, 1, "", "fmt"]], "Bio.Align.bed.AlignmentWriter": [[35, 5, 1, "", "__abstractmethods__"], [35, 2, 1, "", "__init__"], [35, 2, 1, "", "format_alignment"]], "Bio.Align.bigbed": [[36, 3, 1, "", "AlignmentIterator"], [36, 3, 1, "", "AlignmentWriter"], [36, 3, 1, "", "AutoSQLTable"], [36, 3, 1, "", "Field"]], "Bio.Align.bigbed.AlignmentIterator": [[36, 5, 1, "", "__abstractmethods__"], [36, 2, 1, "", "__len__"], [36, 5, 1, "", "fmt"], [36, 5, 1, "", "mode"], [36, 2, 1, "", "search"]], "Bio.Align.bigbed.AlignmentWriter": [[36, 5, 1, "", "__abstractmethods__"], [36, 2, 1, "", "__init__"], [36, 5, 1, "", "fmt"], [36, 5, 1, "", "mode"], [36, 2, 1, "", "write_alignments"], [36, 2, 1, "", "write_file"]], "Bio.Align.bigbed.AutoSQLTable": [[36, 5, 1, "", "__annotations__"], [36, 2, 1, "", "__bytes__"], [36, 2, 1, "", "__getitem__"], [36, 2, 1, "", "__init__"], [36, 2, 1, "", "__str__"], [36, 5, 1, "", "default"], [36, 2, 1, "", "from_bytes"], [36, 2, 1, "", "from_string"]], "Bio.Align.bigbed.Field": [[36, 2, 1, "", "__getnewargs__"], [36, 2, 1, "", "__new__"], [36, 2, 1, "", "__repr__"], [36, 5, 1, "", "__slots__"], [36, 5, 1, "", "as_type"], [36, 5, 1, "", "comment"], [36, 5, 1, "", "name"]], "Bio.Align.bigmaf": [[37, 3, 1, "", "AlignmentIterator"], [37, 3, 1, "", "AlignmentWriter"]], "Bio.Align.bigmaf.AlignmentIterator": [[37, 5, 1, "", "__abstractmethods__"], [37, 2, 1, "", "__init__"], [37, 5, 1, "", "fmt"], [37, 5, 1, "", "mode"]], "Bio.Align.bigmaf.AlignmentWriter": [[37, 5, 1, "", "__abstractmethods__"], [37, 2, 1, "", "__init__"], [37, 5, 1, "", "fmt"], [37, 2, 1, "", "write_file"]], "Bio.Align.bigpsl": [[38, 3, 1, "", "AlignmentIterator"], [38, 3, 1, "", "AlignmentWriter"]], "Bio.Align.bigpsl.AlignmentIterator": [[38, 5, 1, "", "__abstractmethods__"], [38, 5, 1, "", "fmt"]], "Bio.Align.bigpsl.AlignmentWriter": [[38, 5, 1, "", "__abstractmethods__"], [38, 2, 1, "", "__init__"], [38, 5, 1, "", "fmt"], [38, 2, 1, "", "write_file"]], "Bio.Align.chain": [[39, 3, 1, "", "AlignmentIterator"], [39, 3, 1, "", "AlignmentWriter"]], "Bio.Align.chain.AlignmentIterator": [[39, 5, 1, "", "__abstractmethods__"], [39, 5, 1, "", "fmt"]], "Bio.Align.chain.AlignmentWriter": [[39, 5, 1, "", "__abstractmethods__"], [39, 5, 1, "", "fmt"], [39, 2, 1, "", "format_alignment"]], "Bio.Align.clustal": [[40, 3, 1, "", "AlignmentIterator"], [40, 3, 1, "", "AlignmentWriter"]], "Bio.Align.clustal.AlignmentIterator": [[40, 5, 1, "", "__abstractmethods__"], [40, 5, 1, "", "fmt"]], "Bio.Align.clustal.AlignmentWriter": [[40, 5, 1, "", "__abstractmethods__"], [40, 5, 1, "", "fmt"], [40, 2, 1, "", "format_alignment"], [40, 2, 1, "", "write_header"]], "Bio.Align.emboss": [[41, 3, 1, "", "AlignmentIterator"]], "Bio.Align.emboss.AlignmentIterator": [[41, 5, 1, "", "__abstractmethods__"], [41, 5, 1, "", "fmt"]], "Bio.Align.exonerate": [[42, 3, 1, "", "AlignmentIterator"], [42, 3, 1, "", "AlignmentWriter"]], "Bio.Align.exonerate.AlignmentIterator": [[42, 5, 1, "", "__abstractmethods__"], [42, 5, 1, "", "fmt"]], "Bio.Align.exonerate.AlignmentWriter": [[42, 5, 1, "", "__abstractmethods__"], [42, 2, 1, "", "__init__"], [42, 5, 1, "", "fmt"], [42, 2, 1, "", "write_footer"], [42, 2, 1, "", "write_header"]], "Bio.Align.fasta": [[43, 3, 1, "", "AlignmentIterator"], [43, 3, 1, "", "AlignmentWriter"]], "Bio.Align.fasta.AlignmentIterator": [[43, 5, 1, "", "__abstractmethods__"], [43, 5, 1, "", "fmt"]], "Bio.Align.fasta.AlignmentWriter": [[43, 5, 1, "", "__abstractmethods__"], [43, 5, 1, "", "fmt"], [43, 2, 1, "", "format_alignment"]], "Bio.Align.hhr": [[44, 3, 1, "", "AlignmentIterator"]], "Bio.Align.hhr.AlignmentIterator": [[44, 5, 1, "", "__abstractmethods__"], [44, 2, 1, "", "__len__"], [44, 5, 1, "", "fmt"]], "Bio.Align.interfaces": [[45, 3, 1, "", "AlignmentIterator"], [45, 3, 1, "", "AlignmentWriter"]], "Bio.Align.interfaces.AlignmentIterator": [[45, 5, 1, "", "__abstractmethods__"], [45, 5, 1, "", "__annotations__"], [45, 2, 1, "", "__enter__"], [45, 2, 1, "", "__exit__"], [45, 2, 1, "", "__getitem__"], [45, 2, 1, "", "__init__"], [45, 2, 1, "", "__len__"], [45, 2, 1, "", "__next__"], [45, 5, 1, "", "fmt"], [45, 5, 1, "", "mode"], [45, 2, 1, "", "rewind"]], "Bio.Align.interfaces.AlignmentWriter": [[45, 5, 1, "", "__abstractmethods__"], [45, 5, 1, "", "__annotations__"], [45, 2, 1, "", "__init__"], [45, 5, 1, "", "fmt"], [45, 2, 1, "", "format_alignment"], [45, 5, 1, "", "mode"], [45, 2, 1, "", "write"], [45, 2, 1, "", "write_alignments"], [45, 2, 1, "", "write_file"], [45, 2, 1, "", "write_footer"], [45, 2, 1, "", "write_header"], [45, 2, 1, "", "write_multiple_alignments"], [45, 2, 1, "", "write_single_alignment"]], "Bio.Align.maf": [[46, 3, 1, "", "AlignmentIterator"], [46, 3, 1, "", "AlignmentWriter"]], "Bio.Align.maf.AlignmentIterator": [[46, 5, 1, "", "__abstractmethods__"], [46, 5, 1, "", "empty_status_characters"], [46, 5, 1, "", "fmt"], [46, 5, 1, "", "status_characters"]], "Bio.Align.maf.AlignmentWriter": [[46, 5, 1, "", "__abstractmethods__"], [46, 5, 1, "", "fmt"], [46, 2, 1, "", "format_alignment"], [46, 2, 1, "", "write_header"]], "Bio.Align.mauve": [[47, 3, 1, "", "AlignmentIterator"], [47, 3, 1, "", "AlignmentWriter"]], "Bio.Align.mauve.AlignmentIterator": [[47, 5, 1, "", "__abstractmethods__"], [47, 5, 1, "", "fmt"]], "Bio.Align.mauve.AlignmentWriter": [[47, 5, 1, "", "__abstractmethods__"], [47, 2, 1, "", "__init__"], [47, 5, 1, "", "fmt"], [47, 2, 1, "", "format_alignment"], [47, 2, 1, "", "write_file"], [47, 2, 1, "", "write_header"]], "Bio.Align.msf": [[48, 3, 1, "", "AlignmentIterator"]], "Bio.Align.msf.AlignmentIterator": [[48, 5, 1, "", "__abstractmethods__"], [48, 5, 1, "", "fmt"]], "Bio.Align.nexus": [[49, 3, 1, "", "AlignmentIterator"], [49, 3, 1, "", "AlignmentWriter"]], "Bio.Align.nexus.AlignmentIterator": [[49, 5, 1, "", "__abstractmethods__"], [49, 5, 1, "", "fmt"]], "Bio.Align.nexus.AlignmentWriter": [[49, 5, 1, "", "__abstractmethods__"], [49, 2, 1, "", "__init__"], [49, 5, 1, "", "fmt"], [49, 2, 1, "", "format_alignment"], [49, 2, 1, "", "write_alignment"], [49, 2, 1, "", "write_alignments"], [49, 2, 1, "", "write_file"]], "Bio.Align.phylip": [[50, 3, 1, "", "AlignmentIterator"], [50, 3, 1, "", "AlignmentWriter"]], "Bio.Align.phylip.AlignmentIterator": [[50, 5, 1, "", "__abstractmethods__"], [50, 5, 1, "", "fmt"]], "Bio.Align.phylip.AlignmentWriter": [[50, 5, 1, "", "__abstractmethods__"], [50, 5, 1, "", "fmt"], [50, 2, 1, "", "format_alignment"]], "Bio.Align.psl": [[51, 3, 1, "", "AlignmentIterator"], [51, 3, 1, "", "AlignmentWriter"]], "Bio.Align.psl.AlignmentIterator": [[51, 5, 1, "", "__abstractmethods__"], [51, 5, 1, "", "fmt"]], "Bio.Align.psl.AlignmentWriter": [[51, 5, 1, "", "__abstractmethods__"], [51, 2, 1, "", "__init__"], [51, 5, 1, "", "fmt"], [51, 2, 1, "", "format_alignment"], [51, 2, 1, "", "write_header"]], "Bio.Align.sam": [[52, 3, 1, "", "AlignmentIterator"], [52, 3, 1, "", "AlignmentWriter"]], "Bio.Align.sam.AlignmentIterator": [[52, 5, 1, "", "__abstractmethods__"], [52, 5, 1, "", "fmt"]], "Bio.Align.sam.AlignmentWriter": [[52, 5, 1, "", "__abstractmethods__"], [52, 2, 1, "", "__init__"], [52, 5, 1, "", "fmt"], [52, 2, 1, "", "format_alignment"], [52, 2, 1, "", "write_header"]], "Bio.Align.stockholm": [[53, 3, 1, "", "AlignmentIterator"], [53, 3, 1, "", "AlignmentWriter"]], "Bio.Align.stockholm.AlignmentIterator": [[53, 5, 1, "", "__abstractmethods__"], [53, 5, 1, "", "fmt"], [53, 5, 1, "", "gc_mapping"], [53, 5, 1, "", "gf_mapping"], [53, 5, 1, "", "gr_mapping"], [53, 5, 1, "", "gs_mapping"], [53, 5, 1, "", "key"], [53, 5, 1, "", "keyword"], [53, 5, 1, "", "value"]], "Bio.Align.stockholm.AlignmentWriter": [[53, 5, 1, "", "__abstractmethods__"], [53, 5, 1, "", "fmt"], [53, 2, 1, "", "format_alignment"], [53, 5, 1, "", "gc_mapping"], [53, 5, 1, "", "gf_mapping"], [53, 5, 1, "", "gr_mapping"], [53, 5, 1, "", "gs_mapping"]], "Bio.Align.substitution_matrices": [[54, 3, 1, "", "Array"], [54, 4, 1, "", "load"], [54, 4, 1, "", "read"]], "Bio.Align.substitution_matrices.Array": [[54, 2, 1, "", "__array_finalize__"], [54, 2, 1, "", "__array_prepare__"], [54, 2, 1, "", "__array_ufunc__"], [54, 2, 1, "", "__array_wrap__"], [54, 2, 1, "", "__contains__"], [54, 2, 1, "", "__format__"], [54, 2, 1, "", "__getitem__"], [54, 2, 1, "", "__new__"], [54, 2, 1, "", "__reduce__"], [54, 2, 1, "", "__repr__"], [54, 2, 1, "", "__setitem__"], [54, 2, 1, "", "__setstate__"], [54, 2, 1, "", "__str__"], [54, 6, 1, "", "alphabet"], [54, 2, 1, "", "copy"], [54, 2, 1, "", "format"], [54, 2, 1, "", "get"], [54, 2, 1, "", "items"], [54, 2, 1, "", "keys"], [54, 2, 1, "", "select"], [54, 2, 1, "", "transpose"], [54, 2, 1, "", "update"], [54, 2, 1, "", "values"]], "Bio.Align.tabular": [[55, 3, 1, "", "AlignmentIterator"], [55, 3, 1, "", "State"]], "Bio.Align.tabular.AlignmentIterator": [[55, 5, 1, "", "__abstractmethods__"], [55, 5, 1, "", "fmt"], [55, 2, 1, "", "parse_btop"], [55, 2, 1, "", "parse_cigar"]], "Bio.Align.tabular.State": [[55, 5, 1, "", "MATCH"], [55, 5, 1, "", "NONE"], [55, 5, 1, "", "QUERY_GAP"], [55, 5, 1, "", "TARGET_GAP"]], "Bio.AlignIO": [[57, 0, 0, "-", "ClustalIO"], [58, 0, 0, "-", "EmbossIO"], [59, 0, 0, "-", "FastaIO"], [60, 0, 0, "-", "Interfaces"], [61, 0, 0, "-", "MafIO"], [62, 0, 0, "-", "MauveIO"], [63, 0, 0, "-", "MsfIO"], [64, 0, 0, "-", "NexusIO"], [65, 0, 0, "-", "PhylipIO"], [66, 0, 0, "-", "StockholmIO"], [56, 4, 1, "", "convert"], [56, 4, 1, "", "parse"], [56, 4, 1, "", "read"], [56, 4, 1, "", "write"]], "Bio.AlignIO.ClustalIO": [[57, 3, 1, "", "ClustalIterator"], [57, 3, 1, "", "ClustalWriter"]], "Bio.AlignIO.ClustalIO.ClustalIterator": [[57, 2, 1, "", "__next__"]], "Bio.AlignIO.ClustalIO.ClustalWriter": [[57, 2, 1, "", "write_alignment"]], "Bio.AlignIO.EmbossIO": [[58, 3, 1, "", "EmbossIterator"]], "Bio.AlignIO.EmbossIO.EmbossIterator": [[58, 2, 1, "", "__next__"]], "Bio.AlignIO.FastaIO": [[59, 4, 1, "", "FastaM10Iterator"]], "Bio.AlignIO.Interfaces": [[60, 3, 1, "", "AlignmentIterator"], [60, 3, 1, "", "AlignmentWriter"], [60, 3, 1, "", "SequentialAlignmentWriter"]], "Bio.AlignIO.Interfaces.AlignmentIterator": [[60, 2, 1, "", "__init__"], [60, 2, 1, "", "__iter__"], [60, 2, 1, "", "__next__"]], "Bio.AlignIO.Interfaces.AlignmentWriter": [[60, 2, 1, "", "__init__"], [60, 2, 1, "", "clean"], [60, 2, 1, "", "write_file"]], "Bio.AlignIO.Interfaces.SequentialAlignmentWriter": [[60, 2, 1, "", "__init__"], [60, 2, 1, "", "write_alignment"], [60, 2, 1, "", "write_file"], [60, 2, 1, "", "write_footer"], [60, 2, 1, "", "write_header"]], "Bio.AlignIO.MafIO": [[61, 3, 1, "", "MafIndex"], [61, 4, 1, "", "MafIterator"], [61, 3, 1, "", "MafWriter"]], "Bio.AlignIO.MafIO.MafIndex": [[61, 2, 1, "", "__init__"], [61, 2, 1, "", "__len__"], [61, 2, 1, "", "__repr__"], [61, 2, 1, "", "close"], [61, 2, 1, "", "get_spliced"], [61, 2, 1, "", "search"]], "Bio.AlignIO.MafIO.MafWriter": [[61, 2, 1, "", "write_alignment"], [61, 2, 1, "", "write_header"]], "Bio.AlignIO.MauveIO": [[62, 3, 1, "", "MauveIterator"], [62, 3, 1, "", "MauveWriter"]], "Bio.AlignIO.MauveIO.MauveIterator": [[62, 5, 1, "", "__annotations__"], [62, 2, 1, "", "__next__"]], "Bio.AlignIO.MauveIO.MauveWriter": [[62, 2, 1, "", "__init__"], [62, 2, 1, "", "write_alignment"]], "Bio.AlignIO.MsfIO": [[63, 3, 1, "", "MsfIterator"]], "Bio.AlignIO.MsfIO.MsfIterator": [[63, 2, 1, "", "__next__"]], "Bio.AlignIO.NexusIO": [[64, 4, 1, "", "NexusIterator"], [64, 3, 1, "", "NexusWriter"]], "Bio.AlignIO.NexusIO.NexusWriter": [[64, 2, 1, "", "write_alignment"], [64, 2, 1, "", "write_file"]], "Bio.AlignIO.PhylipIO": [[65, 3, 1, "", "PhylipIterator"], [65, 3, 1, "", "PhylipWriter"], [65, 3, 1, "", "RelaxedPhylipIterator"], [65, 3, 1, "", "RelaxedPhylipWriter"], [65, 3, 1, "", "SequentialPhylipIterator"], [65, 3, 1, "", "SequentialPhylipWriter"], [65, 4, 1, "", "sanitize_name"]], "Bio.AlignIO.PhylipIO.PhylipIterator": [[65, 2, 1, "", "__next__"], [65, 5, 1, "", "id_width"]], "Bio.AlignIO.PhylipIO.PhylipWriter": [[65, 2, 1, "", "write_alignment"]], "Bio.AlignIO.PhylipIO.RelaxedPhylipWriter": [[65, 2, 1, "", "write_alignment"]], "Bio.AlignIO.PhylipIO.SequentialPhylipIterator": [[65, 2, 1, "", "__next__"]], "Bio.AlignIO.PhylipIO.SequentialPhylipWriter": [[65, 2, 1, "", "write_alignment"]], "Bio.AlignIO.StockholmIO": [[66, 3, 1, "", "StockholmIterator"], [66, 3, 1, "", "StockholmWriter"]], "Bio.AlignIO.StockholmIO.StockholmIterator": [[66, 2, 1, "", "__next__"], [66, 5, 1, "", "pfam_gc_mapping"], [66, 5, 1, "", "pfam_gr_mapping"], [66, 5, 1, "", "pfam_gs_mapping"]], "Bio.AlignIO.StockholmIO.StockholmWriter": [[66, 5, 1, "", "pfam_gc_mapping"], [66, 5, 1, "", "pfam_gr_mapping"], [66, 5, 1, "", "pfam_gs_mapping"], [66, 2, 1, "", "write_alignment"]], "Bio.Application": [[67, 3, 1, "", "AbstractCommandline"], [67, 1, 1, "", "ApplicationError"]], "Bio.Application.AbstractCommandline": [[67, 2, 1, "", "__call__"], [67, 2, 1, "", "__init__"], [67, 2, 1, "", "__repr__"], [67, 2, 1, "", "__setattr__"], [67, 2, 1, "", "__str__"], [67, 5, 1, "", "parameters"], [67, 2, 1, "", "set_parameter"]], "Bio.Application.ApplicationError": [[67, 2, 1, "", "__init__"], [67, 2, 1, "", "__repr__"], [67, 2, 1, "", "__str__"]], "Bio.Blast": [[69, 0, 0, "-", "Applications"], [68, 1, 1, "", "CorruptedXMLError"], [68, 3, 1, "", "HSP"], [68, 3, 1, "", "Hit"], [70, 0, 0, "-", "NCBIWWW"], [71, 0, 0, "-", "NCBIXML"], [68, 1, 1, "", "NotXMLError"], [68, 3, 1, "", "Record"], [68, 3, 1, "", "Records"], [68, 4, 1, "", "parse"], [68, 4, 1, "", "qblast"], [68, 4, 1, "", "read"], [68, 4, 1, "", "write"]], "Bio.Blast.Applications": [[69, 3, 1, "", "NcbiblastformatterCommandline"], [69, 3, 1, "", "NcbiblastnCommandline"], [69, 3, 1, "", "NcbiblastpCommandline"], [69, 3, 1, "", "NcbiblastxCommandline"], [69, 3, 1, "", "NcbideltablastCommandline"], [69, 3, 1, "", "NcbimakeblastdbCommandline"], [69, 3, 1, "", "NcbipsiblastCommandline"], [69, 3, 1, "", "NcbirpsblastCommandline"], [69, 3, 1, "", "NcbirpstblastnCommandline"], [69, 3, 1, "", "NcbitblastnCommandline"], [69, 3, 1, "", "NcbitblastxCommandline"]], "Bio.Blast.Applications.NcbiblastformatterCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "archive"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "rid"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "version"]], "Bio.Blast.Applications.NcbiblastnCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "dust"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "filtering_db"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "index_name"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "min_raw_gapped_score"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "no_greedy"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "off_diagonal_range"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "penalty"], [69, 6, 1, "", "perc_identity"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "reward"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "template_length"], [69, 6, 1, "", "template_type"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_index"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_masker_db"], [69, 6, 1, "", "window_masker_taxid"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbiblastpCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbiblastxCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "frame_shift_penalty"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_intron_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_gencode"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbideltablastCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "domain_inclusion_ethresh"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gap_trigger"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "inclusion_ethresh"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_iterations"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "out_ascii_pssm"], [69, 6, 1, "", "out_pssm"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "pseudocount"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "rpsdb"], [69, 6, 1, "", "save_each_pssm"], [69, 6, 1, "", "save_pssm_after_last_round"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_domain_hits"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbimakeblastdbCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "blastdb_version"], [69, 6, 1, "", "dbtype"], [69, 6, 1, "", "gi_mask"], [69, 6, 1, "", "gi_mask_name"], [69, 6, 1, "", "h"], [69, 6, 1, "", "hash_index"], [69, 6, 1, "", "help"], [69, 6, 1, "", "input_file"], [69, 6, 1, "", "input_type"], [69, 6, 1, "", "logfile"], [69, 6, 1, "", "mask_data"], [69, 6, 1, "", "mask_desc"], [69, 6, 1, "", "mask_id"], [69, 6, 1, "", "max_file_sz"], [69, 6, 1, "", "out"], [69, 6, 1, "", "parse_seqids"], [69, 6, 1, "", "taxid"], [69, 6, 1, "", "taxid_map"], [69, 6, 1, "", "title"], [69, 6, 1, "", "version"]], "Bio.Blast.Applications.NcbipsiblastCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gap_trigger"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "ignore_msa_master"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "in_msa"], [69, 6, 1, "", "in_pssm"], [69, 6, 1, "", "inclusion_ethresh"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "msa_master_idx"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_iterations"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "out_ascii_pssm"], [69, 6, 1, "", "out_pssm"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "phi_pattern"], [69, 6, 1, "", "pseudocount"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "save_each_pssm"], [69, 6, 1, "", "save_pssm_after_last_round"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbirpsblastCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbirpstblastnCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_gencode"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbitblastnCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_gencode"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "frame_shift_penalty"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "in_pssm"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_intron_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbitblastxCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_gencode"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_intron_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_gencode"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.CorruptedXMLError": [[68, 2, 1, "", "__init__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.HSP": [[68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.Hit": [[68, 5, 1, "", "__abstractmethods__"], [68, 2, 1, "", "__getitem__"], [68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.NCBIWWW": [[70, 4, 1, "", "qblast"]], "Bio.Blast.NCBIXML": [[71, 3, 1, "", "Alignment"], [71, 3, 1, "", "Blast"], [71, 3, 1, "", "BlastParser"], [71, 3, 1, "", "DatabaseReport"], [71, 3, 1, "", "Description"], [71, 3, 1, "", "DescriptionExt"], [71, 3, 1, "", "DescriptionExtItem"], [71, 3, 1, "", "HSP"], [71, 3, 1, "", "Header"], [71, 3, 1, "", "MultipleAlignment"], [71, 3, 1, "", "PSIBlast"], [71, 3, 1, "", "Parameters"], [71, 3, 1, "", "Round"], [71, 4, 1, "", "fmt_"], [71, 4, 1, "", "parse"], [71, 4, 1, "", "read"]], "Bio.Blast.NCBIXML.Alignment": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.Blast": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.BlastParser": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "reset"], [71, 2, 1, "", "set_hit_accession"], [71, 2, 1, "", "set_hit_def"], [71, 2, 1, "", "set_hit_id"], [71, 2, 1, "", "set_hit_len"]], "Bio.Blast.NCBIXML.DatabaseReport": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.Description": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.DescriptionExt": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "append_item"]], "Bio.Blast.NCBIXML.DescriptionExtItem": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.HSP": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.Header": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.MultipleAlignment": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "to_generic"]], "Bio.Blast.NCBIXML.PSIBlast": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.Parameters": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.Round": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NotXMLError": [[68, 2, 1, "", "__init__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.Record": [[68, 2, 1, "", "__contains__"], [68, 2, 1, "", "__getitem__"], [68, 2, 1, "", "__init__"], [68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"], [68, 2, 1, "", "index"], [68, 2, 1, "", "keys"]], "Bio.Blast.Records": [[68, 5, 1, "", "__abstractmethods__"], [68, 2, 1, "", "__enter__"], [68, 2, 1, "", "__exit__"], [68, 2, 1, "", "__getitem__"], [68, 2, 1, "", "__init__"], [68, 2, 1, "", "__iter__"], [68, 2, 1, "", "__next__"], [68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"], [68, 6, 1, "", "data"]], "Bio.CAPS": [[72, 1, 1, "", "AlignmentHasDifferentLengthsError"], [72, 3, 1, "", "CAPSMap"], [72, 3, 1, "", "DifferentialCutsite"]], "Bio.CAPS.CAPSMap": [[72, 2, 1, "", "__init__"]], "Bio.CAPS.DifferentialCutsite": [[72, 2, 1, "", "__init__"]], "Bio.Cluster": [[73, 3, 1, "", "Node"], [73, 3, 1, "", "Record"], [73, 3, 1, "", "Tree"], [73, 4, 1, "", "clustercentroids"], [73, 4, 1, "", "clusterdistance"], [73, 4, 1, "", "distancematrix"], [73, 4, 1, "", "kcluster"], [73, 4, 1, "", "kmedoids"], [73, 4, 1, "", "pca"], [73, 4, 1, "", "read"], [73, 4, 1, "", "somcluster"], [73, 4, 1, "", "treecluster"]], "Bio.Cluster.Record": [[73, 2, 1, "", "__init__"], [73, 2, 1, "", "clustercentroids"], [73, 2, 1, "", "clusterdistance"], [73, 2, 1, "", "distancematrix"], [73, 2, 1, "", "kcluster"], [73, 2, 1, "", "save"], [73, 2, 1, "", "somcluster"], [73, 2, 1, "", "treecluster"]], "Bio.Cluster.Tree": [[73, 2, 1, "", "cut"], [73, 2, 1, "", "sort"]], "Bio.Compass": [[74, 3, 1, "", "Record"], [74, 4, 1, "", "parse"], [74, 4, 1, "", "read"]], "Bio.Compass.Record": [[74, 2, 1, "", "__init__"], [74, 2, 1, "", "hit_coverage"], [74, 2, 1, "", "query_coverage"]], "Bio.Data": [[76, 0, 0, "-", "CodonTable"], [77, 0, 0, "-", "IUPACData"], [78, 0, 0, "-", "PDBData"]], "Bio.Data.CodonTable": [[76, 3, 1, "", "AmbiguousCodonTable"], [76, 3, 1, "", "AmbiguousForwardTable"], [76, 3, 1, "", "CodonTable"], [76, 3, 1, "", "NCBICodonTable"], [76, 3, 1, "", "NCBICodonTableDNA"], [76, 3, 1, "", "NCBICodonTableRNA"], [76, 1, 1, "", "TranslationError"], [76, 4, 1, "", "list_ambiguous_codons"], [76, 4, 1, "", "list_possible_proteins"], [76, 4, 1, "", "make_back_table"], [76, 4, 1, "", "register_ncbi_table"]], "Bio.Data.CodonTable.AmbiguousCodonTable": [[76, 2, 1, "", "__getattr__"], [76, 2, 1, "", "__init__"]], "Bio.Data.CodonTable.AmbiguousForwardTable": [[76, 2, 1, "", "__contains__"], [76, 2, 1, "", "__getitem__"], [76, 2, 1, "", "__init__"], [76, 2, 1, "", "get"]], "Bio.Data.CodonTable.CodonTable": [[76, 5, 1, "", "__annotations__"], [76, 2, 1, "", "__init__"], [76, 2, 1, "", "__str__"], [76, 5, 1, "", "back_table"], [76, 5, 1, "", "forward_table"], [76, 5, 1, "", "start_codons"], [76, 5, 1, "", "stop_codons"]], "Bio.Data.CodonTable.NCBICodonTable": [[76, 5, 1, "", "__annotations__"], [76, 2, 1, "", "__init__"], [76, 2, 1, "", "__repr__"], [76, 5, 1, "", "nucleotide_alphabet"], [76, 5, 1, "", "protein_alphabet"]], "Bio.Data.CodonTable.NCBICodonTableDNA": [[76, 5, 1, "", "nucleotide_alphabet"]], "Bio.Data.CodonTable.NCBICodonTableRNA": [[76, 5, 1, "", "nucleotide_alphabet"]], "Bio.Emboss": [[80, 0, 0, "-", "Applications"], [81, 0, 0, "-", "Primer3"], [82, 0, 0, "-", "PrimerSearch"]], "Bio.Emboss.Applications": [[80, 3, 1, "", "DiffseqCommandline"], [80, 3, 1, "", "EInvertedCommandline"], [80, 3, 1, "", "ETandemCommandline"], [80, 3, 1, "", "Est2GenomeCommandline"], [80, 3, 1, "", "FConsenseCommandline"], [80, 3, 1, "", "FDNADistCommandline"], [80, 3, 1, "", "FDNAParsCommandline"], [80, 3, 1, "", "FNeighborCommandline"], [80, 3, 1, "", "FProtDistCommandline"], [80, 3, 1, "", "FProtParsCommandline"], [80, 3, 1, "", "FSeqBootCommandline"], [80, 3, 1, "", "FTreeDistCommandline"], [80, 3, 1, "", "FuzznucCommandline"], [80, 3, 1, "", "FuzzproCommandline"], [80, 3, 1, "", "IepCommandline"], [80, 3, 1, "", "NeedleCommandline"], [80, 3, 1, "", "NeedleallCommandline"], [80, 3, 1, "", "PalindromeCommandline"], [80, 3, 1, "", "Primer3Commandline"], [80, 3, 1, "", "PrimerSearchCommandline"], [80, 3, 1, "", "SeqmatchallCommandline"], [80, 3, 1, "", "SeqretCommandline"], [80, 3, 1, "", "StretcherCommandline"], [80, 3, 1, "", "TranalignCommandline"], [80, 3, 1, "", "WaterCommandline"]], "Bio.Emboss.Applications.DiffseqCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aoutfeat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "boutfeat"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "wordsize"]], "Bio.Emboss.Applications.EInvertedCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gap"], [80, 6, 1, "", "help"], [80, 6, 1, "", "match"], [80, 6, 1, "", "maxrepeat"], [80, 6, 1, "", "mismatch"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.ETandemCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "maxrepeat"], [80, 6, 1, "", "minrepeat"], [80, 6, 1, "", "mismatch"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "uniform"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.Est2GenomeCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "align"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "best"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "est"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gappenalty"], [80, 6, 1, "", "genome"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intronpenalty"], [80, 6, 1, "", "match"], [80, 6, 1, "", "minscore"], [80, 6, 1, "", "mismatch"], [80, 6, 1, "", "mode"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "reverse"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "shuffle"], [80, 6, 1, "", "space"], [80, 6, 1, "", "splice"], [80, 6, 1, "", "splicepenalty"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "width"]], "Bio.Emboss.Applications.FConsenseCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "method"], [80, 6, 1, "", "mlfrac"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "root"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FDNADistCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "basefreq"], [80, 6, 1, "", "categories"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "freqsfrom"], [80, 6, 1, "", "gamma"], [80, 6, 1, "", "gammacoefficient"], [80, 6, 1, "", "help"], [80, 6, 1, "", "invarfrac"], [80, 6, 1, "", "lower"], [80, 6, 1, "", "method"], [80, 6, 1, "", "ncategories"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rate"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "ttratio"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"]], "Bio.Emboss.Applications.FDNAParsCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dotdiff"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "maxtrees"], [80, 6, 1, "", "njumble"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "rearrange"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "thorough"], [80, 6, 1, "", "thresh"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "transversion"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"]], "Bio.Emboss.Applications.FNeighborCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "jumble"], [80, 6, 1, "", "matrixtype"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "progress"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "treeprint"], [80, 6, 1, "", "treetype"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FProtDistCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aacateg"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "basefreq"], [80, 6, 1, "", "catergories"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "ease"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gamma"], [80, 6, 1, "", "gammacoefficient"], [80, 6, 1, "", "help"], [80, 6, 1, "", "invarcoefficient"], [80, 6, 1, "", "method"], [80, 6, 1, "", "ncategories"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rate"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "ttratio"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"], [80, 6, 1, "", "whichcode"]], "Bio.Emboss.Applications.FProtParsCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dotdiff"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "njumble"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "thresh"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"], [80, 6, 1, "", "whichcode"]], "Bio.Emboss.Applications.FSeqBootCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "blocksize"], [80, 6, 1, "", "catergories"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dotdiff"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "fracsample"], [80, 6, 1, "", "help"], [80, 6, 1, "", "jusweights"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "regular"], [80, 6, 1, "", "reps"], [80, 6, 1, "", "rewriteformat"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "seqtype"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "test"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"]], "Bio.Emboss.Applications.FTreeDistCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dtype"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "noroot"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "pairing"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "style"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FuzznucCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "complement"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "pattern"], [80, 6, 1, "", "pmismatch"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FuzzproCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "pattern"], [80, 6, 1, "", "pmismatch"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.IepCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "amino"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "carboxyl"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "disulphides"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "lysinemodified"], [80, 6, 1, "", "notermini"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.NeedleCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "brief"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "endextend"], [80, 6, 1, "", "endopen"], [80, 6, 1, "", "endweight"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "nobrief"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "similarity"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.NeedleallCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "brief"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "endextend"], [80, 6, 1, "", "endopen"], [80, 6, 1, "", "endweight"], [80, 6, 1, "", "error"], [80, 6, 1, "", "errorfile"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "minscore"], [80, 6, 1, "", "nobrief"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "similarity"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.PalindromeCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gaplimit"], [80, 6, 1, "", "help"], [80, 6, 1, "", "maxpallen"], [80, 6, 1, "", "minpallen"], [80, 6, 1, "", "nummismatches"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "overlap"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.Primer3Commandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dnaconc"], [80, 6, 1, "", "error"], [80, 6, 1, "", "excludedregion"], [80, 6, 1, "", "explainflag"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "forwardinput"], [80, 6, 1, "", "gcclamp"], [80, 6, 1, "", "help"], [80, 6, 1, "", "hybridprobe"], [80, 6, 1, "", "includedregion"], [80, 6, 1, "", "maxdifftm"], [80, 6, 1, "", "maxgc"], [80, 6, 1, "", "maxmispriming"], [80, 6, 1, "", "maxpolyx"], [80, 6, 1, "", "maxsize"], [80, 6, 1, "", "maxtm"], [80, 6, 1, "", "mingc"], [80, 6, 1, "", "minsize"], [80, 6, 1, "", "mintm"], [80, 6, 1, "", "mishyblibraryfile"], [80, 6, 1, "", "mispriminglibraryfile"], [80, 6, 1, "", "numreturn"], [80, 6, 1, "", "oanyself"], [80, 6, 1, "", "odnaconc"], [80, 6, 1, "", "oendself"], [80, 6, 1, "", "oexcludedregion"], [80, 6, 1, "", "ogcmax"], [80, 6, 1, "", "ogcmin"], [80, 6, 1, "", "ogcopt"], [80, 6, 1, "", "ogcpercent"], [80, 6, 1, "", "oligoinput"], [80, 6, 1, "", "omaxsize"], [80, 6, 1, "", "ominsize"], [80, 6, 1, "", "omishybmax"], [80, 6, 1, "", "opolyxmax"], [80, 6, 1, "", "options"], [80, 6, 1, "", "opttm"], [80, 6, 1, "", "osaltconc"], [80, 6, 1, "", "osize"], [80, 6, 1, "", "osizeopt"], [80, 6, 1, "", "otm"], [80, 6, 1, "", "otmmax"], [80, 6, 1, "", "otmmin"], [80, 6, 1, "", "otmopt"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "prange"], [80, 6, 1, "", "psizeopt"], [80, 6, 1, "", "ptmmax"], [80, 6, 1, "", "ptmmin"], [80, 6, 1, "", "ptmopt"], [80, 6, 1, "", "reverseinput"], [80, 6, 1, "", "saltconc"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "target"], [80, 6, 1, "", "task"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.PrimerSearchCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "infile"], [80, 6, 1, "", "mismatchpercent"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "seqall"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.SeqmatchallCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "wordsize"]], "Bio.Emboss.Applications.SeqretCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "osformat"], [80, 6, 1, "", "outseq"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "sformat"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.StretcherCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.TranalignCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outseq"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "table"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.WaterCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "brief"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "nobrief"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "similarity"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Primer3": [[81, 3, 1, "", "Primers"], [81, 3, 1, "", "Record"], [81, 4, 1, "", "parse"], [81, 4, 1, "", "read"]], "Bio.Emboss.Primer3.Primers": [[81, 2, 1, "", "__init__"], [81, 2, 1, "", "__len__"]], "Bio.Emboss.Primer3.Record": [[81, 2, 1, "", "__init__"]], "Bio.Emboss.PrimerSearch": [[82, 3, 1, "", "Amplifier"], [82, 3, 1, "", "InputRecord"], [82, 3, 1, "", "OutputRecord"], [82, 4, 1, "", "read"]], "Bio.Emboss.PrimerSearch.Amplifier": [[82, 2, 1, "", "__init__"]], "Bio.Emboss.PrimerSearch.InputRecord": [[82, 2, 1, "", "__init__"], [82, 2, 1, "", "__str__"], [82, 2, 1, "", "add_primer_set"]], "Bio.Emboss.PrimerSearch.OutputRecord": [[82, 2, 1, "", "__init__"]], "Bio.Entrez": [[84, 0, 0, "-", "Parser"], [83, 4, 1, "", "ecitmatch"], [83, 4, 1, "", "efetch"], [83, 4, 1, "", "egquery"], [83, 4, 1, "", "einfo"], [83, 4, 1, "", "elink"], [83, 4, 1, "", "epost"], [83, 4, 1, "", "esearch"], [83, 4, 1, "", "espell"], [83, 4, 1, "", "esummary"], [83, 4, 1, "", "parse"], [83, 4, 1, "", "read"]], "Bio.Entrez.Parser": [[84, 1, 1, "", "CorruptedXMLError"], [84, 3, 1, "", "DataHandler"], [84, 3, 1, "", "DataHandlerMeta"], [84, 3, 1, "", "DictionaryElement"], [84, 3, 1, "", "ErrorElement"], [84, 3, 1, "", "IntegerElement"], [84, 3, 1, "", "ListElement"], [84, 3, 1, "", "NoneElement"], [84, 1, 1, "", "NotXMLError"], [84, 3, 1, "", "OrderedListElement"], [84, 3, 1, "", "StringElement"], [84, 1, 1, "", "ValidationError"]], "Bio.Entrez.Parser.CorruptedXMLError": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__str__"]], "Bio.Entrez.Parser.DataHandler": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "characterDataHandlerEscape"], [84, 2, 1, "", "characterDataHandlerRaw"], [84, 2, 1, "", "elementDecl"], [84, 2, 1, "", "endElementHandler"], [84, 2, 1, "", "endErrorElementHandler"], [84, 2, 1, "", "endIntegerElementHandler"], [84, 2, 1, "", "endNamespaceDeclHandler"], [84, 2, 1, "", "endRawElementHandler"], [84, 2, 1, "", "endSkipElementHandler"], [84, 2, 1, "", "endStringElementHandler"], [84, 2, 1, "", "externalEntityRefHandler"], [84, 5, 1, "", "global_dtd_dir"], [84, 5, 1, "", "global_xsd_dir"], [84, 2, 1, "", "handleMissingDocumentDefinition"], [84, 5, 1, "", "local_dtd_dir"], [84, 5, 1, "", "local_xsd_dir"], [84, 2, 1, "", "open_dtd_file"], [84, 2, 1, "", "open_xsd_file"], [84, 2, 1, "", "parse"], [84, 2, 1, "", "parse_xsd"], [84, 2, 1, "", "read"], [84, 2, 1, "", "save_dtd_file"], [84, 2, 1, "", "save_xsd_file"], [84, 2, 1, "", "schemaHandler"], [84, 2, 1, "", "skipCharacterDataHandler"], [84, 2, 1, "", "startElementHandler"], [84, 2, 1, "", "startNamespaceDeclHandler"], [84, 2, 1, "", "startRawElementHandler"], [84, 2, 1, "", "startSkipElementHandler"], [84, 2, 1, "", "xmlDeclHandler"]], "Bio.Entrez.Parser.DataHandlerMeta": [[84, 2, 1, "", "__init__"], [84, 6, 1, "", "directory"]], "Bio.Entrez.Parser.DictionaryElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__repr__"], [84, 2, 1, "", "store"]], "Bio.Entrez.Parser.ErrorElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__new__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.IntegerElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__new__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.ListElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__repr__"], [84, 2, 1, "", "store"]], "Bio.Entrez.Parser.NoneElement": [[84, 2, 1, "", "__eq__"], [84, 5, 1, "", "__hash__"], [84, 2, 1, "", "__init__"], [84, 2, 1, "", "__ne__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.NotXMLError": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__str__"]], "Bio.Entrez.Parser.OrderedListElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__repr__"], [84, 2, 1, "", "store"]], "Bio.Entrez.Parser.StringElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__new__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.ValidationError": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__str__"]], "Bio.ExPASy": [[86, 0, 0, "-", "Enzyme"], [87, 0, 0, "-", "Prodoc"], [88, 0, 0, "-", "Prosite"], [89, 0, 0, "-", "ScanProsite"], [90, 0, 0, "-", "cellosaurus"], [85, 4, 1, "", "get_prodoc_entry"], [85, 4, 1, "", "get_prosite_entry"], [85, 4, 1, "", "get_prosite_raw"], [85, 4, 1, "", "get_sprot_raw"]], "Bio.ExPASy.Enzyme": [[86, 3, 1, "", "Record"], [86, 4, 1, "", "parse"], [86, 4, 1, "", "read"]], "Bio.ExPASy.Enzyme.Record": [[86, 2, 1, "", "__init__"], [86, 2, 1, "", "__repr__"], [86, 2, 1, "", "__str__"]], "Bio.ExPASy.Prodoc": [[87, 3, 1, "", "Record"], [87, 3, 1, "", "Reference"], [87, 4, 1, "", "parse"], [87, 4, 1, "", "read"]], "Bio.ExPASy.Prodoc.Record": [[87, 2, 1, "", "__init__"]], "Bio.ExPASy.Prodoc.Reference": [[87, 2, 1, "", "__init__"]], "Bio.ExPASy.Prosite": [[88, 3, 1, "", "Record"], [88, 4, 1, "", "parse"], [88, 4, 1, "", "read"]], "Bio.ExPASy.Prosite.Record": [[88, 2, 1, "", "__init__"]], "Bio.ExPASy.ScanProsite": [[89, 3, 1, "", "ContentHandler"], [89, 3, 1, "", "Parser"], [89, 3, 1, "", "Record"], [89, 4, 1, "", "read"], [89, 4, 1, "", "scan"]], "Bio.ExPASy.ScanProsite.ContentHandler": [[89, 2, 1, "", "__init__"], [89, 2, 1, "", "characters"], [89, 2, 1, "", "endElement"], [89, 5, 1, "", "integers"], [89, 2, 1, "", "startElement"], [89, 5, 1, "", "strings"]], "Bio.ExPASy.ScanProsite.Parser": [[89, 2, 1, "", "__init__"], [89, 2, 1, "", "feed"]], "Bio.ExPASy.ScanProsite.Record": [[89, 2, 1, "", "__init__"]], "Bio.ExPASy.cellosaurus": [[90, 3, 1, "", "Record"], [90, 4, 1, "", "parse"], [90, 4, 1, "", "read"]], "Bio.ExPASy.cellosaurus.Record": [[90, 2, 1, "", "__init__"], [90, 2, 1, "", "__repr__"], [90, 2, 1, "", "__str__"]], "Bio.File": [[91, 4, 1, "", "as_handle"]], "Bio.GenBank": [[92, 3, 1, "", "FeatureParser"], [92, 3, 1, "", "Iterator"], [92, 1, 1, "", "ParserFailureError"], [93, 0, 0, "-", "Record"], [92, 3, 1, "", "RecordParser"], [94, 0, 0, "-", "Scanner"], [92, 4, 1, "", "parse"], [92, 4, 1, "", "read"], [95, 0, 0, "-", "utils"]], "Bio.GenBank.FeatureParser": [[92, 2, 1, "", "__init__"], [92, 2, 1, "", "parse"]], "Bio.GenBank.Iterator": [[92, 2, 1, "", "__init__"], [92, 2, 1, "", "__iter__"], [92, 2, 1, "", "__next__"]], "Bio.GenBank.Record": [[93, 3, 1, "", "Feature"], [93, 3, 1, "", "Qualifier"], [93, 3, 1, "", "Record"], [93, 3, 1, "", "Reference"]], "Bio.GenBank.Record.Feature": [[93, 2, 1, "", "__init__"], [93, 2, 1, "", "__repr__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.Record.Qualifier": [[93, 2, 1, "", "__init__"], [93, 2, 1, "", "__repr__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.Record.Record": [[93, 5, 1, "", "BASE_FEATURE_FORMAT"], [93, 5, 1, "", "BASE_FORMAT"], [93, 5, 1, "", "GB_BASE_INDENT"], [93, 5, 1, "", "GB_FEATURE_INDENT"], [93, 5, 1, "", "GB_FEATURE_INTERNAL_INDENT"], [93, 5, 1, "", "GB_INTERNAL_INDENT"], [93, 5, 1, "", "GB_LINE_LENGTH"], [93, 5, 1, "", "GB_OTHER_INTERNAL_INDENT"], [93, 5, 1, "", "GB_SEQUENCE_INDENT"], [93, 5, 1, "", "INTERNAL_FEATURE_FORMAT"], [93, 5, 1, "", "INTERNAL_FORMAT"], [93, 5, 1, "", "OTHER_INTERNAL_FORMAT"], [93, 5, 1, "", "SEQUENCE_FORMAT"], [93, 2, 1, "", "__init__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.Record.Reference": [[93, 2, 1, "", "__init__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.RecordParser": [[92, 2, 1, "", "__init__"], [92, 2, 1, "", "parse"]], "Bio.GenBank.Scanner": [[94, 3, 1, "", "EmblScanner"], [94, 3, 1, "", "GenBankScanner"], [94, 3, 1, "", "InsdcScanner"]], "Bio.GenBank.Scanner.EmblScanner": [[94, 5, 1, "", "EMBL_INDENT"], [94, 5, 1, "", "EMBL_SPACER"], [94, 5, 1, "", "FEATURE_END_MARKERS"], [94, 5, 1, "", "FEATURE_QUALIFIER_INDENT"], [94, 5, 1, "", "FEATURE_QUALIFIER_SPACER"], [94, 5, 1, "", "FEATURE_START_MARKERS"], [94, 5, 1, "", "HEADER_WIDTH"], [94, 5, 1, "", "RECORD_START"], [94, 5, 1, "", "SEQUENCE_HEADERS"], [94, 2, 1, "", "parse_footer"]], "Bio.GenBank.Scanner.GenBankScanner": [[94, 5, 1, "", "FEATURE_END_MARKERS"], [94, 5, 1, "", "FEATURE_QUALIFIER_INDENT"], [94, 5, 1, "", "FEATURE_QUALIFIER_SPACER"], [94, 5, 1, "", "FEATURE_START_MARKERS"], [94, 5, 1, "", "GENBANK_INDENT"], [94, 5, 1, "", "GENBANK_SPACER"], [94, 5, 1, "", "HEADER_WIDTH"], [94, 5, 1, "", "RECORD_START"], [94, 5, 1, "", "SEQUENCE_HEADERS"], [94, 5, 1, "", "STRUCTURED_COMMENT_DELIM"], [94, 5, 1, "", "STRUCTURED_COMMENT_END"], [94, 5, 1, "", "STRUCTURED_COMMENT_START"], [94, 5, 1, "", "__annotations__"], [94, 2, 1, "", "parse_footer"]], "Bio.GenBank.Scanner.InsdcScanner": [[94, 5, 1, "", "FEATURE_END_MARKERS"], [94, 5, 1, "", "FEATURE_QUALIFIER_INDENT"], [94, 5, 1, "", "FEATURE_QUALIFIER_SPACER"], [94, 5, 1, "", "FEATURE_START_MARKERS"], [94, 5, 1, "", "HEADER_WIDTH"], [94, 5, 1, "", "RECORD_START"], [94, 5, 1, "", "SEQUENCE_HEADERS"], [94, 2, 1, "", "__init__"], [94, 2, 1, "", "feed"], [94, 2, 1, "", "find_start"], [94, 2, 1, "", "parse"], [94, 2, 1, "", "parse_cds_features"], [94, 2, 1, "", "parse_feature"], [94, 2, 1, "", "parse_features"], [94, 2, 1, "", "parse_footer"], [94, 2, 1, "", "parse_header"], [94, 2, 1, "", "parse_records"], [94, 2, 1, "", "set_handle"]], "Bio.GenBank.utils": [[95, 3, 1, "", "FeatureValueCleaner"]], "Bio.GenBank.utils.FeatureValueCleaner": [[95, 2, 1, "", "__init__"], [95, 2, 1, "", "__repr__"], [95, 2, 1, "", "clean_value"], [95, 5, 1, "", "keys_to_process"]], "Bio.Geo": [[97, 0, 0, "-", "Record"], [96, 4, 1, "", "parse"]], "Bio.Geo.Record": [[97, 3, 1, "", "Record"], [97, 4, 1, "", "out_block"]], "Bio.Geo.Record.Record": [[97, 2, 1, "", "__init__"], [97, 2, 1, "", "__str__"]], "Bio.Graphics": [[99, 0, 0, "-", "BasicChromosome"], [100, 0, 0, "-", "ColorSpiral"], [101, 0, 0, "-", "Comparative"], [102, 0, 0, "-", "DisplayRepresentation"], [103, 0, 0, "-", "Distribution"], [104, 0, 0, "-", "GenomeDiagram"], [105, 0, 0, "-", "KGML_vis"]], "Bio.Graphics.BasicChromosome": [[99, 3, 1, "", "AnnotatedChromosomeSegment"], [99, 3, 1, "", "Chromosome"], [99, 3, 1, "", "ChromosomeSegment"], [99, 3, 1, "", "Organism"], [99, 3, 1, "", "SpacerSegment"], [99, 3, 1, "", "TelomereSegment"]], "Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment": [[99, 2, 1, "", "__init__"]], "Bio.Graphics.BasicChromosome.Chromosome": [[99, 2, 1, "", "__init__"], [99, 2, 1, "", "draw"], [99, 2, 1, "", "subcomponent_size"]], "Bio.Graphics.BasicChromosome.ChromosomeSegment": [[99, 2, 1, "", "__init__"], [99, 2, 1, "", "draw"]], "Bio.Graphics.BasicChromosome.Organism": [[99, 2, 1, "", "__init__"], [99, 2, 1, "", "draw"]], "Bio.Graphics.BasicChromosome.SpacerSegment": [[99, 2, 1, "", "draw"]], "Bio.Graphics.BasicChromosome.TelomereSegment": [[99, 2, 1, "", "__init__"]], "Bio.Graphics.ColorSpiral": [[100, 3, 1, "", "ColorSpiral"], [100, 4, 1, "", "get_color_dict"], [100, 4, 1, "", "get_colors"]], "Bio.Graphics.ColorSpiral.ColorSpiral": [[100, 2, 1, "", "__init__"], [100, 6, 1, "", "a"], [100, 6, 1, "", "b"], [100, 2, 1, "", "get_colors"], [100, 6, 1, "", "jitter"], [100, 6, 1, "", "v_final"], [100, 6, 1, "", "v_init"]], "Bio.Graphics.Comparative": [[101, 3, 1, "", "ComparativeScatterPlot"]], "Bio.Graphics.Comparative.ComparativeScatterPlot": [[101, 2, 1, "", "__init__"], [101, 2, 1, "", "draw_to_file"]], "Bio.Graphics.DisplayRepresentation": [[102, 3, 1, "", "ChromosomeCounts"]], "Bio.Graphics.DisplayRepresentation.ChromosomeCounts": [[102, 2, 1, "", "__init__"], [102, 2, 1, "", "add_count"], [102, 2, 1, "", "add_label"], [102, 2, 1, "", "fill_chromosome"], [102, 2, 1, "", "get_segment_info"], [102, 2, 1, "", "scale_segment_value"], [102, 2, 1, "", "set_scale"]], "Bio.Graphics.Distribution": [[103, 3, 1, "", "BarChartDistribution"], [103, 3, 1, "", "DistributionPage"], [103, 3, 1, "", "LineDistribution"]], "Bio.Graphics.Distribution.BarChartDistribution": [[103, 2, 1, "", "__init__"], [103, 2, 1, "", "draw"]], "Bio.Graphics.Distribution.DistributionPage": [[103, 2, 1, "", "__init__"], [103, 2, 1, "", "draw"]], "Bio.Graphics.Distribution.LineDistribution": [[103, 2, 1, "", "__init__"], [103, 2, 1, "", "draw"]], "Bio.Graphics.GenomeDiagram": [[104, 3, 1, "", "ColorTranslator"], [104, 3, 1, "", "CrossLink"], [104, 3, 1, "", "Diagram"], [104, 3, 1, "", "Feature"], [104, 3, 1, "", "FeatureSet"], [104, 3, 1, "", "GraphData"], [104, 3, 1, "", "GraphSet"], [104, 3, 1, "", "Track"]], "Bio.Graphics.GenomeDiagram.ColorTranslator": [[104, 2, 1, "", "__init__"], [104, 2, 1, "", "artemis_color"], [104, 2, 1, "", "float1_color"], [104, 2, 1, "", "get_artemis_colorscheme"], [104, 2, 1, "", "get_colorscheme"], [104, 2, 1, "", "int255_color"], [104, 2, 1, "", "read_colorscheme"], [104, 2, 1, "", "scheme_color"], [104, 2, 1, "", "translate"]], "Bio.Graphics.GenomeDiagram.CrossLink": [[104, 2, 1, "", "__init__"], [104, 6, 1, "", "endA"], [104, 6, 1, "", "endB"], [104, 6, 1, "", "startA"], [104, 6, 1, "", "startB"]], "Bio.Graphics.GenomeDiagram.Diagram": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_track"], [104, 2, 1, "", "del_track"], [104, 2, 1, "", "draw"], [104, 2, 1, "", "get_drawn_levels"], [104, 2, 1, "", "get_levels"], [104, 2, 1, "", "get_tracks"], [104, 2, 1, "", "move_track"], [104, 2, 1, "", "new_track"], [104, 2, 1, "", "range"], [104, 2, 1, "", "renumber_tracks"], [104, 2, 1, "", "set_all_tracks"], [104, 2, 1, "", "write"], [104, 2, 1, "", "write_to_string"]], "Bio.Graphics.GenomeDiagram.Feature": [[104, 2, 1, "", "__getattr__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "get_feature"], [104, 2, 1, "", "set_color"], [104, 2, 1, "", "set_colour"], [104, 2, 1, "", "set_feature"]], "Bio.Graphics.GenomeDiagram.FeatureSet": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__len__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_feature"], [104, 2, 1, "", "del_feature"], [104, 2, 1, "", "get_features"], [104, 2, 1, "", "get_ids"], [104, 2, 1, "", "range"], [104, 2, 1, "", "set_all_features"], [104, 2, 1, "", "to_string"]], "Bio.Graphics.GenomeDiagram.GraphData": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__len__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_point"], [104, 2, 1, "", "get_data"], [104, 2, 1, "", "mean"], [104, 2, 1, "", "quartiles"], [104, 2, 1, "", "range"], [104, 2, 1, "", "set_data"], [104, 2, 1, "", "stdev"]], "Bio.Graphics.GenomeDiagram.GraphSet": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__len__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "data_quartiles"], [104, 2, 1, "", "del_graph"], [104, 2, 1, "", "get_graphs"], [104, 2, 1, "", "get_ids"], [104, 2, 1, "", "new_graph"], [104, 2, 1, "", "range"], [104, 2, 1, "", "to_string"]], "Bio.Graphics.GenomeDiagram.Track": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_set"], [104, 2, 1, "", "del_set"], [104, 2, 1, "", "get_ids"], [104, 2, 1, "", "get_sets"], [104, 2, 1, "", "new_set"], [104, 2, 1, "", "range"], [104, 2, 1, "", "to_string"]], "Bio.Graphics.KGML_vis": [[105, 3, 1, "", "KGMLCanvas"], [105, 4, 1, "", "color_to_reportlab"], [105, 4, 1, "", "darken"], [105, 4, 1, "", "get_temp_imagefilename"]], "Bio.Graphics.KGML_vis.KGMLCanvas": [[105, 2, 1, "", "__init__"], [105, 2, 1, "", "draw"]], "Bio.HMM": [[107, 0, 0, "-", "DynamicProgramming"], [108, 0, 0, "-", "MarkovModel"], [109, 0, 0, "-", "Trainer"], [110, 0, 0, "-", "Utilities"]], "Bio.HMM.DynamicProgramming": [[107, 3, 1, "", "AbstractDPAlgorithms"], [107, 3, 1, "", "LogDPAlgorithms"], [107, 3, 1, "", "ScaledDPAlgorithms"]], "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms": [[107, 2, 1, "", "__init__"], [107, 2, 1, "", "backward_algorithm"], [107, 2, 1, "", "forward_algorithm"]], "Bio.HMM.DynamicProgramming.LogDPAlgorithms": [[107, 2, 1, "", "__init__"]], "Bio.HMM.DynamicProgramming.ScaledDPAlgorithms": [[107, 2, 1, "", "__init__"]], "Bio.HMM.MarkovModel": [[108, 3, 1, "", "HiddenMarkovModel"], [108, 3, 1, "", "MarkovModelBuilder"]], "Bio.HMM.MarkovModel.HiddenMarkovModel": [[108, 2, 1, "", "__init__"], [108, 2, 1, "", "get_blank_emissions"], [108, 2, 1, "", "get_blank_transitions"], [108, 2, 1, "", "transitions_from"], [108, 2, 1, "", "transitions_to"], [108, 2, 1, "", "viterbi"]], "Bio.HMM.MarkovModel.MarkovModelBuilder": [[108, 5, 1, "", "DEFAULT_PSEUDO"], [108, 2, 1, "", "__init__"], [108, 2, 1, "", "allow_all_transitions"], [108, 2, 1, "", "allow_transition"], [108, 2, 1, "", "destroy_transition"], [108, 2, 1, "", "get_markov_model"], [108, 2, 1, "", "set_emission_pseudocount"], [108, 2, 1, "", "set_emission_score"], [108, 2, 1, "", "set_equal_probabilities"], [108, 2, 1, "", "set_initial_probabilities"], [108, 2, 1, "", "set_random_emission_probabilities"], [108, 2, 1, "", "set_random_initial_probabilities"], [108, 2, 1, "", "set_random_probabilities"], [108, 2, 1, "", "set_random_transition_probabilities"], [108, 2, 1, "", "set_transition_pseudocount"], [108, 2, 1, "", "set_transition_score"]], "Bio.HMM.Trainer": [[109, 3, 1, "", "AbstractTrainer"], [109, 3, 1, "", "BaumWelchTrainer"], [109, 3, 1, "", "KnownStateTrainer"], [109, 3, 1, "", "TrainingSequence"]], "Bio.HMM.Trainer.AbstractTrainer": [[109, 2, 1, "", "__init__"], [109, 2, 1, "", "estimate_params"], [109, 2, 1, "", "log_likelihood"], [109, 2, 1, "", "ml_estimator"]], "Bio.HMM.Trainer.BaumWelchTrainer": [[109, 2, 1, "", "__init__"], [109, 2, 1, "", "train"], [109, 2, 1, "", "update_emissions"], [109, 2, 1, "", "update_transitions"]], "Bio.HMM.Trainer.KnownStateTrainer": [[109, 2, 1, "", "__init__"], [109, 2, 1, "", "train"]], "Bio.HMM.Trainer.TrainingSequence": [[109, 2, 1, "", "__init__"]], "Bio.HMM.Utilities": [[110, 4, 1, "", "pretty_print_prediction"]], "Bio.KEGG": [[112, 0, 0, "-", "Compound"], [113, 0, 0, "-", "Enzyme"], [114, 0, 0, "-", "Gene"], [115, 0, 0, "-", "KGML"], [118, 0, 0, "-", "Map"], [119, 0, 0, "-", "REST"]], "Bio.KEGG.Compound": [[112, 3, 1, "", "Record"], [112, 4, 1, "", "parse"]], "Bio.KEGG.Compound.Record": [[112, 2, 1, "", "__init__"], [112, 2, 1, "", "__str__"]], "Bio.KEGG.Enzyme": [[113, 3, 1, "", "Record"], [113, 4, 1, "", "parse"], [113, 4, 1, "", "read"]], "Bio.KEGG.Enzyme.Record": [[113, 2, 1, "", "__init__"], [113, 2, 1, "", "__str__"]], "Bio.KEGG.Gene": [[114, 3, 1, "", "Record"], [114, 4, 1, "", "parse"]], "Bio.KEGG.Gene.Record": [[114, 2, 1, "", "__init__"], [114, 2, 1, "", "__str__"]], "Bio.KEGG.KGML": [[116, 0, 0, "-", "KGML_parser"], [117, 0, 0, "-", "KGML_pathway"]], "Bio.KEGG.KGML.KGML_parser": [[116, 3, 1, "", "KGMLParser"], [116, 4, 1, "", "parse"], [116, 4, 1, "", "read"]], "Bio.KEGG.KGML.KGML_parser.KGMLParser": [[116, 2, 1, "", "__init__"], [116, 2, 1, "", "parse"]], "Bio.KEGG.KGML.KGML_pathway": [[117, 3, 1, "", "Component"], [117, 3, 1, "", "Entry"], [117, 3, 1, "", "Graphics"], [117, 3, 1, "", "Pathway"], [117, 3, 1, "", "Reaction"], [117, 3, 1, "", "Relation"]], "Bio.KEGG.KGML.KGML_pathway.Component": [[117, 2, 1, "", "__init__"], [117, 6, 1, "", "element"], [117, 6, 1, "", "id"]], "Bio.KEGG.KGML.KGML_pathway.Entry": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 2, 1, "", "add_component"], [117, 2, 1, "", "add_graphics"], [117, 6, 1, "", "bounds"], [117, 6, 1, "", "element"], [117, 6, 1, "", "id"], [117, 6, 1, "", "is_reactant"], [117, 6, 1, "", "name"], [117, 6, 1, "", "reaction"], [117, 2, 1, "", "remove_component"], [117, 2, 1, "", "remove_graphics"]], "Bio.KEGG.KGML.KGML_pathway.Graphics": [[117, 2, 1, "", "__init__"], [117, 6, 1, "", "bgcolor"], [117, 6, 1, "", "bounds"], [117, 6, 1, "", "centre"], [117, 6, 1, "", "coords"], [117, 6, 1, "", "element"], [117, 6, 1, "", "fgcolor"], [117, 6, 1, "", "height"], [117, 6, 1, "", "width"], [117, 6, 1, "", "x"], [117, 6, 1, "", "y"]], "Bio.KEGG.KGML.KGML_pathway.Pathway": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 2, 1, "", "add_entry"], [117, 2, 1, "", "add_reaction"], [117, 2, 1, "", "add_relation"], [117, 6, 1, "", "bounds"], [117, 6, 1, "", "compounds"], [117, 6, 1, "", "element"], [117, 6, 1, "", "genes"], [117, 2, 1, "", "get_KGML"], [117, 6, 1, "", "maps"], [117, 6, 1, "", "name"], [117, 6, 1, "", "number"], [117, 6, 1, "", "orthologs"], [117, 6, 1, "", "reaction_entries"], [117, 6, 1, "", "reactions"], [117, 6, 1, "", "relations"], [117, 2, 1, "", "remove_entry"], [117, 2, 1, "", "remove_reaction"], [117, 2, 1, "", "remove_relation"]], "Bio.KEGG.KGML.KGML_pathway.Reaction": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 2, 1, "", "add_product"], [117, 2, 1, "", "add_substrate"], [117, 6, 1, "", "element"], [117, 6, 1, "", "entry"], [117, 6, 1, "", "id"], [117, 6, 1, "", "name"], [117, 6, 1, "", "products"], [117, 6, 1, "", "reactant_ids"], [117, 6, 1, "", "substrates"]], "Bio.KEGG.KGML.KGML_pathway.Relation": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 6, 1, "", "element"], [117, 6, 1, "", "entry1"], [117, 6, 1, "", "entry2"]], "Bio.KEGG.Map": [[118, 4, 1, "", "parse"]], "Bio.KEGG.REST": [[119, 4, 1, "", "kegg_conv"], [119, 4, 1, "", "kegg_find"], [119, 4, 1, "", "kegg_get"], [119, 4, 1, "", "kegg_info"], [119, 4, 1, "", "kegg_link"], [119, 4, 1, "", "kegg_list"]], "Bio.LogisticRegression": [[120, 3, 1, "", "LogisticRegression"], [120, 4, 1, "", "calculate"], [120, 4, 1, "", "classify"], [120, 4, 1, "", "train"]], "Bio.LogisticRegression.LogisticRegression": [[120, 2, 1, "", "__init__"]], "Bio.MarkovModel": [[121, 3, 1, "", "MarkovModel"], [121, 4, 1, "", "find_states"], [121, 4, 1, "", "itemindex"], [121, 4, 1, "", "load"], [121, 4, 1, "", "save"], [121, 4, 1, "", "train_bw"], [121, 4, 1, "", "train_visible"]], "Bio.MarkovModel.MarkovModel": [[121, 2, 1, "", "__init__"], [121, 2, 1, "", "__str__"]], "Bio.MaxEntropy": [[122, 3, 1, "", "MaxEntropy"], [122, 4, 1, "", "calculate"], [122, 4, 1, "", "classify"], [122, 4, 1, "", "train"]], "Bio.MaxEntropy.MaxEntropy": [[122, 2, 1, "", "__init__"]], "Bio.Medline": [[123, 3, 1, "", "Record"], [123, 4, 1, "", "parse"], [123, 4, 1, "", "read"]], "Bio.NMR": [[125, 0, 0, "-", "NOEtools"], [126, 0, 0, "-", "xpktools"]], "Bio.NMR.NOEtools": [[125, 4, 1, "", "predictNOE"]], "Bio.NMR.xpktools": [[126, 3, 1, "", "Peaklist"], [126, 3, 1, "", "XpkEntry"], [126, 4, 1, "", "data_table"], [126, 4, 1, "", "replace_entry"]], "Bio.NMR.xpktools.Peaklist": [[126, 2, 1, "", "__init__"], [126, 2, 1, "", "residue_dict"], [126, 2, 1, "", "write_header"]], "Bio.NMR.xpktools.XpkEntry": [[126, 2, 1, "", "__init__"]], "Bio.NaiveBayes": [[127, 3, 1, "", "NaiveBayes"], [127, 4, 1, "", "calculate"], [127, 4, 1, "", "classify"], [127, 4, 1, "", "train"]], "Bio.NaiveBayes.NaiveBayes": [[127, 2, 1, "", "__init__"]], "Bio.Nexus": [[129, 0, 0, "-", "Nexus"], [130, 0, 0, "-", "Nodes"], [131, 0, 0, "-", "StandardData"], [132, 0, 0, "-", "Trees"]], "Bio.Nexus.Nexus": [[129, 3, 1, "", "Block"], [129, 3, 1, "", "CharBuffer"], [129, 3, 1, "", "Commandline"], [129, 3, 1, "", "Nexus"], [129, 1, 1, "", "NexusError"], [129, 3, 1, "", "StepMatrix"], [129, 4, 1, "", "combine"], [129, 4, 1, "", "get_start_end"], [129, 4, 1, "", "quotestrip"], [129, 4, 1, "", "safename"]], "Bio.Nexus.Nexus.Block": [[129, 2, 1, "", "__init__"]], "Bio.Nexus.Nexus.CharBuffer": [[129, 2, 1, "", "__init__"], [129, 2, 1, "", "__next__"], [129, 2, 1, "", "next_nonwhitespace"], [129, 2, 1, "", "next_until"], [129, 2, 1, "", "next_word"], [129, 2, 1, "", "peek"], [129, 2, 1, "", "peek_nonwhitespace"], [129, 2, 1, "", "peek_word"], [129, 2, 1, "", "rest"], [129, 2, 1, "", "skip_whitespace"]], "Bio.Nexus.Nexus.Commandline": [[129, 2, 1, "", "__init__"]], "Bio.Nexus.Nexus.Nexus": [[129, 2, 1, "", "__init__"], [129, 2, 1, "", "add_sequence"], [129, 2, 1, "", "append_sets"], [129, 2, 1, "", "bootstrap"], [129, 2, 1, "", "constant"], [129, 2, 1, "", "crop_matrix"], [129, 2, 1, "", "cstatus"], [129, 2, 1, "", "export_fasta"], [129, 2, 1, "", "export_phylip"], [129, 2, 1, "", "gaponly"], [129, 2, 1, "", "insert_gap"], [129, 2, 1, "", "invert"], [129, 2, 1, "", "read"], [129, 2, 1, "", "terminal_gap_to_missing"], [129, 2, 1, "", "weighted_stepmatrix"], [129, 2, 1, "", "write_nexus_data"], [129, 2, 1, "", "write_nexus_data_partitions"]], "Bio.Nexus.Nexus.StepMatrix": [[129, 2, 1, "", "__init__"], [129, 2, 1, "", "add"], [129, 2, 1, "", "set"], [129, 2, 1, "", "smprint"], [129, 2, 1, "", "sum"], [129, 2, 1, "", "transformation"], [129, 2, 1, "", "weighting"]], "Bio.Nexus.Nodes": [[130, 3, 1, "", "Chain"], [130, 1, 1, "", "ChainException"], [130, 3, 1, "", "Node"], [130, 1, 1, "", "NodeException"]], "Bio.Nexus.Nodes.Chain": [[130, 2, 1, "", "__init__"], [130, 2, 1, "", "add"], [130, 2, 1, "", "all_ids"], [130, 2, 1, "", "collapse"], [130, 2, 1, "", "is_parent_of"], [130, 2, 1, "", "kill"], [130, 2, 1, "", "link"], [130, 2, 1, "", "trace"], [130, 2, 1, "", "unlink"]], "Bio.Nexus.Nodes.Node": [[130, 2, 1, "", "__init__"], [130, 2, 1, "", "add_succ"], [130, 2, 1, "", "get_data"], [130, 2, 1, "", "get_id"], [130, 2, 1, "", "get_prev"], [130, 2, 1, "", "get_succ"], [130, 2, 1, "", "remove_succ"], [130, 2, 1, "", "set_data"], [130, 2, 1, "", "set_id"], [130, 2, 1, "", "set_prev"], [130, 2, 1, "", "set_succ"]], "Bio.Nexus.StandardData": [[131, 1, 1, "", "NexusError"], [131, 3, 1, "", "StandardData"]], "Bio.Nexus.StandardData.StandardData": [[131, 2, 1, "", "__getitem__"], [131, 2, 1, "", "__init__"], [131, 2, 1, "", "__iter__"], [131, 2, 1, "", "__len__"], [131, 2, 1, "", "__next__"], [131, 2, 1, "", "__str__"], [131, 2, 1, "", "raw"]], "Bio.Nexus.Trees": [[132, 3, 1, "", "NodeData"], [132, 3, 1, "", "Tree"], [132, 1, 1, "", "TreeError"], [132, 4, 1, "", "consensus"]], "Bio.Nexus.Trees.NodeData": [[132, 2, 1, "", "__init__"]], "Bio.Nexus.Trees.Tree": [[132, 2, 1, "", "__init__"], [132, 2, 1, "", "__str__"], [132, 2, 1, "", "branchlength2support"], [132, 2, 1, "", "collapse_genera"], [132, 2, 1, "", "common_ancestor"], [132, 2, 1, "", "convert_absolute_support"], [132, 2, 1, "", "count_terminals"], [132, 2, 1, "", "display"], [132, 2, 1, "", "distance"], [132, 2, 1, "", "get_taxa"], [132, 2, 1, "", "get_terminals"], [132, 2, 1, "", "has_support"], [132, 2, 1, "", "is_bifurcating"], [132, 2, 1, "", "is_compatible"], [132, 2, 1, "", "is_identical"], [132, 2, 1, "", "is_internal"], [132, 2, 1, "", "is_monophyletic"], [132, 2, 1, "", "is_preterminal"], [132, 2, 1, "", "is_terminal"], [132, 2, 1, "", "merge_with_support"], [132, 2, 1, "", "node"], [132, 2, 1, "", "prune"], [132, 2, 1, "", "randomize"], [132, 2, 1, "", "root_with_outgroup"], [132, 2, 1, "", "search_taxon"], [132, 2, 1, "", "set_subtree"], [132, 2, 1, "", "split"], [132, 2, 1, "", "sum_branchlength"], [132, 2, 1, "", "to_string"], [132, 2, 1, "", "unroot"]], "Bio.PDB": [[134, 0, 0, "-", "AbstractPropertyMap"], [135, 0, 0, "-", "Atom"], [136, 0, 0, "-", "Chain"], [137, 0, 0, "-", "DSSP"], [138, 0, 0, "-", "Dice"], [139, 0, 0, "-", "Entity"], [140, 0, 0, "-", "FragmentMapper"], [141, 0, 0, "-", "HSExposure"], [142, 0, 0, "-", "MMCIF2Dict"], [143, 0, 0, "-", "MMCIFParser"], [144, 0, 0, "-", "Model"], [145, 0, 0, "-", "NACCESS"], [146, 0, 0, "-", "NeighborSearch"], [147, 0, 0, "-", "PDBExceptions"], [148, 0, 0, "-", "PDBIO"], [149, 0, 0, "-", "PDBList"], [150, 0, 0, "-", "PDBMLParser"], [151, 0, 0, "-", "PDBParser"], [152, 0, 0, "-", "PICIO"], [153, 0, 0, "-", "PSEA"], [154, 0, 0, "-", "Polypeptide"], [155, 0, 0, "-", "Residue"], [156, 0, 0, "-", "ResidueDepth"], [157, 0, 0, "-", "SASA"], [158, 0, 0, "-", "SCADIO"], [159, 0, 0, "-", "Selection"], [160, 0, 0, "-", "Structure"], [161, 0, 0, "-", "StructureAlignment"], [162, 0, 0, "-", "StructureBuilder"], [163, 0, 0, "-", "Superimposer"], [164, 0, 0, "-", "alphafold_db"], [165, 0, 0, "-", "binary_cif"], [166, 0, 0, "-", "cealign"], [167, 0, 0, "-", "ic_data"], [168, 0, 0, "-", "ic_rebuild"], [169, 0, 0, "-", "internal_coords"], [170, 0, 0, "-", "mmcifio"], [171, 0, 0, "-", "mmtf"], [174, 0, 0, "-", "parse_pdb_header"], [175, 0, 0, "-", "qcprot"], [176, 0, 0, "-", "vectors"]], "Bio.PDB.AbstractPropertyMap": [[134, 3, 1, "", "AbstractAtomPropertyMap"], [134, 3, 1, "", "AbstractPropertyMap"], [134, 3, 1, "", "AbstractResiduePropertyMap"]], "Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap": [[134, 2, 1, "", "__init__"]], "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap": [[134, 2, 1, "", "__contains__"], [134, 2, 1, "", "__getitem__"], [134, 2, 1, "", "__init__"], [134, 2, 1, "", "__iter__"], [134, 2, 1, "", "__len__"], [134, 2, 1, "", "keys"]], "Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap": [[134, 2, 1, "", "__init__"]], "Bio.PDB.Atom": [[135, 3, 1, "", "Atom"], [135, 3, 1, "", "DisorderedAtom"]], "Bio.PDB.Atom.Atom": [[135, 2, 1, "", "__eq__"], [135, 2, 1, "", "__ge__"], [135, 2, 1, "", "__gt__"], [135, 2, 1, "", "__hash__"], [135, 2, 1, "", "__init__"], [135, 2, 1, "", "__le__"], [135, 2, 1, "", "__lt__"], [135, 2, 1, "", "__ne__"], [135, 2, 1, "", "__repr__"], [135, 2, 1, "", "__sub__"], [135, 2, 1, "", "copy"], [135, 2, 1, "", "detach_parent"], [135, 2, 1, "", "flag_disorder"], [135, 2, 1, "", "get_altloc"], [135, 2, 1, "", "get_anisou"], [135, 2, 1, "", "get_bfactor"], [135, 2, 1, "", "get_charge"], [135, 2, 1, "", "get_coord"], [135, 2, 1, "", "get_full_id"], [135, 2, 1, "", "get_fullname"], [135, 2, 1, "", "get_id"], [135, 2, 1, "", "get_level"], [135, 2, 1, "", "get_name"], [135, 2, 1, "", "get_occupancy"], [135, 2, 1, "", "get_parent"], [135, 2, 1, "", "get_radius"], [135, 2, 1, "", "get_serial_number"], [135, 2, 1, "", "get_sigatm"], [135, 2, 1, "", "get_siguij"], [135, 2, 1, "", "get_vector"], [135, 2, 1, "", "is_disordered"], [135, 2, 1, "", "set_altloc"], [135, 2, 1, "", "set_anisou"], [135, 2, 1, "", "set_bfactor"], [135, 2, 1, "", "set_charge"], [135, 2, 1, "", "set_coord"], [135, 2, 1, "", "set_occupancy"], [135, 2, 1, "", "set_parent"], [135, 2, 1, "", "set_radius"], [135, 2, 1, "", "set_serial_number"], [135, 2, 1, "", "set_sigatm"], [135, 2, 1, "", "set_siguij"], [135, 2, 1, "", "strictly_equals"], [135, 2, 1, "", "transform"]], "Bio.PDB.Atom.DisorderedAtom": [[135, 2, 1, "", "__init__"], [135, 2, 1, "", "__iter__"], [135, 2, 1, "", "__repr__"], [135, 2, 1, "", "center_of_mass"], [135, 2, 1, "", "disordered_add"], [135, 2, 1, "", "disordered_get_list"], [135, 2, 1, "", "disordered_remove"], [135, 2, 1, "", "transform"]], "Bio.PDB.Chain": [[136, 3, 1, "", "Chain"]], "Bio.PDB.Chain.Chain": [[136, 2, 1, "", "__contains__"], [136, 2, 1, "", "__delitem__"], [136, 2, 1, "", "__ge__"], [136, 2, 1, "", "__getitem__"], [136, 2, 1, "", "__gt__"], [136, 2, 1, "", "__init__"], [136, 2, 1, "", "__le__"], [136, 2, 1, "", "__lt__"], [136, 5, 1, "", "__orig_bases__"], [136, 5, 1, "", "__parameters__"], [136, 2, 1, "", "__repr__"], [136, 2, 1, "", "atom_to_internal_coordinates"], [136, 2, 1, "", "get_atoms"], [136, 2, 1, "", "get_residues"], [136, 2, 1, "", "get_unpacked_list"], [136, 2, 1, "", "has_id"], [136, 2, 1, "", "internal_to_atom_coordinates"]], "Bio.PDB.DSSP": [[137, 3, 1, "", "DSSP"], [137, 4, 1, "", "dssp_dict_from_pdb_file"], [137, 4, 1, "", "make_dssp_dict"], [137, 4, 1, "", "ss_to_index"], [137, 4, 1, "", "version"]], "Bio.PDB.DSSP.DSSP": [[137, 2, 1, "", "__init__"]], "Bio.PDB.Dice": [[138, 3, 1, "", "ChainSelector"], [138, 4, 1, "", "extract"]], "Bio.PDB.Dice.ChainSelector": [[138, 2, 1, "", "__init__"], [138, 2, 1, "", "accept_atom"], [138, 2, 1, "", "accept_chain"], [138, 2, 1, "", "accept_model"], [138, 2, 1, "", "accept_residue"]], "Bio.PDB.Entity": [[139, 3, 1, "", "DisorderedEntityWrapper"], [139, 3, 1, "", "Entity"]], "Bio.PDB.Entity.DisorderedEntityWrapper": [[139, 2, 1, "", "__contains__"], [139, 2, 1, "", "__ge__"], [139, 2, 1, "", "__getattr__"], [139, 2, 1, "", "__getitem__"], [139, 2, 1, "", "__gt__"], [139, 2, 1, "", "__init__"], [139, 2, 1, "", "__iter__"], [139, 2, 1, "", "__le__"], [139, 2, 1, "", "__len__"], [139, 2, 1, "", "__lt__"], [139, 2, 1, "", "__setitem__"], [139, 2, 1, "", "__sub__"], [139, 2, 1, "", "copy"], [139, 2, 1, "", "detach_parent"], [139, 2, 1, "", "disordered_add"], [139, 2, 1, "", "disordered_get"], [139, 2, 1, "", "disordered_get_id_list"], [139, 2, 1, "", "disordered_get_list"], [139, 2, 1, "", "disordered_has_id"], [139, 2, 1, "", "disordered_remove"], [139, 2, 1, "", "disordered_select"], [139, 2, 1, "", "get_id"], [139, 2, 1, "", "get_parent"], [139, 2, 1, "", "is_disordered"], [139, 2, 1, "", "set_parent"], [139, 2, 1, "", "strictly_equals"]], "Bio.PDB.Entity.Entity": [[139, 5, 1, "", "__annotations__"], [139, 2, 1, "", "__contains__"], [139, 2, 1, "", "__delitem__"], [139, 2, 1, "", "__eq__"], [139, 2, 1, "", "__ge__"], [139, 2, 1, "", "__getitem__"], [139, 2, 1, "", "__gt__"], [139, 2, 1, "", "__hash__"], [139, 2, 1, "", "__init__"], [139, 2, 1, "", "__iter__"], [139, 2, 1, "", "__le__"], [139, 2, 1, "", "__len__"], [139, 2, 1, "", "__lt__"], [139, 2, 1, "", "__ne__"], [139, 5, 1, "", "__orig_bases__"], [139, 5, 1, "", "__parameters__"], [139, 2, 1, "", "add"], [139, 2, 1, "", "center_of_mass"], [139, 5, 1, "", "child_dict"], [139, 5, 1, "", "child_list"], [139, 2, 1, "", "copy"], [139, 2, 1, "", "detach_child"], [139, 2, 1, "", "detach_parent"], [139, 2, 1, "", "get_full_id"], [139, 2, 1, "", "get_id"], [139, 2, 1, "", "get_iterator"], [139, 2, 1, "", "get_level"], [139, 2, 1, "", "get_list"], [139, 2, 1, "", "get_parent"], [139, 2, 1, "", "has_id"], [139, 6, 1, "", "id"], [139, 2, 1, "", "insert"], [139, 5, 1, "", "level"], [139, 5, 1, "", "parent"], [139, 2, 1, "", "set_parent"], [139, 2, 1, "", "strictly_equals"], [139, 2, 1, "", "transform"]], "Bio.PDB.FragmentMapper": [[140, 3, 1, "", "Fragment"], [140, 3, 1, "", "FragmentMapper"]], "Bio.PDB.FragmentMapper.Fragment": [[140, 2, 1, "", "__init__"], [140, 2, 1, "", "__len__"], [140, 2, 1, "", "__repr__"], [140, 2, 1, "", "__sub__"], [140, 2, 1, "", "add_residue"], [140, 2, 1, "", "get_coords"], [140, 2, 1, "", "get_id"], [140, 2, 1, "", "get_resname_list"]], "Bio.PDB.FragmentMapper.FragmentMapper": [[140, 2, 1, "", "__contains__"], [140, 2, 1, "", "__getitem__"], [140, 2, 1, "", "__init__"]], "Bio.PDB.HSExposure": [[141, 3, 1, "", "ExposureCN"], [141, 3, 1, "", "HSExposureCA"], [141, 3, 1, "", "HSExposureCB"]], "Bio.PDB.HSExposure.ExposureCN": [[141, 2, 1, "", "__init__"]], "Bio.PDB.HSExposure.HSExposureCA": [[141, 2, 1, "", "__init__"], [141, 2, 1, "", "pcb_vectors_pymol"]], "Bio.PDB.HSExposure.HSExposureCB": [[141, 2, 1, "", "__init__"]], "Bio.PDB.MMCIF2Dict": [[142, 3, 1, "", "MMCIF2Dict"]], "Bio.PDB.MMCIF2Dict.MMCIF2Dict": [[142, 2, 1, "", "__init__"]], "Bio.PDB.MMCIFParser": [[143, 3, 1, "", "FastMMCIFParser"], [143, 3, 1, "", "MMCIFParser"]], "Bio.PDB.MMCIFParser.FastMMCIFParser": [[143, 2, 1, "", "__init__"], [143, 2, 1, "", "get_structure"]], "Bio.PDB.MMCIFParser.MMCIFParser": [[143, 2, 1, "", "__init__"], [143, 2, 1, "", "get_structure"]], "Bio.PDB.Model": [[144, 3, 1, "", "Model"]], "Bio.PDB.Model.Model": [[144, 2, 1, "", "__init__"], [144, 5, 1, "", "__orig_bases__"], [144, 5, 1, "", "__parameters__"], [144, 2, 1, "", "__repr__"], [144, 2, 1, "", "atom_to_internal_coordinates"], [144, 2, 1, "", "get_atoms"], [144, 2, 1, "", "get_chains"], [144, 2, 1, "", "get_residues"], [144, 2, 1, "", "internal_to_atom_coordinates"]], "Bio.PDB.NACCESS": [[145, 3, 1, "", "NACCESS"], [145, 3, 1, "", "NACCESS_atomic"], [145, 4, 1, "", "process_asa_data"], [145, 4, 1, "", "process_rsa_data"], [145, 4, 1, "", "run_naccess"]], "Bio.PDB.NACCESS.NACCESS": [[145, 2, 1, "", "__init__"]], "Bio.PDB.NACCESS.NACCESS_atomic": [[145, 2, 1, "", "__init__"]], "Bio.PDB.NeighborSearch": [[146, 3, 1, "", "NeighborSearch"]], "Bio.PDB.NeighborSearch.NeighborSearch": [[146, 2, 1, "", "__init__"], [146, 2, 1, "", "search"], [146, 2, 1, "", "search_all"]], "Bio.PDB.PDBExceptions": [[147, 1, 1, "", "PDBConstructionException"], [147, 1, 1, "", "PDBConstructionWarning"], [147, 1, 1, "", "PDBException"], [147, 1, 1, "", "PDBIOException"]], "Bio.PDB.PDBIO": [[148, 3, 1, "", "PDBIO"], [148, 3, 1, "", "Select"], [148, 3, 1, "", "StructureIO"]], "Bio.PDB.PDBIO.PDBIO": [[148, 2, 1, "", "__init__"], [148, 2, 1, "", "save"]], "Bio.PDB.PDBIO.Select": [[148, 2, 1, "", "__repr__"], [148, 2, 1, "", "accept_atom"], [148, 2, 1, "", "accept_chain"], [148, 2, 1, "", "accept_model"], [148, 2, 1, "", "accept_residue"]], "Bio.PDB.PDBIO.StructureIO": [[148, 2, 1, "", "__init__"], [148, 2, 1, "", "set_structure"]], "Bio.PDB.PDBList": [[149, 3, 1, "", "PDBList"]], "Bio.PDB.PDBList.PDBList": [[149, 5, 1, "", "PDB_REF"], [149, 2, 1, "", "__init__"], [149, 2, 1, "", "download_all_assemblies"], [149, 2, 1, "", "download_entire_pdb"], [149, 2, 1, "", "download_obsolete_entries"], [149, 2, 1, "", "download_pdb_files"], [149, 2, 1, "", "get_all_assemblies"], [149, 2, 1, "", "get_all_entries"], [149, 2, 1, "", "get_all_obsolete"], [149, 2, 1, "", "get_recent_changes"], [149, 2, 1, "", "get_seqres_file"], [149, 2, 1, "", "get_status_list"], [149, 2, 1, "", "retrieve_assembly_file"], [149, 2, 1, "", "retrieve_pdb_file"], [149, 2, 1, "", "update_pdb"]], "Bio.PDB.PDBMLParser": [[150, 3, 1, "", "PDBMLParser"]], "Bio.PDB.PDBMLParser.PDBMLParser": [[150, 2, 1, "", "__init__"], [150, 2, 1, "", "get_structure"]], "Bio.PDB.PDBParser": [[151, 3, 1, "", "PDBParser"]], "Bio.PDB.PDBParser.PDBParser": [[151, 2, 1, "", "__init__"], [151, 2, 1, "", "get_header"], [151, 2, 1, "", "get_structure"], [151, 2, 1, "", "get_trailer"]], "Bio.PDB.PICIO": [[152, 4, 1, "", "enumerate_atoms"], [152, 4, 1, "", "pdb_date"], [152, 4, 1, "", "read_PIC"], [152, 4, 1, "", "read_PIC_seq"], [152, 4, 1, "", "write_PIC"]], "Bio.PDB.PSEA": [[153, 3, 1, "", "PSEA"], [153, 4, 1, "", "annotate"], [153, 4, 1, "", "psea"], [153, 4, 1, "", "psea2HEC"], [153, 4, 1, "", "run_psea"]], "Bio.PDB.PSEA.PSEA": [[153, 2, 1, "", "__init__"], [153, 2, 1, "", "get_seq"]], "Bio.PDB.Polypeptide": [[154, 3, 1, "", "CaPPBuilder"], [154, 3, 1, "", "PPBuilder"], [154, 3, 1, "", "Polypeptide"], [154, 4, 1, "", "index_to_one"], [154, 4, 1, "", "index_to_three"], [154, 4, 1, "", "is_aa"], [154, 4, 1, "", "is_nucleic"], [154, 4, 1, "", "one_to_index"], [154, 4, 1, "", "three_to_index"]], "Bio.PDB.Polypeptide.CaPPBuilder": [[154, 2, 1, "", "__init__"]], "Bio.PDB.Polypeptide.PPBuilder": [[154, 2, 1, "", "__init__"]], "Bio.PDB.Polypeptide.Polypeptide": [[154, 2, 1, "", "__repr__"], [154, 2, 1, "", "get_ca_list"], [154, 2, 1, "", "get_phi_psi_list"], [154, 2, 1, "", "get_sequence"], [154, 2, 1, "", "get_tau_list"], [154, 2, 1, "", "get_theta_list"]], "Bio.PDB.Residue": [[155, 3, 1, "", "DisorderedResidue"], [155, 3, 1, "", "Residue"]], "Bio.PDB.Residue.DisorderedResidue": [[155, 2, 1, "", "__init__"], [155, 2, 1, "", "__repr__"], [155, 2, 1, "", "add"], [155, 2, 1, "", "disordered_add"], [155, 2, 1, "", "disordered_remove"], [155, 2, 1, "", "sort"]], "Bio.PDB.Residue.Residue": [[155, 2, 1, "", "__init__"], [155, 5, 1, "", "__orig_bases__"], [155, 5, 1, "", "__parameters__"], [155, 2, 1, "", "__repr__"], [155, 2, 1, "", "add"], [155, 2, 1, "", "flag_disordered"], [155, 2, 1, "", "get_atoms"], [155, 2, 1, "", "get_resname"], [155, 2, 1, "", "get_segid"], [155, 2, 1, "", "get_unpacked_list"], [155, 2, 1, "", "is_disordered"], [155, 2, 1, "", "strictly_equals"]], "Bio.PDB.ResidueDepth": [[156, 3, 1, "", "ResidueDepth"], [156, 4, 1, "", "ca_depth"], [156, 4, 1, "", "get_surface"], [156, 4, 1, "", "min_dist"], [156, 4, 1, "", "residue_depth"]], "Bio.PDB.ResidueDepth.ResidueDepth": [[156, 2, 1, "", "__init__"]], "Bio.PDB.SASA": [[157, 3, 1, "", "ShrakeRupley"]], "Bio.PDB.SASA.ShrakeRupley": [[157, 2, 1, "", "__init__"], [157, 2, 1, "", "compute"]], "Bio.PDB.SCADIO": [[158, 4, 1, "", "write_SCAD"]], "Bio.PDB.Selection": [[159, 4, 1, "", "get_unique_parents"], [159, 4, 1, "", "unfold_entities"], [159, 4, 1, "", "uniqueify"]], "Bio.PDB.Structure": [[160, 3, 1, "", "Structure"]], "Bio.PDB.Structure.Structure": [[160, 2, 1, "", "__init__"], [160, 5, 1, "", "__orig_bases__"], [160, 5, 1, "", "__parameters__"], [160, 2, 1, "", "__repr__"], [160, 2, 1, "", "atom_to_internal_coordinates"], [160, 2, 1, "", "get_atoms"], [160, 2, 1, "", "get_chains"], [160, 2, 1, "", "get_models"], [160, 2, 1, "", "get_residues"], [160, 2, 1, "", "internal_to_atom_coordinates"]], "Bio.PDB.StructureAlignment": [[161, 3, 1, "", "StructureAlignment"]], "Bio.PDB.StructureAlignment.StructureAlignment": [[161, 2, 1, "", "__init__"], [161, 2, 1, "", "get_iterator"], [161, 2, 1, "", "get_maps"]], "Bio.PDB.StructureBuilder": [[162, 3, 1, "", "StructureBuilder"]], "Bio.PDB.StructureBuilder.StructureBuilder": [[162, 2, 1, "", "__init__"], [162, 2, 1, "", "get_structure"], [162, 2, 1, "", "init_atom"], [162, 2, 1, "", "init_chain"], [162, 2, 1, "", "init_model"], [162, 2, 1, "", "init_residue"], [162, 2, 1, "", "init_seg"], [162, 2, 1, "", "init_structure"], [162, 2, 1, "", "set_anisou"], [162, 2, 1, "", "set_header"], [162, 2, 1, "", "set_line_counter"], [162, 2, 1, "", "set_sigatm"], [162, 2, 1, "", "set_siguij"], [162, 2, 1, "", "set_symmetry"]], "Bio.PDB.Superimposer": [[163, 3, 1, "", "Superimposer"]], "Bio.PDB.Superimposer.Superimposer": [[163, 2, 1, "", "__init__"], [163, 2, 1, "", "apply"], [163, 2, 1, "", "set_atoms"]], "Bio.PDB.alphafold_db": [[164, 4, 1, "", "download_cif_for"], [164, 4, 1, "", "get_predictions"], [164, 4, 1, "", "get_structural_models_for"]], "Bio.PDB.binary_cif": [[165, 3, 1, "", "BinaryCIFParser"]], "Bio.PDB.binary_cif.BinaryCIFParser": [[165, 2, 1, "", "__init__"], [165, 2, 1, "", "get_structure"]], "Bio.PDB.cealign": [[166, 3, 1, "", "CEAligner"]], "Bio.PDB.cealign.CEAligner": [[166, 2, 1, "", "__init__"], [166, 2, 1, "", "align"], [166, 2, 1, "", "get_guide_coord_from_structure"], [166, 2, 1, "", "set_reference"]], "Bio.PDB.ic_rebuild": [[168, 4, 1, "", "IC_duplicate"], [168, 4, 1, "", "compare_residues"], [168, 4, 1, "", "report_IC"], [168, 4, 1, "", "structure_rebuild_test"], [168, 4, 1, "", "write_PDB"]], "Bio.PDB.internal_coords": [[169, 3, 1, "", "AtomKey"], [169, 3, 1, "", "Dihedron"], [169, 3, 1, "", "Edron"], [169, 3, 1, "", "Hedron"], [169, 1, 1, "", "HedronMatchError"], [169, 3, 1, "", "IC_Chain"], [169, 3, 1, "", "IC_Residue"], [169, 1, 1, "", "MissingAtomError"], [169, 4, 1, "", "set_accuracy_95"]], "Bio.PDB.internal_coords.AtomKey": [[169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__eq__"], [169, 2, 1, "", "__ge__"], [169, 2, 1, "", "__gt__"], [169, 2, 1, "", "__hash__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "__le__"], [169, 2, 1, "", "__lt__"], [169, 2, 1, "", "__ne__"], [169, 2, 1, "", "__repr__"], [169, 2, 1, "", "altloc_match"], [169, 2, 1, "", "atm"], [169, 5, 1, "", "atom_re"], [169, 2, 1, "", "cr_class"], [169, 5, 1, "", "d2h"], [169, 5, 1, "", "fieldNames"], [169, 5, 1, "", "fields"], [169, 2, 1, "", "is_backbone"]], "Bio.PDB.internal_coords.Dihedron": [[169, 2, 1, "", "__init__"], [169, 2, 1, "", "__repr__"], [169, 6, 1, "", "angle"], [169, 2, 1, "", "angle_avg"], [169, 2, 1, "", "angle_dif"], [169, 2, 1, "", "angle_pop_sd"], [169, 2, 1, "", "bits"], [169, 2, 1, "", "difference"]], "Bio.PDB.internal_coords.Edron": [[169, 2, 1, "", "__contains__"], [169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__eq__"], [169, 2, 1, "", "__ge__"], [169, 2, 1, "", "__gt__"], [169, 2, 1, "", "__hash__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "__le__"], [169, 2, 1, "", "__lt__"], [169, 2, 1, "", "__ne__"], [169, 2, 1, "", "__repr__"], [169, 5, 1, "", "edron_re"], [169, 2, 1, "", "gen_key"], [169, 2, 1, "", "gen_tuple"], [169, 2, 1, "", "is_backbone"]], "Bio.PDB.internal_coords.Hedron": [[169, 2, 1, "", "__init__"], [169, 2, 1, "", "__repr__"], [169, 6, 1, "", "angle"], [169, 2, 1, "", "get_length"], [169, 6, 1, "", "len12"], [169, 6, 1, "", "len23"], [169, 2, 1, "", "set_length"]], "Bio.PDB.internal_coords.IC_Chain": [[169, 5, 1, "", "AAsiz"], [169, 5, 1, "", "MaxPeptideBond"], [169, 5, 1, "", "ParallelAssembleResidues"], [169, 5, 1, "", "__annotations__"], [169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "assemble_residues"], [169, 2, 1, "", "assemble_residues_ser"], [169, 5, 1, "", "atomArray"], [169, 2, 1, "", "atom_to_internal_coordinates"], [169, 2, 1, "", "build_atomArray"], [169, 2, 1, "", "build_edraArrays"], [169, 2, 1, "", "clear_ic"], [169, 2, 1, "", "copy_initNCaCs"], [169, 5, 1, "", "dCoordSpace"], [169, 5, 1, "", "dcsValid"], [169, 2, 1, "", "dihedral_signs"], [169, 2, 1, "", "distance_plot"], [169, 2, 1, "", "distance_to_internal_coordinates"], [169, 2, 1, "", "distplot_to_dh_arrays"], [169, 2, 1, "", "init_atom_coords"], [169, 2, 1, "", "init_edra"], [169, 2, 1, "", "internal_to_atom_coordinates"], [169, 2, 1, "", "make_extended"], [169, 2, 1, "", "propagate_changes"], [169, 2, 1, "", "update_dCoordSpace"]], "Bio.PDB.internal_coords.IC_Residue": [[169, 5, 1, "", "__annotations__"], [169, 2, 1, "", "__contains__"], [169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "__repr__"], [169, 5, 1, "", "accept_atoms"], [169, 5, 1, "", "accept_backbone"], [169, 5, 1, "", "accept_deuteriums"], [169, 5, 1, "", "accept_hydrogens"], [169, 5, 1, "", "accept_mainchain"], [169, 5, 1, "", "accept_resnames"], [169, 5, 1, "", "accept_sidechain"], [169, 2, 1, "", "applyMtx"], [169, 2, 1, "", "assemble"], [169, 5, 1, "", "atom_chain"], [169, 5, 1, "", "atom_sernum"], [169, 2, 1, "", "bond_rotate"], [169, 2, 1, "", "bond_set"], [169, 2, 1, "", "clear_transforms"], [169, 2, 1, "", "get_angle"], [169, 2, 1, "", "get_length"], [169, 5, 1, "", "gly_Cbeta"], [169, 5, 1, "", "no_altloc"], [169, 2, 1, "", "pdb_residue_string"], [169, 5, 1, "", "picFlagsDefault"], [169, 5, 1, "", "picFlagsDict"], [169, 5, 1, "", "pic_accuracy"], [169, 5, 1, "", "pic_flags"], [169, 2, 1, "", "pick_angle"], [169, 2, 1, "", "pick_length"], [169, 2, 1, "", "pretty_str"], [169, 2, 1, "", "rak"], [169, 2, 1, "", "set_angle"], [169, 2, 1, "", "set_flexible"], [169, 2, 1, "", "set_hbond"], [169, 2, 1, "", "set_length"], [169, 2, 1, "", "split_akl"]], "Bio.PDB.mmcifio": [[170, 3, 1, "", "MMCIFIO"]], "Bio.PDB.mmcifio.MMCIFIO": [[170, 2, 1, "", "__init__"], [170, 2, 1, "", "save"], [170, 2, 1, "", "set_dict"]], "Bio.PDB.mmtf": [[172, 0, 0, "-", "DefaultParser"], [171, 3, 1, "", "MMTFParser"], [171, 4, 1, "", "get_from_decoded"], [173, 0, 0, "-", "mmtfio"]], "Bio.PDB.mmtf.DefaultParser": [[172, 3, 1, "", "StructureDecoder"]], "Bio.PDB.mmtf.DefaultParser.StructureDecoder": [[172, 2, 1, "", "__init__"], [172, 2, 1, "", "finalize_structure"], [172, 2, 1, "", "init_structure"], [172, 2, 1, "", "set_atom_info"], [172, 2, 1, "", "set_bio_assembly_trans"], [172, 2, 1, "", "set_chain_info"], [172, 2, 1, "", "set_entity_info"], [172, 2, 1, "", "set_group_bond"], [172, 2, 1, "", "set_group_info"], [172, 2, 1, "", "set_header_info"], [172, 2, 1, "", "set_inter_group_bond"], [172, 2, 1, "", "set_model_info"], [172, 2, 1, "", "set_xtal_info"]], "Bio.PDB.mmtf.MMTFParser": [[171, 2, 1, "", "get_structure"], [171, 2, 1, "", "get_structure_from_url"]], "Bio.PDB.mmtf.mmtfio": [[173, 3, 1, "", "MMTFIO"]], "Bio.PDB.mmtf.mmtfio.MMTFIO": [[173, 2, 1, "", "__init__"], [173, 2, 1, "", "save"]], "Bio.PDB.parse_pdb_header": [[174, 4, 1, "", "parse_pdb_header"]], "Bio.PDB.qcprot": [[175, 3, 1, "", "QCPSuperimposer"], [175, 4, 1, "", "qcp"]], "Bio.PDB.qcprot.QCPSuperimposer": [[175, 2, 1, "", "__init__"], [175, 2, 1, "", "apply"], [175, 2, 1, "", "get_init_rms"], [175, 2, 1, "", "get_rms"], [175, 2, 1, "", "get_rotran"], [175, 2, 1, "", "get_transformed"], [175, 2, 1, "", "run"], [175, 2, 1, "", "set"], [175, 2, 1, "", "set_atoms"]], "Bio.PDB.vectors": [[176, 3, 1, "", "Vector"], [176, 4, 1, "", "calc_angle"], [176, 4, 1, "", "calc_dihedral"], [176, 4, 1, "", "coord_space"], [176, 4, 1, "", "get_spherical_coordinates"], [176, 4, 1, "", "homog_rot_mtx"], [176, 4, 1, "", "homog_scale_mtx"], [176, 4, 1, "", "homog_trans_mtx"], [176, 4, 1, "", "m2rotaxis"], [176, 4, 1, "", "multi_coord_space"], [176, 4, 1, "", "multi_rot_Y"], [176, 4, 1, "", "multi_rot_Z"], [176, 4, 1, "", "refmat"], [176, 4, 1, "", "rotaxis"], [176, 4, 1, "", "rotaxis2m"], [176, 4, 1, "", "rotmat"], [176, 4, 1, "", "set_X_homog_rot_mtx"], [176, 4, 1, "", "set_Y_homog_rot_mtx"], [176, 4, 1, "", "set_Z_homog_rot_mtx"], [176, 4, 1, "", "set_homog_trans_mtx"], [176, 4, 1, "", "vector_to_axis"]], "Bio.PDB.vectors.Vector": [[176, 2, 1, "", "__add__"], [176, 2, 1, "", "__contains__"], [176, 2, 1, "", "__getitem__"], [176, 2, 1, "", "__init__"], [176, 2, 1, "", "__mul__"], [176, 2, 1, "", "__neg__"], [176, 2, 1, "", "__pow__"], [176, 2, 1, "", "__repr__"], [176, 2, 1, "", "__setitem__"], [176, 2, 1, "", "__sub__"], [176, 2, 1, "", "__truediv__"], [176, 2, 1, "", "angle"], [176, 2, 1, "", "copy"], [176, 2, 1, "", "get_array"], [176, 2, 1, "", "left_multiply"], [176, 2, 1, "", "norm"], [176, 2, 1, "", "normalize"], [176, 2, 1, "", "normalized"], [176, 2, 1, "", "normsq"], [176, 2, 1, "", "right_multiply"]], "Bio.Pathway": [[177, 3, 1, "", "Interaction"], [177, 3, 1, "", "Network"], [177, 3, 1, "", "Reaction"], [178, 0, 0, "-", "Rep"], [177, 3, 1, "", "System"]], "Bio.Pathway.Interaction": [[177, 2, 1, "", "__hash__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"]], "Bio.Pathway.Network": [[177, 2, 1, "", "__init__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"], [177, 2, 1, "", "add_interaction"], [177, 2, 1, "", "add_species"], [177, 2, 1, "", "interactions"], [177, 2, 1, "", "sink"], [177, 2, 1, "", "sink_interactions"], [177, 2, 1, "", "source"], [177, 2, 1, "", "source_interactions"], [177, 2, 1, "", "species"]], "Bio.Pathway.Reaction": [[177, 2, 1, "", "__eq__"], [177, 2, 1, "", "__hash__"], [177, 2, 1, "", "__init__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"], [177, 2, 1, "", "reverse"], [177, 2, 1, "", "species"]], "Bio.Pathway.Rep": [[179, 0, 0, "-", "Graph"], [180, 0, 0, "-", "MultiGraph"]], "Bio.Pathway.Rep.Graph": [[179, 3, 1, "", "Graph"]], "Bio.Pathway.Rep.Graph.Graph": [[179, 2, 1, "", "__eq__"], [179, 5, 1, "", "__hash__"], [179, 2, 1, "", "__init__"], [179, 2, 1, "", "__repr__"], [179, 2, 1, "", "__str__"], [179, 2, 1, "", "add_edge"], [179, 2, 1, "", "add_node"], [179, 2, 1, "", "child_edges"], [179, 2, 1, "", "children"], [179, 2, 1, "", "edges"], [179, 2, 1, "", "labels"], [179, 2, 1, "", "nodes"], [179, 2, 1, "", "parent_edges"], [179, 2, 1, "", "parents"], [179, 2, 1, "", "remove_edge"], [179, 2, 1, "", "remove_node"]], "Bio.Pathway.Rep.MultiGraph": [[180, 3, 1, "", "MultiGraph"], [180, 4, 1, "", "bf_search"], [180, 4, 1, "", "df_search"]], "Bio.Pathway.Rep.MultiGraph.MultiGraph": [[180, 2, 1, "", "__eq__"], [180, 5, 1, "", "__hash__"], [180, 2, 1, "", "__init__"], [180, 2, 1, "", "__repr__"], [180, 2, 1, "", "__str__"], [180, 2, 1, "", "add_edge"], [180, 2, 1, "", "add_node"], [180, 2, 1, "", "child_edges"], [180, 2, 1, "", "children"], [180, 2, 1, "", "edges"], [180, 2, 1, "", "labels"], [180, 2, 1, "", "nodes"], [180, 2, 1, "", "parent_edges"], [180, 2, 1, "", "parents"], [180, 2, 1, "", "remove_edge"], [180, 2, 1, "", "remove_node"]], "Bio.Pathway.System": [[177, 2, 1, "", "__init__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"], [177, 2, 1, "", "add_reaction"], [177, 2, 1, "", "reactions"], [177, 2, 1, "", "remove_reaction"], [177, 2, 1, "", "species"], [177, 2, 1, "", "stochiometry"]], "Bio.Phylo": [[182, 0, 0, "-", "Applications"], [183, 0, 0, "-", "BaseTree"], [184, 0, 0, "-", "CDAO"], [185, 0, 0, "-", "CDAOIO"], [186, 0, 0, "-", "Consensus"], [187, 0, 0, "-", "NeXML"], [188, 0, 0, "-", "NeXMLIO"], [189, 0, 0, "-", "Newick"], [190, 0, 0, "-", "NewickIO"], [191, 0, 0, "-", "NexusIO"], [192, 0, 0, "-", "PAML"], [197, 0, 0, "-", "PhyloXML"], [198, 0, 0, "-", "PhyloXMLIO"], [199, 0, 0, "-", "TreeConstruction"]], "Bio.Phylo.Applications": [[182, 3, 1, "", "FastTreeCommandline"], [182, 3, 1, "", "PhymlCommandline"], [182, 3, 1, "", "RaxmlCommandline"]], "Bio.Phylo.Applications.FastTreeCommandline": [[182, 2, 1, "", "__init__"], [182, 6, 1, "", "bionj"], [182, 6, 1, "", "boot"], [182, 6, 1, "", "cat"], [182, 6, 1, "", "close"], [182, 6, 1, "", "constraintWeight"], [182, 6, 1, "", "constraints"], [182, 6, 1, "", "expert"], [182, 6, 1, "", "fastest"], [182, 6, 1, "", "gamma"], [182, 6, 1, "", "gtr"], [182, 6, 1, "", "gtrfreq"], [182, 6, 1, "", "gtrrates"], [182, 6, 1, "", "help"], [182, 6, 1, "", "input"], [182, 6, 1, "", "intree"], [182, 6, 1, "", "intree1"], [182, 6, 1, "", "log"], [182, 6, 1, "", "makematrix"], [182, 6, 1, "", "matrix"], [182, 6, 1, "", "mlacc"], [182, 6, 1, "", "mllen"], [182, 6, 1, "", "mlnni"], [182, 6, 1, "", "n"], [182, 6, 1, "", "nj"], [182, 6, 1, "", "nni"], [182, 6, 1, "", "no2nd"], [182, 6, 1, "", "nocat"], [182, 6, 1, "", "nomatrix"], [182, 6, 1, "", "nome"], [182, 6, 1, "", "noml"], [182, 6, 1, "", "nopr"], [182, 6, 1, "", "nosupport"], [182, 6, 1, "", "notop"], [182, 6, 1, "", "nt"], [182, 6, 1, "", "out"], [182, 6, 1, "", "pseudo"], [182, 6, 1, "", "quiet"], [182, 6, 1, "", "quote"], [182, 6, 1, "", "rawdist"], [182, 6, 1, "", "refresh"], [182, 6, 1, "", "second"], [182, 6, 1, "", "seed"], [182, 6, 1, "", "slow"], [182, 6, 1, "", "slownni"], [182, 6, 1, "", "spr"], [182, 6, 1, "", "sprlength"], [182, 6, 1, "", "top"], [182, 6, 1, "", "topm"], [182, 6, 1, "", "wag"]], "Bio.Phylo.Applications.PhymlCommandline": [[182, 2, 1, "", "__init__"], [182, 6, 1, "", "alpha"], [182, 6, 1, "", "bootstrap"], [182, 6, 1, "", "datatype"], [182, 6, 1, "", "frequencies"], [182, 6, 1, "", "input"], [182, 6, 1, "", "input_tree"], [182, 6, 1, "", "model"], [182, 6, 1, "", "multiple"], [182, 6, 1, "", "n_rand_starts"], [182, 6, 1, "", "nclasses"], [182, 6, 1, "", "optimize"], [182, 6, 1, "", "pars"], [182, 6, 1, "", "print_site_lnl"], [182, 6, 1, "", "print_trace"], [182, 6, 1, "", "prop_invar"], [182, 6, 1, "", "quiet"], [182, 6, 1, "", "r_seed"], [182, 6, 1, "", "rand_start"], [182, 6, 1, "", "run_id"], [182, 6, 1, "", "search"], [182, 6, 1, "", "sequential"], [182, 6, 1, "", "ts_tv_ratio"]], "Bio.Phylo.Applications.RaxmlCommandline": [[182, 2, 1, "", "__init__"], [182, 6, 1, "", "algorithm"], [182, 6, 1, "", "binary_constraint"], [182, 6, 1, "", "bipartition_filename"], [182, 6, 1, "", "bootstrap_branch_lengths"], [182, 6, 1, "", "bootstrap_seed"], [182, 6, 1, "", "checkpoints"], [182, 6, 1, "", "cluster_threshold"], [182, 6, 1, "", "cluster_threshold_fast"], [182, 6, 1, "", "epsilon"], [182, 6, 1, "", "exclude_filename"], [182, 6, 1, "", "grouping_constraint"], [182, 6, 1, "", "model"], [182, 6, 1, "", "name"], [182, 6, 1, "", "num_bootstrap_searches"], [182, 6, 1, "", "num_categories"], [182, 6, 1, "", "num_replicates"], [182, 6, 1, "", "outgroup"], [182, 6, 1, "", "parsimony"], [182, 6, 1, "", "parsimony_seed"], [182, 6, 1, "", "partition_branch_lengths"], [182, 6, 1, "", "partition_filename"], [182, 6, 1, "", "protein_model"], [182, 6, 1, "", "random_starting_tree"], [182, 6, 1, "", "rapid_bootstrap_seed"], [182, 6, 1, "", "rearrangements"], [182, 6, 1, "", "sequences"], [182, 6, 1, "", "starting_tree"], [182, 6, 1, "", "threads"], [182, 6, 1, "", "version"], [182, 6, 1, "", "weight_filename"], [182, 6, 1, "", "working_dir"]], "Bio.Phylo.BaseTree": [[183, 3, 1, "", "BranchColor"], [183, 3, 1, "", "Clade"], [183, 3, 1, "", "Tree"], [183, 3, 1, "", "TreeElement"], [183, 3, 1, "", "TreeMixin"]], "Bio.Phylo.BaseTree.BranchColor": [[183, 2, 1, "", "__init__"], [183, 2, 1, "", "__repr__"], [183, 2, 1, "", "__str__"], [183, 5, 1, "", "color_names"], [183, 2, 1, "", "from_hex"], [183, 2, 1, "", "from_name"], [183, 2, 1, "", "to_hex"], [183, 2, 1, "", "to_rgb"]], "Bio.Phylo.BaseTree.Clade": [[183, 2, 1, "", "__bool__"], [183, 2, 1, "", "__getitem__"], [183, 2, 1, "", "__init__"], [183, 2, 1, "", "__iter__"], [183, 2, 1, "", "__len__"], [183, 2, 1, "", "__str__"], [183, 6, 1, "", "color"], [183, 2, 1, "", "is_terminal"], [183, 6, 1, "", "root"]], "Bio.Phylo.BaseTree.Tree": [[183, 2, 1, "", "__format__"], [183, 2, 1, "", "__init__"], [183, 2, 1, "", "__str__"], [183, 2, 1, "", "as_phyloxml"], [183, 6, 1, "", "clade"], [183, 2, 1, "", "format"], [183, 2, 1, "", "from_clade"], [183, 2, 1, "", "is_terminal"], [183, 2, 1, "", "randomized"], [183, 2, 1, "", "root_at_midpoint"], [183, 2, 1, "", "root_with_outgroup"]], "Bio.Phylo.BaseTree.TreeElement": [[183, 2, 1, "", "__repr__"], [183, 2, 1, "", "__str__"]], "Bio.Phylo.BaseTree.TreeMixin": [[183, 2, 1, "", "collapse"], [183, 2, 1, "", "collapse_all"], [183, 2, 1, "", "common_ancestor"], [183, 2, 1, "", "count_terminals"], [183, 2, 1, "", "depths"], [183, 2, 1, "", "distance"], [183, 2, 1, "", "find_any"], [183, 2, 1, "", "find_clades"], [183, 2, 1, "", "find_elements"], [183, 2, 1, "", "get_nonterminals"], [183, 2, 1, "", "get_path"], [183, 2, 1, "", "get_terminals"], [183, 2, 1, "", "is_bifurcating"], [183, 2, 1, "", "is_monophyletic"], [183, 2, 1, "", "is_parent_of"], [183, 2, 1, "", "is_preterminal"], [183, 2, 1, "", "ladderize"], [183, 2, 1, "", "prune"], [183, 2, 1, "", "split"], [183, 2, 1, "", "total_branch_length"], [183, 2, 1, "", "trace"]], "Bio.Phylo.CDAO": [[184, 3, 1, "", "Clade"], [184, 3, 1, "", "Tree"]], "Bio.Phylo.CDAO.Clade": [[184, 2, 1, "", "__init__"]], "Bio.Phylo.CDAO.Tree": [[184, 2, 1, "", "__init__"]], "Bio.Phylo.CDAOIO": [[185, 3, 1, "", "Parser"], [185, 3, 1, "", "Writer"], [185, 4, 1, "", "format_label"], [185, 4, 1, "", "parse"], [185, 4, 1, "", "qUri"], [185, 4, 1, "", "write"]], "Bio.Phylo.CDAOIO.Parser": [[185, 2, 1, "", "__init__"], [185, 2, 1, "", "from_string"], [185, 2, 1, "", "get_node_info"], [185, 2, 1, "", "new_clade"], [185, 2, 1, "", "parse"], [185, 2, 1, "", "parse_children"], [185, 2, 1, "", "parse_graph"], [185, 2, 1, "", "parse_handle_to_graph"]], "Bio.Phylo.CDAOIO.Writer": [[185, 2, 1, "", "__init__"], [185, 2, 1, "", "add_stmt_to_handle"], [185, 5, 1, "", "prefixes"], [185, 2, 1, "", "process_clade"], [185, 2, 1, "", "write"]], "Bio.Phylo.Consensus": [[186, 4, 1, "", "adam_consensus"], [186, 4, 1, "", "bootstrap"], [186, 4, 1, "", "bootstrap_consensus"], [186, 4, 1, "", "bootstrap_trees"], [186, 4, 1, "", "get_support"], [186, 4, 1, "", "majority_consensus"], [186, 4, 1, "", "strict_consensus"]], "Bio.Phylo.NeXML": [[187, 3, 1, "", "Clade"], [187, 3, 1, "", "Tree"]], "Bio.Phylo.NeXML.Clade": [[187, 2, 1, "", "__init__"]], "Bio.Phylo.NeXML.Tree": [[187, 2, 1, "", "__init__"]], "Bio.Phylo.NeXMLIO": [[188, 1, 1, "", "NeXMLError"], [188, 3, 1, "", "Parser"], [188, 3, 1, "", "Writer"], [188, 4, 1, "", "cdao_to_obo"], [188, 4, 1, "", "matches"], [188, 4, 1, "", "parse"], [188, 4, 1, "", "qUri"], [188, 4, 1, "", "write"]], "Bio.Phylo.NeXMLIO.Parser": [[188, 2, 1, "", "__init__"], [188, 2, 1, "", "add_annotation"], [188, 2, 1, "", "from_string"], [188, 2, 1, "", "parse"]], "Bio.Phylo.NeXMLIO.Writer": [[188, 2, 1, "", "__init__"], [188, 2, 1, "", "new_label"], [188, 2, 1, "", "write"]], "Bio.Phylo.Newick": [[189, 3, 1, "", "Clade"], [189, 3, 1, "", "Tree"]], "Bio.Phylo.Newick.Clade": [[189, 2, 1, "", "__init__"]], "Bio.Phylo.Newick.Tree": [[189, 2, 1, "", "__init__"]], "Bio.Phylo.NewickIO": [[190, 1, 1, "", "NewickError"], [190, 3, 1, "", "Parser"], [190, 3, 1, "", "Writer"], [190, 4, 1, "", "parse"], [190, 4, 1, "", "write"]], "Bio.Phylo.NewickIO.Parser": [[190, 2, 1, "", "__init__"], [190, 2, 1, "", "from_string"], [190, 2, 1, "", "new_clade"], [190, 2, 1, "", "parse"], [190, 2, 1, "", "process_clade"]], "Bio.Phylo.NewickIO.Writer": [[190, 2, 1, "", "__init__"], [190, 2, 1, "", "to_strings"], [190, 2, 1, "", "write"]], "Bio.Phylo.NexusIO": [[191, 4, 1, "", "parse"], [191, 4, 1, "", "write"]], "Bio.Phylo.PAML": [[193, 0, 0, "-", "baseml"], [194, 0, 0, "-", "chi2"], [195, 0, 0, "-", "codeml"], [196, 0, 0, "-", "yn00"]], "Bio.Phylo.PAML.baseml": [[193, 3, 1, "", "Baseml"], [193, 1, 1, "", "BasemlError"], [193, 4, 1, "", "read"]], "Bio.Phylo.PAML.baseml.Baseml": [[193, 2, 1, "", "__init__"], [193, 2, 1, "", "read_ctl_file"], [193, 2, 1, "", "run"], [193, 2, 1, "", "write_ctl_file"]], "Bio.Phylo.PAML.chi2": [[194, 4, 1, "", "cdf_chi2"]], "Bio.Phylo.PAML.codeml": [[195, 3, 1, "", "Codeml"], [195, 1, 1, "", "CodemlError"], [195, 4, 1, "", "read"]], "Bio.Phylo.PAML.codeml.Codeml": [[195, 2, 1, "", "__init__"], [195, 2, 1, "", "print_options"], [195, 2, 1, "", "read_ctl_file"], [195, 2, 1, "", "run"], [195, 2, 1, "", "write_ctl_file"]], "Bio.Phylo.PAML.yn00": [[196, 3, 1, "", "Yn00"], [196, 1, 1, "", "Yn00Error"], [196, 4, 1, "", "read"]], "Bio.Phylo.PAML.yn00.Yn00": [[196, 2, 1, "", "__init__"], [196, 2, 1, "", "read_ctl_file"], [196, 2, 1, "", "run"], [196, 2, 1, "", "write_ctl_file"]], "Bio.Phylo.PhyloXML": [[197, 3, 1, "", "Accession"], [197, 3, 1, "", "Annotation"], [197, 3, 1, "", "BinaryCharacters"], [197, 3, 1, "", "BranchColor"], [197, 3, 1, "", "Clade"], [197, 3, 1, "", "CladeRelation"], [197, 3, 1, "", "Confidence"], [197, 3, 1, "", "Date"], [197, 3, 1, "", "Distribution"], [197, 3, 1, "", "DomainArchitecture"], [197, 3, 1, "", "Events"], [197, 3, 1, "", "Id"], [197, 3, 1, "", "MolSeq"], [197, 3, 1, "", "Other"], [197, 3, 1, "", "PhyloElement"], [197, 1, 1, "", "PhyloXMLWarning"], [197, 3, 1, "", "Phylogeny"], [197, 3, 1, "", "Phyloxml"], [197, 3, 1, "", "Point"], [197, 3, 1, "", "Polygon"], [197, 3, 1, "", "Property"], [197, 3, 1, "", "ProteinDomain"], [197, 3, 1, "", "Reference"], [197, 3, 1, "", "Sequence"], [197, 3, 1, "", "SequenceRelation"], [197, 3, 1, "", "Taxonomy"], [197, 3, 1, "", "Uri"]], "Bio.Phylo.PhyloXML.Accession": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Annotation": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "re_ref"]], "Bio.Phylo.PhyloXML.BinaryCharacters": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.BranchColor": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Clade": [[197, 2, 1, "", "__init__"], [197, 6, 1, "", "confidence"], [197, 2, 1, "", "from_clade"], [197, 6, 1, "", "taxonomy"], [197, 2, 1, "", "to_phylogeny"]], "Bio.Phylo.PhyloXML.CladeRelation": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Confidence": [[197, 2, 1, "", "__new__"], [197, 6, 1, "", "value"]], "Bio.Phylo.PhyloXML.Date": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Distribution": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.DomainArchitecture": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Events": [[197, 2, 1, "", "__contains__"], [197, 2, 1, "", "__delitem__"], [197, 2, 1, "", "__getitem__"], [197, 2, 1, "", "__init__"], [197, 2, 1, "", "__iter__"], [197, 2, 1, "", "__len__"], [197, 2, 1, "", "__setitem__"], [197, 2, 1, "", "items"], [197, 2, 1, "", "keys"], [197, 5, 1, "", "ok_type"], [197, 2, 1, "", "values"]], "Bio.Phylo.PhyloXML.Id": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.MolSeq": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"], [197, 5, 1, "", "re_value"]], "Bio.Phylo.PhyloXML.Other": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__iter__"]], "Bio.Phylo.PhyloXML.Phylogeny": [[197, 2, 1, "", "__init__"], [197, 6, 1, "", "alignment"], [197, 2, 1, "", "as_phyloxml"], [197, 6, 1, "", "confidence"], [197, 2, 1, "", "from_clade"], [197, 2, 1, "", "from_tree"], [197, 2, 1, "", "to_alignment"], [197, 2, 1, "", "to_phyloxml_container"]], "Bio.Phylo.PhyloXML.Phyloxml": [[197, 2, 1, "", "__getitem__"], [197, 2, 1, "", "__init__"], [197, 2, 1, "", "__iter__"], [197, 2, 1, "", "__len__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Point": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Polygon": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Property": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "ok_applies_to"], [197, 5, 1, "", "ok_datatype"], [197, 5, 1, "", "re_ref"]], "Bio.Phylo.PhyloXML.ProteinDomain": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "from_seqfeature"], [197, 2, 1, "", "to_seqfeature"]], "Bio.Phylo.PhyloXML.Reference": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "re_doi"]], "Bio.Phylo.PhyloXML.Sequence": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "from_seqrecord"], [197, 5, 1, "", "re_symbol"], [197, 2, 1, "", "to_seqrecord"], [197, 5, 1, "", "types"]], "Bio.Phylo.PhyloXML.SequenceRelation": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "ok_type"]], "Bio.Phylo.PhyloXML.Taxonomy": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"], [197, 5, 1, "", "ok_rank"], [197, 5, 1, "", "re_code"]], "Bio.Phylo.PhyloXML.Uri": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXMLIO": [[198, 3, 1, "", "Parser"], [198, 1, 1, "", "PhyloXMLError"], [198, 3, 1, "", "Writer"], [198, 4, 1, "", "parse"], [198, 4, 1, "", "read"], [198, 4, 1, "", "write"]], "Bio.Phylo.PhyloXMLIO.Parser": [[198, 2, 1, "", "__init__"], [198, 2, 1, "", "accession"], [198, 2, 1, "", "annotation"], [198, 2, 1, "", "binary_characters"], [198, 2, 1, "", "clade_relation"], [198, 2, 1, "", "color"], [198, 2, 1, "", "confidence"], [198, 2, 1, "", "date"], [198, 2, 1, "", "distribution"], [198, 2, 1, "", "domain"], [198, 2, 1, "", "domain_architecture"], [198, 2, 1, "", "events"], [198, 2, 1, "", "id"], [198, 2, 1, "", "mol_seq"], [198, 2, 1, "", "other"], [198, 2, 1, "", "parse"], [198, 2, 1, "", "point"], [198, 2, 1, "", "polygon"], [198, 2, 1, "", "property"], [198, 2, 1, "", "read"], [198, 2, 1, "", "reference"], [198, 2, 1, "", "sequence_relation"], [198, 2, 1, "", "uri"]], "Bio.Phylo.PhyloXMLIO.Writer": [[198, 2, 1, "", "__init__"], [198, 2, 1, "", "accession"], [198, 2, 1, "", "alt"], [198, 2, 1, "", "annotation"], [198, 2, 1, "", "bc"], [198, 2, 1, "", "binary_characters"], [198, 2, 1, "", "blue"], [198, 2, 1, "", "branch_length"], [198, 2, 1, "", "clade"], [198, 2, 1, "", "clade_relation"], [198, 2, 1, "", "code"], [198, 2, 1, "", "color"], [198, 2, 1, "", "common_name"], [198, 2, 1, "", "confidence"], [198, 2, 1, "", "date"], [198, 2, 1, "", "desc"], [198, 2, 1, "", "description"], [198, 2, 1, "", "distribution"], [198, 2, 1, "", "domain"], [198, 2, 1, "", "domain_architecture"], [198, 2, 1, "", "duplications"], [198, 2, 1, "", "events"], [198, 2, 1, "", "green"], [198, 2, 1, "", "id"], [198, 2, 1, "", "lat"], [198, 2, 1, "", "location"], [198, 2, 1, "", "long"], [198, 2, 1, "", "losses"], [198, 2, 1, "", "maximum"], [198, 2, 1, "", "minimum"], [198, 2, 1, "", "mol_seq"], [198, 2, 1, "", "name"], [198, 2, 1, "", "node_id"], [198, 2, 1, "", "other"], [198, 2, 1, "", "phylogeny"], [198, 2, 1, "", "phyloxml"], [198, 2, 1, "", "point"], [198, 2, 1, "", "polygon"], [198, 2, 1, "", "property"], [198, 2, 1, "", "rank"], [198, 2, 1, "", "red"], [198, 2, 1, "", "reference"], [198, 2, 1, "", "scientific_name"], [198, 2, 1, "", "sequence"], [198, 2, 1, "", "sequence_relation"], [198, 2, 1, "", "speciations"], [198, 2, 1, "", "symbol"], [198, 2, 1, "", "synonym"], [198, 2, 1, "", "taxonomy"], [198, 2, 1, "", "type"], [198, 2, 1, "", "uri"], [198, 2, 1, "", "value"], [198, 2, 1, "", "width"], [198, 2, 1, "", "write"]], "Bio.Phylo.TreeConstruction": [[199, 3, 1, "", "DistanceCalculator"], [199, 3, 1, "", "DistanceMatrix"], [199, 3, 1, "", "DistanceTreeConstructor"], [199, 3, 1, "", "NNITreeSearcher"], [199, 3, 1, "", "ParsimonyScorer"], [199, 3, 1, "", "ParsimonyTreeConstructor"], [199, 3, 1, "", "Scorer"], [199, 3, 1, "", "TreeConstructor"], [199, 3, 1, "", "TreeSearcher"]], "Bio.Phylo.TreeConstruction.DistanceCalculator": [[199, 2, 1, "", "__init__"], [199, 5, 1, "", "dna_models"], [199, 2, 1, "", "get_distance"], [199, 5, 1, "", "models"], [199, 5, 1, "", "protein_models"]], "Bio.Phylo.TreeConstruction.DistanceMatrix": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "__setitem__"], [199, 2, 1, "", "format_phylip"]], "Bio.Phylo.TreeConstruction.DistanceTreeConstructor": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "build_tree"], [199, 5, 1, "", "methods"], [199, 2, 1, "", "nj"], [199, 2, 1, "", "upgma"]], "Bio.Phylo.TreeConstruction.NNITreeSearcher": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "search"]], "Bio.Phylo.TreeConstruction.ParsimonyScorer": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "get_score"]], "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "build_tree"]], "Bio.Phylo.TreeConstruction.Scorer": [[199, 2, 1, "", "get_score"]], "Bio.Phylo.TreeConstruction.TreeConstructor": [[199, 2, 1, "", "build_tree"]], "Bio.Phylo.TreeConstruction.TreeSearcher": [[199, 2, 1, "", "search"]], "Bio.PopGen": [[201, 0, 0, "-", "GenePop"]], "Bio.PopGen.GenePop": [[202, 0, 0, "-", "Controller"], [203, 0, 0, "-", "EasyController"], [204, 0, 0, "-", "FileParser"], [205, 0, 0, "-", "LargeFileParser"], [201, 3, 1, "", "Record"], [201, 4, 1, "", "get_indiv"], [201, 4, 1, "", "read"]], "Bio.PopGen.GenePop.Controller": [[202, 3, 1, "", "GenePopController"]], "Bio.PopGen.GenePop.Controller.GenePopController": [[202, 2, 1, "", "__init__"], [202, 2, 1, "", "calc_allele_genotype_freqs"], [202, 2, 1, "", "calc_diversities_fis_with_identity"], [202, 2, 1, "", "calc_diversities_fis_with_size"], [202, 2, 1, "", "calc_fst_all"], [202, 2, 1, "", "calc_fst_pair"], [202, 2, 1, "", "calc_ibd_diplo"], [202, 2, 1, "", "calc_ibd_haplo"], [202, 2, 1, "", "calc_rho_all"], [202, 2, 1, "", "calc_rho_pair"], [202, 2, 1, "", "create_contingency_tables"], [202, 2, 1, "", "estimate_nm"], [202, 2, 1, "", "test_genic_diff_all"], [202, 2, 1, "", "test_genic_diff_pair"], [202, 2, 1, "", "test_genotypic_diff_all"], [202, 2, 1, "", "test_genotypic_diff_pair"], [202, 2, 1, "", "test_global_hz_deficiency"], [202, 2, 1, "", "test_global_hz_excess"], [202, 2, 1, "", "test_ld"], [202, 2, 1, "", "test_pop_hz_deficiency"], [202, 2, 1, "", "test_pop_hz_excess"], [202, 2, 1, "", "test_pop_hz_prob"]], "Bio.PopGen.GenePop.EasyController": [[203, 3, 1, "", "EasyController"]], "Bio.PopGen.GenePop.EasyController.EasyController": [[203, 2, 1, "", "__init__"], [203, 2, 1, "", "calc_ibd"], [203, 2, 1, "", "estimate_nm"], [203, 2, 1, "", "get_allele_frequency"], [203, 2, 1, "", "get_alleles"], [203, 2, 1, "", "get_alleles_all_pops"], [203, 2, 1, "", "get_avg_fis"], [203, 2, 1, "", "get_avg_fst_pair"], [203, 2, 1, "", "get_avg_fst_pair_locus"], [203, 2, 1, "", "get_basic_info"], [203, 2, 1, "", "get_f_stats"], [203, 2, 1, "", "get_fis"], [203, 2, 1, "", "get_genotype_count"], [203, 2, 1, "", "get_heterozygosity_info"], [203, 2, 1, "", "get_multilocus_f_stats"], [203, 2, 1, "", "test_hw_global"], [203, 2, 1, "", "test_hw_pop"], [203, 2, 1, "", "test_ld_all_pair"]], "Bio.PopGen.GenePop.FileParser": [[204, 3, 1, "", "FileRecord"], [204, 4, 1, "", "read"]], "Bio.PopGen.GenePop.FileParser.FileRecord": [[204, 2, 1, "", "__init__"], [204, 2, 1, "", "__str__"], [204, 2, 1, "", "get_individual"], [204, 2, 1, "", "remove_loci_by_name"], [204, 2, 1, "", "remove_loci_by_position"], [204, 2, 1, "", "remove_locus_by_name"], [204, 2, 1, "", "remove_locus_by_position"], [204, 2, 1, "", "remove_population"], [204, 2, 1, "", "seek_position"], [204, 2, 1, "", "skip_header"], [204, 2, 1, "", "skip_population"], [204, 2, 1, "", "start_read"]], "Bio.PopGen.GenePop.LargeFileParser": [[205, 3, 1, "", "Record"], [205, 4, 1, "", "get_indiv"], [205, 4, 1, "", "read"]], "Bio.PopGen.GenePop.LargeFileParser.Record": [[205, 2, 1, "", "__init__"], [205, 2, 1, "", "data_generator"]], "Bio.PopGen.GenePop.Record": [[201, 2, 1, "", "__init__"], [201, 2, 1, "", "__str__"], [201, 2, 1, "", "remove_locus_by_name"], [201, 2, 1, "", "remove_locus_by_position"], [201, 2, 1, "", "remove_population"], [201, 2, 1, "", "split_in_loci"], [201, 2, 1, "", "split_in_pops"]], "Bio.Restriction": [[207, 0, 0, "-", "PrintFormat"], [208, 0, 0, "-", "Restriction_Dictionary"]], "Bio.Restriction.PrintFormat": [[207, 3, 1, "", "PrintFormat"]], "Bio.Restriction.PrintFormat.PrintFormat": [[207, 5, 1, "", "Cmodulo"], [207, 5, 1, "", "ConsoleWidth"], [207, 5, 1, "", "Indent"], [207, 5, 1, "", "MaxSize"], [207, 5, 1, "", "NameWidth"], [207, 5, 1, "", "PrefWidth"], [207, 2, 1, "", "format_output"], [207, 5, 1, "", "linesize"], [207, 2, 1, "", "make_format"], [207, 2, 1, "", "print_as"], [207, 2, 1, "", "print_that"]], "Bio.SCOP": [[209, 3, 1, "", "Astral"], [210, 0, 0, "-", "Cla"], [211, 0, 0, "-", "Des"], [212, 0, 0, "-", "Dom"], [209, 3, 1, "", "Domain"], [213, 0, 0, "-", "Hie"], [209, 3, 1, "", "Node"], [214, 0, 0, "-", "Raf"], [215, 0, 0, "-", "Residues"], [209, 3, 1, "", "Scop"], [209, 4, 1, "", "cmp_sccs"], [209, 4, 1, "", "parse_domain"], [209, 4, 1, "", "search"]], "Bio.SCOP.Astral": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "domainsClusteredByEv"], [209, 2, 1, "", "domainsClusteredById"], [209, 2, 1, "", "getAstralDomainsFromFile"], [209, 2, 1, "", "getAstralDomainsFromSQL"], [209, 2, 1, "", "getSeq"], [209, 2, 1, "", "getSeqBySid"], [209, 2, 1, "", "hashedDomainsByEv"], [209, 2, 1, "", "hashedDomainsById"], [209, 2, 1, "", "isDomainInEv"], [209, 2, 1, "", "isDomainInId"], [209, 2, 1, "", "writeToSQL"]], "Bio.SCOP.Cla": [[210, 3, 1, "", "Index"], [210, 3, 1, "", "Record"], [210, 4, 1, "", "parse"]], "Bio.SCOP.Cla.Index": [[210, 2, 1, "", "__getitem__"], [210, 2, 1, "", "__init__"]], "Bio.SCOP.Cla.Record": [[210, 2, 1, "", "__init__"], [210, 2, 1, "", "__str__"]], "Bio.SCOP.Des": [[211, 3, 1, "", "Record"], [211, 4, 1, "", "parse"]], "Bio.SCOP.Des.Record": [[211, 2, 1, "", "__init__"], [211, 2, 1, "", "__str__"]], "Bio.SCOP.Dom": [[212, 3, 1, "", "Record"], [212, 4, 1, "", "parse"]], "Bio.SCOP.Dom.Record": [[212, 2, 1, "", "__init__"], [212, 2, 1, "", "__str__"]], "Bio.SCOP.Domain": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "__str__"], [209, 2, 1, "", "toClaRecord"], [209, 2, 1, "", "toDesRecord"]], "Bio.SCOP.Hie": [[213, 3, 1, "", "Record"], [213, 4, 1, "", "parse"]], "Bio.SCOP.Hie.Record": [[213, 2, 1, "", "__init__"], [213, 2, 1, "", "__str__"]], "Bio.SCOP.Node": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "__str__"], [209, 2, 1, "", "getAscendent"], [209, 2, 1, "", "getChildren"], [209, 2, 1, "", "getDescendents"], [209, 2, 1, "", "getParent"], [209, 2, 1, "", "toDesRecord"], [209, 2, 1, "", "toHieRecord"]], "Bio.SCOP.Raf": [[214, 3, 1, "", "Res"], [214, 3, 1, "", "SeqMap"], [214, 3, 1, "", "SeqMapIndex"], [214, 4, 1, "", "normalize_letters"], [214, 4, 1, "", "parse"]], "Bio.SCOP.Raf.Res": [[214, 2, 1, "", "__init__"]], "Bio.SCOP.Raf.SeqMap": [[214, 2, 1, "", "__add__"], [214, 2, 1, "", "__getitem__"], [214, 2, 1, "", "__iadd__"], [214, 2, 1, "", "__init__"], [214, 2, 1, "", "append"], [214, 2, 1, "", "extend"], [214, 2, 1, "", "getAtoms"], [214, 2, 1, "", "index"]], "Bio.SCOP.Raf.SeqMapIndex": [[214, 2, 1, "", "__getitem__"], [214, 2, 1, "", "__init__"], [214, 2, 1, "", "getSeqMap"]], "Bio.SCOP.Residues": [[215, 3, 1, "", "Residues"]], "Bio.SCOP.Residues.Residues": [[215, 2, 1, "", "__init__"], [215, 2, 1, "", "__str__"]], "Bio.SCOP.Scop": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "getAscendentFromSQL"], [209, 2, 1, "", "getDescendentsFromSQL"], [209, 2, 1, "", "getDomainBySid"], [209, 2, 1, "", "getDomainFromSQL"], [209, 2, 1, "", "getDomains"], [209, 2, 1, "", "getNodeBySunid"], [209, 2, 1, "", "getRoot"], [209, 2, 1, "", "write_cla"], [209, 2, 1, "", "write_cla_sql"], [209, 2, 1, "", "write_des"], [209, 2, 1, "", "write_des_sql"], [209, 2, 1, "", "write_hie"], [209, 2, 1, "", "write_hie_sql"]], "Bio.SVDSuperimposer": [[216, 3, 1, "", "SVDSuperimposer"]], "Bio.SVDSuperimposer.SVDSuperimposer": [[216, 2, 1, "", "__init__"], [216, 2, 1, "", "get_init_rms"], [216, 2, 1, "", "get_rms"], [216, 2, 1, "", "get_rotran"], [216, 2, 1, "", "get_transformed"], [216, 2, 1, "", "run"], [216, 2, 1, "", "set"]], "Bio.SearchIO": [[218, 0, 0, "-", "BlastIO"], [221, 0, 0, "-", "BlatIO"], [222, 0, 0, "-", "ExonerateIO"], [226, 0, 0, "-", "FastaIO"], [227, 0, 0, "-", "HHsuiteIO"], [229, 0, 0, "-", "HmmerIO"], [234, 0, 0, "-", "InterproscanIO"], [217, 4, 1, "", "convert"], [217, 4, 1, "", "index"], [217, 4, 1, "", "index_db"], [217, 4, 1, "", "parse"], [217, 4, 1, "", "read"], [217, 4, 1, "", "to_dict"], [217, 4, 1, "", "write"]], "Bio.SearchIO.BlastIO": [[219, 0, 0, "-", "blast_tab"], [220, 0, 0, "-", "blast_xml"]], "Bio.SearchIO.BlastIO.blast_tab": [[219, 3, 1, "", "BlastTabIndexer"], [219, 3, 1, "", "BlastTabParser"], [219, 3, 1, "", "BlastTabWriter"]], "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer": [[219, 5, 1, "", "__abstractmethods__"], [219, 2, 1, "", "__init__"], [219, 2, 1, "", "__iter__"], [219, 2, 1, "", "get_raw"]], "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser": [[219, 2, 1, "", "__init__"], [219, 2, 1, "", "__iter__"]], "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter": [[219, 2, 1, "", "__init__"], [219, 2, 1, "", "write_file"]], "Bio.SearchIO.BlastIO.blast_xml": [[220, 3, 1, "", "BlastXmlIndexer"], [220, 3, 1, "", "BlastXmlParser"], [220, 3, 1, "", "BlastXmlWriter"]], "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer": [[220, 5, 1, "", "__abstractmethods__"], [220, 2, 1, "", "__init__"], [220, 2, 1, "", "__iter__"], [220, 5, 1, "", "block_size"], [220, 2, 1, "", "get_raw"], [220, 5, 1, "", "qend_mark"], [220, 5, 1, "", "qstart_mark"]], "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser": [[220, 2, 1, "", "__init__"], [220, 2, 1, "", "__iter__"]], "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter": [[220, 2, 1, "", "__init__"], [220, 2, 1, "", "write_file"]], "Bio.SearchIO.BlatIO": [[221, 3, 1, "", "BlatPslIndexer"], [221, 3, 1, "", "BlatPslParser"], [221, 3, 1, "", "BlatPslWriter"]], "Bio.SearchIO.BlatIO.BlatPslIndexer": [[221, 5, 1, "", "__abstractmethods__"], [221, 2, 1, "", "__init__"], [221, 2, 1, "", "__iter__"], [221, 2, 1, "", "get_raw"]], "Bio.SearchIO.BlatIO.BlatPslParser": [[221, 2, 1, "", "__init__"], [221, 2, 1, "", "__iter__"]], "Bio.SearchIO.BlatIO.BlatPslWriter": [[221, 2, 1, "", "__init__"], [221, 2, 1, "", "write_file"]], "Bio.SearchIO.ExonerateIO": [[223, 0, 0, "-", "exonerate_cigar"], [224, 0, 0, "-", "exonerate_text"], [225, 0, 0, "-", "exonerate_vulgar"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar": [[223, 3, 1, "", "ExonerateCigarIndexer"], [223, 3, 1, "", "ExonerateCigarParser"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer": [[223, 5, 1, "", "__abstractmethods__"], [223, 2, 1, "", "get_qresult_id"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser": [[223, 5, 1, "", "__abstractmethods__"], [223, 2, 1, "", "parse_alignment_block"]], "Bio.SearchIO.ExonerateIO.exonerate_text": [[224, 3, 1, "", "ExonerateTextIndexer"], [224, 3, 1, "", "ExonerateTextParser"]], "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer": [[224, 5, 1, "", "__abstractmethods__"], [224, 2, 1, "", "get_qresult_id"], [224, 2, 1, "", "get_raw"]], "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser": [[224, 5, 1, "", "__abstractmethods__"], [224, 2, 1, "", "parse_alignment_block"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar": [[225, 3, 1, "", "ExonerateVulgarIndexer"], [225, 3, 1, "", "ExonerateVulgarParser"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer": [[225, 5, 1, "", "__abstractmethods__"], [225, 5, 1, "", "__annotations__"], [225, 2, 1, "", "get_qresult_id"], [225, 2, 1, "", "get_raw"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser": [[225, 5, 1, "", "__abstractmethods__"], [225, 2, 1, "", "parse_alignment_block"]], "Bio.SearchIO.FastaIO": [[226, 3, 1, "", "FastaM10Indexer"], [226, 3, 1, "", "FastaM10Parser"]], "Bio.SearchIO.FastaIO.FastaM10Indexer": [[226, 5, 1, "", "__abstractmethods__"], [226, 2, 1, "", "__init__"], [226, 2, 1, "", "__iter__"], [226, 2, 1, "", "get_raw"]], "Bio.SearchIO.FastaIO.FastaM10Parser": [[226, 2, 1, "", "__init__"], [226, 2, 1, "", "__iter__"]], "Bio.SearchIO.HHsuiteIO": [[228, 0, 0, "-", "hhsuite2_text"]], "Bio.SearchIO.HHsuiteIO.hhsuite2_text": [[228, 3, 1, "", "Hhsuite2TextParser"]], "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser": [[228, 2, 1, "", "__init__"], [228, 2, 1, "", "__iter__"]], "Bio.SearchIO.HmmerIO": [[230, 0, 0, "-", "hmmer2_text"], [231, 0, 0, "-", "hmmer3_domtab"], [232, 0, 0, "-", "hmmer3_tab"], [233, 0, 0, "-", "hmmer3_text"]], "Bio.SearchIO.HmmerIO.hmmer2_text": [[230, 3, 1, "", "Hmmer2TextIndexer"], [230, 3, 1, "", "Hmmer2TextParser"]], "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer": [[230, 5, 1, "", "__abstractmethods__"], [230, 2, 1, "", "__iter__"], [230, 5, 1, "", "qresult_end"], [230, 5, 1, "", "qresult_start"]], "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser": [[230, 2, 1, "", "__init__"], [230, 2, 1, "", "__iter__"], [230, 2, 1, "", "parse_hits"], [230, 2, 1, "", "parse_hsp_alignments"], [230, 2, 1, "", "parse_hsps"], [230, 2, 1, "", "parse_key_value"], [230, 2, 1, "", "parse_preamble"], [230, 2, 1, "", "parse_qresult"], [230, 2, 1, "", "push_back"], [230, 2, 1, "", "read_next"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab": [[231, 3, 1, "", "Hmmer3DomtabHmmhitIndexer"], [231, 3, 1, "", "Hmmer3DomtabHmmhitParser"], [231, 3, 1, "", "Hmmer3DomtabHmmhitWriter"], [231, 3, 1, "", "Hmmer3DomtabHmmqueryIndexer"], [231, 3, 1, "", "Hmmer3DomtabHmmqueryParser"], [231, 3, 1, "", "Hmmer3DomtabHmmqueryWriter"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer": [[231, 5, 1, "", "__abstractmethods__"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser": [[231, 5, 1, "", "hmm_as_hit"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter": [[231, 2, 1, "", "__init__"], [231, 5, 1, "", "hmm_as_hit"], [231, 2, 1, "", "write_file"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer": [[231, 5, 1, "", "__abstractmethods__"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser": [[231, 5, 1, "", "hmm_as_hit"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter": [[231, 5, 1, "", "hmm_as_hit"]], "Bio.SearchIO.HmmerIO.hmmer3_tab": [[232, 3, 1, "", "Hmmer3TabIndexer"], [232, 3, 1, "", "Hmmer3TabParser"], [232, 3, 1, "", "Hmmer3TabWriter"]], "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer": [[232, 5, 1, "", "__abstractmethods__"], [232, 2, 1, "", "__iter__"], [232, 2, 1, "", "get_raw"]], "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser": [[232, 2, 1, "", "__init__"], [232, 2, 1, "", "__iter__"]], "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter": [[232, 2, 1, "", "__init__"], [232, 2, 1, "", "write_file"]], "Bio.SearchIO.HmmerIO.hmmer3_text": [[233, 3, 1, "", "Hmmer3TextIndexer"], [233, 3, 1, "", "Hmmer3TextParser"]], "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer": [[233, 5, 1, "", "__abstractmethods__"], [233, 2, 1, "", "__iter__"], [233, 5, 1, "", "qresult_end"], [233, 5, 1, "", "qresult_start"]], "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser": [[233, 2, 1, "", "__init__"], [233, 2, 1, "", "__iter__"]], "Bio.SearchIO.InterproscanIO": [[235, 0, 0, "-", "interproscan_xml"]], "Bio.SearchIO.InterproscanIO.interproscan_xml": [[235, 3, 1, "", "InterproscanXmlParser"]], "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser": [[235, 2, 1, "", "__init__"], [235, 2, 1, "", "__iter__"]], "Bio.Seq": [[236, 3, 1, "", "MutableSeq"], [236, 3, 1, "", "Seq"], [236, 3, 1, "", "SequenceDataAbstractBaseClass"], [236, 1, 1, "", "UndefinedSequenceError"], [236, 4, 1, "", "back_transcribe"], [236, 4, 1, "", "complement"], [236, 4, 1, "", "complement_rna"], [236, 4, 1, "", "reverse_complement"], [236, 4, 1, "", "reverse_complement_rna"], [236, 4, 1, "", "transcribe"], [236, 4, 1, "", "translate"]], "Bio.Seq.MutableSeq": [[236, 5, 1, "", "__abstractmethods__"], [236, 2, 1, "", "__delitem__"], [236, 2, 1, "", "__init__"], [236, 2, 1, "", "__setitem__"], [236, 2, 1, "", "append"], [236, 2, 1, "", "extend"], [236, 2, 1, "", "insert"], [236, 2, 1, "", "pop"], [236, 2, 1, "", "remove"], [236, 2, 1, "", "reverse"]], "Bio.Seq.Seq": [[236, 5, 1, "", "__abstractmethods__"], [236, 5, 1, "", "__annotations__"], [236, 2, 1, "", "__hash__"], [236, 2, 1, "", "__init__"]], "Bio.Seq.SequenceDataAbstractBaseClass": [[236, 5, 1, "", "__abstractmethods__"], [236, 2, 1, "", "__add__"], [236, 2, 1, "", "__bytes__"], [236, 2, 1, "", "__contains__"], [236, 2, 1, "", "__eq__"], [236, 2, 1, "", "__ge__"], [236, 2, 1, "", "__getitem__"], [236, 2, 1, "", "__gt__"], [236, 2, 1, "", "__hash__"], [236, 2, 1, "", "__init__"], [236, 2, 1, "", "__le__"], [236, 2, 1, "", "__len__"], [236, 2, 1, "", "__lt__"], [236, 2, 1, "", "__mul__"], [236, 2, 1, "", "__radd__"], [236, 5, 1, "", "__slots__"], [236, 2, 1, "", "count"], [236, 2, 1, "", "decode"], [236, 6, 1, "", "defined"], [236, 6, 1, "", "defined_ranges"], [236, 2, 1, "", "endswith"], [236, 2, 1, "", "find"], [236, 2, 1, "", "index"], [236, 2, 1, "", "islower"], [236, 2, 1, "", "isupper"], [236, 2, 1, "", "lower"], [236, 2, 1, "", "lstrip"], [236, 2, 1, "", "removeprefix"], [236, 2, 1, "", "removesuffix"], [236, 2, 1, "", "replace"], [236, 2, 1, "", "rfind"], [236, 2, 1, "", "rindex"], [236, 2, 1, "", "rsplit"], [236, 2, 1, "", "rstrip"], [236, 2, 1, "", "split"], [236, 2, 1, "", "startswith"], [236, 2, 1, "", "strip"], [236, 2, 1, "", "translate"], [236, 2, 1, "", "upper"]], "Bio.SeqFeature": [[237, 3, 1, "", "AfterPosition"], [237, 3, 1, "", "BeforePosition"], [237, 3, 1, "", "BetweenPosition"], [237, 3, 1, "", "CompoundLocation"], [237, 3, 1, "", "ExactPosition"], [237, 5, 1, "", "FeatureLocation"], [237, 3, 1, "", "Location"], [237, 1, 1, "", "LocationParserError"], [237, 3, 1, "", "OneOfPosition"], [237, 3, 1, "", "Position"], [237, 3, 1, "", "Reference"], [237, 3, 1, "", "SeqFeature"], [237, 3, 1, "", "SimpleLocation"], [237, 3, 1, "", "UncertainPosition"], [237, 3, 1, "", "UnknownPosition"], [237, 3, 1, "", "WithinPosition"]], "Bio.SeqFeature.AfterPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.BeforePosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.BetweenPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__getnewargs__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.CompoundLocation": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__contains__"], [237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__iter__"], [237, 2, 1, "", "__len__"], [237, 2, 1, "", "__nonzero__"], [237, 2, 1, "", "__radd__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"], [237, 6, 1, "", "end"], [237, 2, 1, "", "extract"], [237, 6, 1, "", "ref"], [237, 6, 1, "", "ref_db"], [237, 6, 1, "", "start"], [237, 6, 1, "", "strand"]], "Bio.SeqFeature.ExactPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.Location": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "fromstring"]], "Bio.SeqFeature.OneOfPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__getnewargs__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.Position": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "fromstring"]], "Bio.SeqFeature.Reference": [[237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.SeqFeature": [[237, 2, 1, "", "__bool__"], [237, 2, 1, "", "__contains__"], [237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__iter__"], [237, 2, 1, "", "__len__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"], [237, 2, 1, "", "extract"], [237, 6, 1, "", "ref"], [237, 6, 1, "", "ref_db"], [237, 6, 1, "", "strand"], [237, 2, 1, "", "translate"]], "Bio.SeqFeature.SimpleLocation": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__contains__"], [237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__iter__"], [237, 2, 1, "", "__len__"], [237, 2, 1, "", "__nonzero__"], [237, 2, 1, "", "__radd__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"], [237, 2, 1, "", "__sub__"], [237, 6, 1, "", "end"], [237, 2, 1, "", "extract"], [237, 2, 1, "", "fromstring"], [237, 6, 1, "", "parts"], [237, 6, 1, "", "start"], [237, 6, 1, "", "strand"]], "Bio.SeqFeature.UncertainPosition": [[237, 5, 1, "", "__abstractmethods__"]], "Bio.SeqFeature.UnknownPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__hash__"], [237, 2, 1, "", "__repr__"]], "Bio.SeqFeature.WithinPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__getnewargs__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqIO": [[239, 0, 0, "-", "AbiIO"], [240, 0, 0, "-", "AceIO"], [241, 0, 0, "-", "FastaIO"], [242, 0, 0, "-", "GckIO"], [243, 0, 0, "-", "GfaIO"], [244, 0, 0, "-", "IgIO"], [245, 0, 0, "-", "InsdcIO"], [246, 0, 0, "-", "Interfaces"], [247, 0, 0, "-", "NibIO"], [248, 0, 0, "-", "PdbIO"], [249, 0, 0, "-", "PhdIO"], [250, 0, 0, "-", "PirIO"], [251, 0, 0, "-", "QualityIO"], [252, 0, 0, "-", "SeqXmlIO"], [253, 0, 0, "-", "SffIO"], [254, 0, 0, "-", "SnapGeneIO"], [255, 0, 0, "-", "SwissIO"], [256, 0, 0, "-", "TabIO"], [257, 0, 0, "-", "TwoBitIO"], [258, 0, 0, "-", "UniprotIO"], [259, 0, 0, "-", "XdnaIO"], [238, 4, 1, "", "convert"], [238, 4, 1, "", "index"], [238, 4, 1, "", "index_db"], [238, 4, 1, "", "parse"], [238, 4, 1, "", "read"], [238, 4, 1, "", "to_dict"], [238, 4, 1, "", "write"]], "Bio.SeqIO.AbiIO": [[239, 3, 1, "", "AbiIterator"]], "Bio.SeqIO.AbiIO.AbiIterator": [[239, 5, 1, "", "__abstractmethods__"], [239, 2, 1, "", "__init__"], [239, 2, 1, "", "__next__"], [239, 5, 1, "", "__parameters__"], [239, 2, 1, "", "parse"]], "Bio.SeqIO.AceIO": [[240, 4, 1, "", "AceIterator"]], "Bio.SeqIO.FastaIO": [[241, 3, 1, "", "FastaIterator"], [241, 3, 1, "", "FastaTwoLineIterator"], [241, 4, 1, "", "FastaTwoLineParser"], [241, 3, 1, "", "FastaTwoLineWriter"], [241, 3, 1, "", "FastaWriter"], [241, 4, 1, "", "SimpleFastaParser"], [241, 4, 1, "", "as_fasta"], [241, 4, 1, "", "as_fasta_2line"]], "Bio.SeqIO.FastaIO.FastaIterator": [[241, 5, 1, "", "__abstractmethods__"], [241, 2, 1, "", "__init__"], [241, 5, 1, "", "__parameters__"], [241, 2, 1, "", "iterate"], [241, 2, 1, "", "parse"]], "Bio.SeqIO.FastaIO.FastaTwoLineIterator": [[241, 5, 1, "", "__abstractmethods__"], [241, 2, 1, "", "__init__"], [241, 5, 1, "", "__parameters__"], [241, 2, 1, "", "iterate"], [241, 2, 1, "", "parse"]], "Bio.SeqIO.FastaIO.FastaTwoLineWriter": [[241, 2, 1, "", "__init__"]], "Bio.SeqIO.FastaIO.FastaWriter": [[241, 2, 1, "", "__init__"], [241, 2, 1, "", "write_record"]], "Bio.SeqIO.GckIO": [[242, 3, 1, "", "GckIterator"]], "Bio.SeqIO.GckIO.GckIterator": [[242, 5, 1, "", "__abstractmethods__"], [242, 2, 1, "", "__init__"], [242, 5, 1, "", "__parameters__"], [242, 2, 1, "", "parse"]], "Bio.SeqIO.GfaIO": [[243, 4, 1, "", "Gfa1Iterator"], [243, 4, 1, "", "Gfa2Iterator"]], "Bio.SeqIO.IgIO": [[244, 3, 1, "", "IgIterator"]], "Bio.SeqIO.IgIO.IgIterator": [[244, 5, 1, "", "__abstractmethods__"], [244, 2, 1, "", "__init__"], [244, 5, 1, "", "__parameters__"], [244, 2, 1, "", "iterate"], [244, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO": [[245, 3, 1, "", "EmblCdsFeatureIterator"], [245, 3, 1, "", "EmblIterator"], [245, 3, 1, "", "EmblWriter"], [245, 3, 1, "", "GenBankCdsFeatureIterator"], [245, 3, 1, "", "GenBankIterator"], [245, 3, 1, "", "GenBankWriter"], [245, 3, 1, "", "ImgtIterator"], [245, 3, 1, "", "ImgtWriter"]], "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.EmblIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.EmblWriter": [[245, 5, 1, "", "BLOCKS_PER_LINE"], [245, 5, 1, "", "FEATURE_HEADER"], [245, 5, 1, "", "HEADER_WIDTH"], [245, 5, 1, "", "LETTERS_PER_BLOCK"], [245, 5, 1, "", "LETTERS_PER_LINE"], [245, 5, 1, "", "POSITION_PADDING"], [245, 5, 1, "", "QUALIFIER_INDENT"], [245, 5, 1, "", "QUALIFIER_INDENT_STR"], [245, 5, 1, "", "QUALIFIER_INDENT_TMP"], [245, 2, 1, "", "write_record"]], "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.GenBankIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.GenBankWriter": [[245, 5, 1, "", "HEADER_WIDTH"], [245, 5, 1, "", "LETTERS_PER_LINE"], [245, 5, 1, "", "QUALIFIER_INDENT"], [245, 5, 1, "", "SEQUENCE_INDENT"], [245, 5, 1, "", "STRUCTURED_COMMENT_DELIM"], [245, 5, 1, "", "STRUCTURED_COMMENT_END"], [245, 5, 1, "", "STRUCTURED_COMMENT_START"], [245, 2, 1, "", "write_record"]], "Bio.SeqIO.InsdcIO.ImgtIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.ImgtWriter": [[245, 5, 1, "", "FEATURE_HEADER"], [245, 5, 1, "", "HEADER_WIDTH"], [245, 5, 1, "", "QUALIFIER_INDENT"], [245, 5, 1, "", "QUALIFIER_INDENT_STR"], [245, 5, 1, "", "QUALIFIER_INDENT_TMP"]], "Bio.SeqIO.Interfaces": [[246, 3, 1, "", "SequenceIterator"], [246, 3, 1, "", "SequenceWriter"]], "Bio.SeqIO.Interfaces.SequenceIterator": [[246, 5, 1, "", "__abstractmethods__"], [246, 2, 1, "", "__init__"], [246, 2, 1, "", "__iter__"], [246, 2, 1, "", "__next__"], [246, 5, 1, "", "__orig_bases__"], [246, 5, 1, "", "__parameters__"], [246, 2, 1, "", "parse"]], "Bio.SeqIO.Interfaces.SequenceWriter": [[246, 2, 1, "", "__init__"], [246, 2, 1, "", "clean"], [246, 2, 1, "", "write_file"], [246, 2, 1, "", "write_footer"], [246, 2, 1, "", "write_header"], [246, 2, 1, "", "write_record"], [246, 2, 1, "", "write_records"]], "Bio.SeqIO.NibIO": [[247, 3, 1, "", "NibIterator"], [247, 3, 1, "", "NibWriter"]], "Bio.SeqIO.NibIO.NibIterator": [[247, 5, 1, "", "__abstractmethods__"], [247, 2, 1, "", "__init__"], [247, 5, 1, "", "__parameters__"], [247, 2, 1, "", "iterate"], [247, 2, 1, "", "parse"]], "Bio.SeqIO.NibIO.NibWriter": [[247, 2, 1, "", "__init__"], [247, 2, 1, "", "write_file"], [247, 2, 1, "", "write_header"], [247, 2, 1, "", "write_record"]], "Bio.SeqIO.PdbIO": [[248, 4, 1, "", "AtomIterator"], [248, 4, 1, "", "CifAtomIterator"], [248, 4, 1, "", "CifSeqresIterator"], [248, 4, 1, "", "PdbAtomIterator"], [248, 3, 1, "", "PdbSeqresIterator"]], "Bio.SeqIO.PdbIO.PdbSeqresIterator": [[248, 5, 1, "", "__abstractmethods__"], [248, 2, 1, "", "__init__"], [248, 2, 1, "", "__next__"], [248, 5, 1, "", "__parameters__"], [248, 2, 1, "", "parse"]], "Bio.SeqIO.PhdIO": [[249, 4, 1, "", "PhdIterator"], [249, 3, 1, "", "PhdWriter"]], "Bio.SeqIO.PhdIO.PhdWriter": [[249, 2, 1, "", "__init__"], [249, 2, 1, "", "write_record"]], "Bio.SeqIO.PirIO": [[250, 3, 1, "", "PirIterator"], [250, 3, 1, "", "PirWriter"]], "Bio.SeqIO.PirIO.PirIterator": [[250, 5, 1, "", "__abstractmethods__"], [250, 2, 1, "", "__init__"], [250, 2, 1, "", "__next__"], [250, 5, 1, "", "__parameters__"], [250, 2, 1, "", "parse"]], "Bio.SeqIO.PirIO.PirWriter": [[250, 2, 1, "", "__init__"], [250, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO": [[251, 4, 1, "", "FastqGeneralIterator"], [251, 4, 1, "", "FastqIlluminaIterator"], [251, 3, 1, "", "FastqIlluminaWriter"], [251, 3, 1, "", "FastqPhredIterator"], [251, 3, 1, "", "FastqPhredWriter"], [251, 4, 1, "", "FastqSolexaIterator"], [251, 3, 1, "", "FastqSolexaWriter"], [251, 4, 1, "", "PairedFastaQualIterator"], [251, 3, 1, "", "QualPhredIterator"], [251, 3, 1, "", "QualPhredWriter"], [251, 4, 1, "", "as_fastq"], [251, 4, 1, "", "as_fastq_illumina"], [251, 4, 1, "", "as_fastq_solexa"], [251, 4, 1, "", "as_qual"], [251, 4, 1, "", "phred_quality_from_solexa"], [251, 4, 1, "", "solexa_quality_from_phred"]], "Bio.SeqIO.QualityIO.FastqIlluminaWriter": [[251, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO.FastqPhredIterator": [[251, 5, 1, "", "__abstractmethods__"], [251, 2, 1, "", "__init__"], [251, 5, 1, "", "__orig_bases__"], [251, 5, 1, "", "__parameters__"], [251, 2, 1, "", "iterate"], [251, 2, 1, "", "parse"]], "Bio.SeqIO.QualityIO.FastqPhredWriter": [[251, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO.FastqSolexaWriter": [[251, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO.QualPhredIterator": [[251, 5, 1, "", "__abstractmethods__"], [251, 2, 1, "", "__init__"], [251, 5, 1, "", "__parameters__"], [251, 2, 1, "", "iterate"], [251, 2, 1, "", "parse"]], "Bio.SeqIO.QualityIO.QualPhredWriter": [[251, 2, 1, "", "__init__"], [251, 2, 1, "", "write_record"]], "Bio.SeqIO.SeqXmlIO": [[252, 3, 1, "", "ContentHandler"], [252, 3, 1, "", "SeqXmlIterator"], [252, 3, 1, "", "SeqXmlWriter"]], "Bio.SeqIO.SeqXmlIO.ContentHandler": [[252, 2, 1, "", "__init__"], [252, 2, 1, "", "characters"], [252, 2, 1, "", "endDBRefElement"], [252, 2, 1, "", "endDescriptionElement"], [252, 2, 1, "", "endEntryElement"], [252, 2, 1, "", "endPropertyElement"], [252, 2, 1, "", "endSeqXMLElement"], [252, 2, 1, "", "endSequenceElement"], [252, 2, 1, "", "endSpeciesElement"], [252, 2, 1, "", "startDBRefElement"], [252, 2, 1, "", "startDescriptionElement"], [252, 2, 1, "", "startDocument"], [252, 2, 1, "", "startEntryElement"], [252, 2, 1, "", "startEntryFieldElement"], [252, 2, 1, "", "startEntryFieldElementVersion01"], [252, 2, 1, "", "startPropertyElement"], [252, 2, 1, "", "startSeqXMLElement"], [252, 2, 1, "", "startSequenceElement"], [252, 2, 1, "", "startSpeciesElement"]], "Bio.SeqIO.SeqXmlIO.SeqXmlIterator": [[252, 5, 1, "", "BLOCK"], [252, 5, 1, "", "__abstractmethods__"], [252, 2, 1, "", "__init__"], [252, 2, 1, "", "__next__"], [252, 5, 1, "", "__parameters__"], [252, 2, 1, "", "parse"]], "Bio.SeqIO.SeqXmlIO.SeqXmlWriter": [[252, 2, 1, "", "__init__"], [252, 2, 1, "", "write_footer"], [252, 2, 1, "", "write_header"], [252, 2, 1, "", "write_record"]], "Bio.SeqIO.SffIO": [[253, 4, 1, "", "ReadRocheXmlManifest"], [253, 3, 1, "", "SffIterator"], [253, 3, 1, "", "SffWriter"]], "Bio.SeqIO.SffIO.SffIterator": [[253, 5, 1, "", "__abstractmethods__"], [253, 2, 1, "", "__init__"], [253, 5, 1, "", "__parameters__"], [253, 2, 1, "", "iterate"], [253, 2, 1, "", "parse"]], "Bio.SeqIO.SffIO.SffWriter": [[253, 2, 1, "", "__init__"], [253, 2, 1, "", "write_file"], [253, 2, 1, "", "write_header"], [253, 2, 1, "", "write_record"]], "Bio.SeqIO.SnapGeneIO": [[254, 3, 1, "", "SnapGeneIterator"]], "Bio.SeqIO.SnapGeneIO.SnapGeneIterator": [[254, 5, 1, "", "__abstractmethods__"], [254, 2, 1, "", "__init__"], [254, 5, 1, "", "__parameters__"], [254, 2, 1, "", "iterate"], [254, 2, 1, "", "parse"]], "Bio.SeqIO.SwissIO": [[255, 4, 1, "", "SwissIterator"]], "Bio.SeqIO.TabIO": [[256, 3, 1, "", "TabIterator"], [256, 3, 1, "", "TabWriter"], [256, 4, 1, "", "as_tab"]], "Bio.SeqIO.TabIO.TabIterator": [[256, 5, 1, "", "__abstractmethods__"], [256, 2, 1, "", "__init__"], [256, 5, 1, "", "__parameters__"], [256, 2, 1, "", "iterate"], [256, 2, 1, "", "parse"]], "Bio.SeqIO.TabIO.TabWriter": [[256, 2, 1, "", "write_record"]], "Bio.SeqIO.TwoBitIO": [[257, 3, 1, "", "TwoBitIterator"]], "Bio.SeqIO.TwoBitIO.TwoBitIterator": [[257, 5, 1, "", "__abstractmethods__"], [257, 2, 1, "", "__getitem__"], [257, 2, 1, "", "__init__"], [257, 2, 1, "", "__len__"], [257, 5, 1, "", "__parameters__"], [257, 2, 1, "", "keys"], [257, 2, 1, "", "parse"]], "Bio.SeqIO.UniprotIO": [[258, 3, 1, "", "Parser"], [258, 4, 1, "", "UniprotIterator"]], "Bio.SeqIO.UniprotIO.Parser": [[258, 2, 1, "", "__init__"], [258, 2, 1, "", "parse"]], "Bio.SeqIO.XdnaIO": [[259, 3, 1, "", "XdnaIterator"], [259, 3, 1, "", "XdnaWriter"]], "Bio.SeqIO.XdnaIO.XdnaIterator": [[259, 5, 1, "", "__abstractmethods__"], [259, 2, 1, "", "__init__"], [259, 5, 1, "", "__parameters__"], [259, 2, 1, "", "iterate"], [259, 2, 1, "", "parse"]], "Bio.SeqIO.XdnaIO.XdnaWriter": [[259, 2, 1, "", "__init__"], [259, 2, 1, "", "write_file"]], "Bio.SeqRecord": [[260, 3, 1, "", "SeqRecord"]], "Bio.SeqRecord.SeqRecord": [[260, 2, 1, "", "__add__"], [260, 5, 1, "", "__annotations__"], [260, 2, 1, "", "__bool__"], [260, 2, 1, "", "__bytes__"], [260, 2, 1, "", "__contains__"], [260, 2, 1, "", "__eq__"], [260, 2, 1, "", "__format__"], [260, 2, 1, "", "__ge__"], [260, 2, 1, "", "__getitem__"], [260, 2, 1, "", "__gt__"], [260, 5, 1, "", "__hash__"], [260, 2, 1, "", "__init__"], [260, 2, 1, "", "__iter__"], [260, 2, 1, "", "__le__"], [260, 2, 1, "", "__len__"], [260, 2, 1, "", "__lt__"], [260, 2, 1, "", "__ne__"], [260, 2, 1, "", "__radd__"], [260, 2, 1, "", "__repr__"], [260, 2, 1, "", "__str__"], [260, 5, 1, "", "annotations"], [260, 2, 1, "", "count"], [260, 5, 1, "", "dbxrefs"], [260, 2, 1, "", "format"], [260, 2, 1, "", "islower"], [260, 2, 1, "", "isupper"], [260, 6, 1, "", "letter_annotations"], [260, 2, 1, "", "lower"], [260, 2, 1, "", "reverse_complement"], [260, 6, 1, "", "seq"], [260, 2, 1, "", "translate"], [260, 2, 1, "", "upper"]], "Bio.SeqUtils": [[262, 0, 0, "-", "CheckSum"], [261, 3, 1, "", "CodonAdaptationIndex"], [261, 4, 1, "", "GC123"], [261, 4, 1, "", "GC_skew"], [263, 0, 0, "-", "IsoelectricPoint"], [264, 0, 0, "-", "MeltingTemp"], [265, 0, 0, "-", "ProtParam"], [266, 0, 0, "-", "ProtParamData"], [261, 4, 1, "", "gc_fraction"], [267, 0, 0, "-", "lcc"], [261, 4, 1, "", "molecular_weight"], [261, 4, 1, "", "nt_search"], [261, 4, 1, "", "seq1"], [261, 4, 1, "", "seq3"], [261, 4, 1, "", "six_frame_translations"], [261, 4, 1, "", "xGC_skew"]], "Bio.SeqUtils.CheckSum": [[262, 4, 1, "", "crc32"], [262, 4, 1, "", "crc64"], [262, 4, 1, "", "gcg"], [262, 4, 1, "", "seguid"]], "Bio.SeqUtils.CodonAdaptationIndex": [[261, 2, 1, "", "__init__"], [261, 2, 1, "", "__str__"], [261, 2, 1, "", "calculate"], [261, 2, 1, "", "optimize"]], "Bio.SeqUtils.IsoelectricPoint": [[263, 3, 1, "", "IsoelectricPoint"]], "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint": [[263, 2, 1, "", "__init__"], [263, 2, 1, "", "charge_at_pH"], [263, 2, 1, "", "pi"]], "Bio.SeqUtils.MeltingTemp": [[264, 4, 1, "", "Tm_GC"], [264, 4, 1, "", "Tm_NN"], [264, 4, 1, "", "Tm_Wallace"], [264, 4, 1, "", "chem_correction"], [264, 4, 1, "", "make_table"], [264, 4, 1, "", "salt_correction"]], "Bio.SeqUtils.ProtParam": [[265, 3, 1, "", "ProteinAnalysis"]], "Bio.SeqUtils.ProtParam.ProteinAnalysis": [[265, 2, 1, "", "__init__"], [265, 6, 1, "", "amino_acids_percent"], [265, 2, 1, "", "aromaticity"], [265, 2, 1, "", "charge_at_pH"], [265, 2, 1, "", "count_amino_acids"], [265, 2, 1, "", "flexibility"], [265, 2, 1, "", "get_amino_acids_percent"], [265, 2, 1, "", "gravy"], [265, 2, 1, "", "instability_index"], [265, 2, 1, "", "isoelectric_point"], [265, 2, 1, "", "molar_extinction_coefficient"], [265, 2, 1, "", "molecular_weight"], [265, 2, 1, "", "protein_scale"], [265, 2, 1, "", "secondary_structure_fraction"]], "Bio.SeqUtils.lcc": [[267, 4, 1, "", "lcc_mult"], [267, 4, 1, "", "lcc_simp"]], "Bio.Sequencing": [[269, 0, 0, "-", "Ace"], [270, 0, 0, "-", "Applications"], [271, 0, 0, "-", "Phd"]], "Bio.Sequencing.Ace": [[269, 3, 1, "", "ACEFileRecord"], [269, 3, 1, "", "Contig"], [269, 3, 1, "", "Reads"], [269, 3, 1, "", "af"], [269, 3, 1, "", "bs"], [269, 3, 1, "", "ct"], [269, 3, 1, "", "ds"], [269, 4, 1, "", "parse"], [269, 3, 1, "", "qa"], [269, 3, 1, "", "rd"], [269, 4, 1, "", "read"], [269, 3, 1, "", "rt"], [269, 3, 1, "", "wa"], [269, 3, 1, "", "wr"]], "Bio.Sequencing.Ace.ACEFileRecord": [[269, 2, 1, "", "__init__"], [269, 2, 1, "", "sort"]], "Bio.Sequencing.Ace.Contig": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.Reads": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.af": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.bs": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.ct": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.ds": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.qa": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.rd": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.rt": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.wa": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.wr": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Applications": [[270, 3, 1, "", "BwaAlignCommandline"], [270, 3, 1, "", "BwaBwaswCommandline"], [270, 3, 1, "", "BwaIndexCommandline"], [270, 3, 1, "", "BwaMemCommandline"], [270, 3, 1, "", "BwaSampeCommandline"], [270, 3, 1, "", "BwaSamseCommandline"], [270, 3, 1, "", "NovoalignCommandline"], [270, 3, 1, "", "SamtoolsCalmdCommandline"], [270, 3, 1, "", "SamtoolsCatCommandline"], [270, 3, 1, "", "SamtoolsFaidxCommandline"], [270, 3, 1, "", "SamtoolsFixmateCommandline"], [270, 3, 1, "", "SamtoolsIdxstatsCommandline"], [270, 3, 1, "", "SamtoolsIndexCommandline"], [270, 3, 1, "", "SamtoolsMergeCommandline"], [270, 3, 1, "", "SamtoolsMpileupCommandline"], [270, 3, 1, "", "SamtoolsPhaseCommandline"], [270, 3, 1, "", "SamtoolsReheaderCommandline"], [270, 3, 1, "", "SamtoolsRmdupCommandline"], [270, 5, 1, "", "SamtoolsSortCommandline"], [270, 3, 1, "", "SamtoolsTargetcutCommandline"], [270, 3, 1, "", "SamtoolsVersion0xSortCommandline"], [270, 3, 1, "", "SamtoolsVersion1xSortCommandline"], [270, 3, 1, "", "SamtoolsViewCommandline"]], "Bio.Sequencing.Applications.BwaAlignCommandline": [[270, 6, 1, "", "B"], [270, 6, 1, "", "E"], [270, 6, 1, "", "I"], [270, 6, 1, "", "M"], [270, 6, 1, "", "N"], [270, 6, 1, "", "O"], [270, 6, 1, "", "R"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "b1"], [270, 6, 1, "", "b2"], [270, 6, 1, "", "c"], [270, 6, 1, "", "d"], [270, 6, 1, "", "e"], [270, 6, 1, "", "i"], [270, 6, 1, "", "k"], [270, 6, 1, "", "l"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"], [270, 6, 1, "", "q"], [270, 6, 1, "", "read_file"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "t"]], "Bio.Sequencing.Applications.BwaBwaswCommandline": [[270, 6, 1, "", "N"], [270, 6, 1, "", "T"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "a"], [270, 6, 1, "", "b"], [270, 6, 1, "", "c"], [270, 6, 1, "", "mate_file"], [270, 6, 1, "", "q"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "s"], [270, 6, 1, "", "t"], [270, 6, 1, "", "w"], [270, 6, 1, "", "z"]], "Bio.Sequencing.Applications.BwaIndexCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "algorithm"], [270, 6, 1, "", "c"], [270, 6, 1, "", "infile"], [270, 6, 1, "", "prefix"]], "Bio.Sequencing.Applications.BwaMemCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "B"], [270, 6, 1, "", "C"], [270, 6, 1, "", "E"], [270, 6, 1, "", "H"], [270, 6, 1, "", "L"], [270, 6, 1, "", "M"], [270, 6, 1, "", "O"], [270, 6, 1, "", "P"], [270, 6, 1, "", "R"], [270, 6, 1, "", "T"], [270, 6, 1, "", "U"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "a"], [270, 6, 1, "", "c"], [270, 6, 1, "", "d"], [270, 6, 1, "", "k"], [270, 6, 1, "", "p"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file1"], [270, 6, 1, "", "read_file2"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "t"], [270, 6, 1, "", "v"], [270, 6, 1, "", "w"]], "Bio.Sequencing.Applications.BwaSampeCommandline": [[270, 6, 1, "", "N"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "a"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file1"], [270, 6, 1, "", "read_file2"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "sai_file1"], [270, 6, 1, "", "sai_file2"]], "Bio.Sequencing.Applications.BwaSamseCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "n"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "sai_file"]], "Bio.Sequencing.Applications.NovoalignCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "adapter3"], [270, 6, 1, "", "adapter5"], [270, 6, 1, "", "cores"], [270, 6, 1, "", "database"], [270, 6, 1, "", "format"], [270, 6, 1, "", "fragment"], [270, 6, 1, "", "gap_extend"], [270, 6, 1, "", "gap_open"], [270, 6, 1, "", "good_bases"], [270, 6, 1, "", "homopolymer"], [270, 6, 1, "", "miRNA"], [270, 6, 1, "", "qual_digits"], [270, 6, 1, "", "quality"], [270, 6, 1, "", "r_method"], [270, 6, 1, "", "read_cal"], [270, 6, 1, "", "readfile"], [270, 6, 1, "", "recorded"], [270, 6, 1, "", "repeats"], [270, 6, 1, "", "report"], [270, 6, 1, "", "threshold"], [270, 6, 1, "", "trimming"], [270, 6, 1, "", "truncate"], [270, 6, 1, "", "unconverted"], [270, 6, 1, "", "variation"], [270, 6, 1, "", "write_cal"]], "Bio.Sequencing.Applications.SamtoolsCalmdCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "C"], [270, 6, 1, "", "E"], [270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "e"], [270, 6, 1, "", "input_bam"], [270, 6, 1, "", "r"], [270, 6, 1, "", "ref"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Applications.SamtoolsCatCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "bams"], [270, 6, 1, "", "h"], [270, 6, 1, "", "o"]], "Bio.Sequencing.Applications.SamtoolsFaidxCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "ref"]], "Bio.Sequencing.Applications.SamtoolsFixmateCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "output_file"]], "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_bam"]], "Bio.Sequencing.Applications.SamtoolsIndexCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_bam"]], "Bio.Sequencing.Applications.SamtoolsMergeCommandline": [[270, 6, 1, "", "R"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "bam"], [270, 6, 1, "", "f"], [270, 6, 1, "", "fast_bam"], [270, 6, 1, "", "h"], [270, 6, 1, "", "n"], [270, 6, 1, "", "output"], [270, 6, 1, "", "r"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Applications.SamtoolsMpileupCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "B"], [270, 6, 1, "", "C"], [270, 6, 1, "", "D"], [270, 6, 1, "", "E"], [270, 6, 1, "", "I"], [270, 6, 1, "", "L"], [270, 6, 1, "", "M"], [270, 6, 1, "", "Q"], [270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "d"], [270, 6, 1, "", "e"], [270, 6, 1, "", "f"], [270, 6, 1, "", "g"], [270, 6, 1, "", "h"], [270, 6, 1, "", "illumina_13"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "l"], [270, 6, 1, "", "o"], [270, 6, 1, "", "p"], [270, 6, 1, "", "q"], [270, 6, 1, "", "r"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Applications.SamtoolsPhaseCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "F"], [270, 6, 1, "", "Q"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "in_bam"], [270, 6, 1, "", "k"], [270, 6, 1, "", "q"]], "Bio.Sequencing.Applications.SamtoolsReheaderCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "bam_file"], [270, 6, 1, "", "sam_file"]], "Bio.Sequencing.Applications.SamtoolsRmdupCommandline": [[270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "output_file"], [270, 6, 1, "", "s"]], "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline": [[270, 6, 1, "", "Q"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "em0"], [270, 6, 1, "", "em1"], [270, 6, 1, "", "em2"], [270, 6, 1, "", "f"], [270, 6, 1, "", "i"], [270, 6, 1, "", "in_bam"]], "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input"], [270, 6, 1, "", "m"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"], [270, 6, 1, "", "out_prefix"]], "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline": [[270, 6, 1, "", "I"], [270, 6, 1, "", "O"], [270, 6, 1, "", "T"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "input"], [270, 6, 1, "", "m"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"]], "Bio.Sequencing.Applications.SamtoolsViewCommandline": [[270, 6, 1, "", "F"], [270, 6, 1, "", "H"], [270, 6, 1, "", "R"], [270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "c"], [270, 6, 1, "", "f"], [270, 6, 1, "", "fast_bam"], [270, 6, 1, "", "h"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "l"], [270, 6, 1, "", "o"], [270, 6, 1, "", "q"], [270, 6, 1, "", "r"], [270, 6, 1, "", "region"], [270, 6, 1, "", "t"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Phd": [[271, 3, 1, "", "Record"], [271, 4, 1, "", "parse"], [271, 4, 1, "", "read"]], "Bio.Sequencing.Phd.Record": [[271, 2, 1, "", "__init__"]], "Bio.SwissProt": [[272, 3, 1, "", "FeatureTable"], [273, 0, 0, "-", "KeyWList"], [272, 3, 1, "", "Record"], [272, 3, 1, "", "Reference"], [272, 1, 1, "", "SwissProtParserError"], [272, 4, 1, "", "parse"], [272, 4, 1, "", "read"]], "Bio.SwissProt.KeyWList": [[273, 3, 1, "", "Record"], [273, 4, 1, "", "parse"]], "Bio.SwissProt.KeyWList.Record": [[273, 2, 1, "", "__init__"]], "Bio.SwissProt.Record": [[272, 2, 1, "", "__init__"]], "Bio.SwissProt.Reference": [[272, 2, 1, "", "__init__"]], "Bio.SwissProt.SwissProtParserError": [[272, 2, 1, "", "__init__"]], "Bio.TogoWS": [[274, 4, 1, "", "convert"], [274, 4, 1, "", "entry"], [274, 4, 1, "", "search"], [274, 4, 1, "", "search_count"], [274, 4, 1, "", "search_iter"]], "Bio.UniGene": [[275, 3, 1, "", "ProtsimLine"], [275, 3, 1, "", "Record"], [275, 3, 1, "", "STSLine"], [275, 3, 1, "", "SequenceLine"], [275, 4, 1, "", "parse"], [275, 4, 1, "", "read"]], "Bio.UniGene.ProtsimLine": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniGene.Record": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniGene.STSLine": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniGene.SequenceLine": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniProt": [[277, 0, 0, "-", "GOA"], [276, 4, 1, "", "search"]], "Bio.UniProt.GOA": [[277, 4, 1, "", "gafbyproteiniterator"], [277, 4, 1, "", "gafiterator"], [277, 4, 1, "", "gpa_iterator"], [277, 4, 1, "", "gpi_iterator"], [277, 4, 1, "", "record_has"], [277, 4, 1, "", "writebyproteinrec"], [277, 4, 1, "", "writerec"]], "Bio.bgzf": [[278, 4, 1, "", "BgzfBlocks"], [278, 3, 1, "", "BgzfReader"], [278, 3, 1, "", "BgzfWriter"], [278, 4, 1, "", "make_virtual_offset"], [278, 4, 1, "", "open"], [278, 4, 1, "", "split_virtual_offset"]], "Bio.bgzf.BgzfReader": [[278, 2, 1, "", "__enter__"], [278, 2, 1, "", "__exit__"], [278, 2, 1, "", "__init__"], [278, 2, 1, "", "__iter__"], [278, 2, 1, "", "__next__"], [278, 2, 1, "", "close"], [278, 2, 1, "", "fileno"], [278, 2, 1, "", "isatty"], [278, 2, 1, "", "read"], [278, 2, 1, "", "readline"], [278, 2, 1, "", "seek"], [278, 2, 1, "", "seekable"], [278, 2, 1, "", "tell"]], "Bio.bgzf.BgzfWriter": [[278, 2, 1, "", "__enter__"], [278, 2, 1, "", "__exit__"], [278, 2, 1, "", "__init__"], [278, 2, 1, "", "close"], [278, 2, 1, "", "fileno"], [278, 2, 1, "", "flush"], [278, 2, 1, "", "isatty"], [278, 2, 1, "", "seekable"], [278, 2, 1, "", "tell"], [278, 2, 1, "", "write"]], "Bio.codonalign": [[279, 4, 1, "", "build"], [280, 0, 0, "-", "codonalignment"], [281, 0, 0, "-", "codonseq"]], "Bio.codonalign.codonalignment": [[280, 3, 1, "", "CodonAlignment"], [280, 4, 1, "", "mktest"]], "Bio.codonalign.codonalignment.CodonAlignment": [[280, 2, 1, "", "__add__"], [280, 2, 1, "", "__getitem__"], [280, 2, 1, "", "__init__"], [280, 2, 1, "", "__str__"], [280, 2, 1, "", "from_msa"], [280, 2, 1, "", "get_aln_length"], [280, 2, 1, "", "get_dn_ds_matrix"], [280, 2, 1, "", "get_dn_ds_tree"], [280, 2, 1, "", "toMultipleSeqAlignment"]], "Bio.codonalign.codonseq": [[281, 3, 1, "", "CodonSeq"], [281, 4, 1, "", "cal_dn_ds"]], "Bio.codonalign.codonseq.CodonSeq": [[281, 5, 1, "", "__abstractmethods__"], [281, 2, 1, "", "__init__"], [281, 2, 1, "", "from_seq"], [281, 2, 1, "", "full_translate"], [281, 2, 1, "", "get_codon"], [281, 2, 1, "", "get_codon_num"], [281, 2, 1, "", "get_full_rf_table"], [281, 2, 1, "", "toSeq"], [281, 2, 1, "", "translate"], [281, 2, 1, "", "ungap"]], "Bio.kNN": [[282, 4, 1, "", "calculate"], [282, 4, 1, "", "classify"], [282, 4, 1, "", "equal_weight"], [282, 3, 1, "", "kNN"], [282, 4, 1, "", "train"]], "Bio.kNN.kNN": [[282, 2, 1, "", "__init__"]], "Bio.motifs": [[283, 3, 1, "", "Instances"], [283, 3, 1, "", "Motif"], [284, 0, 0, "-", "alignace"], [285, 0, 0, "-", "applications"], [286, 0, 0, "-", "clusterbuster"], [283, 4, 1, "", "create"], [287, 0, 0, "-", "jaspar"], [289, 0, 0, "-", "mast"], [290, 0, 0, "-", "matrix"], [291, 0, 0, "-", "meme"], [292, 0, 0, "-", "minimal"], [283, 4, 1, "", "parse"], [293, 0, 0, "-", "pfm"], [283, 4, 1, "", "read"], [294, 0, 0, "-", "thresholds"], [295, 0, 0, "-", "transfac"], [283, 4, 1, "", "write"], [296, 0, 0, "-", "xms"]], "Bio.motifs.Instances": [[283, 2, 1, "", "__init__"], [283, 2, 1, "", "__str__"], [283, 2, 1, "", "count"], [283, 2, 1, "", "reverse_complement"], [283, 2, 1, "", "search"]], "Bio.motifs.Motif": [[283, 2, 1, "", "__format__"], [283, 2, 1, "", "__getitem__"], [283, 2, 1, "", "__init__"], [283, 2, 1, "", "__len__"], [283, 2, 1, "", "__str__"], [283, 6, 1, "", "anticonsensus"], [283, 6, 1, "", "background"], [283, 6, 1, "", "consensus"], [283, 6, 1, "", "degenerate_consensus"], [283, 2, 1, "", "format"], [283, 6, 1, "", "instances"], [283, 6, 1, "", "mask"], [283, 6, 1, "", "pseudocounts"], [283, 6, 1, "", "pssm"], [283, 6, 1, "", "pwm"], [283, 6, 1, "", "relative_entropy"], [283, 2, 1, "", "reverse_complement"], [283, 2, 1, "", "weblogo"]], "Bio.motifs.alignace": [[284, 3, 1, "", "Record"], [284, 4, 1, "", "read"]], "Bio.motifs.alignace.Record": [[284, 2, 1, "", "__init__"]], "Bio.motifs.clusterbuster": [[286, 3, 1, "", "Record"], [286, 4, 1, "", "read"], [286, 4, 1, "", "write"]], "Bio.motifs.clusterbuster.Record": [[286, 2, 1, "", "__str__"]], "Bio.motifs.jaspar": [[287, 3, 1, "", "Motif"], [287, 3, 1, "", "Record"], [287, 4, 1, "", "calculate_pseudocounts"], [288, 0, 0, "-", "db"], [287, 4, 1, "", "read"], [287, 4, 1, "", "split_jaspar_id"], [287, 4, 1, "", "write"]], "Bio.motifs.jaspar.Motif": [[287, 2, 1, "", "__eq__"], [287, 2, 1, "", "__hash__"], [287, 2, 1, "", "__init__"], [287, 2, 1, "", "__str__"], [287, 6, 1, "", "base_id"], [287, 6, 1, "", "version"]], "Bio.motifs.jaspar.Record": [[287, 2, 1, "", "__init__"], [287, 2, 1, "", "__str__"], [287, 2, 1, "", "to_dict"]], "Bio.motifs.jaspar.db": [[288, 3, 1, "", "JASPAR5"]], "Bio.motifs.jaspar.db.JASPAR5": [[288, 2, 1, "", "__init__"], [288, 2, 1, "", "__str__"], [288, 2, 1, "", "fetch_motif_by_id"], [288, 2, 1, "", "fetch_motifs"], [288, 2, 1, "", "fetch_motifs_by_name"]], "Bio.motifs.mast": [[289, 3, 1, "", "Record"], [289, 4, 1, "", "read"]], "Bio.motifs.mast.Record": [[289, 2, 1, "", "__getitem__"], [289, 2, 1, "", "__init__"]], "Bio.motifs.matrix": [[290, 3, 1, "", "FrequencyPositionMatrix"], [290, 3, 1, "", "GenericPositionMatrix"], [290, 3, 1, "", "PositionSpecificScoringMatrix"], [290, 3, 1, "", "PositionWeightMatrix"]], "Bio.motifs.matrix.FrequencyPositionMatrix": [[290, 2, 1, "", "normalize"]], "Bio.motifs.matrix.GenericPositionMatrix": [[290, 2, 1, "", "__getitem__"], [290, 2, 1, "", "__init__"], [290, 2, 1, "", "__str__"], [290, 6, 1, "", "anticonsensus"], [290, 2, 1, "", "calculate_consensus"], [290, 6, 1, "", "consensus"], [290, 6, 1, "", "degenerate_consensus"], [290, 6, 1, "", "gc_content"], [290, 2, 1, "", "reverse_complement"]], "Bio.motifs.matrix.PositionSpecificScoringMatrix": [[290, 2, 1, "", "calculate"], [290, 2, 1, "", "dist_pearson"], [290, 2, 1, "", "dist_pearson_at"], [290, 2, 1, "", "distribution"], [290, 6, 1, "", "gc_content"], [290, 6, 1, "", "max"], [290, 2, 1, "", "mean"], [290, 6, 1, "", "min"], [290, 2, 1, "", "search"], [290, 2, 1, "", "std"]], "Bio.motifs.matrix.PositionWeightMatrix": [[290, 2, 1, "", "__init__"], [290, 2, 1, "", "log_odds"]], "Bio.motifs.meme": [[291, 3, 1, "", "Instance"], [291, 3, 1, "", "Motif"], [291, 3, 1, "", "Record"], [291, 4, 1, "", "read"]], "Bio.motifs.meme.Instance": [[291, 5, 1, "", "__abstractmethods__"], [291, 2, 1, "", "__init__"]], "Bio.motifs.meme.Motif": [[291, 2, 1, "", "__init__"]], "Bio.motifs.meme.Record": [[291, 2, 1, "", "__getitem__"], [291, 2, 1, "", "__init__"]], "Bio.motifs.minimal": [[292, 3, 1, "", "Record"], [292, 4, 1, "", "read"]], "Bio.motifs.minimal.Record": [[292, 2, 1, "", "__getitem__"], [292, 2, 1, "", "__init__"]], "Bio.motifs.pfm": [[293, 3, 1, "", "Record"], [293, 4, 1, "", "read"], [293, 4, 1, "", "write"]], "Bio.motifs.pfm.Record": [[293, 2, 1, "", "__str__"]], "Bio.motifs.thresholds": [[294, 3, 1, "", "ScoreDistribution"]], "Bio.motifs.thresholds.ScoreDistribution": [[294, 2, 1, "", "__init__"], [294, 2, 1, "", "modify"], [294, 2, 1, "", "threshold_balanced"], [294, 2, 1, "", "threshold_fnr"], [294, 2, 1, "", "threshold_fpr"], [294, 2, 1, "", "threshold_patser"]], "Bio.motifs.transfac": [[295, 3, 1, "", "Motif"], [295, 3, 1, "", "Record"], [295, 4, 1, "", "read"], [295, 4, 1, "", "write"]], "Bio.motifs.transfac.Motif": [[295, 2, 1, "", "__getitem__"], [295, 5, 1, "", "multiple_value_keys"], [295, 5, 1, "", "reference_keys"]], "Bio.motifs.transfac.Record": [[295, 2, 1, "", "__init__"], [295, 2, 1, "", "__str__"]], "Bio.motifs.xms": [[296, 3, 1, "", "Record"], [296, 3, 1, "", "XMSScanner"], [296, 4, 1, "", "read"]], "Bio.motifs.xms.Record": [[296, 2, 1, "", "__str__"]], "Bio.motifs.xms.XMSScanner": [[296, 2, 1, "", "__init__"], [296, 2, 1, "", "get_acgt"], [296, 2, 1, "", "get_property_value"], [296, 2, 1, "", "get_text"], [296, 2, 1, "", "handle_motif"]], "Bio.pairwise2": [[297, 3, 1, "", "Alignment"], [297, 3, 1, "", "affine_penalty"], [297, 4, 1, "", "calc_affine_penalty"], [297, 3, 1, "", "dictionary_match"], [297, 4, 1, "", "format_alignment"], [297, 3, 1, "", "identity_match"], [297, 4, 1, "", "print_matrix"]], "Bio.pairwise2.Alignment": [[297, 2, 1, "", "__getnewargs__"], [297, 2, 1, "", "__new__"], [297, 2, 1, "", "__repr__"], [297, 5, 1, "", "__slots__"], [297, 5, 1, "", "end"], [297, 5, 1, "", "score"], [297, 5, 1, "", "seqA"], [297, 5, 1, "", "seqB"], [297, 5, 1, "", "start"]], "Bio.pairwise2.affine_penalty": [[297, 2, 1, "", "__call__"], [297, 2, 1, "", "__init__"]], "Bio.pairwise2.dictionary_match": [[297, 2, 1, "", "__call__"], [297, 2, 1, "", "__init__"]], "Bio.pairwise2.identity_match": [[297, 2, 1, "", "__call__"], [297, 2, 1, "", "__init__"]], "Bio.phenotype": [[298, 4, 1, "", "parse"], [299, 0, 0, "-", "phen_micro"], [300, 0, 0, "-", "pm_fitting"], [298, 4, 1, "", "read"], [298, 4, 1, "", "write"]], "Bio.phenotype.phen_micro": [[299, 4, 1, "", "CsvIterator"], [299, 4, 1, "", "JsonIterator"], [299, 3, 1, "", "JsonWriter"], [299, 3, 1, "", "PlateRecord"], [299, 3, 1, "", "WellRecord"]], "Bio.phenotype.phen_micro.JsonWriter": [[299, 2, 1, "", "__init__"], [299, 2, 1, "", "write"]], "Bio.phenotype.phen_micro.PlateRecord": [[299, 2, 1, "", "__add__"], [299, 2, 1, "", "__contains__"], [299, 2, 1, "", "__delitem__"], [299, 2, 1, "", "__eq__"], [299, 2, 1, "", "__getitem__"], [299, 5, 1, "", "__hash__"], [299, 2, 1, "", "__init__"], [299, 2, 1, "", "__iter__"], [299, 2, 1, "", "__len__"], [299, 2, 1, "", "__repr__"], [299, 2, 1, "", "__setitem__"], [299, 2, 1, "", "__str__"], [299, 2, 1, "", "__sub__"], [299, 2, 1, "", "get_column"], [299, 2, 1, "", "get_row"], [299, 2, 1, "", "subtract_control"]], "Bio.phenotype.phen_micro.WellRecord": [[299, 2, 1, "", "__add__"], [299, 2, 1, "", "__eq__"], [299, 2, 1, "", "__getitem__"], [299, 5, 1, "", "__hash__"], [299, 2, 1, "", "__init__"], [299, 2, 1, "", "__iter__"], [299, 2, 1, "", "__len__"], [299, 2, 1, "", "__repr__"], [299, 2, 1, "", "__setitem__"], [299, 2, 1, "", "__str__"], [299, 2, 1, "", "__sub__"], [299, 2, 1, "", "fit"], [299, 2, 1, "", "get_raw"], [299, 2, 1, "", "get_signals"], [299, 2, 1, "", "get_times"]], "Bio.phenotype.pm_fitting": [[300, 4, 1, "", "fit"], [300, 4, 1, "", "get_area"], [300, 4, 1, "", "gompertz"], [300, 4, 1, "", "guess_lag"], [300, 4, 1, "", "guess_plateau"], [300, 4, 1, "", "logistic"], [300, 4, 1, "", "richards"]], "BioSQL": [[302, 0, 0, "-", "BioSeq"], [303, 0, 0, "-", "BioSeqDatabase"], [304, 0, 0, "-", "DBUtils"], [305, 0, 0, "-", "Loader"]], "BioSQL.BioSeq": [[302, 3, 1, "", "DBSeqRecord"]], "BioSQL.BioSeq.DBSeqRecord": [[302, 2, 1, "", "__init__"], [302, 6, 1, "", "annotations"], [302, 6, 1, "", "dbxrefs"], [302, 6, 1, "", "features"], [302, 6, 1, "", "seq"]], "BioSQL.BioSeqDatabase": [[303, 3, 1, "", "Adaptor"], [303, 3, 1, "", "BioSeqDatabase"], [303, 3, 1, "", "DBServer"], [303, 3, 1, "", "MysqlConnectorAdaptor"], [303, 4, 1, "", "open_database"]], "BioSQL.BioSeqDatabase.Adaptor": [[303, 2, 1, "", "__init__"], [303, 2, 1, "", "autocommit"], [303, 2, 1, "", "close"], [303, 2, 1, "", "commit"], [303, 2, 1, "", "execute"], [303, 2, 1, "", "execute_and_fetch_col0"], [303, 2, 1, "", "execute_and_fetchall"], [303, 2, 1, "", "execute_one"], [303, 2, 1, "", "executemany"], [303, 2, 1, "", "fetch_dbid_by_dbname"], [303, 2, 1, "", "fetch_seqid_by_accession"], [303, 2, 1, "", "fetch_seqid_by_display_id"], [303, 2, 1, "", "fetch_seqid_by_identifier"], [303, 2, 1, "", "fetch_seqid_by_version"], [303, 2, 1, "", "fetch_seqids_by_accession"], [303, 2, 1, "", "get_subseq_as_string"], [303, 2, 1, "", "last_id"], [303, 2, 1, "", "list_any_ids"], [303, 2, 1, "", "list_biodatabase_names"], [303, 2, 1, "", "list_bioentry_display_ids"], [303, 2, 1, "", "list_bioentry_ids"], [303, 2, 1, "", "rollback"]], "BioSQL.BioSeqDatabase.BioSeqDatabase": [[303, 2, 1, "", "__contains__"], [303, 2, 1, "", "__delitem__"], [303, 2, 1, "", "__getitem__"], [303, 2, 1, "", "__init__"], [303, 2, 1, "", "__iter__"], [303, 2, 1, "", "__len__"], [303, 2, 1, "", "__repr__"], [303, 2, 1, "", "get_Seq_by_acc"], [303, 2, 1, "", "get_Seq_by_id"], [303, 2, 1, "", "get_Seq_by_ver"], [303, 2, 1, "", "get_Seqs_by_acc"], [303, 2, 1, "", "items"], [303, 2, 1, "", "keys"], [303, 2, 1, "", "load"], [303, 2, 1, "", "lookup"], [303, 2, 1, "", "values"]], "BioSQL.BioSeqDatabase.DBServer": [[303, 2, 1, "", "__contains__"], [303, 2, 1, "", "__delitem__"], [303, 2, 1, "", "__getitem__"], [303, 2, 1, "", "__init__"], [303, 2, 1, "", "__iter__"], [303, 2, 1, "", "__len__"], [303, 2, 1, "", "__repr__"], [303, 2, 1, "", "close"], [303, 2, 1, "", "commit"], [303, 2, 1, "", "items"], [303, 2, 1, "", "keys"], [303, 2, 1, "", "load_database_sql"], [303, 2, 1, "", "new_database"], [303, 2, 1, "", "rollback"], [303, 2, 1, "", "values"]], "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor": [[303, 2, 1, "", "execute_and_fetch_col0"], [303, 2, 1, "", "execute_and_fetchall"], [303, 2, 1, "", "execute_one"]], "BioSQL.DBUtils": [[304, 3, 1, "", "Generic_dbutils"], [304, 3, 1, "", "Mysql_dbutils"], [304, 3, 1, "", "Pgdb_dbutils"], [304, 3, 1, "", "Psycopg2_dbutils"], [304, 3, 1, "", "Sqlite_dbutils"], [304, 4, 1, "", "get_dbutils"]], "BioSQL.DBUtils.Generic_dbutils": [[304, 2, 1, "", "__init__"], [304, 2, 1, "", "autocommit"], [304, 2, 1, "", "execute"], [304, 2, 1, "", "executemany"], [304, 2, 1, "", "last_id"], [304, 2, 1, "", "tname"]], "BioSQL.DBUtils.Mysql_dbutils": [[304, 2, 1, "", "last_id"]], "BioSQL.DBUtils.Pgdb_dbutils": [[304, 2, 1, "", "autocommit"]], "BioSQL.DBUtils.Psycopg2_dbutils": [[304, 2, 1, "", "autocommit"]], "BioSQL.DBUtils.Sqlite_dbutils": [[304, 2, 1, "", "execute"], [304, 2, 1, "", "executemany"]], "BioSQL.Loader": [[305, 3, 1, "", "DatabaseLoader"], [305, 3, 1, "", "DatabaseRemover"]], "BioSQL.Loader.DatabaseLoader": [[305, 2, 1, "", "__init__"], [305, 2, 1, "", "load_seqrecord"]], "BioSQL.Loader.DatabaseRemover": [[305, 2, 1, "", "__init__"], [305, 2, 1, "", "remove"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "exception", "Python exception"], "2": ["py", "method", "Python method"], "3": ["py", "class", "Python class"], "4": ["py", "function", "Python function"], "5": ["py", "attribute", "Python attribute"], "6": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:exception", "2": "py:method", "3": "py:class", "4": "py:function", "5": "py:attribute", "6": "py:property"}, "terms": {"": [0, 2, 3, 5, 6, 8, 9, 10, 11, 12, 13, 14, 16, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 36, 37, 55, 56, 59, 61, 65, 66, 67, 68, 69, 70, 71, 73, 76, 80, 81, 83, 84, 90, 93, 96, 99, 100, 104, 111, 112, 113, 114, 115, 117, 119, 122, 129, 130, 132, 137, 139, 140, 141, 146, 149, 152, 154, 156, 157, 159, 168, 169, 172, 177, 178, 182, 183, 185, 188, 190, 193, 195, 196, 197, 199, 202, 205, 209, 217, 218, 220, 221, 222, 226, 229, 234, 237, 238, 239, 240, 241, 244, 245, 247, 248, 249, 250, 251, 253, 256, 257, 259, 260, 261, 262, 263, 264, 265, 268, 269, 270, 272, 274, 275, 278, 280, 281, 287, 288, 290, 293, 296, 297, 298, 299, 304, 305, 307], "0": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 35, 36, 46, 51, 53, 54, 61, 62, 66, 67, 68, 69, 70, 71, 73, 80, 83, 87, 88, 89, 90, 92, 94, 99, 100, 104, 105, 108, 112, 113, 114, 120, 122, 126, 129, 132, 135, 137, 138, 139, 140, 141, 148, 152, 154, 156, 157, 161, 168, 169, 170, 173, 176, 177, 182, 183, 184, 186, 187, 189, 190, 195, 197, 199, 202, 203, 204, 207, 214, 216, 217, 222, 229, 230, 233, 234, 236, 237, 238, 240, 243, 246, 247, 249, 251, 252, 253, 260, 261, 263, 264, 265, 270, 277, 278, 280, 281, 283, 286, 288, 289, 290, 291, 292, 294, 297, 299, 303], "00": [0, 2, 11, 12, 16, 32, 53, 169, 176, 216, 251, 261, 263, 264, 288, 299], "000": [6, 11, 32, 126, 182, 207, 278], "0000": [0, 11, 13], "000000": [0, 11, 13, 182, 199, 299], "000000001": 251, "00000001": 251, "00001": [6, 202, 203], "0000313": 25, "0000417": 0, "0001": [11, 25], "0001068": 53, "0002": [0, 13, 25], "00029": 0, "0003": 0, "0005260": 267, "0006": 13, "0008270": 197, "0009490": 182, "001": [3, 11, 24, 69, 80, 182], "0012": 13, "0013": 13, "0019": 13, "001991": 11, "002": [11, 69], "00206457": 13, "0021": 13, "0022": [2, 137], "002263": 11, "002387": 11, "002418": 11, "0025": 32, "002613": 11, "002850": 11, "002868": 11, "003": 11, "00332": 11, "003922": 104, "003964": 11, "004030": 11, "004352": 11, "004470": 11, "004653": 11, "005": 11, "0051537": 25, "005737": 11, "006": 11, "006667": 11, "007769": 11, "0080635": 137, "008165": 11, "0089": 13, "009": [0, 2, 11], "0095": [12, 13], "00961538461538462": 11, "00e": 11, "01": [0, 11, 16, 21, 68, 149, 185, 214, 216, 251], "010": [11, 126], "0108695652173913": 11, "0112": 13, "012": [0, 11], "012345": 182, "0132": 13, "013277": 11, "014": 11, "0142": 13, "01421": 199, "014631": 11, "01477186": 11, "016": 11, "0162": 13, "016304347826087": 11, "0166": [12, 13], "017663": 11, "019": 2, "0194": 13, "019497": 11, "0197": [12, 13], "01e": [216, 291], "02": [0, 4, 11, 16, 73, 105, 149, 185, 216, 251, 264], "020": 11, "02024": 2, "020643": 11, "021": 126, "0215": 13, "0217391304347826": 11, "0224": 13, "023": 11, "0230646871686108": 11, "023194": 13, "023344": 11, "024": 32, "025": 32, "025056": 11, "0251": [12, 13], "025231": 11, "025414": 11, "026": 11, "026128": 11, "026652": 11, "026732": 11, "026737": 11, "0268": [12, 13], "026928": 11, "027444": 11, "028": 11, "02832e": 3, "0284994697773065": 11, "0288": [12, 13], "029759": 11, "02e": 216, "03": [0, 7, 11, 32, 86, 149, 168, 176, 216], "0301021": 13, "03370807": 11, "0339342523860021": 11, "034": 3, "0342": [12, 13], "036": 13, "037": 11, "03734159": 11, "037406": 11, "038461538461538464": 199, "038860": 11, "0397": 13, "04": [0, 3, 7, 11, 149, 216, 251, 264, 270, 277], "040264": 11, "0406": [12, 13], "04066086": 11, "040694591728526": 11, "041": 68, "04194000000000003": 199, "043": 11, "0436": [12, 13], "04403040513919": 169, "045": 11, "0461293743372216": 11, "0465": [12, 13], "0466": 13, "047": 11, "047316": 11, "04807692307692307": 199, "049537": 11, "0499": 13, "04e": 216, "05": [0, 2, 7, 11, 12, 69, 100, 104, 263, 270, 280], "050": [0, 11], "0502386002120891": 11, "051282051282051266": 199, "0518": [12, 13], "052017": 11, "053296": 13, "054": 11, "0546": 13, "0553": [12, 13], "056317": 11, "0585": 13, "058787": 11, "059": 24, "05e": 291, "06": [0, 3, 7, 11, 13, 17, 20, 149, 291], "060204": 13, "060312": 11, "06172252": 11, "062": 11, "062462": 11, "0627": 13, "0631": 13, "0660": [12, 13], "067715": 13, "068": 11, "068728": 13, "0691940615058324": 11, "069475": 13, "06e": 216, "07": [0, 11, 185, 216, 291], "0705": [12, 13], "070505": 2, "071113_eas56_0053": 251, "0740": 13, "07477": 199, "0752": [12, 13], "076117": 11, "07692307692307693": 199, "077066": 11, "078208": 11, "07922333291745": 11, "0793": 13, "07e": 216, "08": [11, 149, 291], "081202": 32, "081468": 13, "0833333": 11, "0833333334583333": 11, "08531": 199, "089579": 11, "0896076352067868": 11, "08e": 291, "09": [7, 11, 216, 277], "090": 11, "0939": 13, "0976": [12, 13], "098612": 11, "09919716": 11, "0b100": 0, "0b1000101": 0, "0c": 169, "0cc864": 183, "0e": [3, 11, 122], "0pdb": 158, "0x": [0, 30, 68], "0x10403d850": [30, 68], "0xc356b0": 11, "1": [0, 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 51, 53, 55, 56, 61, 62, 65, 66, 68, 69, 70, 71, 73, 74, 76, 80, 83, 92, 93, 94, 99, 100, 101, 102, 104, 105, 108, 109, 113, 120, 122, 126, 129, 132, 135, 136, 137, 139, 148, 149, 152, 154, 155, 156, 157, 158, 161, 169, 170, 172, 173, 176, 182, 183, 184, 186, 187, 189, 190, 195, 197, 199, 201, 204, 205, 206, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 221, 222, 234, 236, 237, 238, 241, 243, 245, 247, 251, 252, 253, 256, 260, 261, 264, 265, 270, 274, 277, 278, 281, 282, 283, 288, 289, 290, 291, 292, 294, 295, 297, 299, 303, 304, 307], "10": [0, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 16, 17, 20, 22, 23, 24, 30, 31, 32, 50, 53, 56, 59, 65, 66, 67, 68, 69, 70, 73, 80, 83, 87, 88, 91, 93, 100, 104, 119, 122, 125, 126, 137, 139, 140, 146, 169, 175, 182, 197, 202, 206, 207, 215, 217, 218, 221, 222, 226, 236, 237, 238, 240, 245, 249, 251, 252, 253, 260, 262, 264, 265, 267, 270, 272, 274, 276, 278, 279, 290, 291, 294], "100": [0, 3, 4, 6, 7, 8, 11, 15, 20, 21, 22, 23, 25, 32, 61, 69, 80, 122, 157, 182, 183, 207, 217, 237, 238, 253, 261, 264, 265, 270, 274, 278], "1000": [0, 4, 11, 13, 14, 15, 22, 32, 36, 49, 53, 64, 69, 215, 237, 261, 270], "10000": [0, 8, 122, 182, 202, 203, 270], "100000": [270, 278], "1000000": 8, "100000028": 7, "100002": 0, "1002": [2, 13, 137, 149, 262], "100598": 13, "1006": 2, "1007": 2, "10076": 62, "10090": [7, 11], "101": [0, 20, 217, 218], "1010b": 214, "1011": 69, "1011751523": 68, "101564639": 7, "101574747": 7, "101582229": 7, "101585369": 7, "101586429": 7, "101589678": 7, "1016": [2, 137], "101627224": 7, "101639023": 7, "101645372": 7, "101647801": 7, "101647835": 7, "101649614": 7, "101653734": 7, "101657941": 7, "101659814": 7, "101660833": 7, "101661657": 7, "101664671": 7, "101669877": 7, "101671907": 7, "101_9001_1242061629": 7, "101m": 0, "102": [0, 17, 32], "1020": 22, "1021": [7, 169], "1023": 263, "1024": [169, 252], "10256410256410259": 199, "10271783": 0, "10271816": 0, "103": [0, 11, 13, 278], "1030": 6, "1031": 263, "10328": 137, "10338": 2, "1038": [32, 100, 267], "104": [66, 169, 278], "10458": 10, "104968": 11, "105": [68, 217, 237], "105172": 237, "105173": 237, "1055": 0, "10557": 32, "10562": 32, "10574": 0, "106": [0, 11, 206, 253], "10638": 21, "10666704": [34, 281], "107": [2, 6, 11, 24], "107212": 278, "107263": 278, "107264": 278, "1073": 2, "1074592421627525": 11, "108": [2, 68, 217, 237], "1081": [7, 260], "1083": 288, "108462": 237, "109": 264, "10915": 2, "10919": 2, "1093": [2, 73, 251, 252], "1098": 0, "10a": 214, "10mb": 270, "10th": 0, "11": [0, 2, 3, 4, 6, 7, 8, 11, 13, 20, 21, 22, 30, 32, 36, 67, 68, 73, 94, 104, 137, 157, 166, 209, 236, 237, 251, 260, 261, 264, 265, 270, 281, 299], "110": [16, 237], "1101": [0, 2], "1102": 288, "1104": 2, "1105": 2, "11057692307692304": 199, "1107": 175, "1109": 6, "111": [3, 6, 16, 20, 222], "1110": 3, "1111": 3, "111776384": [0, 30], "111776784": [0, 30], "111776785": [0, 30], "111982717": [0, 30], "111982775": [0, 30], "111987921": [0, 30], "111988073": [0, 30], "112": [0, 3, 11, 16, 149], "112009200": [0, 30], "112009302": [0, 30], "112019962": [0, 30], "112019978": [0, 30], "1125": 0, "1128": 2, "113": [13, 15, 16, 32, 156], "114": [6, 16, 183, 222], "1141": 7, "1144": 0, "1145": 2, "1146": 2, "114619004": 7, "11464971": [20, 217, 218], "115": [16, 237], "11538461538461536": 199, "116": [0, 11, 12], "1160": [68, 217], "116576": 7, "1166": [68, 217], "1167": 0, "116834": 0, "116835": 0, "116837": 0, "116856": 0, "116872": 0, "11691a": 11, "116l": 149, "117": [3, 7, 16, 237], "117054": 11, "1173": 3, "117512670": 22, "117512683": 22, "117512690": 22, "117512700": 22, "118": [0, 13, 56, 126, 264], "1186": [2, 69, 197], "119": [6, 13, 56], "119000876": 22, "1190160": 7, "1195311108": 278, "1198066": 0, "11e": 291, "12": [0, 2, 3, 7, 8, 10, 11, 12, 13, 16, 17, 20, 21, 22, 25, 30, 31, 32, 35, 36, 38, 69, 73, 93, 94, 99, 104, 125, 137, 141, 149, 183, 206, 207, 215, 218, 221, 237, 245, 251, 253, 260, 263, 264, 265, 281, 288, 299], "120": [0, 3, 13, 15, 16, 30, 32, 56, 169, 237, 253, 264], "1200": [0, 207], "1200166": 21, "1201": 7, "120217": 11, "1205": [68, 217], "120626": 32, "121": [0, 7], "1219041180": 3, "122": [3, 11, 68, 169, 237], "122114": 0, "122250000": [0, 30], "122250400": [0, 30], "12230038": 7, "1226": 0, "1226m3m1m": 0, "122835789": [0, 30], "122835847": [0, 30], "122840993": [0, 30], "122841145": [0, 30], "1229": 0, "122907212": [0, 30], "122907314": [0, 30], "122909818": [0, 30], "122909819": [0, 30], "122909835": [0, 30], "123": [32, 68, 169, 237, 256], "1230": 0, "12300": 0, "12301": 0, "12318": 0, "1234593": 222, "1234630": 222, "1235": [12, 13], "12368254": 7, "124": [0, 13, 56, 237, 288], "124556": 278, "124602": 278, "124653": 278, "125": [6, 8, 17, 56], "1250": 299, "126": [0, 251, 264, 278], "1261": 7, "12654095": 68, "126722851": 7, "127": [0, 11, 24, 299], "127706": 13, "128": [0, 6, 16, 17, 169, 183, 253], "1281": 261, "129": [0, 11, 16, 222], "1295": 261, "129628": 68, "129993255": 0, "13": [0, 2, 3, 7, 8, 11, 12, 13, 14, 15, 20, 21, 22, 30, 38, 68, 87, 104, 113, 137, 153, 183, 199, 206, 217, 222, 237, 249, 251, 260, 297, 299], "130": [11, 13, 237, 253], "1302": 7, "130382477": 0, "130383872": 0, "130383910": 0, "130383918": 0, "130383920": 0, "130383943": 0, "130383946": 0, "130383958": 0, "130384222": 0, "130388520": 0, "1305": 169, "130607995": 0, "130611000": 0, "130611008": 0, "130611010": 0, "130611033": 0, "130611036": 0, "130611048": 0, "130620657": 0, "130881": 278, "130946": 278, "131": 0, "131007": 11, "131071": 278, "131072": 278, "1313": [68, 217], "1318045": 0, "1318046": 0, "1318075": 0, "1319220": 222, "1319271": 0, "1319274": 0, "1319275": [0, 222], "132": [0, 16], "132427": 11, "1327": 149, "132953340402969": 11, "13298": 260, "133": [0, 68], "133105": 0, "133919957": 0, "133922962": 0, "133922970": 0, "133922972": 0, "133922995": 0, "133922998": 0, "133923010": 0, "133924947": 0, "133926309": 0, "133926312": 0, "133932620": 0, "134": [0, 2, 253], "1347369": 68, "1348912": 238, "1348917": 238, "135": [0, 11], "1353": [2, 283], "136": 16, "1361": [2, 283], "136185": 0, "136186": 0, "1362": 0, "136245": 0, "136286": 0, "13687943": 11, "13691": 199, "137": 0, "1371": [137, 182], "137181": 7, "138": [0, 4, 11, 256], "13813": 3, "13819": 6, "1383": [68, 217], "13919613": 23, "13925890": 23, "1394": 2, "13990994": 238, "13f": 169, "14": [0, 2, 3, 7, 8, 11, 13, 15, 20, 22, 30, 32, 68, 69, 71, 104, 113, 149, 206, 237, 249, 251, 253, 260, 263, 264, 281, 299], "140": [16, 183], "1403": 2, "14098": 169, "141213431": 0, "1415": 157, "14150838": [21, 23], "142": [13, 16], "1422": 2, "1423": 2, "143": [11, 16, 278], "143444": 2, "144": [0, 15], "14423076923076922": 199, "145": [0, 11, 256], "1453": 2, "14530136": 182, "1454": 2, "145469": 13, "145707": 3, "14580": 6, "146": [0, 30], "1460": 264, "14630660": [7, 83], "146364022": 0, "1465": 264, "1467": 7, "147": [13, 25], "1471": [2, 69, 197, 218], "1475": 240, "148": [0, 11, 30], "14863": 2, "14868": 2, "14871861": 7, "1488655": 21, "149": [11, 12, 13, 116], "14918518": 11, "14939": 278, "149736546": 22, "149742490": 7, "14986": 209, "149m1d7m1i17m3d60m5i6m1i13m2i13m4i30m2i6m2d112m": 0, "15": [0, 2, 3, 7, 8, 11, 13, 16, 20, 31, 32, 53, 69, 83, 87, 88, 104, 206, 237, 249, 251, 253, 260, 261, 263, 264, 270, 278, 281, 283, 299], "150": [2, 8, 11, 30, 237, 253], "15000": 0, "1501": 2, "1505": 13, "15073": 278, "151": 2, "151104725": 0, "152": [15, 140, 156], "152_d_c": 15, "152_d_ca": 15, "152_d_cb": 15, "152_d_cg": 15, "152_d_n": 15, "153": [11, 15, 251], "1530": 0, "1531": 2, "15310": 90, "1532": 0, "153846": 199, "15384615384615383": 199, "154478": [237, 278], "155": [68, 265], "155029160": 0, "155029206": 0, "155184381": 0, "155563": 7, "155784573": 0, "155784581": 0, "155784583": 0, "155784606": 0, "155784609": 0, "155784621": 0, "155814782": 0, "155814790": 0, "155814792": 0, "155814815": 0, "155814818": 0, "155814830": 0, "155c_": 214, "156": [0, 30], "1560": 0, "15613794": 11, "156330991": 22, "156354347": 0, "156354348": 0, "156630997": [68, 217], "1567": 0, "156859": 13, "156861": 13, "156863": 13, "156865": 13, "156867": 13, "156869": 13, "156871": 13, "156873": 13, "156875": 13, "156877": 13, "156879": 13, "157": [0, 140], "157128497": 0, "157137496": 0, "1575": 0, "157519211": 0, "157519257": 0, "158": 0, "1580": 288, "158040939": 0, "158048983": 0, "1581": 13, "158330": 7, "1584": 0, "158545518": 0, "15870786": 0, "1589": [152, 169], "159": [0, 237], "1591": [152, 169], "1592936": 238, "159345973": 22, "15973002": 175, "159745316": 0, "15985178": 7, "159862546986584": 11, "15e": 216, "15m2i17m2d11m1i58m1i11m1d7m1d8m": 0, "15n": 126, "15n2": 126, "16": [0, 2, 3, 4, 7, 11, 12, 13, 14, 20, 25, 30, 32, 53, 69, 73, 87, 93, 104, 129, 169, 206, 251, 253, 260, 264, 265, 270, 278, 299], "160": [0, 222], "160039680": 0, "160127253446448": 11, "16080617": [20, 218], "16082683": 21, "161": [0, 222, 265], "16131885": 260, "161576975": 0, "16161448": 0, "161824586": 22, "162": 0, "1620": 0, "163": 0, "1632": 32, "16348228": [299, 300], "16377612": 7, "16384": [169, 220], "16389355": 0, "164": [0, 11, 29, 30], "16403221": 7, "165": [0, 6, 183], "1658": 253, "166": 0, "166667": 11, "1668": 0, "167": 0, "1672": 116, "167234445": 238, "167376": 0, "167877390": 238, "168": 29, "1680": 0, "1688586483": 262, "168904": 0, "169": 0, "1697": [12, 13], "16e": 216, "17": [0, 2, 3, 7, 8, 11, 12, 13, 20, 23, 25, 30, 32, 104, 113, 169, 206, 237, 249, 251, 260, 261, 264, 281], "170": 29, "170899992": 0, "171": 0, "17103": 265, "1711": 0, "17121776": 7, "1716": 237, "1717": 237, "172": [0, 11, 169, 253], "17292": 278, "173": 0, "173163865": 22, "17342": 278, "17353": 278, "17390": 278, "173908612": 0, "174": [2, 29], "17420": 265, "174210431": 0, "174256650": 0, "174256662": 0, "174256685": 0, "174256689": 0, "174256691": 0, "174256699": 0, "174256702": 0, "175": [0, 250], "1750": 237, "1751": 237, "17523": 199, "175231": 0, "175262": 0, "175316": 0, "17545": 265, "176": [0, 6], "1760": 237, "176504": 11, "1767": [2, 251], "17708": 278, "17709": 278, "1771": [2, 251], "17715": 278, "17728": 278, "17762460233298": 11, "177k": 222, "1780": 0, "178247": 0, "17857": 278, "1792": 32, "1795": 13, "17989604": 7, "17beta": 113, "17e": 216, "17m1d6m": 0, "18": [0, 3, 8, 11, 12, 13, 15, 16, 20, 21, 22, 23, 53, 68, 69, 80, 90, 109, 149, 206, 216, 251, 260, 278, 281, 299], "180": [13, 15, 169, 183, 288], "18004": 278, "18017": 278, "181": [0, 7], "181217": 0, "18190": 278, "18195": 278, "182": [29, 251], "18207101": 22, "18223": 278, "18239": 278, "18248": 278, "18269230769230765": 199, "1827": 0, "18299": 278, "183": 129, "183925984": 0, "183925985": 0, "183925990": 0, "183926028": 0, "184": [2, 222], "1848": 13, "185": [0, 53], "18575690": 7, "18575811": 7, "18579475": 7, "18585042": 8, "18589523": 7, "18591784": 7, "18594007": 7, "186": [7, 15], "18606172": 7, "18612381": 7, "18627452": 7, "18627489": 7, "1863": 197, "18661158": 7, "18665331": 7, "18665981": 11, "18680603": 7, "18689808": 7, "187237168": 7, "1873": 0, "187371129": 0, "18749999999999994": 199, "187676": 7, "188": [2, 29, 250], "188111581": 0, "188158351": 0, "188162918": 0, "188162930": 0, "188162953": 0, "188162957": 0, "188162959": 0, "188162967": 0, "188162970": 0, "188171225": 0, "188228261": 0, "188236997": 0, "1888": [6, 237], "18m22": 0, "19": [0, 2, 3, 8, 11, 12, 13, 20, 29, 30, 84, 88, 152, 154, 169, 206, 221, 249, 251, 260, 264, 270, 299], "190": 0, "1901": 237, "190214555": 13, "1904993": [34, 280], "191": [0, 53], "191154276": 0, "19159": 0, "192": [0, 183], "193": [2, 11, 29], "19304878": [7, 83], "193835": 0, "19450287": 7, "1949": 0, "195": [0, 11, 264], "195230749": [68, 217], "1956": 264, "1958": 32, "196": 129, "1960": 260, "1961": 264, "1962": 264, "196364": 278, "1964": 32, "196429": 278, "1965": 264, "196608": 278, "1967": 80, "196734": 278, "19698094": 7, "197": [0, 2], "1970": 288, "19705359": 8, "1971": 2, "1972": 109, "1973": [2, 157], "19732999999999998": 199, "1977": 149, "197793": 11, "1978": 2, "1979": 2, "198": [29, 222], "1980": 21, "1981": 129, "1982": 265, "198295559": [0, 13], "198365852": 22, "1984": 2, "1985": [2, 13, 34, 281], "1986": [2, 13, 34, 264, 281], "1987": [2, 137, 261, 283], "1988": [0, 2, 32, 59, 237], "1989": [2, 216], "1990": [2, 129, 265, 299, 300], "1990656": 13, "1991": [83, 264], "1992": [2, 32, 182], "19923": 83, "1993": [13, 72, 169, 263, 264, 265], "1994": [2, 13, 32, 34, 137, 169, 263, 265, 281], "1995": 264, "199577": 11, "1996": [2, 264], "1997": [2, 3, 4, 68, 129, 153, 264], "1998": [2, 32, 53, 87, 93, 166, 264], "1999": [2, 4, 69, 87, 185, 264, 294], "19mb": 6, "1_k_ca": 169, "1_k_cb": 169, "1_k_cd": 169, "1_k_cg": 169, "1_modifi": 0, "1a": [215, 264], "1a8o": [15, 140, 148, 154, 156, 170, 173, 248], "1a91": 238, "1abc": [15, 139], "1acgt2tgca3atgc4cgta": 264, "1asrukw": 238, "1b4o": 0, "1bba": 215, "1c": 169, "1ca": 169, "1d": [0, 4, 30, 73], "1e": [0, 13, 73, 168, 292], "1e4": 104, "1e6": 104, "1ejg": 15, "1en2": 15, "1f": [6, 30, 54, 251, 264], "1fat": [15, 137], "1ffk": 15, "1fkk": 15, "1g": 11, "1gb": [23, 69], "1gbt": 15, "1hft": 149, "1hfv": 149, "1hg6": 149, "1hhb": 149, "1hid": 149, "1hiu": 149, "1hke": 149, "1ifk": 12, "1ifl": 12, "1jic": 0, "1joi": 260, "1k7t_a": 0, "1k7u_a": 0, "1k7v_a": 0, "1kl12": 0, "1kl120": 0, "1lcd": 157, "1mot": 137, "1n": 169, "1nh4": 12, "1r": 25, "1rnd": [15, 169], "1s6m4i38m1": 0, "1sso": 0, "1st": [126, 169], "1t": 264, "1t0w_a": 0, "1ulk_a": 0, "1uuz": 149, "1wga": 0, "1wgc_a": 0, "1wgt_a": 0, "2": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 36, 42, 45, 53, 55, 56, 59, 62, 66, 68, 69, 71, 73, 80, 83, 93, 101, 104, 108, 112, 113, 114, 117, 118, 122, 132, 137, 139, 140, 149, 157, 168, 169, 176, 182, 183, 195, 197, 201, 202, 204, 205, 206, 209, 210, 211, 216, 217, 218, 222, 227, 228, 230, 234, 236, 237, 238, 241, 243, 247, 251, 252, 253, 260, 264, 265, 269, 270, 277, 278, 279, 287, 288, 291, 297, 299, 303], "20": [0, 2, 3, 6, 7, 8, 11, 12, 13, 15, 20, 21, 22, 25, 30, 32, 53, 66, 67, 69, 80, 87, 88, 109, 113, 140, 154, 169, 182, 183, 202, 203, 206, 215, 216, 236, 237, 247, 251, 253, 260, 264, 270, 272, 280, 299], "200": [18, 21, 23, 32, 69, 80, 83, 182, 183, 201, 204, 205, 237], "2000": [0, 2, 7, 9, 13, 14, 16, 21, 32, 34, 111, 115, 119, 185, 196, 264, 281], "2000000": 237, "200000016": 7, "2001": [2, 4, 69, 149, 182, 211, 213, 237, 264], "20010710": 263, "2002": [0, 2, 7, 8, 32, 140, 185], "20020916": 7, "2003": [2, 9, 15, 65, 74, 122, 137, 152, 169, 182], "20030606": 7, "20031006": 149, "20031013": 149, "2004": [0, 2, 9, 11, 32, 36, 73, 264], "20041117": 7, "20049947": 262, "2005": [2, 32, 69, 175, 264, 267], "2006": [2, 8, 9, 23, 182], "200600032": 262, "2007": [7, 25, 32, 83, 87], "2008": [7, 21, 32, 210, 253, 264], "2009": [2, 3, 7, 8, 9, 17, 20, 23, 25, 32, 69, 86, 87, 88, 93, 197, 278], "201": [0, 18, 53, 201, 204, 205], "2010": [2, 6, 7, 9, 32, 182, 251, 264], "2011": [32, 238, 252], "201197": 13, "201198": 13, "2012": [2, 7, 8, 9, 17, 83, 264], "2013": [11, 32, 137, 288], "2014": 15, "2014248": 83, "2015": [12, 13, 23], "2016": [7, 9, 90, 265, 277], "20161961": 7, "2017": [0, 9, 88], "2017_03": 88, "2019": [0, 2, 15, 76, 152, 169], "202": [0, 2, 11], "2020": 0, "2024": 208, "2026": 13, "203": [0, 31, 183], "20370": 29, "20379": 2, "204": [0, 2, 11], "2048": 169, "205": [11, 32, 237], "20517297": 288, "205754": 13, "206": 0, "20605": 29, "206124072110286": 11, "2073": 25, "207551": 13, "2078": 2, "2079": [2, 12, 13], "208": [0, 264], "208639": 222, "208677": 222, "209": [2, 264], "20945": 29, "20m": 0, "21": [0, 2, 3, 8, 11, 12, 20, 21, 30, 53, 69, 93, 94, 109, 149, 172, 176, 182, 183, 206, 245, 251, 253, 260, 264, 288], "210": [0, 11, 23, 183, 237, 288], "2105": [2, 69, 197, 218], "211": 11, "211387": 11, "212": 32, "2120": 7, "21300": 29, "2134": 0, "214": [0, 11], "21438": 29, "21455": 29, "2146": 0, "215": [0, 2, 183, 237], "216": [0, 2, 11, 15, 53, 68, 217], "2164": 2, "216l": 149, "217": [13, 14, 32, 237], "2170": 23, "218451749734889": 11, "21871": 29, "21883": 29, "219": [244, 253], "21e": [11, 291], "22": [0, 2, 3, 6, 7, 11, 12, 15, 20, 21, 36, 69, 87, 122, 182, 185, 206, 216, 217, 218, 249, 251, 253, 260, 288, 292], "220": [0, 7, 237], "221": 253, "22104": 29, "22144": 278, "22177": 29, "222": [2, 53, 237], "222222": 199, "22230": 278, "223": 13, "223616942": 0, "224": 0, "224244399": [0, 30], "225584828": 0, "227": 264, "228": [0, 13], "228573443": [0, 30], "2289704": 2, "22909249": 7, "229193": 21, "229202": 2, "23": [0, 3, 6, 11, 13, 17, 20, 21, 22, 32, 53, 69, 175, 206, 216, 221, 237, 251, 253, 260, 299], "230": 237, "2300": 0, "2303": 0, "230769": 199, "2308": 2, "231": 11, "2310": 2, "231336967110781": 11, "23181": 6, "23186": 6, "2325": 0, "23262": 0, "233": 53, "23344455555555555555544433": 0, "2337": 13, "234": [11, 29], "234666677777777777766666655544332223333": 0, "23470805": 8, "235": [2, 264], "235949098621421": 11, "236": [0, 251], "2360": [12, 13], "23891310": 0, "23891349": 0, "239": [11, 20, 217], "23927": 199, "239940": 0, "23e": 216, "24": [0, 3, 6, 7, 8, 11, 12, 13, 17, 20, 21, 25, 29, 30, 32, 69, 74, 183, 206, 249, 251, 260, 261], "240": [13, 62, 104], "241": [7, 11, 13, 288], "241163": 0, "242": [0, 30], "242193529": 13, "243199373": 0, "2433": 0, "2434": 253, "2444": [2, 59], "2448": [2, 13, 59], "246": 3, "247": 68, "2475": 7, "2480607": 11, "248343840": 22, "248956422": [0, 13, 36, 37, 38], "249": 261, "249053267": 0, "249182": 0, "249250621": 0, "249999999875": 11, "25": [0, 2, 3, 6, 8, 11, 12, 13, 16, 17, 20, 21, 29, 32, 68, 99, 104, 113, 182, 202, 206, 237, 245, 251, 260, 261, 264, 270, 299], "250": [8, 182, 183, 270], "2500": 207, "250000": [199, 299], "2505": 13, "250645": 11, "2514": 13, "255": [0, 12, 17, 104, 183], "256": [0, 13, 36, 37, 169, 236, 253, 278], "256374": 7, "2569": [12, 13], "2587879": 8, "259": 264, "259112547756697": 11, "25g14g2c34a12a9": 0, "25m": 0, "25mb": 23, "26": [0, 3, 6, 7, 8, 11, 13, 20, 21, 29, 30, 32, 69, 206, 217, 218, 234, 251, 253, 260], "260": [0, 253, 256], "2606": 7, "261": [0, 253], "2611": 29, "261883": 278, "261948": 278, "262144": 278, "262205": 3, "262205281": [3, 20], "262205290": [3, 20], "262205298": [3, 20], "262205302": [3, 20], "262205309": [3, 20], "262205317": [3, 20], "262205330": [3, 20], "262205423": [3, 20], "262205429": [3, 20], "262205445": [3, 20], "262205451": [3, 20], "2625807": 8, "263": [0, 250], "264": 244, "2643": 237, "2644": 237, "26466274": 11, "2647": 13, "265": [0, 253], "26503372": 11, "265207": 13, "26585": [0, 30], "266": [0, 253], "266435125": 0, "2669": 29, "267": [68, 244], "268": 156, "2682512": 7, "2683": 288, "2688": 182, "269": [129, 253], "2690": 182, "2697049": [25, 276], "26992728": 8, "27": [0, 3, 7, 11, 12, 13, 16, 20, 68, 69, 206, 236, 251, 253, 260, 264], "270": [11, 13], "270132717": [3, 20], "270133": 3, "270133242": [3, 20], "270133247": [3, 20], "270133254": [3, 20], "270133306": [3, 20], "2705363": 7, "271": 253, "2715": 11, "272": 0, "272646": 7, "272960": 23, "273": 0, "2732620": 94, "274": 0, "2743": [12, 13], "2744707": 7, "274597": 11, "275": [8, 11, 129], "27578828": 0, "27578829": 0, "27578831": 0, "27578850": 0, "27578866": 0, "2759": 29, "276": 2, "2762": 29, "2765564": 19, "2765583": 23, "2765596": 23, "2765613": 23, "2765646": 23, "2765658": [19, 23], "276694": 11, "2767712": 21, "27699739": 0, "277": [2, 7, 11, 20, 217, 253], "27707221": 0, "278": 253, "2783487": 169, "27884615384615385": 199, "279": 0, "2792": 29, "2795": 29, "28": [0, 2, 3, 7, 8, 11, 20, 22, 30, 93, 111, 113, 115, 119, 149, 217, 249, 251, 253, 260, 278], "280": [0, 13], "281": [0, 253], "2810": 29, "281474976710656": 278, "283": 0, "2830": 6, "2836": [2, 137], "283785": 11, "284": [7, 68, 222, 264], "285": 6, "2852": 0, "286": 32, "2868": 237, "287": [0, 253], "28741140": 0, "28741141": 0, "28741143": 0, "28741162": 0, "28741178": 0, "288": 7, "28862317": 0, "28869787": 0, "289": 0, "29": [0, 2, 3, 8, 11, 13, 20, 22, 29, 69, 111, 115, 119, 149, 222, 251, 260, 261, 264, 265], "290": [11, 264], "2907": 2, "290900": 11, "291": 153, "2912": 2, "2914": 29, "292": [13, 14, 253], "2923": 199, "2931": 0, "2934173": 68, "2936": [3, 20], "294118": 104, "2947": 32, "2948": 32, "295": [153, 253], "296": 7, "296143": 0, "296143771": 0, "2963": 260, "297": [140, 288], "2976": 29, "297814701": [3, 20], "297911": 222, "297993": 222, "298": 32, "299": 253, "2994": 69, "2996219": 21, "299651": 12, "29e": 216, "2_a_c": 169, "2_r1": [15, 152, 169], "2beg": 154, "2bit": [0, 23, 257], "2cp": 12, "2cpb": 12, "2cvr": 0, "2cwg_a": 0, "2d": [0, 2, 4, 11, 12, 13, 15, 30, 73, 101, 169, 177, 303], "2drca": 214, "2e": [0, 291], "2f": [11, 12, 13, 16, 183, 190, 216, 251, 261, 263, 264, 265], "2fe": 25, "2fm5fnyyy07j4": 238, "2gb": 270, "2hft": 149, "2hhb": 149, "2hid": 149, "2hiu": 149, "2j5x": 149, "2l": 25, "2l3j": 53, "2l3j_b_ss": 53, "2line": [238, 241], "2mb": 6, "2nd": [2, 69, 169, 182, 216], "2uvo": 0, "2uvo_a": 0, "2uvo_hhblit": 0, "2uvoah": 0, "2wga": 0, "2wgc_a": 0, "2x3t_a": 0, "2x52_a": 0, "3": [0, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 45, 53, 55, 56, 62, 65, 68, 69, 73, 80, 83, 84, 93, 94, 101, 104, 109, 112, 113, 126, 135, 137, 139, 140, 154, 157, 162, 168, 169, 176, 182, 183, 197, 201, 204, 205, 207, 214, 217, 218, 221, 222, 228, 229, 233, 236, 237, 238, 241, 247, 249, 251, 253, 260, 261, 263, 264, 265, 269, 270, 272, 275, 278, 279, 280, 281, 283, 288, 290, 291, 294, 297, 299], "30": [0, 2, 4, 6, 8, 11, 12, 13, 21, 23, 30, 32, 59, 68, 69, 70, 166, 169, 182, 216, 237, 251, 260, 270], "300": [10, 182, 207, 237, 261], "300256": 11, "3005": 69, "300mb": 25, "301": [7, 68, 217], "301171": 3, "301171146": [3, 20], "301171153": [3, 20], "301171211": [3, 20], "301171259": [3, 20], "301171267": [3, 20], "301171276": [3, 20], "301171311": [3, 20], "301171322": [3, 20], "301171354": [3, 20], "301171394": [3, 20], "301171401": [3, 20], "301171428": [3, 20], "301171437": [3, 20], "301171447": [3, 20], "3014644": 0, "3014689": 0, "3014742": 0, "3014778": 0, "3017743": 0, "3018000": 0, "3018161": 0, "3018230": 0, "3018359": 0, "3018482": 0, "3018644": 0, "3018822": 0, "3018932": 0, "3019": 2, "3019000": 0, "3019271": 0, "3019377": 0, "3019435": 0, "3019465": 0, "302": [7, 32], "3021": 2, "303": 244, "3030": 2, "30367": 7, "30432563": 8, "305": [2, 11], "305622": 278, "3056429": 3, "3059": 32, "306": 244, "3066": 32, "307": [11, 13, 140, 182], "308": [0, 11], "3085": 11, "309": [238, 244, 260], "31": [0, 2, 8, 11, 116, 149, 222, 251, 260, 288], "310": [10, 253], "310520": 11, "3109": 210, "311": 0, "312": 256, "312544902": 22, "31278684": 7, "31298": 20, "3130377": 0, "31359": 20, "314": 11, "315": 6, "3165": 13, "317": 74, "3171620263517245": 11, "317338282078473": 11, "31744": 169, "3176602": [238, 260], "319": [68, 222], "3190": 6, "31_i86win32": 32, "32": [0, 2, 11, 12, 13, 16, 22, 30, 32, 69, 169, 251, 260, 264], "320": 32, "321": 0, "321580063626723": 11, "3218": [12, 13], "323": 140, "324": [126, 238], "3246": 2, "3248": [2, 83], "325053704": [68, 217], "3251": [3, 20], "326": 74, "32611": 7, "326933": 0, "327294": 278, "327359": 278, "327680": 278, "32930": 278, "3298468": [241, 260], "32bp": 270, "33": [0, 6, 8, 11, 16, 32, 53, 100, 169, 238, 251, 260, 261, 264, 265, 270], "330": [32, 244], "330443": 0, "330443520": 0, "330443688": 0, "3305": [12, 13], "331078": 0, "3318709": 238, "33211": 217, "33212": 217, "33213": 217, "333333": 11, "335": [0, 11], "336": [2, 16], "3376": 0, "338": 0, "3389": [3, 68], "34": [0, 2, 11, 13, 25, 29, 111, 115, 119, 221, 251, 260], "340": [32, 256], "3402": [3, 68], "340200303": 137, "341": 126, "341303": 11, "342": 244, "343": 0, "344": [0, 30], "3444411": [34, 281], "344556666666666666566555543333223333321": 0, "345": [2, 68], "3459481": 68, "346": [0, 11], "3470": 6, "348": [7, 238, 244], "34_222_": 249, "35": [0, 11, 16, 30, 32, 156, 226, 251, 260, 264, 270], "350783": 11, "351": 11, "3512": 0, "3512432070271259": 11, "352": 2, "3537": 264, "354": 244, "35483340": 0, "35483510": 0, "355": 6, "35538": 8, "3554": 264, "3555": 264, "355556": 199, "356": [0, 197], "3562": 264, "356517317": [3, 20], "356543101": [3, 20], "357": 256, "358": 222, "35847450464382": 11, "359464": 0, "35m": 0, "36": [0, 2, 11, 13, 22, 74, 216, 226, 251, 253, 260, 299], "360": 169, "36001014": 169, "3601": 0, "3609329790": 278, "361": [6, 7], "361464": 11, "362": [0, 11], "3628": 116, "36438": 278, "364552": 11, "36462": 278, "36489": 278, "365": 7, "365806": 13, "3661": 29, "368": 264, "369048": 199, "37": [0, 3, 11, 13, 16, 20, 183, 249, 251, 260, 265, 270], "371502086": [68, 217], "372": [13, 32], "374": [2, 32], "375": [8, 11], "37613720253387": 11, "3765": 260, "378": 2, "37n": 270, "38": [0, 2, 7, 11, 16, 21, 23, 29, 216, 251, 260, 278], "382": 222, "38240": 6, "38347": 8, "384": [0, 56, 299], "3842": 260, "384615": 199, "3857": 6, "386123": 222, "386207": 222, "387": 244, "388": 222, "39": [0, 3, 11, 13, 20, 30, 104, 237, 251, 260, 264], "390": 244, "390332043": [3, 20], "390332045": [3, 20], "3910647": 12, "3916709": [34, 281], "392760": 278, "392825": 278, "393": 156, "393216": 278, "393333": 251, "394": 23, "39429784": 11, "3957471": [15, 158], "396": [11, 288], "397513516": [3, 20], "397623": 11, "398": 11, "399": [0, 11, 68], "3_p_ca": 169, "3_p_n": 169, "3a": 68, "3c": 118, "3d": [4, 7, 25, 26, 135, 158, 169, 171, 175, 176, 248, 307], "3dcoffe": 32, "3e": [3, 20], "3f": 11, "3fe": 25, "3g": 11, "3hhb": 149, "3j92": 149, "3jb9": 53, "3pbl": 15, "3rd": [169, 253], "3x": 71, "3x3": [135, 139, 176], "3x4": 169, "4": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 22, 23, 24, 25, 29, 30, 31, 32, 45, 53, 55, 68, 69, 73, 76, 80, 101, 104, 113, 126, 129, 137, 149, 154, 158, 169, 175, 176, 182, 201, 204, 206, 207, 209, 214, 216, 217, 218, 221, 222, 237, 238, 247, 251, 253, 260, 263, 264, 265, 270, 272, 278, 283, 288, 290, 297, 299], "40": [0, 7, 8, 11, 21, 32, 56, 157, 206, 216, 237, 251, 260, 261, 265, 270, 283], "400": [3, 8, 10, 182, 207, 253], "4005": 0, "401": [13, 288], "403": 2, "404": [10, 208], "40568": 6, "407": [0, 30], "4079": [3, 20], "408": 0, "4082": [3, 20], "40832722": 11, "409": 15, "409215": 11, "4096": 169, "40a": 0, "40e": 264, "41": [0, 3, 6, 11, 13, 16, 21, 251, 260, 264, 265], "410": 2, "411": [0, 11, 56], "41253757072521": 11, "413": [0, 3, 238], "4145": 0, "415": 2, "41614797": 94, "416667": 11, "418": 2, "41833273": 22, "41892": 6, "419": 11, "42": [0, 8, 11, 21, 183], "420": [182, 244], "421": [7, 69, 218], "42144400": 0, "42144436": 0, "42291": [3, 20], "42322": 222, "42326848": 22, "42372": 2, "42381": 2, "4249": 6, "425": 288, "42530895": 0, "42530922": 0, "42530955": 0, "42530958": 0, "42532020": 0, "42532039": 0, "42532095": 0, "42532515": 0, "42532563": 0, "42532575": 0, "42532606": 0, "425_103_": 249, "425_7_": 249, "426": 2, "4284": 0, "42991": 20, "43": [0, 2, 11, 12, 20, 87, 88, 157, 264], "4300": [0, 21], "4301": 0, "431": 2, "4310": 237, "4311": 237, "43177247": 11, "4320": 0, "433": 0, "4342": 21, "4343": 21, "43458748": 11, "4347": 237, "43478": 278, "435": 3, "4350": 21, "44": [0, 2, 11, 16, 18, 183, 217, 251, 260], "440": 30, "441039751299748": 11, "4414": 16, "44157214": 7, "443": 238, "44334329": 11, "444": 11, "4457": 7, "44576": 7, "447": 238, "449": 222, "45": [0, 6, 7, 8, 9, 11, 13, 15, 30, 104, 207, 264], "4512": 0, "453": 264, "454": [6, 21, 238, 251, 253], "45478711": 21, "45478712": 256, "45478713": 256, "45478714": 256, "45478715": 256, "45478716": [21, 256], "45478717": [238, 256], "45478718": 256, "45478719": 256, "45478720": 256, "45478721": 256, "455": 237, "455991516436904": 11, "456": 237, "456614": 278, "456679": 278, "457": 237, "46": [0, 2, 11, 22, 62, 129, 209, 216], "461538": 199, "4622798": 0, "463": 7, "465": 15, "4660": 0, "46757": 0, "46785": 0, "46845": 0, "46875": 22, "468851": 25, "46m1827n82m3376n76m12h": 0, "47": [0, 3, 11, 20, 30, 216, 264], "470": 0, "47031477": 0, "471": [11, 238], "4722596": 7, "473": [2, 3], "47448759": 0, "4749": 0, "47545159": 0, "47545187": 0, "47545247": 0, "476": 126, "478": 175, "4780": [6, 21], "48": [0, 2, 8, 11, 13, 16, 216, 264, 278], "480": [11, 21, 175], "4800": 21, "48000000": 0, "481": 7, "4814": 6, "482": 3, "48663767": 0, "48663768": 0, "48663795": 0, "48663796": 0, "48663813": 0, "48665640": 0, "48665716": 0, "48665722": 0, "48669098": 0, "48669174": 0, "487327": 222, "487387": 222, "4877": 25, "488": 0, "488889": 199, "49": [0, 4, 8, 11, 12, 15, 22, 29, 73, 216], "4900": 0, "49000000": 0, "490883": 94, "490885": 94, "491": 6, "491055": 11, "4923": 260, "492621": 11, "4927836298652875": 11, "49340": 15, "493976": 199, "49598789": 11, "496": 169, "498070": 11, "49840": 126, "498454": 0, "4990": 0, "4aml_a": 0, "4cup": 15, "4e": 0, "4f": [12, 13, 261], "4gb": 23, "4lgy": 169, "4th": 169, "4x4": [169, 176], "4yyaj7ibmqgnkxdxq": 23, "4z8i_a": 0, "5": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 67, 68, 69, 73, 80, 93, 94, 99, 100, 101, 104, 108, 113, 122, 126, 132, 135, 137, 140, 169, 176, 182, 183, 186, 199, 207, 209, 216, 217, 218, 234, 236, 237, 238, 245, 251, 260, 261, 264, 265, 270, 272, 275, 288, 290, 291, 297, 299], "50": [0, 3, 6, 8, 11, 12, 23, 25, 30, 32, 65, 68, 70, 155, 169, 202, 207, 214, 216, 237, 247, 249, 251, 253, 261, 264, 270, 299], "500": [7, 21, 68, 69, 70, 264, 270, 276], "5000": [0, 202, 203], "500000": 299, "501": 251, "502": 30, "5062": 0, "50977498": 11, "51": [0, 2, 3, 8, 9, 11, 15, 20, 216], "510": 11, "511": [32, 275], "512": [0, 36, 37, 149, 169], "51304566": 0, "51343240527031": 11, "5147": 25, "516": 0, "518": [0, 32], "5199": 169, "519a": 3, "52": [0, 3, 7, 11, 12, 20, 169, 182, 216, 251], "5203": 0, "5204": 0, "5209": 13, "520b": [3, 20], "520c": [3, 20], "521": 11, "525": 169, "528": 264, "529": 263, "52_g_ca": 169, "52_g_ca_0": 169, "52_g_ca_b_0": 169, "52b_g_ca": 169, "53": [9, 11, 13, 15, 32, 104, 263, 264, 278], "530": 68, "53215344": 0, "53215346": 0, "53215347": 0, "53215366": 0, "53215382": 0, "53303881": 0, "5331": 0, "53310102": 0, "5336": 264, "535": 149, "5353": 264, "53575980": 0, "53575997": 0, "53729353": [68, 217], "538462": 199, "539": [32, 263], "54": [0, 1, 6, 8, 9, 11, 17, 207, 216, 240, 251, 261, 264], "540": 238, "54006": 17, "541": 7, "5416": 62, "5417": 62, "54178987": 20, "54179038": 20, "54185425": 20, "54185486": 20, "54189735": 20, "54189795": 20, "54197657": 20, "54197717": 20, "54198476": 20, "54198536": 20, "542": 149, "54201651": 20, "54201712": 20, "54204480": 20, "54204541": 20, "54206009": 20, "54206061": 20, "54210720": 20, "54210780": 20, "54212018": 20, "54212071": 20, "54233104": 20, "54233122": 20, "54234278": 20, "54234321": 20, "54238143": 20, "54238196": 20, "54240175": 20, "54254477": 20, "54255662": 20, "54255723": 20, "54260071": 20, "54264420": 20, "54264463": 20, "54265610": 20, "54265671": 20, "54442": 278, "54479": 278, "54493": 278, "54503e": 3, "5463": 7, "5465132509466635": 11, "54723985087516": 11, "547619": 199, "55": [3, 6, 7, 8, 9, 11, 16, 17, 20, 108, 211, 212, 213, 264], "5500": 15, "55074": 278, "55423": 222, "556": 68, "559292": 277, "56": [0, 11, 17, 222], "5601": 0, "56122354": 238, "56325207": 22, "56422281": 11, "566265": 199, "567": [0, 7], "5688": 262, "5690369": 3, "56e": 291, "57": [0, 9, 11, 21, 23, 108, 240], "57096847": [0, 53], "572": 6, "57240071": 7, "57240072": 7, "573": 100, "5763814": 21, "5781": 11, "579": 11, "58": [0, 11, 13, 16, 17, 65, 107, 216, 264], "58037": 21, "582000": 0, "582060": 0, "582120": 0, "582180": 0, "582228": 0, "583333": 11, "583333333208333": 11, "585366": 199, "585505": 68, "59": [0, 2, 7, 8, 9, 11, 17, 21, 104, 107, 182, 237, 251, 264], "590": [2, 129], "5900": [0, 6], "5901": 0, "590402969247084": 11, "591": 0, "59128983": [0, 20], "592": [6, 19, 23], "5923": 6, "5925": 0, "594": 0, "5960": 0, "5968": 62, "5969": 62, "5974": 6, "599": 126, "59e": 291, "5a": 68, "5alpha": 90, "5e": [0, 3], "5f": [11, 169, 190], "5gb": 25, "5xx": 83, "6": [0, 2, 3, 4, 7, 8, 11, 12, 13, 17, 20, 21, 29, 30, 32, 68, 69, 73, 80, 93, 101, 104, 105, 113, 126, 129, 135, 137, 149, 154, 172, 207, 217, 218, 237, 238, 245, 249, 251, 253, 260, 261, 264, 265, 270, 278, 281, 288, 290, 291, 297, 299], "60": [0, 3, 11, 13, 15, 16, 20, 23, 30, 68, 69, 83, 126, 155, 207, 237, 241, 245, 250, 251, 264, 280], "600": [14, 264, 277], "6000": 0, "6002": [3, 20], "601": [7, 11], "60124254": 11, "6015": 62, "6016975": 11, "6026": 2, "6036": 2, "605": 11, "608": 264, "609": 11, "60966679": 22, "61": [0, 3, 7, 8, 11, 16, 20, 116, 175, 261, 299], "6146": 0, "6150": 30, "615385": 199, "616": 2, "61646095": 0, "61646111": 0, "617": 2, "6182": 0, "62": [3, 7, 13, 21, 29, 32, 113, 149, 251, 264], "620": 11, "621": [2, 129], "622": 11, "62230396": 11, "6228": 0, "625": 3, "627328": 0, "6273284": [0, 7, 12, 30], "6273285": [0, 7, 12, 30], "6273286": [0, 7, 12, 30], "6273287": [0, 7, 12, 30], "6273289": [0, 7, 12, 23, 30], "627329": 0, "6273290": [0, 7, 12, 23, 30], "6273291": [0, 7, 12, 23, 30], "6283": 0, "628313891834571": 11, "62959": 2, "62969": 2, "6298": 6, "62e": 291, "63": [0, 11, 13, 16], "630": 68, "6308": 0, "6311": 0, "633": 238, "63398": 278, "6340": 4, "63459": 3, "63854": 278, "63m1062n75m468n43m": 0, "64": [0, 4, 6, 13, 16, 68, 69, 73, 157, 169, 238, 251, 256, 264, 270, 278], "640": 288, "64000": 15, "641682": 222, "6421": 6, "646": 0, "64668512": 11, "646m": 0, "64bit": 23, "64kb": 278, "65": [0, 9, 11, 22, 104, 216, 234, 236, 264], "650": [207, 264], "6500": 197, "652": 0, "6523201955933": 11, "65409": 278, "65411": 278, "65434": 278, "65466": 278, "65472": 278, "65483": 278, "655": 0, "65519": 278, "65535": 278, "65536": 278, "6553600000": 278, "6553600001": 278, "6553600010": 278, "65537": 278, "65540": 278, "656": [2, 221], "65614533": 11, "656680805938494": 11, "657": 0, "657m": 0, "659": 11, "66": [0, 7, 9, 11, 264], "661": 7, "663": 126, "663044098": 3, "66312982331297": 11, "6636": 0, "664": 2, "664268": 13, "665": 11, "6654": 6, "666667": 11, "6667": 261, "666990": 0, "667": 11, "667050": 0, "667109": 0, "667168": 0, "667216": 0, "66807541": 0, "67": [11, 14, 16, 21, 29, 264], "673143725": 3, "675": 264, "67518": 23, "6754794": 7, "679": 0, "6796999": 11, "68": [9, 11, 13, 113, 216, 240, 264], "682194862932": 169, "684409690": 3, "68521": 278, "69": [0, 9, 11, 13, 65, 238, 264], "694": 0, "69599e": 68, "696": 182, "6979": 13, "6982": 0, "6989": 7, "69e": 291, "6a": 113, "6e": 0, "6mb": 278, "6mer": 32, "6merpair": 32, "7": [0, 2, 3, 4, 6, 7, 8, 11, 12, 13, 17, 20, 27, 29, 30, 31, 32, 55, 69, 73, 74, 101, 104, 105, 113, 116, 117, 126, 137, 140, 154, 169, 206, 207, 217, 236, 237, 238, 249, 251, 253, 260, 263, 264, 265, 288, 291], "70": [9, 11, 12, 53, 129, 183, 207, 209, 237, 264, 270, 278], "700": [6, 11, 23, 207], "70000": 278, "700000": 199, "70143": 278, "7024864140542533": 11, "703928": 11, "704": [6, 182], "7053": 157, "706746561638717": 11, "7087": 0, "709": 6, "7093": 0, "71": [0, 8, 11, 16, 216, 236, 249, 297], "712": [251, 288], "71483e": 3, "71525": [0, 30], "7165707818416": 11, "7168": 169, "71795": 278, "717b": 32, "718": [6, 11], "71821": 278, "71846": 278, "71917": 222, "72": [0, 11, 12, 13, 14, 68, 104, 240, 264, 265], "720": 13, "721": 7, "723": [2, 23], "7235": 23, "7236": 0, "725": 2, "726": 6, "727": 0, "728": 2, "73": [0, 3, 4, 11, 12, 16, 20, 210, 264], "730": 6, "733": 6, "7331": 0, "73414803": 11, "736": 2, "738": 11, "7381525": 11, "739": [11, 166], "74": [0, 7, 23], "740": [6, 19, 23], "74100009": 238, "74196805": 0, "74196831": 0, "742": 2, "744": 6, "747": 166, "748": 6, "749": 2, "74907211028632": 11, "75": [0, 2, 3, 7, 11, 15, 16, 17, 23, 32, 104, 110, 182, 251, 261, 263, 264, 270, 299], "750": 11, "750000": 299, "7525076": 238, "753": 6, "755": 11, "7564": 0, "7592839": 11, "76": [0, 7, 11, 29, 263, 299], "7602": 6, "761": 11, "76216221": 11, "763": 2, "768": 13, "77": [0, 8, 9, 11, 14, 251, 264], "772259": 11, "772949": 11, "77304": 278, "77363485291994": 11, "774": [2, 11], "775": [13, 263], "7788": 6, "78": [3, 9, 11, 21, 68, 104, 107, 238, 264], "780": 11, "78077248": 0, "781": 7, "782996e": 11, "783": [3, 25], "7860": 126, "789": 6, "79": [0, 7, 11, 13, 93, 238, 264], "7902972158110341": 11, "792": 238, "793": 2, "7968486": [34, 281], "797": 3, "797852598091198": 11, "798957": 13, "79999999999999999999999999999999999999999999999999999999999999999999999999999999": 0, "799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998899999999999999999999999999999999999999999999999999999999999999999999999999986": 0, "7a": 0, "7b": 0, "7e": 0, "7kd": 0, "7kd_dna_bind": 0, "7rsa": 169, "7wga_a": 0, "8": [0, 2, 3, 4, 7, 8, 11, 12, 13, 16, 17, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 73, 90, 101, 104, 109, 126, 137, 154, 166, 169, 182, 206, 226, 236, 237, 238, 247, 249, 251, 260, 261, 264, 278, 281, 288, 291, 299], "80": [0, 3, 11, 14, 15, 20, 30, 53, 68, 97, 175, 182, 207, 249, 250, 251, 278], "800": [11, 15], "801": 11, "803": 288, "80360": 2, "8044": 0, "806": 2, "807": 13, "8080": 7, "808080": 17, "8087": 6, "81": [0, 11, 12, 13, 15, 32, 104, 249, 264], "8106085": 72, "8124": 6, "81344243": 0, "81344245": 0, "81344264": 0, "81344267": 0, "81344283": 0, "814": 7, "81444246": 0, "81519121131782": 11, "8192": 169, "82": [0, 11, 176, 238, 265], "8230": 126, "82356262": 11, "827": 6, "83": [11, 12, 32, 251, 253], "831": 11, "832": 0, "8332116": [1, 3], "833333": 11, "84": [0, 7, 11, 149, 253, 264, 265], "841": 7, "84337": 278, "844": 0, "844049228115868": 11, "844718": 278, "8465": 6, "847": 32, "84771": 278, "84962463": 11, "84962511": 11, "85": [0, 2, 3, 11, 20, 26, 59, 100, 216, 238, 240, 264, 307], "85010": 0, "85061": 0, "8526": 7, "853516785566917": 299, "854": 13, "854375": 11, "85454": 278, "85737865": 0, "85737906": 0, "85843": 278, "85e": 291, "86": [2, 3, 11, 15, 20, 24, 206, 264], "8637051322628": 11, "86436": 238, "8660": 4, "87": [0, 2, 8, 11, 137], "870": 11, "870876719950774": 11, "873": 25, "8741": 6, "875": 22, "87558226865211": 11, "87661": 0, "877470982533044": 11, "879": 94, "87e": 291, "88": [0, 8, 11, 29, 83, 216, 251, 264], "8800": 7, "880567338282079": 11, "881": 7, "883079837598544": 11, "8859": 278, "88765292": 0, "88765304": 0, "88765327": 0, "88765331": 0, "88765333": 0, "88765335": 0, "88765343": 0, "88765346": 0, "888": 149, "88857985": 0, "88857997": 0, "88858020": 0, "88858024": 0, "88858026": 0, "88858028": 0, "88858036": 0, "88858039": 0, "89": [0, 2, 206, 288], "892": [7, 83], "893": [7, 264], "894": 7, "895": 7, "89503": 278, "89536": 278, "89554": 278, "896": 7, "89741": 279, "898": 3, "898197242841994": 11, "899": [7, 23], "899024": 11, "8b8": 0, "8cb": [0, 55], "8cc": [0, 55], "8e": 0, "8gb": 23, "8h": 0, "8p22": 7, "9": [0, 2, 3, 4, 7, 8, 11, 12, 13, 16, 20, 21, 22, 24, 29, 30, 32, 73, 80, 84, 93, 104, 113, 126, 137, 156, 157, 166, 169, 206, 207, 217, 237, 245, 247, 249, 251, 253, 260, 263, 264, 265, 270, 279, 280, 281, 288], "90": [0, 6, 7, 8, 11, 17, 30, 53, 169, 206, 216, 240, 251, 256], "900": 0, "90038": 137, "901": 7, "90165": 2, "902": [7, 23, 69], "9044": 6, "90478": 2, "906": 12, "9085": 0, "909": 288, "9097": 13, "9099": 13, "90e": 216, "91": [0, 4, 8, 11], "91001": [21, 238], "9101": 13, "9103": 13, "9106": 0, "911": 69, "91102552": 11, "91307e": [3, 20], "9169": 0, "9183534": 153, "918728": 11, "919596": 11, "92": [11, 32], "9217": 13, "9219": 13, "9221": 13, "9223": 13, "9223372036854775807": [0, 13], "92243": 278, "9225": 13, "9227": 13, "9229": 13, "923": 264, "9231": 13, "9233": 13, "9235": 13, "9237": 13, "9239": 13, "923902": 12, "926": 7, "926202": 11, "9264": 6, "9290": 0, "93": [0, 6, 8, 11, 251], "9316": 2, "9317": 0, "935284": 11, "936213": 11, "9373": 0, "93827754": 11, "939": 11, "94": [0, 6, 8, 11, 19, 23, 149, 250], "940": 11, "9407": 0, "941176": 104, "9428": 62, "9429": 62, "943": 11, "943639": 11, "94630059171354": 299, "94707528": 0, "94708176": 0, "94708178": 0, "94708718": 0, "9475": 62, "9476": 62, "9478129": 53, "9483": 0, "948570": 260, "948639": 11, "949": 261, "94967506": 56, "94e": 216, "95": [0, 2, 8, 11, 15, 217, 238, 240, 261, 264, 265, 299], "95160479": 0, "95160520": 0, "95186205": 0, "95186217": 0, "95186220": 0, "95186243": 0, "95186245": 0, "95186253": 0, "95225": 0, "9525": 2, "95871737667187": 11, "9598": 7, "96": [2, 11, 16, 149, 206, 251, 264, 298, 299], "960": [0, 157], "9606": [68, 288], "9609": [6, 21], "961": 7, "965": 11, "968132": 11, "96820": 0, "97": [3, 8, 11, 20, 32, 149, 264], "970": [11, 13], "971": 13, "971153846153846": 11, "972": [0, 11], "974": 11, "9758318": 0, "9758326": 0, "9758328": 0, "9758351": 0, "9758354": 0, "9758366": 0, "976567": 11, "97769": 222, "978": 0, "9786631": 0, "9787941": 0, "9788508": 0, "9790455": 0, "9790463": 0, "9790465": 0, "9790488": 0, "9790491": 0, "9790503": 0, "9795062": 0, "9795065": 0, "9795737": 0, "9796": 7, "9796821": 166, "97e": 11, "98": [3, 7, 8, 11, 20, 25, 104, 206, 265], "980": 11, "9805": 11, "981": 13, "983797": 11, "984": 11, "9876543210": 251, "987828735": 278, "989200": 11, "99": [0, 3, 8, 11, 16, 20, 116, 207, 216, 256, 264, 270], "990": [13, 251], "997": [11, 261], "9974": 0, "998": 251, "9986": 7, "999": 207, "9997": 0, "9999": 0, "99999": 149, "99999699899": 0, "9999969989999999999999998699989997": 0, "99999999": 7, "99999999986": 0, "99999999999988999999999999999999999999999999999999999999999999999999999999999999": 0, "9999999999999869998": 0, "9999999999999999999": 0, "99999999999999999999999": 0, "9999999999999999999999999999999999999999999999": 0, "9_": 197, "9e": [0, 3, 20], "9wga_a": 0, "A": [0, 1, 2, 3, 4, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 21, 22, 23, 24, 25, 30, 31, 32, 33, 35, 36, 37, 38, 45, 46, 47, 49, 51, 53, 55, 56, 60, 61, 64, 65, 66, 68, 71, 72, 73, 76, 80, 81, 84, 92, 93, 94, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 112, 113, 114, 117, 118, 119, 121, 123, 127, 129, 130, 135, 137, 139, 140, 141, 146, 149, 150, 152, 154, 155, 156, 157, 159, 164, 165, 169, 172, 175, 177, 179, 180, 182, 183, 197, 199, 202, 207, 209, 210, 212, 214, 215, 217, 222, 236, 237, 238, 246, 247, 248, 251, 260, 261, 262, 263, 264, 265, 268, 270, 271, 272, 275, 277, 280, 281, 283, 287, 288, 289, 290, 291, 296, 297, 298, 299, 300, 302, 303], "AND": [7, 25, 149, 251, 276], "AS": [0, 11, 53, 66, 90, 270, 295], "AT": [30, 31, 264], "And": [6, 7, 12, 20, 23, 30, 80, 182, 251, 260], "As": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 38, 39, 45, 46, 51, 61, 68, 73, 81, 169, 217, 222, 236, 238, 247, 250, 251, 253, 270, 275, 278, 283], "At": [3, 7, 8, 11, 15, 20, 24, 25, 30, 68, 260, 270, 274, 277], "But": [0, 3, 7, 15, 17, 20, 23, 217, 222, 237, 251, 305], "By": [0, 3, 4, 6, 7, 8, 11, 12, 13, 15, 17, 20, 22, 23, 24, 25, 30, 32, 54, 67, 69, 83, 92, 99, 102, 108, 109, 127, 135, 149, 182, 183, 217, 237, 241, 250, 251, 260, 261, 265, 270, 274, 278, 286, 290, 297, 299, 303], "For": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 20, 21, 22, 23, 24, 25, 30, 31, 41, 50, 53, 54, 55, 56, 58, 59, 61, 62, 65, 66, 67, 68, 69, 73, 81, 83, 85, 94, 99, 108, 112, 113, 114, 117, 119, 125, 137, 157, 168, 169, 177, 182, 183, 197, 205, 212, 215, 217, 218, 221, 222, 229, 234, 237, 238, 239, 241, 247, 249, 251, 252, 253, 255, 256, 260, 262, 264, 265, 270, 274, 275, 278, 283, 295, 297, 298, 299, 305], "IN": [53, 60, 66, 129, 151], "INS": 32, "IT": 66, "If": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 36, 37, 38, 44, 45, 47, 51, 52, 54, 56, 66, 67, 68, 69, 73, 80, 81, 83, 84, 92, 93, 94, 95, 99, 101, 102, 104, 108, 109, 113, 117, 127, 129, 132, 135, 136, 137, 139, 143, 149, 151, 154, 158, 166, 169, 176, 180, 182, 183, 193, 195, 196, 197, 205, 207, 209, 214, 217, 218, 221, 222, 229, 236, 237, 238, 241, 251, 253, 260, 261, 263, 264, 265, 269, 270, 277, 278, 281, 282, 283, 286, 288, 290, 297, 298, 299, 300], "In": [0, 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 30, 31, 56, 60, 65, 66, 67, 68, 73, 94, 107, 135, 144, 154, 176, 182, 183, 197, 201, 205, 214, 215, 217, 218, 221, 222, 234, 236, 237, 238, 248, 251, 260, 264, 270, 274, 277, 278, 297], "It": [0, 3, 4, 6, 7, 8, 9, 11, 13, 14, 15, 17, 19, 20, 21, 23, 24, 25, 27, 30, 31, 45, 46, 56, 60, 61, 65, 67, 68, 71, 94, 103, 104, 121, 122, 139, 140, 146, 149, 155, 182, 183, 197, 199, 201, 204, 207, 209, 217, 218, 221, 229, 236, 237, 238, 246, 251, 252, 257, 264, 265, 270, 278, 280, 281, 283, 291, 294], "Its": [0, 12, 15, 197, 263], "NO": 182, "NOT": [7, 27, 30, 32, 59, 66, 80, 94, 129, 159, 169, 179, 180, 246, 251, 260, 261], "No": [0, 3, 4, 32, 65, 104, 122, 126, 182, 207, 217, 236, 251, 265, 297, 303], "Not": [3, 15, 17, 20, 23, 25, 31, 69, 71, 132, 182, 183, 237], "OF": [83, 149], "ON": 32, "ONE": [49, 64, 182], "OR": [32, 142, 143, 151, 152, 154], "Of": [6, 7, 15, 19, 68, 251, 253, 278], "On": [1, 3, 15, 23, 222], "One": [1, 6, 7, 8, 9, 11, 12, 13, 14, 15, 19, 21, 23, 25, 30, 32, 56, 119, 135, 154, 197, 211, 217, 251, 278, 303], "Or": [3, 8, 11, 12, 15, 17, 20, 22, 23, 25, 30, 238, 241, 249, 250, 251, 253, 260, 278, 283, 298, 299], "Such": [12, 13, 15, 22, 27, 238], "THAT": 60, "THE": 151, "THESE": 151, "TO": [15, 151, 169], "That": [6, 7, 17, 19, 20, 21, 23, 183, 229], "The": [1, 2, 5, 6, 8, 9, 10, 12, 14, 16, 17, 18, 19, 22, 23, 25, 26, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39, 44, 45, 46, 48, 50, 51, 52, 53, 54, 56, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 80, 83, 84, 85, 88, 89, 92, 93, 94, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 112, 113, 114, 116, 117, 118, 119, 122, 123, 125, 126, 127, 128, 135, 136, 137, 139, 140, 143, 144, 149, 150, 151, 152, 155, 156, 157, 158, 160, 162, 164, 166, 169, 176, 177, 182, 183, 185, 186, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 222, 226, 229, 234, 236, 237, 238, 241, 242, 244, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 263, 264, 265, 267, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 282, 283, 286, 287, 288, 289, 290, 291, 293, 295, 296, 297, 298, 299, 300, 303, 307], "Their": [0, 177], "Then": [3, 7, 8, 15, 17, 23, 25, 94, 251], "There": [0, 3, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 20, 23, 24, 25, 30, 69, 73, 85, 116, 117, 169, 217, 222, 238, 250, 251, 256, 269, 278, 288, 299], "These": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 66, 67, 73, 76, 80, 91, 94, 99, 103, 104, 109, 122, 123, 143, 148, 151, 169, 170, 173, 178, 215, 217, 218, 221, 226, 236, 237, 245, 251, 264, 270, 283, 295], "To": [0, 3, 4, 5, 6, 7, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 61, 84, 92, 108, 119, 146, 149, 156, 169, 176, 182, 183, 198, 204, 209, 221, 229, 236, 239, 248, 250, 251, 252, 260, 264, 274, 278, 288, 297, 299], "WILL": 66, "WITH": 278, "Will": [31, 32, 92, 202, 237, 261, 275], "With": [0, 1, 4, 7, 11, 12, 13, 14, 17, 20, 69, 182, 236, 237, 260, 270, 297], "_": [4, 6, 12, 13, 17, 73, 169, 197, 214, 226, 238, 251], "_7_": 100, "__": [0, 12], "___": 12, "_____": 12, "______": 12, "________": 17, "_________": 17, "__________": [12, 17], "___________": 17, "______________": 17, "_______________": 12, "________________": 17, "_________________": 12, "__________________": 17, "________________________": 17, "__________________________": 12, "___________________________": 17, "___________________________________________": 17, "___________________________________________________________________________": 17, "__abstractmethods__": [27, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 68, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 233, 236, 237, 238, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259, 279, 281, 283, 291], "__add__": [27, 30, 133, 176, 209, 214, 236, 237, 260, 279, 280, 298, 299], "__annotations__": [27, 30, 36, 45, 56, 62, 75, 76, 92, 94, 133, 139, 169, 222, 225, 236, 260], "__array__": [27, 30], "__array_finalize__": [30, 54], "__array_prepare__": [30, 54], "__array_ufunc__": [30, 54], "__array_wrap__": [30, 54], "__bool__": [27, 181, 183, 237, 260], "__bytes__": [27, 30, 36, 236, 260], "__call__": [27, 67, 297], "__contains__": [27, 30, 54, 68, 75, 76, 133, 134, 136, 139, 140, 169, 176, 181, 197, 236, 237, 260, 298, 299, 301, 303], "__deepcopy__": [133, 169], "__delitem__": [27, 30, 133, 136, 139, 181, 197, 236, 298, 299, 301, 303], "__dict__": 20, "__doc__": 25, "__enter__": [27, 30, 45, 68, 278], "__eq__": [27, 30, 83, 84, 133, 135, 139, 169, 177, 178, 179, 180, 236, 237, 260, 283, 287, 298, 299], "__exit__": [27, 30, 45, 68, 278], "__format__": [27, 30, 54, 181, 183, 260, 283], "__ge__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__getattr__": [75, 76, 98, 104, 133, 139], "__getitem__": [27, 30, 31, 36, 45, 54, 68, 75, 76, 98, 104, 128, 131, 133, 134, 136, 139, 140, 176, 181, 183, 197, 209, 210, 214, 236, 238, 257, 260, 279, 280, 283, 289, 290, 291, 292, 295, 298, 299, 301, 303], "__getnewargs__": [27, 30, 36, 237, 297], "__getstate__": [27, 30], "__gt__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__hash__": [27, 30, 83, 84, 133, 135, 139, 169, 177, 178, 179, 180, 236, 237, 260, 283, 287, 298, 299], "__iadd__": [209, 214], "__init__": [9, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 42, 45, 47, 49, 51, 52, 56, 60, 61, 62, 67, 68, 69, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 114, 115, 116, 117, 120, 121, 122, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 148, 149, 150, 151, 153, 154, 155, 156, 157, 160, 161, 162, 163, 165, 166, 169, 170, 171, 172, 173, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 187, 188, 189, 190, 192, 193, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 263, 265, 268, 269, 270, 271, 272, 273, 275, 278, 279, 280, 281, 282, 283, 284, 287, 288, 289, 290, 291, 292, 294, 295, 296, 297, 298, 299, 301, 302, 303, 304, 305], "__iter__": [27, 30, 56, 60, 68, 92, 128, 131, 133, 134, 135, 139, 181, 183, 197, 217, 218, 219, 220, 221, 226, 227, 228, 229, 230, 232, 233, 234, 235, 237, 238, 246, 260, 278, 298, 299, 301, 303], "__le__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__len__": [27, 30, 36, 44, 45, 56, 61, 79, 81, 98, 104, 128, 131, 133, 134, 139, 140, 181, 183, 197, 236, 237, 238, 257, 260, 283, 298, 299, 301, 303], "__lt__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__main__": 24, "__module__": [25, 278], "__mul__": [27, 133, 176, 236], "__name__": [24, 303], "__ne__": [27, 30, 83, 84, 133, 135, 139, 169, 260], "__neg__": [133, 176], "__new__": [27, 30, 36, 54, 83, 84, 181, 197, 237, 297], "__next__": [27, 30, 45, 56, 57, 58, 60, 62, 63, 65, 66, 68, 92, 128, 129, 131, 238, 239, 246, 248, 250, 252, 278], "__nonzero__": [27, 237], "__orig_bases__": [133, 136, 139, 144, 155, 160, 238, 246, 251], "__parameters__": [133, 136, 139, 144, 155, 160, 238, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259], "__pow__": [133, 176], "__radd__": [27, 236, 237, 260], "__reduce__": [30, 54], "__repr__": [27, 30, 36, 54, 56, 61, 67, 68, 75, 76, 83, 84, 85, 86, 90, 92, 93, 95, 133, 135, 136, 140, 144, 148, 154, 155, 160, 169, 176, 177, 178, 179, 180, 181, 183, 237, 260, 275, 297, 298, 299, 301, 303], "__setattr__": [27, 30, 67], "__setitem__": [27, 30, 54, 133, 139, 176, 181, 197, 199, 236, 298, 299], "__setstate__": [27, 30, 54], "__slots__": [27, 30, 36, 236, 297], "__str__": [27, 30, 31, 36, 54, 67, 68, 71, 75, 76, 79, 82, 83, 84, 85, 86, 90, 92, 93, 96, 97, 98, 104, 111, 112, 113, 114, 115, 117, 121, 128, 131, 132, 177, 178, 179, 180, 181, 183, 197, 200, 201, 204, 209, 210, 211, 212, 213, 215, 237, 260, 261, 279, 280, 283, 286, 287, 288, 290, 293, 295, 296, 298, 299], "__sub__": [27, 133, 135, 139, 140, 176, 237, 298, 299], "__truediv__": [133, 176], "__version__": 9, "_abstracthsexposur": 141, "_all": 20, "_allbond": 169, "_alphabet": 13, "_atom_sit": [15, 248], "_atomt": 135, "_attr_tagnam": 252, "_backward_recurs": 107, "_base": 225, "_baseexonerateindex": [224, 225], "_baseexoneratepars": [223, 224, 225], "_basehmmertextindex": [230, 233], "_bit": 226, "_bitstr": 186, "_calc_ibd": 202, "_child": 139, "_chromosomecompon": 99, "_cl": [30, 36, 297], "_color": 104, "_create_edra": 169, "_data": 236, "_default_field": 219, "_draw_seg": 99, "_elem_tagnam": 252, "_embosscommandlin": 80, "_embossminimalcommandlin": 80, "_end_tag": 71, "_entity_poly_seq": 248, "_expect": 226, "_exptl_cryst": 15, "_fastam10parser__parse_hit_t": 226, "_fasttre": [24, 182], "_featur": 104, "_featureconsum": 94, "_forward_recurs": 107, "_gc_valu": 261, "_grei": 104, "_hedradict2chain": 169, "_id": 62, "_ident": 226, "_init1": 226, "_initn": 226, "_insdcwrit": 245, "_io": 24, "_item": 20, "_make_": 207, "_matric": 11, "_matrix": 199, "_ncbibaseblastcommandlin": 69, "_ncbiblast2seqcommandlin": 69, "_ncbiblastcommandlin": 69, "_ncbiblastmain2seqcommandlin": 69, "_open": [83, 209], "_opt": 226, "_parent": 139, "_parser": 225, "_pdbx_poly_seq": 248, "_pdbx_poly_seq_schem": [238, 248], "_per_letter_annot": 260, "_phylip_id_width": 65, "_phyml_lk": 182, "_phyml_stat": 17, "_phyml_trac": 182, "_phyml_tre": 17, "_posit": 99, "_postgresql_dbutil": 304, "_ppbuilder": 154, "_pseudcount": 11, "_query_mark": 225, "_rc": 260, "_read_next_align": 45, "_recordconsum": 269, "_residuet": 155, "_restricteddict": 260, "_score": 226, "_select": [148, 170, 173], "_self": 139, "_seqabstractbaseclass": 236, "_sim": 226, "_start_tag": 71, "_struct_ref_seq": 248, "_tba_c": 0, "_tba_right": 0, "_toopm": 299, "_translate_id": 136, "_twobitsequencedata": [236, 257], "_uk": 167, "_undefinedsequencedata": 236, "_uniprotsearchresult": 276, "_util": 24, "_xmlparser": 71, "_z": 226, "a0": [17, 176, 183], "a00022": 245, "a00028": 245, "a00031": 245, "a00034": 245, "a00060": 245, "a00071": 245, "a00072": 245, "a00078": 245, "a01": [16, 299], "a02": [16, 299], "a026236": 2, "a03": [16, 249, 299], "a040153": 2, "a040343": 2, "a040410": 2, "a05": 299, "a1": [0, 17, 30, 169, 176, 183, 264], "a12": [16, 299], "a1bg": 7, "a2": [0, 30, 169, 176], "a202": 15, "a203": 15, "a204": 15, "a2d_map": 169, "a2da_map": 169, "a2h_map": 169, "a2ha_map": 169, "a2l": 154, "a2m": [7, 27, 30, 32], "a2mp": 7, "a3": [15, 104, 169, 176], "a3c184c": 30, "a4": [8, 169], "a4yea2": 0, "a_": 109, "a_color": 8, "a_kei": 137, "a_rec": 8, "a_rod": 244, "a_u455": 244, "a_vs_b": 8, "aa": [0, 7, 11, 13, 22, 30, 31, 32, 66, 104, 137, 154, 182, 275], "aa1": 13, "aa2": 13, "aa3": 13, "aa_cont": 263, "aa_end": 6, "aa_multiple_align": 0, "aa_onli": 154, "aa_start": 6, "aaa": [0, 13, 22, 30, 222, 260, 280, 281], "aaaa": 22, "aaaaaaa": 30, "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa": 56, "aaaaaaaaattt": 30, "aaaaaaaacccccccaaaaaaaaaaaggggggaaaaaaaa": [0, 13, 30], "aaaaaaaggggggngaaaaa": 0, "aaaaaatacc": 7, "aaaaaattt": 30, "aaaaac": 12, "aaaaaccg": 0, "aaaaaccgg": 0, "aaaaagaaag": 7, "aaaaaggcattgtggtgggaat": 0, "aaaac": [0, 30], "aaaacaggtt": 7, "aaaacc": 12, "aaaaccc": 13, "aaaacgt": 30, "aaaacgtcg": 280, "aaaacgtt": [0, 30], "aaaag": [0, 30], "aaaagagacagatggtcactaataaaatctgt": 0, "aaaagattcc": 7, "aaaagcaatt": 7, "aaaagg": [0, 30], "aaaaggt": 30, "aaaaggtgg": 280, "aaaagtacag": 7, "aaaatatcag": 7, "aaaauugaauaucguuuuacuuguuuau": 66, "aaac": [0, 13, 30], "aaacaa": 12, "aaacaaa": [0, 13, 30], "aaacatgtgaaggttcttcaagacgaaaaactcccatttgatttgactctgtgcggttcg": 260, "aaacca": 12, "aaaccc": 12, "aaacccccccaaaaaaaaacaaaaaaaaaaaaaaaaaaaa": 56, "aaacct": 0, "aaacgtttaa": 7, "aaag": [0, 13, 30], "aaaga": 253, "aaagaaa": [0, 13, 30], "aaagaagtaaggtaaataac": 253, "aaagacaact": 278, "aaagacaagtggtatcaacg": 253, "aaagannnnn": 253, "aaaggggctt": [30, 68], "aaai": 2, "aaanccagtcacctttctcctaggtaatgagtagtgctgttcatattactntaagttcta": 238, "aaatcttggt": 7, "aaatgagggcccagggtatgctt": 62, "aaatgta": 0, "aaattcattt": 7, "aaattt": 30, "aaatttcccgg": 281, "aaatttcccgggaa": 281, "aaatttgggccaaattt": 281, "aac": [13, 22, 222], "aac62543": 21, "aacaac": 12, "aacagtcttc": 7, "aacateg": [79, 80], "aacc": [13, 22], "aaccaaaaag": 7, "aaccc": 11, "aacccc": 12, "aaccgg": 22, "aacctgtgga": 7, "aacg": 30, "aacgagcgttccg": 222, "aacgcc": [283, 295], "aacgcca": [283, 295], "aacgtacgt": 30, "aacgtg": 11, "aacgtgacagccctcc": 11, "aacgtgcacatcgtcc": 11, "aacgtggccacat": 199, "aacp": 7, "aactattcct": 7, "aactcc": [283, 295], "aactccg": [283, 295], "aactcgacggtcg": 236, "aactcgacgtcg": 236, "aactg": 30, "aactgg": 30, "aactggagttccg": 222, "aactt": 13, "aacttaatagcc": 0, "aadac": 7, "aaf": [15, 169], "aag": [13, 22, 30], "aagaa": 30, "aagaaagctcctcatgatcatcacggcggtcatggtccaggcaaacatcaccgctaa": 22, "aagaaatgga": 7, "aagcagcaatgtacaaga": 251, "aagcagtggtatcaacgcag": 253, "aagcccc": [30, 68], "aagccccttt": [30, 68], "aagccctcctagcacacacccggagtgg": 0, "aagccctgc": 0, "aagctt": 8, "aaggtcgccacac": 199, "aagtacgt": 0, "aagttccctccataattccttcctcccacccccaca": 0, "aah00859": 68, "aai": 15, "aak33142": 23, "aak49457": 23, "aak54648": [21, 23], "aalpetkdwredg": 0, "aamatrix": [30, 32], "aamp": 7, "aanat": 7, "aandx": [15, 169], "aani": 206, "aapkk": 250, "aar": 7, "aaron": 2, "aaseq": [10, 119], "aasiz": [15, 133, 169], "aat": [12, 13, 22], "aataa": 30, "aatatttccc": 7, "aatcatccac": 253, "aatcatccacttttta": 253, "aatcatccactttttaacgt": 253, "aatccggaggaccggtgtactcagctcaccgggggcattgctcccgtggtgaccctgatttgttgttggg": [19, 23], "aatcg": 236, "aatcgtggctattactgggatggaggtcactggcgcgaccacggctggtggaaacaacat": 22, "aatctagttt": 7, "aatg": 30, "aatgc": 11, "aatgcgaata": 7, "aatgggaatgttaagcaaacga": 0, "aatt": 13, "aattgntttgcccttttgggtttnttnttggtaaannnttcccgggtgggggnggtnnngaaa": 238, "aatttacgat": 7, "aatttcatct": 7, "aatttttggt": 7, "aattttttga": 7, "aaucg": 236, "aav74328": 238, "aavs1": 7, "aaymfflilv": 250, "aaymfllil": 250, "aaz99217": 238, "ab": [3, 7, 73, 123, 169, 182], "ab01234": 93, "ab1": 249, "ab811634": 23, "abacu": 17, "abasi": 206, "abbrevi": [0, 7, 12, 119, 123], "abc": [30, 45, 236, 237, 246], "abcd": 13, "abcdefghij": 260, "abcdejt": 251, "abd": 11, "abda_cell_fbgn0000014": 11, "abecasi": 2, "abi": [238, 239], "abif_file_format": 239, "abiio": [27, 238], "abiiter": [27, 238, 239], "abil": [0, 8, 9, 13, 19, 20, 30, 169], "abl": [0, 1, 3, 5, 7, 12, 17, 20, 23, 31, 42, 66, 108, 218, 221, 222, 264], "aboderin": 265, "abort": 56, "about": [3, 5, 6, 8, 9, 11, 12, 15, 17, 21, 22, 23, 25, 26, 27, 30, 31, 32, 59, 67, 71, 73, 77, 83, 84, 93, 99, 100, 102, 104, 117, 132, 149, 183, 185, 198, 214, 218, 222, 227, 234, 243, 246, 251, 253, 260, 262, 264, 269, 270, 273, 289, 307], "abov": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 56, 66, 83, 94, 104, 108, 152, 168, 169, 177, 202, 205, 217, 221, 237, 238, 250, 251, 252, 253, 256, 260, 263, 265, 270, 278, 283, 290, 297, 298], "abrahamleo": 265, "abs_scor": 11, "abs_score_threshold": 11, "absent": [0, 69, 182, 197, 270, 273], "absent_count": 197, "absolut": [11, 13, 15, 32, 73, 80, 100, 132, 193, 195], "abstract": [21, 30, 107, 123, 177, 178, 179, 180, 209, 236, 237, 246], "abstractatompropertymap": [27, 133, 134, 145], "abstractcommandlin": [27, 32, 67, 69, 80, 182, 270], "abstractdpalgorithm": [27, 106, 107], "abstractpropertymap": [24, 27, 133, 141, 156], "abstractresiduepropertymap": [27, 133, 134, 137, 145], "abstracttrain": [27, 106, 109], "abund": [102, 265], "abus": 7, "ac": [0, 6, 11, 12, 13, 14, 15, 17, 25, 27, 30, 32, 53, 66, 68, 90, 104, 129, 145, 169, 176, 182, 209, 210, 211, 212, 222, 234, 238, 240, 245, 250, 268, 273, 277, 295, 297], "ac007323": 238, "ac12345": 21, "aca": [13, 22, 23], "acaaattttt": 7, "acacatttat": 7, "acactacgactacgactcagactacaan": 256, "acad": [83, 264], "academ": [15, 137], "academi": [2, 32], "acagctgaaaata": 0, "acat": 13, "acataaatca": 249, "acataaatcaaattactnaccaacacacaaaccngtctcgcgtagtggag": 249, "acatttgaat": 7, "acc": [7, 11, 13, 22, 23, 83, 229, 275, 287], "acc1": [11, 291], "acc99456": 7, "acc_arrai": 137, "acc_avg": 229, "acc_list": 7, "accaac": 12, "accagtgtact": 19, "accal": 145, "acccaa": 12, "acccagctaatttttgtatttttgttagagacagtg": 251, "acccca": 12, "accccatccc": 7, "accccc": 12, "acccccgt": 297, "acccgagcgcggt": 67, "acccgggcgcggt": 67, "accd": 83, "acceler": [69, 182], "accept": [0, 3, 4, 7, 9, 13, 15, 17, 20, 22, 23, 30, 38, 46, 51, 61, 67, 68, 80, 83, 99, 104, 138, 169, 217, 218, 237, 251, 270, 277, 281, 303], "accept_atom": [15, 133, 138, 148, 152, 168, 169, 170, 173], "accept_backbon": [15, 133, 169], "accept_chain": [15, 133, 138, 148, 170, 173], "accept_deuterium": [133, 169], "accept_hydrogen": [133, 169], "accept_mainchain": [133, 169], "accept_model": [15, 133, 138, 148, 170, 173], "accept_residu": [15, 133, 138, 148, 170, 173], "accept_resnam": [15, 133, 169], "accept_sidechain": [133, 169], "acceptor": 80, "access": [0, 3, 4, 6, 8, 9, 12, 13, 17, 19, 20, 21, 22, 23, 26, 27, 30, 31, 49, 53, 56, 64, 66, 67, 68, 71, 73, 83, 85, 87, 88, 89, 90, 92, 93, 117, 119, 126, 134, 136, 137, 145, 149, 156, 157, 164, 169, 181, 183, 197, 198, 209, 210, 214, 217, 218, 229, 234, 236, 237, 238, 240, 248, 251, 253, 255, 263, 264, 270, 272, 273, 274, 275, 278, 288, 289, 291, 292, 295, 297, 299, 303, 307], "accession_vers": 218, "accg": [0, 30, 297], "accgacggcagctaaaaggg": 283, "accgagacggcaaaggctagcataggtatgagacttccttcctgccagtgctgaggaactgggagcctac": 21, "accgcc": [283, 295], "accgccc": [283, 295], "accgg": 30, "accggatgta": 238, "accggttt": 30, "accgt": [30, 68, 297], "accident": [0, 22, 30], "accii": 206, "acclim": [2, 3], "accomplish": [4, 7, 17, 25], "accord": [0, 15, 17, 32, 47, 59, 65, 99, 102, 129, 149, 158, 169, 172, 183, 217, 236, 263, 264, 265, 270], "accordingli": [4, 11, 50, 66, 169, 229, 260], "account": [6, 11, 12, 15, 30, 31, 32, 104, 182, 237, 270], "acct": 0, "acctgatgcttttataagccattgtgattaggatgactgttacaggcttagctttgtgtg": 238, "accttaagagctccacatagttgccatttgcagtacatggctaacatggattcaattgct": 260, "accumul": [261, 270], "accur": [32, 140, 182], "accuraci": [15, 32, 152, 166, 168, 169, 229, 264, 270], "acdefghiklmnpqrstvwi": 76, "acdq": 13, "acefilerecord": [27, 268, 269], "aceio": [27, 238], "aceiter": [27, 238, 240], "acet": 113, "acetylesteras": 113, "acetyltransferas": 7, "acg": [13, 22, 30, 260, 264, 297], "acga": 260, "acgc": 30, "acgcatacttg": 30, "acgccgct": 30, "acgccttttc": 7, "acgg": 30, "acggaaacat": 7, "acggcggt": 30, "acggcgtt": 30, "acgggtt": 30, "acgt": [11, 12, 13, 21, 22, 24, 30, 68, 236, 260, 264, 283, 287, 295, 297], "acgta": 241, "acgtaaccgg": 22, "acgtaaccggtt": 22, "acgtacct": 0, "acgtacgt": [0, 22, 260], "acgtacgtacgt": 262, "acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtn": 251, "acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtnnnnnn": [251, 260], "acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtnnnnnnact": 260, "acgtcggt": 30, "acgtcgtt": 30, "acgtnnnnnn": 260, "acgtt": 30, "acgttgcaatgccgta": 264, "acgtuacgtuxyzxyz": 236, "acgu": 13, "achiev": [197, 251, 260], "acid": [0, 2, 3, 11, 12, 14, 15, 23, 30, 32, 68, 71, 76, 111, 115, 119, 137, 154, 166, 169, 182, 214, 222, 236, 245, 248, 251, 261, 262, 263, 265, 272, 283, 290, 297], "acidocaldariu": 0, "acii": 206, "acm": 2, "acnq": 13, "aconitas": 83, "acoordmatchcount": 168, "acquaint": 17, "acquir": 6, "acr": 94, "across": [3, 12, 15, 99, 103, 217, 229, 288], "act": [0, 6, 12, 13, 23, 30, 105, 117, 237, 241, 260, 274, 278, 303], "act_sit": 272, "acta": [83, 175], "actaccgctagctcagaag": 12, "actacgac": 12, "actacgactagctcag": 12, "actacgactagctcagg": 12, "actacggcaagcacagg": 12, "actacggctagcacagaag": 12, "actacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtnnnnnn": 260, "actagtacag": 12, "actagtacagct": 12, "actagtacagctg": 12, "actagtta": 0, "actccta": 12, "actcgacgt": 236, "actcgacgtc": 236, "actcgacgtcg": 236, "actcgacgtcga": 236, "actcgacgtcgattt": 236, "actcgnnntcg": 236, "actcgtcgtcg": 236, "actg": [22, 261], "actgctagat": 30, "actgctagatag": 30, "actgctagct": [12, 30], "actgctagctag": [12, 30], "actgctagdt": 12, "actgctagdtag": 12, "actgn": [236, 261], "actgssss": 261, "actgswu": 261, "actgtn": 261, "actin": 197, "action": [12, 20, 71, 169], "activ": [15, 16, 17, 24, 25, 53, 86, 136, 139, 169, 272, 303], "active_sit": 66, "actm": 197, "acttcgactt": 7, "actttcttctttaccgtaac": 253, "actual": [6, 7, 8, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 69, 83, 99, 108, 109, 110, 217, 222, 226, 237, 238, 245, 246, 251, 260, 278, 294], "acugn": 236, "acxq": 13, "acyltransferas": 23, "ad": [4, 6, 8, 11, 12, 13, 15, 17, 23, 24, 30, 31, 32, 67, 69, 73, 76, 80, 99, 102, 111, 115, 117, 123, 132, 149, 155, 177, 182, 183, 209, 211, 237, 256, 260, 265, 269, 277, 280, 290, 303], "adaisrd": 0, "adaisrddylnapgetysvklta": 0, "adam": 186, "adam_consensu": [27, 181, 186], "adapt": [13, 20, 104, 166, 182, 253, 261, 262, 270, 283], "adapter3": [268, 270], "adapter5": [268, 270], "adaptor": [21, 301, 302, 303, 305], "adaptor3": 270, "add": [0, 5, 6, 7, 8, 9, 10, 11, 12, 15, 17, 19, 21, 22, 23, 24, 30, 31, 32, 45, 49, 60, 64, 71, 76, 82, 84, 99, 100, 102, 104, 105, 108, 109, 117, 121, 128, 129, 130, 132, 133, 135, 139, 140, 149, 155, 169, 172, 177, 179, 180, 182, 183, 185, 188, 197, 218, 221, 222, 226, 227, 229, 234, 236, 237, 246, 251, 260, 264, 265, 270, 278, 296, 299, 303], "add_annot": [181, 188], "add_compon": [115, 117], "add_count": [98, 102], "add_edg": [178, 179, 180], "add_entri": [115, 117], "add_featur": [8, 98, 104], "add_graph": [115, 117], "add_interact": [27, 177], "add_label": [98, 102], "add_nod": [178, 179, 180], "add_point": [98, 104], "add_primer_set": [79, 82], "add_product": [115, 117], "add_react": [27, 115, 117, 177], "add_rel": [115, 117], "add_residu": [133, 140], "add_sequ": [128, 129], "add_set": [8, 98, 104], "add_speci": [27, 177], "add_stmt_to_handl": [181, 185], "add_substr": [115, 117], "add_succ": [128, 130], "add_track": [8, 98, 104], "addit": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 35, 36, 38, 45, 60, 62, 66, 68, 69, 73, 80, 97, 99, 158, 166, 169, 177, 182, 183, 185, 198, 209, 211, 214, 215, 217, 221, 237, 246, 248, 253, 260, 264, 269, 270, 272, 278, 287], "addition": [5, 21, 56, 238, 247, 264, 278], "address": [6, 7, 20, 30, 68, 158], "adh": 13, "adh_zinc": 88, "adjac": [15, 169, 226], "adjust": [4, 6, 8, 9, 12, 21, 32, 68, 69, 70, 117, 129, 152, 169, 182, 217, 222, 229, 253, 260, 264, 270], "adjustdirect": [30, 32], "adjustdirectionaccur": [30, 32], "adlakslshkqllmspgqststtfpadapageytfycephrgagmvgkit": 0, "admin": 221, "administr": 3, "adocbl": 53, "adopt": [15, 20, 27], "adrian": 2, "adult": 7, "advanc": [3, 14, 15, 17, 27, 90, 169], "advantag": [3, 7, 8, 20, 22, 23, 237, 253], "advic": 8, "ae": [0, 16], "ae007476": 66, "aegddp": 12, "aegddpakaafdslqasateyigyawamvvvivgatigiklfkkfaska": 12, "aegddpakaafdslqasateyigyawamvvvivgatigiklfkkftska": 12, "aegddpakaafnslqasateyigyawamvvvivgatigiklfkkftska": 12, "aegothel": 0, "aepnaa": 12, "aepnaaateamdslktqaidlisqtwpvvttvvvaglviklfkkfvsra": 12, "aepnaaateamdslktqaidlisqtwpvvttvvvaglvirlfkkfsska": 12, "aepnaatnya": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvikl": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglviklfkkfv": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglviklfkkfvsra": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvirl": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvirlfkkfss": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvirlfkkfsska": 12, "aequinoctial": 7, "aerodramu": 0, "aessss": 12, "aestivum": 0, "af": [13, 27, 268, 269, 270], "af053945": 21, "af158246": 3, "af191": [0, 12, 30], "af191658": [0, 7, 12, 30], "af191659": [0, 7, 12, 30], "af191660": [0, 7, 12, 30], "af191661": [0, 7, 12, 30], "af191663": [0, 7, 12, 23, 30], "af191664": [0, 7, 12, 23, 30], "af191665": [0, 7, 12, 23, 30], "af283004": 3, "af297471": [238, 245], "af323668": 8, "af376133_1": [21, 23], "afai": 206, "afc": [30, 32], "afc_v": [30, 32], "affect": [4, 15, 20, 30, 32, 169, 182, 270], "affi": [24, 27], "affili": [7, 123], "affin": [14, 32, 42, 222, 297], "affine_penalti": [27, 297], "affl": 7, "affy_v3_exampl": 29, "affy_v4_exampl": 29, "affymetrix": [28, 29], "aformat": [79, 80], "african": 250, "after": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 17, 19, 20, 21, 22, 23, 24, 30, 56, 68, 69, 83, 93, 126, 169, 182, 183, 198, 202, 204, 222, 237, 238, 251, 253, 260, 269, 270, 278, 298], "afterposit": [21, 27, 237], "afterward": 3, "ag": [0, 7, 12, 30, 90, 182, 222], "aga": [12, 22, 30], "agaaatcaaa": 7, "agaacatctt": 7, "agaact": 14, "agaactc": 13, "agaattcttt": 7, "agagctattt": 278, "agagg": 240, "agagtcagtcaaggatagt": 22, "again": [0, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 18, 20, 21, 22, 23, 25, 30, 68, 71, 217, 218, 221, 237, 241, 251, 264], "against": [0, 3, 4, 6, 11, 12, 13, 17, 20, 24, 25, 30, 32, 68, 69, 70, 83, 168, 183, 218, 270, 290], "agatttc": 0, "agc": [22, 260, 261], "agccccgggc": 240, "agcccgtgggaaagtcgccgggtaatgcaccg": 22, "agcctttgccgtc": 21, "agcgcgcgtg": 283, "ageygyycephqgagmvgkii": 0, "ageygyycephqgagmvgkiiv": 0, "agg": [22, 30], "aggaatcgcgtgc": 11, "aggcatgcatc": 22, "aggctcggtta": 238, "aggctta": 0, "agggaactct": 7, "aggggtgcagagccgagtcacggggttgccagcac": 0, "agglutinin": 0, "aggreg": [15, 143, 151], "aggt": 0, "aggttt": 0, "aggtttgtt": 260, "aggua": 66, "agl3": 11, "agnost": [25, 169], "ago": 197, "agre": [12, 260], "agreement": 9, "agt": 22, "agtaaggtaaataacaaacg": 253, "agtacactggt": [19, 22], "agtacttgtg": 7, "agtatcttct": 7, "agttt": 0, "agtttaa": 0, "agtttatatataaatttcctttttattgga": 23, "ahcgscwtf": 0, "ahead": [3, 19, 278], "ahki": 13, "ahmad": 137, "ahr_si": 11, "ahsen": 264, "aid": [100, 123, 167], "aidlisqtwp": 12, "aiftddlpva": 0, "aik": 6, "aim": [17, 23, 27, 109, 119, 209, 237, 274], "airlfkkfss": 12, "aj237582": [238, 245], "ak": 169, "ak_set": 169, "ak_spec": 169, "ak_tpl": 169, "aka": [22, 238, 241, 250, 255, 278, 304], "akaafdslqasateyigyawamvvvivgatigikl": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkfa": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkfaska": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkft": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkftska": 12, "akaafdsltaqatemsgyawalvvlvvgatvgiklfkkfvsra": 12, "akaafnslqasateyigyawamvvvivgatigikl": 12, "akaafnslqasateyigyawamvvvivgatigiklfkkft": 12, "akaafnslqasateyigyawamvvvivgatigiklfkkftska": 12, "akc": 169, "akl": [15, 169], "akset": 169, "akstr": 169, "aktupl": 169, "al": [0, 4, 6, 7, 8, 9, 13, 17, 32, 34, 65, 69, 73, 107, 108, 109, 137, 140, 238, 252, 264, 265, 281, 299, 300], "al109969": 21, "al391218": 237, "al_con": 226, "ala": [13, 15, 154, 169], "alan": 2, "alanin": 112, "alcohol": 113, "alec": 2, "alejandro": [3, 68], "alert": 27, "aleu_horv": 0, "aleu_horvu": [0, 56], "aleu_horvumaharvlllalavlataavavassssfadsnpirpvtdraastlesavlgalgrtrhalrfarfavrygksyesaaevrrrfrifsesleevrstn": 0, "algebra": [2, 177], "algol": 4, "algorithm": [2, 9, 12, 13, 14, 15, 20, 30, 32, 68, 69, 70, 73, 107, 108, 109, 121, 127, 157, 166, 169, 175, 177, 181, 182, 186, 199, 216, 238, 263, 268, 270, 282, 297], "algotyp": 270, "algrtrhalr": 0, "ali": 229, "ali1": 74, "ali2": 74, "alia": [23, 30, 36, 104, 218, 237, 238, 251, 270, 297], "alias": 0, "alifrom": 229, "alig": 238, "align": [2, 3, 4, 6, 9, 11, 15, 17, 19, 20, 21, 22, 23, 26, 27, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 74, 79, 80, 133, 161, 166, 169, 175, 181, 182, 186, 193, 195, 196, 197, 199, 216, 217, 218, 221, 222, 223, 224, 225, 229, 230, 244, 250, 264, 270, 275, 278, 279, 280, 281, 283, 287, 289, 290, 291, 295, 297, 307], "align1": [12, 30, 297], "align2": [12, 30, 297], "align2model": [0, 33], "align3": 12, "align_arrai": [0, 12], "align_cmd": 270, "align_format": 0, "align_length": 71, "alignac": [11, 27, 283], "aligned_col": 0, "aligned_sequ": 0, "aligninfo": [12, 27, 30], "alignio": [0, 1, 9, 12, 17, 19, 20, 27, 30, 32, 91, 199, 217, 238, 250, 274], "alignment1": [0, 13, 30], "alignment2": [0, 13, 30], "alignment3": [0, 13], "alignment_format": 66, "alignment_iterator1": 0, "alignment_iterator2": 0, "alignment_list": 0, "alignment_n": 32, "alignment_ord": [30, 32], "alignment_view": [68, 70], "alignmentcount": [0, 27, 30], "alignmentfil": 182, "alignmenthasdifferentlengthserror": [27, 72], "alignmentiter": [0, 27, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 60, 62, 63, 65, 66], "alignments1": [13, 30], "alignments2": [13, 30], "alignments3": 13, "alignmentsabstractbaseclass": [0, 27, 30, 45], "alignmentwrit": [27, 30, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 46, 47, 49, 50, 51, 52, 53, 56, 60, 64], "alignmnet": 32, "alignn": [66, 274], "alignret": 58, "alito": 229, "all": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 36, 42, 56, 59, 61, 68, 69, 70, 71, 72, 73, 76, 80, 83, 88, 91, 93, 94, 97, 98, 99, 102, 104, 108, 109, 112, 117, 123, 129, 130, 132, 135, 139, 146, 149, 152, 154, 155, 156, 157, 158, 161, 164, 166, 167, 169, 177, 179, 180, 182, 183, 185, 186, 195, 197, 198, 199, 202, 203, 206, 209, 211, 214, 217, 218, 221, 222, 229, 236, 237, 238, 248, 251, 252, 253, 260, 261, 262, 264, 265, 269, 270, 271, 274, 276, 277, 278, 280, 282, 287, 288, 290, 295, 297, 298, 299, 303], "all_id": [128, 130], "all_qresult": 222, "all_speci": 23, "all_vers": 288, "allawi": 264, "allclos": [15, 168, 169], "allel": [18, 201, 202, 203, 204, 205], "allele1": 202, "allele2": 202, "allenzym": 206, "alloc": [8, 99, 176], "allow": [0, 1, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 27, 30, 31, 32, 42, 45, 56, 61, 65, 66, 68, 69, 71, 80, 83, 84, 99, 102, 103, 104, 105, 107, 108, 117, 119, 121, 123, 139, 182, 183, 197, 207, 217, 222, 236, 237, 238, 246, 251, 253, 257, 258, 261, 264, 269, 270, 274, 278, 280, 281, 288, 297, 302, 303], "allow_all_transit": [106, 108], "allow_transit": [106, 108], "allowed_tag": 84, "almost": [6, 8, 12, 15, 17, 19, 20, 21, 84, 251, 278], "aln": [0, 7, 12, 13, 20, 30, 32, 56, 62, 199, 238, 270, 275, 279], "aln_al": 20, "aln_annot": [218, 222, 226, 229], "aln_bam": 270, "aln_cod": 0, "aln_span": [20, 218, 229, 234], "alok": [2, 4], "alon": [4, 15, 182, 278], "along": [0, 4, 5, 6, 8, 11, 12, 15, 17, 20, 21, 31, 73, 100, 102, 169, 183, 197, 237, 261, 265, 299], "alpha": [0, 3, 8, 12, 13, 14, 15, 27, 30, 105, 113, 122, 137, 140, 154, 166, 169, 172, 181, 182, 199, 238, 241, 250, 260, 272, 280], "alphabet": [0, 11, 12, 30, 54, 76, 77, 78, 94, 108, 121, 135, 207, 214, 238, 241, 246, 251, 253, 258, 283, 287, 290, 291, 295], "alphabet_dna": 283, "alphafold": 164, "alphafold_db": [27, 133], "alphanumer": [4, 253], "alreadi": [3, 4, 7, 12, 15, 17, 19, 20, 22, 23, 24, 30, 67, 94, 108, 117, 169, 199, 217, 238, 297], "alrt": 182, "also": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 49, 52, 56, 59, 64, 65, 66, 68, 69, 71, 72, 73, 76, 83, 89, 94, 99, 100, 103, 104, 119, 135, 149, 150, 154, 169, 176, 181, 182, 183, 185, 189, 209, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 240, 245, 247, 249, 251, 253, 255, 257, 258, 259, 260, 261, 264, 270, 274, 276, 278, 280, 281, 283, 288, 290, 297, 299], "alst": 169, "alt": [68, 70, 117, 181, 197, 198], "alt_id": 169, "alt_nam": 76, "alt_unit": 197, "altcolor": 104, "altcolour": 104, "alter": [18, 23, 217, 272], "altern": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 30, 31, 32, 45, 67, 76, 81, 83, 86, 90, 92, 99, 117, 120, 134, 135, 152, 158, 162, 168, 169, 172, 182, 236, 237, 238, 246, 251, 252, 271, 272, 282, 289, 290, 291], "alternative_location_id": 172, "although": [6, 7, 8, 11, 12, 15, 22, 23, 25, 42, 68, 70, 127, 218, 222, 237, 251, 260, 278], "altitud": 197, "altloc": [135, 158, 162, 169], "altloc_match": [133, 169], "altnam": 23, "altschul": [2, 3, 32, 68], "altschul1990": [0, 2, 13], "alubi": 206, "alui": 206, "alwai": [0, 3, 4, 6, 7, 8, 13, 14, 15, 20, 30, 32, 83, 157, 169, 182, 183, 217, 218, 222, 236, 237, 238, 241, 242, 247, 251, 254, 259, 260, 265, 278, 288, 297], "am": [0, 2, 3, 7], "amano": 25, "ambigu": [11, 13, 22, 30, 31, 76, 236, 251, 260, 261, 264, 270], "ambiguous_nucleotid": 76, "ambiguous_nucleotide_alphabet": 76, "ambiguous_nucleotide_valu": 76, "ambiguous_protein": 76, "ambiguous_protein_alphabet": 76, "ambiguous_protein_valu": 76, "ambiguouscodont": [27, 75, 76], "ambiguousforwardt": [27, 75, 76], "amen": 15, "amend": 260, "american": 8, "amid": [152, 169], "amino": [0, 2, 3, 11, 12, 14, 15, 23, 30, 32, 68, 71, 76, 79, 80, 137, 154, 169, 182, 214, 222, 236, 245, 248, 260, 261, 262, 263, 265, 272, 290, 297], "amino_acid": 0, "amino_acids_cont": 265, "amino_acids_perc": [261, 265], "aminoacid": [167, 265], "among": [4, 13, 15, 18, 20, 32, 80, 217, 275], "amount": [0, 6, 11, 13, 71, 92, 100, 169, 237, 264], "amplicon": 80, "amplif": 82, "amplifi": [27, 72, 79, 80, 82, 253], "an": [2, 3, 4, 5, 6, 8, 9, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 80, 81, 83, 84, 85, 86, 89, 90, 91, 92, 93, 94, 97, 99, 100, 102, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 125, 126, 127, 129, 130, 132, 134, 135, 136, 139, 140, 142, 143, 144, 149, 151, 152, 153, 154, 155, 156, 157, 158, 159, 161, 164, 169, 170, 172, 175, 177, 179, 180, 182, 183, 185, 188, 190, 193, 195, 196, 197, 198, 199, 202, 203, 204, 205, 209, 210, 214, 215, 216, 217, 218, 222, 236, 237, 238, 239, 240, 241, 245, 246, 248, 250, 251, 252, 253, 256, 258, 259, 260, 261, 264, 265, 267, 269, 270, 272, 273, 274, 275, 276, 277, 278, 279, 282, 283, 284, 291, 295, 296, 297, 298, 299, 302, 303, 304, 306], "anacaacao": 169, "anal": 264, "analog": [0, 3, 20, 21, 237], "analys": [23, 182], "analysi": [0, 2, 3, 6, 7, 9, 13, 15, 16, 17, 21, 25, 26, 27, 30, 32, 73, 109, 129, 169, 177, 182, 185, 193, 195, 206, 207, 208, 238, 265, 283, 307], "analyz": [0, 2, 4, 6, 26, 84, 169, 182, 307], "anc": [30, 32], "ancenstor": 209, "ancestor": [17, 132, 183], "ancestr": 32, "anchor": [30, 32, 80, 221], "anchor_len": [30, 279], "anchorspac": [30, 32], "ander": 2, "andrew": 2, "andrzej": 267, "angl": [100, 104, 133, 136, 144, 152, 154, 160, 169, 176], "angle2": 158, "angle_avg": [133, 169], "angle_dif": [133, 169], "angle_kei": 169, "angle_pop_sd": [133, 169], "angle_rad": 176, "angstrom": [15, 158, 169], "ani": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 45, 52, 53, 56, 60, 65, 66, 67, 68, 73, 80, 83, 86, 93, 94, 103, 104, 105, 108, 117, 119, 129, 132, 136, 139, 140, 144, 150, 152, 160, 168, 169, 172, 176, 177, 182, 183, 186, 197, 198, 217, 218, 222, 229, 236, 237, 238, 240, 241, 246, 248, 251, 252, 253, 256, 258, 260, 261, 262, 264, 265, 269, 272, 274, 277, 278, 281, 288, 297, 299, 305], "anisimova": 182, "anisotrop": [15, 135, 162], "anisou_arrai": [135, 162], "anl": 262, "ann": [0, 53, 197], "anneal": 80, "annot": [0, 2, 3, 6, 12, 17, 19, 20, 22, 23, 25, 26, 27, 30, 32, 37, 39, 46, 52, 53, 56, 62, 66, 68, 99, 104, 133, 149, 153, 181, 183, 188, 197, 198, 221, 222, 229, 237, 244, 245, 248, 250, 251, 252, 253, 255, 256, 260, 272, 277, 301, 302, 303, 307], "annotatedchromosomeseg": [8, 27, 98, 99], "annotation_upd": [25, 272], "announc": [9, 69], "annual": 2, "annurev": 2, "anomal": 270, "anoth": [3, 4, 5, 6, 7, 8, 11, 12, 14, 15, 16, 17, 20, 21, 22, 23, 30, 57, 62, 65, 66, 104, 130, 139, 152, 159, 163, 166, 169, 197, 204, 214, 216, 217, 222, 237, 238, 251, 253, 260, 270, 272, 278, 299], "answer": [5, 6, 19, 169, 279], "antao": [2, 7, 26], "anticip": 7, "anticonsensu": [11, 27, 283, 290], "antoni": 2, "anymor": [9, 251, 258], "anyon": [5, 24, 30, 237, 299], "anystr": 246, "anyth": [3, 7, 17, 22, 30, 31, 91, 99, 103, 134, 152, 253, 299], "anyuri": 197, "anywai": [0, 3], "anywher": [6, 269], "aoacacaacb": 169, "aoutfeat": [79, 80], "ap": [11, 272], "ap001509": 66, "apaf": 183, "apai": 207, "apalsnt": 0, "apalsntklriapgsfysvtlgt": 0, "apart": [22, 237, 256], "api": [7, 14, 15, 17, 18, 23, 68, 70, 83, 99, 119, 164, 177, 209, 217, 237, 252, 274, 276, 303, 307], "api_kei": [7, 83], "aplca": 197, "aplysia": 197, "apmap": 134, "appar": [0, 20, 56, 238, 251], "appear": [0, 3, 11, 12, 13, 15, 17, 36, 37, 38, 73, 80, 93, 108, 123, 126, 132, 183, 207, 238, 244, 251, 269, 273], "append": [0, 6, 8, 10, 12, 13, 22, 23, 25, 27, 30, 32, 60, 84, 129, 182, 209, 214, 236, 260, 270, 278], "append_item": [68, 71], "append_set": [128, 129], "appendix": [26, 182, 307], "appl": [5, 153], "appli": [0, 3, 4, 6, 11, 12, 13, 15, 16, 17, 20, 21, 23, 32, 56, 68, 69, 70, 73, 80, 133, 135, 139, 153, 163, 166, 169, 175, 183, 197, 217, 237, 238, 239, 251, 260, 264, 267, 270, 274, 278, 280, 281, 288], "applic": [0, 2, 4, 6, 7, 9, 13, 15, 18, 22, 24, 27, 30, 68, 71, 73, 79, 83, 158, 169, 177, 181, 197, 218, 236, 264, 268, 283], "applicationerror": [27, 67], "appliedbiosystem": 239, "applies_to": 197, "applymtx": [133, 169], "approach": [3, 4, 6, 7, 8, 9, 13, 20, 32, 84, 99, 100, 107, 169, 238, 251, 264, 269, 294], "approci": 3, "appropri": [0, 4, 6, 9, 12, 13, 15, 21, 23, 30, 83, 84, 104, 121, 169, 182, 222, 237, 238, 251, 253, 260, 269, 278, 287, 288, 293, 294], "approv": 7, "approxim": [6, 11, 13, 32, 141, 182, 251, 264, 270, 294], "approximationfor": 32, "apr": [7, 83, 149, 278], "aptahdslpspat": 12, "aq": 0, "aqcbl": 53, "aqrk": 250, "aqua": 183, "aqvk": 13, "aqvkghgkkvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaah": 13, "ar": [0, 1, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 73, 76, 80, 81, 82, 83, 84, 88, 91, 92, 93, 94, 97, 99, 100, 101, 102, 103, 104, 107, 108, 109, 110, 117, 118, 119, 121, 122, 123, 125, 126, 127, 129, 130, 132, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 146, 149, 151, 152, 154, 155, 157, 158, 160, 164, 166, 167, 168, 169, 172, 174, 177, 178, 182, 183, 197, 198, 199, 201, 204, 207, 209, 210, 214, 215, 217, 218, 221, 222, 226, 227, 229, 231, 234, 236, 237, 238, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 255, 256, 258, 260, 261, 262, 263, 264, 265, 269, 270, 272, 273, 274, 275, 277, 278, 280, 281, 283, 287, 288, 289, 290, 292, 294, 295, 297, 298, 299, 303], "arab1": 238, "arabidopsi": [3, 8, 20, 23, 238, 275, 278], "arabidopsis_thaliana": 8, "arabinos": 260, "arac": 260, "arang": 13, "arbit": 214, "arbitrari": [11, 12, 13, 16, 17, 104, 130, 177, 180, 183, 197, 198, 253], "arbitrarili": [11, 13, 158, 169], "archaebacterium": 0, "archaeohip": 56, "archaeopteryx": 17, "architectur": [15, 69, 197, 198], "archiv": [5, 6, 8, 9, 15, 68, 69, 94, 149, 251, 275], "area": [5, 15, 16, 99, 137, 145, 157, 299, 300], "aren": [9, 17, 21, 102, 149, 251], "arg": [13, 29, 30, 62, 69, 84, 104, 131, 169, 183, 197, 230, 233, 272, 291, 303, 304], "arginin": 263, "argmax_x": 270, "argo": 265, "argter": 261, "arguabl": [20, 22], "argument": [0, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 17, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 42, 45, 47, 49, 51, 52, 54, 55, 56, 60, 64, 67, 68, 69, 71, 73, 80, 83, 85, 86, 88, 89, 90, 91, 92, 94, 99, 100, 101, 102, 103, 104, 107, 108, 109, 110, 116, 119, 120, 126, 127, 135, 136, 137, 142, 143, 144, 146, 149, 151, 155, 156, 162, 169, 182, 183, 193, 195, 197, 201, 204, 205, 206, 207, 210, 211, 212, 213, 214, 217, 218, 221, 236, 237, 238, 241, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 258, 259, 260, 261, 263, 264, 265, 269, 270, 271, 272, 274, 278, 279, 280, 281, 282, 283, 288, 290, 297, 299, 302, 303], "aris": 15, "arithmet": [4, 17, 73, 199], "arkin": 182, "arndcqeghilkmfpstwyvbzx": 13, "arnt": 11, "aromat": [261, 265], "around": [1, 4, 9, 15, 19, 32, 53, 66, 100, 129, 141, 146, 155, 158, 176, 177, 238], "arrai": [4, 6, 7, 11, 15, 18, 29, 30, 54, 68, 73, 127, 135, 139, 140, 146, 156, 162, 169, 172, 175, 176, 177, 216, 270, 275, 283, 290, 299], "arrang": [12, 16], "arrow": [15, 104], "arrowhead_length": [8, 104], "arrowshaft_height": [8, 104], "art": 17, "artemi": [8, 99, 104], "artemis_color": [98, 104], "articl": [7, 15, 17, 83, 100, 123, 197, 234, 237], "articletitl": 7, "artifici": [11, 251], "arylamin": 7, "as_con": 53, "as_fasta": [27, 238, 241], "as_fasta_2lin": [27, 238, 241], "as_fastq": [27, 238, 251], "as_fastq_illumina": [27, 238, 251], "as_fastq_solexa": [27, 238, 251], "as_handl": [27, 91, 152, 158], "as_phyloxml": [17, 181, 183, 197], "as_qual": [27, 238, 251], "as_tab": [27, 238, 256], "as_typ": [30, 36], "asa": [137, 145, 157], "asap": 260, "ascend": [6, 209], "asci": 251, "ascii": [6, 17, 23, 25, 69, 214, 236, 238, 251, 260, 270, 278], "asequ": [12, 67, 79, 80], "asi": 67, "asid": [12, 66], "ask": [0, 6, 7, 8, 11, 19, 20, 23, 61, 207], "asldkfla": 13, "asn": [3, 7, 13, 15, 69, 70, 162], "asn_glycosyl": 25, "asp": [13, 15, 34, 280], "asparagal": 7, "asparagin": [13, 14], "aspart": [13, 14, 263], "aspect": 24, "aspgluserileasn": 222, "asplei": 206, "aspttgaatgatgaaaata": 222, "assembl": [133, 158, 169, 243, 268], "assemble_residu": [133, 169], "assemble_residues_s": [133, 169], "assembli": [0, 6, 13, 30, 136, 149, 152, 158, 169, 238, 243, 253, 268, 269], "assembly_num": 149, "assemblyv": 238, "assert": [0, 12, 13, 15, 23, 59, 169, 238, 278], "assertalmostequ": 24, "assertequ": 24, "assess": [13, 32, 74, 182], "assign": [3, 4, 7, 8, 12, 14, 15, 17, 20, 21, 22, 67, 69, 73, 100, 120, 121, 122, 125, 127, 143, 153, 157, 176, 182, 197, 251, 264, 265, 277, 282, 299], "assist": 186, "associ": [0, 6, 12, 13, 21, 27, 30, 32, 52, 54, 66, 68, 69, 73, 80, 129, 132, 139, 149, 177, 182, 197, 198, 209, 217, 237, 245, 255, 257, 270, 275, 277, 290, 295, 303], "assort": [23, 262, 276], "assum": [0, 3, 4, 6, 7, 11, 12, 15, 19, 23, 24, 30, 32, 60, 67, 71, 94, 125, 135, 151, 153, 157, 183, 209, 217, 231, 237, 238, 251, 252, 253, 261, 265, 270, 277, 287, 290, 303], "assumpt": [7, 12, 125, 127, 238, 246], "aster": [241, 260], "aster_no_wrap": 241, "asterisk": [0, 13, 22, 236, 250, 261], "astlesavlg": 0, "astqkaekev": 250, "astral": [7, 15, 27, 123, 209, 214], "astral_fil": 209, "astronom": 30, "asx": 261, "asym": 172, "ata": 22, "ataaatagattattccaaataatttatttatgtaagaacaggatgggaggggga": 21, "ataaatcttc": 7, "atacttacctgacaggggaggcaccatgatcacacaggtggtcctcccagggcgaggctc": 30, "atacttacctgacaggggaggcaccatgatcacacaggtggtcctcccagggcgaggctcttccattgcactgcgggagggttgacccctgcgatttccccaaatgtgggaaactcgactgtataatttgtggtagtgggggactgcgttcgcgctatcccccg": 30, "atacttacctggcaggggagataccatgatcacgaaggtggttttcccagggcgaggctt": 30, "atacttacctggcaggggagataccatgatcacgaaggtggttttcccagggcgaggcttatccattgcactccggatgtgctgacccctgcgatttccccaaatgtgggaaactcgactgcataatttgtggtagtgggggactgcgttcgcgctttcccctg": 30, "atagccccag": 7, "atagtctcat": 7, "ataset": 80, "atataattct": 7, "atc": [22, 30], "atccatctgg": 7, "atccattgcactccggatgtgctgacccctgcgatttccccaaatgtgggaaactcgact": 30, "atcccg": 22, "atcctatgct": 7, "atcg": [12, 30], "atcgacgtcg": 236, "atcgswu": 261, "atctactaat": 7, "atctcagaggatggatggacca": 0, "atctgataccttgttcagatttcaaaatagttgtagccttatcctggttttacagatgtgaaactttcaa": 238, "atcttatcaacaaaactcaaagttcctaactgagacacgcaacaggggataagacaaggcacacaggggataggnnnnnnnnnnn": 253, "atdlidqtwp": 12, "ateamdslktqaidlisqtwpvvttvvvaglviklfkkfvsra": 12, "ateamdslktqaidlisqtwpvvttvvvaglvirlfkkfsska": 12, "ateamnslktqatdlidqtwpvvtsvavaglairlfkkfsska": 12, "atemsgyawa": 12, "ateyigyawa": 12, "atg": [22, 260, 279], "atgactca": 11, "atgactcatc": 11, "atgc": [17, 182, 240, 264], "atgcgt": 279, "atgctgggctcgaacgagtcc": 30, "atgctgggctcgaacgagtccgtgtatgccctaagctgagcccgtcg": 30, "atggaagaag": 7, "atggcacggaagtga": 236, "atggccattgtaatgggccgctgaaagggtgcccgatag": 22, "atggcgtttaccttgaccaacaagaacgtggttttcgtggccggtctgggaggcattggt": 13, "atgggaaccgcg": 13, "atgggaaccgcgctgcttttgctactggccgcgctctgcgccgcaggtggggccctggag": 13, "atgggcaatatccttcggaaaggtcagcaaat": 222, "atgggccgc": 22, "atgnnnnnnnnnnatcccgnnnnnnnnnnttgca": 22, "atgtaaaaat": 7, "atgtcgtttactttgaccaacaagaacgtgattttcgttgccggtctgggaggcattggt": 13, "atgtctcgt": [30, 279], "athel": 2, "atla": [2, 53], "atm": [15, 133, 169], "atmnamendx": [15, 169], "atol": 168, "atom": [25, 27, 31, 119, 133, 134, 136, 138, 139, 141, 143, 144, 145, 146, 148, 149, 151, 152, 154, 155, 156, 157, 158, 159, 160, 162, 163, 166, 167, 168, 169, 170, 172, 173, 175, 176, 209, 214, 238, 248], "atom1": [15, 135], "atom2": [15, 135], "atom3": 15, "atom4": 15, "atom_chain": [133, 169], "atom_coord": 169, "atom_count": 172, "atom_index_on": 172, "atom_index_two": 172, "atom_list": [15, 146, 163, 175], "atom_nam": [135, 172], "atom_r": [133, 169], "atom_sernum": [133, 169], "atom_to_internal_coordin": [15, 133, 136, 144, 158, 160, 168, 169], "atomarrai": [133, 168, 169], "atomarrayca": 169, "atomarrayindex": [15, 169], "atomarrayph": 169, "atomarrayvalid": 169, "atomcoordsin": 169, "atomic_radii": 157, "atomiter": [27, 238, 248], "atomkei": [15, 27, 133, 152, 168, 169], "atomndx": 169, "atomscal": 158, "atr": [4, 73], "att": [13, 22], "attach": [17, 130, 132, 157, 183, 197, 270], "attccattct": 7, "attcgatacc": 7, "attctgatat": 7, "attempt": [3, 7, 13, 19, 20, 21, 22, 29, 30, 71, 125, 218, 222, 237, 260, 270, 278, 288], "attent": 278, "attgtctctcagtgtg": 0, "attgtctcttacggtg": 0, "attqkaekev": 250, "attr": [84, 89, 104, 252], "attract": 17, "attribut": [3, 4, 7, 8, 11, 12, 17, 20, 21, 23, 30, 31, 35, 36, 37, 38, 39, 42, 45, 46, 47, 51, 52, 62, 67, 68, 71, 73, 76, 83, 84, 87, 88, 93, 94, 97, 99, 101, 103, 104, 112, 113, 114, 117, 120, 126, 127, 136, 144, 152, 157, 160, 161, 168, 169, 177, 183, 193, 197, 199, 204, 207, 209, 210, 211, 212, 213, 214, 217, 218, 221, 222, 226, 229, 234, 237, 252, 260, 265, 269, 272, 275, 282, 287, 295, 297], "attributeerror": [0, 17], "attttcactt": 7, "attttttacg": 7, "attttttacgaacctgtggaaatttttggttatgacaataaatctagtttagta": 7, "atwtrtaass": 0, "atwtrtavss": 0, "au": [0, 4, 7, 18, 53, 123, 201, 204, 274], "au099534": 7, "aucguuuuac": 66, "auggccauug": 261, "auggccauuguaaugggccgcuga": 261, "auggccauuguaaugggccgcugaaagggugcccgauag": 22, "augucucgu": 30, "august": [2, 9], "auml": 3, "auspic": 17, "austrocylindropuntia": 7, "ausubel": 72, "auth": [7, 172], "auth_chain": 143, "auth_residu": 143, "authent": 7, "author": [7, 11, 15, 21, 25, 26, 53, 87, 93, 123, 133, 143, 174, 197, 237, 272, 274, 295, 303], "author_nam": 83, "auto": [30, 32, 67, 79, 80, 250, 283], "auto_format": [68, 70], "autocommit": [301, 303, 304], "autodoc": 306, "autom": [2, 3, 7], "automat": [2, 3, 4, 7, 9, 11, 12, 13, 17, 19, 22, 23, 24, 25, 30, 32, 67, 68, 69, 80, 83, 149, 152, 183, 197, 217, 237, 238, 251, 253, 260, 264, 269, 270, 306], "automz": 0, "autosql": [0, 36, 38], "autosql_data": 0, "autosqlt": [0, 27, 30, 36], "auwera": [2, 8], "auxiliari": 7, "avail": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 30, 34, 52, 62, 67, 68, 70, 71, 73, 76, 83, 84, 88, 99, 104, 126, 134, 149, 158, 166, 168, 172, 182, 199, 202, 209, 217, 218, 221, 222, 226, 227, 229, 234, 251, 263, 264, 270, 274, 280, 281, 287, 290, 299, 300], "averag": [4, 11, 15, 16, 32, 73, 108, 152, 156, 169, 182, 186, 203, 264, 265, 270], "average_height": [16, 299], "avg": 169, "avg_rslt": 169, "avhasldkflasvstvltskyr": 12, "avmgrwkggraag": 22, "avoid": [3, 4, 6, 7, 8, 9, 11, 15, 17, 21, 24, 27, 31, 60, 67, 80, 108, 119, 149, 169, 176, 182, 183, 209, 238, 246, 251, 270, 274, 278], "avp": 23, "avpgr": 68, "avtpvknq": 0, "avtpvknqgqcgscwsf": 0, "avtpvknqgqcgscwsfsttgnvegqhfisqnklvslseqnlvdcdhecmeyegeeacdegcngglqpnaynyiiknggiqtessypytaetgtqcnfnsanigakisnftmip": 0, "awai": [8, 68, 80], "awar": [7, 15, 32, 218, 221, 229, 237], "ax": [54, 104, 300], "axi": [4, 8, 12, 13, 15, 31, 100, 104, 117, 126, 169, 176], "axis_label": 104, "axis_seq": 31, "axislabel": 126, "ay851611": 7, "ay851612": [7, 83], "ayako": 2, "ayass": 7, "azimuth": 176, "azup_achc": 0, "azup_achci": 0, "b": [0, 2, 3, 4, 7, 8, 11, 13, 17, 22, 27, 30, 32, 36, 37, 45, 53, 62, 67, 73, 80, 83, 84, 98, 100, 104, 107, 108, 109, 118, 126, 135, 136, 137, 149, 152, 162, 169, 172, 177, 182, 183, 206, 209, 210, 211, 215, 220, 230, 233, 236, 238, 247, 248, 249, 250, 261, 263, 264, 265, 268, 269, 270, 278, 280, 295], "b01": [16, 299], "b02": 299, "b03": 299, "b04": 299, "b05": 299, "b06": 299, "b1": [0, 30, 268, 270], "b1174": 114, "b1175": 114, "b12": 299, "b2": [0, 30, 268, 270], "b3_649_fc8437_r1_1_1_183_714": 251, "b3_649_fc8437_r1_1_1_362_549": 251, "b3_649_fc8437_r1_1_1_397_389": 251, "b3_649_fc8437_r1_1_1_610_79": 251, "b3_649_fc8437_r1_1_1_850_123": 251, "b4059": 260, "b64": 15, "b65": 15, "b66": 15, "b67": 15, "b7": 0, "b9": 0, "b_": 11, "b_8148": 0, "b_color": 8, "b_ehoa": 244, "b_factor": 162, "b_hxb2r": 244, "b_i": 11, "b_rec": 8, "b_vs_c": 8, "ba": [7, 11, 295], "baa31520": [241, 260], "baa33523": 238, "baboon": 0, "bac": [21, 103, 270], "bacillu": 13, "back": [3, 6, 7, 11, 12, 15, 17, 19, 21, 22, 23, 25, 55, 76, 84, 159, 168, 169, 191, 197, 209, 214, 236, 251, 258, 260, 274, 278, 303, 305], "back_tabl": [75, 76], "back_transcrib": [22, 27, 236], "backbon": [15, 140, 158, 167, 169], "backbonefil": [0, 62], "backboneonli": 158, "backboneselect": 169, "backend": 209, "background": [8, 11, 13, 27, 104, 117, 283, 287, 290, 294], "backslash": 270, "backtranscrib": 264, "backward": [12, 21, 30, 104, 107, 109, 207, 237, 260, 265, 303], "backward_algorithm": [106, 107], "backward_var": 109, "bacteri": [6, 16, 22, 238], "bacteria": [2, 22, 93], "bacteriologi": 2, "bacteriophag": 8, "bad": [21, 23, 251, 260, 278], "bailei": 2, "bailey1994": [2, 11], "baj87517": 25, "balaena": 272, "balaenoptera": 272, "balanc": [11, 21], "ball": 157, "baltimor": 216, "bam": [0, 23, 268, 270, 278], "bam_fil": [268, 270], "bamhi": [8, 207], "ban": [7, 65], "ban04711": 25, "band": [270, 275], "bang": 100, "bank": [88, 149, 214, 238, 245], "baq": 270, "bar": [4, 8, 103, 104, 270], "barbatum": 23, "barchartdistribut": [27, 98, 103], "barcod": 270, "barlei": 25, "barrier": 5, "bartek": [2, 26], "bartram": 7, "base": [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 123, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 160, 161, 162, 163, 165, 166, 169, 170, 171, 172, 173, 175, 176, 177, 179, 180, 182, 183, 184, 185, 187, 188, 189, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 230, 231, 232, 233, 234, 235, 236, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 268, 269, 270, 271, 272, 273, 274, 275, 278, 280, 281, 282, 283, 284, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 299, 302, 303, 304, 305], "base64binari": 197, "base_count": 93, "base_feature_format": [92, 93], "base_format": [92, 93], "base_id": [283, 287], "basefreq": [79, 80], "baselin": 104, "baseml": [17, 181, 192], "basemlerror": [181, 192, 193], "basetre": [13, 27, 181, 197, 198], "bashrc": 149, "basi": [4, 11, 95, 149, 295], "basic": [0, 1, 2, 3, 6, 8, 9, 11, 12, 15, 17, 18, 19, 21, 22, 23, 24, 67, 94, 101, 107, 139, 177, 218, 236, 237], "basicchromosom": [8, 27, 98], "bass": 263, "bassi": 262, "batch": [7, 12, 25, 59, 182, 202, 203, 274, 276], "batch_siz": [7, 25, 276], "bateman": 0, "batzogl": 32, "baum": [109, 121], "baumwelchtrain": [27, 106, 109], "bay": [9, 122, 127], "bb": 0, "bbcol": [0, 62], "bbr025": 252, "bbtacgcbb": 11, "bbtpgrp3": 0, "bc": [169, 181, 183, 198, 270, 278], "bc015878": 7, "bc067218": 7, "bcf": 270, "bchuh": 270, "bcif": 15, "bcjt": 251, "bct": [21, 93], "bdata": 83, "bdbbccdd": 0, "bdhkmnrvxy": 261, "bdist_rpm": 5, "be037100": 1, "beauti": 19, "becam": [3, 15], "becaus": [3, 6, 7, 8, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 30, 65, 66, 88, 95, 108, 139, 182, 183, 198, 209, 217, 218, 221, 222, 238, 251, 265, 269, 278], "becom": [4, 5, 6, 7, 11, 17, 20, 22, 23, 84, 94, 217, 218, 237, 245, 251, 255, 270], "bed": [13, 27, 30, 36, 38, 270], "bed12": [0, 38], "bed3": 0, "bed6": 0, "bedexample2": 0, "bedmaf": 0, "bedn": [0, 35, 36], "bedtobigb": [0, 36, 37], "been": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 19, 20, 21, 24, 25, 30, 32, 67, 68, 83, 94, 104, 108, 120, 122, 127, 132, 149, 154, 182, 199, 212, 217, 248, 251, 253, 260, 264, 270, 277, 278, 282, 290], "befor": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 65, 73, 83, 84, 88, 92, 99, 117, 121, 125, 169, 183, 198, 222, 237, 241, 252, 261, 270, 278, 290, 297], "beforehand": [25, 252], "beforeposit": [21, 27, 237], "begin": [0, 3, 4, 6, 7, 11, 15, 17, 20, 22, 30, 36, 44, 45, 56, 61, 89, 136, 169, 217, 230, 236, 237, 250, 251, 265, 279, 297], "beginn": 5, "begun": 20, "behav": [4, 15, 17, 20, 68, 135, 236, 237, 260], "behavior": [0, 4, 11, 16, 17, 20, 23, 30, 183, 217, 218, 237], "behaviour": [30, 64, 76, 260, 264, 288, 294, 297], "being": [1, 3, 4, 7, 8, 12, 13, 15, 16, 18, 21, 23, 30, 31, 32, 61, 65, 73, 108, 162, 182, 237, 260, 270, 278], "believ": 275, "belong": [4, 11, 13, 15, 32, 73, 84, 88, 93, 132, 272, 282, 288, 299], "below": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 16, 17, 19, 21, 22, 23, 24, 71, 72, 80, 90, 119, 149, 158, 169, 198, 203, 217, 251, 253, 263, 274, 278, 279, 288, 290], "bend": [15, 137], "benefit": [0, 1, 5, 6, 13, 15, 19, 158, 169, 217, 238, 278], "benner22": [13, 199], "benner6": [13, 199], "benner74": [13, 199], "benzoat": 113, "bep": 25, "berg": 265, "berkelei": [211, 212, 283], "berlin": 2, "bernard": 2, "bernstein": 149, "bertil": 32, "besid": [11, 217], "best": [2, 4, 5, 6, 11, 12, 13, 14, 15, 19, 20, 23, 24, 30, 32, 69, 73, 79, 80, 175, 182, 199, 216, 229, 238, 270, 297], "best_hit_overhang": [68, 69], "best_hit_score_edg": [68, 69], "bestn": 0, "bestscor": 270, "beta": [0, 4, 12, 13, 14, 15, 27, 30, 112, 120, 137, 152, 169, 172, 199, 211, 238, 241, 272, 280], "better": [4, 6, 7, 8, 13, 14, 15, 17, 71, 182, 237, 260, 261, 297], "between": [0, 3, 6, 7, 11, 13, 14, 15, 16, 17, 20, 21, 22, 30, 32, 35, 36, 56, 68, 69, 73, 80, 83, 94, 99, 100, 101, 104, 108, 109, 117, 127, 130, 132, 135, 138, 140, 143, 156, 161, 163, 166, 169, 172, 175, 176, 177, 182, 183, 186, 197, 198, 204, 209, 214, 217, 222, 226, 237, 238, 251, 261, 264, 265, 270, 278, 282, 289, 297, 299, 300], "betweenposit": [21, 27, 237], "bewar": [11, 21, 278], "beyer": [13, 30], "beyond": [8, 11, 20, 21, 30, 217], "bf": [11, 295], "bf_search": [177, 178, 180], "bfac": 152, "bfactor": [135, 152, 169], "bfile": 11, "bg": 11, "bg569293": 7, "bg_prob": 294, "bgcolor": [115, 117], "bgz": [23, 217, 238, 278], "bgzf": [23, 27, 217, 238], "bgzfblock": [27, 278], "bgzfreader": [27, 278], "bgzfwriter": [27, 278], "bgzip": [23, 278], "bia": [6, 229, 270], "bias": [237, 272], "bib": 252, "bibiserv": 32, "bibliograph": 7, "bibliographi": [26, 307], "bidiagon": 4, "bielefeld": 32, "bif72": 238, "bifurc": [17, 132, 183], "big": [0, 5, 6, 7, 12, 149, 204, 237, 278], "big_fil": 6, "bigarrow": 8, "bigb": [27, 30, 37, 38], "bigendian": 23, "bigger": [32, 207, 222], "biggest": 20, "bigmaf": [27, 30], "bigpsl": [27, 30], "bil285": 8, "bill": [12, 56, 59, 217, 226], "bin": [0, 6, 85, 265], "binari": [0, 1, 3, 6, 7, 23, 25, 27, 32, 36, 37, 38, 45, 54, 67, 68, 83, 145, 153, 182, 186, 197, 198, 202, 203, 238, 242, 247, 251, 252, 253, 254, 259, 260, 270, 278], "binary_charact": [181, 197, 198], "binary_cif": [15, 27, 133], "binary_constraint": [181, 182], "binarycharact": [27, 181, 197], "binarycif": 165, "binarycifpars": [15, 27, 133, 165], "bind": [0, 2, 11, 25, 53, 177, 185, 256, 260, 264, 272, 288, 295], "bindin": 0, "binomi": [2, 4], "bio": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 303, 306, 307], "bio_assembly_index": 172, "bioassembli": 172, "bioassmbli": 172, "bioch": [59, 226], "biochem": [53, 177, 264], "biochemistri": 264, "biochimica": 83, "biocomput": 3, "biocorba": 237, "biodatabas": 303, "bioentri": 303, "bioinf": 250, "bioinformat": [0, 2, 4, 5, 7, 8, 9, 15, 19, 20, 22, 32, 69, 73, 83, 152, 169, 182, 262], "bioinformatician": 15, "biojava": [6, 7, 9, 251], "biol": [0, 74, 129, 140, 149, 157, 264], "biolog": [2, 10, 15, 20, 22, 27, 75, 109, 149, 197, 236, 237, 272, 299, 301, 303], "biologi": [0, 2, 5, 7, 9, 19, 21, 23, 27, 32, 83, 130, 182], "biologist": [0, 7, 12, 15, 19, 21], "biomed": [2, 238, 250, 253], "biomedcentr": 218, "bionj": [181, 182], "bioperl": [6, 7, 9, 20, 66, 237, 238, 251, 255, 261, 262, 303], "biophysica": 83, "biopolym": [2, 264], "biopython": [0, 1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 30, 31, 32, 56, 65, 67, 68, 69, 70, 80, 81, 83, 84, 92, 104, 112, 113, 114, 118, 119, 152, 156, 158, 167, 168, 169, 171, 172, 177, 178, 181, 182, 198, 209, 210, 217, 226, 234, 236, 237, 238, 240, 249, 251, 253, 256, 264, 270, 274, 280, 281, 297, 298, 301, 302, 303, 304, 305, 306], "biopythondeprecationwarn": 27, "biopythonexperimentalwarn": 27, "biopythonparserwarn": 27, "biopythonwarn": [27, 147, 197, 236], "biopythooon": [7, 83], "biorubi": [9, 251], "biosci": 153, "bioscienc": 2, "bioseq": 301, "bioseqdatabas": [301, 302, 305], "biosoftwar": 242, "biospam": 24, "biospamtestaddit": 24, "biospamtestdivis": 24, "biosql": [7, 9, 19, 237, 306, 307], "biostar": 279, "biosynthesi": [23, 25], "biosystem": [238, 239], "biotech": 254, "biovar": [6, 8, 21, 238], "bipartit": [94, 182], "bipartition_filenam": [181, 182], "bipoython": 158, "birch": [2, 7], "birnei": [2, 237], "bisect": 263, "bisection_method": 263, "bisulfit": 270, "bit": [0, 3, 5, 6, 8, 11, 12, 13, 17, 19, 20, 23, 31, 68, 69, 71, 75, 133, 169, 182, 183, 238, 247, 251, 253, 270, 278, 283], "bit_scor": 3, "bitmap": [8, 104], "bitmask": 169, "bitscor": [20, 218, 226, 229, 234], "bitscore_raw": [20, 218], "bitwis": [0, 52], "bj": 83, "bjellqvist": 263, "bl": [30, 32], "bl_ord_id": 218, "black": [6, 8, 104, 183], "blackbriar": 0, "blackmould": 265, "blackshield": 32, "blanco": 7, "blank": [0, 5, 71, 139, 162, 214, 241, 256, 260], "blanklin": 206, "blast": [2, 5, 8, 9, 13, 26, 27, 32, 55, 67, 217, 219, 220, 221, 226, 229, 270, 274, 307], "blast_cutoff": 71, "blast_formatt": 69, "blast_frag": 20, "blast_hit": 20, "blast_hsp": 20, "blast_id": 218, "blast_qresult": 20, "blast_record": 3, "blast_record_copi": 3, "blast_recordt": 3, "blast_slic": [3, 20], "blast_tab": [217, 218], "blast_xml": [217, 218], "blastal": [3, 69], "blastallcommandlin": 69, "blastdb": [68, 70], "blastdb_vers": [68, 69], "blastio": [20, 27, 217, 221], "blastjson": 3, "blastn": [3, 13, 20, 30, 68, 69, 70, 71, 199, 218], "blastoutput2": 3, "blastoutput_db": 218, "blastoutput_program": 218, "blastoutput_refer": 218, "blastoutput_vers": 218, "blastp": [3, 13, 30, 68, 69, 70, 71, 199, 218], "blastpars": [27, 68, 71], "blastpgp": [3, 69, 71], "blastpgpcommandlin": 69, "blasttabindex": [217, 218, 219], "blasttabpars": [217, 218, 219], "blasttabwrit": [217, 218, 219], "blastx": [3, 68, 69, 70, 71, 218], "blastxml": 71, "blastxmlindex": [217, 218, 220], "blastxmlpars": [217, 218, 220], "blastxmlwrit": [217, 218, 220], "blat": [0, 2, 3, 20, 30, 45, 217, 221], "blat4": 221, "blat_frag": 20, "blat_hit": 20, "blat_hsp": 20, "blat_hsp2": 20, "blat_qresult": 20, "blatio": [20, 27, 217], "blatpslindex": [27, 217, 221], "blatpslpars": [27, 217, 221], "blatpslwrit": [27, 217, 221], "blatspec": 221, "blattner": 2, "bleasbi": 2, "bloack": 0, "block": [0, 2, 3, 7, 12, 13, 20, 23, 24, 27, 36, 37, 39, 46, 61, 62, 66, 68, 72, 73, 97, 128, 129, 220, 221, 222, 223, 224, 225, 226, 229, 230, 238, 250, 252, 253, 278], "block_siz": [218, 220], "block_start_offset": 278, "blockcount": [0, 36], "blocked_in": 72, "blocks_5": 13, "blocks_per_lin": [238, 245], "blocksiz": [0, 36, 37, 79, 80, 129, 221], "blog": 61, "blosum": [13, 14, 32], "blosum45": [13, 68, 70, 182, 199], "blosum50": [13, 199], "blosum62": [3, 11, 13, 14, 30, 32, 68, 69, 182, 199, 290, 297], "blosum62mt": 32, "blosum80": [68, 70, 199], "blosum90": 199, "blown": 59, "blue": [8, 9, 15, 17, 99, 104, 169, 181, 183, 198], "blunt": 206, "bm": [0, 53, 145], "bmc": [2, 32, 69], "bmedi": 206, "bmp": [8, 104], "bmr": 32, "bob": [2, 124], "bodi": 8, "bogusparamet": 80, "boil": 23, "bolser": 2, "bommarito": 264, "bond": [136, 144, 152, 158, 160, 169, 172, 265, 272], "bond_count": 172, "bond_ord": 172, "bond_rot": [133, 152, 169], "bond_set": [133, 152, 169], "bondradiu": 158, "bone": 7, "bonu": [6, 278], "book": [6, 7, 17, 83, 218], "bool": [15, 54, 135, 136, 139, 144, 149, 152, 155, 158, 160, 162, 166, 168, 169, 176, 183, 197, 260], "boolean": [6, 17, 32, 67, 69, 80, 94, 104, 127, 129, 143, 148, 151, 152, 154, 162, 169, 182, 183, 197, 218, 221, 229, 236, 237, 253, 260, 270, 297, 303], "boot": [181, 182], "bootlabel": [30, 32], "bootseq": 12, "bootstrap": [12, 27, 30, 32, 80, 128, 129, 132, 181, 182, 183, 186, 197, 238], "bootstrap_branch_length": [181, 182], "bootstrap_consensu": [27, 181, 186], "bootstrap_se": [181, 182], "bootstrap_tre": [27, 181, 186], "border": [8, 104], "bore": 11, "botani": 7, "both": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 20, 21, 23, 25, 30, 32, 56, 59, 63, 65, 69, 71, 80, 104, 109, 135, 158, 169, 182, 183, 188, 197, 214, 217, 218, 221, 222, 229, 234, 237, 251, 260, 264, 270, 278, 290, 297, 299], "bother": 15, "botstein": 2, "bottom": [21, 99, 104], "bought": 6, "bound": [8, 13, 21, 104, 115, 117, 156, 197, 198, 274], "boundari": [11, 21, 35, 46, 51, 61, 237], "bourn": 166, "boutfeat": [79, 80], "bowden": 2, "box": [8, 104], "bp": [0, 6, 7, 8, 11, 21, 23, 30, 83, 207, 222, 270, 278, 283], "bp_length": 99, "bpatomarrai": 169, "bq": 270, "br": 278, "bracket": [4, 215], "bracteata": 23, "brad": [2, 26], "bradtiana": 23, "bradtianaa": 23, "branch": [32, 80, 132, 182, 183, 186, 197, 198], "branch_label": 17, "branch_length": [13, 17, 181, 183, 184, 187, 189, 197, 198, 199], "branch_length_onli": 190, "branch_length_unit": 197, "branch_stdev": 183, "branchcolor": [27, 181, 183, 197], "branchlength": 132, "branchlength2support": [128, 132], "branchlength_sd": 132, "branchlengths_onli": 132, "brandon": 2, "brassica": 238, "breadth": [17, 180, 183], "break": [0, 3, 6, 7, 8, 13, 15, 17, 18, 19, 23, 66, 94, 99, 149, 158, 169, 198, 207, 222, 242, 245, 251, 255, 260, 278], "breez": 20, "brenner": [30, 32], "breslauer": 264, "brian": 2, "brice": 149, "bridg": [15, 80, 137, 203, 265, 272], "brief": [7, 9, 15, 32, 79, 80, 123], "briefli": [3, 7, 19, 23, 32], "bright": [23, 100], "bring": [12, 23, 278], "broad": [2, 23], "broken": 8, "brought": 17, "brown": [2, 8, 32, 183], "browser": [3, 7, 10, 35, 61], "bruce": 2, "brudno": 32, "brush": 19, "brute": [6, 21], "bryan": 2, "br\u00fcssow": 2, "bs_tree": 132, "bsd": 9, "bsequenc": [12, 67, 79, 80], "bsh1236i": 206, "bshfi": 206, "bsni": 206, "bspani": 206, "bsthhi": 206, "bstree": 132, "bsubtili": 13, "bt": 275, "btg299": 2, "btgst": 0, "bth078": [2, 73], "bth349": 2, "btk021": 2, "btop": [55, 218], "btp163": 2, "btp352": 2, "btpe": 4, "btw": 15, "bu": 286, "bucket": 146, "bucket_s": 146, "buffer": [0, 129, 168], "bug": [17, 24, 42, 130, 210, 218, 222, 226, 277], "bug6yxxskwecffh0l08jzalghq": 238, "build": [3, 5, 6, 8, 23, 24, 25, 27, 32, 45, 53, 60, 67, 69, 80, 108, 109, 148, 162, 166, 169, 182, 186, 193, 195, 196, 198, 199, 209, 217, 237, 238, 246, 270, 279, 285, 303], "build_atomarrai": [133, 169], "build_edraarrai": [133, 169], "build_peptid": [15, 154], "build_tre": [181, 199], "builder": 108, "built": [0, 1, 3, 5, 6, 9, 11, 12, 15, 19, 20, 21, 22, 23, 24, 27, 32, 61, 67, 169, 183, 209, 221, 260, 274, 278, 283, 299], "builtin": [91, 278], "bulb": 264, "bulk": [16, 20], "bullbrees": 265, "bunch": [7, 23, 103, 123, 182], "bundl": [8, 36, 37, 149, 251], "burden": 67, "buri": 5, "burrow": 270, "bussel": 124, "buster": [11, 283, 286, 293], "butterworth": 7, "bwa": [0, 270], "bwaaligncommandlin": [268, 270], "bwabwaswcommandlin": [268, 270], "bwaindexcommandlin": [268, 270], "bwamemcommandlin": [268, 270], "bwasampecommandlin": [268, 270], "bwasamsecommandlin": [268, 270], "bwasw": 270, "bwasw_cmd": 270, "bwt": 270, "bwtsw": 270, "by_seri": 7, "bypass": 13, "byte": [0, 3, 6, 17, 22, 23, 30, 36, 90, 91, 104, 150, 164, 197, 219, 220, 221, 225, 226, 232, 236, 238, 241, 245, 246, 247, 249, 251, 256, 257, 260, 278, 303], "bytearrai": [0, 22, 236, 303], "byteord": 247, "bytesio": 238, "bytestream": 90, "bz2": 23, "bzip": 11, "bzip2": [1, 23], "c": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 17, 19, 22, 23, 29, 30, 31, 32, 46, 62, 66, 67, 69, 73, 76, 80, 84, 118, 129, 135, 137, 139, 140, 146, 149, 152, 154, 157, 159, 166, 168, 169, 172, 175, 177, 182, 183, 218, 222, 229, 236, 247, 251, 260, 261, 263, 264, 268, 269, 270, 278, 280, 288, 296, 297, 299], "c00017": 112, "c00023": 112, "c00099": 112, "c00294": 112, "c00298": 112, "c00348": 112, "c00349": 112, "c01": [16, 299], "c01386": 112, "c02": 299, "c03": [16, 299], "c05": 299, "c1": [0, 30], "c12": 299, "c2": [0, 30], "c2h2": 11, "c4": [166, 222], "c4fbb762c4a87ebd": 262, "c_": 11, "c_alpha": 153, "c_color": 8, "c_rec": 8, "c_seq": 264, "c_ug268a": 244, "ca": [0, 11, 25, 86, 90, 135, 136, 140, 141, 152, 154, 156, 162, 166, 169, 172, 273], "ca1": 15, "ca2": 15, "ca3": 15, "ca_a_0": 169, "ca_b_0": 169, "ca_bind": 272, "ca_coord": [15, 140, 169], "ca_depth": [15, 27, 133, 156], "caa": [0, 22], "caa63439": 21, "caa90861": 21, "caaa": [0, 13, 30], "caaaaaaaaaaaaaaaacacaaaaaaaaaaaaaaaaaaaa": 56, "caaaacacaaacag": 253, "caaacaacaacaaaaaaaacaaaaaaaaaaaaaaaaaaaa": 56, "caaacc": 12, "caagccctgc": 0, "caagccctgcgcgctcagccggagtgtcccgggccctgctttccttttc": 0, "caagtggtatcaacgcagag": 253, "caatgccgga": 7, "cab531": 21, "cabio": 2, "cac": 22, "caccuaacaauaaguaagucagcagugagau": 66, "cacga": 66, "cacgagaggagcggaggcgaggggtgaacgcggagcactccaatcgctcccaactagaggtccacccaggacccagagacctggatttgaggctgctgggcggcagatggagcgatcagaagaccaggagacgggagctggagtgcagtggctgttcacaagcgtgaaagcaaagattaaaaaatttgtttttatattaaaaaa": 0, "cacgtg": 11, "cacgtgatgtcctc": 11, "cacgtgccgcgcgc": 11, "cacgtgggaggtac": 11, "cach": [0, 6, 7, 36, 44, 45, 84, 149, 169, 265, 278, 297], "cactacea": 7, "cacti": 7, "cactu": 12, "cad": [13, 15], "cadist": [15, 169], "cag": 22, "cagaaaa": 222, "cagcccgggggatccactagttctagagcggccgccaccgcggtggagctc": 206, "caggctgcgcggtttctatttatgaagaacaaggtccgtatgatagttgattgtcatgca": 260, "cagttcgccacaa": 199, "cagttttcgttaagagaacttaacattttcttatgacgtaaatga": 23, "cai": 261, "caiatcasyp": 0, "cal_dn_d": [27, 279, 281], "calc_affine_penalti": [27, 297], "calc_allele_genotype_freq": [201, 202], "calc_angl": [15, 27, 133, 176], "calc_dihedr": [15, 27, 133, 176], "calc_diversities_fis_with_ident": [201, 202], "calc_diversities_fis_with_s": [201, 202], "calc_fs_exposur": 15, "calc_fst_al": [201, 202], "calc_fst_pair": [201, 202], "calc_hs_exposur": 15, "calc_ibd": [201, 203], "calc_ibd_diplo": [201, 202], "calc_ibd_haplo": [201, 202], "calc_rho_al": [201, 202], "calc_rho_pair": [201, 202], "calceolu": 7, "calcium": [15, 172, 272], "calcul": [0, 6, 9, 11, 17, 20, 22, 23, 27, 30, 31, 32, 34, 36, 44, 45, 52, 73, 80, 107, 108, 109, 120, 122, 127, 129, 132, 134, 135, 137, 141, 145, 156, 157, 166, 169, 175, 176, 182, 183, 186, 194, 199, 202, 203, 216, 221, 257, 261, 262, 263, 264, 265, 267, 270, 281, 282, 283, 287, 290, 294, 297, 299, 300], "calculate_consensu": [11, 12, 283, 290], "calculate_dn_d": [13, 27, 30, 34], "calculate_dn_ds_matrix": [13, 27, 30, 34], "calculate_pseudocount": [11, 283, 287], "calibr": [53, 270], "calif": 83, "california": [2, 6, 197], "californica": 197, "californicum": 23, "calippu": 56, "caljac1": 0, "caljac3": 0, "caljac3tocaljac4": 0, "caljac4": 0, "call": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 21, 22, 23, 24, 25, 30, 41, 45, 49, 54, 56, 58, 59, 60, 61, 64, 66, 67, 68, 71, 73, 80, 84, 85, 89, 99, 104, 108, 119, 121, 122, 135, 139, 143, 149, 151, 153, 156, 157, 158, 168, 169, 176, 182, 185, 197, 199, 202, 203, 205, 209, 217, 236, 237, 238, 241, 245, 246, 247, 248, 250, 251, 252, 253, 255, 260, 264, 265, 268, 270, 271, 274, 277, 278, 281, 283, 287, 288, 293, 297, 298, 299, 303, 305], "callabl": [183, 251], "callback": [3, 20, 120, 121, 122, 217, 238, 297], "calledprocesserror": 67, "caller": [68, 199, 270, 277], "calmd": 270, "calmd_cmd": 270, "calpha": 154, "cam": [15, 209, 210, 211, 212], "camacho": 69, "cambridg": 2, "came": [93, 278], "camp_phospho_sit": 25, "can": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 35, 45, 46, 51, 54, 56, 59, 60, 61, 66, 67, 68, 69, 71, 72, 73, 80, 81, 83, 84, 88, 89, 91, 92, 94, 99, 101, 102, 104, 107, 108, 109, 119, 121, 130, 134, 135, 137, 140, 146, 148, 149, 152, 154, 157, 158, 169, 172, 180, 182, 183, 185, 186, 197, 199, 202, 205, 207, 209, 210, 211, 212, 213, 214, 217, 218, 221, 222, 229, 236, 237, 238, 241, 242, 245, 246, 247, 249, 250, 251, 252, 253, 254, 256, 258, 260, 261, 263, 264, 265, 269, 270, 271, 272, 273, 274, 278, 281, 288, 289, 290, 291, 292, 297, 298, 299, 305, 306, 307], "cancerchromosom": 7, "candid": [6, 21, 270], "canfam2": 0, "canfam3": 22, "cannarozzi": 2, "cannot": [0, 3, 4, 7, 12, 15, 23, 27, 30, 45, 56, 68, 72, 152, 169, 188, 190, 198, 236, 238, 246, 251, 269, 278], "canon": [15, 86, 90, 99, 154, 272, 275], "cantor": 182, "canva": 105, "cap": [27, 89, 270], "capabl": [15, 95, 99], "capit": [9, 11, 20, 198, 202, 203], "capmapq": 270, "cappbuild": [15, 27, 133, 154], "capqcoef": 270, "capsid": 15, "capsmap": [27, 72], "caption": 99, "captur": [2, 11, 12, 15, 67, 169, 197], "car": 122, "carbohyd": 272, "carbohydr": 0, "carbon": [135, 169, 172], "carboxyl": [25, 79, 80], "care": [3, 4, 5, 6, 7, 12, 15, 17, 21, 23, 24, 109, 130, 237, 243, 274], "carlsward": 7, "carolin": 2, "carri": [65, 73], "cartesian": 169, "cartn_i": 15, "caryophyllal": 7, "casari": 265, "casava": [238, 251], "casbon": [7, 71], "cascad": [17, 197], "case": [0, 1, 3, 4, 7, 8, 9, 11, 12, 13, 17, 19, 20, 21, 23, 24, 30, 32, 33, 38, 51, 56, 67, 68, 69, 70, 73, 83, 94, 95, 104, 107, 117, 135, 154, 162, 169, 176, 182, 183, 197, 205, 214, 217, 218, 221, 222, 226, 234, 236, 237, 238, 241, 251, 253, 260, 261, 262, 270, 275, 283, 288, 290, 297, 298], "caselect": [15, 169], "casual": 17, "cat": [22, 181, 182, 270, 278], "cataatttga": 7, "catalyst": 177, "catalyt": [25, 53, 86], "catalyz": 118, "catch": [8, 23, 25, 32, 278], "catcnagatgacactacgactacgactcagactac": 256, "categor": [3, 100, 182], "categori": [5, 6, 7, 79, 80, 90, 100, 182, 248, 273], "catergori": [79, 80], "catgggcaaatattatacgcaaggcgacaaggtgctgatgccgctggcgattca": 260, "cath_huma": 0, "cath_human": [0, 56], "cation": 264, "catmix": 182, "catt": 30, "cattatgttc": 7, "cattctggaa": 7, "cattgttgagatcacataataattgatcgagttaatctggaggatctgtttact": [19, 23], "catttattgc": 7, "caught": [21, 27, 135, 151], "caus": [3, 4, 13, 15, 20, 21, 68, 72, 92, 169, 182, 251, 270], "caution": 237, "cautiou": 21, "caven": [2, 11, 283], "cavener1987": [2, 11], "caviti": 158, "cb": [15, 53, 141, 152, 169], "cb_at_origin": 15, "cbcbgggttbbcgggceecttsbeebshhhhsttccbsscssccbcbgggttbccsttceecttsbeebshhhhsttccb": 0, "cbcbgggttbbcgggceecttsbeebshhhhsttccbsscssccbcbgggttbccsttceecttsbeebshhhhsttccbsscssccbcbgggttbccgggceecttsbeebshhhhsttccbsscssccccbtttttbccsttceecttsceebshhhhsttccbsscc": 0, "cbeta": 158, "cc": [0, 11, 22, 25, 30, 53, 86, 90, 222, 295], "cc_author": 88, "cc_ft_desc": 88, "cc_ft_kei": 88, "cc_matrix_typ": 88, "cc_max_repeat": 88, "cc_scaling_db": 88, "cc_site": 88, "cc_skip_flag": 88, "cc_taxo_rang": 88, "cc_version": 88, "cca": 22, "ccaaac": 12, "ccaaccacaacccacaccccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccacaaccccacacccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccaccacccacaccccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccaccaccccacacccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccccccccccacacccaaaaaaaaaaaaaaaaaaaa": 56, "ccacca": 12, "ccaccccccacccccaca": 0, "ccacgaatat": 7, "ccacgctaagagaagtgccggag": 283, "ccatg": 11, "ccatggcccgggggggagctccagctgccatagctattcgaactatagcttaag": 207, "ccc": 22, "cccaaa": 12, "cccaac": 12, "cccaagtgttctgatagctaatgtgaaaaagaagcatgtgcccaccagtaagctttgtgg": 0, "cccaagtgttctgattgcctctgtgaaaaagaaacatgggcccgctaataagatttgcaa": 0, "cccacc": 12, "cccacccccccccacaccccaaaaaaaaaaaaaaaaaaaa": 56, "cccc": [0, 4, 13, 30], "ccccaa": 12, "ccccaaaaaaaaaaagggg": [0, 13, 30], "ccccagcattctggcagacacagtg": 0, "ccccatttg": [30, 68], "ccccca": 12, "ccccccc": [0, 13, 30], "cccccccaaaaaaaaaaagggggg": [0, 13, 30], "ccccccccccc": 0, "cccccccccccccccccccccccccc": 0, "ccccccccccccccccccccccccccccccccccccccc": 0, "ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccceeccchhhc": 0, "cccccccccccccccceecccceeccccccccccccccccccccccccccccccccccccccccceeccccccccccccc": 0, "cccccccccccccccceecccceeccccccccccccccccccccccccccccccccccccccccceecccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccceeccchhhcccccccccccc": 0, "cccccccgggggg": [0, 13, 30], "ccccgggg": [0, 13, 30], "cccggg": 8, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaag": 20, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttc": 3, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttccttt": [3, 20], "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttccttttagagg": 3, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttccttttagaggg": 20, "ccctctagagggaagcgctttctgtggtctgaaagaaaagaaagtgcttc": 3, "cccttcttgtcttcagcgtt": 21, "cccttcttgtcttcagcgttctcc": 21, "cccttcttgtcttcagcgtttctcc": [21, 238, 251], "cccttttgggtttnttnttggtaaannnttcccgggtgggggnggtnnngaaa": 238, "cccxc": [0, 30], "cccxccc": 30, "cccxccxc": [0, 30], "ccg": [6, 22], "ccgcc": 241, "ccgcccaaagt": 222, "ccgcg": 30, "ccgg": [30, 66], "ccgggccgtactttcctttt": 0, "ccggttttt": 0, "ccgtatagga": 7, "ccgtg": 11, "ccguaaa": 66, "ccp4": 15, "ccp4mg": 15, "cct": 22, "cctact": 12, "cctatacctttctttcatgagaa": 0, "cctatacctttcttttatgagaa": 0, "cctatttaat": 278, "cctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttcc": 3, "cctgaatgtg": 22, "cctgtacc": 0, "ccz78521": 23, "cd": [0, 3, 7, 8, 21, 22, 23, 38, 68, 94, 169, 236, 237, 238, 245, 260, 275, 278], "cd1": 169, "cd2": 169, "cdao": [17, 27, 181, 185, 188], "cdao_to_obo": [27, 181, 188], "cdaoio": [27, 181], "cdata": [4, 73], "cdd": 7, "cdd_delta": 69, "cdf_chi2": [181, 192, 194], "cdg": 0, "cdii": 206, "cdkl": 13, "cdna": 25, "cdna2genom": [0, 42, 222], "cdot": 4, "cdt": [4, 73], "ce": [166, 169], "ce1": 169, "ce2": 169, "ce3": 169, "cealign": [27, 133], "cel": [28, 29], "celest": 2, "celfil": [24, 27, 28], "celi": 263, "cell": [0, 2, 4, 10, 16, 73, 90, 162, 172, 263], "celldata": [4, 73], "cellosauru": [27, 85], "cellular": 7, "center": [4, 8, 15, 30, 32, 73, 104, 135, 139, 146, 169, 175, 265], "center_of_mass": [133, 135, 139], "centr": [7, 8, 104, 115, 117, 141, 263], "central": [5, 7, 19, 22, 104, 123, 140, 169, 253, 265], "centroid": 73, "cephalotaxu": 17, "certain": [5, 8, 11, 12, 15, 17, 19, 21, 23, 67, 102, 139, 182, 203, 204, 238, 299], "cf": [86, 209, 211, 216], "cfoi": 206, "cfreq": [13, 34, 281], "cg": [0, 11, 15, 30, 169, 182, 297], "cg1": 169, "cg2": 169, "cga": [22, 30, 236], "cgactcagaggtt": 283, "cgactcgcgcttacaagg": 283, "cgat": 30, "cgatcg": 30, "cgatcgagtgaatccggaggaccggtgtactcagctcaccgggggcattgctcccgtggt": 23, "cgaut": 236, "cgc": [19, 22, 23], "cgcgc": 241, "cgcgtg": 11, "cgct": 30, "cgctaaaagctaggatatatccgggtagctag": 22, "cgg": [22, 30], "cggagccagcgagcatatgctgcatgaggacctttctatcttacattatggctgggaatc": 238, "cggagccagcgagcatatgctgcatgaggacctttctatcttacattatggctgggaatcttactctttc": 238, "cggccgggcctctcatcggt": 253, "cgggatccca": 249, "cggt": [0, 30], "cggttttt": 0, "cgi": [3, 19, 22, 85, 209, 253, 265], "cgl": 15, "cglaacasyp": 0, "cgt": [22, 30, 260, 279], "cgta": 264, "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgatgagaccgtgg": [19, 23], "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgatgagaccgtggaataaa": 23, "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgatgagaccgtggaataaacgatcgagtg": [19, 23], "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgttgagatcacat": 23, "cgtac": 270, "cgtc": 241, "cgtcgcaatt": 7, "cgtgtatgccctaagctgagcccgtcg": 30, "cgtt": 30, "cgttcca1agatgtgggcatgagcttac": 264, "cgttccaaagatgtgggcatgagcttac": 264, "cgu": [66, 260], "cguuccaaagaugugggcaugagcuuac": 264, "cguuucuacaa": 66, "cguuucuacaaggug": 66, "cgvsnfvst": 0, "ch": 263, "ch2": 169, "ch34": 2, "chaaa": 0, "chain": [2, 12, 13, 27, 30, 128, 130, 132, 133, 134, 135, 137, 138, 139, 140, 143, 144, 146, 148, 149, 152, 154, 155, 156, 157, 158, 159, 160, 162, 168, 169, 170, 172, 173, 176, 184, 187, 189, 214, 215, 248, 250, 272], "chain_a": 15, "chain_count": 172, "chain_id": [15, 134, 137, 138, 162, 172], "chain_indic": 172, "chain_list": 15, "chain_nam": 172, "chainexcept": [27, 128, 130], "chainid": [137, 138, 152, 168, 214, 215], "chainselector": [27, 133, 138], "chalcon": [21, 23, 25], "challeng": 19, "chanc": [3, 6, 12, 15, 68], "chang": [2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 17, 19, 21, 23, 26, 27, 30, 34, 68, 70, 80, 83, 84, 85, 103, 108, 109, 126, 145, 149, 152, 158, 162, 169, 176, 177, 182, 183, 191, 217, 236, 237, 241, 260, 261, 265, 270, 277, 280, 297, 303], "changed_this_week": 15, "changedir": 24, "channel": [8, 105], "chaperon": 104, "chapman": [2, 7, 9, 26], "chapman2000": [2, 9], "chapter": [0, 3, 5, 6, 7, 8, 11, 12, 13, 14, 16, 17, 19, 20, 21, 22, 23, 24, 56, 236, 238], "chapter4": 83, "char": [0, 15, 36, 97, 134, 146, 152, 159, 169, 176, 197, 236, 260, 297], "chara": 297, "charact": [0, 4, 6, 11, 12, 13, 14, 15, 16, 17, 22, 23, 30, 31, 32, 38, 50, 51, 56, 65, 66, 83, 84, 85, 89, 94, 129, 176, 182, 197, 198, 214, 236, 238, 241, 244, 248, 250, 251, 252, 253, 260, 261, 264, 269, 278, 281, 290, 297, 299], "character": 25, "characterdatahandlerescap": [83, 84], "characterdatahandlerraw": [83, 84], "characterist": [15, 17, 175, 183, 272], "charb": 297, "charbuff": [27, 128, 129], "charg": [12, 13, 15, 80, 135, 162, 172, 263, 265], "charge_at_ph": [261, 263, 265], "charit": 149, "charl": 2, "charlist": 129, "charpartit": 129, "chars_to_ignor": [12, 31], "charset": 129, "chart": [8, 103], "chchhhhcccctcccttchhhhhhhhhhhhhhhhhhhhctt": 12, "check": [0, 3, 4, 6, 7, 9, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 32, 68, 70, 76, 80, 83, 84, 104, 119, 125, 129, 130, 134, 136, 139, 140, 148, 152, 154, 155, 168, 169, 182, 183, 188, 193, 222, 236, 237, 251, 253, 260, 264, 270, 303], "check_output": 67, "checkpoint": [69, 181, 182], "checksum": [27, 238, 261], "chem": [0, 264], "chem_correct": [27, 261, 264], "chemcomp": 172, "chemic": [16, 112, 117, 119, 214, 264, 265, 272], "chen": 264, "cheng": 2, "chenna": 32, "chenopodium": 3, "chester": 264, "chhhhhhtt": 0, "chi": [2, 15, 152, 169, 194], "chi1": [15, 152, 169], "chi2": [152, 169, 181, 182, 192, 202], "chi3": [152, 169], "chi4": [152, 169], "chi5": [152, 169], "chicken": 30, "child": [12, 15, 17, 130, 131, 135, 139, 155, 159, 169, 179, 180, 183, 185, 197, 209], "child_dict": [133, 139], "child_edg": [178, 179, 180], "child_ent": 15, "child_id": 15, "child_list": [15, 133, 139], "children": [15, 17, 135, 139, 157, 178, 179, 180, 183, 197, 198, 209, 213, 252], "chimer": 270, "chimera": [15, 158], "chimp": [0, 22], "chimpanze": [0, 30], "chip": [11, 288], "chiral": [15, 169], "chitin": 0, "chix": 169, "chloroplast": [7, 23, 272, 278], "chn": [168, 169], "chn1": 15, "cho1": [11, 291], "cho2": [11, 291], "choic": [6, 9, 11, 12, 15, 17, 20, 22, 23, 100, 237, 290], "choli": 0, "choos": [3, 4, 6, 7, 8, 11, 13, 20, 23, 30, 80, 287], "chop": 138, "chosen": [4, 13, 76, 152, 260, 261, 269, 270], "chr": [8, 251], "chr1": [0, 13, 30, 36, 37, 38], "chr10": 0, "chr14": 22, "chr18": 0, "chr19": [0, 20], "chr2": [0, 13], "chr22": 0, "chr3": [0, 13, 22, 45], "chr4": [0, 13, 22], "chr6": [0, 22], "chr7": [0, 22], "chr8": [0, 22], "chr9": 0, "chr_diagram": 8, "chr_i": 8, "chr_ii": 8, "chr_iii": 8, "chr_iv": 8, "chr_percent": 99, "chr_v": 8, "christian": [2, 259], "christoph": 2, "chrom": [0, 13, 36], "chromatogram": 269, "chromend": [0, 36], "chromosom": [0, 3, 7, 13, 22, 23, 27, 30, 36, 37, 38, 46, 61, 98, 99, 102, 103, 197, 238, 245, 270, 275], "chromosome_nam": 99, "chromosomecount": [27, 98, 102], "chromosomeseg": [8, 27, 98, 99, 102], "chromsiz": 0, "chromstart": [0, 36], "chrun_ki270385v1": 13, "chrun_ki270392v1": 13, "chrun_ki270394v1": 13, "chrun_ki270423v1": 13, "chs3_brofi": [23, 85], "chung": 2, "chunk": [0, 23, 30, 94], "chunksiz": 290, "chy": 0, "chykaenaavqvldsvnitlnaedelknavglvrpvsvafqvi": 0, "chykaenaavqvldsvnitlnaedelknavglvrpvsvafqvidgfrqyksgvytsdhcgttpddvnhavlavgygvengv": 0, "chylomicron": 25, "ci": [11, 123, 283, 286], "cic": [15, 169], "cic2": [15, 169], "cid": 265, "cif": [15, 170, 173, 214, 238, 248], "cifatomiter": [27, 238, 248], "cifseqresiter": [27, 238, 248], "cifsyntax": 170, "cigar": [0, 42, 55, 217, 223], "cin": 123, "cine": 245, "circl": [8, 99, 117], "circle_cor": [8, 104], "circleci": 84, "circular": [8, 21, 93, 104, 237, 250, 261, 278], "circumv": [7, 152], "citat": [83, 87, 153, 272], "citation_1": 83, "cite": [7, 9, 264], "citi": 73, "ciz78533": [19, 23], "cj": 7, "ckf": 0, "ckfqpgkaigfvkdvanitiydeeamveavalynpvsfafevt": 0, "ckfqpgkaigfvkdvanitiydeeamveavalynpvsfafevtqdfmmyrtgiysstschktpdkvnhavlavgygekngi": 0, "cl": [0, 53, 54, 84, 122, 197, 209, 211, 237], "cl0020": 53, "cl0049": 0, "cla": [6, 27, 32, 209, 211], "cla_handl": 209, "clade": [13, 25, 27, 132, 181, 183, 184, 185, 186, 187, 189, 190, 197, 198, 199], "clade_rel": [181, 197, 198], "claderel": [27, 181, 197], "cladist": 129, "claim": 265, "clan": [0, 53], "clarifi": [15, 21, 22], "clash": 169, "class": [2, 4, 6, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 24, 25, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 158, 160, 161, 162, 163, 165, 166, 169, 170, 171, 172, 173, 175, 176, 177, 179, 180, 182, 183, 184, 185, 186, 187, 188, 189, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 219, 220, 221, 223, 224, 225, 226, 228, 230, 231, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 263, 265, 269, 270, 271, 272, 273, 275, 278, 280, 281, 282, 283, 284, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 299, 302, 303, 304, 305], "classic": [11, 15, 30, 69, 152, 169, 283, 291], "classic_b": [152, 169], "classif": [7, 9, 11, 53, 93, 113, 120, 127, 140, 209, 210, 211, 272, 282, 295], "classifi": [13, 27, 30, 84, 120, 122, 127, 140, 282], "classmethod": [30, 36, 183, 185, 188, 190, 197, 280, 281], "classnam": [10, 113], "classproperti": 84, "claus": 9, "clavata": 23, "claw": 250, "clean": [15, 56, 60, 92, 95, 238, 246, 251], "clean_valu": [92, 95], "cleandata": 17, "cleaner": [92, 95], "cleanup": 172, "clear": [6, 9, 12, 15, 25, 67, 119, 169, 198, 260, 274], "clear_ic": [133, 169], "clear_transform": [133, 169], "clearer": [8, 238], "clearest": 6, "clearli": [5, 12, 15, 24], "cleav": 72, "clever": 6, "clf1_schpo": 53, "click": 5, "client": [68, 183, 197], "climb": 182, "clin": 264, "cline": [32, 67, 69, 80], "clip": [0, 6, 52, 253, 270], "clip11262": 8, "clip_qual_left": 253, "clip_qual_right": 253, "clog": 24, "clone": [7, 21, 25, 93, 103, 206, 238, 275], "cloner": 259, "close": [1, 3, 7, 8, 9, 11, 13, 20, 22, 23, 24, 27, 30, 56, 61, 68, 83, 91, 129, 181, 182, 217, 238, 241, 250, 252, 253, 278, 298, 301, 303], "closer": [4, 20, 25, 92], "closest": [4, 176], "closur": 61, "cloud": 4, "clu": [32, 229], "clustal": [0, 12, 13, 23, 27, 30, 32, 56, 57, 238, 246], "clustal_consensu": 0, "clustal_data": 12, "clustalio": [27, 56], "clustaliter": [27, 56, 57], "clustalo": 32, "clustalomega_clin": 32, "clustalomegacommandlin": [30, 32], "clustalout": [30, 32], "clustalw": [5, 9, 13, 19, 30, 32, 40, 50, 56, 57, 238], "clustalw2": [12, 32], "clustalw_aln": 32, "clustalw_clin": 32, "clustalw_ex": 12, "clustalwcommandlin": [30, 32], "clustalwrit": [27, 56, 57], "clustalx": 12, "cluster": [2, 7, 9, 11, 13, 24, 25, 26, 27, 30, 32, 123, 182, 209, 217, 275, 283, 286, 288, 293, 307], "cluster1": [30, 32], "cluster2": [30, 32], "cluster_num": 229, "cluster_threshold": [181, 182], "cluster_threshold_fast": [181, 182], "clusterbust": [27, 283], "clustercentroid": [4, 27, 73], "clusterdist": [4, 27, 73], "clusterid": [4, 73], "clusteringout": [30, 32], "clusters": [30, 32], "clutter": 251, "clw": [30, 32], "clwout": [30, 32], "clwstrict": [30, 32], "clwstrictout": [30, 32], "cm": 8, "cmap": [15, 169], "cmask": [4, 73], "cmbi": [15, 137, 250], "cmd": [3, 12, 17, 32, 67, 69, 80, 182, 253, 270], "cmeyegeeac": 0, "cml": 17, "cmodulo": [206, 207], "cmp_scc": [27, 209], "cn": 123, "cnr": 15, "co": [11, 94, 269, 295], "coa": 113, "coatb_bpi2": 12, "coatb_bpi22": 12, "coatb_bpif": 12, "coatb_bpif1": 12, "coatb_bpik": 12, "coatb_bpm1": 12, "coatb_bpm13": 12, "coatb_bpzj": 12, "coatb_bpzj2": 12, "cochran": [2, 4], "cock": [2, 6, 7, 9, 26, 133, 251], "cock2009": [2, 9], "cock2010": [2, 6, 9], "cockerham": [202, 203], "codata": 32, "code": [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 34, 49, 55, 59, 64, 65, 67, 68, 69, 70, 71, 74, 76, 79, 80, 81, 82, 83, 84, 85, 87, 89, 90, 91, 92, 94, 100, 106, 111, 112, 113, 114, 115, 119, 120, 122, 123, 124, 131, 136, 137, 138, 139, 143, 149, 152, 154, 158, 162, 165, 166, 169, 172, 175, 181, 183, 196, 197, 198, 201, 204, 205, 209, 214, 215, 222, 236, 237, 238, 241, 248, 250, 251, 260, 261, 268, 272, 273, 274, 276, 278, 279, 280, 281, 282, 297, 298, 304, 305, 306], "codec": 236, "coded_bi": [3, 68], "codeml": [17, 181, 192], "codeml_nssites_al": 17, "codemlerror": [181, 192, 195], "codeset": 0, "coding2cod": [42, 222], "coding_and_optim": 69, "coding_dna": [22, 236], "coding_dna2": 236, "coding_dna3": 236, "coding_sequ": 6, "codon": [0, 2, 6, 21, 22, 30, 32, 34, 36, 76, 195, 222, 236, 237, 261, 279, 280, 281], "codon_align": 13, "codon_aln": [279, 280], "codon_seq1": 281, "codon_seq2": 281, "codon_start": [7, 21, 94, 237], "codon_t": [13, 30, 34, 76, 279, 280, 281], "codonadaptationindex": [27, 261], "codonalign": [27, 30], "codonfreq": 17, "codonposit": 0, "codonposset": 0, "codons_block": 129, "codons_onli": 129, "codonseq": [27, 279, 280], "codont": [22, 27, 30, 75, 236, 237, 261], "coef": 177, "coeffici": [11, 177, 265, 270], "cofactor": [86, 113], "coffe": [32, 48, 63], "coffset": 278, "cog1583": 94, "cohort": 197, "coil": [234, 272], "col": [0, 30, 31, 299], "col_def": 97, "cold": 3, "coli": [6, 13, 22, 83, 209, 260], "collab": 94, "collabor": [6, 94, 245], "collaps": [17, 128, 130, 132, 181, 183, 222], "collapse_al": [17, 181, 183], "collapse_genera": [128, 132], "collect": [0, 5, 6, 9, 11, 12, 13, 16, 25, 27, 30, 75, 102, 110, 117, 139, 149, 160, 177, 178, 209, 214, 215, 237, 270, 279, 287, 288, 299], "collis": [15, 23], "colloc": 153, "colon": [182, 230, 244, 250], "color": [0, 6, 8, 16, 25, 99, 100, 102, 104, 105, 117, 181, 183, 197, 198, 270], "color0": 283, "color1": 283, "color2": 283, "color3": 283, "color4": 283, "color_auto": 283, "color_nam": [181, 183], "color_schem": [102, 283], "color_to_reportlab": [27, 98, 105], "colorimetr": 16, "colornam": 183, "colorschem": 104, "colorspir": [27, 98], "colortransl": [98, 104], "colour": [8, 99, 100, 104], "columba": 174, "column": [0, 3, 4, 6, 7, 10, 12, 13, 16, 20, 30, 31, 32, 33, 35, 36, 38, 49, 51, 52, 53, 56, 61, 62, 64, 66, 68, 69, 73, 129, 149, 176, 182, 199, 207, 209, 218, 221, 229, 238, 256, 276, 279, 280, 283, 290, 296, 299, 303], "column_annot": [0, 27, 30, 53, 66], "columnmean": [4, 73], "com": [3, 4, 5, 7, 15, 23, 25, 32, 99, 140, 158, 169, 218, 227, 234, 239, 270, 283, 299], "combin": [0, 2, 4, 6, 7, 8, 10, 12, 15, 22, 23, 25, 27, 30, 32, 52, 56, 80, 95, 128, 129, 169, 182, 199, 237, 238, 241, 250, 251, 260, 264, 272, 278, 280], "combinatori": [129, 166], "combined_matrix": 129, "come": [0, 1, 3, 8, 11, 12, 15, 20, 21, 23, 30, 169, 221, 222, 278, 303], "comjnl": 2, "comma": [0, 7, 9, 10, 16, 32, 36, 69, 83, 182, 270, 274], "command": [0, 1, 3, 4, 6, 9, 11, 12, 14, 15, 17, 19, 23, 24, 27, 32, 56, 59, 67, 68, 69, 80, 129, 156, 169, 182, 193, 195, 196, 218, 234, 251, 260, 270, 285, 303, 304, 306], "commandlin": [27, 32, 67, 69, 80, 128, 129], "commenc": 22, "comment": [0, 6, 11, 20, 21, 24, 25, 30, 36, 53, 81, 86, 88, 90, 93, 104, 113, 123, 129, 132, 152, 169, 177, 182, 184, 187, 189, 201, 204, 205, 217, 218, 219, 237, 241, 244, 258, 270, 272, 287, 288, 295], "comment_lin": [201, 204, 205], "commentari": 244, "comments_are_confid": 190, "commerci": [7, 11], "commiss": 25, "commit": [301, 303], "common": [1, 6, 7, 9, 11, 12, 13, 17, 19, 20, 21, 22, 23, 30, 31, 56, 68, 70, 107, 132, 152, 169, 183, 186, 197, 217, 238, 251, 290], "common_ancestor": [17, 128, 132, 181, 183], "common_nam": [181, 197, 198], "commonli": [0, 1, 4, 8, 17, 23, 30, 73, 83, 295], "commun": [2, 6, 7], "comp": 7, "comp_auto": 283, "comp_based_stat": [68, 69], "compact": [0, 20, 23, 42, 94, 222], "compactli": 209, "compani": 15, "compar": [2, 4, 6, 7, 8, 9, 13, 16, 17, 20, 21, 27, 34, 80, 98, 104, 132, 135, 139, 155, 168, 169, 182, 183, 185, 222, 236, 237, 260, 270, 278, 280, 290, 294, 297, 299], "comparativescatterplot": [27, 98, 101], "compare_coordin": [135, 139, 155], "compare_residu": [27, 133, 168], "comparison": [2, 3, 6, 7, 9, 11, 12, 13, 16, 22, 42, 71, 74, 80, 137, 168, 169, 196, 222, 236, 237, 251, 260, 263, 283], "compass": 27, "compat": [0, 3, 5, 10, 12, 16, 18, 21, 30, 37, 69, 104, 132, 151, 169, 183, 190, 197, 207, 237, 251, 260, 265, 270, 278, 297, 303], "compbia": 272, "competit": 9, "compil": [5, 6, 24, 169, 197, 288], "complain": [20, 152], "complement": [6, 8, 13, 19, 27, 30, 68, 79, 80, 94, 157, 236, 237, 260, 264, 269, 270, 278, 283, 290, 305], "complement_rna": [27, 236], "complementar": 80, "complementari": [11, 80, 264], "complet": [0, 3, 4, 6, 7, 8, 11, 14, 17, 19, 20, 21, 22, 23, 25, 45, 56, 61, 67, 68, 71, 73, 83, 104, 123, 169, 183, 198, 222, 236, 237, 238, 246, 247, 250, 258, 260, 270, 275, 278, 298, 303], "complete_protein": 279, "complex": [0, 6, 7, 15, 17, 21, 23, 24, 25, 32, 117, 158, 169, 237, 238, 264, 267, 274], "compli": [65, 283], "complianc": 197, "compliant": 11, "complic": [6, 7, 15, 21, 22, 23, 24, 31, 240], "compon": [2, 20, 24, 73, 99, 111, 115, 117, 169, 287], "compos": [18, 201, 204, 209, 263], "composit": [7, 32, 69, 99, 263, 267, 283], "composition": 272, "composition_based_statist": [68, 70], "compound": [10, 15, 21, 27, 111, 115, 116, 117, 119, 174, 237, 274], "compoundloc": [27, 237], "comprehens": [6, 20, 23, 24, 25, 182], "compress": [0, 1, 7, 12, 15, 25, 36, 37, 38, 149, 217, 238, 270, 278], "compresslevel": 278, "compris": [16, 17, 104, 169, 183, 278], "comput": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 15, 19, 20, 21, 23, 25, 27, 32, 69, 83, 108, 127, 132, 133, 149, 153, 157, 169, 176, 177, 182, 194, 199, 202, 216, 217, 221, 237, 263, 265, 267, 270, 278, 283, 287, 290], "computation": 8, "con": [11, 53, 123, 290], "concaten": [46, 53, 56, 60, 66, 71, 95, 214, 238, 260, 270, 278], "concentr": [80, 264], "concept": [15, 20, 21, 169, 269], "concern": 5, "concis": [12, 23, 25, 179, 180, 209, 210, 211, 215, 260], "conclus": [7, 251], "concord": [30, 297], "conda": 5, "condit": [0, 4, 14, 17, 20, 23, 24, 69, 73, 127, 182, 183, 186, 217, 229], "confer": 2, "confid": [0, 27, 181, 183, 184, 187, 189, 197, 198], "confidence_as_branch_length": 190, "config": [22, 84], "configur": [7, 24, 83, 99, 169, 193, 195, 196], "confirm": [0, 15, 21, 169, 275], "conflict": 272, "conform": [169, 185, 217, 265, 270], "confus": [1, 3, 9, 17, 20, 21], "confusingli": 251, "congruenc": 132, "congruenti": 4, "coniferal": 17, "conjunct": 152, "conn": [303, 304], "connect": [3, 7, 11, 17, 23, 37, 46, 56, 83, 103, 130, 132, 169, 176, 177, 179, 180, 183, 209, 278, 283, 288, 303, 304, 305], "connectiong": 132, "connector": 303, "cons": [238, 249, 268, 271], "consecut": [0, 4, 73, 100, 104, 141, 154, 221, 272, 277], "consed_sampl": 240, "consel": 182, "consens": [80, 132], "consensu": [0, 2, 17, 27, 30, 31, 53, 66, 80, 128, 132, 181, 240, 269, 270, 283, 290], "consensus_tre": 132, "consequ": 15, "conserv": [0, 2, 12, 69, 94, 104, 182, 260], "consid": [0, 2, 4, 5, 7, 9, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 30, 32, 53, 62, 66, 73, 120, 183, 221, 226, 236, 237, 238, 251, 256, 260, 264, 270, 276, 278, 281, 282, 298, 299], "consider": [0, 3, 4], "consist": [0, 3, 4, 6, 7, 11, 12, 13, 14, 15, 17, 20, 24, 30, 32, 38, 51, 52, 63, 66, 68, 73, 83, 99, 102, 135, 158, 169, 214, 215, 217, 221, 237, 238, 251, 255, 256, 260, 297], "consol": [24, 32, 207], "consolewidth": [206, 207], "consortium": 93, "consre": 132, "consrtm": 93, "constant": [32, 128, 129, 177, 182, 264], "constitu": [21, 155], "constitut": 22, "constrain": 182, "constraint": [181, 182], "constraintweight": [181, 182], "constre": 132, "construct": [0, 3, 6, 11, 12, 15, 17, 22, 23, 30, 32, 67, 68, 69, 119, 129, 143, 151, 154, 162, 183, 188, 190, 197, 198, 199, 209, 237, 238, 242, 270, 274, 280, 281, 287, 288], "constructor": [13, 21, 183, 186, 197, 199, 209, 265], "consult": [6, 27, 30, 182], "consum": [32, 92, 94, 162, 204], "consumpt": [14, 23], "cont": 24, "contact": [3, 7, 27], "contain": [0, 1, 3, 4, 6, 8, 11, 12, 13, 14, 16, 17, 19, 20, 21, 23, 24, 25, 30, 32, 33, 35, 36, 37, 39, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 58, 59, 60, 61, 62, 64, 66, 67, 68, 69, 73, 74, 76, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 92, 94, 99, 100, 101, 104, 105, 107, 108, 109, 113, 120, 121, 124, 128, 135, 139, 141, 144, 146, 149, 150, 155, 160, 169, 182, 183, 185, 186, 191, 197, 198, 199, 201, 202, 204, 205, 209, 217, 222, 226, 234, 236, 238, 242, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 259, 263, 264, 265, 269, 270, 271, 273, 274, 275, 277, 278, 280, 281, 282, 283, 286, 290, 293, 295, 296, 297, 298, 299, 303], "content": [0, 2, 3, 11, 13, 15, 18, 23, 29, 31, 36, 37, 38, 50, 84, 89, 90, 129, 149, 158, 202, 220, 221, 236, 264, 265, 273, 278, 288, 290], "contenthandl": [27, 85, 89, 238, 252], "context": [4, 22, 54, 84, 91, 99, 185, 236, 261], "contextu": 59, "contig": [6, 22, 27, 93, 94, 238, 240, 268, 269, 270, 271], "contig1": 240, "contig2": 240, "contig3": 269, "contig6394": 0, "contigu": [0, 16, 20, 169, 217, 270], "conting": 202, "continu": [0, 3, 6, 7, 8, 9, 13, 15, 24, 31, 188, 190, 198, 236, 237, 270], "contrari": 21, "contrast": [0, 3, 11, 20, 236], "contribut": [1, 4, 6, 11, 19, 24, 26, 109, 124, 133, 169, 275, 290, 307], "contributor": 5, "control": [8, 12, 13, 17, 19, 30, 32, 67, 69, 80, 99, 100, 152, 169, 182, 193, 195, 196, 200, 201, 203, 207, 238, 261, 265, 270, 272, 278, 298, 299], "conv": 119, "conveni": [0, 13, 15, 17, 20, 108, 169, 183, 237, 253], "convent": [4, 8, 11, 12, 15, 21, 22, 27, 61, 66, 73, 104, 197, 229, 236, 251, 278, 290, 297], "converg": [4, 71, 109, 122], "convers": [4, 6, 11, 20, 22, 23, 27, 32, 105, 221, 229, 251, 274], "convert": [0, 3, 4, 7, 9, 11, 13, 15, 17, 22, 27, 30, 32, 52, 56, 68, 69, 83, 90, 93, 119, 132, 152, 158, 168, 169, 183, 188, 191, 198, 209, 214, 217, 236, 237, 238, 248, 251, 253, 261, 262, 264, 270, 274, 280, 281, 299, 303], "convert_absolute_support": [128, 132], "cookbook": [17, 19, 23, 83, 169, 307], "cooki": 7, "cool": [3, 5, 7, 19, 23, 25, 26, 307], "cooper": 197, "coord": [15, 115, 117, 135, 140, 152, 156, 162, 168, 169, 175, 176, 216, 253], "coord_spac": [27, 133, 176], "coordin": [3, 4, 6, 8, 13, 16, 20, 21, 22, 25, 27, 30, 32, 35, 39, 46, 51, 52, 53, 55, 61, 68, 73, 99, 101, 117, 125, 126, 135, 136, 139, 140, 141, 143, 144, 149, 152, 155, 158, 160, 162, 166, 167, 168, 169, 172, 175, 176, 197, 198, 202, 214, 216, 221, 222, 226, 229, 231, 237, 238, 270], "coordinates1": 0, "coordinates2": 0, "coords1": 175, "coords2": 175, "coot": 15, "cope": [7, 12, 22, 42, 65, 71, 222, 237, 251, 261], "copi": [0, 3, 6, 8, 12, 17, 19, 21, 24, 30, 36, 54, 133, 135, 139, 149, 157, 169, 176, 236, 237, 260, 270, 281, 297, 299], "copy_initncac": [15, 133, 169], "copyright": [11, 123, 295], "cor6_6": [238, 245], "core": [3, 7, 11, 17, 20, 30, 32, 53, 80, 169, 268, 270, 280, 281, 283, 288], "cornel": 124, "corner": 8, "cornish": 2, "cornish1985": [2, 11], "corpor": 123, "corr": 264, "corr_dict": 279, "correct": [6, 7, 9, 16, 23, 32, 68, 83, 123, 182, 202, 214, 251, 260, 264, 304], "correctedqueri": [7, 83], "correctli": [4, 7, 15, 71], "correl": [11, 73, 182, 263, 290], "correspond": [0, 3, 4, 7, 10, 11, 13, 15, 16, 17, 21, 22, 25, 30, 37, 46, 61, 67, 68, 73, 83, 84, 86, 104, 108, 117, 139, 141, 154, 158, 161, 167, 176, 182, 183, 184, 187, 189, 197, 237, 248, 253, 270, 278, 279, 280, 287, 295, 303], "corrupt": [21, 68, 84], "corruptedxmlerror": [7, 27, 68, 83, 84], "coru": 269, "cosin": 169, "cost": [3, 11, 13, 14, 32, 68, 69, 80, 222, 270], "could": [0, 1, 3, 6, 7, 8, 9, 12, 15, 20, 21, 22, 23, 24, 25, 30, 31, 56, 63, 76, 88, 99, 103, 137, 197, 217, 236, 237, 248, 251, 253, 264, 274, 278], "couldn": 9, "count": [6, 11, 13, 14, 15, 17, 21, 22, 23, 27, 30, 31, 32, 34, 56, 60, 61, 68, 69, 71, 83, 93, 94, 102, 108, 109, 121, 132, 168, 169, 182, 183, 186, 197, 202, 203, 221, 236, 237, 238, 253, 260, 261, 264, 265, 270, 274, 280, 283, 287, 290, 295, 297, 303], "count_amino_acid": [261, 265], "count_termin": [17, 128, 132, 181, 183], "counterpart": [7, 20, 217], "coupl": [7, 11, 15, 17, 23, 169, 182], "cours": [3, 4, 5, 6, 7, 12, 15, 19, 20, 21, 23, 56, 238, 251, 253, 260, 278, 298, 299], "coval": [158, 169, 272], "covari": [4, 300], "cover": [3, 5, 7, 8, 12, 17, 19, 20, 21, 22, 23, 24, 59, 74, 217, 237, 274], "coverag": [5, 69], "cowan3": 265, "cowan7": 265, "cox": [2, 7, 269], "cprev": 182, "cpu": [0, 53, 69, 182, 278], "cpython": [217, 238], "cpzant": 244, "cpzgab": 244, "cq": 0, "cq797900": 245, "cqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggcdg": 0, "cr": [7, 278], "cr407631": 7, "cr_class": [133, 169], "crab_anapl": 250, "crab_bovin": 250, "crab_pir": 250, "crafqyhskeqqcvimaenrkssiiirmrdvvlfekkvylsecktgngknyrgtmsktkn": 25, "cram": 270, "crash": 182, "crc": 262, "crc32": [27, 261, 262, 272], "crc64": [23, 27, 261, 262], "cre_class": 169, "creat": [3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 17, 18, 19, 20, 22, 23, 24, 25, 27, 30, 31, 32, 33, 35, 36, 37, 38, 42, 45, 47, 49, 51, 52, 54, 60, 64, 67, 69, 72, 73, 80, 81, 83, 84, 88, 99, 102, 104, 105, 108, 121, 123, 129, 131, 135, 136, 137, 140, 143, 144, 146, 148, 149, 151, 152, 158, 160, 161, 162, 169, 172, 176, 182, 183, 185, 186, 188, 197, 198, 202, 204, 207, 209, 210, 217, 222, 236, 237, 238, 241, 245, 246, 250, 251, 252, 257, 260, 264, 270, 272, 278, 283, 288, 290, 295, 297, 298, 302, 303, 304, 305], "create_contingency_t": [201, 202], "created": 7, "creation": [15, 61, 169], "credenti": 288, "cress": 23, "crf": 123, "cri": 123, "cricetulu": 3, "crick": [22, 32], "crit": 264, "criteria": [11, 20, 288], "criterion": [15, 122], "critic": 238, "crn_drome": 53, "cron": 149, "cronjob": 15, "crook": 7, "crop": 6, "crop_matrix": [128, 129], "cross": [7, 12, 15, 21, 90, 93, 104, 119, 176, 248, 252, 260, 272, 302], "cross_refer": [25, 272], "cross_track_link": [8, 104], "crosslink": [8, 98, 104], "crosslnk": 272, "crossmatch": 269, "crosspeak": 125, "crp0": 289, "crystal": [83, 133, 175, 216], "crystallin": 250, "crystallogr": 175, "crystallograph": [15, 172, 238], "crystallographi": [25, 144], "csa": 53, "csa_con": 53, "csb": 169, "csblab": 140, "csd": [6, 248], "cse": 221, "csequenc": 67, "cshlp": 221, "csqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcggg": 0, "css": 183, "cst": [15, 169], "cstatu": [128, 129], "csv": [16, 298, 299], "csviter": [27, 298, 299], "ct": [0, 12, 27, 182, 240, 268, 269], "cta": [12, 22], "ctaaatgatatacgattccacta": 0, "ctaaatgatatacgattccactatgtaaggtctttgaatcatatcataaaagacaatgta": 0, "ctaaccagcagcacgaccacccttccaacgacccataacagc": 22, "ctacg": 264, "ctactacag": 12, "ctactacaggtg": 12, "ctagct": [12, 30], "ctagctacccggatatatcctagcttttagcg": 22, "ctagctag": [12, 30], "ctagtagtgt": 7, "ctatcgggcaccctttcagcggcccattacaatggccat": 22, "ctattcattc": 7, "ctc": [13, 22], "ctcaaggttgttgcaagggggtctatgtgaacaaa": 0, "ctcaattttg": 7, "ctcatttttc": 7, "ctcc": 21, "ctccgtaagaaggtgctgcc": 253, "ctccgtcgga": 249, "ctcctgctgctggctgcgctcggcgccgcaggtggagcactggag": 13, "ctcgacgtcg": 236, "ctg": [12, 13, 21, 22, 30, 62], "ctgaaaa": 222, "ctgaaaacctaagtaggagaatcaactaaggataat": 22, "ctgaaaacctaagtaggagagacagttaaagataat": 22, "ctgaaatcctgaatgtgagagtcaatcaaggatggt": 22, "ctgcacctagctacgagtgag": 283, "ctgcccagaat": 222, "ctgctgatxgcacgaggttatgg": 264, "ctgctgctgctggctgcgctctgcgccgcaggtggggcgctggag": 13, "ctggaacgtacttgctggtttcgctactatttcaaacaagttagaggccgttacctcgggcgaacgtataaaccattctg": 62, "ctggacaccagcaaggagctgctcaagcgcgatctgaagaacctggtgatcctcgaccgc": 13, "ctggagtctt": 7, "ctggcgtccggagctgggacgt": 0, "ctggcttcaa": 7, "ctgtc": [30, 31], "ctl_file": [193, 195, 196], "ctt": [22, 62], "cttgaagaaa": 7, "ctttggtgagaatttttgtttcagtgttaaaagtttg": 0, "cttttgctactggccgcgctctgcgccgcaggtggggccctggag": 13, "cube": 145, "cucuac": 66, "cucumi": [21, 23], "cue": 17, "cuga": 22, "cull": [69, 152, 169], "culling_limit": [68, 69], "cullpdb_pc20_res2": [15, 152, 169], "cultivar": 197, "cultur": 16, "cumbersom": [15, 18], "cumul": [17, 183, 194], "cur_chromosom": 8, "cur_diagram": 99, "cur_draw": [99, 103], "curat": [11, 25], "curl": 23, "current": [0, 3, 4, 5, 6, 7, 10, 11, 12, 13, 15, 16, 17, 18, 19, 24, 29, 32, 34, 37, 46, 66, 67, 68, 80, 85, 99, 100, 102, 103, 104, 107, 108, 109, 119, 122, 124, 125, 126, 139, 149, 153, 162, 164, 169, 182, 193, 195, 196, 197, 198, 199, 204, 211, 237, 250, 263, 270, 274, 276, 278, 281, 283, 302, 303, 304], "current_angl": 169, "current_releas": 23, "current_sect": 10, "cursor": [303, 304], "curtin": [18, 201, 204], "curv": [16, 299, 300], "curve_fit": 300, "custom": [0, 7, 8, 10, 11, 16, 17, 30, 36, 38, 67, 99, 149, 158, 169, 182, 217, 218, 241, 251, 261, 304], "custom_field": 218, "custom_map": 261, "cut": [3, 4, 8, 27, 69, 72, 73, 80, 158, 206, 207, 260], "cutoff": [15, 53, 68, 69, 70, 186], "cuts_in": 72, "cutsit": 72, "cutter": 206, "cv": 11, "cvcl_xxxx": 90, "cviaii": 206, "cvla": 13, "cw": [30, 32, 203], "cwd": 67, "cxc": [0, 30], "cy": [13, 15, 155, 238, 265], "cyan": [8, 183], "cyanel": 272, "cyano": 4, "cyano_result": 4, "cyano_result_k_a2": 4, "cyano_result_k_g2": 4, "cyano_result_k_g2_a2": 4, "cyanobacteri": 2, "cycl": 32, "cyg": [15, 169], "cylind": [15, 100, 158, 169], "cymon": [2, 269], "cypripedioidea": [7, 19], "cypripedium": [7, 19, 23], "cys1_dicd": 0, "cys1_dicdi": [0, 56], "cys2his2": [11, 283], "cysargtyrhi": 222, "cystein": [25, 265], "cystin": 265, "cytoband": [7, 275], "cytolog": 275, "cytosin": 270, "cytosol": 4, "cz": 169, "cz2": 169, "cz3": 169, "d": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 17, 22, 25, 27, 30, 32, 34, 59, 62, 68, 69, 80, 118, 131, 149, 169, 177, 182, 222, 237, 251, 261, 263, 264, 265, 268, 269, 270, 280, 281, 283, 297, 300], "d05": 299, "d0lrbacxx": 0, "d1": [169, 250], "d1anu1": [211, 212], "d1d": 169, "d1danl2": 210, "d1tpt_1": 209, "d2": 169, "d2a_map": 169, "d2d": 169, "d2h": [15, 133, 168, 169], "d3": [15, 169], "d5hbib_": 209, "d90040": 7, "d90042": 7, "d_": 4, "d_eli": 244, "d_mm251": 244, "da": [7, 13, 123, 154, 169], "da2": 169, "da3": 169, "da4509dc64a87ebd": 262, "dad": 274, "dai": 15, "daili": 15, "dali": 32, "dalk": [2, 7], "dan": 2, "danger": 17, "dangl": 264, "dark": 8, "darken": [27, 98, 105], "darker": 105, "darkgreen": 8, "darkseagreen": 104, "darl": 2, "darling2004": [0, 2], "dash": [0, 12, 15, 30, 33, 43, 68, 117], "dat": [11, 13, 23, 25, 86, 88, 272], "data": [2, 3, 7, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 46, 52, 53, 54, 56, 61, 63, 66, 67, 68, 69, 71, 73, 83, 84, 86, 87, 88, 89, 90, 92, 93, 94, 97, 100, 101, 103, 104, 109, 111, 115, 119, 120, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 137, 143, 145, 149, 150, 151, 152, 158, 164, 166, 168, 169, 172, 177, 178, 182, 183, 185, 198, 199, 201, 202, 204, 205, 209, 214, 236, 238, 245, 251, 252, 253, 257, 260, 261, 264, 269, 271, 272, 274, 275, 277, 278, 281, 282, 288, 289, 291, 295, 298, 299, 300, 303, 307], "data_class": [25, 272], "data_file_divis": [21, 23, 93], "data_gener": [201, 205], "data_quartil": [98, 104], "data_t": [27, 124, 126], "data_typ": [11, 287, 288], "data_upd": 88, "databa": 303, "databas": [0, 3, 9, 10, 12, 13, 15, 17, 18, 20, 21, 22, 26, 61, 66, 68, 69, 70, 71, 80, 83, 90, 93, 94, 111, 112, 113, 114, 115, 117, 119, 152, 164, 174, 177, 209, 217, 218, 226, 229, 238, 245, 248, 250, 252, 260, 268, 270, 272, 274, 275, 276, 277, 283, 287, 288, 295, 301, 302, 303, 304, 305, 307], "database_length": 71, "database_lett": 71, "database_nam": 71, "database_sequ": 71, "databaseload": [301, 305], "databaseremov": [301, 305], "databasereport": [27, 68, 71], "datafil": [11, 23, 79, 80, 169], "datahandl": [27, 83, 84], "datahandlermeta": [27, 83, 84], "datalabel": 126, "dataset": [6, 7, 10, 15, 126, 182, 264], "datatyp": [0, 56, 181, 182, 197], "date": [0, 3, 5, 7, 9, 11, 12, 19, 21, 23, 27, 67, 71, 83, 88, 90, 93, 123, 133, 152, 169, 172, 181, 197, 198, 272, 295], "datestamp": 214, "datestr": 152, "datetim": 197, "datetyp": 7, "datom": 169, "datoms_needs_upd": 169, "datum": 197, "daunt": 20, "davi": 7, "david": [2, 3, 68, 263], "dayhoff": [2, 182, 199], "dayhoff1978": [2, 13], "daylateanddollarshort": 15, "db": [3, 7, 11, 23, 68, 69, 71, 83, 113, 119, 152, 169, 174, 234, 238, 245, 270, 272, 274, 283, 287, 303, 305], "db1": 169, "db2": 169, "db3": 169, "db_gencod": [68, 69], "db_genetic_cod": [68, 70], "db_handl": 209, "db_hard_mask": [68, 69], "db_idx": 217, "db_name": [303, 305], "db_object_id": 277, "db_object_nam": 277, "db_ref": 237, "db_soft_mask": [68, 69], "db_sourc": 93, "db_xref": [7, 21, 94], "dbcl": 274, "dbd": 288, "dbentri": 119, "dbfrom": [7, 83], "dbg": 80, "dbid": [303, 305], "dbinfo": 7, "dbj": [238, 241, 260], "dblink": [21, 93, 112, 113, 114], "dblist": [7, 83], "dbname": [7, 83, 272, 303], "dbref": [248, 252], "dbref1": 248, "dbref2": 248, "dbseqrecord": [301, 302, 303], "dbserver": [301, 303, 305], "dbsize": [68, 69], "dbto": 7, "dbtype": [68, 69], "dbutil": [301, 303], "dbxref": [0, 3, 12, 20, 21, 23, 27, 68, 234, 248, 260, 301, 302], "dc": [69, 250], "dc525629": [0, 30], "dcmut": 182, "dcom": [7, 123], "dcoordspac": [133, 169], "dcsvalid": [133, 169], "dct": 207, "dcut": 72, "dd": [88, 152], "dd1": 169, "dd11": 169, "dd12": 169, "dd13": 169, "dd2": 169, "dd21": 169, "dd22": 169, "dd23": 169, "dd3": 169, "dd728": 0, "ddassaatsk": 250, "ddbj": [94, 237, 245, 274, 275], "ddd": 0, "ddddbffff7a": 0, "ddefault": [69, 270], "ddmpn": 13, "ddpeeksavnn": 14, "ddvnhavlav": 0, "de": [0, 2, 4, 6, 7, 9, 15, 25, 26, 27, 32, 53, 66, 73, 86, 130, 149, 169, 174, 209, 250, 273, 289, 295], "de1": 169, "de2": 169, "de21": 169, "de22": 169, "de3": 169, "de_tabl": 264, "deactiv": 182, "deal": [1, 6, 7, 9, 11, 12, 15, 19, 21, 22, 23, 24, 27, 28, 30, 59, 74, 84, 95, 107, 108, 110, 129, 133, 139, 162, 217, 222, 237, 238, 251, 261, 268, 275, 276, 279, 280, 281, 298], "dealign": [30, 32], "dealt": [7, 15, 20, 95], "debug": [3, 12, 17, 30, 32, 67, 71, 76, 79, 80, 92, 93, 94, 148, 177, 182, 183, 237, 260, 270, 275, 278, 297, 299], "debug_level": 92, "dec": 13, "decemb": 25, "decept": 7, "decid": [7, 17, 20, 22, 23, 32, 67, 69, 80, 84, 182, 270, 285], "decim": [11, 119, 197, 251, 270, 286], "decis": [104, 264], "declar": [0, 36, 84, 252], "decod": [0, 3, 7, 14, 25, 27, 108, 109, 171, 236, 238, 278], "decoded_data": 15, "decomposit": [2, 4, 15, 216], "decompress": [15, 23, 25, 270, 278], "decor": 15, "decreas": [0, 4, 30, 182, 222, 264], "dedic": [0, 16, 24], "deduc": 7, "deduct": [30, 270, 297], "deep": [2, 169, 176], "deepcopi": [3, 17, 169], "deeper": 20, "deepest": [17, 183], "def": [3, 6, 8, 13, 15, 20, 23, 24, 32, 68, 70, 122, 218, 238, 241, 251, 253, 297], "default": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 16, 17, 20, 21, 22, 23, 24, 27, 30, 31, 32, 35, 36, 37, 38, 42, 49, 51, 52, 54, 64, 65, 67, 68, 69, 70, 72, 73, 80, 83, 84, 89, 92, 99, 102, 104, 108, 109, 127, 129, 132, 135, 136, 137, 138, 140, 143, 144, 145, 148, 149, 151, 152, 154, 157, 158, 160, 164, 166, 168, 169, 182, 183, 186, 195, 197, 199, 207, 217, 218, 221, 222, 229, 236, 237, 238, 241, 250, 251, 260, 261, 263, 264, 265, 270, 274, 276, 277, 278, 282, 283, 286, 288, 290, 297, 298, 299, 303, 304], "default_encod": 198, "default_feature_color": 99, "default_pseudo": [106, 108], "default_stop_codon": 76, "default_str": 71, "defaultpars": [133, 171], "defici": [202, 203], "defin": [0, 2, 3, 4, 6, 7, 10, 11, 14, 15, 16, 21, 23, 24, 27, 30, 31, 32, 35, 36, 37, 38, 39, 45, 46, 51, 52, 55, 61, 73, 84, 89, 91, 99, 100, 104, 116, 117, 132, 134, 135, 136, 141, 145, 147, 152, 153, 166, 167, 169, 172, 176, 177, 182, 183, 197, 202, 203, 209, 236, 237, 238, 247, 251, 253, 260, 261, 263, 265, 269, 270, 272, 278, 290, 291, 296, 297, 300, 303], "defined_rang": [27, 236], "definit": [0, 3, 7, 11, 13, 21, 23, 53, 68, 69, 71, 88, 105, 114, 117, 135, 139, 140, 155, 167, 169, 177, 197, 210, 212, 215, 251, 273, 278], "deflin": 69, "deg": 202, "degc": 264, "degcngglqp": 0, "degener": [11, 253, 283, 290], "degenerate_consensu": [11, 27, 283, 290], "degrad": [104, 152, 197], "degre": [8, 15, 32, 100, 104, 169], "dehal": 182, "dehek": [12, 13], "dehkr": [12, 13], "dehoon2004": [2, 4, 9], "dehydrogenas": 113, "del": [0, 6, 67, 236, 260], "del_featur": [98, 104], "del_graph": [98, 104], "del_set": [98, 104], "del_track": [98, 104], "delai": [32, 83], "deleg": 21, "delet": [0, 13, 15, 17, 30, 33, 55, 61, 67, 69, 80, 104, 129, 130, 136, 169, 183, 197, 222, 236, 251, 260, 270], "deliber": [6, 8, 21, 22, 56], "delimit": [4, 51, 83, 104, 236, 238, 256, 270], "delin": 2, "delknavglv": 0, "delta": [4, 12, 30, 169, 199, 241, 264], "deltablast": 69, "delv": 19, "demand": [5, 23, 30, 236, 238], "demarc": 0, "dememor": [202, 203], "demo": [0, 30], "demonstr": [8, 10, 15, 23, 169, 251], "dendrogram": [4, 17, 73], "dendropi": 17, "denomin": 4, "denot": [6, 15, 20, 73, 104, 217, 229, 236], "densiti": [25, 218, 294], "density_percent_sol": 15, "dep": [24, 123], "depart": 7, "depend": [0, 3, 4, 5, 7, 8, 11, 12, 13, 15, 16, 17, 20, 22, 23, 24, 25, 27, 30, 32, 71, 73, 80, 83, 104, 157, 169, 217, 229, 236, 237, 238, 264, 274, 278, 287, 297, 299, 300], "deposit": [15, 152, 172], "deposition_d": [15, 172, 174], "deprec": [3, 9, 14, 21, 27, 30, 32, 67, 83, 85, 92, 120, 127, 209, 212, 237, 265, 275, 282, 283], "deprecationwarn": 27, "depth": [12, 13, 17, 23, 156, 180, 181, 183, 197, 270], "der": [2, 8], "deriv": [0, 5, 15, 16, 22, 24, 25, 32, 60, 83, 99, 102, 107, 125, 144, 148, 182, 183, 198, 207, 214, 237, 248, 288], "des_handl": 209, "desc": [88, 181, 197, 198, 234], "descend": [3, 17, 20, 132, 183, 197, 209], "describ": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 17, 22, 23, 25, 30, 32, 36, 39, 46, 51, 55, 56, 61, 68, 69, 72, 73, 74, 80, 81, 84, 87, 88, 100, 104, 107, 109, 117, 121, 123, 136, 144, 149, 158, 160, 169, 175, 182, 185, 197, 210, 211, 213, 234, 237, 238, 250, 251, 253, 260, 261, 270, 272, 274, 278, 291, 296, 298, 299], "descript": [0, 3, 4, 6, 7, 10, 11, 13, 15, 17, 19, 20, 21, 23, 25, 27, 30, 33, 43, 68, 69, 70, 71, 72, 73, 88, 89, 93, 94, 104, 109, 113, 117, 121, 123, 132, 169, 172, 179, 180, 181, 197, 198, 209, 210, 211, 217, 218, 222, 226, 229, 234, 238, 241, 247, 250, 251, 252, 253, 256, 260, 270, 272, 275, 277, 295, 297, 303, 305], "descriptionext": [27, 68, 71], "descriptionextitem": [27, 68, 71], "descriptor": 278, "desier": 2, "design": [0, 4, 6, 8, 9, 11, 12, 15, 19, 21, 24, 30, 73, 81, 95, 101, 102, 103, 108, 177, 222, 238, 251, 253, 261, 263, 264, 278, 281], "desir": [4, 12, 15, 16, 21, 23, 30, 61, 73, 104, 176, 182, 209, 217, 251, 270], "desktop": 25, "despit": [15, 20, 23, 193, 195], "destin": [9, 68, 83, 108, 164], "destroy_transit": [106, 108], "detach": 139, "detach_child": [133, 139], "detach_par": [133, 135, 139], "detail": [0, 3, 6, 7, 8, 11, 12, 13, 14, 15, 17, 19, 20, 21, 23, 24, 27, 30, 59, 67, 68, 69, 83, 92, 135, 169, 182, 201, 202, 217, 221, 222, 239, 247, 248, 251, 253, 260, 264, 269, 270, 274, 276, 303], "detect": [0, 2, 3, 4, 7, 11, 15, 23, 25, 29, 32, 66, 68, 83, 125, 158, 169, 217, 238, 250, 251, 264], "detectednuc": 125, "determin": [0, 4, 11, 12, 20, 23, 50, 56, 80, 84, 104, 146, 152, 169, 182, 207, 238, 261, 265, 270, 288], "determinist": [4, 73], "deuter": 168, "deuterium": 169, "dev": [0, 9, 27, 67, 152, 169], "dev0": [9, 26, 307], "develop": [3, 5, 6, 9, 15, 16, 17, 19, 21, 24, 25, 27, 32, 59, 157, 158, 169, 182, 275], "developerinfo": 3, "deviat": [4, 11, 15, 104, 135, 152, 162, 169, 175, 216, 270, 290, 300], "devic": 278, "devot": 5, "df": [17, 183, 194], "df_search": [177, 178, 180], "dfwd": 169, "dg": [2, 32, 169], "dg1": 169, "dg11": 169, "dg12": 169, "dg13": 169, "dg2": 169, "dg21": 169, "dg22": 169, "dg23": 169, "dg3": 169, "dgfrqyksgv": 0, "dgfrqyksgvytsdhcgttpddvnhavlavgygvengv": 0, "dgtsta": 12, "dgtstaateamnslktqatdlidqtwpvvtsvavaglairlfkkfsska": 12, "dgtstatsya": 12, "dgtstatsyateamnslktqatdlidqtwpvvtsvavaglairl": 12, "dgtstatsyateamnslktqatdlidqtwpvvtsvavaglairlfkkfss": 12, "dgtstatsyateamnslktqatdlidqtwpvvtsvavaglairlfkkfsska": 12, "dh": 169, "dh11": 169, "dh12": 169, "dh1ndx": 169, "dh2": 169, "dh21": 169, "dh22": 169, "dh2ndx": 169, "dhhkk": [12, 13], "di": [15, 25, 90, 152, 169], "diabet": 274, "diacylglycerol": 25, "diag": [30, 32], "diagbreak": [30, 32], "diaglength": [30, 32], "diagmargin": [30, 32], "diagnos": 67, "diagon": [6, 12, 30, 32, 69, 125, 199, 270], "diagram": [3, 4, 15, 98, 99, 104], "dialign": 32, "dialign2": 32, "dialign_clin": 32, "dialigncommandlin": [30, 32], "diamond": 15, "diaz": 7, "dic": [170, 248, 263], "dice": [15, 27, 133], "dict": [8, 13, 54, 76, 84, 86, 90, 123, 126, 127, 139, 142, 157, 164, 168, 169, 177, 183, 197, 209, 210, 214, 217, 236, 238, 260, 261, 265, 273, 279, 290, 295, 302], "dict_kei": [7, 21, 23], "dict_on": 6, "dict_two": 6, "dictionarai": 84, "dictionari": [0, 3, 6, 7, 8, 9, 11, 12, 13, 15, 17, 18, 20, 21, 22, 25, 30, 31, 39, 52, 53, 66, 67, 68, 76, 82, 83, 84, 86, 90, 100, 102, 104, 107, 108, 109, 117, 121, 123, 126, 127, 134, 137, 139, 141, 142, 157, 161, 169, 170, 172, 174, 185, 197, 201, 202, 203, 207, 210, 214, 217, 222, 236, 237, 238, 240, 244, 248, 251, 253, 257, 260, 261, 263, 264, 265, 272, 273, 277, 282, 287, 290, 295, 297, 299, 303], "dictionary_match": [27, 297], "dictionaryel": [27, 83, 84], "dictyostelium": 93, "did": [0, 4, 8, 11, 12, 65, 69, 94, 251], "didddddddddddddddddddddddddddddddddddddddddddddddiddidddddddddddddddddddddddiiidddddddddddddddddddddd": 0, "didn": [7, 12], "die": [79, 80], "differ": [0, 1, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 42, 56, 65, 66, 68, 69, 72, 73, 80, 83, 84, 94, 99, 100, 101, 102, 104, 121, 126, 133, 135, 143, 144, 146, 168, 169, 177, 182, 199, 204, 207, 214, 217, 222, 226, 229, 238, 243, 248, 251, 253, 260, 261, 263, 264, 265, 270, 272, 274, 278, 281, 287, 288, 297, 300], "differenc": 80, "differenti": [2, 18, 66, 72, 202], "differentialcutsit": [27, 72], "difficult": [3, 4, 6, 7, 8, 15, 23], "difficulti": [8, 20, 24], "diffseq": 80, "diffseqcommandlin": [27, 79, 80], "dig": 12, "digest": [6, 8, 206], "digit": [16, 118, 182, 201, 204, 205, 214, 270], "diglycerid": 25, "dih": 168, "dihdral": 169, "dihedr": [136, 144, 154, 160, 169, 176], "dihedra": [15, 152, 158, 167, 168, 169], "dihedra_sign": 169, "dihedraangl": [15, 169], "dihedraanglerad": 169, "dihedrakei": 169, "dihedral14": 169, "dihedral_sign": [15, 133, 169], "dihedralen": 169, "dihedrandx": [15, 169], "dihedron": [15, 27, 133, 152, 169], "dihydroxypterocarpan": 113, "diiron": 25, "dilemma": 2, "dim": [13, 54, 127, 175, 216], "dimens": [0, 4, 11, 56, 73, 120, 175, 216], "dimension": [4, 13, 25, 127, 169, 263, 272, 290], "dimer": [30, 32], "dineen": 32, "dinucleotid": 21, "dipcn": 0, "diploid": [202, 203, 205], "dir": [25, 149, 209, 210], "dir_path": 209, "dirac": 15, "direct": [4, 6, 7, 8, 15, 16, 17, 22, 32, 67, 71, 91, 92, 94, 100, 109, 117, 141, 156, 177, 178, 179, 180, 183, 229, 237, 264, 278], "directli": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 20, 21, 23, 24, 30, 32, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 69, 80, 83, 84, 92, 99, 105, 107, 108, 125, 169, 182, 183, 185, 191, 197, 218, 222, 236, 238, 247, 251, 253, 255, 256, 260, 270, 271, 283, 285, 294, 298, 305], "directori": [0, 5, 7, 9, 12, 13, 15, 17, 18, 24, 67, 69, 83, 84, 124, 140, 149, 153, 157, 164, 182, 193, 195, 196, 202, 203, 209, 251, 270], "direntri": 91, "dirqgpkepfrdyvdrfyktlraeqasqevknw": 154, "dirti": [23, 31, 132], "disabl": [32, 69, 80, 169, 218, 270, 303], "disadvantag": 3, "disallow": [7, 13, 108, 270], "discard": [0, 6, 32, 226, 264, 270], "discoideum": 93, "disconcord": 270, "disconnect": 130, "discontigu": 69, "discontinu": 7, "discount": 169, "discourag": [9, 24, 71, 92, 251, 278], "discov": [2, 11, 19, 21, 83], "discoveri": 11, "discrep": [11, 169, 214], "discret": [12, 127, 182], "discuss": [5, 6, 7, 8, 11, 12, 15, 19, 21, 22, 108, 169], "diseas": [90, 113, 264], "disembl": 15, "disequilibrium": [18, 202, 203], "disk": [7, 12, 23, 25, 30, 56, 83, 217, 238, 278, 298], "disord": [135, 136, 139, 155, 158, 169], "disorderd": 139, "disordered_add": [133, 135, 139, 155], "disordered_get": [133, 139], "disordered_get_id_list": [133, 139], "disordered_get_list": [133, 135, 139], "disordered_has_id": [15, 133, 139], "disordered_remov": [133, 135, 139, 155], "disordered_select": [15, 133, 135, 139], "disorderedatom": [15, 27, 133, 135, 139, 155], "disorderedentitywrapp": [15, 27, 133, 135, 139, 155], "disorderedresidu": [15, 27, 133, 136, 139, 155], "disp": 209, "displai": [0, 2, 4, 6, 12, 15, 17, 20, 32, 36, 80, 94, 99, 101, 102, 103, 104, 119, 128, 132, 169, 182, 183, 197, 222, 297, 303], "display_id": 303, "display_info": [101, 103], "displayrepresent": [27, 98], "disput": 19, "dissimilar": 182, "dist": [4, 5, 8, 9, 32, 73, 80, 83, 132, 156], "dist_pearson": [11, 283, 290], "dist_pearson_at": [283, 290], "distanc": [11, 17, 32, 73, 80, 100, 128, 132, 135, 154, 156, 169, 181, 182, 183, 197, 199, 202, 203, 237, 270, 282], "distance1": [30, 32], "distance2": [30, 32], "distance_calcul": 199, "distance_fn": 282, "distance_matrix": 199, "distance_plot": [15, 133, 169], "distance_to_internal_coordin": [15, 133, 169], "distancecalcul": [27, 181, 199], "distancematrix": [4, 13, 27, 73, 181, 199], "distancetreeconstructor": [13, 27, 181, 199], "distant": [17, 183], "distinct": [3, 4, 6, 15, 17, 20, 69, 182, 221, 270], "distinguish": [0, 6, 15, 23, 30, 68, 100, 222], "distmat": 32, "distmat_ful": [30, 32], "distmat_full_it": [30, 32], "distmat_in": [30, 32], "distmat_out": [30, 32], "distplot": 169, "distplot_to_dh_arrai": [15, 133, 169], "distribut": [0, 4, 6, 7, 9, 11, 12, 13, 17, 25, 27, 98, 100, 101, 108, 152, 167, 181, 182, 194, 197, 198, 270, 283, 290, 294], "distributionpag": [27, 98, 103], "disulfid": [265, 272], "disulphid": [79, 80], "div": 169, "diverg": [11, 32], "divers": 202, "divid": [4, 7, 11, 12, 13, 15, 16, 30, 73, 102, 104, 108, 241, 256, 264, 270, 278, 290], "divis": [7, 12, 24, 93, 104, 197, 261], "djacent": 80, "dkt": 169, "dkvnhavlav": 0, "dl": [13, 175, 250], "dlen": 176, "dlp": 6, "dlqllikavnlfpagtnsrwevianymnihsssgvkrtakdvigkakslqkldp": 68, "dlqllikavnlfpagtnsrwevianymnihsssgvkrtakdvigkakslqkldphqkddinkkafdkfkkehgvvpqadnatpserf": 68, "dlshg": 13, "dm": [199, 209, 211], "dmb_prot": 250, "dmitrovski": 2, "dmso": 264, "dmsofactor": 264, "dmvvveipklgkeaavkaikewgq": 23, "dn": [13, 34, 280, 281], "dn7_mets5": 0, "dn7a_sac": 0, "dn7a_sacs2": 0, "dn7a_sacs2tvkfkykgeekqvdiskikkvwrvgkmisftydegggktgrgavsekdapkellqmlek": 0, "dn7e_sula": 0, "dn7e_sulac": 0, "dn7e_sulackvrfkykgeekevdtskikkvwrvgkmvsftydd": 0, "dn_constructor": 13, "dn_ds_method": 280, "dn_tree": 13, "dna": [0, 2, 6, 7, 10, 11, 12, 13, 19, 21, 22, 23, 30, 31, 32, 56, 76, 80, 83, 93, 154, 168, 182, 196, 197, 199, 236, 237, 238, 245, 250, 251, 252, 253, 259, 260, 261, 264, 267, 272, 278, 281, 290], "dna_bind": 272, "dna_de1": 264, "dna_imm1": 264, "dna_model": [181, 199], "dna_nn1": 264, "dna_nn2": 264, "dna_nn3": 264, "dna_nn4": 264, "dna_protein": 32, "dna_rna": [0, 45], "dna_seq": 22, "dna_tmm1": 264, "dnac1": 264, "dnac2": 264, "dnaconc": [79, 80], "dnadist": 80, "dnafreq": [30, 32], "dnamatrix": [30, 32], "dnaml": 17, "dnapar": 80, "dnastrid": 32, "dnd": [12, 17, 32], "dntp": 264, "do": [0, 1, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 36, 37, 38, 39, 46, 49, 51, 52, 60, 64, 68, 80, 84, 92, 117, 120, 129, 158, 169, 182, 197, 206, 207, 216, 217, 221, 229, 236, 237, 238, 240, 245, 246, 248, 249, 251, 260, 264, 269, 270, 271, 278, 282, 288, 297, 302, 303, 305, 307], "do_featur": 94, "doc": [0, 1, 3, 8, 9, 10, 12, 19, 20, 24, 25, 32, 50, 65, 68, 70, 83, 87, 88, 94, 105, 117, 126, 164, 199, 245, 253, 272, 273, 277, 296], "docstr": [3, 5, 8, 9, 19, 24, 83, 297, 306], "docsum": 7, "docsumlist": 7, "doctest_suit": 24, "doctestsuit": 24, "doctyp": 7, "document": [0, 1, 3, 6, 7, 9, 10, 11, 12, 14, 15, 17, 18, 19, 20, 21, 23, 24, 27, 30, 32, 56, 65, 67, 68, 83, 85, 86, 88, 89, 94, 99, 135, 169, 182, 197, 201, 204, 217, 221, 222, 234, 236, 237, 238, 243, 248, 251, 252, 253, 272, 295, 296], "documentor": 19, "doe": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 20, 21, 22, 23, 24, 25, 30, 54, 59, 66, 68, 70, 76, 83, 85, 99, 119, 136, 144, 152, 158, 160, 168, 169, 182, 202, 204, 217, 222, 229, 236, 237, 238, 241, 250, 251, 260, 261, 269, 270, 274, 278, 283, 288, 297, 303], "does_not_exist": 85, "doesn": [3, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31, 99, 104, 108, 149, 176, 197, 269, 270], "dog": [0, 22], "doi": [2, 32, 69, 73, 100, 137, 175, 182, 197, 251, 252, 262, 267], "dom": [9, 27, 209, 229, 252], "domain": [0, 7, 15, 21, 25, 27, 69, 181, 197, 198, 209, 210, 211, 212, 214, 215, 217, 229, 231, 237, 260, 272, 288], "domain_architectur": [181, 197, 198], "domain_exp_num": 229, "domain_included_num": 229, "domain_inclusion_ethresh": [68, 69], "domain_index": 229, "domain_obs_num": 229, "domain_reported_num": 229, "domainarchitectur": [27, 181, 197], "domainsclusteredbyev": [27, 209], "domainsclusteredbyid": [27, 209], "domest": 122, "domtab": [217, 231], "don": [0, 3, 5, 7, 8, 9, 12, 17, 20, 21, 22, 23, 25, 32, 99, 108, 143, 152, 182, 191, 237, 251, 260, 264, 270, 297], "donat": 15, "done": [0, 1, 3, 4, 5, 6, 7, 8, 11, 15, 17, 19, 21, 22, 23, 24, 67, 95, 125, 127, 182, 204, 221, 236, 248, 253, 299, 302, 303], "donna": 2, "donor": [80, 90], "doolitl": 265, "doolittl": 265, "dopamin": 15, "dot": [4, 12, 13, 15, 20, 30, 32, 65, 73, 80, 104, 169, 176, 216, 237, 297], "dotdiff": [79, 80], "doti": 264, "doubl": [4, 8, 9, 12, 21, 22, 129, 158, 169, 172, 197, 236, 261, 264], "double_strand": 261, "dougla": [2, 32, 175], "douthart": 169, "douw": 2, "down": [11, 15, 17, 20, 22, 23, 24, 71, 139, 157, 250, 270, 296], "downgrad": 270, "download": [0, 1, 3, 6, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 84, 90, 105, 149, 164, 221, 238, 245, 274, 283], "download_all_assembli": [133, 149], "download_cif_for": [27, 133, 164], "download_entire_pdb": [15, 133, 149], "download_obsolete_entri": [133, 149], "download_pdb_fil": [133, 149], "downsid": 23, "downstream": [21, 83, 132, 183], "downward": 132, "dp": [7, 32, 123], "dp_method": 109, "dpi": 104, "dpparttre": [30, 32], "dq110336": 7, "dr": [0, 11, 12, 25, 53, 86, 90, 295], "dr_false_neg": 88, "dr_false_po": 88, "dr_posit": 88, "dr_potenti": 88, "dr_unknown": 88, "draft": 20, "drain": 169, "dramat": 270, "draw": [4, 6, 8, 17, 98, 99, 102, 103, 104, 105, 182], "draw_ascii": [12, 17], "draw_graphviz": 17, "draw_rel": 105, "draw_to_fil": [98, 101], "drawback": 3, "drawn": [4, 8, 17, 99, 104], "dread": 237, "drev": 169, "drill": 20, "drive5": 32, "driver": [303, 304, 305], "droadhc": 13, "droadhca": 13, "droadhcb": 13, "droadhcc": 13, "droadhcd": 13, "droadhcf": 13, "droadhcg": 13, "droadhch": 13, "droadhci": 13, "droadhcj": 13, "droadhck": 13, "drop": [0, 17, 21, 66, 183, 270, 305], "dropoff": [69, 270], "dropoff_1st_pass": 71, "drosophila": [2, 13, 283], "drug": [119, 274], "drwxrwxr": 149, "ds_constructor": 13, "ds_of_read4": 269, "ds_tree": 13, "dset": 169, "dsetvalid": 169, "dshdppphl": 0, "dsname": 7, "dssp": [0, 27, 133, 172], "dssp_dict": 137, "dssp_dict_from_pdb_fil": [27, 133, 137], "dssp_tupl": 137, "dssp_version": 137, "dstype": 7, "dstypenam": 7, "dsvnitlna": 0, "dt": [11, 90, 295], "dtaselect": 263, "dtd": [3, 68, 71, 83, 84, 117, 218], "dtring": 69, "dtype": [0, 4, 11, 13, 15, 30, 54, 73, 79, 80, 169], "dual": [9, 236], "ductap": 16, "due": [4, 6, 7, 9, 11, 13, 15, 16, 17, 24, 67, 85, 145, 151, 158, 222, 229, 270, 278, 303], "duf57": 94, "dufayard": 182, "duke": 269, "dumb_consensu": [12, 30, 31], "dummi": [30, 99, 237, 260, 278, 282], "dunbrack": [15, 152, 169], "dunker": 169, "dup": 241, "duplex": 264, "duplic": [3, 23, 155, 168, 181, 197, 198, 226, 238, 241, 270], "durat": 197, "durbin": [2, 13, 52, 107, 108, 109], "durbin1998": [2, 11, 13], "dure": [2, 4, 13, 15, 16, 17, 30, 32, 80, 107, 148, 158, 169, 182, 183, 199], "dust": [68, 69], "dustmask": 69, "dvanitiyd": 0, "dvllganggvlvfepndfsvkagetitfknnagyphnvvfdedavpsgvdvski": 0, "dy": 80, "dye": 16, "dylddefin": 0, "dylnapgetysvklta": 0, "dynam": [13, 30, 69, 107, 109, 193, 195, 196, 294, 297], "dynamicprogram": [27, 106], "dz": 169, "dz1": 169, "dz2": 169, "dz3": 169, "e": [0, 1, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 16, 17, 20, 21, 22, 23, 24, 30, 31, 32, 34, 45, 53, 54, 56, 67, 68, 69, 70, 71, 73, 76, 80, 81, 83, 88, 94, 99, 104, 108, 109, 118, 119, 126, 129, 132, 135, 137, 139, 145, 146, 149, 155, 158, 159, 162, 164, 166, 169, 172, 182, 183, 197, 199, 207, 209, 210, 211, 212, 214, 215, 217, 221, 226, 229, 236, 237, 238, 241, 248, 250, 251, 253, 260, 261, 263, 264, 265, 268, 269, 270, 272, 274, 278, 280, 283, 287, 288, 297, 299, 303], "e0": 168, "e06": 299, "e1": 168, "e12": 299, "e3mfgyr02_random_10_read": [6, 253], "e3mfgyr02f7z7g": 253, "e3mfgyr02fr9g7": 253, "e3mfgyr02ftg": 253, "e3mfgyr02gazm": 253, "e3mfgyr02gfkuc": 253, "e3mfgyr02gpgb1": 253, "e3mfgyr02hhz8o": 253, "e3mfgyr02ja6il": 253, "e3mfgyr02jhd4h": 253, "e3mfgyr02jwq7t": 253, "e9490": 182, "e_": 109, "e_class": 169, "e_freq_t": [12, 31], "e_value_thresh": 3, "eac": 73, "each": [0, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 34, 35, 36, 37, 38, 39, 42, 43, 46, 51, 52, 53, 56, 60, 62, 63, 65, 66, 67, 68, 69, 71, 72, 73, 80, 81, 83, 84, 86, 90, 94, 99, 100, 101, 102, 103, 104, 108, 109, 116, 117, 120, 121, 122, 127, 129, 130, 131, 139, 146, 155, 157, 158, 161, 168, 169, 175, 176, 177, 182, 183, 185, 186, 198, 201, 202, 203, 204, 209, 210, 211, 212, 213, 214, 216, 217, 218, 221, 222, 236, 238, 240, 241, 244, 245, 247, 248, 250, 251, 253, 256, 257, 258, 260, 261, 265, 269, 270, 271, 274, 276, 278, 280, 282, 283, 290, 297, 299, 303], "eaifegftfyktvsiririnrgeavyigtlwkelnvyrkldkeerefykflydcglg": 94, "eal": 14, "eamveavali": 0, "earli": [7, 15, 27, 69, 251, 253], "earlier": [3, 6, 12, 13, 14, 17, 20, 21, 22, 23, 32, 251], "earrai": 238, "eas": [15, 79, 80, 222, 264], "eas51_64": 0, "eas54_6_r1_2_1_413_324": [238, 251], "eas54_6_r1_2_1_443_348": [238, 251], "eas54_6_r1_2_1_540_792": [238, 251], "eas56_57": 0, "easi": [0, 5, 6, 7, 8, 9, 11, 12, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 56, 82, 93, 97, 99, 102, 137, 217, 237, 238, 251], "easier": [3, 5, 6, 7, 8, 9, 12, 16, 19, 20, 21, 23, 119, 169, 183, 203, 217, 274, 283], "easiest": [5, 8, 15, 207, 260, 303], "easili": [5, 6, 9, 11, 15, 17, 21, 22, 23, 251, 260], "easter": [7, 23], "eastern": 3, "easycontrol": [200, 201], "ebi": [0, 6, 32, 209, 222, 234, 245, 250, 274, 277], "eblosum62": [0, 11, 290], "ebml": 274, "ebug": 270, "ebyntm": 22, "ec": [10, 23, 25, 86, 112, 113, 117, 118, 123, 197], "ec_5": 10, "echo": 214, "echtel1": 0, "ecitmatch": [27, 83], "ecnumb": 25, "eco": 25, "ecoli": 13, "ecori": [8, 207], "ecosystem": 10, "ecuy": [2, 4], "ed": [2, 216], "edat": 123, "eddi": 2, "eddylab": 229, "edg": [8, 69, 169, 177, 178, 179, 180, 183, 265], "edgar": 32, "edgssaatsk": 250, "edit": [0, 2, 6, 8, 12, 21, 22, 94, 236, 237, 251, 260, 270], "editor": [8, 12, 17, 19, 23], "edkflhlnyvsdlliphpihleilvqilqcrikdvpslhllrllfheyhnlnslitsk": 7, "ednaful": [11, 290], "edra": 169, "edron": [27, 133, 169], "edron_r": [133, 169], "eds40773": 238, "edu": [0, 15, 18, 32, 35, 36, 37, 38, 39, 46, 50, 51, 59, 61, 65, 124, 156, 190, 199, 201, 204, 209, 211, 212, 214, 221, 226, 247, 263, 269], "eeee2": 0, "eeeeesssseeeeettteeeeeesssseeeee": 0, "eek": 13, "eeubsr": 270, "ef1": 4, "ef590892": 83, "ef590893": 83, "efetch": [8, 9, 23, 27, 83, 274], "eff": [3, 68], "effect": [3, 4, 11, 15, 68, 69, 71, 182, 183, 217, 236, 238, 270, 283], "effective_database_length": 71, "effective_hsp_length": 71, "effective_query_length": 71, "effective_search_spac": 71, "effective_search_space_us": 71, "effector": 113, "effici": [2, 4, 6, 15, 23, 25, 56, 153, 182, 198, 203, 238, 253, 257, 269, 278], "effort": [3, 6], "efg23vgg": 238, "efr": 123, "eft": 13, "eg": [15, 32, 135, 140, 175, 182, 216, 234], "eggert": [2, 13], "egmqcscgpd": 250, "egmqcscgvd": 250, "egqueri": [27, 83], "egqueryresult": [7, 83], "ei": 14, "eigenvalu": [4, 73], "eigenvector": 4, "eight": [4, 7, 11, 80, 264], "ein": 123, "einfo": [27, 83], "einfo3": 7, "einfo_020511": 7, "einforesult": 7, "einvert": 80, "einvertedcommandlin": [27, 79, 80], "eisen": [2, 4, 73], "eisen1998": [2, 4], "eisenberg": 265, "either": [0, 3, 4, 5, 7, 8, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 25, 31, 32, 56, 67, 69, 73, 76, 80, 83, 91, 99, 104, 123, 126, 129, 137, 182, 183, 193, 195, 197, 198, 199, 205, 209, 217, 218, 222, 226, 229, 236, 237, 238, 241, 250, 261, 263, 269, 272, 274, 278, 297, 298, 303], "ekdrfsvnld": 250, "eksmikkrymhlteeilkenpnicaymapsldarqdivvvevpklgkeaaqkaikewgqp": 23, "ekyfnftlipkkdiienkryyliisspdkrfievlhnkikdldiitiglaqfqlrktk": 94, "el": 267, "elabor": [11, 17, 20], "electron": [123, 272], "electrophoresi": 263, "eleg": 6, "elegantli": 3, "elem": [116, 198, 258], "element": [0, 2, 4, 6, 7, 9, 12, 13, 15, 17, 18, 22, 23, 25, 30, 31, 53, 54, 69, 73, 83, 84, 104, 105, 108, 115, 116, 117, 120, 126, 135, 139, 158, 162, 168, 169, 172, 183, 197, 198, 199, 201, 202, 218, 234, 252, 265, 282, 297], "elementdecl": [83, 84], "elementtre": 198, "eleven": [6, 7, 25], "elh": 13, "elif": [6, 297], "elink": [27, 83], "elkan": 2, "ellipsoid": 4, "elong": 4, "els": [0, 6, 8, 12, 13, 15, 19, 23, 30, 93, 99, 169, 275, 299], "elsewher": [0, 6, 22, 81, 210, 211, 212, 213], "elw": 182, "em": [4, 32, 73], "em0": [268, 270], "em1": [268, 270], "em2": [268, 270], "email": [3, 7, 23, 68, 70, 83], "emb": [13, 19, 21, 23, 24, 253], "embed": [244, 278], "embl": [15, 21, 22, 23, 25, 32, 92, 94, 234, 237, 238, 245, 260, 274, 275], "embl_ind": [92, 94], "embl_spac": [92, 94], "emblcdsfeatureiter": [27, 238, 245], "embliter": [27, 238, 245], "emblscann": [27, 92, 94], "emblwrit": [27, 238, 245], "emboss": [2, 5, 9, 11, 13, 14, 27, 30, 56, 58, 66, 67, 208, 238, 250, 251, 255, 290], "emboss_consensu": 0, "embossio": [27, 56], "embossiter": [27, 56, 58], "embryophyta": [7, 25], "emerg": 174, "emiss": [30, 32, 107, 108, 109, 110, 121], "emission_alphabet": 108, "emission_count": 109, "emission_lett": 108, "emission_prob": 108, "emission_pseudo": 108, "emission_st": 108, "emission_titl": 110, "emissions_count": 109, "emit": [108, 121], "emmseqdgylaesinkdieecnaiieqfidylr": 260, "empir": [2, 32, 80, 182, 264], "emploi": [0, 30, 168, 197], "empti": [0, 3, 4, 8, 11, 13, 15, 25, 30, 36, 37, 38, 46, 49, 64, 67, 72, 99, 104, 108, 109, 135, 159, 169, 172, 197, 205, 209, 211, 230, 236, 241, 261, 278, 295, 299], "empty_status_charact": [30, 46], "en": [7, 53, 66, 263, 274], "ena": 6, "enabl": [6, 11, 15, 17, 18, 32, 67, 69, 169, 217, 270, 303], "encapsul": [8, 15, 21, 107, 122], "encephalosi": 23, "encod": [0, 3, 6, 7, 13, 14, 22, 25, 68, 76, 83, 84, 90, 182, 198, 236, 238, 251, 253, 260, 261, 270, 278, 297], "encount": [4, 7, 11, 20, 83, 84, 222], "encourag": [5, 6, 22, 23, 24, 92, 251], "encyclopedia": [111, 115, 119], "end": [0, 3, 4, 5, 6, 8, 9, 11, 12, 13, 14, 15, 17, 20, 21, 22, 23, 24, 27, 30, 31, 32, 35, 36, 46, 51, 56, 61, 62, 63, 66, 68, 71, 80, 84, 89, 90, 94, 95, 99, 104, 125, 130, 136, 138, 154, 169, 182, 183, 197, 204, 214, 215, 217, 221, 222, 226, 229, 234, 236, 237, 238, 245, 252, 260, 261, 264, 265, 269, 270, 274, 275, 278, 297, 299, 303], "end1": 236, "end2": 236, "end_extend_gap_scor": 13, "end_gap_scor": 13, "end_i": 103, "end_open_gap_scor": 13, "end_po": 21, "end_x": 103, "end_x_posit": 99, "end_y_posit": 99, "enda": [98, 104], "endara": 7, "endb": [98, 104], "enddbrefel": [238, 252], "enddescriptionel": [238, 252], "endeavor": 3, "endel": [85, 89], "endelementhandl": [83, 84], "endentryel": [238, 252], "enderrorelementhandl": [83, 84], "endextend": [79, 80], "endgap": [30, 32], "endian": 0, "endintegerelementhandl": [83, 84], "endnamespacedeclhandl": [83, 84], "endopen": [79, 80], "endoribonucleas": 0, "endpoint": [10, 68, 70], "endpropertyel": [238, 252], "endrawelementhandl": [83, 84], "endresid": 215, "endsequenceel": [238, 252], "endseqxmlel": [238, 252], "endskipelementhandl": [83, 84], "endspeciesel": [238, 252], "endstringelementhandl": [83, 84], "endswith": [27, 236], "endweight": [79, 80], "energi": [19, 104], "enf": 13, "enforc": [7, 32, 117, 197, 217], "engelman": 265, "engin": [166, 253, 265], "english": [3, 7], "enhanc": 69, "enjoi": 19, "enough": [3, 5, 6, 8, 15, 19, 20, 21, 23, 127, 251, 270], "ensg00000197372": 11, "ensur": [3, 4, 7, 11, 22, 23, 24, 30, 68, 71, 91, 104, 108, 152, 217, 237, 238, 280], "ent": [11, 15, 169], "enter": [7, 65, 182], "enterobacteri": 2, "entir": [1, 7, 17, 20, 21, 23, 31, 60, 64, 66, 183, 185, 209, 214, 237, 253, 261, 265, 267], "entirerli": 269, "entireti": 65, "entiti": [15, 27, 84, 133, 134, 136, 144, 146, 148, 152, 155, 157, 158, 159, 160, 168, 170, 172, 173], "entity_1": 134, "entity_2": 134, "entity_attribut": 97, "entity_id": [15, 97], "entity_list": 159, "entity_property_list": 134, "entity_typ": [97, 172], "entrez": [3, 8, 9, 19, 22, 23, 24, 26, 27, 68, 69, 70, 76, 119, 123, 238, 274, 275, 303, 307], "entrez_links_new_window": [68, 70], "entrez_queri": [68, 69, 70], "entrezf": 7, "entrezgene_gen": 7, "entrezgene_track": 7, "entri": [0, 7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 25, 27, 30, 60, 66, 83, 84, 85, 86, 87, 88, 90, 92, 111, 112, 113, 114, 115, 116, 117, 119, 125, 126, 139, 140, 149, 152, 167, 168, 169, 176, 182, 201, 212, 222, 226, 234, 237, 238, 241, 246, 248, 251, 252, 258, 260, 272, 273, 274, 275, 303], "entropi": [3, 13, 68, 122, 264, 283], "entry1": [115, 117], "entry2": [115, 117], "entry_nam": [25, 85, 272], "entrynum": 126, "enum": 55, "enum_test": [202, 203], "enumer": [0, 6, 8, 12, 22, 55, 68, 158, 169, 202], "enumerate_atom": [27, 133, 152], "env": [67, 229], "env_end": 229, "env_endtyp": 229, "env_num": 229, "env_start": 229, "envelop": [69, 217, 229], "environ": [7, 12, 15, 67, 83, 149, 157, 169], "envis": 102, "envlist": 24, "envpython": 24, "envz": 260, "enzmy": 206, "enzym": [7, 9, 10, 27, 72, 85, 111, 112, 118, 206, 207, 272, 274], "eof": 278, "eorder": [4, 73], "ep": [8, 30, 32], "epislon": 12, "epo_prt_select": 245, "epoch": 4, "epost": [27, 83], "epost_020511": 7, "epostresult": 7, "eprimer3": [80, 81], "epsilon": [12, 13, 30, 181, 182, 199], "epsilon_prot": 265, "epub": 175, "epubd": 7, "eqal": 68, "eqnlvdcdh": 0, "eqqlvdcagg": 0, "eqqlvdcaqd": 0, "equal": [0, 4, 6, 7, 11, 12, 13, 14, 15, 17, 20, 22, 25, 30, 68, 73, 84, 104, 108, 135, 136, 139, 150, 155, 157, 168, 169, 177, 179, 180, 183, 237, 251, 260, 261, 264, 270, 282, 290, 294, 297, 299], "equal_weight": [27, 282], "equat": [6, 11, 15], "equcab1": 0, "equilibrium": [13, 182], "equin": 23, "equiv": 4, "equival": [0, 3, 4, 7, 15, 22, 24, 30, 69, 139, 169, 197, 237, 238, 241, 245, 248, 251, 261, 264, 270, 274, 278, 300, 302], "equiveal": 161, "equvial": 270, "eras": 214, "erbos": 80, "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggat": 0, "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqc": 0, "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqg": 0, "eric": [2, 26, 122, 133], "err": [67, 182], "err_output": 67, "errata": 32, "erratum": 123, "erron": [15, 21], "error": [3, 4, 6, 12, 14, 17, 21, 24, 25, 27, 29, 32, 67, 68, 73, 79, 80, 83, 84, 89, 107, 119, 125, 145, 149, 168, 169, 182, 193, 195, 196, 198, 209, 214, 238, 251, 258, 261, 270, 272, 294, 298], "errorel": [7, 27, 83, 84], "errorfil": [79, 80], "erw": 68, "escap": [83, 84], "escherichia": [13, 209], "esearch": [27, 83, 274], "esearch1": 83, "esfviymfiv": 250, "esfviymfvv": 250, "esk": 6, "esoter": 93, "especi": [3, 5, 7, 9, 10, 12, 19, 102, 177, 260, 270], "espel": [27, 83], "essenc": [3, 4, 183], "essenti": [1, 3, 5, 6, 10, 13, 14, 15, 17, 20, 21, 22, 32, 100, 236, 258, 260, 270, 274], "est": [0, 7, 30, 79, 80, 275], "est2genom": [42, 80, 222], "est2genomecommandlin": [27, 79, 80], "est48004": 68, "establish": [0, 11], "estim": [2, 6, 13, 18, 32, 80, 108, 109, 121, 127, 152, 182, 196, 202, 203, 251, 253, 264], "estimate_nm": [201, 202, 203], "estimate_param": [106, 109], "estradiol": 113, "esummari": [27, 83], "esyvvymfvv": 250, "et": [4, 6, 8, 9, 11, 13, 17, 32, 34, 65, 69, 73, 83, 107, 108, 109, 137, 140, 238, 252, 264, 265, 281, 288, 299, 300], "eta": 12, "etandem": 80, "etandemcommandlin": [27, 79, 80], "etc": [5, 6, 7, 8, 9, 11, 14, 21, 30, 99, 117, 133, 152, 159, 169, 182, 217, 221, 229, 237, 253, 260, 261, 264, 269, 272, 275, 278, 288, 303], "etglsemrl": 250, "ethan": 2, "etherington": 2, "etre": 198, "ets1": 288, "eu": 222, "eu490707": 7, "euarc": 0, "euclidean": [73, 282], "eudicotyledon": 7, "eugen": 2, "eukaryot": [6, 16, 21], "eukaryota": [7, 23, 25], "euphyllophyta": 7, "european": [0, 2, 278], "eutil": 7, "eva": 2, "eval": [30, 68], "evalu": [0, 3, 4, 11, 17, 20, 68, 69, 143, 151, 182, 183, 209, 218, 226, 229, 234, 237, 260, 264, 291, 292], "evalue_cond": 229, "even": [4, 5, 7, 9, 11, 12, 13, 17, 19, 20, 21, 22, 23, 27, 30, 31, 32, 56, 80, 104, 222, 237, 238, 251, 264, 278, 288], "evenli": [100, 108], "event": [4, 6, 11, 13, 17, 27, 94, 181, 183, 197, 198, 252], "eventu": [20, 67, 191], "ever": [3, 79, 127, 149, 228], "everi": [3, 6, 8, 15, 16, 17, 23, 24, 30, 61, 67, 71, 84, 127, 169, 215, 234, 245, 255, 260, 264, 270, 278, 282, 288, 299], "everybodi": 3, "everydai": [4, 22], "everyth": [3, 5, 6, 7, 11, 12, 19, 21, 23, 69, 94, 95, 99, 101, 148, 152, 252, 305], "evid": [15, 21, 197, 240, 272, 277], "evl": [30, 297], "evo": 182, "evol": 7, "evolut": [2, 13, 19, 50, 65, 182, 190, 199], "evolutionari": [2, 12, 13, 32, 182], "evolutionaryontologi": 185, "evrnak": 22, "evrnakacgt": 22, "evrstn": 0, "evssvstspv": 250, "ewan": [2, 237], "eweight": [4, 73], "ex": [12, 32, 67, 182, 221], "ex1": [0, 278], "ex1_head": [0, 278], "ex1_refresh": 278, "exact": [6, 7, 17, 20, 21, 45, 61, 99, 119, 152, 222, 237], "exact_loc": 21, "exact_mass": 119, "exactli": [0, 3, 4, 7, 8, 10, 11, 12, 15, 17, 20, 21, 23, 25, 30, 86, 87, 88, 90, 92, 93, 113, 135, 217, 238, 241, 251, 253, 283, 288, 298, 299], "exactposit": [21, 27, 68, 237], "examin": [15, 270, 282], "exampl": [0, 1, 3, 6, 9, 10, 11, 12, 14, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 35, 36, 37, 38, 41, 46, 51, 53, 56, 58, 59, 60, 61, 62, 66, 67, 68, 69, 73, 80, 83, 85, 91, 94, 101, 104, 108, 109, 112, 113, 114, 116, 117, 122, 125, 126, 133, 134, 135, 139, 140, 148, 152, 154, 157, 158, 169, 170, 173, 176, 182, 183, 197, 199, 201, 204, 207, 215, 217, 218, 221, 222, 229, 234, 236, 237, 238, 241, 244, 246, 249, 250, 251, 252, 253, 256, 260, 261, 263, 264, 270, 272, 274, 277, 279, 282, 283, 288, 291, 292, 297, 298, 299, 303, 305], "example_do": 238, "example_filenam": 272, "examplealign": 182, "exampletre": 182, "exc_traceback": [45, 68], "exc_typ": [45, 68], "exc_valu": [45, 68], "exce": [32, 221], "exceed": 15, "excel": [6, 7, 23], "except": [0, 4, 6, 12, 13, 15, 16, 17, 21, 22, 23, 25, 27, 29, 30, 32, 37, 46, 56, 67, 68, 69, 72, 76, 83, 84, 92, 94, 113, 129, 130, 131, 132, 136, 144, 147, 151, 152, 160, 168, 169, 188, 190, 193, 195, 196, 197, 198, 217, 222, 236, 237, 238, 241, 251, 253, 260, 261, 270, 272, 278, 283, 288, 295, 297, 298, 299, 305], "excerpt": 22, "excess": [0, 4, 7, 202, 241, 270], "exchang": 4, "excit": [5, 8], "exclam": 251, "exclud": [0, 8, 15, 17, 22, 24, 32, 80, 129, 130, 169, 182, 183, 234, 236, 270], "exclude_doctest_modul": 24, "exclude_filenam": [181, 182], "excludedregion": [79, 80], "exclus": [20, 222, 263], "excus": 22, "execut": [3, 4, 12, 24, 25, 32, 67, 68, 69, 89, 137, 156, 169, 183, 202, 221, 301, 303, 304], "execute_and_fetch_col0": [301, 303], "execute_and_fetchal": [301, 303], "execute_on": [301, 303], "executemani": [301, 303, 304], "exelixi": [17, 182], "exercis": 158, "exhaust": [23, 42, 182, 222, 270], "exist": [3, 4, 12, 13, 14, 15, 17, 18, 19, 20, 21, 23, 24, 25, 32, 56, 83, 85, 104, 117, 129, 139, 149, 152, 169, 176, 183, 193, 209, 217, 238, 251, 260, 264, 265, 270, 272, 303], "exit": [32, 67, 91, 182], "exn": [0, 30, 222], "exn_22_m_cdna2genome_vulgar": 0, "exn_22_m_coding2coding_fshift": 222, "exn_22_m_genome2genom": 222, "exn_22_m_ner_cigar": 30, "exon": [20, 21, 61, 237], "exoner": [20, 27, 30, 217, 223, 224, 225], "exonerate_cigar": [217, 222], "exonerate_text": [217, 222], "exonerate_vulgar": [217, 222], "exoneratecigarindex": [217, 222, 223], "exoneratecigarpars": [217, 222, 223], "exonerateio": [27, 217], "exoneratetextindex": [217, 222, 224], "exoneratetextpars": [217, 222, 224], "exoneratevulgarindex": [217, 222, 223, 225], "exoneratevulgarpars": [217, 222, 225], "exp": [100, 229, 270], "exp_ca": 15, "exp_cb": 15, "exp_f": 15, "expand": 169, "expasi": [9, 19, 23, 24, 26, 27, 265, 272, 307], "expasy_url": 85, "expatpars": 89, "expclust": [4, 73], "expect": [0, 2, 3, 4, 6, 7, 8, 9, 12, 13, 15, 20, 21, 23, 27, 31, 32, 35, 36, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 70, 71, 90, 94, 99, 102, 104, 152, 182, 197, 198, 202, 203, 221, 222, 229, 237, 238, 240, 241, 244, 245, 247, 249, 250, 251, 252, 253, 255, 256, 259, 278, 290, 298], "expect_high": [68, 70], "expect_low": [68, 70], "expected_frequ": [12, 13], "expens": 32, "experi": [4, 15, 16, 19, 20, 21, 23, 144, 152, 214, 264], "experiment": [4, 10, 16, 21, 25, 27, 172, 197, 214, 270, 272], "experimnetal_method": 172, "expert": [181, 182], "expid": [4, 73], "explain": [4, 5, 7, 12, 15, 20, 21, 24, 30, 83, 121, 203, 251, 278], "explainflag": [79, 80], "explan": [0, 68, 83, 108, 182, 209], "explanatori": 11, "explicit": [8, 9, 12, 17, 21, 24, 61, 158, 237, 238, 260, 261, 278], "explicitli": [0, 3, 7, 8, 9, 12, 20, 21, 22, 23, 32, 104, 158, 169, 177, 218, 237, 251, 260, 288], "explor": [11, 15, 17, 182], "exponenti": [11, 16], "export": [11, 149, 158, 169], "export_fasta": [128, 129], "export_phylip": [128, 129], "export_search_strategi": [68, 69], "expos": [15, 169, 236, 278], "exposur": [2, 141, 157], "exposurecn": [27, 133, 141], "express": [0, 2, 4, 5, 6, 7, 17, 20, 21, 23, 30, 56, 73, 96, 169, 183, 197, 215, 238, 251, 261, 275], "exptre": 4, "ext": 202, "extend": [3, 5, 6, 8, 9, 10, 12, 13, 14, 15, 20, 24, 27, 30, 32, 36, 68, 69, 71, 76, 80, 169, 177, 186, 209, 214, 217, 218, 236, 264, 270, 272, 297], "extend_gap_scor": [13, 30], "extend_penalti": 0, "extenda": 297, "extendb": 297, "extens": [2, 3, 6, 9, 13, 14, 15, 18, 22, 23, 24, 32, 35, 68, 69, 71, 80, 129, 137, 153, 166, 222, 237, 253, 270, 297], "extent": 272, "extern": [11, 12, 15, 24, 27, 83, 84, 183, 197, 198, 295], "externalentityrefhandl": [83, 84], "extinct": 265, "extra": [0, 11, 17, 21, 23, 36, 38, 56, 168, 226, 237, 238, 248, 251, 278], "extra_indic": 36, "extract": [0, 3, 6, 7, 8, 10, 12, 13, 17, 19, 20, 21, 22, 25, 27, 30, 31, 62, 68, 94, 126, 133, 138, 182, 191, 201, 205, 214, 217, 218, 226, 237, 238, 251, 253, 260, 270, 274, 296, 299, 300, 306], "extraindex": [0, 36, 38], "extrem": [6, 13, 19, 21, 23, 272], "exu": 80, "ey": 13, "eyltapgetfsvtltv": 0, "f": [0, 2, 3, 7, 8, 11, 12, 13, 14, 15, 16, 17, 22, 30, 32, 54, 68, 69, 76, 80, 107, 135, 139, 149, 169, 182, 203, 216, 237, 251, 253, 260, 261, 263, 264, 265, 268, 270, 278, 289, 291, 292, 299], "f001": 238, "f002": 238, "f1": [237, 250], "f1x4": [13, 34, 281], "f2": 237, "f2cxe6": 25, "f3": 237, "f3x4": [13, 34, 281], "f61": [13, 34, 281], "f81": 182, "f84": 182, "f_": 18, "f_bz163a": 244, "f_handl": 6, "fa": [0, 6, 13, 30, 32, 38, 62, 80, 182, 209, 211, 238, 270], "faa": [12, 13, 14, 23, 56, 69, 80, 238], "faadda": 12, "faaddaakaafdsltaqatemsgyawalvvlvvgatvgiklfkkfvsra": 12, "faaddatsqa": 12, "faaddatsqakaafdsltaqatemsgyawalvvlvvgatvgikl": 12, "faaddatsqakaafdsltaqatemsgyawalvvlvvgatvgiklfkkfv": 12, "faaddatsqakaafdsltaqatemsgyawalvvlvvgatvgiklfkkfvsra": 12, "face": [25, 149], "facil": [11, 15], "facilit": [11, 15, 177, 260, 278], "fact": [3, 15, 19, 23, 25, 56, 193, 195, 236, 251], "facto": 6, "factor": [4, 11, 25, 32, 105, 135, 152, 162, 169, 172, 264, 288, 295], "faei": 206, "fafbyproteinrec": 277, "fai": 270, "faidx": 270, "faii": 206, "fail": [3, 4, 7, 9, 13, 16, 18, 24, 68, 80, 83, 84, 85, 92, 152, 168, 169, 193, 195, 196, 236, 251, 270, 303], "failobj": 76, "failur": [7, 24, 83, 92, 236, 237], "fairli": [1, 5, 7, 15, 21], "fake": 251, "fall": [6, 21, 237, 260], "fals": [0, 3, 4, 7, 8, 11, 15, 17, 20, 21, 22, 30, 31, 32, 36, 37, 38, 49, 51, 52, 64, 67, 68, 69, 70, 73, 80, 83, 88, 91, 94, 104, 105, 127, 129, 132, 135, 136, 139, 140, 143, 144, 148, 149, 151, 152, 153, 154, 155, 158, 160, 162, 166, 168, 169, 170, 176, 183, 184, 185, 187, 188, 189, 190, 193, 195, 196, 199, 202, 204, 218, 219, 220, 221, 226, 231, 236, 237, 238, 239, 253, 258, 260, 261, 264, 265, 270, 277, 279, 281, 283, 288, 294, 297, 299, 303, 305], "famili": [0, 2, 7, 8, 11, 12, 19, 25, 68, 197, 209, 211, 288], "familiar": [7, 11, 12, 20, 24, 30, 299], "famou": 13, "fan": 19, "fanci": [15, 31, 91, 169], "fancier": 31, "fanhfmvlcg": 250, "faq": [35, 46, 51, 61, 221, 247], "faqblat": 221, "faqformat": [35, 46, 51, 61, 247], "far": [4, 8, 19, 20, 21, 100, 251, 278], "farfavrygk": 0, "farfavrygksyesaaevrrrfrifsesleevrstn": 0, "fas1": [11, 291], "fas2": [11, 291], "fasciculatum": 23, "fashion": 23, "fasman": 265, "fast": [0, 2, 12, 14, 23, 30, 31, 32, 69, 146, 182, 253, 270, 278], "fast_bam": [268, 270], "fasta": [1, 3, 7, 8, 9, 11, 12, 13, 14, 15, 20, 22, 27, 30, 32, 55, 56, 59, 60, 62, 66, 67, 69, 80, 91, 129, 161, 182, 209, 217, 238, 241, 246, 250, 251, 252, 253, 256, 260, 270, 274, 278], "fasta36": 0, "fasta_align": 161, "fasta_aln": 32, "fasta_data": 23, "fasta_format_str": 22, "fasta_guid": 226, "fasta_list2": 226, "fasta_seq": 32, "fasta_sourc": 251, "fasta_str": 3, "fasta_www2": 226, "fastaio": [6, 23, 27, 56, 217, 238, 251], "fastaiter": [27, 238, 241, 246], "fastam10index": [27, 217, 226], "fastam10iter": [27, 56, 59], "fastam10pars": [27, 217, 226], "fastaout": [30, 32], "fastapair": [30, 32], "fastaparttre": [30, 32], "fastatwolineiter": [27, 238, 241], "fastatwolinepars": [27, 238, 241], "fastatwolinewrit": [27, 238, 241], "fastawrit": [27, 238, 241], "faster": [0, 3, 4, 6, 7, 8, 14, 23, 32, 36, 37, 84, 94, 166, 169, 182, 217, 238, 270, 297], "fastest": [11, 56, 92, 181, 182, 238, 270], "fastmmcifpars": [27, 133, 143], "fastq": [2, 9, 21, 238, 240, 249, 251, 253, 260, 270, 278], "fastq_dict": 238, "fastqgeneraliter": [6, 23, 27, 238, 251], "fastqilluminaiter": [27, 238, 251], "fastqilluminawrit": [27, 238, 251], "fastqphrediter": [27, 238, 251], "fastqphredwrit": [27, 238, 251], "fastqsolexaiter": [27, 238, 251], "fastqsolexawrit": [27, 238, 251], "fasttre": [17, 182], "fasttree_ex": 182, "fasttreecommandlin": [181, 182], "fasttreewin32": 182, "fatal": 151, "fati": 206, "fau": 123, "faucher": 265, "favor": [7, 275], "favorit": [7, 11, 12, 17, 19, 20, 23, 265], "fbgn0000210": 11, "fc": 182, "fconsens": 80, "fconsensecommandlin": [27, 79, 80], "fcygrllctv": 250, "fcygrlvctv": 250, "fdir": 140, "fdnadist": 80, "fdnadistcommandlin": [27, 79, 80], "fdnapar": 80, "fdnaparscommandlin": [27, 79, 80], "fe2": 25, "fe2s2": 25, "feat": 197, "featur": [0, 3, 6, 7, 9, 14, 15, 19, 20, 22, 23, 25, 27, 38, 68, 80, 92, 93, 94, 95, 98, 99, 104, 122, 127, 158, 177, 182, 217, 222, 238, 245, 251, 255, 260, 272, 282, 301, 302], "feature_clean": 92, "feature_end_mark": [92, 94], "feature_fn": 122, "feature_head": [238, 245], "feature_i": 8, "feature_id": 104, "feature_kei": 94, "feature_loc": 237, "feature_qualifier_ind": [92, 94], "feature_qualifier_spac": [92, 94], "feature_seq": 21, "feature_start_mark": [92, 94], "feature_t": 94, "feature_x": 8, "featurea": 104, "featureb": 104, "featureloc": [27, 237], "featurepars": [27, 92], "featureposit": 21, "featureset": [8, 98, 104], "featuret": [27, 272], "featurevalueclean": [27, 92, 95], "feb": [0, 7, 74, 83, 88, 261], "februari": [9, 20, 87], "fed": 12, "feed": [25, 85, 89, 92, 94, 191], "feedback": [5, 6, 27], "feedstock": 5, "feel": [5, 19, 108, 146], "fefec": 0, "felcat3": 0, "felsenstein": [0, 17, 65, 129], "feng": 199, "fennel": 2, "fesfgdl": 13, "fetch": [3, 7, 11, 15, 20, 23, 25, 83, 85, 149, 274, 288, 303], "fetch_dbid_by_dbnam": [301, 303], "fetch_motif": [11, 287, 288], "fetch_motif_by_id": [11, 287, 288], "fetch_motifs_by_nam": [11, 287, 288], "fetch_ncbi_taxonomi": [303, 305], "fetch_seqid_by_access": [301, 303], "fetch_seqid_by_display_id": [301, 303], "fetch_seqid_by_identifi": [301, 303], "fetch_seqid_by_vers": [301, 303], "fetch_seqids_by_access": [301, 303], "few": [0, 3, 8, 10, 12, 15, 17, 18, 20, 23, 25, 31, 68, 251, 264], "fewer": 270, "ff": [0, 30, 32], "ff8000": 183, "ffer": 3, "fffdfhghhhjjjijjjjijjjgedhhgghgbgiigiiab": 0, "fft": [30, 32], "fg": 182, "fgcolor": [115, 117], "fgkeftppvqaayqkvvagvanalahkyh": 13, "fh": [0, 11, 94, 245], "fhfkswmskhrkty": 0, "fhv": 6, "fi": [202, 203], "fibronectin": 211, "fid": 140, "fiddli": 6, "field": [0, 2, 4, 7, 15, 17, 18, 20, 23, 25, 27, 30, 36, 38, 51, 61, 66, 83, 119, 126, 133, 139, 162, 169, 218, 219, 248, 251, 252, 256, 258, 263, 270, 274, 275, 276, 277, 278, 295, 297], "field_nam": 277, "fieldlist": 7, "fieldn": 126, "fieldnam": [133, 169], "fieldval": 277, "fifteen": 16, "fifth": 278, "fifti": 6, "fig": [6, 8, 15, 17], "figur": [3, 6, 8, 19, 22, 102], "file": [1, 2, 3, 8, 9, 10, 16, 17, 18, 22, 24, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 76, 78, 80, 82, 83, 84, 86, 87, 88, 90, 92, 93, 94, 95, 96, 99, 101, 103, 104, 105, 112, 113, 114, 116, 117, 121, 123, 125, 126, 128, 129, 133, 135, 137, 140, 141, 142, 143, 145, 148, 149, 150, 151, 152, 153, 154, 158, 162, 164, 165, 167, 168, 169, 170, 171, 173, 174, 182, 183, 185, 188, 190, 191, 193, 195, 196, 198, 199, 201, 202, 203, 204, 205, 208, 209, 210, 211, 212, 213, 214, 217, 218, 219, 220, 221, 222, 226, 229, 232, 234, 236, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 283, 284, 286, 287, 293, 295, 296, 299, 303], "file_format": 149, "file_handl": 209, "file_nam": 270, "file_path": 171, "file_typ": 137, "fileformat": 238, "filehandl": [142, 143, 148, 151, 170], "filenam": [0, 1, 6, 7, 8, 9, 12, 13, 15, 17, 19, 20, 23, 30, 32, 56, 67, 68, 73, 80, 83, 84, 104, 105, 126, 129, 137, 138, 141, 142, 143, 149, 153, 158, 171, 182, 209, 210, 214, 217, 219, 220, 221, 223, 224, 225, 226, 231, 232, 238, 241, 250, 251, 270, 278, 298, 303], "fileno": [27, 278], "fileobj": 278, "filepars": [200, 201], "filepath": [170, 173], "fileprefix": 182, "filerecord": [200, 201, 204], "fill": [0, 5, 11, 15, 89, 99, 102, 104, 169, 248, 270, 287], "fill_chromosom": [98, 102], "fill_color": 99, "filt": 7, "filter": [7, 10, 15, 17, 20, 21, 56, 67, 68, 69, 70, 79, 80, 169, 183, 238, 270, 277], "filter_and_trim": 253, "filter_func": [3, 20], "filtered_qresult": 20, "filtering_db": [68, 69], "fin": [136, 158, 169, 272], "final": [0, 3, 4, 7, 12, 15, 17, 20, 21, 23, 32, 45, 66, 69, 99, 100, 104, 169, 182, 190, 193, 195, 196, 202, 214, 221, 246, 251, 253, 260, 269, 270, 278], "final_optim": 166, "finalize_structur": [171, 172], "find": [1, 3, 4, 5, 6, 8, 10, 12, 13, 15, 17, 18, 19, 21, 23, 24, 25, 27, 30, 32, 36, 68, 80, 81, 83, 84, 85, 94, 119, 121, 146, 154, 167, 169, 175, 183, 186, 214, 216, 226, 229, 236, 237, 270, 278, 283, 289, 290, 291, 292, 294, 297], "find_ani": [17, 181, 183], "find_clad": [17, 181, 183], "find_el": [17, 181, 183], "find_orfs_with_tran": 6, "find_start": [92, 94], "find_stat": [27, 121], "finder": 11, "fine": [6, 8, 9, 13, 20, 278], "finer": 169, "finger": [11, 272, 283], "fingerprint": 88, "finish": [8, 12, 17, 19, 22, 67, 130, 169, 183, 198, 252], "fir": 123, "firebrick": 8, "first": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 30, 31, 32, 35, 46, 51, 56, 61, 65, 67, 68, 69, 73, 80, 99, 104, 109, 117, 126, 129, 132, 137, 149, 154, 169, 172, 180, 182, 183, 197, 204, 221, 222, 236, 237, 238, 241, 247, 249, 251, 256, 260, 261, 265, 269, 270, 274, 276, 277, 278, 283, 288, 297, 298, 299, 303], "first_align": 12, "first_index": 283, "first_lin": 1, "first_model": 15, "first_pag": 83, "first_primer_seq": 82, "first_record": [23, 30], "first_row": 299, "first_tag": 84, "firstli": [3, 6, 8, 251], "firstlin": 126, "fisher": 202, "fit": [0, 2, 4, 5, 7, 8, 16, 21, 27, 30, 120, 127, 178, 202, 203, 216, 229, 237, 243, 251, 270, 280, 298, 299, 300], "fitch": [32, 199], "fite": 0, "fitzgerald": 2, "five": [0, 7, 8, 12, 16, 20, 21, 51, 118, 251], "fix": [0, 11, 15, 21, 24, 32, 146, 152, 163, 175, 176, 182, 270, 277, 278, 303], "fix_alpha": 17, "fixedbranch": [30, 32], "fixmat": 270, "fixmate_cmd": 270, "fkauff": [130, 269], "fkkkkf": 30, "fknyylnnk": 0, "fknyylnnkeaiftddlpvadylddefinsiptafdwrtrg": 0, "fkskinenykvtfta": 0, "fkswmskhrk": 0, "fkswmskhrkty": 0, "fl": [7, 13], "fl1": 237, "fl2": 237, "fl3": 237, "fla": 7, "flag": [0, 3, 15, 17, 20, 52, 104, 135, 136, 152, 154, 155, 158, 162, 169, 214, 217, 218, 221, 222, 226, 229, 270, 297, 303], "flag_disord": [133, 135, 155], "flank": [2, 59, 80, 141, 283], "flat": [7, 10, 11, 13, 23, 94, 238, 255, 275], "flavanoid": 25, "flavonoid": 23, "flavor": [4, 15, 20, 71, 218, 226, 229], "flefqdkfnk": 0, "flefqdkfnkki": 0, "flength": 140, "flexibl": [4, 6, 7, 9, 15, 19, 23, 169, 177, 207, 261, 265], "flickr": 19, "flicwvpyai": 250, "flight": 123, "flip": [6, 8, 104], "float": [3, 4, 6, 17, 24, 54, 68, 69, 71, 73, 80, 104, 135, 140, 141, 146, 152, 157, 158, 162, 166, 168, 169, 176, 182, 183, 197, 216, 251, 261, 263, 265, 267, 270, 286], "float0": [135, 162], "float1_color": [98, 104], "float32": 11, "float64": [4, 15, 73, 169], "float64p4": 169, "florian": 2, "florida": 7, "flow": [6, 253], "flow_index": 253, "flow_kei": 253, "flow_valu": 253, "flowgram": [6, 238, 253], "fluorophor": 261, "flush": [27, 30, 56, 68, 238, 278, 298], "flvcwvpya": 250, "flx": 6, "fly": [6, 13, 20, 25], "flyfactorsurvei": [11, 283], "fm": 140, "fmd": 264, "fmdfactor": 264, "fmdmethod": 264, "fme": 154, "fmn": 53, "fmodel": [30, 32], "fmt": [0, 3, 4, 13, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 68, 183, 246, 283], "fmt_": [27, 68, 71], "fn": [30, 32], "fn_list": 126, "fna": [6, 7, 8, 21], "fname": [153, 202, 203, 204, 218, 222, 283], "fneighbor": 80, "fneighborcommandlin": [27, 79, 80], "fnnf": 0, "fnny": 0, "fnr": [11, 294], "focu": [19, 21, 22, 25], "focus": [8, 12, 15, 16, 19, 263], "focuss": 8, "fold": [209, 211, 272], "folder": [6, 8, 20, 21, 24, 149, 166], "folk": 3, "follow": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 42, 43, 45, 52, 54, 56, 59, 62, 65, 66, 68, 73, 76, 80, 86, 88, 90, 92, 94, 99, 104, 123, 135, 137, 140, 148, 158, 169, 170, 173, 177, 182, 197, 204, 207, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 241, 246, 247, 248, 250, 251, 253, 256, 260, 261, 272, 274, 280, 283, 290, 295, 297, 298, 299], "font": [8, 104], "fontnam": 105, "fontsiz": 105, "foo": [17, 270], "foo1": 17, "foo2": 17, "foo3": 17, "footer": [42, 45, 56, 59, 60, 238, 240, 246, 269], "fop": [30, 32], "forc": [6, 12, 15, 20, 21, 30, 32, 148, 169, 240, 270], "force_gener": 297, "foreground": 117, "forg": 5, "forget": [7, 15, 251], "forgotten": 5, "forkhead": 11, "form": [0, 3, 4, 6, 7, 9, 11, 15, 16, 25, 30, 45, 69, 72, 84, 93, 107, 126, 137, 140, 169, 182, 197, 237, 272, 278, 290], "formal": 172, "formaldehyd": 264, "formamid": 264, "format": [1, 2, 4, 6, 7, 8, 9, 10, 13, 16, 17, 18, 20, 22, 24, 25, 27, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 71, 73, 78, 80, 82, 83, 85, 87, 88, 89, 92, 93, 94, 97, 99, 104, 105, 117, 118, 129, 132, 148, 149, 150, 151, 152, 158, 162, 165, 169, 181, 182, 183, 185, 188, 190, 197, 198, 199, 201, 204, 207, 209, 210, 211, 213, 214, 219, 220, 223, 224, 225, 227, 228, 230, 231, 232, 233, 235, 236, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 264, 268, 270, 271, 272, 274, 275, 276, 277, 278, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 297, 299, 303], "format1": 35, "format2": 51, "format23": 248, "format5": [46, 61], "format_align": [14, 27, 30, 33, 35, 39, 40, 43, 45, 46, 47, 49, 50, 51, 52, 53, 297], "format_alignemt": 297, "format_branch_length": 190, "format_confid": 190, "format_entrez_queri": [68, 70], "format_label": [27, 181, 185], "format_object": [68, 70], "format_output": [206, 207], "format_phylip": [181, 199], "format_spec": [30, 71, 183, 260, 283], "format_typ": [3, 68, 70], "formatt": 54, "formatvers": [0, 62], "former": [0, 11, 15, 257], "formfe": 236, "formula": [11, 12, 109, 112, 119, 221, 251, 264], "formuleaa": 167, "fortran": 9, "fortun": [3, 12], "forum": 5, "forward": [0, 6, 7, 8, 11, 12, 13, 15, 34, 76, 80, 104, 107, 109, 135, 139, 169, 237, 251, 252, 261, 280], "forward_algorithm": [106, 107], "forward_gc": 81, "forward_length": 81, "forward_seq": 81, "forward_start": 81, "forward_t": [22, 75, 76], "forward_tm": 81, "forward_var": 109, "forwardinput": [79, 80], "forwardref": [136, 144, 155, 160], "foster": 2, "found": [0, 3, 4, 5, 6, 7, 9, 12, 13, 15, 17, 18, 22, 23, 24, 25, 30, 53, 54, 56, 67, 68, 71, 72, 73, 80, 84, 102, 104, 140, 169, 172, 182, 183, 195, 198, 210, 211, 212, 213, 214, 217, 236, 237, 238, 251, 252, 253, 258, 270, 271, 274, 275, 283, 290, 295, 298, 299, 300], "foundat": [2, 5, 238, 250], "four": [0, 4, 8, 15, 17, 20, 23, 25, 149, 169, 176, 217, 251, 261, 264, 283], "fourcolumn": 11, "fourrow": 11, "fourth": [0, 11, 15, 20, 23, 169, 251, 278], "fout": 31, "fp": [7, 91, 123], "fphf": 13, "fpr": [11, 294], "fprotdist": 80, "fprotdistcommandlin": [27, 79, 80], "fprotpar": 80, "fprotparscommandlin": [27, 79, 80], "fq": 270, "fq_dict": 6, "fqatrl": 0, "fr": [13, 15, 17, 153, 182, 245], "frac": [4, 6, 11, 12, 16], "fracsampl": [79, 80], "fraction": [23, 80, 264, 265, 270, 290], "fractur": 260, "fragaria": 23, "fragil": 24, "fragment": [7, 8, 20, 22, 27, 32, 83, 88, 104, 133, 140, 169, 214, 215, 217, 221, 222, 229, 238, 243, 250, 268, 270, 278], "fragment1": 140, "fragment2": 140, "fragment_data": 140, "fragment_s": 104, "fragmentmapp": [27, 133], "frame": [0, 4, 13, 20, 22, 27, 30, 69, 71, 218, 222, 236, 237, 261, 281], "frame_shift_penalti": [68, 69], "frameshift": [13, 71, 222, 272, 281], "frameshift_minus_one_scor": 13, "frameshift_minus_scor": 13, "frameshift_minus_two_scor": 13, "frameshift_one_scor": 13, "frameshift_plus_one_scor": 13, "frameshift_plus_scor": 13, "frameshift_plus_two_scor": 13, "frameshift_scor": [13, 30], "frameshift_two_scor": 13, "framework": [3, 5, 26, 32, 177, 307], "francisco": 83, "franck": 7, "frank": [2, 130, 269], "frederick": 2, "free": [3, 5, 6, 7, 11, 15, 19, 24, 69, 87, 88, 93, 137, 172, 197, 244, 250, 270, 272], "freedom": 202, "freeli": [2, 5, 7, 9, 27, 83], "frefix": 270, "freier": 264, "freq": [11, 80], "freqsfrom": [79, 80], "frequenc": [11, 12, 13, 27, 30, 31, 32, 34, 80, 132, 181, 182, 202, 203, 265, 275, 281, 283, 286, 290, 293], "frequencypositionmatrix": [27, 283, 290], "frequent": [1, 11, 251, 265], "frg": 32, "fri": 0, "frick": 2, "friedberg": [2, 26], "friend": [7, 19], "friendli": 7, "frog": 250, "from": [2, 3, 4, 6, 8, 9, 10, 14, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 29, 30, 31, 32, 40, 41, 45, 47, 50, 52, 53, 54, 55, 56, 57, 58, 59, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 76, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 99, 100, 102, 104, 108, 109, 111, 112, 113, 114, 115, 116, 117, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 132, 135, 136, 137, 139, 140, 144, 146, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 160, 165, 166, 168, 169, 170, 171, 172, 173, 174, 176, 177, 180, 182, 183, 185, 186, 190, 193, 194, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 206, 207, 209, 210, 214, 215, 216, 217, 218, 219, 220, 221, 222, 224, 225, 226, 232, 236, 237, 238, 240, 242, 245, 247, 248, 249, 251, 252, 253, 254, 255, 256, 258, 260, 261, 263, 264, 265, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 283, 286, 287, 288, 289, 290, 291, 292, 293, 295, 296, 297, 298, 299, 303, 305, 306, 307], "from_byt": [30, 36], "from_clad": [181, 183, 197], "from_hex": [181, 183], "from_level": 104, "from_msa": [279, 280], "from_nam": [181, 183], "from_seq": [279, 281], "from_seqfeatur": [181, 197], "from_seqrecord": [181, 197], "from_stat": 108, "from_str": [0, 30, 36, 181, 185, 188, 190], "from_tre": [17, 181, 197], "fromstr": [27, 237], "front": [183, 236], "frozen": 23, "frozenset": [30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 68, 219, 220, 221, 223, 224, 225, 226, 230, 231, 232, 233, 236, 237, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259, 281, 291], "fruit": 13, "frustrat": 19, "frutig": 263, "fsa": 182, "fseqboot": 80, "fseqbootcommandlin": [27, 79, 80], "fsm": [30, 32], "fst": [202, 203], "ft": [94, 182, 245], "ftable_doc": 245, "ftid": 272, "ftitmytslh": 250, "ftp": [6, 7, 8, 15, 22, 23, 25, 76, 90, 93, 94, 153, 277], "ftreedist": 80, "ftreedistcommandlin": [27, 79, 80], "ftvtmytsmh": 250, "ftvtmytsmn": 250, "fuchsia": 183, "fucosyltransferas": 113, "fujii": 25, "fulfil": [0, 3], "full": [0, 3, 4, 6, 8, 9, 10, 12, 13, 14, 15, 17, 20, 22, 23, 24, 25, 32, 45, 59, 67, 80, 104, 108, 123, 131, 135, 139, 140, 152, 155, 168, 188, 197, 217, 221, 226, 229, 236, 237, 238, 256, 257, 260, 261, 269, 278, 281, 288], "full_id": [15, 139], "full_rf_tabl": 281, "full_sequ": [14, 297], "full_transl": [279, 281], "fullhelp": [30, 32], "fulli": [11, 21, 22, 23, 36, 73, 169, 260, 270, 278, 288, 305], "fullnam": [7, 135, 162], "fun": [8, 19], "function": [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 35, 36, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 73, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 99, 100, 104, 105, 108, 109, 110, 112, 113, 114, 116, 119, 120, 121, 122, 123, 127, 130, 138, 149, 169, 172, 176, 182, 183, 185, 186, 188, 190, 191, 194, 198, 201, 204, 205, 209, 217, 218, 237, 238, 240, 241, 244, 245, 247, 248, 249, 250, 251, 253, 255, 256, 259, 260, 261, 262, 263, 269, 270, 271, 272, 273, 274, 277, 278, 280, 282, 283, 290, 291, 292, 297, 298, 299, 300, 303, 305], "fund": 19, "further": [0, 3, 4, 5, 6, 7, 11, 15, 20, 61, 68, 69, 89, 91, 99, 104, 169, 182, 237, 252, 258, 260, 303], "furthermor": [8, 20, 237, 278], "fusion": 197, "futur": [0, 3, 7, 15, 16, 23, 27, 30, 32, 67, 68, 69, 70, 80, 83, 92, 177, 182, 209, 236, 237, 260, 270, 277, 285], "fuzzi": [6, 92, 237], "fuzznuc": 80, "fuzznuccommandlin": [27, 79, 80], "fuzzpro": 80, "fuzzprocommandlin": [27, 79, 80], "fwghkhffsshfssqmvsegfgvileipfssqlvssleekkipkyqnlrsihsifpfl": 7, "fwsqpyrihikqlsnysfsflgyfssvlenhlvvrnqmlensfiinlltkkfdtiapv": 7, "g": [0, 1, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, 24, 30, 31, 32, 53, 56, 62, 66, 67, 68, 69, 70, 73, 76, 80, 88, 94, 99, 104, 108, 109, 119, 123, 129, 132, 135, 137, 139, 145, 146, 149, 152, 153, 155, 158, 159, 162, 164, 169, 172, 179, 180, 182, 183, 197, 199, 202, 203, 209, 210, 211, 212, 214, 215, 216, 217, 221, 226, 229, 236, 237, 238, 241, 247, 248, 249, 250, 251, 253, 260, 261, 263, 264, 265, 268, 269, 270, 272, 274, 278, 280, 287, 288, 296, 297, 299], "g116295259": 7, "g116295260": 7, "g13550663": 7, "g13576946": 7, "g16198419": 7, "g16198420": 7, "g219411": 7, "g219412": 7, "g219415": 7, "g219416": 7, "g25137": 68, "g26680": 238, "g26684": 68, "g26685": 238, "g29385": 238, "g45501306": 7, "g45501307": 7, "g47115198": 7, "g47115199": 7, "g59899": 7, "ga": [0, 13, 14, 30, 53], "gaa": [0, 7, 22, 76], "gaaa": [0, 13, 30], "gaaaaggaaagtacggcccggccactccgggtgtgtgctaggagggctta": 0, "gaaattgtat": 278, "gaac": 14, "gaact": [13, 30], "gaactgg": 30, "gaacttaacattttcttatgacgtaaatgaagtttatatataaatttcctttttattgga": 23, "gaactttggc": 7, "gaagaggaaaagtagatccctggcgtccggagctgggacgt": 0, "gaaqtcsatlagnhlmrda": 0, "gaattactat": 240, "gaattc": [8, 260], "gabor": 2, "gabriel": 262, "gac": [14, 22], "gacagctag": 12, "gaccagagcctcgcatggggg": 283, "gaccctgatttgttgttgggccgcctcgggagcgtccatggcgggt": 23, "gacct": 30, "gacctg": 30, "gacgaaagtattaat": 222, "gacgccggggat": 283, "gacgscwtf": 0, "gacttaatagcc": 0, "gae": 23, "gaf": [276, 277], "gaf20field": 277, "gafbyproteiniter": [27, 276, 277], "gafiter": [27, 276, 277], "gag": [22, 76], "gagatcagagggccg": 283, "gagatctccgccc": 199, "gagatttactgactttcctagaatagtttctctactggaaacctgatgcttttataagccattgtgatta": 238, "gagatttccgcct": 199, "gagavivgsdpdlsverplyelvwtgatllpdsegaidghlrevgltfhllkdvpglisk": [21, 23], "gagcqsggcdg": 0, "gagggtgttgatcatgatgatggcg": 251, "gahageygaeal": 13, "gain": [14, 197], "gained_count": 197, "gainesvil": 7, "gamma": [0, 12, 30, 79, 80, 172, 181, 182, 199, 241, 280], "gammacoeffici": [79, 80], "gammai": 182, "gammalogtopaup": 182, "gander": 3, "gap": [3, 7, 9, 12, 14, 20, 27, 30, 31, 32, 33, 39, 42, 43, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 68, 69, 71, 79, 80, 129, 158, 166, 182, 197, 218, 221, 222, 236, 237, 240, 260, 261, 270, 281, 295, 297], "gap_a_fn": 297, "gap_b_fn": 297, "gap_char": [279, 281, 297], "gap_consensu": [30, 31], "gap_extend": [3, 268, 270], "gap_funct": 297, "gap_num": [20, 218], "gap_open": [3, 268, 270], "gap_penalti": [0, 71], "gap_scor": [12, 13, 30], "gap_trigg": [68, 69, 71], "gap_x_dropoff": 71, "gap_x_dropoff_fin": 71, "gapcost": [68, 70], "gapdist": [30, 32], "gapext": [30, 32], "gapextend": [12, 30, 32, 67, 68, 69, 79, 80], "gaplimit": [79, 80], "gaponli": [128, 129], "gapopen": [12, 30, 32, 67, 68, 69, 79, 80, 218], "gapopen_num": [218, 221], "gappenalti": [79, 80], "gaprat": [30, 32], "garcia": 2, "gari": 2, "gascuel": [65, 182], "gaston": 2, "gat": [13, 22, 30, 222], "gatacgcagtcatattttttacacaattctctaatcccgacaaggtcgtaggtc": 21, "gatatcaagg": 7, "gatc": [21, 76], "gatcctcaaa": 7, "gatcg": 22, "gatcgatgggcctatataggatcgaaaatcgc": 22, "gatctggacc": 7, "gatgacggtgt": 6, "gatgggaaacccatggccgagtgggaagaaaccagctgaggtcacatcaccagaggagggagagtgtggcccctgactcagtccatcagcttgtggagctg": 0, "gatgggcc": 22, "gatgtgcaatacctttgtagaggaa": 251, "gather": [22, 53], "gattattaga": 7, "gattgctttt": 7, "gatttctcgg": 7, "gattttgggg": 7, "gau": 66, "gauc": 76, "gaugagggu": 66, "gaugagggucucuac": 66, "gave": [7, 8, 12, 19, 71], "gavlimfpstcnqywdehkr": [15, 169], "gb": [0, 1, 3, 6, 7, 8, 12, 13, 21, 23, 30, 32, 68, 83, 92, 237, 238, 245, 260, 278], "gb_base_ind": [92, 93], "gb_feature_ind": [92, 93], "gb_feature_internal_ind": [92, 93], "gb_internal_ind": [92, 93], "gb_line_length": [92, 93], "gb_other_internal_ind": [92, 93], "gb_sequence_ind": [92, 93], "gb_vrl": 23, "gbgtw": 11, "gbk": [3, 7, 8, 19, 23], "gbrel": 93, "gbrows": 305, "gbseq_access": 7, "gbseq_creat": 7, "gbseq_definit": 7, "gbseq_divis": 7, "gbseq_featur": 7, "gbseq_length": 7, "gbseq_locu": 7, "gbseq_moltyp": 7, "gbseq_organ": 7, "gbseq_oth": 7, "gbseq_primari": 7, "gbseq_refer": 7, "gbseq_sequ": 7, "gbseq_sourc": 7, "gbseq_stranded": 7, "gbseq_taxonomi": 7, "gbseq_topologi": 7, "gbseq_upd": 7, "gbvrl": 23, "gbvrl1": 23, "gbvrl2": 23, "gbvrl3": 23, "gbvrl38": 23, "gbvrl4": 23, "gbwithpart": 7, "gc": [0, 8, 11, 12, 22, 23, 30, 53, 66, 76, 80, 261, 264, 290], "gc123": [27, 261], "gc_content": [283, 290], "gc_fraction": [0, 6, 22, 27, 30, 261], "gc_frame": 261, "gc_map": [30, 53], "gc_skew": [27, 261], "gc_valu": 6, "gca": [22, 76], "gcaaggcttctacacccgtactcgaatg": 264, "gcaattatcc": 7, "gcacaagcat": 7, "gcacaggctgcggaaattacgttagtcccgtcagtaaaattacagataggcgatcgtgat": 22, "gcacgtccctgagca": 283, "gcagctgaaaaca": 0, "gcataatttgtggtagtgggggactgcgttcgcgctttcccctg": 30, "gcatt": 11, "gcc": [5, 19, 22, 23], "gccacgtaatgggccgctgaaagggtgcccga": 22, "gccactagcagagcagggggc": 283, "gccatcgtaatgggccgctgaaagggtgcccga": 22, "gccattgtaatgggccgctgaaagggtgcccga": 22, "gcccagttcgttcagttgtg": 62, "gcccatatatgg": [11, 283], "gccggttgctgttcattagg": 283, "gcclamp": [79, 80], "gcg": [22, 27, 32, 48, 56, 63, 76, 261, 262], "gcg_checksum": 262, "gcgattttcgatcctatataggcccatcgatc": 22, "gcgctcagccggagtgtcccgggccctgc": 0, "gcgctcagccggagtgtcccgggccctgctttcctttt": 0, "gcgctggag": 13, "gcggcatgtgaaa": 11, "gcgta": 11, "gck": [238, 242], "gckio": [27, 238], "gckiter": [27, 238, 242], "gclmkkssivatiitilsgsanaassqlip": 6, "gcngglp": 0, "gcngglpsqafeyikyng": 0, "gcngglpsqafeyikynggidteesypykgvngv": 0, "gcq": 0, "gcqgglp": 0, "gcqgglpsqafeyilynk": 0, "gcqgglpsqafeyilynkgimgedtypyqgkdgi": 0, "gct": [22, 236], "gctaa": 236, "gctagcggagtgtatactggcttactatgttggcactgatgagggtgtcagtga": 260, "gctgtagtaag": 22, "gctgttatgggtcgttggaagggtggtcgtgctgctggttag": 22, "gcttatgtaa": [11, 283], "gcu": 236, "gcuaa": 236, "gcuguuaugggucguuggaaggguggucgugcugcugguuag": 22, "gd": 7, "gd_diagram": 8, "gd_feature_set": 8, "gd_labels_default": 8, "gd_track_for_featur": 8, "gdai": 197, "gdb": 7, "gdct": 104, "gdd": [8, 104], "gddiagram": 8, "gde": 32, "gdfeatureset": 8, "gds16": 7, "gds_featur": 8, "gdt_featur": 8, "gdutil": 8, "gdvv": 261, "ge": [7, 13], "geal": 14, "gee": 0, "geez": 3, "geffer": 2, "geialwslvv": 250, "gemkeqtewhrvvlfgklaevaseylrkgsqvyiegqlrtrkwtdq": 260, "gen": 18, "gen_kei": [133, 169], "gen_tupl": [133, 169], "genafpair": [30, 32], "genbank": [3, 6, 8, 9, 22, 24, 27, 32, 68, 80, 104, 237, 238, 245, 256, 260, 274, 275, 278], "genbank_ind": [92, 94], "genbank_spac": [92, 94], "genbankcdsfeatureiter": [27, 238, 245], "genbankiter": [27, 238, 245], "genbankscann": [27, 92, 94], "genbankwrit": [27, 238, 245], "gene": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 17, 19, 21, 22, 23, 27, 34, 73, 96, 99, 104, 111, 113, 115, 117, 119, 123, 182, 197, 202, 237, 238, 242, 260, 273, 274, 275, 277, 280], "gene2xml": 7, "gene_associ": 277, "gene_color": 8, "gene_descript": 10, "gene_id": [7, 10, 275], "gene_identifi": 10, "gene_nam": [25, 272], "gene_record": 260, "gene_symbol": 10, "geneclust": [4, 73], "geneid": [4, 7, 21, 73, 94, 260, 278], "genellina": 262, "genenam": [4, 7, 73], "geneontologi": 277, "genepop": [27, 200], "genepop_dir": [202, 203], "genepopcontrol": [200, 201, 202, 203], "gener": [0, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 42, 44, 45, 52, 55, 56, 59, 60, 61, 66, 67, 68, 71, 76, 80, 83, 91, 93, 96, 99, 100, 107, 108, 109, 110, 116, 123, 125, 126, 127, 132, 139, 158, 168, 169, 176, 178, 182, 183, 185, 186, 188, 190, 197, 198, 205, 217, 218, 222, 237, 238, 239, 241, 242, 244, 245, 246, 247, 251, 252, 253, 254, 256, 258, 259, 260, 261, 264, 269, 270, 272, 273, 274, 283, 288, 290, 296, 297, 299], "genera": 19, "generic_by_id": 76, "generic_dbutil": [301, 304], "genericpositionmatrix": [27, 283, 290], "genesymbol": 0, "genet": [0, 2, 6, 13, 22, 26, 30, 50, 65, 69, 76, 80, 99, 190, 199, 200, 236, 237, 260, 261, 264, 307], "genetic_cod": [68, 70, 261], "geneticcod": 7, "genetre": 4, "genic": 202, "genom": [0, 2, 3, 7, 8, 10, 11, 13, 20, 21, 22, 30, 32, 35, 36, 37, 38, 39, 46, 51, 52, 61, 79, 80, 93, 104, 111, 115, 119, 197, 200, 221, 237, 238, 245, 247, 270, 275, 278], "genome2genom": [42, 222], "genome_align": 0, "genomediagram": [2, 7, 9, 26, 27, 98, 99, 123, 307], "genomeprj": 7, "genomeproject": 21, "genotyp": [202, 203, 270], "genpept": [7, 238], "gensat": 7, "genu": [93, 132, 197], "genuin": 20, "geo": 27, "geodet": 197, "geodetic_datum": 197, "geograph": [197, 198], "geometr": [4, 139], "geometri": [139, 169], "georg": 2, "gerald": 2, "germ": 0, "get": [3, 5, 6, 7, 8, 10, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 30, 31, 32, 34, 49, 54, 60, 64, 67, 68, 70, 75, 76, 82, 83, 85, 92, 93, 97, 104, 108, 109, 117, 119, 132, 139, 140, 149, 154, 156, 159, 164, 169, 171, 175, 179, 180, 182, 183, 197, 199, 202, 204, 205, 209, 214, 216, 236, 237, 238, 245, 246, 248, 251, 252, 253, 258, 260, 265, 274, 276, 278, 280, 281, 296, 297, 299, 300, 303], "get_acc": 23, "get_access": 23, "get_acgt": [283, 296], "get_alignment_length": [12, 27, 30, 56, 59], "get_all_assembli": [133, 149], "get_all_entri": [133, 149], "get_all_obsolet": [15, 133, 149], "get_allel": [201, 203], "get_allele_frequ": [201, 203], "get_alleles_all_pop": [201, 203], "get_aln_length": [279, 280], "get_altloc": [15, 133, 135], "get_amino_acids_perc": [261, 265], "get_angl": [15, 133, 169], "get_anis": [15, 133, 135], "get_area": [27, 298, 300], "get_arrai": [133, 176], "get_artemis_colorschem": [98, 104], "get_atom": [15, 133, 136, 144, 155, 160], "get_avg_fi": [201, 203], "get_avg_fst_pair": [201, 203], "get_avg_fst_pair_locu": [201, 203], "get_basic_info": [201, 203], "get_bfactor": [15, 133, 135], "get_blank_emiss": [106, 108], "get_blank_transit": [106, 108], "get_ca_list": [133, 154], "get_chain": [133, 144, 160], "get_charg": [133, 135], "get_codon": [279, 281], "get_codon_num": [279, 281], "get_color": [27, 98, 100], "get_color_dict": [27, 98, 100], "get_colorschem": [98, 104], "get_column": [30, 31, 298, 299], "get_coord": [15, 133, 135, 140], "get_data": [98, 104, 128, 130], "get_dbutil": [301, 304], "get_dist": [181, 199], "get_dn_ds_matrix": [279, 280], "get_dn_ds_tre": [279, 280], "get_drawn_level": [98, 104], "get_f_stat": [201, 203], "get_featur": [8, 98, 104], "get_fi": [201, 203], "get_from_decod": [133, 171], "get_full_id": [15, 133, 135, 139], "get_full_rf_t": [279, 281], "get_fullnam": [15, 133, 135], "get_genotype_count": [201, 203], "get_gi": 238, "get_graph": [98, 104], "get_guide_coord_from_structur": [133, 166], "get_head": [15, 133, 151], "get_heterozygosity_info": [201, 203], "get_id": [15, 98, 104, 128, 130, 133, 135, 139, 140], "get_indiv": [200, 201, 205], "get_individu": [201, 204], "get_init_rm": [27, 133, 175, 216], "get_iter": [133, 139, 161], "get_kgml": [115, 117], "get_length": [15, 133, 169], "get_level": [98, 104, 133, 135, 139], "get_list": [15, 133, 139], "get_map": [133, 161], "get_markov_model": [106, 108], "get_matrix_by_nam": 288, "get_model": [133, 160], "get_multilocus_f_stat": [201, 203], "get_nam": [15, 133, 135], "get_node_info": [181, 185], "get_nontermin": [17, 181, 183], "get_occup": [15, 133, 135], "get_par": [15, 133, 135, 139], "get_path": [17, 181, 183], "get_phi_psi_list": [133, 154], "get_predict": [27, 133, 164], "get_prev": [128, 130], "get_prodoc_entri": [25, 27, 85], "get_property_valu": [283, 296], "get_prosite_entri": [25, 27, 85], "get_prosite_raw": [25, 27, 85], "get_qresult_id": [222, 223, 224, 225], "get_radiu": [133, 135], "get_raw": [6, 23, 217, 218, 219, 220, 221, 222, 224, 225, 226, 229, 232, 238, 298, 299], "get_recent_chang": [133, 149], "get_residu": [15, 30, 31, 133, 136, 144, 160, 169], "get_resnam": [15, 133, 154, 155], "get_resname_list": [133, 140], "get_rm": [27, 133, 175, 216], "get_rotran": [27, 133, 175, 216], "get_row": [298, 299], "get_scor": [181, 199], "get_segid": [15, 133, 155], "get_segment_info": [98, 102], "get_seq": [133, 153], "get_seq_by_acc": [301, 303], "get_seq_by_id": [301, 303], "get_seq_by_v": [301, 303], "get_seqres_fil": [133, 149], "get_seqs_by_acc": [301, 303], "get_sequ": [15, 133, 154], "get_serial_numb": [133, 135], "get_set": [98, 104], "get_sigatm": [15, 133, 135], "get_sign": [298, 299], "get_siguij": [15, 133, 135], "get_spherical_coordin": [27, 133, 176], "get_splic": [56, 61], "get_sprot_raw": [23, 25, 27, 85], "get_start_end": [27, 128, 129], "get_status_list": [133, 149], "get_structur": [15, 133, 137, 140, 143, 148, 150, 151, 154, 156, 157, 162, 165, 169, 170, 171, 173], "get_structural_models_for": [27, 133, 164], "get_structure_from_url": [15, 133, 171], "get_subseq_as_str": [301, 303], "get_succ": [128, 130], "get_support": [27, 181, 186], "get_surfac": [15, 27, 133, 156], "get_tau_list": [133, 154], "get_taxa": [128, 132], "get_temp_imagefilenam": [27, 98, 105], "get_termin": [17, 128, 132, 181, 183], "get_text": [283, 296], "get_theta_list": [133, 154], "get_tim": [298, 299], "get_track": [98, 104], "get_trail": [15, 133, 151], "get_transform": [27, 133, 175, 216], "get_unique_par": [27, 133, 159], "get_unpacked_list": [15, 133, 136, 155], "get_vector": [15, 133, 135], "getascend": [27, 209], "getascendentfromsql": [27, 209], "getastraldomainsfromfil": [27, 209], "getastraldomainsfromsql": [27, 209], "getatom": [209, 214], "getattr": 16, "getchildren": [27, 209], "getdescend": [27, 209], "getdescendentsfromsql": [27, 209], "getdomain": [27, 209], "getdomainbysid": [27, 209], "getdomainfromsql": [27, 209], "getnodebysunid": [27, 209], "getpar": [27, 209], "getroot": [27, 209], "getseq": [27, 209], "getseqbysid": [27, 209], "getseqmap": [209, 214], "getter": 169, "getvalu": [0, 12, 23, 56, 238, 253], "gevalwslvv": 250, "gf": [0, 53, 66], "gf_map": [30, 53], "gfa": 243, "gfa1": [238, 243], "gfa1iter": [27, 238, 243], "gfa2": [238, 243], "gfa2iter": [27, 238, 243], "gfaio": [27, 238], "gff": 274, "gff3": 237, "gfiarefnrk": 250, "gfpvnfltlf": 250, "gg": [0, 30], "gga": [21, 22, 76], "ggaaacaaagtttttctcaacatag": 251, "ggactacgacaatagctcagg": 12, "ggactc": 0, "ggatcc": 8, "ggatctacttttcctcttc": 0, "ggatgactgttacaggcttagctttgtgtgaaanccagtcacctttctcctaggtaatgagtagtgctgt": 238, "ggaucuucggaucu": 261, "ggc": 22, "ggcaccctggaggccatccagtggaccaagcactgggactccggcatc": 13, "ggcaccctggaggccatccagtggtccaagcactgggactccggcatc": 13, "ggege8bb": 0, "ggg": [0, 3, 20, 22, 76], "gggaatgttaaccaaatga": 0, "gggaggagatcgccccaaacgtatggtgagtcgggcg": 62, "gggccgcuga": 261, "gggccgtac": 0, "gggcgaacgtataaaccattctg": 62, "gggg": [0, 13, 30], "ggggatgctaagccaatgagttgttgtctctcaatgtg": 0, "gggggg": [0, 13, 30], "ggggtatttt": 7, "gggt": 30, "gggta": 11, "gggtt": [11, 30], "ggh": 241, "gghvnpavtfgafvggnitllrgivyiiaqllgstvaclllkfvtndmavgvfslsagvg": 260, "ggt": [0, 22, 23, 30], "ggtaccctggaggccatccagtggtccaagcactgggactccggcatc": 13, "ggtaccgggccccccctcgaggtcgacggtatcgataagcttgatatcgaattc": 207, "ggtaccgggccccccctcgaggtcgacggtatcgataagcttgatatcgaattcctg": 206, "ggtcatccta": 7, "ggtctacatgttggttaacc": 253, "ggtgcagagccgagtcacggggttgccagcacagg": 0, "ggtggggg": 0, "ggtt": [13, 22], "ggttacacttaccgataatgtctctgatga": 237, "ggtttgagaaagagaaatgagataa": 251, "ggtttt": 0, "ggua": 66, "ggug": 66, "ggwktcsgtcttststrhrgrsgw": 0, "ggwktcsgtcttststrhrgrsgwsartttaaclrasrksmraacsrsag": 0, "ghnvetikgmipdg": 0, "gi": [0, 1, 3, 7, 12, 13, 19, 20, 21, 23, 30, 56, 68, 69, 70, 93, 94, 217, 218, 238, 241, 256, 260, 275, 303], "gi_al": 218, "gi_list": 7, "gi_mask": [68, 69], "gi_mask_nam": [68, 69], "gi_str": 7, "gibson": 32, "gidteesypi": 0, "gidteesypykgvngv": 0, "gif": [8, 104], "giideibcff": 0, "giklfkkfa": 12, "giklfkkft": 12, "giklfkkfv": 12, "gilist": [68, 69], "gimgedtypi": 0, "gimgedtypyqgkdgi": 0, "gina": 2, "giqtessypi": 0, "giqtessypytaetgtqcnfnsanigakisnftmip": 0, "gish": 2, "github": [5, 9, 27, 140, 227, 234, 243], "githubusercont": [4, 25], "give": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 19, 21, 22, 23, 24, 27, 30, 35, 46, 51, 56, 61, 67, 68, 70, 71, 83, 94, 99, 100, 104, 107, 112, 113, 114, 117, 122, 126, 132, 214, 217, 237, 238, 241, 250, 251, 260, 269, 271, 274, 278, 282, 297, 298, 299, 303], "given": [0, 4, 6, 7, 8, 11, 12, 14, 15, 17, 20, 22, 23, 30, 31, 32, 34, 56, 60, 64, 69, 71, 73, 76, 83, 91, 94, 102, 104, 108, 116, 119, 120, 121, 122, 126, 127, 129, 136, 139, 140, 146, 149, 150, 159, 162, 169, 171, 180, 182, 183, 185, 186, 187, 188, 190, 191, 197, 199, 201, 203, 209, 214, 217, 219, 221, 224, 225, 232, 236, 237, 238, 245, 251, 253, 257, 261, 262, 263, 264, 265, 270, 281, 282, 283, 288, 290, 294, 297, 299, 300, 303, 305], "gkg108": 2, "gkheerqdeh": 250, "gkp1137": [2, 251], "gl": 13, "glai": 206, "glenn": 2, "gln": 13, "glncsffsicnwkfidyinrlfqiiylckn": 6, "glob": [23, 217, 238], "global": [4, 12, 13, 14, 17, 30, 80, 83, 109, 183, 202, 203, 226, 262, 297], "global_dtd_dir": [83, 84], "global_xsd_dir": [83, 84], "globald": 14, "globaldx": 297, "globalm": 297, "globalmc": 297, "globalmx": 297, "globalpair": [30, 32], "globalxx": [14, 297], "glossari": [127, 282], "glpinfmtlf": 250, "glpinfmtli": 250, "gltpfngyta": 0, "gltpfngytaatwtrtavssvgmnipyhgasylvrnqelrswtaadkaaqmpwr": 0, "gltpfngytaatwtrtavssvgmnipyhgasylvrnqelrswtaadkaaqmpwrrnrqsc": 0, "gltpsngyta": 0, "gltpsngytaatwtrtaassvgmnipydgasylvrnqelrswtaadkaaqmpwrrnmqsc": 0, "gltpssgyta": 0, "gltpssgytaatwtrtavssvgmnipyhgasylvrnqelrswtaadkaaqmpwrrnrqsc": 0, "glu": [13, 15], "gluconeogenesi": 116, "glucos": 3, "glue": [8, 214], "glutam": 13, "glutamin": 13, "gly": [13, 15, 140, 169], "gly_cbeta": [15, 133, 169], "gly_onli": 15, "glycan": [119, 274], "glycin": [3, 15, 20, 169], "glycolysi": 116, "glyconnect": 272, "glycoprotein": 113, "glycosyl": 272, "glyselect": 15, "gmonth": 197, "gmonthdai": 197, "gn": 123, "gnfvspvknq": 0, "gnl": 218, "gnm_terminu": 275, "gnu": [23, 278], "gnvl": 13, "go": [0, 1, 3, 4, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 67, 99, 109, 197, 234, 238, 251, 273, 274, 277, 307], "goa": [27, 276], "goa_uniprot": 277, "goa_yeast": 277, "goal": [20, 217], "goe": [4, 24, 27, 84, 149], "gojobori": [2, 13, 34, 281], "gol": 0, "gold": [0, 2, 183], "goldenpath": [0, 36, 37, 38, 39, 221], "goldman": [2, 13, 32, 34, 182, 281], "goldman1994": [2, 13], "goldsack": 265, "golub": [2, 15, 216], "golub1971": [2, 4], "golub1989": [2, 15], "gompertz": [16, 27, 298, 299, 300], "goncalo": 2, "gone": 260, "gonnet": [2, 32], "gonnet1992": 199, "gonzalez": 7, "good": [3, 5, 6, 7, 8, 12, 15, 19, 20, 23, 24, 109, 251, 270], "good_bas": [268, 270], "good_qual": 6, "good_read": 6, "goodi": 7, "googl": [17, 19, 197], "gorder": [4, 73], "got": [0, 3, 5, 6, 7, 8, 12, 19, 20, 241, 278], "goto": [2, 111, 115, 119, 251], "gotoh": [13, 30], "gov": [3, 7, 8, 12, 19, 22, 23, 68, 70, 71, 76, 83, 93, 94, 96, 97, 218, 234, 245, 253, 262, 272], "gp": [0, 7, 23, 201], "gp_inform": 277, "gpa": [276, 277], "gpa_iter": [27, 276, 277], "gpad": 277, "gpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgyc": 0, "gpi": [3, 276, 277], "gpi_iter": [27, 276, 277], "gpipe": 68, "gpl": 5, "gpl28": 7, "gplaiaadav": 0, "gpssr": 0, "gpyppsvdwrkkgnfvspvknqgacgscwtf": 0, "gpyppsvdwrkkgnfvspvknqgacgscwtfsttgalesaiaiatgkmlslaeqqlvdcaqdfnni": 0, "gpytdftp": 68, "gqcgscwsf": 0, "gr": [0, 2, 12, 13, 14, 53, 66, 123], "gr_map": [30, 53], "grab": [7, 25], "gradat": 100, "gradient": 263, "gradual": 6, "graem": 2, "graham": 2, "grai": [6, 17, 183], "grain": 13, "grand": 265, "grandchild": 130, "grant": 123, "graph": [6, 8, 103, 104, 117, 177, 178, 180, 185], "graph_id": 104, "graphdata": [98, 104], "graphic": [4, 9, 12, 17, 26, 27, 111, 115, 117, 183, 197, 238, 243, 261, 307], "graphset": [8, 98, 104], "grasp": 21, "grate": 5, "gravi": [261, 265], "great": [5, 7, 23, 272], "greater": [3, 17, 19, 21, 31, 32, 135, 136, 139, 152, 169, 182, 241, 260, 275], "greatli": [5, 270], "greedi": 69, "green": [0, 4, 8, 17, 104, 181, 183, 198], "greener": 133, "greenhous": 19, "grei": [8, 104, 183], "grep": 6, "greytrack": [8, 104], "greytrack_font": 104, "greytrack_font_color": 104, "greytrack_font_colour": 104, "greytrack_font_rot": 104, "greytrack_fonts": 104, "greytrack_label": 104, "gri_agm677": 244, "grid": [4, 73], "griseu": 3, "grishin": [2, 74], "gritti": 21, "grossli": 20, "ground": 23, "group": [0, 4, 9, 11, 15, 30, 32, 84, 103, 117, 132, 139, 172, 199, 217, 221, 226, 251, 270, 272, 288], "group_nam": 172, "group_numb": 172, "group_typ": 172, "grouping_constraint": [181, 182], "groupsiz": [30, 32], "grow": [11, 20], "grown": [6, 16], "growth": [16, 300], "grusonia": 23, "gs_map": [30, 53], "gse16": 7, "gse16_famili": 7, "gse21512": 11, "gskgcatgtgaaa": [11, 291], "gsl": 254, "gst": 0, "gt": [0, 30, 68, 182, 222], "gta": [0, 22, 76], "gtaacagaaaataaaatttaaatagaaacttaaaggcc": 0, "gtaacagaaaataaaatttaaatagaagcttaaaggct": 0, "gtac": 22, "gtat": 31, "gtataatttgtggtagtgggggactgcgttcgcgctatcccccg": 30, "gtatc": [30, 31], "gtatcaacag": 7, "gtatcagaag": 7, "gtattatttaatggcatacactcaa": 251, "gtc": [0, 22], "gtcagc": 12, "gtcagctag": 12, "gtccatcgcaaagcgtggggc": 283, "gtcccagtattcggatttgtctgccaaaacaatgaaattgacacagtttacaac": 6, "gtg": [12, 22, 76, 236], "gtgaaaaagatgcaatctatcgtactcgcactttccctggttctggtcgctcccatggca": 22, "gtgcaagtat": 278, "gtgccctaagcatactaggcg": 283, "gtgccgttaccatcggtgacgaaagtattaat": 222, "gtggccattgtaatgggccgc": 236, "gtggccattgtaatgggccgctgaaagggtgcccgatag": 236, "gtgta": 11, "gtleaiqwskhwdsgi": 13, "gtleaiqwtkhwdsgi": 13, "gtr": [4, 73, 181, 182], "gtrcat": 182, "gtrcat_gamma": 182, "gtrcat_gammai": 182, "gtrfreq": [181, 182], "gtrgamma": 182, "gtrgammai": 182, "gtrmix": 182, "gtrmixi": 182, "gtrrate": [181, 182], "gtt": [0, 22, 30], "gttacccgg": 11, "gttctaccacaaaagaaaaagagactttggggtttggtagtttgtcataacactactccg": 260, "gttgcttctggcgtgggtggggggg": [238, 251], "gttgtaattc": 7, "gttgtctcttatggtg": 0, "gttt": 0, "gttttggagt": 7, "gttttt": 0, "gua": 76, "guanidinium": 53, "guarante": [4, 11, 83, 108, 109, 183, 218, 288], "gucgugaau": 66, "guess": [3, 6, 7, 12, 15, 20, 21, 23, 149, 222, 300], "guess_lag": [27, 298, 300], "guess_plateau": [27, 298, 300], "guest": 288, "gug": 76, "gui": [2, 4, 7, 9, 222, 265], "guiba": 140, "guid": [3, 8, 12, 32, 166, 218, 221, 226, 229], "guidelin": [3, 5, 23, 104, 119, 274], "guidetre": 32, "guidetree_in": [30, 32], "guidetree_out": [30, 32], "guindon": [65, 182], "gunzip": [15, 23], "guruprasad": 265, "gv": [15, 137], "gva": 6, "gvltvngprk": 250, "gweight": [4, 73], "gyear": 197, "gyearmonth": 197, "gyfifgptgc": 250, "gyfvfgptmc": 250, "gyfvfgqtgc": 250, "gygekngi": 0, "gygvengv": 0, "gymnosperm": 17, "gysakntifr": 0, "gytyr": 237, "gz": [1, 4, 6, 7, 15, 23, 25, 94, 277], "gzip": [1, 4, 7, 23, 25, 217, 238, 270, 278], "g\u00e9raldin": 2, "g\u00f6\u00dfling": 2, "h": [2, 3, 7, 12, 13, 14, 15, 16, 17, 22, 23, 25, 32, 68, 69, 71, 80, 113, 137, 145, 152, 153, 162, 169, 182, 251, 260, 261, 268, 270, 272, 275, 299], "h0": 0, "h01": [16, 299], "h02": 299, "h03": 299, "h05": 299, "h1": [0, 125, 126, 169], "h12": 299, "h1d_map": 169, "h1kei": 169, "h2": 169, "h2aa": 169, "h2kei": 169, "h3": 169, "h_": [11, 15], "h_glc": 15, "h_j": 11, "ha": [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 45, 56, 67, 68, 73, 83, 92, 99, 100, 104, 107, 108, 109, 117, 120, 122, 127, 130, 132, 134, 139, 143, 149, 158, 169, 172, 182, 183, 201, 202, 205, 209, 212, 217, 221, 222, 229, 236, 237, 248, 251, 253, 260, 261, 265, 270, 274, 277, 278, 282, 283, 290, 299], "ha2": 169, "ha3": 169, "hack": [15, 169], "had": [1, 3, 6, 7, 15, 20, 23, 31, 101, 217, 240], "haimov": 265, "half": [20, 53, 61, 84, 99, 141, 182, 217, 221, 265, 275], "hall": 7, "halt": 4, "hamelryck": [2, 7, 9, 15, 26, 133], "hamelryck2003a": [2, 9, 15], "hamelryck2003b": [2, 15], "hamelryck2005": [2, 15], "han": 197, "hand": [0, 3, 7, 8, 11, 12, 13, 15, 19, 20, 21, 22, 23, 25, 84, 264], "handbook": 2, "handi": [7, 15, 25, 134], "handicap": 12, "handl": [0, 3, 5, 6, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 23, 24, 25, 29, 30, 32, 54, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 71, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 99, 101, 103, 104, 112, 113, 114, 116, 118, 119, 121, 123, 126, 129, 132, 137, 143, 152, 158, 169, 172, 182, 183, 185, 188, 190, 191, 198, 199, 201, 205, 209, 210, 211, 212, 213, 214, 217, 219, 220, 221, 222, 223, 224, 225, 226, 228, 230, 231, 232, 233, 235, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 259, 260, 261, 269, 271, 272, 273, 274, 275, 277, 278, 283, 284, 286, 287, 289, 291, 292, 293, 295, 296, 298, 299, 305], "handle_motif": [283, 296], "handleish": 91, "handlemissingdocumentdefinit": [83, 84], "handler": [84, 252], "handsak": 2, "hang": 5, "hansson": 7, "haploid": [201, 202, 203, 204, 270], "happen": [6, 7, 8, 12, 15, 17, 20, 21, 22, 56, 99, 169, 214, 251, 253, 260, 278], "happi": [5, 19], "harald": 2, "hard": [0, 5, 7, 8, 12, 14, 20, 23, 52, 64, 69, 238, 240, 248, 249, 270, 278, 298], "hard_clip_left": [0, 52], "hard_clip_right": [0, 52], "hardi": [18, 202, 203], "hardli": 127, "hare": 197, "haruo": 2, "has_id": [15, 133, 136, 139], "has_missing_residu": 15, "has_support": [128, 132], "hasegawa": 182, "hash": [23, 69, 139, 169, 236, 237, 287], "hash_index": [68, 69], "hashcod": 177, "hasheddomainsbyev": [27, 209], "hasheddomainsbyid": [27, 209], "hasn": [5, 7], "hat": 53, "hatom": 169, "hatoms_needs_upd": 169, "hatomsr": 169, "haubrock": 2, "haunsberg": 2, "haussler": 2, "have": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 35, 36, 37, 38, 43, 46, 47, 51, 56, 61, 62, 66, 67, 68, 69, 71, 72, 73, 80, 83, 92, 94, 99, 102, 104, 107, 108, 109, 117, 123, 135, 136, 137, 143, 144, 146, 148, 149, 152, 154, 155, 157, 158, 160, 168, 169, 170, 172, 173, 175, 176, 182, 183, 191, 195, 197, 199, 202, 205, 207, 214, 217, 218, 221, 222, 229, 236, 237, 238, 246, 247, 251, 253, 260, 261, 264, 265, 270, 278, 285, 288, 290, 297, 299, 300], "haven": [1, 20], "hb": 169, "hb1": 169, "hb2": 169, "hb3": 169, "hba_human": [12, 13, 14], "hbb_human": [12, 13, 14], "hbond": 169, "hc": [11, 295], "hcoordspac": 169, "hcut": 152, "hd": 0, "hd1": 169, "hd11": 169, "hd12": 169, "hd13": 169, "hd2": 169, "hd21": 169, "hd22": 169, "hd23": 169, "hd3": 169, "hdpi": [11, 283], "hdr": 168, "he": 169, "he1": 169, "he2": 169, "he21": 169, "he22": 169, "he3": 169, "head": [7, 8, 15, 104, 174], "header": [0, 11, 13, 15, 27, 32, 33, 40, 42, 43, 45, 46, 47, 51, 52, 56, 59, 60, 61, 68, 71, 94, 126, 151, 152, 162, 168, 169, 172, 174, 204, 209, 217, 221, 223, 224, 225, 238, 244, 246, 247, 248, 253, 259, 270, 277, 278], "header_dict": 15, "header_sam_fil": 270, "header_width": [92, 94, 238, 245], "headlin": 126, "hear": 12, "heat": [8, 104], "heavi": 7, "heavili": [0, 21, 237], "hec": 153, "heck": [3, 9, 12, 23, 83], "hed": 168, "hedgehog": 238, "hedra": [15, 152, 158, 167, 168, 169], "hedraangl": [15, 169], "hedrakei": 169, "hedral12": [15, 169], "hedral23": [15, 169], "hedralen": 169, "hedrandx": 169, "hedron": [27, 133, 152, 158, 169], "hedron1": 169, "hedron2": 169, "hedrondispatch": 158, "hedronmatcherror": [27, 133, 169], "hedronomet": [15, 169], "hedronometr": 169, "hehl": 2, "hei": 3, "height": [8, 16, 104, 115, 117], "hein": 2, "held": [6, 12, 23, 117, 238, 251, 269, 289], "helic": [15, 260], "helix": [9, 11, 15, 32, 53, 137, 236, 260, 265, 272], "helixendin": [30, 32], "helixendout": [30, 32], "helixgap": [30, 32], "helloworld": 67, "help": [0, 3, 6, 7, 8, 9, 12, 17, 18, 19, 21, 23, 24, 25, 30, 32, 36, 37, 38, 39, 67, 68, 69, 70, 79, 80, 95, 99, 104, 108, 129, 181, 182, 209, 217, 221, 250, 262, 270, 281, 286, 297, 306], "help_input": [201, 204], "help_mkt": [34, 280], "helper": [8, 12, 23, 92, 100, 238, 251, 298, 303, 304], "helvetica": [104, 105], "hematopoiet": 2, "hemoglobin": [13, 14], "henc": [4, 15, 20, 73, 238], "henerargiyerfvvvh": 53, "heng": [2, 52], "henikoff": 2, "henikoff1992": [2, 13], "henrik": 9, "her": [143, 151], "here": [0, 1, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 23, 24, 26, 30, 66, 68, 73, 83, 99, 137, 143, 158, 169, 182, 197, 201, 204, 207, 217, 218, 221, 222, 234, 237, 238, 251, 260, 264, 275, 276, 277, 278, 288, 299, 307], "heringa": 32, "heron": [15, 169], "hertz": [11, 294], "het": [0, 15, 270], "hetatm": [15, 143, 145, 154, 168, 169, 248], "hetatom": 214, "hetero": [136, 139, 162], "heterogen": 182, "heterozyg": 270, "heterozygos": 203, "heterozygot": [202, 203, 270], "hetfield": 15, "hetflag": 15, "heuer": [2, 251], "heurist": [2, 182, 270], "hevein": 0, "hex": [17, 30, 68, 105, 117], "hexadecim": 183, "hexbinari": 197, "hexstr": 183, "hf": 7, "hfgkeft": 13, "hflipliii": 250, "hflvpfviif": 250, "hftiplivif": 250, "hg": [13, 135, 162, 169], "hg1": 169, "hg11": 169, "hg12": 169, "hg13": 169, "hg16": 0, "hg18": 0, "hg18_dna": 0, "hg18kgchr7": 0, "hg19": [0, 20], "hg19_dna": [0, 221], "hg19tohg38": 0, "hg2": 169, "hg21": 169, "hg22": 169, "hg23": 169, "hg3": 169, "hg38": [0, 13, 22], "hgapresidu": [30, 32], "hgdownload": 221, "hgfedcba": 251, "hgfisrefhr": 250, "hgkheerqd": 250, "hgkkv": 13, "hh": [2, 44, 169, 227], "hh11": 169, "hh12": 169, "hh2": 169, "hh21": 169, "hh22": 169, "hhai": 206, "hhblit": [0, 44], "hhhh": 12, "hhhhhh": [12, 53], "hhhhhhh": 12, "hhhhhhhh": 12, "hhhhhhhhhhhhh": 53, "hhhhhhhhhhhhhh": [12, 53], "hhhhhhhhhhhhhhhhhhhhh": 12, "hhhhhhhhhhhhhhhhhhhhhhh": 12, "hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh": 12, "hhhhhttthhhhhhhhhhhhhhhhhhhhhh": 260, "hhr": [0, 22, 27, 30], "hhsearch": [0, 44], "hhsuit": [217, 227, 228], "hhsuite2": 217, "hhsuite2_text": [217, 227], "hhsuite2textpars": [217, 227, 228], "hhsuiteio": [27, 217], "hi": [13, 25, 90, 130, 143, 151, 273], "hick": 264, "hicut": 69, "hidden": [0, 2, 9, 32, 44, 104, 106, 108, 229], "hiddenmarkovmodel": [27, 106, 108], "hide": [15, 104, 136], "hie": [27, 209], "hie_handl": 209, "hierarch": [13, 73], "hierarchi": [15, 17, 20, 90, 139, 209, 210, 211, 212, 213, 217, 273], "higgin": 32, "high": [2, 3, 6, 7, 10, 11, 15, 16, 17, 20, 23, 32, 68, 92, 101, 104, 123, 169, 217, 251, 303], "higher": [6, 12, 13, 14, 15, 21, 69, 99, 157, 237, 251, 264, 270, 275, 286, 290, 300], "highest": [11, 13, 15, 104, 135, 236, 275], "highli": [3, 32, 149, 297], "highlight": [3, 8, 15], "hihara": [2, 4], "hihara2001": [2, 4], "hill": [182, 202, 203], "hin1ii": 206, "hin6i": 206, "hindiii": 8, "hinp1i": 206, "hist": 6, "histidin": 260, "histor": [24, 71, 151, 297], "histori": [90, 123], "hit": [0, 7, 19, 25, 27, 68, 69, 70, 71, 74, 88, 182, 217, 218, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 234, 270, 290], "hit_access": 218, "hit_al": 20, "hit_coverag": [27, 74], "hit_def": [71, 218], "hit_end": [218, 221, 222, 226, 229, 234], "hit_endtyp": 229, "hit_filt": 20, "hit_fram": [218, 222], "hit_frame_al": 222, "hit_gap_num": 221, "hit_gapopen_num": 221, "hit_id": [20, 71, 218], "hit_inter_rang": [20, 222], "hit_inter_span": 20, "hit_kei": 20, "hit_len": 218, "hit_map": 20, "hit_placehold": 230, "hit_rang": 20, "hit_range_al": 20, "hit_span": 20, "hit_span_al": [20, 221], "hit_split_codon": 222, "hit_start": [20, 218, 221, 222, 226, 229, 234], "hit_start_al": 221, "hit_strand": [20, 221, 222, 226, 229], "hitlist_s": [68, 70], "hiu": 12, "hiv": 15, "hivb": 182, "hivw": 182, "hke": 56, "hkt": 169, "hky2": 32, "hky85": 182, "hla": [245, 250], "hla00489": 250, "hla00490": 250, "hla00491": 250, "hla00492": 250, "hla00493": 250, "hla01083": 250, "hllesdlfpa": 250, "hllvvccnsfqrilcflkdpfmhyvryqgkailaskgtlilmkkwkfhlvnfwqsyfh": 7, "hlmrda": 0, "hlqesellpa": 250, "hm": 202, "hmm": [0, 27, 32, 53, 229, 231, 234], "hmm_as_hit": [229, 231], "hmm_descript": 0, "hmm_input": [30, 32], "hmm_name": 0, "hmmbuild": [0, 53], "hmmer": [20, 217, 229, 230, 231, 232, 233], "hmmer2": [217, 230], "hmmer2_text": [217, 229], "hmmer2textindex": [217, 229, 230], "hmmer2textpars": [217, 229, 230], "hmmer3": [217, 231, 232, 234], "hmmer3_domtab": [217, 229], "hmmer3_tab": [217, 229], "hmmer3_text": [217, 229], "hmmer3domtabhmmhitindex": [217, 229, 231], "hmmer3domtabhmmhitpars": [217, 229, 231], "hmmer3domtabhmmhitwrit": [217, 229, 231], "hmmer3domtabhmmqueryindex": [217, 229, 231], "hmmer3domtabhmmquerypars": [217, 229, 231], "hmmer3domtabhmmquerywrit": [217, 229, 231], "hmmer3domtabpars": 231, "hmmer3tabindex": [217, 229, 231, 232], "hmmer3tabpars": [217, 229, 232], "hmmer3tabwrit": [217, 229, 232], "hmmer3textindex": [217, 229, 233], "hmmer3textpars": [217, 229, 233], "hmmerio": [27, 217], "hmmfrom": 229, "hmmpfam": [217, 229], "hmmscan": [217, 229], "hmmscan3": 229, "hmmscore": [0, 33], "hmmsearch": [0, 53, 217, 229], "hmmsearch3": 229, "hmmto": 229, "hn": 126, "hoc": 256, "hochstrass": 263, "hocomoco": [11, 283], "hoh": 152, "hokc": 260, "hold": [6, 7, 12, 15, 16, 19, 21, 23, 27, 30, 49, 56, 64, 66, 71, 74, 86, 87, 88, 90, 93, 97, 99, 102, 104, 105, 109, 112, 113, 114, 120, 121, 122, 123, 125, 127, 169, 201, 204, 205, 210, 211, 212, 213, 217, 238, 251, 260, 269, 271, 272, 278, 282, 289, 291, 292], "holder": [134, 158], "homag": 20, "home": [7, 84, 222], "homeo": 288, "homepag": 182, "homer": [2, 11, 283], "hominida": 272, "homo": [3, 20, 68, 90, 93], "homo_sapien": 7, "homodimer": 260, "homog_rot_mtx": [27, 133, 176], "homog_scale_mtx": [27, 133, 176], "homog_trans_mtx": [27, 133, 176], "homogen": [15, 169, 176], "homol": [7, 275], "homolog": 3, "homologen": 7, "homologi": [2, 275], "homologu": 274, "homopolym": [253, 268, 270], "homozygot": [202, 203], "hood": [17, 217], "hoon": [2, 4, 7, 9, 26, 73], "hope": [9, 21, 23, 108, 169], "hopefulli": [3, 5, 7, 8, 12, 19, 21, 30], "hopeless": 3, "hopkin": 216, "hordeum": 25, "hordijk": 182, "hori": 25, "horizont": [4, 6, 8, 73], "hornisch": 2, "hors": [0, 56], "host": [2, 5, 11, 209, 272, 288, 303, 305], "host_organ": [25, 272], "host_taxonomy_id": 272, "hostnam": [0, 288, 303], "hot": [15, 169], "houdt": 2, "hour": [4, 7, 16, 32, 182], "household": 4, "how": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 23, 25, 30, 31, 68, 73, 80, 83, 84, 100, 104, 132, 137, 182, 219, 231, 232, 237, 243, 248, 251, 253, 264, 274, 278], "howev": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 25, 30, 56, 66, 68, 73, 83, 94, 182, 217, 218, 221, 222, 236, 237, 238, 240, 243, 251, 253, 260, 261, 269, 274, 278, 283, 298, 299], "hoxd70": 199, "hp": [11, 295], "hpc": 182, "hpych4iv": 206, "hpyse526i": 206, "hr": [22, 222], "hs_exp": 141, "hsa": [10, 119], "hse": [15, 141], "hsealpha": 15, "hsebeta": 15, "hsexposur": [15, 27, 133], "hsexposureca": [27, 133, 141], "hsexposurecb": [27, 133, 141], "hsi08034": 7, "hsiung": 2, "hsp": [27, 68, 69, 71, 217, 218, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 234], "hsp70": 4, "hsp92ii": 206, "hsp_align": 218, "hsp_bit": 218, "hsp_densiti": 218, "hsp_evalu": 218, "hsp_filter": 20, "hsp_gap": 218, "hsp_hit": 218, "hsp_hseq": 218, "hsp_ident": 218, "hsp_map": 20, "hsp_midlin": 218, "hsp_pattern": 218, "hsp_posit": 218, "hsp_qseq": 218, "hsp_queri": 218, "hsp_score": 218, "hspai": 206, "hspfragment": [217, 218, 221, 222, 226, 229, 234], "hsps_gap": 71, "hsps_no_gap": 71, "hsps_prelim_gap": 71, "hsps_prelim_gapped_attemp": 71, "hsv": 100, "ht": [202, 288], "htc": 275, "html": [0, 3, 9, 10, 15, 17, 25, 30, 32, 35, 36, 37, 38, 39, 46, 50, 51, 53, 56, 61, 65, 66, 68, 69, 70, 83, 85, 89, 94, 119, 182, 183, 190, 199, 201, 204, 209, 210, 211, 212, 214, 221, 236, 238, 243, 245, 247, 248, 250, 272, 274, 286], "htmlout": [30, 32], "htselex": 288, "htslib": 52, "http": [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 18, 19, 21, 22, 23, 25, 27, 32, 34, 35, 36, 37, 38, 39, 46, 50, 51, 52, 53, 56, 59, 61, 65, 66, 68, 69, 70, 71, 73, 83, 85, 86, 87, 88, 89, 90, 94, 96, 97, 99, 100, 105, 111, 115, 116, 117, 119, 122, 137, 140, 145, 149, 150, 156, 158, 167, 169, 170, 181, 182, 185, 188, 190, 197, 199, 201, 204, 209, 210, 211, 212, 214, 218, 221, 226, 227, 229, 234, 237, 239, 243, 245, 247, 248, 250, 251, 252, 253, 258, 262, 263, 265, 267, 270, 272, 273, 274, 277, 278, 279, 280, 283, 286, 299, 301], "http_proxi": [7, 149], "httprespons": 68, "hu": 122, "huge": [1, 3, 13, 31, 32, 182], "hugh": 263, "hughei": 2, "hughey1996": [0, 2], "human": [0, 7, 10, 11, 13, 15, 20, 21, 22, 23, 25, 30, 45, 68, 93, 117, 119, 197, 221, 238, 260, 263, 264, 270, 272, 274, 299], "human_pathwai": 10, "hundr": [4, 19, 20], "hunt": 6, "hurt": 270, "hutchinson": 265, "hvdp": 13, "hwi": 0, "hxkei": 169, "hyb": 80, "hybrid": [7, 20, 264, 275], "hybridis": 80, "hybridprob": [79, 80], "hydro": [30, 32], "hydrocarbon": 7, "hydrofactor": [30, 32], "hydrogen": [15, 138, 158, 169, 272], "hydrolyz": 25, "hydropathi": 265, "hydrophil": [32, 265], "hydrophob": [32, 265], "hyilp": 80, "hyper": 0, "hyperlink": 83, "hypohippu": 56, "hypothet": [3, 12, 94, 104], "hz": 169, "hz1": 169, "hz2": 169, "hz3": 169, "i": [0, 2, 3, 4, 5, 6, 8, 10, 11, 12, 13, 14, 16, 18, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 42, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56, 59, 61, 62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 85, 86, 88, 89, 90, 91, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 118, 119, 120, 121, 122, 123, 125, 126, 127, 129, 130, 132, 134, 135, 136, 137, 138, 139, 140, 141, 143, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 162, 163, 164, 166, 168, 169, 170, 172, 173, 175, 176, 177, 178, 179, 180, 182, 183, 185, 186, 188, 190, 191, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 216, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 268, 269, 270, 271, 272, 274, 275, 277, 278, 280, 281, 282, 283, 286, 287, 288, 290, 291, 294, 295, 296, 297, 298, 299, 300, 302, 303, 305, 306, 307], "i51200": 250, "i_thresh": [68, 70], "ia": 68, "iahpggpaildqvelklglkqeklkatrkvlsnygnmssacvlfildemrkasakeglgt": 23, "iaiiie65i": 251, "ian": 2, "iatgkmlsla": 0, "ibarra": 7, "ic": [11, 31, 168, 169, 273, 294], "ic_": [12, 158], "ic_chain": [15, 27, 133, 158, 169], "ic_data": [15, 27, 133, 152, 169], "ic_data_sidechain": 169, "ic_dupl": [15, 27, 133, 168, 169], "ic_rebuild": [15, 27, 133, 169], "ic_residu": [15, 27, 133, 152, 158, 168, 169], "ic_vector": 31, "icm": 288, "icod": [15, 162, 169, 214], "id": [0, 1, 3, 4, 6, 8, 9, 11, 12, 13, 15, 16, 19, 20, 21, 22, 23, 25, 27, 30, 32, 34, 36, 37, 38, 39, 45, 47, 53, 59, 60, 61, 62, 65, 66, 68, 69, 71, 76, 83, 85, 86, 88, 90, 93, 94, 104, 112, 113, 114, 115, 116, 117, 118, 123, 130, 132, 133, 134, 135, 136, 137, 139, 140, 143, 144, 149, 151, 152, 155, 160, 162, 165, 168, 169, 171, 172, 181, 183, 184, 187, 189, 197, 198, 209, 211, 212, 214, 215, 217, 218, 221, 222, 223, 224, 225, 226, 229, 234, 237, 238, 240, 241, 244, 245, 246, 248, 249, 250, 251, 252, 253, 255, 256, 260, 270, 272, 273, 274, 275, 278, 279, 280, 287, 288, 295, 298, 299, 302, 303, 304, 305], "id1": 272, "id123456": 256, "id123457": 256, "id2": 272, "id3": [169, 272], "id32": 169, "id32_dh_index": 169, "id3_dh": 169, "id3_dh_index": 169, "id_al": 218, "id_dict": 238, "id_fil": 6, "id_handl": 6, "id_i": 8, "id_list": 7, "id_of_previous_nod": 132, "id_ref": 197, "id_ref_0": 197, "id_ref_1": 197, "id_sourc": 197, "id_width": [56, 65], "id_x": 8, "idcod": [152, 158, 168], "iddo": [2, 26], "idea": [1, 5, 7, 12, 15, 19, 21, 23, 108, 238, 278], "ideal": [0, 5, 7, 12, 19, 20, 23, 24, 27, 99, 270], "ident": [3, 4, 8, 11, 12, 13, 17, 19, 20, 21, 22, 23, 27, 30, 32, 68, 69, 71, 80, 132, 168, 176, 199, 202, 203, 209, 221, 236, 238, 251, 270, 290, 297], "ident_num": [20, 218, 221], "ident_pct": [218, 221, 226], "identif": [2, 20, 169, 250], "identifi": [0, 3, 4, 8, 11, 12, 15, 16, 19, 20, 21, 23, 25, 30, 47, 53, 56, 65, 68, 69, 70, 71, 73, 83, 85, 90, 93, 104, 112, 114, 117, 119, 123, 129, 135, 136, 137, 138, 139, 140, 144, 154, 155, 160, 162, 169, 182, 183, 197, 198, 209, 210, 211, 213, 217, 226, 236, 237, 238, 241, 251, 252, 256, 260, 262, 270, 272, 273, 274, 275, 280, 295, 299, 303], "identity_match": [27, 297], "idiom": 15, "idiosyncrat": [0, 42], "idlist": [7, 83], "idmmpmm": [11, 283], "idtglsemrl": 250, "idtyp": [7, 83], "idx": [20, 23], "idx_filenam": 217, "idx_nam": 238, "idxstat": 270, "ie": [15, 31, 92, 93, 99, 108, 136, 137, 140, 156, 176, 237], "ieee": 7, "ieislnqikdgwkiidvkdryydfrnksfsafsnwlrdlkeqslrkynnfcgknfyf": 94, "iep": [80, 263], "iep_clin": 80, "iepcommandlin": [27, 79, 80], "if6hivcnrsqdvniaoefazysc6i4": 262, "iff": 177, "ifound": 4, "ifwcnf2pi": 23, "ifxa": 292, "ifyepveifgydnksslvlvkrlitrmyqqnflissvndsnqkg": 7, "ig": [32, 56, 238, 244], "igio": [27, 238], "igiter": [27, 238, 244], "ignment": 0, "ignor": [4, 11, 12, 13, 15, 20, 21, 23, 24, 27, 31, 32, 59, 66, 67, 69, 88, 94, 141, 152, 167, 169, 182, 198, 218, 238, 240, 244, 251, 256, 261, 264, 270, 278, 283, 290, 298], "ignore_com": 132, "ignore_error": [7, 83, 84], "ignore_lower_cas": 283, "ignore_msa_mast": [68, 69], "ihgfedcba": 251, "ii": [0, 4, 8, 73, 122, 183, 251, 294], "iieqfidylr": 260, "iii": [8, 211, 251], "iiiiii1": 251, "iiiiiii": 251, "iiiiiiiiiiiiciigiiiii": 251, "iiiiiiiiiiiiiiicdiiiii": 251, "iiiiiiiiiiiiiiiiiiiiiiiiiiiiicii": 251, "iij": 13, "iis_converg": 122, "iiv": 0, "ij": [11, 12], "ik": 7, "ikawa": 25, "ikeuchi": 2, "ikhkylwsep": 0, "ikhkylwsepqncsat": 0, "il": [13, 15], "ill": 80, "illumina": [2, 6, 238, 251, 270], "illumina_13": [268, 270], "illumina_fak": 251, "illumnia": 238, "illustr": [0, 2, 6, 7, 8, 13, 20, 21, 23, 30, 134, 135, 139, 140, 251], "ilmfq": 270, "im": 32, "imag": [6, 7, 8, 15, 17, 19, 68, 99, 104, 105, 116, 117, 119, 169, 197], "imagin": [18, 20], "imgt": [167, 238, 245], "imgteduc": 167, "imgtiter": [27, 238, 245], "imgtwrit": [27, 238, 245], "imit": [3, 8], "imm_tabl": 264, "immedi": [3, 7, 20, 21, 169, 278], "immobil": 263, "immun": 21, "immut": [4, 13, 22, 23, 236], "imoto": [2, 7], "implement": [2, 4, 6, 7, 10, 11, 12, 13, 15, 17, 21, 30, 32, 34, 67, 73, 76, 83, 92, 100, 107, 108, 109, 123, 126, 139, 143, 146, 148, 151, 158, 169, 175, 177, 178, 179, 180, 183, 185, 199, 217, 229, 236, 237, 238, 246, 252, 257, 260, 261, 264, 265, 270, 278, 280, 288, 290, 291, 302, 303, 304], "impli": [20, 117], "implic": 53, "implicit": 20, "implicitli": 0, "import": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 32, 45, 53, 54, 56, 59, 62, 66, 67, 68, 69, 73, 76, 80, 83, 85, 90, 91, 92, 99, 104, 116, 122, 123, 126, 135, 137, 139, 140, 148, 154, 156, 157, 169, 170, 173, 176, 182, 183, 199, 206, 207, 216, 217, 218, 221, 222, 236, 237, 238, 240, 245, 247, 248, 249, 251, 253, 260, 261, 262, 263, 264, 265, 269, 270, 272, 274, 276, 277, 278, 279, 280, 281, 282, 283, 288, 289, 291, 292, 295, 297, 298, 299, 303, 305], "import_imagemap": 105, "import_search_strategi": [68, 69], "importantli": [5, 8], "importerror": 27, "impos": [15, 238], "imposs": [21, 95, 222], "impract": 7, "improv": [2, 3, 6, 8, 15, 17, 19, 23, 32, 122, 152, 182, 248, 270, 278, 300], "imshow": [6, 15, 169], "in1": [30, 32, 270], "in2": [30, 32, 270], "in_bam": [268, 270], "in_con": 53, "in_fil": [32, 56, 137, 217, 238], "in_fmt": 217, "in_format": [56, 217, 238, 274], "in_handl": [6, 23, 85, 238], "in_kwarg": 217, "in_msa": [68, 69], "in_plac": 20, "in_pssm": [68, 69], "in_rad": 169, "inappropri": [0, 30], "inbox": 5, "inc": [229, 242], "incent": 23, "incept": 9, "inch": 104, "includ": [0, 1, 3, 4, 5, 6, 7, 9, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 36, 38, 47, 52, 56, 59, 66, 67, 68, 69, 72, 76, 80, 83, 94, 99, 129, 130, 133, 135, 136, 139, 145, 149, 152, 154, 158, 162, 169, 176, 183, 197, 207, 214, 237, 238, 240, 243, 248, 251, 253, 260, 261, 264, 265, 269, 270, 272, 274, 276, 278, 280, 281, 283, 288, 291, 295, 297, 299, 307], "include_codon": 129, "include_miss": 129, "includecod": 158, "includedregion": [79, 80], "inclus": [3, 6, 61, 68, 69, 215, 217, 229, 251], "inclusion_ethresh": [68, 69], "incompat": [6, 69, 251, 278, 297, 303], "incompatibli": 108, "incomplet": [0, 2, 10, 15, 134, 135, 139, 140, 182, 278], "inconsist": [4, 13, 214], "incorpor": 32, "incorrect": [7, 27, 108, 270], "incorrectli": 15, "increas": [0, 4, 7, 30, 73, 183, 270, 297], "increasingli": 20, "incred": 19, "increment": [1, 35, 36, 37, 38, 39, 42, 46, 51, 52, 53, 66, 71, 143, 166, 169, 183, 198, 299], "ind1": [18, 201, 204, 205], "ind2": [18, 201, 204], "inde": [6, 12, 25], "indel": 270, "indent": [12, 198, 206, 207, 238, 245], "independ": [0, 17, 80, 127, 169, 229], "index": [2, 3, 7, 8, 9, 11, 12, 13, 15, 16, 17, 21, 22, 27, 30, 36, 37, 38, 45, 47, 54, 61, 68, 69, 72, 73, 83, 91, 94, 104, 125, 126, 131, 137, 149, 154, 169, 172, 176, 183, 197, 201, 209, 210, 214, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 233, 236, 238, 241, 253, 257, 260, 261, 265, 270, 278, 279, 280, 281, 289, 290, 291, 292, 297, 299, 303], "index1": [4, 73], "index2": [4, 73], "index_cmd": 270, "index_db": [6, 9, 20, 23, 27, 217, 238], "index_filenam": [217, 238], "index_nam": [68, 69], "index_to_on": [27, 133, 154], "index_to_thre": [27, 133, 154], "indexerror": 13, "indic": [3, 4, 6, 7, 10, 11, 12, 13, 15, 16, 17, 20, 21, 22, 24, 27, 30, 32, 68, 73, 92, 104, 105, 109, 119, 121, 127, 129, 135, 139, 143, 149, 151, 158, 169, 172, 182, 183, 197, 214, 215, 217, 222, 236, 237, 248, 264, 266, 270, 272, 275, 278, 280, 297, 299], "indirectli": [7, 278, 303], "indiv": 204, "individu": [0, 4, 8, 13, 15, 18, 20, 21, 24, 25, 30, 45, 83, 90, 157, 158, 167, 177, 182, 197, 201, 202, 204, 205, 217, 222, 238, 260, 286, 289, 291, 292, 293, 295, 296], "indraneel": 2, "ineffici": 20, "inequ": [0, 4, 17, 109, 135, 139, 169, 237], "inexact": 21, "inf": [11, 122, 202, 270], "infect": 6, "infer": [0, 17, 30, 137, 182, 270], "infer_coordin": [27, 30], "infil": [12, 30, 32, 79, 80, 174, 268, 270], "infin": [11, 251], "infinit": 7, "influenc": 108, "infmt": [30, 32], "infn": 126, "info": [3, 5, 7, 15, 31, 92, 93, 101, 102, 103, 112, 113, 114, 119, 168, 169, 183, 191, 202, 203, 237, 269, 275], "info_cont": 12, "info_upd": 88, "inform": [1, 2, 3, 4, 5, 6, 9, 10, 11, 13, 15, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 35, 36, 37, 38, 42, 45, 46, 50, 51, 52, 53, 59, 62, 65, 66, 68, 71, 72, 73, 74, 77, 80, 81, 82, 83, 84, 86, 87, 88, 90, 92, 93, 94, 97, 99, 101, 102, 103, 104, 113, 117, 120, 122, 123, 127, 129, 132, 135, 143, 153, 158, 169, 172, 182, 183, 185, 197, 201, 203, 204, 205, 209, 210, 211, 212, 213, 214, 218, 221, 222, 226, 227, 229, 234, 238, 241, 243, 247, 248, 250, 251, 252, 253, 256, 257, 260, 262, 269, 270, 271, 272, 273, 275, 277, 278, 282, 283, 286, 287, 288, 293, 295, 296, 299, 305], "information_cont": [12, 30, 31], "infraclass": 197, "infracohort": 197, "infradivis": 197, "infrakingdom": 197, "infralegion": 197, "infraphylum": 197, "infratrib": 197, "ingar": 263, "ingo": 2, "inh": 270, "inher": 4, "inherit": [0, 3, 11, 15, 17, 45, 68, 71, 183, 237, 280, 281, 286, 289, 291, 293, 295, 296], "inhibitor": 113, "ini": 24, "init": [4, 169, 264], "init1_scor": 226, "init_a": 264, "init_atom": [133, 162], "init_atom_coord": [133, 169], "init_chain": [133, 162], "init_edra": [133, 169], "init_g": 264, "init_met": 272, "init_model": [133, 162], "init_residu": [133, 162], "init_seg": [133, 162], "init_structur": [133, 162, 171, 172], "initatom": [152, 169], "initi": [0, 4, 13, 15, 17, 20, 21, 29, 30, 31, 32, 36, 60, 62, 67, 68, 69, 71, 72, 73, 74, 76, 80, 81, 82, 84, 86, 87, 88, 89, 90, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 138, 139, 140, 141, 144, 145, 149, 150, 152, 153, 154, 155, 156, 157, 158, 160, 161, 162, 163, 165, 168, 169, 172, 175, 176, 177, 179, 180, 182, 183, 184, 185, 187, 188, 189, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 215, 216, 219, 220, 221, 226, 228, 230, 231, 232, 233, 235, 237, 247, 249, 252, 253, 258, 259, 263, 264, 265, 269, 270, 271, 272, 273, 275, 278, 280, 281, 282, 283, 284, 287, 289, 290, 291, 292, 294, 295, 297, 299, 305], "initial_prob": 108, "initialid": [4, 73], "initialis": [29, 148, 149, 169, 170, 173], "initn_scor": 226, "initncac": 169, "inittau": [4, 73], "inlin": 158, "inner": [12, 13, 272], "inner1": [13, 199], "inner2": [13, 199], "inner3": 199, "inner4": 199, "innocua": 8, "ino1": [11, 291], "ino_up800": [11, 291], "inorgan": 25, "inosin": 112, "inpenalti": 270, "inplac": 236, "input": [0, 3, 4, 6, 7, 8, 10, 11, 12, 13, 15, 17, 19, 21, 22, 24, 25, 26, 27, 30, 31, 32, 37, 45, 50, 54, 59, 60, 65, 66, 67, 68, 69, 73, 80, 81, 82, 83, 91, 94, 104, 116, 119, 125, 126, 129, 153, 156, 157, 166, 169, 171, 175, 176, 181, 182, 193, 195, 196, 199, 229, 241, 246, 248, 249, 251, 258, 261, 268, 270, 274, 278, 297, 299, 307], "input1": [30, 32], "input_bam": [268, 270], "input_bam1": 270, "input_bam2": 270, "input_bam_fil": 270, "input_chain_indic": 172, "input_fil": [6, 68, 69, 268, 270], "input_head": 270, "input_sorted_bam": 270, "input_transform": 172, "input_tre": [181, 182], "input_typ": [68, 69], "inputfil": [50, 65], "inputord": [30, 32], "inputrecord": [27, 79, 82], "inrec": 277, "insdc": [94, 237, 245], "insdcio": [27, 238], "insdcscann": [27, 92, 94], "insect": [11, 288], "insensit": [0, 22, 30, 68, 261, 270], "insert": [0, 12, 15, 22, 27, 30, 32, 33, 55, 133, 136, 139, 143, 162, 169, 172, 214, 215, 221, 236, 270, 275, 295], "insert_gap": [128, 129], "insertion_cod": 172, "insertpenalti": 270, "insid": [20, 25, 32, 104, 149, 169, 270], "insist": [7, 9, 23], "insosin": 264, "inspect": [15, 17, 278, 299], "inspir": [8, 100, 201, 261], "instability_index": [261, 265], "instabl": 265, "instal": [3, 5, 6, 7, 8, 12, 15, 16, 17, 19, 24, 67, 99, 104, 288, 299], "instanc": [3, 4, 7, 9, 12, 13, 16, 17, 21, 23, 24, 27, 30, 31, 36, 54, 67, 91, 109, 129, 132, 135, 140, 160, 162, 182, 183, 185, 188, 190, 193, 195, 196, 197, 198, 209, 214, 234, 236, 237, 260, 265, 269, 272, 283, 287, 288, 291, 292, 295, 297, 299, 303], "instant": 6, "instantan": 6, "instanti": [99, 107, 143, 151, 169, 185, 187, 190, 198], "instead": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 38, 45, 51, 56, 63, 65, 67, 69, 71, 73, 80, 83, 84, 92, 102, 108, 120, 132, 139, 143, 151, 169, 182, 183, 185, 186, 197, 217, 218, 221, 229, 236, 238, 240, 241, 250, 251, 253, 255, 256, 265, 269, 270, 275, 278, 282, 283, 285, 290, 294, 298, 303], "institut": [7, 52, 251, 253], "instruct": [5, 7, 12, 104], "instrument": [6, 16, 251], "insulin": [25, 157], "insur": 125, "int": [0, 7, 8, 13, 17, 21, 36, 54, 64, 71, 83, 84, 88, 99, 104, 117, 125, 126, 130, 134, 136, 139, 140, 141, 144, 148, 149, 150, 152, 157, 158, 162, 164, 169, 176, 186, 197, 236, 237, 238, 251, 253, 260, 262, 270, 276, 302], "int255_color": [98, 104], "int32": [0, 13], "int_node_label": 17, "intact": 17, "integ": [0, 3, 4, 6, 8, 12, 15, 17, 20, 21, 23, 30, 32, 34, 54, 56, 68, 69, 71, 73, 80, 83, 84, 85, 89, 104, 117, 136, 152, 172, 182, 183, 197, 217, 236, 237, 238, 251, 260, 263, 267, 272, 274, 278, 282, 286, 298, 299, 302], "integerel": [27, 83, 84], "integr": [8, 9, 15, 19, 20, 68, 104, 217, 264, 274], "intellig": [2, 104], "intelligenet": [56, 238, 244], "intend": [3, 6, 11, 20, 30, 45, 59, 67, 84, 91, 92, 94, 99, 129, 177, 178, 182, 197, 217, 237, 246, 256], "intens": [29, 104], "intent": 9, "intention": 177, "inter": [15, 23], "interact": [3, 5, 15, 17, 19, 20, 27, 69, 79, 80, 82, 164, 165, 169, 177, 182, 276, 306], "interacton": 177, "interat": 277, "interatom": 169, "interchang": [177, 182, 199, 237, 251], "interconvert": [80, 169], "intereact": 15, "interest": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 32, 40, 83, 88, 93, 97, 99, 143, 169, 272, 278], "interestingli": 21, "interfac": [6, 7, 9, 10, 12, 15, 17, 20, 21, 23, 27, 30, 56, 59, 67, 80, 83, 85, 92, 99, 108, 123, 145, 156, 166, 177, 185, 193, 195, 196, 202, 203, 204, 217, 218, 234, 238, 251, 259, 302, 303], "interfer": 0, "interlac": [0, 23, 56, 65, 66, 238, 246], "interlaced2": 182, "interleav": [0, 32, 49, 50, 64, 65, 66, 129, 182, 270], "interleave_by_partit": 129, "intermedi": [80, 168, 182, 278], "intermediari": 104, "intern": [2, 7, 12, 13, 17, 19, 22, 23, 27, 30, 49, 56, 61, 63, 64, 68, 71, 80, 83, 92, 94, 103, 104, 116, 132, 136, 138, 144, 152, 160, 167, 168, 169, 183, 209, 236, 238, 241, 245, 247, 248, 251, 253, 260, 264, 271, 272, 274, 278, 299, 302, 303, 304], "internal_coord": [27, 133, 136, 152, 158, 160], "internal_extend_gap_scor": 13, "internal_feature_format": [92, 93], "internal_format": [92, 93], "internal_gap_scor": 13, "internal_gc": 81, "internal_length": 81, "internal_open_gap_scor": 13, "internal_seq": 81, "internal_start": 81, "internal_tm": 81, "internal_to_atom": 169, "internal_to_atom_coord": [158, 169], "internal_to_atom_coordin": [15, 133, 136, 144, 158, 160, 169], "internet": [4, 7, 11, 19, 23, 25, 68, 70, 149, 238, 283], "interpol": [8, 15, 22, 169, 299], "interpret": [2, 7, 8, 9, 11, 12, 13, 15, 17, 20, 27, 65, 95, 123, 183, 197, 236, 238, 241, 248, 251, 253, 260], "interpro": [0, 53, 234], "interproscan": [217, 235], "interproscan_xml": [217, 234], "interproscanio": [27, 217], "interproscanxmlpars": [217, 234, 235], "intersect": 6, "interv": [16, 20, 104, 107, 217, 263, 265, 270, 275], "interven": 20, "interwork": 5, "intestin": 7, "intramem": 272, "intramolecular": 10, "intre": [181, 182], "intree1": [181, 182], "intreefil": [79, 80], "intrins": 25, "intro": 209, "introduc": [6, 8, 9, 11, 12, 17, 19, 20, 21, 22, 23, 88, 226, 238, 250, 251, 258], "introduct": [12, 19, 20, 21, 23, 26, 27, 209, 307], "intron": [0, 3, 6, 7, 21, 53, 66, 69, 80, 222, 237], "intronpenalti": [79, 80], "intuit": [16, 21, 237], "invalid": [10, 25, 56, 65, 67, 80, 129, 169, 236, 237, 238, 251], "invar": 182, "invarcoeffici": [79, 80], "invarfrac": [79, 80], "invari": [15, 80, 177, 182], "invent": 4, "invergo": 2, "invers": [6, 8], "inverse_indic": [0, 27, 30], "invert": [8, 99, 104, 128, 129], "investig": [6, 15, 123], "invoc": 270, "invok": [3, 12, 20, 32, 67, 68, 69, 70, 80, 104, 182, 221, 238, 270, 283, 285, 298], "involv": [11, 19, 21, 24, 25, 169, 177, 182, 272], "io": [0, 1, 4, 12, 15, 17, 23, 32, 56, 64, 90, 133, 148, 169, 170, 173, 238, 241, 243, 245, 246, 249, 251, 253, 256], "ioerror": 209, "ion": [253, 264, 272], "iota": 12, "iowa": 2, "ip": [7, 123, 263], "ipf": 260, "iplv": 0, "ipmsnktgvv": 250, "ippeeq": 0, "ipr": 234, "ipr001472": 94, "ipr002743": 94, "ipr003107": 53, "ipr003212": 0, "iptafdwrtr": 0, "ipython": 17, "ir": [30, 32, 123], "irad": 123, "irapeanum": [19, 23], "iron": [25, 112], "irrespect": [13, 119], "irrevers": 117, "is20aa": 169, "is_aa": [15, 27, 133, 154], "is_align": 197, "is_backbon": [133, 169], "is_bifurc": [17, 128, 132, 181, 183], "is_compat": [128, 132], "is_diplo": 203, "is_disord": [15, 133, 135, 139, 155], "is_frag": 20, "is_ident": [128, 132], "is_includ": 229, "is_intern": [128, 132], "is_monophylet": [17, 128, 132, 181, 183], "is_nucl": [27, 133, 154], "is_parent_of": [17, 128, 130, 181, 183], "is_pqr": [15, 148, 151, 162], "is_pretermin": [17, 128, 132, 181, 183], "is_react": [115, 117], "is_termin": [17, 128, 132, 181, 183], "isaccept": 169, "isatti": [27, 278], "isbn": 169, "isdomaininev": [27, 209], "isdomaininid": [27, 209], "isfil": [7, 12], "isfin": 89, "isfortran": 54, "isinst": [3, 68, 237], "isiz": 270, "islic": [25, 276], "isligslskaqfctvlghpiskpiwtdfsdsdildrfcricrnlcryhsgsskkqvli": 7, "islow": [27, 236, 260], "isn": [3, 7, 8, 9, 12, 20, 21, 23, 56, 71, 183, 251, 278, 305], "iso": [104, 278], "isoelectr": [80, 263, 265], "isoelectric_point": [261, 263, 265], "isoelectricpoint": [27, 261, 265], "isoform": 272, "isol": [15, 23, 137, 202, 203, 272, 278], "isolectin": 0, "isoleucin": 15, "isomeras": [3, 10], "isotop": 265, "isotrop": [15, 135], "isotropt": 135, "isprofil": [30, 32], "isqnklvsl": 0, "issn": 123, "issu": [3, 5, 7, 11, 15, 22, 23, 27, 67, 68, 123, 143, 151, 158, 168, 169, 237, 251, 261, 278, 288], "isupp": [27, 236, 260], "ital": 7, "item": [0, 3, 4, 9, 15, 20, 22, 30, 36, 37, 54, 71, 73, 83, 109, 131, 136, 159, 181, 197, 199, 201, 210, 214, 217, 236, 238, 301, 302, 303], "itemindex": [27, 121], "itemrgb": [0, 36], "itemsperslot": [0, 36, 37], "iter": [0, 3, 4, 6, 7, 9, 10, 12, 16, 17, 20, 22, 25, 27, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 71, 73, 74, 81, 83, 87, 88, 92, 94, 100, 108, 109, 112, 113, 114, 116, 120, 121, 122, 123, 129, 131, 134, 135, 139, 154, 159, 161, 164, 169, 183, 185, 186, 188, 190, 197, 198, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 217, 219, 220, 221, 226, 228, 230, 232, 233, 235, 237, 238, 239, 240, 241, 242, 244, 246, 247, 248, 249, 250, 251, 253, 254, 256, 257, 258, 259, 260, 261, 269, 270, 271, 273, 274, 276, 277, 278, 286, 293, 296, 298, 299, 303], "iteration_queri": 218, "iterative_refin": [30, 32], "itertool": [25, 276], "ith": 177, "itoh": 25, "itreekpavt": 250, "its": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 32, 36, 44, 45, 49, 52, 53, 61, 64, 65, 68, 69, 80, 83, 99, 104, 117, 119, 132, 135, 139, 141, 149, 155, 156, 157, 169, 182, 183, 198, 209, 217, 218, 222, 229, 237, 238, 251, 252, 260, 263, 264, 269, 270, 278, 282, 287, 288, 289, 291, 292, 298, 299, 303], "its1": [19, 23], "its2": [19, 23], "itself": [0, 1, 3, 4, 7, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 24, 25, 30, 59, 68, 84, 93, 108, 117, 143, 151, 183, 185, 197, 201, 209, 214, 222, 236, 250, 251, 260, 263, 264], "itv": 0, "iub": 32, "iucr": 170, "iupac": [11, 22, 77, 80, 172, 214, 261, 265], "iupacdata": [27, 75], "iv": 8, "ivspvknq": 0, "ivspvknqahcgscwtf": 0, "ivspvknqahcgscwtfsttgaleaaytqatgknislseqqlvdcaggfnnf": 0, "iw": [30, 32], "ix": [4, 73], "ixi_234": 0, "ixi_235": 0, "iyfl005w": 11, "iystsehtgeqvmrtldeviasrspesqtr": 6, "j": [0, 2, 3, 4, 6, 7, 11, 12, 13, 17, 30, 32, 59, 68, 73, 74, 80, 125, 126, 129, 140, 149, 153, 157, 177, 182, 197, 251, 261, 263, 264, 269, 270], "ja": [2, 7, 13, 157], "jag": 8, "jaggi": 8, "jame": [2, 71], "jan": [0, 21, 149], "jannaschii": 94, "januari": [11, 88], "japan": [245, 274], "japanes": 250, "jaroslaw": 2, "jason": 166, "jaspar": [27, 283], "jaspar2014": 287, "jaspar2018": 288, "jaspar5": [11, 283, 287, 288], "jaspar_db_host": [11, 288], "jaspar_db_nam": [11, 288], "jaspar_db_pass": [11, 288], "jaspar_db_us": [11, 288], "jaspar_dflt_collect": 288, "jaspar_motif": 11, "java": [2, 4, 73], "jb": 2, "jc69": 182, "jd": 32, "jdb": [11, 288], "jeff": [2, 26], "jeffrei": 2, "jennif": 2, "jf": 182, "jfashya": 23, "jid": 123, "jill": 2, "jim": 247, "jinghui": [3, 68], "jitter": [98, 100], "jmb": 32, "jmbi": 2, "jn0120": 250, "joao": [133, 166], "job": [19, 82, 149, 182, 217], "jobnam": [4, 73], "joe": [0, 17, 65, 133], "johann": 2, "john": [2, 216, 262], "johnson": 199, "join": [4, 5, 6, 7, 10, 21, 22, 80, 94, 158, 169, 182, 199, 237, 260, 278], "joint": [6, 169], "jointli": 270, "jonathan": 2, "jone": [2, 7, 32, 182, 199, 265], "jorja": 2, "jour": 7, "journal": [2, 7, 8, 17, 21, 83, 93, 123, 137, 182, 197, 237], "journal_refer": [15, 174], "journal_titl": 83, "jp": [10, 32, 105, 111, 115, 116, 117, 119, 245, 274], "jpeg": 8, "jpg": 104, "jq660890": 7, "jq660906": 7, "jq660907": 7, "jq660908": 7, "jq660909": 7, "jr": [149, 152, 169], "json": [3, 16, 274, 298, 299], "json2": [3, 68], "jsoniter": [27, 298, 299], "jsonwrit": [27, 298, 299], "jt": [7, 123], "jth": 177, "jtreeview": 4, "jtt": [30, 32, 182], "juan": 2, "judg": [12, 15], "judici": 15, "jue": 2, "jueown6dphgz9nayowsgtod9tto": 23, "juke": 182, "jul": [7, 21, 93, 149, 175], "juli": [9, 87, 90, 210, 211, 213], "jumbl": [79, 80], "jump": [3, 5, 17, 19, 217, 238, 278], "jun": [7, 23, 175], "june": [7, 9, 25], "jupe": [2, 8], "jupe2012": [2, 8], "juret": 265, "jussieu": 153, "just": [0, 3, 5, 6, 7, 8, 9, 11, 12, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 49, 56, 64, 67, 71, 80, 83, 93, 94, 97, 99, 101, 104, 107, 108, 110, 129, 132, 152, 169, 182, 183, 191, 197, 203, 218, 236, 237, 238, 240, 241, 243, 251, 253, 255, 260, 264, 265, 278, 288, 297, 298, 303, 304, 305], "justic": 83, "justif": 25, "justweight": 80, "jusweight": [79, 80], "k": [0, 2, 3, 7, 9, 11, 12, 13, 14, 15, 17, 20, 22, 23, 25, 30, 32, 34, 53, 68, 71, 73, 80, 100, 109, 169, 182, 183, 260, 264, 265, 267, 268, 270, 281, 282], "k12": 22, "k80": 182, "k_i": 11, "ka": [2, 12], "ka_param": 71, "ka_params_gap": 71, "kaa": 6, "kaafdslqa": 12, "kaafdsltaq": 12, "kaafnslqa": 12, "kachitvichyanukul": [2, 4], "kachitvichyanukul1988": [2, 4], "kaenaavqvl": 0, "kag": [4, 73], "kamei": 2, "kamiya": 25, "kanamori": 25, "kanehisa": [2, 111, 115, 119], "kaplan": 2, "kappa": [3, 17, 30, 32, 68, 217], "kara": 2, "karlin": [3, 68], "karplu": 32, "katoh": 32, "katrin": 2, "katsuhara": 25, "kauff": [2, 130, 269], "kb": 7, "kbp": 104, "kcf": 119, "kcluster": [4, 27, 73], "kd": [4, 15, 146], "kdaggrvctnnyccskwgscgigpgycgag": 0, "kdkfsvnldv": 250, "kdtree": [15, 146], "keaaaaqq": 250, "keaaaqqq": 250, "keep": [0, 3, 4, 6, 7, 9, 10, 11, 12, 17, 19, 20, 21, 23, 24, 67, 69, 133, 183, 197, 222, 238, 249, 251, 260, 270], "keftppvqaayqkvvagvanalahkyh": 12, "kegg": [26, 27, 105, 197, 274, 307], "kegg_conv": [27, 111, 119], "kegg_find": [10, 27, 111, 119], "kegg_get": [10, 27, 111, 119], "kegg_info": [27, 111, 119], "kegg_link": [27, 111, 119], "kegg_list": [10, 27, 111, 119], "keggapi": [10, 119], "keggid": 117, "kei": [0, 3, 6, 7, 8, 11, 13, 15, 17, 18, 20, 21, 22, 24, 25, 27, 30, 37, 39, 46, 53, 54, 66, 68, 76, 82, 83, 84, 85, 86, 90, 93, 94, 95, 100, 104, 107, 108, 117, 121, 126, 127, 133, 134, 137, 141, 155, 169, 174, 181, 183, 197, 201, 202, 209, 210, 214, 217, 219, 221, 226, 230, 232, 233, 236, 237, 238, 240, 244, 245, 251, 257, 260, 263, 264, 270, 272, 273, 277, 278, 283, 287, 289, 290, 291, 292, 295, 297, 299, 301, 303], "keidrareiyerfvyvh": 53, "keidrareiyerfvyvhpdvknwikfarfe": 53, "keidrarsvyqrflhvhginvqnwikyakf": 53, "keidraruiyerfvavh": 53, "kel": 2, "keller": 53, "kendal": 73, "kennard": 149, "kent": [2, 221, 247], "kent2002": [0, 2], "kept": [3, 6, 7, 15, 21, 23, 32, 151, 198, 260, 269, 299], "ker20427": 3, "kevla": [30, 297], "key_func": 217, "key_funct": [20, 23, 217, 238], "key_nam": [95, 296], "keyatom": 126, "keyerror": [3, 6, 8, 45, 76, 102, 108, 305], "keys_to_process": [92, 95], "keywd": [83, 209], "keywlist": [25, 27, 272], "keyword": [0, 3, 7, 14, 15, 17, 20, 21, 23, 30, 53, 67, 72, 73, 83, 89, 93, 104, 119, 169, 183, 197, 217, 218, 221, 260, 272, 273, 297, 299], "kfdpklrfpwvtitpivlregkivilkgdkyykvfvkrleelkkynlikkkepileep": 94, "kfgakf": 281, "kfiyafskrkkrflwllynsyvyeceylfqflrkqssylrstssgvflerthlyvki": 7, "kfppwv": 281, "kgar": [22, 236], "kgg": [4, 73], "kgml": [27, 105, 111, 119], "kgml_parser": [111, 115], "kgml_pathwai": [111, 115, 116], "kgml_vi": [27, 98], "kgmlcanva": [27, 98, 105], "kgmlparser": [111, 115, 116], "kgtfatl": 13, "kgvngv": 0, "khfspeelkv": 250, "kidera": 265, "kieelnliai": 0, "kikfkykgqdlevdiskvkkvwkvgkmvsftydd": 0, "kikuta": 25, "kilivddqygirillnevfnkegyqtfqaanglqaldivtk": 56, "kill": [128, 130], "kim": 265, "kimmen": 2, "kimron1": 23, "kimura": [30, 32], "kin": 238, "kinahn": 0, "kinas": 113, "kind": [4, 5, 7, 8, 11, 12, 13, 19, 20, 21, 25, 30, 84, 92, 93, 101, 102, 103, 107, 110, 217, 264], "kindli": 53, "kingdom": 197, "kit": [238, 242], "kitareewan": 2, "kkvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaahlpaeftp": 12, "kl": [109, 130], "kloo": 2, "klr": 13, "klriapgsfysvtlgt": 0, "kmedoid": [4, 27, 73], "kml": 197, "kne": 0, "knetvmagyivstgplaiaadav": 0, "knew": 25, "knmpywivkn": 0, "knn": 27, "know": [0, 3, 5, 7, 9, 12, 16, 17, 19, 20, 21, 23, 24, 30, 67, 209, 229, 277, 278], "knowledg": [15, 19], "knowledgebas": [23, 25, 255, 272], "known": [0, 3, 4, 7, 11, 12, 15, 20, 21, 22, 29, 30, 67, 109, 152, 154, 209, 214, 236, 251, 290, 297], "knownstatetrain": [27, 106, 109], "ko": [116, 117], "ko00010": 116, "ko01100": 116, "koehl": 140, "koetzl": 149, "kohonen": [2, 4], "kohonen1997": [2, 4], "kolodni": 140, "konieczni": 72, "konopka": 267, "kpmanfrfg": 250, "kpmgnfrfgn": 250, "kpmsnfrfge": 250, "kqfrnclitt": 250, "kqfrncmitt": 250, "kreitman": [34, 280], "krishna": 2, "kristian": [15, 133, 174], "krogh": 2, "krogh1994": [0, 2], "krp": 292, "kr\u00f3l": 2, "ksgelrqtppasstlhlrlilqrsgvmmel": 6, "kskithlvfcttsgvdmpgcdyqltkllglrpsvkrfmmyqqgcfaggtvlrmakdlaen": 23, "ksnylrgt": 0, "ktn": 13, "ktupl": [30, 32], "kullback": 11, "kuma": 32, "kumar": 2, "kun": 250, "kunzmann": 9, "kurita": 25, "kvkfkykgeekevdiskikkvwrvgkmvsftydd": 0, "kvlgdmveih": 250, "kvrfkykgeekevdtskikkvwrvgkmvsftydd": 0, "kw": [25, 273], "kwarg": [30, 32, 54, 62, 67, 69, 80, 84, 91, 100, 104, 169, 182, 183, 185, 187, 188, 190, 191, 197, 217, 220, 223, 224, 225, 230, 231, 232, 233, 270, 283, 303], "kwd": [72, 283, 291], "kx265011": 7, "kx265012": 7, "kx265013": 7, "kx265014": 7, "kx265015": 7, "ky": 0, "kyh": [12, 14], "kyoto": [111, 115, 119], "kyr": [12, 13, 14], "kyripadvdp": 250, "kyte": 265, "kytedoolitl": 265, "kyushu": 32, "l": [2, 3, 4, 7, 13, 14, 22, 30, 32, 68, 80, 90, 100, 109, 113, 126, 135, 140, 141, 148, 152, 154, 169, 170, 173, 175, 176, 182, 222, 251, 260, 261, 263, 265, 268, 270], "l12": 169, "l13": 169, "l14": 169, "l23": 169, "l31939": [238, 245], "l7gjjfe6w": 238, "la": 123, "laahlpa": 13, "lab": 21, "label": [0, 4, 8, 15, 17, 22, 42, 99, 102, 104, 117, 126, 143, 177, 178, 179, 180, 183, 185, 188, 197, 222, 260], "label_angl": [8, 104], "label_color": [8, 104], "label_compound": 105, "label_font": 104, "label_map": 105, "label_ortholog": 105, "label_posit": [8, 104], "label_reaction_entri": 105, "label_s": [8, 99, 104], "label_sep_perc": 99, "label_strand": 104, "labess": 153, "lack": [15, 17, 183, 260], "lactic": 2, "lactococcu": 8, "ladder": [17, 132, 181, 183, 190], "ladero": 2, "ladi": [7, 19], "laepwkys": 250, "laepwkysvl": 250, "laepwqys": 250, "lag": [16, 300], "laieryiv": 250, "laieryivvc": 250, "laitsslssd": 250, "lambda": [3, 6, 16, 17, 20, 23, 30, 68, 71, 183, 217, 238], "lamprei": [30, 250], "land": 2, "lander": 2, "landscap": [8, 104], "languag": [4, 6, 7, 9, 15, 19, 123, 278], "larg": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 21, 23, 25, 30, 32, 83, 84, 104, 116, 149, 158, 182, 205, 217, 238, 274, 278, 280, 290], "largefilepars": [200, 201], "larger": [6, 7, 13, 20, 23, 32, 71, 169, 237, 265, 270, 278], "largerecord": 205, "largest": [11, 13, 69, 73, 149], "larkin": 32, "larri": 2, "last": [0, 3, 4, 5, 7, 8, 13, 14, 15, 17, 20, 21, 22, 23, 30, 32, 45, 56, 67, 68, 69, 76, 80, 83, 85, 88, 123, 126, 129, 154, 182, 183, 217, 221, 222, 236, 237, 238, 241, 251, 260, 264, 269, 270, 278, 283, 298, 303, 304], "last_align": 12, "last_id": [301, 303, 304], "last_record": [23, 30], "last_row": 299, "lastli": 10, "lastupd": 7, "lat": [181, 197, 198], "later": [0, 4, 6, 7, 8, 9, 13, 15, 17, 19, 20, 21, 23, 32, 48, 63, 65, 67, 69, 73, 169, 260, 278], "latest": [9, 11, 19, 27, 210, 211, 213, 288], "lathyru": 260, "latin": 23, "latin1": 278, "latitud": 197, "latter": [0, 7, 15, 84, 143, 151, 198, 257, 270, 278], "launch": 17, "laveryivvc": 250, "lavlataava": 0, "law": 169, "layout": [15, 22, 23, 51, 66, 68, 70, 94, 99], "lazi": [0, 30, 108, 182, 236, 238], "lc": 15, "lcase_mask": [68, 69, 70], "lcc": [27, 261], "lcc_mult": [27, 261, 267], "lcc_simp": [27, 261, 267], "lccgknpfgd": 250, "lccgknplgd": 250, "ld": 13, "le": [30, 32], "lead": [0, 3, 6, 12, 13, 15, 17, 32, 67, 94, 135, 182, 183, 236, 241, 260, 270, 297], "leaf": [17, 99, 182, 183, 209], "learn": [9, 19, 120, 282], "learner": 127, "least": [1, 2, 3, 4, 6, 7, 14, 15, 19, 22, 25, 32, 69, 72, 146, 169, 217, 238, 251, 275, 283, 288, 298], "leav": [12, 17, 20, 104, 182, 183, 237, 238, 241, 251, 253], "lecb": 12, "lectin": 0, "lecuyer1988": [2, 4], "leeuwenhoek": 2, "lefort": 182, "left": [0, 4, 6, 8, 11, 12, 13, 15, 21, 24, 30, 73, 94, 99, 104, 149, 152, 176, 237, 246, 251, 253, 260, 265, 299], "left_extend_gap_scor": 13, "left_gap_scor": 13, "left_multipli": [15, 133, 176], "left_open_gap_scor": 13, "leftcount": 0, "leftgreedi": 129, "leftstatu": 0, "leg": 169, "legaci": [3, 67, 149, 209, 218, 237, 276], "legal": 5, "legion": 197, "leibler": 11, "leighton": 2, "len": [0, 1, 3, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 45, 59, 62, 66, 68, 81, 116, 131, 169, 186, 217, 218, 221, 236, 237, 238, 240, 244, 247, 250, 251, 253, 256, 260, 270, 278, 283, 298], "len1": 158, "len12": [133, 169], "len23": [133, 169], "len3": 158, "len_adaptor": 6, "len_and_id": 6, "len_prim": 6, "len_record": 6, "len_tre": 186, "length": [0, 3, 4, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, 25, 27, 30, 31, 32, 35, 36, 37, 38, 39, 43, 46, 51, 52, 55, 56, 59, 61, 65, 68, 69, 70, 71, 72, 73, 74, 80, 81, 85, 99, 104, 126, 127, 131, 135, 136, 140, 144, 152, 160, 162, 169, 172, 182, 183, 186, 197, 201, 204, 205, 218, 219, 220, 221, 226, 229, 232, 236, 237, 238, 241, 244, 250, 251, 256, 257, 260, 261, 264, 265, 270, 272, 275, 278, 280, 281, 283, 288, 290, 295, 297, 300], "lenna": 133, "lenton": 262, "leopard": 250, "lep": [30, 32], "leq": 4, "less": [4, 6, 7, 8, 11, 13, 15, 20, 21, 30, 32, 83, 99, 135, 136, 139, 169, 182, 203, 207, 217, 237, 238, 251, 260, 278, 290, 297], "let": [0, 3, 5, 6, 7, 8, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 84, 183, 236, 238, 251, 253, 260, 278], "letter": [6, 11, 12, 13, 14, 15, 19, 21, 22, 25, 30, 31, 33, 53, 54, 59, 66, 71, 76, 80, 107, 108, 109, 149, 154, 169, 172, 209, 214, 215, 222, 236, 248, 250, 251, 260, 261, 263, 290, 295, 297, 299, 302], "letter1": 108, "letter2": 108, "letter_annot": [0, 6, 21, 27, 52, 53, 66, 240, 249, 251, 253, 260], "letters_per_block": [238, 245], "letters_per_lin": [238, 245], "lettter": 30, "leu": [13, 15], "leucin": 13, "level": [6, 7, 8, 10, 15, 17, 20, 21, 22, 24, 25, 27, 32, 36, 37, 67, 69, 84, 89, 99, 101, 104, 119, 123, 133, 135, 139, 145, 146, 152, 157, 158, 159, 168, 169, 172, 182, 183, 197, 198, 209, 217, 229, 238, 241, 251, 256, 270, 274, 278, 303], "level_tag": 89, "levin": 199, "levitt": 140, "lewicki": 2, "lexp": [30, 32], "lf": 278, "lflerleenhyntytskkhaeknwfvglkkngsckrgprthygqkailf": 265, "lfvlavftvf": 0, "lg": [30, 32, 182], "lgs_t": [30, 32], "lgv": 0, "lhah": 13, "lhivvvdddpgtcvyiesvfaelghtcksfvrpeaaeeyilthp": 56, "li": [2, 4, 13, 32, 34, 52, 53, 66, 261, 263, 281], "li1985": [2, 13], "li2009": [0, 2], "li_con": 53, "lib": [8, 24, 84, 99, 102, 275], "librari": [0, 1, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 19, 24, 25, 73, 80, 140, 177, 200, 208, 234, 270, 274, 275, 278, 298], "librdf": 185, "licens": [5, 9, 15, 137, 166], "lid": [7, 123, 275], "lie": [4, 222], "liebold": 0, "life": [12, 19, 21, 253, 265], "lifson": 264, "lift": [0, 30], "lifted_align": 30, "lifted_transcript": 0, "liftov": 0, "liftover_align": 0, "ligan": 112, "ligand": [25, 53, 112, 138], "ligand_bind": 66, "ligas": 113, "light": [2, 8], "lightblu": 8, "lightgreen": 104, "lightgrei": 8, "lightweight": [177, 252], "ligm": 245, "like": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 30, 31, 32, 35, 39, 45, 46, 51, 56, 61, 66, 67, 68, 69, 70, 76, 80, 83, 84, 91, 92, 93, 95, 99, 101, 103, 104, 110, 120, 123, 129, 134, 135, 139, 145, 146, 149, 158, 169, 177, 182, 197, 199, 201, 205, 209, 210, 211, 212, 213, 214, 217, 218, 221, 229, 236, 237, 238, 241, 244, 245, 247, 248, 250, 251, 253, 254, 255, 256, 258, 259, 260, 261, 269, 270, 271, 272, 278, 282, 283, 296, 297, 302, 303], "likelihood": [2, 13, 17, 109, 120, 182, 193, 194, 195, 270], "likelihoood": 121, "likewis": [8, 21, 23, 66], "liliopsida": [7, 25], "lime": 183, "limit": [0, 3, 6, 7, 11, 12, 15, 17, 18, 20, 23, 32, 50, 65, 68, 69, 70, 83, 119, 152, 158, 197, 217, 236, 251, 270, 274, 278], "lin": 9, "lin2566": 8, "lin2567": 8, "lin2568": 8, "lin2570": 8, "lin2571": 8, "lin2572": 8, "lin2573": 8, "lin2574": 8, "lin2575": 8, "lin2576": 8, "lin2577": 8, "lin2578": 8, "lin2579": 8, "lin2580": 8, "lin2581": 8, "linalg": 15, "line": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 21, 22, 23, 24, 25, 27, 30, 32, 33, 35, 37, 42, 43, 46, 51, 52, 53, 56, 59, 61, 65, 66, 67, 68, 69, 71, 80, 81, 83, 88, 90, 94, 99, 103, 104, 117, 123, 126, 129, 132, 143, 149, 152, 154, 156, 162, 168, 169, 174, 176, 182, 190, 201, 204, 205, 207, 210, 211, 212, 213, 214, 217, 218, 222, 223, 224, 225, 226, 230, 234, 238, 241, 244, 245, 248, 250, 251, 255, 256, 260, 269, 270, 271, 272, 273, 274, 275, 277, 278, 280, 285, 295, 297], "line_count": 162, "line_length": [68, 69], "line_width": 110, "lineageex": 7, "linear": [2, 4, 7, 8, 15, 16, 21, 23, 80, 83, 99, 104, 250, 270], "linearlyinterpolatedcolor": 8, "linedistribut": [27, 98, 103], "lines": [206, 207], "linewidth": 104, "link": [2, 4, 7, 9, 15, 19, 69, 83, 93, 104, 112, 114, 117, 119, 128, 130, 158, 167, 169, 177, 197, 218, 226, 227, 229, 234], "link_xi": 8, "linkag": [4, 15, 18, 32, 73, 202, 203, 238, 243], "linker": 69, "linknam": [7, 83], "linkout": 83, "linksetdb": [7, 83], "linn": 129, "linux": [5, 6, 23, 67], "lion": 6, "lip": 32, "lipas": 25, "lipid": 272, "lipl_bovin": 25, "lipl_cavpo": 25, "lipl_chick": 25, "lipl_felca": 25, "lipl_human": 25, "lipl_mous": 25, "lipl_musvi": 25, "lipl_papan": 25, "lipl_pig": 25, "lipl_rat": 25, "lipl_sheep": 25, "lipman": [2, 3, 32, 59, 68], "lipoprotein": 25, "list": [0, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 49, 51, 54, 56, 60, 61, 62, 64, 65, 67, 68, 69, 71, 72, 73, 76, 80, 81, 82, 83, 84, 87, 88, 89, 93, 94, 99, 100, 101, 102, 103, 104, 108, 109, 112, 113, 114, 117, 119, 120, 121, 122, 123, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 137, 139, 140, 146, 149, 152, 154, 155, 156, 159, 163, 167, 169, 172, 175, 177, 179, 180, 182, 183, 186, 197, 198, 201, 202, 203, 204, 205, 207, 209, 210, 214, 217, 218, 222, 226, 236, 237, 238, 246, 248, 251, 257, 259, 260, 261, 265, 267, 269, 270, 272, 273, 274, 276, 277, 280, 282, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 297, 298, 299, 302, 303], "list_ambiguous_codon": [27, 75, 76], "list_any_id": [301, 303], "list_biodatabase_nam": [301, 303], "list_bioentry_display_id": [301, 303], "list_bioentry_id": [301, 303], "list_of_seq": 22, "list_of_tre": 132, "list_possible_protein": [27, 75, 76], "listel": [27, 83, 84], "listeria": 8, "listfil": 149, "liter": 251, "literatur": [3, 7, 11, 12, 13, 15, 68, 197, 198], "littl": [0, 6, 8, 12, 19, 23, 107, 182, 217, 251, 253, 270, 278], "liu": 32, "live": [17, 72], "liver": 7, "ll": [0, 3, 5, 6, 7, 8, 11, 12, 13, 17, 19, 20, 21, 22, 23, 24, 25, 30, 67, 95, 99, 101, 191, 251, 260], "llc": 254, "llk": 6, "lllllaalcaaggal": 13, "llr": 11, "llshc": 13, "llvt": 13, "lmax": [30, 32], "lmb": [15, 209, 210, 211, 212], "lmcp": 153, "ln": [0, 90, 264], "lnl": 17, "lnsmgfgfvntkknsar": 94, "lo": [30, 32, 53, 66], "load": [0, 1, 3, 4, 6, 7, 8, 11, 12, 14, 15, 18, 19, 23, 27, 30, 35, 36, 37, 38, 39, 42, 46, 51, 52, 53, 54, 61, 62, 66, 84, 104, 118, 121, 152, 158, 168, 169, 171, 172, 193, 195, 196, 199, 205, 209, 214, 217, 236, 238, 248, 251, 257, 260, 275, 278, 297, 301, 303, 305], "load_database_sql": [301, 303], "load_seqrecord": [301, 305], "loader": [169, 301], "loadtestsfromnam": 24, "loan": [2, 15, 216], "lobri": 265, "loc": [209, 237], "loc110697660": 3, "loc2": 237, "local": [0, 2, 6, 7, 12, 13, 14, 19, 25, 30, 32, 42, 69, 84, 94, 109, 133, 137, 149, 157, 169, 182, 197, 218, 222, 226, 267, 270, 297], "local_dtd_dir": [83, 84], "local_xsd_dir": [83, 84], "locald": [14, 297], "localhost": 305, "localis": 2, "localm": 14, "localpair": [30, 32], "localpileup": [48, 63], "localtag": 198, "localxx": [14, 297], "locat": [6, 7, 8, 11, 12, 15, 24, 27, 32, 68, 69, 72, 93, 94, 99, 104, 123, 135, 162, 169, 172, 181, 193, 195, 196, 197, 198, 207, 209, 210, 214, 217, 234, 238, 245, 253, 260, 269, 272, 277], "locationparsererror": [27, 237], "loci": [18, 201, 202, 203, 204, 205], "loci_list": [18, 201, 204, 205], "lock": 264, "locu": [7, 8, 18, 21, 23, 83, 93, 94, 201, 202, 203, 204, 237, 245, 260, 278], "locus1": 203, "locus2": 203, "locus_nam": [202, 203], "locus_tag": [8, 21, 94, 99], "locuslink": [7, 275], "locut": 69, "lod": 270, "lofstedt": 7, "log": [4, 6, 9, 11, 12, 13, 30, 32, 67, 69, 93, 107, 109, 120, 122, 127, 158, 181, 182, 202, 203, 251, 264, 270, 288, 290, 294, 297], "log10": 251, "log2": [12, 13, 182], "log_2": [11, 294], "log_bas": [12, 31], "log_likelihood": [106, 109, 121], "log_odd": [11, 283, 290], "loga": [30, 32], "logarith": 251, "logarithm": [4, 11, 12, 13, 14, 31, 100, 127, 129, 251, 294, 297], "logdpalgorithm": [27, 106, 107], "logfil": [68, 69, 182], "logist": [16, 27, 120, 298, 299, 300], "logisticregress": 27, "logo": 9, "logo_end": 283, "logo_label": 283, "logo_start": 283, "logo_titl": 283, "long": [0, 3, 6, 7, 8, 13, 15, 20, 23, 25, 32, 66, 158, 169, 181, 182, 186, 197, 198, 238, 241, 250, 251, 256, 260, 270, 274, 298, 299], "long_vers": [30, 32], "longden": 2, "longer": [3, 4, 6, 7, 8, 12, 13, 14, 15, 17, 21, 23, 56, 65, 68, 70, 76, 83, 132, 149, 182, 183, 209, 238, 245, 246, 251, 258, 270], "longest": [4, 6, 30, 65], "longitud": 197, "longseq": [30, 32], "look": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 38, 53, 66, 80, 84, 93, 97, 101, 149, 169, 209, 251, 253, 260, 261, 278, 282, 297], "lookup": [8, 15, 69, 76, 107, 139, 146, 169, 209, 301, 303], "lookuperror": 17, "loop": [0, 3, 6, 7, 8, 11, 12, 21, 22, 23, 25, 30, 32, 45, 56, 112, 113, 114, 169, 238, 264, 274, 298], "loopgap": [30, 32], "loos": 288, "lop": [30, 32], "lopez": 32, "lose": [0, 13, 20, 30, 222], "loss": [166, 181, 197, 198], "lost": [0, 21, 30, 135, 169, 197, 260], "lost_count": 197, "lot": [1, 3, 5, 6, 7, 8, 9, 11, 12, 17, 19, 21, 22, 23, 24, 25, 31, 32, 99, 204, 238, 274], "lou78617": [238, 260], "love": [3, 12], "loveliesbleed": 260, "low": [6, 13, 15, 16, 25, 99, 104, 145, 238, 251, 264, 270, 274, 278], "lower": [0, 3, 4, 6, 9, 11, 12, 13, 14, 17, 21, 22, 23, 27, 30, 32, 33, 38, 51, 56, 68, 69, 70, 73, 79, 80, 104, 152, 169, 182, 183, 197, 217, 236, 237, 238, 253, 260, 264, 270, 275, 290, 298], "lowercas": [56, 236, 238, 260, 298], "lowerq": 104, "lowest": [11, 36, 37, 104, 236, 251], "lowscor": 25, "loxafr1": 0, "loytynoja": 32, "lpaeftpavhasldkflasvstvltskyr": 13, "lpc": 15, "lpetkdwr": 0, "lpgl": 5, "lpllcagawl": 0, "lplpv": 265, "lr": [7, 120, 123, 182], "lrr": 2, "ls_orchid": [3, 6, 19, 23], "ls_orchid_long": 23, "lsd": 13, "lshtvtdftdqmaqvglcqcvnvfldevtg": 6, "lsize": 140, "lspadktnv": 14, "lspadktnvkaa": [13, 14], "lspadktnvkaawgkvgahageygaealermflsfpttkti": [12, 14], "lspadktnvkaawgkvgahageygaealermflsfpttktyfphf": 13, "lsq": 216, "lsspadktnvkkaa": 14, "lst": 169, "lstring": 0, "lstrip": [27, 236], "lt": [7, 13, 83], "ltnavahv": 13, "lttqkaekev": 250, "lump": 218, "luo": 2, "lvffaedvgsnkgaiiglmvggvvia": 154, "lvvlvvgatv": 12, "lvvyp": 14, "lvvypwt": 13, "lwgkvnvdevg": 13, "lwl85": [13, 34, 280, 281], "ly": [13, 172], "lyrata": [3, 20], "lysatgagcgatgaaaata": 222, "lysin": [14, 80], "lysinemodifi": [79, 80], "lysozym": 157, "m": [0, 2, 3, 4, 7, 11, 12, 13, 14, 15, 16, 22, 25, 30, 32, 46, 55, 56, 59, 68, 73, 80, 111, 115, 119, 139, 140, 146, 149, 152, 153, 154, 157, 159, 168, 176, 182, 183, 197, 201, 217, 218, 226, 236, 237, 251, 253, 261, 265, 268, 270, 279, 283, 294, 297], "m0": 17, "m0_param": 17, "m1": 161, "m10": [27, 56, 59, 217], "m1734_0": 11, "m17827": 13, "m17828": 13, "m17830": 13, "m17831": 13, "m17832": 13, "m17833": 13, "m17834": 13, "m17835": 13, "m17836": 13, "m17837": 13, "m19547": 13, "m2": 161, "m2rotaxi": [27, 133, 176], "m81224": [238, 245], "m_code": 69, "m_cold": [1, 3, 69], "m_reb1": 11, "m_sub": 11, "ma": [3, 7, 20, 30, 32], "ma0001": [11, 288], "ma0002": 11, "ma0004": 11, "ma0047": 287, "ma0049": 288, "ma0052": 11, "ma0098": 288, "maagvkqlad": 260, "maagvkqladdrtllmagvshdlrtpltrirlat": 260, "maagvkqladdrtllmagvshdlrtpltrirlatemmseqdgylaesinkdie": 260, "mac": [5, 278], "macaca": [3, 20], "macaqu": [0, 22], "macclad": 0, "machin": [3, 9, 13, 16, 23, 56, 59, 182, 239, 298], "macintosh": 5, "mackenzi": 2, "macromolecul": 15, "macromolecular": [15, 133, 149, 160, 238], "madden": [3, 68], "maddison": [2, 129], "maddison1997": [0, 2], "made": [3, 4, 12, 13, 15, 18, 19, 21, 22, 31, 100, 183, 237, 251, 260, 283, 303], "maegeittftaltekfnlppgnykkpkllycsngghflrilpdgtvdgt": 265, "maeii": 206, "maf": [22, 27, 30, 37, 61, 278], "maf3": 0, "maf_fil": 61, "maf_project": 0, "mafblock": 0, "mafdot": 0, "mafft": 32, "mafft_clin": 32, "mafft_ex": 32, "mafftcommandlin": [30, 32], "mafindex": [27, 56, 61], "mafio": [27, 56], "mafiter": [27, 56, 61], "maftltnknvvfvaglggigldtskelvkrdlknlvildrienpaaiaelkainpkvtvt": 13, "maftobigmaf": 0, "mafwrit": [27, 56, 61], "magalha": 7, "magenta": 183, "magic": [3, 24, 278], "magnet": [125, 158, 169], "magnitud": [4, 73], "magnoliophyta": [7, 25], "magnoliopsida": 7, "mahabhashyam": 32, "maharvllla": 0, "maharvlllalavlataavavassssfadsnpirpvtdraastl": 56, "maharvlllalavlataavavassssfadsnpirpvtdraastlesavlgalgrtrhalr": 0, "mai": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 36, 37, 38, 45, 46, 52, 53, 56, 60, 65, 66, 67, 68, 70, 71, 73, 76, 81, 83, 84, 92, 93, 100, 104, 107, 116, 119, 137, 158, 169, 182, 183, 193, 195, 196, 197, 198, 209, 211, 214, 217, 218, 221, 222, 226, 229, 234, 237, 238, 240, 246, 248, 251, 260, 261, 264, 270, 272, 277, 278, 288, 297, 298, 303], "mail": [7, 8, 9, 17, 19, 27], "mailing_list": 19, "main": [1, 3, 5, 6, 7, 8, 9, 11, 12, 19, 20, 21, 24, 50, 65, 83, 88, 104, 129, 143, 209, 217, 238, 260, 298], "mainchain": [15, 169], "mainli": 217, "maintain": [9, 12, 83, 100, 217, 238], "mainten": 67, "maivmgr": [22, 260], "maivmgrwkga": 261, "maivmgrwkgar": [22, 236, 261], "maivmgrwkgaxxr": 261, "major": [3, 5, 7, 9, 21, 132, 186], "majority_consensu": [27, 181, 186], "majr": 7, "majumdar": 2, "majumdar2005": [2, 15], "make": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 56, 67, 73, 80, 82, 93, 94, 97, 99, 102, 104, 108, 109, 117, 119, 129, 146, 149, 169, 182, 209, 217, 221, 222, 237, 238, 251, 253, 257, 260, 264, 265, 274, 278, 294, 298, 305], "make_back_t": [27, 75, 76], "make_dssp_dict": [27, 133, 137], "make_extend": [133, 169], "make_format": [206, 207], "make_protein_record": 6, "make_shuffle_record": 6, "make_t": [27, 261, 264], "make_tupl": 238, "make_virtual_offset": [27, 278], "makeblastdb": 69, "makematrix": [181, 182], "maket": 264, "malform": 270, "man": 121, "manag": [11, 91, 107, 129, 130, 131, 132, 169, 197], "mandatori": [7, 12, 21, 69, 182], "manderick": [2, 7, 9, 15], "mangalam": 7, "manhattan": 4, "mani": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 15, 16, 19, 20, 21, 22, 23, 24, 25, 32, 56, 60, 66, 69, 80, 83, 104, 133, 144, 182, 217, 219, 222, 231, 232, 236, 238, 243, 245, 265, 274, 288, 299, 303, 304], "manifest": 253, "manipul": [4, 7, 9, 15, 18, 19, 20, 23, 35, 46, 51, 61, 67, 71, 104, 126, 132, 169, 251], "manlfmvlfg": 250, "mann": 83, "manner": [15, 38, 110, 222, 237], "manor": 8, "manual": [7, 8, 11, 17, 19, 20, 23, 24, 31, 67, 68, 70, 182, 183, 209, 214, 245, 253, 264], "manufactur": 264, "manuscript": [8, 123], "map": [2, 3, 6, 10, 12, 13, 17, 20, 23, 27, 30, 52, 55, 69, 72, 73, 76, 83, 84, 99, 102, 104, 105, 108, 111, 115, 116, 117, 126, 134, 137, 140, 145, 161, 169, 172, 183, 197, 207, 209, 214, 221, 236, 251, 260, 263, 269, 270, 273, 275, 278, 279], "map_func": [3, 20], "mapal": [0, 13, 27, 30], "mapameeirqaqraegpaavlaigtstppnalyqadypdyyfritksehltelk": 23, "mapped_align": 13, "mapped_qresult": 20, "mapq": [52, 270], "maq": 6, "mar": [86, 88, 149], "march": 25, "marck": 259, "marena": 23, "margin": [104, 105, 182], "margouli": 2, "mark": [2, 6, 8, 27, 104, 169, 205, 229, 236, 237, 251, 270], "marker": [18, 72, 99, 201, 204, 205, 251, 275, 278], "marker_len": [201, 204, 205], "markov": [0, 2, 32, 44, 106, 107, 108, 109, 121, 229], "markov_model": [107, 109, 121], "markovmodel": [27, 106], "markovmodelbuild": [27, 106, 108], "marku": 2, "markup": 7, "markw": 236, "marmoset": 0, "marmur": 264, "maroon": 183, "marshak": 264, "marth": 2, "martin": 2, "masahiko": 2, "masatoshi": 2, "mase": [56, 238, 244], "mask": [0, 4, 27, 29, 30, 32, 38, 51, 53, 69, 73, 169, 247, 257, 283], "mask_data": [68, 69], "mask_desc": [68, 69], "mask_id": [68, 69], "maskel": 32, "masrgvnkvilvgnlgqdpevrympnggavanitlatseswrdkat": 260, "masrgvnkvilvgnlgqdpevrympnggavanitlatseswrdkatgemkeqt": 260, "mass": [112, 119, 135, 139, 261, 265], "mast": [27, 283, 291], "master": [4, 17, 25, 69], "mat": [30, 32], "mat_thr": [30, 32], "matbla": 13, "match": [0, 3, 6, 7, 8, 9, 12, 14, 15, 17, 20, 21, 22, 24, 25, 27, 30, 32, 33, 38, 42, 51, 55, 68, 69, 71, 79, 80, 83, 99, 104, 119, 132, 138, 168, 169, 175, 181, 183, 188, 214, 217, 218, 221, 226, 234, 237, 238, 247, 248, 251, 253, 260, 270, 274, 275, 277, 278, 288, 289, 290, 297], "match_column": 0, "match_dict": 297, "match_fn": 297, "match_num": 221, "match_rep_num": 221, "match_scor": [13, 30], "mate": 270, "mate_fil": [268, 270], "materi": 93, "math": [12, 15, 24, 169, 297], "mathdoc": 15, "mathemat": [7, 13], "mathew": 264, "mathml": 7, "mathrm": 12, "mati": 2, "matinits": [30, 32], "matk": 7, "matplotlib": [6, 15, 17, 169, 183], "matr": 7, "matres": [30, 32], "matric": [2, 9, 14, 15, 30, 34, 54, 80, 121, 129, 158, 169, 176, 199, 286, 287, 288, 290, 297, 299], "matrix": [0, 2, 3, 6, 14, 15, 27, 30, 31, 32, 49, 54, 56, 64, 68, 69, 70, 71, 73, 80, 88, 121, 129, 131, 135, 139, 158, 166, 169, 175, 176, 177, 181, 182, 199, 216, 270, 283, 286, 287, 288, 293, 295, 296, 297, 299], "matrix_id": [11, 287, 288], "matrix_nam": [68, 70], "matrixtyp": [79, 80], "matsumoto": 25, "matter": [3, 21, 23, 24, 25, 199], "matur": 272, "maturas": 7, "matys2003": [2, 11], "mau": 2, "mauv": [2, 27, 30, 56, 62], "mauve1": [0, 62], "mauveio": [27, 56], "mauveiter": [27, 56, 62], "mauvewrit": [27, 56, 62], "max": [2, 4, 6, 7, 8, 11, 15, 16, 17, 32, 69, 80, 145, 197, 237, 240, 251, 270, 283, 290, 299], "max_": 263, "max_cach": 278, "max_confid": 190, "max_file_sz": [68, 69], "max_gap": 166, "max_guidetree_iter": [30, 32], "max_hmm_iter": [30, 32], "max_hsp": [68, 69], "max_hsps_per_subject": [68, 69], "max_iis_iter": 122, "max_intron_length": [68, 69], "max_len": 8, "max_link": [30, 32], "max_newton_iter": 122, "max_num_thread": 149, "max_scor": [11, 279], "max_support": 132, "max_target_seq": [68, 69], "max_tri": 83, "maxbranch": [30, 32], "maxcount": 246, "maxdiagbreak": [30, 32], "maxdiff": 270, "maxdifftm": [79, 80], "maxdiv": [30, 32], "maxentropi": 27, "maxgc": [79, 80], "maxhour": [30, 32], "maxim": [2, 4, 207, 237, 270, 290], "maxima": 109, "maximum": [0, 4, 7, 8, 11, 13, 16, 17, 30, 32, 69, 73, 80, 83, 88, 104, 109, 121, 122, 149, 166, 181, 182, 193, 195, 197, 198, 236, 237, 246, 251, 263, 270, 278, 280, 299, 300], "maxit": [30, 32], "maxiter": [30, 32], "maxmem": 270, "maxmisprim": [79, 80], "maxnumseq": [30, 32], "maxocc": 270, "maxpallen": [79, 80], "maxpeptidebond": [15, 133, 158, 169], "maxpolyx": [79, 80], "maxr": 126, "maxrepeat": [79, 80], "maxseqlen": [30, 32], "maxsiz": [79, 80, 206, 207], "maxsplit": 236, "maxtm": [79, 80], "maxtre": [30, 32, 79, 80], "mayb": [5, 6, 7, 15, 274], "mb": 214, "mbed": 32, "mbox": 4, "mbp": 104, "mbstat": [3, 68], "mc": 207, "mcdonald": [34, 280], "mcgettigan": 32, "mclachlan": 199, "mcm": 0, "mcra": [17, 183], "mcwilliam": 32, "md": [0, 30, 52, 270], "mdiaihhpwi": 250, "mdirqgpkepfrdyvdrfyktlraeqasqevknwmtetllvqnanpdcktilkalgpgatleemmtacqg": 154, "mditihnpli": 250, "mdl": 168, "mdm78": 199, "me": [1, 3, 7, 9, 122, 182], "mean": [0, 3, 6, 7, 8, 11, 12, 14, 15, 16, 17, 19, 20, 21, 22, 23, 30, 64, 65, 69, 73, 76, 98, 104, 149, 152, 175, 182, 186, 197, 198, 199, 202, 203, 216, 217, 222, 236, 237, 238, 241, 250, 251, 260, 261, 263, 264, 265, 278, 283, 290, 297, 300], "meaning": [13, 14, 17, 132, 183, 303], "meaningless": 22, "meant": [20, 21, 31, 93, 97, 99, 103, 107, 207, 218, 237], "meantim": 277, "measur": [2, 4, 11, 12, 16, 32, 80, 152, 157, 169, 172], "mechan": [7, 19, 22, 67, 95, 158, 169], "med": [95, 124], "media": [0, 16], "median": 73, "medianq": 104, "medic": 7, "medium": [18, 23, 283], "medlin": [9, 11, 27, 93, 201, 237, 287, 288], "medline_id": [21, 93, 237], "medlinecit": [7, 83], "medoid": 73, "medydpwnlrfqskyksrda": 95, "meet": [183, 288], "mef2a": 11, "mega": [3, 68, 70], "megablast": [13, 30, 68, 69, 70, 199], "mehkevvlllllflksgqgeplddyvntqgaslfsvtkkqlgagsieecaakceedeeft": 25, "meier": 2, "meisner": 122, "melanogast": 13, "melt": [80, 264], "melting_temp": 264, "meltingtemp": [27, 261], "mem": 270, "member": [0, 4, 25, 68, 71, 72, 73, 81, 84, 89, 100, 122, 201, 205], "membership": [3, 6, 17, 20, 169, 183, 237], "membran": [3, 25, 260, 272], "meme": [27, 283, 289, 292], "meme10": 11, "memo": 169, "memoir": 167, "memori": [0, 1, 3, 4, 6, 7, 12, 14, 15, 21, 30, 56, 67, 68, 168, 169, 182, 198, 204, 205, 209, 214, 217, 238, 251, 253, 257, 269, 270, 278, 297], "memoryerror": 7, "memsav": [30, 32], "menlo": 2, "mention": [1, 3, 6, 7, 15, 19, 20, 21, 22, 23], "menunam": 7, "mercuri": [135, 162], "mere": 20, "merg": [4, 8, 32, 132, 270], "merge_bootstrap": 132, "merge_cmd": 270, "merge_with_support": [128, 132], "mergeai": 2, "merychippu": 56, "mesembryanthemum": 1, "mesh": [7, 123, 274], "meshmix": 158, "mesirov": 2, "mesohippu": 56, "mess": [20, 25, 204], "messag": [3, 12, 25, 27, 32, 67, 68, 80, 83, 84, 89, 168, 193, 195, 196, 270, 288], "messeng": 22, "messenger_rna": 22, "messi": 21, "met": [13, 15, 280], "meta": [11, 12, 46, 53, 66, 253, 269, 270], "meta_nod": 188, "metabol": [16, 104, 116], "metaclass": 84, "metadata": [0, 45, 46, 47, 61, 252, 287, 299], "metal": [25, 272], "metalailevalmetglyargtrplysglyala": 261, "metalailevalmetglyargtrplysglyalaarg": 261, "metalailevalmetglyargtrplysglyalaargt": 261, "metalailevalmetglyargtrplysglyalaxaaxaaargt": 261, "metalliduran": 2, "metaphor": 12, "meter": 197, "meth": 169, "methanococcu": 94, "methionin": [22, 154, 236, 272], "method": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 15, 16, 19, 20, 22, 23, 24, 25, 30, 31, 32, 34, 36, 45, 53, 54, 60, 61, 66, 67, 71, 73, 79, 80, 83, 91, 94, 99, 100, 104, 108, 109, 122, 126, 132, 135, 136, 139, 143, 148, 149, 151, 154, 169, 170, 172, 173, 176, 181, 182, 183, 186, 194, 197, 198, 199, 204, 207, 209, 236, 237, 238, 241, 246, 249, 251, 252, 253, 257, 260, 263, 264, 265, 270, 278, 280, 281, 282, 283, 288, 291, 294, 297, 299, 303, 305], "methyl": 112, "metric": [4, 197], "mexipedium": 19, "meyer": 149, "mf": 0, "mfa": 32, "mg": [15, 264], "mg2": 264, "mgc": 275, "mgf": 25, "mgggmisklfclaliflsssglaekntytakdilqnlelntfgnslshgiygkqttfkqteftniksntkkhialinkdnswmislkilgikrdeytvcfedfslirpptyvaihpllikkvksgnfivvkeikksipgctvyyh": 21, "mgltool": 156, "mgnpkvkahgkkvlgafsd": 13, "mgstm1": 0, "mgta": 13, "mgtalllllaalcaaggal": 13, "mh": 123, "mhda": 123, "mhp": 8, "mhz": 15, "mi": [0, 6], "mian": [0, 2], "michael": [2, 4, 73], "michel": [15, 156], "michiel": [2, 26], "microarrai": [2, 238, 298, 299, 300], "microbesonlin": [17, 182], "microphylum": 197, "microrna": [3, 20], "microsequ": 0, "microtu": [6, 8, 21, 238], "mid": 123, "middl": [3, 6, 8, 23, 68, 104], "midlin": [3, 68], "midpoint": [17, 183], "might": [3, 5, 6, 7, 8, 11, 12, 17, 18, 20, 21, 22, 23, 24, 32, 95, 110, 132, 143, 151, 183, 197, 202, 204, 238, 251, 253, 260, 269], "migrant": 202, "migrat": 18, "miller": [2, 3, 32, 68, 133, 137, 169], "millimolar": [80, 264], "million": [6, 23, 197], "milot": 2, "mimic": [6, 218, 221, 226, 264], "mimick": [3, 294], "mimicri": 7, "min": [6, 7, 11, 16, 182, 237, 251, 283, 290, 299], "min_": 263, "min_dist": [27, 133, 156, 202, 203], "min_ic": [11, 288], "min_len": 6, "min_length": 288, "min_link": [30, 32], "min_pro_len": 6, "min_protein_length": 6, "min_raw_gapped_scor": [68, 69], "min_scor": 11, "min_sit": 288, "minbaseq": 270, "minbestcolscor": [30, 32], "mincount": 246, "mind": [4, 7, 12, 19, 73, 103, 114], "mine": 114, "mingc": [79, 80], "minidb": 303, "minim": [0, 4, 8, 11, 15, 24, 27, 35, 46, 51, 61, 163, 166, 175, 177, 191, 198, 216, 237, 238, 270, 283, 290], "minimal_test": 292, "minimis": 209, "minimum": [6, 11, 13, 16, 21, 32, 69, 80, 104, 156, 181, 182, 197, 198, 237, 251, 263, 270, 299], "minlod": 270, "minmapq": 270, "minor": 270, "minoru": 2, "minpallen": [79, 80], "minr": 126, "minrepeat": [79, 80], "minscor": [79, 80], "minseedlen": 270, "minsiz": [79, 80], "minsmoothscor": [30, 32], "mintm": [79, 80], "minu": [15, 20, 63, 69, 119, 221, 222, 237, 251, 270], "minum": 299, "minut": [3, 4, 6, 15, 16, 23, 25], "minw": 11, "mir": [3, 20], "mir519a": 3, "mir520": 20, "mir520b": [3, 20], "mir520c": [3, 20], "mir_1": 217, "mir_2": 217, "mir_3": 217, "mirdita": 2, "mirna": [20, 217, 268, 270], "mirror": [15, 89, 149, 158, 169, 176, 303], "misalign": 270, "misawa": 32, "misc": [22, 76, 94], "miscellan": [21, 104, 261], "mishyblibraryfil": [79, 80], "mislead": [240, 303], "mismatch": [3, 6, 14, 20, 27, 30, 38, 42, 51, 68, 69, 71, 79, 80, 168, 218, 221, 264, 270, 297], "mismatch_num": [20, 218, 221], "mismatch_scor": [13, 30], "mismatchperc": [79, 80], "mismsc": 270, "mispriminglibrari": 80, "mispriminglibraryfil": [79, 80], "miss": [0, 5, 11, 12, 15, 18, 27, 56, 63, 73, 129, 151, 152, 158, 169, 197, 237, 238, 248, 251, 253, 270, 278], "missing_residu": 15, "missingatomerror": [27, 133, 169], "missingexternaldependencyerror": 27, "missingok": 169, "missingpythondependencyerror": 27, "mission": 123, "mistak": [3, 12, 15, 22], "mitchison": 2, "mito_t": 22, "mitochondri": [7, 22], "mitochondria": 8, "mitochondrion": 272, "mitogeneticcod": 7, "mix": [6, 22, 32, 83, 84, 182, 197, 237, 253, 261], "mixi": 182, "mixtur": [2, 6, 129], "miyano": [2, 7], "miyata": 32, "miyazawa": 265, "mj": 7, "mkdssp": 137, "mkkmqsivlalslvlvapmaaqaaeitlvpsvklqigdrdnrgyywdgghwrdh": 22, "mkqhkamivaivicitavvaalvtrkdlcevhirtgqtevavf": 260, "mkqhkamivalivicitavva": 237, "mkqhkamivalivicitavvaalvtrkdlcevhirtgqtevavf": [236, 260], "mkt": [34, 280], "mktest": [13, 27, 30, 34, 279, 280], "mkvil": 0, "mkvillfvlavftvfvss": [0, 56], "ml": [13, 34, 80, 182, 280, 281], "ml_estim": [106, 109], "mlacc": [181, 182], "mle": 121, "mlfrac": [79, 80], "mlgsnesrvcpklsp": 30, "mllen": [181, 182], "mlnni": [181, 182], "mlyi": 206, "mm": [53, 66, 121, 152, 158, 264], "mm10": [0, 22], "mm10tomm39": 0, "mm39": 0, "mm4": 0, "mm9": 0, "mmcif": [133, 137, 142, 143, 149, 150, 164, 169, 170, 172, 238, 248], "mmcif2dict": [15, 27, 133], "mmcif_dict": 15, "mmcif_pars": 164, "mmcif_pdbx_v40": 248, "mmcif_pdbx_v50": 248, "mmcifio": [15, 27, 133], "mmcifpars": [15, 27, 133, 162, 164, 170, 173, 238], "mmcipars": 143, "mmlib": 15, "mmm": [88, 270], "mmtf": [27, 133, 149], "mmtfio": [15, 133, 171], "mmtfparser": [15, 133, 171], "mmtk": 15, "mmtv": 68, "mmyqqgcfaggtvlrlakdlaennrgarvlvvcseitavtfrgpsethldsmvgqalfgd": [21, 23], "mn": 23, "mnemon": 123, "mngtegdnfi": 250, "mngtegpnfi": 250, "mnllltlltnttlalllvfi": 272, "mnmnm": 0, "mnp": 270, "mo_prob": 294, "mod": [11, 149, 218], "mod_r": 272, "mode": [1, 6, 7, 9, 13, 23, 25, 27, 30, 32, 36, 37, 45, 68, 79, 80, 83, 91, 129, 143, 182, 199, 241, 244, 245, 246, 247, 248, 249, 251, 252, 253, 256, 259, 264, 270, 271, 303], "model": [0, 2, 3, 7, 11, 12, 16, 17, 21, 25, 27, 30, 32, 33, 42, 44, 53, 68, 71, 80, 84, 99, 106, 107, 108, 109, 110, 121, 123, 125, 128, 133, 135, 136, 137, 138, 139, 140, 141, 145, 146, 148, 153, 156, 157, 158, 160, 161, 162, 168, 169, 170, 172, 173, 177, 181, 182, 185, 195, 199, 217, 222, 229, 234, 237, 248, 270, 299, 300], "model_id": [15, 138, 162, 172], "model_mask": 66, "model_nr": 15, "moder": [23, 270], "modif": [15, 23, 182, 218, 272], "modifi": [0, 3, 4, 11, 12, 13, 17, 20, 21, 24, 80, 93, 149, 154, 158, 166, 169, 182, 183, 191, 209, 214, 217, 218, 236, 241, 251, 278, 283, 294], "modify_record": [241, 251], "modr": 248, "modul": [0, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 307], "module_nam": [303, 304], "moieti": 272, "mol": [74, 119, 140, 149, 157, 264], "mol_seq": [181, 197, 198], "mol_typ": 7, "mol_weight": [10, 119], "molar": [264, 265], "molar_extinction_coeffici": [261, 265], "molbev": 2, "molecul": [15, 20, 21, 22, 56, 69, 104, 157, 166, 197, 214, 238, 250, 252, 260, 261, 272], "molecular": [0, 2, 7, 9, 10, 12, 19, 23, 27, 32, 83, 112, 119, 156, 169, 197, 198, 261, 265, 272], "molecular_weight": [27, 261, 265], "molecule_typ": [0, 21, 25, 56, 238, 252, 253, 260, 272], "molseq": [27, 181, 197], "moment": [149, 270, 277], "mondom5": 22, "mono": 259, "monoisotop": [261, 265], "monom": 0, "mononucleotid": 80, "monooxygenas": 113, "monophylet": [17, 132, 182, 183], "monoval": 264, "monphyli": 132, "month": 152, "montpelli": [17, 182], "moor": 7, "mopb_rhoca": 68, "more": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 35, 36, 37, 38, 45, 46, 49, 50, 51, 52, 53, 56, 59, 61, 64, 65, 66, 67, 68, 70, 71, 72, 73, 76, 80, 83, 84, 90, 91, 93, 99, 107, 108, 113, 117, 123, 129, 149, 155, 157, 169, 177, 182, 197, 198, 204, 207, 212, 214, 215, 217, 218, 221, 222, 226, 227, 229, 234, 237, 238, 239, 240, 251, 252, 253, 255, 260, 262, 269, 270, 271, 273, 274, 275, 278, 283, 288, 295, 297, 298, 299], "more_target": 183, "more_termin": 183, "moreov": 20, "morgenstern": 32, "mornon": 153, "most": [0, 1, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 45, 50, 56, 59, 65, 66, 67, 68, 69, 80, 83, 85, 99, 101, 108, 139, 149, 152, 177, 182, 183, 197, 201, 209, 217, 221, 222, 236, 237, 238, 241, 248, 251, 260, 264, 265, 278, 283, 298, 303], "mostli": [15, 32], "mot": [30, 32], "motif": [2, 9, 12, 26, 27, 32, 53, 114, 272, 307], "motif1": 11, "motif2": 11, "motif_1": 11, "motif_nam": [11, 291], "motifexplor": 296, "motifsm": 11, "motiv": [7, 19, 23], "mott": 238, "mous": [0, 11, 22, 30, 182], "move": [5, 6, 15, 20, 92, 100, 104, 132, 163, 169, 175, 176, 182, 237, 278], "move_track": [98, 104], "mp": [1, 182], "mp14h09": 1, "mpi": 182, "mpileup": 270, "mpwrrnmqsc": 0, "mpwrrnrqsc": 0, "mr": 80, "mrbay": 129, "mrc": [15, 209, 210, 211, 212], "mrca": [17, 183], "mre": 80, "mrlllelkalnsidkkqlsnyliqgfiynilknteyswlhnwkk": 94, "mrlllelkalnsidkkqlsnyliqgfiynilknteyswlhnwkknekyfnft": 94, "mrna": [3, 7, 21, 22, 68, 238, 275], "mrna1": 0, "mrna2": 0, "msa": [12, 30, 32, 69, 186, 199], "msa_master_idx": [68, 69], "msaprob": 32, "msaprobscommandlin": [30, 32], "msb": 32, "mse": [15, 154], "msei": 206, "msf": [27, 30, 32, 56, 63], "msf_aln": 32, "msfio": [27, 56], "msfiter": [27, 56, 63], "msfout": [30, 32], "msftltnknvifvaglggigldtskellkrdlknlvildrienpaaiaelkainpkvtvt": 13, "msm": [15, 156], "msms_exec": 156, "msms_home": 15, "msr": [30, 279], "mt": [32, 264], "mtart": 182, "mtfglvytvyataidpkkgslgtiapiaigfivgani": 241, "mtmam": 182, "mtrev": 182, "mttranslat": [30, 32], "mtx": [169, 176], "mu": [25, 217], "mu_": 16, "much": [0, 3, 4, 5, 6, 7, 11, 13, 15, 17, 19, 21, 22, 23, 25, 30, 83, 84, 92, 93, 94, 166, 175, 204, 209, 217, 218, 238, 264, 270], "mulatta": [3, 20], "multi": [23, 30, 32, 81, 94, 131, 180, 182, 183, 270, 278, 280], "multi_coord_spac": [27, 133, 176], "multi_rot_i": [27, 133, 176], "multi_rot_z": [27, 133, 176], "multidimension": 2, "multifurc": 182, "multigraph": [177, 178], "multilevel": 83, "multilocu": [202, 203], "multilocusfi": 202, "multilocusfst": 202, "multipass": [3, 68], "multipl": [1, 2, 3, 4, 6, 7, 11, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 43, 44, 45, 46, 53, 56, 59, 61, 62, 65, 66, 69, 71, 74, 81, 83, 84, 86, 88, 90, 92, 94, 99, 103, 104, 116, 130, 132, 149, 154, 169, 172, 181, 182, 186, 197, 199, 206, 217, 234, 236, 237, 241, 244, 246, 250, 251, 253, 260, 261, 267, 270, 271, 272, 275, 278, 281, 283, 288, 298, 307], "multiple_align": 71, "multiple_value_kei": [283, 295], "multiplealign": [27, 68, 71], "multipleseqalign": [0, 3, 9, 12, 20, 27, 30, 56, 59, 60, 61, 64, 65, 66, 71, 186, 197, 199, 217, 279, 280], "multipli": [6, 11, 12, 13, 15, 32, 107, 135, 139, 169, 175, 176, 216, 287], "multist": 131, "multivari": 4, "multiz": 0, "multiz28wayfram": 0, "munteanu": 7, "muscl": [7, 32, 48, 63, 197], "muscle3": 32, "muscle_clin": 32, "muscle_ex": 32, "musclecommandlin": [30, 32], "musculu": 217, "must": [0, 3, 5, 8, 10, 11, 12, 13, 14, 17, 20, 21, 23, 24, 30, 32, 35, 36, 37, 38, 47, 53, 54, 56, 61, 66, 67, 68, 69, 83, 92, 104, 107, 108, 117, 122, 127, 152, 169, 175, 182, 183, 186, 199, 207, 209, 214, 217, 229, 236, 237, 238, 247, 248, 250, 251, 260, 264, 270, 278, 288, 290, 297, 299, 303], "mutabl": [22, 236], "mutable_seq": 22, "mutableseq": [0, 9, 27, 30, 236, 237, 260, 261], "mutagen": 272, "mutagenesi": [264, 272], "mutant": 15, "mutat": [13, 22, 155], "mv": [12, 13, 14], "mvhl": [13, 14], "mvhltpeeksavtalwgkv": [12, 13, 14], "mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk": 12, "mvlspadktnvkaawgkvgahageygaealermflsfpttktyfphfdlshgsaqvkghg": 12, "mvtveefrraqcaegpatvmaigtatpsncvdqstypdyyfritnsehkvelkekfkrmc": 23, "mvvvivgati": 12, "mw": 265, "mwat": 0, "mwatlpllcagawllgv": [0, 56], "my": [3, 8, 9, 15, 17, 19, 23, 25, 32, 84, 108, 169, 207], "my_ace_fil": 269, "my_align": 12, "my_blast": [3, 20], "my_blat": 20, "my_cod": 131, "my_el": 83, "my_exampl": [12, 23], "my_gap_score_funct": 13, "my_info": 1, "my_info_handl": 1, "my_iter": 56, "my_loc": 21, "my_map": 207, "my_partially_defined_sequ": 236, "my_pssm": 12, "my_qblast_output": 3, "my_qblast_output_select": 3, "my_record": [23, 260], "my_seq": [19, 22, 236], "my_seq_featur": 8, "my_snp": 21, "my_str": 22, "my_undefined_sequ": 236, "mya": 197, "myapikei": 7, "myatom1": 15, "myatom2": 15, "mybed12fil": 0, "mybed3fil": 0, "mybed6fil": 0, "mychain": [15, 169], "mychain2": [15, 169], "mycic": 15, "mydatafil": 4, "myer": [2, 32], "myfastaread": 246, "myfil": [0, 7, 60, 246], "myfilenam": 0, "mylocalscript": 7, "mymotif": 11, "myprodocrecord": [25, 85], "myprositefil": 25, "myprositerecord": [25, 85], "myprotein": [15, 169], "myprotein2": [15, 169], "myprotein3": [15, 169], "myrandom": [15, 169], "myrecord": [241, 250], "myresult": 80, "myseq": 264, "mysequ": 80, "mysingleprositerecord": 25, "mysql": [209, 303, 304], "mysql_dbutil": [301, 304], "mysqlconnectoradaptor": [301, 303], "mysqldb": [209, 288, 303, 305], "mystery_seq": [3, 20], "mystr": 264, "myswissprotfil": 25, "mytabl": 264, "mytransfacfil": 11, "mytre": 73, "myunigenefil": 7, "myzipfil": 3, "m\u00fcnch": 2, "n": [0, 1, 3, 4, 6, 7, 10, 11, 12, 13, 14, 15, 17, 22, 23, 25, 30, 32, 38, 46, 51, 74, 80, 94, 119, 126, 129, 132, 135, 136, 149, 152, 153, 154, 166, 169, 175, 181, 182, 183, 185, 201, 207, 216, 221, 229, 237, 238, 245, 247, 251, 257, 260, 261, 263, 264, 265, 268, 270, 278, 290, 297], "n0": 183, "n1": [183, 250], "n15": [125, 126], "n3": 250, "n5kn7umj013": 3, "n5kn7umj013_1": 3, "n_": 12, "n_g": 270, "n_match": [25, 89], "n_num": 221, "n_point": 157, "n_rand_start": [181, 182], "n_seq": [25, 89], "n_x": 4, "n_y": 4, "na": [11, 80, 264, 295], "na_eq": 264, "naccess": [27, 133], "naccess_atom": [27, 133, 145], "naccess_binari": 145, "naccggatgta": 238, "nacgt": 91, "nacgtacgta": 251, "nad": 272, "nadh": [16, 113], "nag": 0, "nagaagagccgcnggcactt": 247, "nagaagagccgcnggcacttgantatcgtcgccaccagncgncttgntgg": 247, "naggctcggtta": 238, "naiv": [6, 7, 9, 76, 122, 127, 251], "naivebay": 27, "name": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45, 47, 49, 50, 51, 52, 53, 54, 56, 59, 61, 65, 67, 68, 69, 71, 73, 76, 80, 82, 83, 84, 86, 87, 88, 89, 90, 92, 93, 94, 99, 100, 101, 102, 103, 104, 112, 113, 114, 115, 117, 119, 121, 123, 125, 126, 129, 132, 135, 137, 139, 140, 141, 142, 143, 149, 151, 152, 154, 155, 158, 162, 167, 169, 172, 175, 181, 182, 183, 184, 185, 187, 189, 197, 198, 199, 201, 202, 204, 205, 207, 211, 217, 218, 221, 229, 234, 236, 237, 238, 241, 247, 249, 250, 251, 252, 253, 256, 257, 259, 260, 263, 269, 270, 272, 275, 278, 280, 287, 288, 289, 291, 292, 295, 296, 297, 299, 303, 304], "name1": 129, "name2": 129, "name_map": 12, "name_qualifi": [99, 104], "namedtupl": [0, 30, 169], "namelength": [30, 32], "namelist": 3, "namespac": [27, 84, 188, 197, 198, 252, 303], "namesrt": 270, "namewidth": [206, 207], "nan": [16, 299], "nannipu": 56, "nanomolar": 80, "naohisa": 2, "nar": [2, 69, 251], "naringenin": 23, "narrow": 129, "nasti": 251, "nat1": 7, "nat2": 7, "nation": [2, 32, 238, 250], "nativ": [11, 12, 20, 140, 218, 238, 253, 254, 270], "natl": [83, 264], "natom": 175, "natur": [20, 22, 100, 260, 294], "navi": 183, "navig": 17, "naynyiikng": 0, "nb": [2, 127, 183, 197], "nbk1762": 218, "nbk25499": 83, "nbk25501": [7, 83], "nbrf": [32, 238, 250], "nc": [0, 11, 53, 169, 207], "nc_000932": [92, 237, 238, 278], "nc_001136": 0, "nc_001145": 0, "nc_002703": 8, "nc_003070": 8, "nc_003071": 8, "nc_003074": 8, "nc_003075": 8, "nc_003076": 8, "nc_003132": 21, "nc_003212": 8, "nc_0058": 21, "nc_005816": [6, 7, 8, 21, 69, 238, 256], "nca": 169, "ncac": 169, "ncackei": 169, "ncaco": 169, "ncategori": [79, 80], "ncbi": [0, 6, 8, 9, 13, 19, 20, 21, 22, 23, 26, 32, 38, 68, 69, 70, 71, 76, 83, 84, 93, 94, 96, 97, 119, 123, 197, 218, 234, 236, 237, 238, 245, 251, 252, 253, 272, 274, 275, 303, 307], "ncbi_blast_url": [68, 70], "ncbi_blastoutput": [68, 71, 218], "ncbi_gi": [68, 70], "ncbi_taxonomi": 197, "ncbiblastformattercommandlin": [27, 68, 69], "ncbiblastncommandlin": [27, 68, 69], "ncbiblastpcommandlin": [27, 68, 69], "ncbiblastxcommandlin": [27, 68, 69], "ncbicodont": [27, 75, 76], "ncbicodontabledna": [27, 75, 76], "ncbicodontablerna": [27, 75, 76], "ncbideltablastcommandlin": [27, 68, 69], "ncbimakeblastdbcommandlin": [27, 68, 69], "ncbipsiblastcommandlin": [27, 68, 69], "ncbirpsblastcommandlin": [27, 68, 69], "ncbirpstblastncommandlin": [27, 68, 69], "ncbisearch": 7, "ncbitaxid": 252, "ncbitblastncommandlin": [27, 68, 69], "ncbitblastxcommandlin": [27, 68, 69], "ncbiwww": [3, 9, 27, 68], "ncbixml": [3, 27, 68], "nchar": [0, 56, 129], "ncid_01_206841095_130": 7, "ncifcrf": 12, "nclass": [181, 182], "ncluster": [4, 73], "ncog1583": 94, "ncol": 29, "ncolumn": 73, "ncontig": 269, "ncount": [0, 30, 38, 51], "ncrna": 32, "nctnctn": 12, "nd": 277, "nd1": 169, "nd2": 169, "ndarrai": [54, 135, 162, 169, 176], "ndg": 0, "ndx": [15, 169], "ne": [3, 169, 202], "ne1": 169, "ne2": 169, "nearest": [9, 15, 169, 182, 199, 223, 224, 225, 251, 253, 264, 282], "nearli": [15, 23], "neat": [6, 12, 22], "necessari": [3, 4, 8, 15, 20, 24, 61, 120, 132, 177, 217, 237, 264, 282], "necessarili": [4, 15, 17, 25, 109, 129, 183, 237], "need": [0, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 55, 61, 67, 73, 84, 90, 95, 99, 109, 137, 140, 152, 158, 168, 169, 172, 176, 178, 182, 191, 207, 209, 218, 221, 229, 236, 237, 238, 251, 260, 264, 269, 277, 278, 280, 298], "needl": [0, 13, 14, 41, 56, 58, 80], "needleal": 80, "needleallcommandlin": [27, 79, 80], "needlecommandlin": [27, 79, 80], "needleman": [12, 13, 30, 32], "needs_upd": 169, "neff": 0, "neg": [4, 11, 13, 30, 32, 69, 71, 73, 88, 99, 197, 237, 251, 270, 294, 297, 299], "negative_gilist": [68, 69], "negative_seqidlist": [68, 69], "negativeinteg": 197, "negcolor": 104, "nei": [2, 13, 34, 281], "nei1986": [2, 13], "neighbor": [4, 9, 15, 80, 141, 146, 182, 199, 264, 265, 282], "neighborbood": 73, "neighborhood": 282, "neighborsearch": [15, 27, 133], "neither": [84, 182, 197, 251], "nematod": 288, "neohippari": 56, "neph": [11, 283], "neq001": 94, "ner": [42, 222], "nescent": 17, "nest": [6, 8, 17, 20, 132, 182, 185, 217], "nestedmica": 296, "net": [4, 7, 15, 25, 32, 177, 270, 274, 278], "network": [4, 7, 23, 27, 83, 177, 209], "neubig": 7, "neural": 4, "neutral": [23, 34, 280], "never": [4, 207], "new": [0, 2, 4, 5, 6, 7, 8, 9, 11, 13, 15, 17, 18, 20, 21, 23, 25, 26, 30, 32, 36, 45, 54, 60, 67, 68, 69, 70, 71, 76, 84, 94, 104, 105, 109, 112, 113, 114, 120, 126, 127, 129, 132, 149, 153, 162, 169, 176, 177, 179, 180, 182, 183, 188, 190, 191, 197, 199, 205, 207, 236, 237, 238, 244, 246, 251, 252, 260, 261, 264, 265, 270, 278, 282, 283, 288, 295, 297, 299, 303, 307], "new_angl": 169, "new_clad": [181, 185, 190], "new_databas": [301, 303, 305], "new_graph": [98, 104], "new_id": [6, 23], "new_label": [181, 188], "new_seq": [22, 71], "new_set": [8, 98, 104], "new_succ": 130, "new_track": [8, 98, 104], "new_tre": 132, "newatomcoord": 169, "newbler": 6, "newentri": 126, "newer": [6, 7, 25, 251], "newest": 149, "newick": [12, 17, 27, 32, 132, 181, 182, 190, 191, 197, 199], "newick_doc": 190, "newickerror": [27, 181, 190], "newickfil": 182, "newickio": [27, 181, 191], "newlength": 169, "newli": [4, 15, 32], "newlin": [60, 65, 69, 94, 236, 238, 246], "newslett": 2, "newtabl": 264, "newton": 122, "newton_converg": 122, "newtre": [17, 30, 32], "newtree1": [30, 32], "newtree2": [30, 32], "nex": [0, 17], "nexml": [17, 27, 181, 188], "nexmlerror": [27, 181, 188], "nexmlio": [27, 181], "nexp": 73, "next": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, 25, 30, 37, 45, 46, 52, 53, 56, 57, 58, 60, 62, 63, 65, 66, 68, 92, 129, 131, 169, 183, 204, 218, 222, 230, 238, 246, 251, 252, 258, 267, 278, 298, 299, 300], "next_nonwhitespac": [128, 129], "next_until": [128, 129], "next_word": [128, 129], "nexu": [2, 12, 17, 27, 30, 32, 56, 64, 182, 183, 184, 185, 187, 188, 189, 190, 191, 197, 238], "nexus_instance1": 129, "nexus_instance2": 129, "nexuserror": [27, 128, 129, 131], "nexusio": [27, 56, 181], "nexusiter": [27, 56, 64], "nexuswrit": [27, 56, 64], "nfh": 245, "nfk": 13, "nfound": [4, 73], "nftmip": 0, "ng86": [13, 34, 280, 281], "ngc": 6, "ngene": 73, "ngktgrgavsekdapkellnmigk": 0, "ngktgrgavsekdapkellsmluk": 0, "ngktgrgavsekdapkelmdmlar": 0, "ngnhtfkmal": 0, "ngnhtfkmalnqfsdmsfa": 0, "ngnhtfkmalnqfsdmsfaeikhkylwsepqncsat": 0, "nh": 137, "nh1": 169, "nh2": 169, "nh2mec": 112, "nh_1_energi": 137, "nh_1_relidx": 137, "nh_2_energi": 137, "nh_2_relidx": 137, "nh_o_1_energi": 137, "nh_o_1_relidx": 137, "nh_o_2_energi": 137, "nh_o_2_relidx": 137, "nhaimgvaft": 250, "nhammgvaft": 250, "nhkadtkfgv": 0, "nib": [238, 247], "nibbl": [238, 247], "nibfrag": 247, "nibio": [27, 238], "nibiter": [27, 238, 247], "nibwrit": [27, 238, 247], "nice": [3, 5, 6, 7, 12, 15, 21, 23, 25, 30, 31, 36, 99, 103, 110, 169, 207, 260, 261, 280, 297], "nicer": [12, 14], "nich": 19, "nick": 2, "nicol": 2, "nicotiana": 23, "nid": [7, 93, 275], "nident": 218, "niekslkeaftplgisdwnstfwiahpggpaildqveaklglkeekmratrevlseygnm": [21, 23], "nielsen": [2, 13, 34, 196, 281], "nig": 245, "nih": [3, 7, 8, 19, 22, 23, 68, 70, 71, 76, 83, 93, 94, 96, 97, 218, 234, 245, 253, 272], "nil": 2, "nine": 0, "ninth": 12, "niter": [4, 73], "nitti": 21, "nj": [32, 80, 181, 182, 199, 280], "njtree": 199, "njumbl": [79, 80], "nkfadlssd": 0, "nkgarvlvvcseitavtfrgpndthldslvgqalfgdgaaaviigsdpipeverplfelv": 23, "nl": [15, 137, 250], "nlaiii": 206, "nlength": 6, "nlib": 0, "nlm": [3, 7, 8, 19, 22, 68, 70, 71, 83, 93, 94, 96, 97, 123, 218, 234, 245, 253, 272], "nlmcatalog": 7, "nm": [0, 123, 203, 264], "nm_000015": 7, "nm_001180731": 0, "nmeth0810": 100, "nmin": 73, "nmkqhkamivalivicitavvaalvtrkdlcevhirtgqtevavf": 260, "nmotif": 11, "nmr": [0, 15, 25, 27, 144], "nmrview": [125, 126], "nn": [169, 264], "nn_tabl": 264, "nna": 32, "nni": [181, 182, 199], "nnitreesearch": [27, 181, 199], "nnn": [30, 236], "nnnn": 270, "nnnnnnacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt": 260, "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn": 30, "no2nd": [181, 182], "no_altloc": [133, 158, 169], "no_greedi": [68, 69], "no_of_seq": 0, "noaa": 197, "noali": 229, "noanchor": [30, 32], "nobrief": [79, 80], "nocat": [181, 182], "nocor": [30, 32], "node": [4, 17, 27, 32, 73, 99, 117, 128, 132, 177, 178, 179, 180, 182, 183, 184, 185, 187, 189, 190, 197, 198, 209, 211, 213, 252, 296], "node1": 132, "node2": 132, "node_dict": 188, "node_id": [130, 132, 181, 197, 198], "node_typ": 209, "nodecodedict": 209, "nodedata": [27, 128, 130, 132, 184, 187, 189], "nodeexcept": [27, 128, 130], "nodelist": 296, "nodetyp": [210, 211], "noe": 125, "noed": 126, "noetool": [27, 124], "nofft": [30, 32], "nohgap": [30, 32], "nois": 53, "noisi": 17, "nolan": [2, 7], "nomatrix": [181, 182], "nome": [181, 182], "nomenclatur": [2, 25, 169], "noml": [181, 182], "non": [0, 3, 4, 7, 11, 12, 13, 14, 15, 17, 21, 22, 25, 30, 32, 45, 60, 67, 69, 73, 84, 85, 117, 126, 129, 143, 149, 154, 158, 169, 172, 183, 197, 198, 218, 221, 222, 230, 236, 237, 238, 246, 251, 253, 260, 261, 264, 272, 275, 297], "non_con": 272, "non_std": 272, "non_ter": 272, "nonconsecut": 221, "noncontigu": 221, "none": [0, 3, 4, 6, 8, 10, 11, 12, 13, 15, 17, 18, 20, 21, 22, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 72, 73, 76, 84, 85, 92, 94, 99, 102, 103, 104, 108, 119, 120, 121, 122, 127, 129, 130, 132, 135, 136, 137, 139, 143, 144, 145, 149, 151, 152, 156, 157, 158, 160, 162, 164, 165, 168, 169, 172, 176, 177, 179, 180, 183, 184, 185, 186, 187, 189, 190, 193, 195, 196, 197, 199, 201, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 215, 217, 236, 237, 238, 240, 241, 246, 248, 249, 250, 251, 252, 253, 258, 260, 261, 263, 264, 269, 270, 272, 274, 275, 276, 278, 279, 280, 281, 282, 283, 287, 288, 290, 291, 292, 294, 295, 299, 303, 304], "noneel": [27, 83, 84], "nonetyp": 160, "nonexist": 7, "nonnegativeinteg": 197, "nonpositiveinteg": 197, "nonsci": 17, "nonsens": 253, "nonsynonym": [2, 196], "nontermin": [17, 183], "nontrivi": 15, "nonumb": 4, "nonzero": [17, 183], "nopgap": [30, 32], "nopost": [30, 32], "nopr": [181, 182], "noqa": 11, "nor": [7, 12, 15, 20, 84, 129, 182, 278], "noreturn": 260, "norm": [15, 133, 176, 251], "normal": [4, 5, 7, 11, 12, 13, 15, 21, 22, 23, 30, 32, 65, 67, 93, 121, 129, 133, 135, 143, 144, 151, 169, 176, 182, 236, 237, 238, 251, 261, 270, 281, 283, 288, 290, 302, 303, 305], "normalize_lett": [27, 209, 214], "normalizedstr": 197, "normsq": [133, 176], "noroot": [79, 80], "northern": 250, "noscor": [30, 32], "nose": 24, "nosecstr1": [30, 32], "nosecstr2": [30, 32], "nostatu": 11, "nosupport": [181, 182], "notabl": 17, "notat": [3, 14, 20, 21, 30, 236, 260, 299], "note": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 21, 22, 23, 24, 27, 30, 32, 45, 49, 56, 59, 60, 62, 64, 66, 67, 68, 69, 70, 71, 73, 76, 81, 83, 90, 94, 95, 99, 108, 117, 121, 123, 125, 129, 135, 137, 143, 149, 153, 158, 159, 168, 169, 177, 182, 202, 210, 211, 212, 213, 214, 217, 218, 221, 222, 226, 229, 236, 237, 238, 240, 242, 245, 246, 247, 248, 249, 251, 253, 254, 257, 259, 260, 261, 262, 263, 264, 265, 269, 270, 272, 274, 278, 287, 288, 290, 294, 297, 298, 299, 302], "notermini": [79, 80], "notextw": 229, "noth": [17, 31, 54, 65, 99, 241, 250, 275, 278], "notic": [4, 5, 6, 8, 11, 12, 19, 20, 21, 22, 23, 67, 166, 218, 222, 237, 238, 251, 253, 260, 278, 295], "notimplementederror": 21, "notion": [11, 108], "notop": [181, 182], "notre": [30, 32], "notredam": 32, "notrim": 6, "notxmlerror": [7, 27, 68, 83, 84], "nov": [23, 149], "novel": [25, 32], "novemb": [87, 122], "novoalign": 270, "novoalign_clin": 270, "novoaligncommandlin": [268, 270], "novocraft": 270, "now": [0, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 67, 71, 83, 92, 108, 149, 169, 209, 236, 237, 238, 250, 251, 253, 260, 278, 297], "nowadai": [3, 11], "noweight": [30, 32], "noxml": [30, 32], "np": [0, 12, 13, 15, 30, 32, 68, 169], "np_001075655": 7, "np_001107837": 238, "np_035004": 7, "np_051101": 238, "np_391444": [20, 218], "np_395230": 21, "np_418483": 260, "np_963295": 94, "np_995567": 256, "np_995568": 256, "np_995569": 256, "np_995570": 256, "np_995571": [21, 256], "np_995572": [238, 256], "np_995573": 256, "np_995574": 256, "np_995575": 256, "np_995576": 256, "np_bind": 272, "npass": [4, 73], "npe": 6, "npg": 267, "npirpvtdra": 0, "npix": 29, "npvsfafevt": 0, "nqfsdmsfae": 0, "nqiqgvicspdsgefmvtfetvmeikilhk": 6, "nr": [3, 68, 69, 70], "nr_030186": [3, 20], "nr_030188": [3, 20], "nr_030190": [3, 20], "nr_030191": [3, 20], "nr_030193": [3, 20], "nr_030194": [3, 20], "nr_030195": [3, 20], "nr_030198": [3, 20], "nr_030217": [3, 20], "nr_030218": [3, 20], "nr_030221": [3, 20], "nr_030222": [3, 20], "nr_032573": [3, 20], "nr_032574": [3, 20], "nr_032575": [3, 20], "nr_032587": [3, 20], "nr_032716": [3, 20], "nr_035837": [3, 20], "nr_035838": [3, 20], "nr_035845": [3, 20], "nr_035850": [3, 20], "nr_035851": [3, 20], "nr_035852": [3, 20], "nr_035856": [3, 20], "nr_035857": [3, 20], "nr_035860": [3, 20], "nr_035865": [3, 20], "nr_035866": [3, 20], "nr_035869": [3, 20], "nr_035870": [3, 20], "nr_035871": [3, 20], "nr_046654": 0, "nr_111921": [0, 45], "nr_children": 15, "nr_false_neg": 88, "nr_false_po": 88, "nr_partial": 88, "nr_posit": 88, "nr_sp_releas": 88, "nr_sp_seq": 88, "nr_total": 88, "nr_unknown": 88, "nread": 269, "nrep": 132, "nrfsdmswee": 0, "nrow": [29, 73], "ns3": 23, "ns_site": 17, "nsanigaki": 0, "nsequence_1": 0, "nsequence_2": 0, "nsldhgiliv": 0, "nssite": 17, "nt": [0, 3, 30, 32, 69, 181, 182, 261, 264], "nt_search": [27, 261], "nta": [30, 32], "ntax": [0, 56, 132], "ntitl": 7, "ntree": 132, "ntseq": 119, "nu": [238, 260], "nu3m_balph": 272, "nuc": [6, 11, 30, 32, 260, 290], "nuc1": 13, "nuc2": 13, "nuc3": 13, "nuc_list": 6, "nuc_rec": 6, "nuc_record": 6, "nuccor": [7, 19, 83, 274], "nucest": [7, 274], "nucgss": [7, 274], "nucl": 69, "nucl_penalti": [68, 70], "nucl_reward": [68, 70], "nucl_seq": 279, "nuclear": [30, 94], "nucleic": [2, 3, 12, 15, 32, 68, 111, 115, 119, 154, 166, 251, 261, 283], "nucleotid": [0, 2, 3, 11, 12, 19, 20, 21, 23, 30, 32, 34, 61, 68, 69, 70, 71, 76, 80, 83, 93, 94, 154, 182, 193, 195, 222, 226, 236, 237, 238, 245, 247, 251, 260, 261, 262, 264, 270, 272, 274, 275, 279, 283, 287, 290], "nucleotide_alphabet": [75, 76], "nucleotide_m8cc": 0, "nucleotide_record": 13, "nucleu": [125, 126], "null": [67, 270], "num": [3, 68, 169, 218], "num_align": [68, 69, 71], "num_bootstrap_search": [181, 182], "num_categori": [181, 182], "num_descript": [68, 69], "num_good_extend": 71, "num_group": 172, "num_hit": 71, "num_iter": [68, 69], "num_letters_in_databas": 71, "num_occurr": 11, "num_repl": [181, 182], "num_seqs_better_": 71, "num_sequ": 71, "num_sequences_in_databas": 71, "num_thread": [32, 68, 69], "number": [0, 2, 3, 6, 7, 8, 9, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 37, 42, 44, 45, 47, 49, 51, 54, 56, 60, 61, 68, 69, 70, 71, 73, 80, 83, 84, 86, 87, 88, 90, 93, 99, 100, 102, 104, 108, 109, 112, 113, 115, 117, 118, 119, 120, 121, 122, 123, 126, 130, 132, 134, 135, 139, 140, 141, 143, 149, 151, 157, 158, 169, 172, 175, 176, 177, 182, 183, 185, 186, 188, 190, 197, 202, 203, 207, 209, 214, 215, 216, 217, 221, 222, 229, 236, 237, 238, 246, 247, 248, 251, 252, 253, 257, 260, 265, 269, 270, 272, 274, 275, 276, 278, 280, 281, 282, 287, 288, 290, 291, 294, 295, 297, 298, 299, 303], "numberofcategori": 182, "numer": [4, 13, 15, 17, 88, 104, 107, 149, 152, 168, 169, 177, 197, 247, 251, 265, 272], "numit": [30, 32], "nummismatch": [79, 80], "numpi": [0, 4, 5, 12, 13, 15, 24, 30, 54, 68, 73, 135, 139, 140, 146, 156, 162, 168, 169, 176, 216, 238, 290, 299], "numreturn": [79, 80], "numthread": [30, 32], "nur1f": 270, "nv": 126, "nvde": 14, "nvdevggealgrllvvypwtqrf": 12, "nvdevggealgrllvvypwtqrff": 14, "nvdevggealgrllvvypwtqrffesfgdlstpdavmgn": 13, "nwk": 17, "nx3": [140, 175, 216], "nxdim": [175, 216], "nxgrid": [4, 73], "nydpwnlrfqskyksrda": 95, "nygrid": [4, 73], "nylrgt": 0, "nz": 169, "o": [2, 5, 7, 11, 12, 15, 23, 25, 30, 32, 53, 66, 85, 91, 97, 99, 137, 148, 149, 152, 157, 169, 170, 173, 182, 185, 188, 190, 191, 221, 251, 253, 261, 268, 270, 283, 295], "o16376": 53, "o16376_caeel": 53, "o23729": [23, 25, 85], "o23730": 25, "o23731": 25, "o46647": 25, "o_1_energi": 137, "o_1_relidx": 137, "o_2_energi": 137, "o_2_relidx": 137, "o_ant70": 244, "o_mvp5180": 244, "o_nh_1_energi": 137, "o_nh_1_relidx": 137, "o_nh_2_energi": 137, "o_nh_2_relidx": 137, "oa": 169, "oab": 123, "oanyself": [79, 80], "ob": 169, "obei": 7, "obf": 6, "obj": [54, 191, 198], "obj_typ": 188, "object": [3, 4, 6, 7, 8, 9, 14, 16, 18, 19, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 42, 45, 46, 47, 49, 51, 52, 54, 56, 59, 60, 61, 64, 66, 67, 68, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 123, 126, 127, 128, 129, 130, 131, 132, 134, 135, 136, 137, 138, 139, 140, 141, 143, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 161, 162, 163, 165, 166, 168, 169, 170, 171, 172, 173, 175, 176, 177, 179, 180, 183, 184, 185, 186, 187, 188, 189, 190, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 224, 225, 226, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 269, 270, 271, 272, 273, 275, 278, 279, 280, 281, 282, 283, 284, 286, 288, 289, 291, 292, 293, 294, 295, 296, 297, 298, 299, 302, 303, 304, 305, 307], "objfun": 11, "objscor": [30, 32], "objwct": 68, "obo": [185, 188], "obolibrari": 185, "obscur": 7, "observ": [4, 11, 12, 13, 16, 22, 52, 109, 120, 121, 122, 127, 169, 202, 203, 214, 229, 251, 282], "observed_frequ": [12, 13], "obsess": 19, "obslt": 149, "obsolet": [12, 15, 32, 67, 69, 71, 80, 92, 94, 149, 182, 186, 207, 237, 241, 251, 270, 285], "obsolete_pdb": 149, "obtain": [0, 12, 13, 14, 22, 25, 30, 68, 92, 119, 140, 182, 203, 209, 221, 222, 270, 299], "obviou": [6, 7, 15, 288], "obvious": [7, 13, 15, 30, 169], "oc": [11, 53, 66, 169, 295], "occ": 169, "occacb": 169, "occasion": [7, 20, 21, 23], "occup": [15, 135, 155, 162, 169, 172], "occupi": 104, "occur": [0, 4, 7, 11, 12, 13, 15, 17, 21, 23, 30, 73, 83, 84, 145, 222, 236, 237, 272], "occurr": [4, 12, 13, 90, 182, 236, 260, 263, 270, 273, 291, 294], "ocd": 0, "ocdhpr": 0, "ochromend": 0, "ochroms": 0, "ochromstart": 0, "oci": 123, "ockholm": 32, "oct": [0, 149, 182], "octagon": 8, "octo": 8, "octob": 7, "octopu": 183, "octvu": 183, "od1": 169, "od2": 169, "odd": [11, 12, 13, 288, 290, 294], "oddsratio": 13, "odnaconc": [79, 80], "odoratu": 260, "oe1": [157, 169], "oe2": 169, "oendself": [79, 80], "oexcludedregion": [79, 80], "off": [0, 3, 8, 21, 23, 32, 68, 69, 70, 80, 117, 119, 125, 158, 182, 251, 270], "off_diagonal_rang": [68, 69], "offend": 272, "offer": [0, 3, 6, 9, 15, 21, 49, 64, 83, 98, 240, 241, 255, 274], "offici": [7, 9, 23, 68, 70, 119, 197, 212, 251], "offlin": 24, "offset": [6, 11, 20, 23, 32, 61, 100, 121, 141, 219, 220, 221, 224, 225, 226, 230, 232, 233, 237, 238, 251, 274, 278, 290], "often": [0, 1, 3, 4, 6, 7, 9, 11, 12, 15, 17, 19, 20, 21, 22, 23, 24, 132, 145, 182, 251, 264], "og": [15, 80, 169], "og1": 169, "ogcmax": [79, 80], "ogcmin": [79, 80], "ogcopt": [79, 80], "ogcperc": [79, 80], "oh": 169, "oi": 90, "oid": 123, "ointment": 6, "ok": [6, 7, 9, 23, 24], "ok_applies_to": [181, 197], "ok_datatyp": [181, 197], "ok_rank": [181, 197], "ok_typ": [181, 197], "old": [0, 6, 9, 12, 19, 21, 23, 26, 32, 68, 69, 70, 94, 182, 191, 236, 237, 251, 258, 260, 264, 278, 307], "old_refseq": 8, "oldatomcoord": 169, "older": [0, 1, 3, 5, 7, 8, 9, 11, 12, 21, 22, 25, 56, 65, 69, 71, 210, 212, 236, 238, 251, 295, 298], "oldtabl": 264, "oligo": [80, 264], "oligoinput": [79, 80], "oligonucleotid": 264, "oliv": 183, "olsen": 263, "omaxs": [79, 80], "omega": [15, 17, 32, 152, 169], "omg": [152, 169], "omia": 7, "omim": 7, "omins": [79, 80], "omishybmax": [79, 80], "omit": [20, 21, 54, 129, 217, 236, 238, 251, 260], "omit_nexu": 129, "omnibu": [7, 96], "onc": [0, 1, 3, 4, 5, 6, 7, 11, 12, 16, 19, 21, 22, 23, 30, 32, 56, 60, 61, 67, 73, 84, 90, 121, 158, 169, 205, 217, 238, 248, 251, 269, 273, 288, 298], "one": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 35, 39, 42, 43, 45, 46, 51, 52, 56, 61, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 80, 81, 83, 86, 87, 88, 90, 92, 93, 101, 104, 112, 113, 114, 116, 117, 119, 123, 130, 137, 139, 146, 149, 154, 157, 161, 163, 166, 169, 172, 177, 182, 183, 186, 197, 201, 204, 205, 207, 210, 211, 212, 213, 214, 215, 217, 221, 222, 228, 237, 238, 242, 245, 247, 249, 250, 251, 252, 254, 256, 259, 261, 264, 267, 269, 270, 271, 272, 273, 274, 275, 277, 278, 282, 283, 287, 288, 290, 295, 297, 298, 299, 300, 303], "one_alignment_onli": [14, 297], "one_letter_cod": 214, "one_to_index": [27, 133, 154], "one_to_one_orthologi": 197, "oneofposit": [21, 27, 237], "ones": [0, 7, 8, 10, 20, 132, 297], "ongo": 9, "onim": 274, "onli": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 33, 34, 36, 40, 45, 49, 52, 56, 59, 60, 64, 65, 68, 69, 70, 71, 73, 76, 80, 81, 83, 91, 92, 104, 116, 117, 119, 125, 129, 137, 138, 140, 143, 144, 149, 152, 158, 168, 169, 177, 182, 183, 197, 198, 199, 202, 205, 217, 222, 226, 228, 236, 237, 238, 241, 242, 245, 247, 249, 251, 252, 253, 254, 256, 257, 259, 260, 261, 265, 269, 270, 272, 274, 275, 277, 278, 281, 283, 287, 288, 290, 297, 298, 299], "onlin": [0, 3, 5, 7, 8, 9, 12, 13, 19, 21, 23, 24, 25, 83, 119, 209, 250], "online_doctest_modul": 24, "onto": [16, 166, 176, 182, 214, 216, 251], "ontologi": [17, 185, 273], "onward": [6, 9, 11, 18, 23, 80, 251], "oop": [11, 289, 291], "oow": 238, "op": [30, 32], "open": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 23, 24, 25, 27, 29, 30, 32, 56, 57, 60, 61, 62, 65, 66, 68, 69, 71, 80, 83, 84, 85, 90, 91, 92, 112, 113, 114, 116, 123, 129, 142, 143, 151, 158, 166, 198, 199, 204, 205, 217, 218, 221, 238, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 256, 259, 260, 269, 270, 271, 272, 277, 278, 283, 289, 291, 292, 297, 298, 303], "open_databas": [301, 303, 305], "open_dtd_fil": [83, 84], "open_gap_scor": [13, 30], "open_xsd_fil": [83, 84], "opena": 297, "openascad": 158, "openb": 297, "openscad": [15, 158, 169], "oper": [5, 6, 7, 9, 13, 15, 17, 22, 30, 32, 55, 56, 67, 80, 169, 176, 182, 183, 186, 237, 238, 251, 264, 278, 290], "operand": [260, 299], "ophri": 7, "opi3": [11, 291], "opisthorchi": 3, "opm": [16, 298], "opolyxmax": [79, 80], "opossum": 22, "oppos": 3, "opposit": [0, 4, 15, 169, 237], "opt": [8, 32, 226], "opt_scor": 226, "optim": [2, 4, 6, 13, 14, 23, 27, 32, 69, 73, 146, 166, 181, 182, 261, 265, 267], "optimis": [32, 56, 182, 238], "optimum": 80, "option": [0, 3, 4, 6, 7, 9, 12, 13, 15, 17, 20, 21, 22, 23, 24, 30, 31, 32, 33, 43, 45, 48, 54, 56, 59, 60, 63, 65, 67, 68, 69, 72, 73, 76, 79, 80, 83, 90, 92, 93, 97, 99, 104, 108, 109, 118, 119, 120, 121, 127, 129, 135, 136, 139, 143, 149, 151, 152, 158, 164, 166, 169, 182, 186, 188, 190, 193, 195, 196, 197, 214, 215, 217, 225, 236, 237, 238, 241, 244, 246, 247, 250, 251, 252, 253, 258, 260, 261, 265, 269, 270, 273, 274, 275, 276, 282, 297, 303], "opttm": [79, 80], "opuntia": [0, 3, 7, 12, 23, 30, 32, 80, 83], "opuntioidea": 7, "orang": [8, 183], "orchid": [6, 7, 19, 23, 25], "orchid_dict": 23, "orchid_rpl16": 7, "orchidacea": [7, 19], "orcutt": 2, "ord": [13, 251], "order": [0, 3, 4, 5, 6, 8, 11, 12, 15, 17, 19, 20, 23, 24, 27, 30, 31, 32, 36, 37, 38, 60, 61, 73, 76, 80, 84, 102, 103, 108, 119, 137, 159, 167, 169, 172, 177, 180, 183, 197, 198, 202, 207, 209, 218, 222, 237, 238, 260, 270, 278, 299], "ordered_aa_ic_list": [15, 169], "orderedlistel": [27, 83, 84], "orderedlocusnam": 272, "ordinari": [15, 23, 217, 238, 278], "orf": [4, 6, 73], "orf10": 8, "orf12": 8, "orf13": 8, "orf14": 8, "orf15": 8, "orf16": 8, "orf17": 8, "orf20": 8, "orf22": 8, "orf23": 8, "orf27": 8, "orf28": 8, "orf29": 8, "orf38": 8, "orf39": 8, "orf4": 8, "orf40": 8, "orf41": 8, "orf42": 8, "orf43": 8, "orf44": 8, "orf46": 8, "orf47": 8, "orf48": 8, "orf49": 8, "orf50": 8, "orf51": 8, "orf52": 8, "orf53": 8, "orf54": 8, "orf55": 8, "orf6": 8, "orf60": 8, "orf7": 8, "orf8": 8, "orf9": 8, "orf_list": 6, "orfnam": 272, "org": [2, 5, 6, 7, 8, 9, 12, 15, 17, 19, 21, 23, 25, 27, 32, 52, 53, 56, 66, 69, 73, 83, 85, 86, 87, 88, 89, 90, 94, 100, 117, 119, 137, 149, 150, 158, 167, 170, 181, 182, 185, 188, 197, 221, 229, 237, 245, 248, 251, 252, 258, 262, 263, 265, 267, 272, 273, 275, 277, 279, 286, 288, 301], "organ": [2, 6, 8, 10, 11, 19, 21, 23, 25, 27, 53, 66, 73, 93, 98, 99, 103, 113, 114, 116, 119, 197, 260, 272, 275], "organel": [7, 25, 272], "organis": 94, "organism_classif": [25, 66, 272], "organism_id": [25, 276], "orgn": [7, 83], "ori": 123, "orient": [8, 9, 22, 80, 104, 169, 295], "origin": [0, 3, 4, 6, 7, 8, 9, 11, 12, 15, 17, 19, 20, 21, 23, 30, 36, 44, 45, 56, 59, 63, 69, 76, 90, 93, 94, 95, 97, 102, 123, 125, 126, 133, 136, 158, 166, 168, 169, 174, 175, 176, 182, 183, 214, 217, 236, 237, 238, 251, 252, 253, 258, 260, 265, 270, 271, 272, 275, 277, 299], "original_blast_record": 3, "original_read": 6, "original_rec": 6, "originnuc": 125, "originresnum": 125, "orlean": 15, "ormandi": 122, "ortholog": [115, 116, 117], "orthologi": [114, 197, 274], "osaltconc": [79, 80], "osequ": 0, "oserror": [193, 195, 196], "osformat": [79, 80], "osiz": [79, 80], "osizeopt": [79, 80], "ossibl": 80, "ostrand": 0, "ot": 123, "other": [0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 21, 23, 24, 25, 26, 27, 30, 31, 32, 40, 52, 56, 57, 65, 66, 67, 69, 72, 73, 83, 84, 88, 91, 93, 99, 100, 102, 104, 105, 108, 117, 119, 123, 133, 135, 136, 139, 140, 146, 149, 155, 161, 166, 169, 175, 176, 181, 182, 183, 195, 197, 198, 199, 211, 214, 216, 217, 218, 222, 226, 229, 236, 237, 238, 241, 250, 256, 260, 261, 264, 265, 278, 280, 287, 288, 290, 295, 297, 299, 307], "other1": [18, 201, 204], "other_advanc": [68, 70], "other_internal_format": [92, 93], "other_tre": 17, "otherwis": [0, 8, 11, 15, 16, 17, 23, 30, 31, 32, 54, 67, 68, 83, 95, 99, 104, 108, 132, 135, 148, 149, 162, 169, 170, 173, 182, 183, 193, 195, 196, 236, 237, 251, 260, 264, 270, 275, 277, 288, 290, 297, 299], "otm": [79, 80], "otmmax": [79, 80], "otmmin": [79, 80], "otmopt": [79, 80], "oto": 123, "otogar1": 0, "otu": [80, 132], "ought": 20, "our": [1, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 17, 19, 20, 21, 23, 24, 27, 56, 67, 236, 238, 251], "ourselv": 20, "out": [0, 3, 5, 6, 7, 8, 9, 11, 12, 13, 16, 17, 19, 20, 21, 23, 24, 25, 30, 31, 32, 68, 69, 73, 80, 82, 92, 99, 102, 103, 110, 116, 131, 138, 148, 152, 170, 173, 181, 182, 195, 218, 221, 251, 253, 260, 265, 270, 278, 283, 292, 297, 303], "out_arr": 54, "out_ascii_pssm": [68, 69], "out_bam": 270, "out_block": [27, 96, 97], "out_dict": 137, "out_fil": [17, 32, 56, 193, 195, 196, 217, 238, 270], "out_fmt": 217, "out_format": [56, 217, 238, 274], "out_handl": [3, 6, 11, 12, 23, 25, 85, 214, 238, 251, 253], "out_kwarg": 217, "out_prefix": [268, 270], "out_pssm": [68, 69], "out_rad": 169, "out_stream": 3, "outdat": 7, "outer": 154, "outfil": [12, 30, 32, 67, 79, 80], "outfmt": [0, 3, 30, 32, 55, 68, 69], "outfn": 126, "outgo": 108, "outgrno": [79, 80], "outgroup": [17, 80, 132, 181, 182, 183], "outgroup_branch_length": 183, "outgroup_target": 183, "outlier": [4, 6, 29], "outlin": [17, 20, 32], "outlist": 126, "outord": [30, 32], "outperform": 15, "outprotrec": 277, "output": [1, 4, 6, 7, 8, 9, 11, 12, 15, 17, 18, 19, 21, 22, 24, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38, 40, 41, 42, 44, 45, 47, 48, 49, 51, 52, 55, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 80, 81, 82, 83, 89, 93, 98, 99, 100, 101, 103, 104, 121, 125, 137, 145, 148, 152, 153, 158, 167, 169, 170, 173, 182, 183, 193, 195, 196, 199, 207, 214, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 237, 240, 241, 243, 245, 246, 247, 249, 250, 251, 252, 253, 259, 260, 261, 268, 269, 270, 271, 274, 277, 278, 280, 283, 284, 291, 292, 303, 307], "output_bam": 270, "output_fil": [6, 99, 101, 103, 268, 270], "output_format": [99, 101, 103], "output_handl": 6, "output_sai_fil": 270, "output_sam_fil": 270, "outputeith": 32, "outputfilenam": 182, "outputformat": 234, "outputord": [30, 32], "outputrecord": [27, 79, 82], "outputtre": [30, 32], "outrec": 277, "outseq": [79, 80], "outsid": [7, 32, 104, 119, 303], "outtreefil": [79, 80], "ov": [11, 229, 295], "over": [0, 1, 4, 6, 7, 8, 9, 11, 12, 17, 19, 20, 21, 22, 25, 30, 36, 44, 45, 56, 60, 61, 65, 66, 67, 68, 70, 73, 74, 81, 83, 84, 85, 87, 88, 92, 104, 116, 123, 129, 131, 134, 139, 149, 161, 164, 185, 188, 190, 197, 198, 205, 207, 209, 210, 211, 212, 213, 214, 217, 219, 220, 221, 226, 228, 230, 232, 233, 237, 238, 240, 241, 244, 246, 247, 248, 250, 251, 253, 254, 256, 257, 258, 260, 261, 264, 267, 269, 271, 274, 276, 277, 278, 288, 298, 299, 303], "overal": [4, 11, 15, 99, 158, 202, 237], "overfit": 11, "overflowerror": 13, "overhang": [69, 158], "overhead": [23, 169, 217], "overlai": 8, "overlap": [8, 15, 22, 32, 36, 61, 79, 80, 152, 158, 167, 169, 182, 236, 260], "overlap_num": 229, "overload": [15, 119, 148, 274], "overrid": [12, 15, 17, 32, 64, 68, 69, 70, 99, 104, 158, 169, 197, 237, 261, 264], "overridden": [30, 45, 104, 207, 237, 246], "overview": [3, 7, 11, 13, 16, 17, 20, 23, 123, 169, 275], "overwork": 19, "overwrit": [23, 32, 56, 149, 238, 270], "overwritten": [12, 23, 149, 183, 197, 238], "ow": [30, 32], "owczarzi": 264, "owl": 185, "own": [0, 3, 6, 7, 11, 12, 13, 14, 17, 19, 20, 22, 23, 24, 61, 117, 123, 143, 151, 169, 218, 222, 229, 251, 253, 260, 264, 278, 291, 297], "owner": 123, "ox": 90, "oxfordjourn": 2, "oxid": 265, "oxopropano": 112, "oxt": 169, "oxygen": 15, "p": [0, 2, 4, 7, 12, 13, 15, 22, 23, 30, 32, 34, 53, 69, 80, 104, 107, 108, 123, 126, 127, 137, 140, 153, 157, 166, 169, 172, 176, 182, 194, 202, 237, 251, 261, 265, 268, 270, 279, 280, 281], "p0": 11, "p00321": 272, "p00520": 164, "p03618": 12, "p03619": 12, "p03620": 12, "p06858": 25, "p07175": 68, "p1": [177, 250], "p11151": 25, "p11152": 25, "p11153": 25, "p11602": 25, "p12497": 248, "p13125": 0, "p13689": 23, "p14921": 288, "p15416": 12, "p17304": 197, "p17886": 53, "p19801": 23, "p2": [0, 177, 237], "p24973": 272, "p33487": 23, "p49060": 25, "p49923": 25, "p53762": 11, "p55031": 25, "p57": 107, "p58": 107, "p61991": 0, "p62": 108, "p64": 109, "p68308": 272, "p69541": 12, "p87312": 53, "p_": [11, 12], "p_condit": 127, "p_e": 6, "p_emiss": 121, "p_initi": 121, "p_prior": 127, "p_transit": 121, "pa": [13, 32, 53, 263], "pablo": [2, 262], "pack": [0, 197], "packag": [0, 2, 3, 5, 7, 11, 16, 18, 25, 84, 100, 129, 137, 150, 156, 193, 195, 196, 303, 306, 307], "pad": [0, 13, 30, 65, 126], "padktnv": [13, 14], "paffakss": 250, "paffakssai": 250, "page": [3, 6, 7, 8, 9, 12, 17, 19, 21, 23, 25, 83, 85, 90, 99, 103, 104, 218, 222, 229, 234], "page_s": 8, "pages": [8, 104], "pagin": 123, "pai": 278, "pair": [0, 3, 6, 8, 12, 13, 14, 15, 18, 20, 23, 30, 32, 41, 54, 56, 58, 68, 79, 80, 81, 95, 99, 146, 161, 169, 176, 177, 179, 180, 182, 197, 199, 201, 202, 203, 204, 230, 251, 253, 270, 295, 297, 299, 303], "pairedfastaqualiter": [6, 27, 238, 251], "pairgap": [30, 32], "pairwis": [4, 6, 12, 15, 26, 30, 32, 34, 35, 36, 38, 39, 41, 42, 44, 51, 52, 55, 56, 58, 59, 68, 69, 73, 169, 196, 222, 270, 297, 307], "pairwise2": [26, 27, 307], "pairwise_align": 0, "pairwise_alignment1": 0, "pairwise_alignment2": 0, "pairwise_codon_align": 13, "pairwisealign": [0, 12, 13, 14, 27, 30, 68], "pale": 8, "palindrom": 80, "palindromecommandlin": [27, 79, 80], "palss": 2, "pam": [13, 14, 32], "pam200": 32, "pam250": 199, "pam30": [68, 70, 199], "pam70": [68, 70, 199], "paml": [9, 27, 181], "pan": [3, 20], "pandit": 265, "panel": 275, "panisc": [3, 20], "panther": 234, "pantro1": 0, "pantro2": 0, "pantro4": 22, "pantro5": [0, 30], "pantro5topantro6": [0, 30], "pantro6": [0, 30], "paper": [4, 7, 12, 19, 21, 59, 72, 264], "paphiopedilum": [19, 23], "paquet": 263, "par": [145, 181, 182], "para_agrtu": 68, "paragraph": 5, "parahippu": 56, "parallel": [8, 25, 169, 182], "parallelassembleresidu": [133, 169], "paralleliz": 9, "paralogi": 197, "param": [3, 16, 32, 68, 136, 169, 176], "param_dict": 265, "param_entrez_queri": 218, "param_evalue_threshold": [20, 218], "param_filt": 218, "param_gap_extend": 218, "param_gap_open": 218, "param_includ": 218, "param_matrix": 218, "param_pattern": 218, "param_score_match": 218, "param_score_mismatch": 218, "paramet": [3, 4, 7, 11, 12, 13, 14, 15, 17, 25, 27, 31, 32, 54, 67, 68, 69, 70, 71, 80, 83, 89, 100, 104, 105, 108, 109, 120, 121, 125, 126, 134, 135, 136, 137, 139, 140, 141, 144, 148, 149, 150, 152, 154, 155, 157, 158, 160, 163, 164, 165, 166, 168, 169, 170, 171, 172, 173, 175, 176, 182, 183, 185, 186, 187, 188, 189, 190, 197, 198, 199, 202, 207, 209, 218, 236, 237, 261, 263, 264, 265, 270, 276, 283, 290, 297, 299, 300], "parameter": 15, "parameters_entrez": 218, "parameters_expect": 218, "parameters_filt": 218, "parameters_gap": 218, "parameters_includ": 218, "parameters_matrix": 218, "parameters_pattern": 218, "parameters_sc": 218, "parametr": [4, 182], "paramfil": [30, 32], "paraphras": 7, "parent": [6, 15, 17, 21, 104, 117, 130, 133, 135, 139, 159, 169, 178, 179, 180, 183, 185, 190, 197, 209, 213, 237, 260], "parent_branch": 197, "parent_edg": [178, 179, 180], "parent_ent": 15, "parent_id": 132, "parent_seq": 237, "parent_sequ": 237, "parenthes": 182, "parenthesi": 20, "parenttaxid": 7, "park": 2, "parker": 265, "parlanc": 3, "pars": [0, 1, 8, 9, 11, 13, 17, 18, 20, 21, 24, 27, 29, 30, 32, 38, 45, 50, 53, 54, 55, 56, 57, 58, 59, 62, 63, 65, 66, 68, 69, 71, 74, 76, 79, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 111, 112, 113, 114, 115, 116, 118, 121, 123, 129, 137, 142, 143, 149, 150, 151, 152, 153, 162, 165, 174, 181, 185, 188, 190, 191, 193, 195, 196, 198, 201, 204, 205, 209, 210, 211, 212, 213, 214, 217, 218, 221, 222, 223, 224, 225, 226, 227, 229, 230, 234, 236, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 268, 269, 271, 272, 273, 275, 278, 279, 283, 284, 286, 289, 291, 292, 293, 295, 296, 298, 299, 303], "pars_tre": 199, "parsabl": 209, "parse_alignment_block": [222, 223, 224, 225], "parse_btop": [30, 55], "parse_cds_featur": [92, 94], "parse_children": [181, 185], "parse_cigar": [30, 55], "parse_deflin": [68, 69], "parse_domain": [27, 209], "parse_featur": [92, 94], "parse_foot": [92, 94], "parse_format": 185, "parse_graph": [181, 185], "parse_handle_to_graph": [181, 185], "parse_head": [92, 94], "parse_hit": [229, 230], "parse_hsp": [229, 230], "parse_hsp_align": [229, 230], "parse_key_valu": [229, 230], "parse_pdb_head": [15, 27, 133, 248], "parse_preambl": [229, 230], "parse_printed_align": [0, 27, 30], "parse_qresult": [229, 230], "parse_record": [92, 94], "parse_seqid": [68, 69], "parse_xsd": [83, 84], "parseabl": 226, "parser": [0, 1, 2, 3, 6, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 25, 27, 29, 30, 41, 42, 45, 50, 52, 55, 56, 58, 59, 60, 63, 66, 68, 71, 83, 85, 88, 89, 90, 92, 96, 123, 128, 133, 140, 143, 148, 150, 151, 156, 164, 165, 169, 170, 173, 181, 185, 188, 190, 191, 198, 205, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 241, 242, 243, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 269, 271, 275, 276, 277, 283, 295, 298, 299], "parsererror": [27, 28, 29], "parserfailureerror": [27, 92], "parsimoni": [80, 129, 181, 182, 199], "parsimony_se": [181, 182], "parsimonyscor": [27, 181, 199], "parsimonytreeconstructor": [27, 181, 199], "parsiomni": 80, "part": [0, 4, 6, 8, 9, 11, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 37, 44, 46, 56, 59, 66, 73, 99, 117, 169, 183, 193, 195, 196, 197, 217, 221, 222, 236, 237, 238, 250, 252, 264, 269, 275, 278, 297, 299], "part_align": [53, 66], "parti": [8, 17, 253], "partial": [0, 3, 6, 7, 11, 21, 36, 66, 104, 119, 123, 201, 236, 238, 260, 263], "particip": 117, "particular": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 17, 19, 20, 21, 23, 30, 31, 83, 104, 108, 109, 183, 214, 236, 238, 260, 278, 299], "particularli": [3, 7, 20, 83, 237], "partit": [32, 129, 182], "partition_branch_length": [181, 182], "partition_filenam": [181, 182], "partli": [15, 21], "partner": 172, "partsiz": [30, 32], "parttre": [30, 32], "pas_con": 53, "pasquali": 263, "pass": [1, 3, 4, 6, 7, 10, 11, 12, 13, 15, 17, 18, 20, 21, 25, 30, 31, 32, 67, 68, 70, 73, 83, 89, 91, 92, 94, 100, 104, 105, 109, 117, 122, 158, 169, 172, 182, 193, 195, 196, 217, 218, 221, 236, 237, 240, 248, 264, 278, 283, 287, 288, 293], "passwd": [303, 305], "password": [11, 68, 70, 288, 303], "past": [24, 158, 236], "patch": 5, "path": [0, 3, 4, 7, 8, 12, 15, 17, 24, 30, 32, 37, 45, 67, 68, 83, 91, 100, 108, 109, 110, 112, 116, 117, 119, 149, 152, 153, 158, 164, 165, 166, 171, 182, 183, 193, 195, 209, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 258, 259, 269, 270, 271, 272, 303], "pathlib": 91, "pathlik": [150, 164, 238, 241, 245, 246, 249, 251, 256], "pathogen": [2, 104], "patholog": 116, "pathwai": [10, 27, 105, 111, 112, 113, 115, 116, 117, 118, 119, 234, 274], "pathway_fil": 10, "patient": 123, "patrick": [2, 9], "patser": [11, 294], "pattern": [1, 2, 3, 7, 25, 51, 68, 69, 79, 80, 88, 117, 283], "pattern_end": 218, "pattern_start": 218, "paul": 2, "paulu": 7, "paup": [32, 129, 132, 190], "pazar": [11, 288], "pazar_id": [11, 287, 288], "pbad30": 260, "pbad30_rc": 260, "pbd": 215, "pbluescript": [206, 207], "pbm": 288, "pbs_mc": [206, 207], "pbz78439": 19, "pc": [15, 73], "pc6": 90, "pca": [4, 27, 73], "pcassai": 7, "pcb_vectors_pymol": [133, 141], "pcc": 11, "pccompound": 7, "pclass": 169, "pcm": 11, "pcr": [80, 253, 264, 270], "pcsubstanc": 7, "pct": [7, 275], "pcut": 152, "pd": 0, "pdat": 7, "pdb": [0, 2, 7, 9, 12, 24, 25, 26, 27, 53, 83, 88, 123, 209, 214, 215, 238, 248, 260, 274, 307], "pdb1fat": 15, "pdb70": 0, "pdb7rsa": 169, "pdb_code": 149, "pdb_date": [27, 133, 152], "pdb_datestamp": 214, "pdb_file": [15, 145], "pdb_handl": 214, "pdb_id": [171, 248], "pdb_object": 148, "pdb_ref": [133, 149], "pdb_residue_str": [15, 133, 169], "pdb_seqr": 149, "pdb_struct": 88, "pdbatomiter": [27, 238, 248], "pdbconstructionexcept": [15, 27, 133, 147, 155], "pdbconstructionwarn": [27, 133, 147], "pdbdata": [27, 75], "pdbdescr": 83, "pdbexcept": [27, 133, 152, 168], "pdbid": [0, 152, 158, 168, 169, 214, 215], "pdbio": [15, 27, 133, 169, 238], "pdbioexcept": [27, 133, 147], "pdbj": 274, "pdbl": 15, "pdblist": [15, 27, 133], "pdbml": [149, 150], "pdbml_parser": 15, "pdbmlparser": [15, 27, 133], "pdbparser": [15, 27, 133, 137, 140, 143, 148, 154, 156, 157, 162, 169], "pdbseqresiter": [27, 238, 248], "pdbstructur": [164, 168], "pdbx": [15, 149], "pdbx_poly_seq_schem": 248, "pdf": [6, 8, 9, 15, 56, 83, 99, 101, 103, 104, 226, 229, 236, 238, 239, 263, 278], "pdir": [15, 149], "pdoc": [25, 88], "pdoc00001": [25, 85], "pdoc00004": 25, "pdoc00005": 25, "pdoc00110": 25, "pdvknwikfarfe": 53, "pdz78471": 23, "pe": 251, "peak": [7, 19, 125], "peaklist": [27, 124, 125, 126], "pear": [7, 12, 23], "pearson": [0, 2, 11, 12, 32, 55, 56, 59, 73, 182, 217, 226, 241, 290], "pearson1988": [0, 2], "peculiar": 4, "peek": [128, 129, 278], "peek_nonwhitespac": [128, 129], "peek_word": [128, 129], "peeksav": [13, 14], "peeksavtalwgkv": 14, "pemslei": 15, "pen": 32, "penal": [13, 14, 270, 297], "penalis": 32, "penalize_end_gap": 297, "penalize_extend_when_open": 297, "penalti": [9, 13, 14, 32, 68, 69, 71, 80, 182, 199, 238, 270, 297], "peopl": [5, 11, 19, 21, 23, 207], "peptid": [22, 32, 154, 169, 263, 272], "peptidoglycan": 0, "per": [0, 6, 7, 15, 18, 21, 30, 53, 56, 60, 64, 66, 69, 83, 85, 104, 119, 121, 149, 158, 167, 169, 182, 197, 201, 202, 204, 205, 217, 229, 238, 241, 251, 259, 260, 264, 270, 273, 274, 275, 278, 302], "perc_id": [68, 70], "perc_ident": [68, 69], "percent": [32, 69, 80, 209, 221, 264, 275], "percentag": [6, 8, 13, 31, 80, 99, 209, 261, 265], "percentcg": 283, "percentid": [30, 32], "perfect": [6, 21, 23, 30], "perfectli": 20, "perform": [7, 9, 11, 12, 15, 20, 22, 30, 32, 34, 56, 65, 69, 73, 80, 149, 182, 203, 238, 251, 270, 278, 290, 300], "perhap": [5, 6, 7, 12, 21, 22, 183, 191, 240, 241, 251], "period": [0, 4, 12, 33, 63, 65], "perl": [23, 288], "permiss": [15, 151], "permit": [100, 117, 169, 237], "permut": 4, "perna": 2, "peroxisom": 272, "perpendicular": [8, 176], "persist": [217, 305], "person": [6, 7, 15, 19, 21, 83, 123], "perspect": 56, "pertain": 20, "pesti": [6, 8, 21, 238], "pesticin": [21, 238], "petabyt": 278, "peter": [2, 26, 133, 263], "peterson": 133, "pevtnwlrwarfee": 53, "peyret": 264, "pf": 234, "pf02184": 53, "pf02294": 0, "pf05371": 12, "pf05371_seed": 12, "pfam": [0, 12, 21, 53, 56, 66], "pfam2": 0, "pfam_gc_map": [56, 66], "pfam_gr_map": [56, 66], "pfam_gs_map": [56, 66], "pfamseq": [0, 53], "pfm": [27, 283, 287, 288, 296], "pfm_format": 293, "pg": [0, 7, 108, 123], "pgdb": 304, "pgdb_dbutil": [301, 304], "pgm": 253, "pgt875": 0, "pgtygfycephagagmvgkvt": 0, "pgtygfycephagagmvgkvtv": 0, "pgtysfyctphrgagmvgtit": 0, "pgtysfyctphrgagmvgtitv": 0, "pgvygvkctphygmgmvgvv": 0, "pgvygvkctphygmgmvgvvev": 0, "ph": [263, 265], "phage": [2, 8, 104], "phage_coat_gp8": 12, "pharmaceut": 15, "phase": [158, 182, 270], "phd": [27, 238, 249, 268], "phd1": 249, "phdio": [27, 238], "phditer": [27, 238, 249], "phdwriter": [27, 238, 249], "phe": [13, 15, 169, 265], "pheatomselect": [15, 169], "phen_micro": [27, 298], "phenotyp": [26, 27, 307], "phenylalanin": [13, 15, 169], "pheromon": 7, "pheselect": 169, "phi": [3, 15, 68, 70, 137, 152, 154, 169], "phi_pattern": [68, 69, 70], "phl": 0, "phlyip": 56, "phmmer": [217, 229], "phmmer3": 229, "phobiou": 234, "phosphat": [3, 112, 261, 272], "phosphomutas": 10, "phosphoryl": 260, "phosphorylas": 209, "phosphotransferas": 10, "photo": 19, "phragmipedium": 19, "phrap": [238, 249, 268, 269, 271], "phred": [6, 238, 240, 249, 251, 253, 268, 270, 271], "phred_qual": [6, 21, 52, 240, 249, 251, 253, 260], "phred_quality_from_solexa": [27, 238, 251], "phrep": 251, "phst": 123, "phx": 183, "phy": [0, 12, 17, 30, 32, 56, 60, 182, 199], "phy_phyml_tre": 17, "phya": 260, "phyi": [30, 32], "phyiout": [30, 32], "phyl": 17, "phylip": [12, 17, 23, 27, 30, 32, 56, 60, 65, 80, 129, 132, 182, 190, 199, 238], "phylip3": 32, "phylipio": [27, 56], "phylipiter": [27, 56, 60, 65], "phylipout": [30, 32], "phylipwrit": [27, 56, 65], "phylo": [0, 2, 9, 12, 13, 24, 26, 27, 132, 307], "phylo_cookbook": 17, "phyloel": [27, 181, 197], "phylogenet": [0, 2, 7, 9, 12, 26, 56, 129, 130, 132, 181, 182, 183, 197, 198, 307], "phylogeni": [0, 17, 27, 32, 132, 181, 182, 183, 197, 198], "phylogent": 80, "phylogeograph": 197, "phylogram": 17, "phyloxml": [27, 181, 183, 198], "phyloxml_exampl": [17, 183], "phyloxmlerror": [27, 181, 198], "phyloxmlio": [27, 181, 183], "phyloxmlwarn": [27, 181, 197], "phylum": 197, "phyml": [17, 65, 182], "phymlcommandlin": [181, 182], "physalu": 272, "physic": [15, 158, 265], "physiol": 7, "physout": [30, 32], "phyto": 2, "phytochrom": 260, "phytopathologi": 2, "phz78458": 23, "pi": [15, 53, 135, 137, 139, 176, 261, 263, 265, 272], "pic": [144, 152, 167, 168, 169], "pic_accuraci": [133, 152, 168, 169], "pic_flag": [15, 133, 152, 169], "picard": 270, "picflag": [15, 152], "picflagsdefault": [133, 152, 169], "picflagsdict": [133, 169], "picio": [15, 27, 133, 169], "pick": [3, 6, 7, 8, 12, 15, 23, 32, 80, 102, 222], "pick_angl": [15, 133, 169], "pick_length": [15, 133, 169], "pickl": [30, 36, 54, 237, 297], "pict": 8, "pictur": [19, 99], "pid": [7, 93, 275], "pident": 218, "piec": [3, 6, 7, 8, 11, 260, 278], "pierr": 2, "pigment": 25, "pil": 8, "pilar": 2, "pileup": [48, 56, 63, 270], "pillow": 24, "pim": [21, 30, 32], "pin": 24, "pink": 183, "pip": 9, "pipe": [12, 17, 23, 270, 297], "pipelin": [6, 7, 238, 251], "pir": [25, 32, 238, 250], "pir_aln": 32, "pir_fram": 250, "pir_seq": 32, "pirio": [27, 238], "piriter": [27, 238, 250], "pirwrit": [27, 238, 250], "pisc": [152, 169], "pixel": 104, "pj": [7, 53], "pk": [3, 53, 263], "pk_ss": 53, "pkc_phospho_sit": 25, "pkvkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahh": 13, "pl": [15, 123, 182, 265, 270], "place": [3, 4, 5, 7, 11, 15, 17, 19, 22, 23, 30, 99, 104, 109, 119, 123, 152, 158, 168, 169, 177, 183, 214, 236, 237, 248, 251, 269, 275, 286], "placehold": [22, 277], "placement": [0, 8, 13, 30, 32], "plai": [7, 146, 221], "plain": [0, 1, 3, 6, 7, 8, 9, 13, 17, 19, 22, 23, 25, 30, 36, 68, 69, 70, 71, 83, 84, 89, 90, 94, 132, 185, 188, 190, 191, 197, 217, 222, 224, 228, 229, 233, 237, 238, 256, 258, 260, 261, 274, 276, 278, 297], "plain_newick": [132, 190], "plaintext": 104, "plan": [7, 18], "plane": [15, 169, 176], "plant": [2, 7, 19, 25, 93, 275], "plas_anav": 0, "plas_anava": 0, "plas_chlr": 0, "plas_horv": 0, "plas_horvu": 0, "plas_proh": 0, "plas_proho": 0, "plasma": [3, 25], "plasmid": [2, 6, 8, 21, 260], "plasmid_circular": 8, "plasmid_circular_nic": 8, "plasmid_linear": 8, "plasmid_linear_nic": 8, "plastid": 7, "plate": [16, 298, 299], "plate2": 299, "plate3": 299, "plateau": [16, 300], "plateid": 299, "platerecord": [16, 27, 298, 299], "platform": [7, 12, 16, 253, 270], "pleas": [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 18, 24, 25, 27, 29, 31, 32, 42, 50, 53, 65, 66, 68, 70, 73, 92, 120, 149, 152, 169, 182, 218, 222, 226, 241, 247, 251, 252, 253, 256, 264, 269, 274, 278, 282, 283, 297], "pleasant": 20, "pleckstrin": 217, "plenti": 9, "plfgwsryip": 250, "pliohippu": 56, "pln": [7, 23, 83, 93, 278], "plnyillnla": 250, "plnyillnlg": 250, "plnyillnlv": 250, "plo": 182, "plor": 15, "plot": [4, 8, 17, 23, 101, 169, 261, 265], "plq": 6, "plt": [15, 169], "plu": [0, 3, 7, 8, 9, 17, 20, 23, 32, 69, 169, 183, 221, 237, 251, 260, 261, 300], "plug": [31, 99], "plural": [0, 3, 11, 290], "plv": 56, "plvgwsryip": 250, "pm": [3, 16, 298, 299, 300], "pm01": [16, 298, 299], "pm09": [16, 298], "pm_fit": [27, 298], "pmc": [7, 83, 123, 234], "pmc310725p3": 7, "pmc3998142": 234, "pmc_id": 7, "pmc_pubm": 7, "pmcid": 7, "pmdml": 149, "pmic": 262, "pmid": [7, 34, 72, 83, 123, 153, 166, 175, 182, 280, 281, 299, 300], "pmismatch": [79, 80], "pmv": 15, "pn": 0, "pna": [2, 59], "pname": 153, "pnext": 52, "png": [6, 8, 11, 99, 104, 116, 283], "pnsldhgilivgysakntifrknmpywivknswgadwgeqg": 0, "pnsldhgilivgysakntifrknmpywivknswgadwgeqgyiylrrgkntcgvsnfvstsii": 0, "po": [11, 18, 31, 88, 129, 139, 201, 204, 223, 224, 225], "poacea": 25, "poal": 25, "pob": 80, "point": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 16, 17, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 36, 37, 65, 68, 73, 80, 84, 100, 101, 104, 129, 155, 157, 169, 175, 176, 177, 181, 182, 197, 198, 207, 216, 237, 251, 260, 263, 265, 278, 281, 282, 297, 299, 300], "pointer": [1, 3, 5, 13, 86, 158], "pointless": 23, "poke": 17, "pol_hv1n5": 248, "polar": [12, 13], "polar_angl": 176, "poll": 3, "pollin": 7, "pollut": 278, "polya": 275, "polygon": [27, 181, 197, 198], "polylin": 117, "polym": [143, 172], "polymorph": 72, "polynomi": 175, "polypeptid": [27, 133, 140, 263, 272], "polypeptide_domain": 0, "polypeptide_list": 15, "polypeptide_repeat": 53, "polypeptidebuild": 15, "polytomi": 132, "pomg": [152, 169], "ponabe2": 0, "pone": [137, 182], "ponnuswami": 265, "pooidea": 25, "poor": [6, 13, 19, 183, 251, 270], "poorli": [30, 270], "pop": [6, 17, 27, 201, 202, 204, 236], "pop_list": 201, "pop_nam": [18, 201, 202], "pop_po": [202, 203], "popen": 12, "popgen": [26, 27, 307], "popset": 7, "popul": [21, 26, 66, 169, 200, 201, 202, 203, 204, 205, 260, 303, 307], "popular": [4, 5, 7, 9, 11, 12, 18, 19, 20, 23], "port": 17, "portabl": 2, "portal": 8, "portion": [12, 61, 138], "portrait": 104, "pos_num": [20, 218], "pos_pct": [218, 226], "pos_specific_score_matrix": [12, 30, 31], "poscolor": 104, "posit": [0, 3, 4, 6, 8, 13, 14, 15, 17, 18, 22, 27, 30, 31, 32, 35, 36, 39, 44, 45, 46, 51, 52, 61, 66, 68, 69, 71, 73, 88, 99, 100, 104, 107, 114, 117, 125, 129, 135, 136, 139, 141, 146, 152, 158, 162, 169, 177, 182, 201, 203, 204, 217, 218, 222, 234, 236, 237, 240, 253, 257, 261, 263, 264, 265, 269, 270, 272, 278, 283, 286, 290, 293, 294, 295, 297, 303], "position_pad": [238, 245], "positionspecificscoringmatrix": [11, 27, 283, 290], "positionweightmatrix": [27, 283, 290], "positiveinteg": 197, "possess": 217, "possibl": [3, 5, 6, 7, 8, 11, 12, 15, 19, 20, 21, 23, 24, 27, 30, 34, 56, 66, 68, 72, 76, 84, 108, 122, 127, 175, 197, 217, 218, 221, 237, 238, 251, 256, 260, 261, 269, 275, 278, 281, 282, 290, 295, 303, 305], "possibli": [20, 30, 36, 68, 69, 88, 169, 197, 198, 237], "post": [6, 7, 19, 71, 83, 221, 253], "posted_d": 71, "posterior": [32, 53], "posterior_prob": 66, "postgresql": 304, "postord": [17, 183], "postscript": [8, 99], "posttransation": 272, "posttransl": 272, "potapov": 2, "potato": 2, "potenti": [3, 5, 6, 11, 12, 15, 20, 21, 23, 27, 88, 99, 177, 237, 251, 270, 278], "pothier": 153, "pou": 288, "power": [6, 7, 15, 23], "pp": [15, 53, 66, 149, 154, 169, 229], "pp_con": 53, "ppawagdrsh": 0, "ppb": [15, 154], "ppbuilder": [15, 27, 133, 154], "ppcp": 21, "ppcp1": [6, 8, 21], "ppo": 218, "ppsflrapsw": 250, "pqqpqggnqfsggaqsrpqqsapaapsneppmdfdddipf": 260, "pqr": [135, 148, 151, 162], "pqr_charg": [135, 162], "pqr_parser": 15, "pr": [7, 25, 86, 88], "practic": [4, 12, 15, 17, 21, 23, 127, 251, 264], "prang": [79, 80], "prank": 32, "prank_clin": 32, "prankcommandlin": [30, 32], "prb": 270, "prbnseq": 270, "pre": [5, 6, 30, 32, 169, 253, 260], "preambl": [94, 230], "precalcul": [4, 54], "preced": [0, 17, 169, 183, 288], "precis": [11, 13, 80, 157, 182, 216, 286, 290, 294], "pred": 122, "predecessor": [130, 132, 218], "predefin": [0, 17, 20, 38, 294], "predict": [0, 3, 15, 20, 25, 53, 110, 125, 164, 263, 275], "predicted_st": 110, "predicted_titl": 110, "predictno": [27, 124, 125], "predictor": [11, 283], "preexist": 104, "prefer": [3, 4, 6, 7, 8, 11, 12, 13, 15, 22, 30, 67, 73, 84, 169, 238, 251, 261, 270, 295], "prefix": [6, 17, 24, 32, 84, 97, 117, 129, 181, 183, 185, 188, 236, 268, 270], "prefwidth": [206, 207], "preker": 53, "prelim": 71, "preliminari": [69, 272], "preorder": [17, 183], "prepar": [12, 49, 64, 149, 163, 169, 175], "prepeptid": 272, "preprocess": 177, "preq1": 53, "prescrib": 104, "presenc": [20, 275, 299], "present": [1, 3, 4, 5, 6, 7, 8, 16, 20, 21, 23, 24, 25, 30, 52, 54, 69, 73, 94, 102, 104, 117, 129, 136, 139, 144, 149, 164, 172, 182, 197, 218, 221, 222, 226, 229, 236, 237, 251, 264, 270, 275, 299], "present_count": 197, "preserv": [0, 8, 15, 17, 20, 21, 23, 30, 84, 159, 183, 217, 222, 238, 253, 260], "preserve_atom_numb": [148, 170], "preset": 15, "press": [2, 169, 216], "presum": [13, 303], "pretend": [6, 253], "pretrain": 32, "pretti": [5, 6, 7, 12, 15, 22, 23, 237, 261], "prettifi": 117, "prettili": 297, "pretty_print_predict": [27, 106, 110], "pretty_str": [15, 133, 169], "prev": 130, "prevent": [0, 7, 11, 12, 24, 30, 32, 107, 236, 240, 251, 303], "previou": [6, 8, 12, 15, 20, 21, 22, 23, 24, 37, 46, 53, 68, 108, 158, 169, 240, 267], "previous": [4, 8, 15, 20, 21, 65, 83, 127, 251], "pri": 93, "price": 182, "prickli": [7, 12, 23], "primari": [21, 52, 83, 88, 152, 169, 303], "primarili": [0, 24, 30, 158], "primary_id": [302, 303], "primat": 93, "prime": 21, "primer": [12, 21, 27, 72, 79, 80, 81, 82, 251, 253, 264], "primer3": [27, 79, 80], "primer3commandlin": [27, 79, 80], "primer3plu": 264, "primer_nam": 82, "primer_read": 6, "primersearch": [27, 79, 80], "primersearchamplifi": 82, "primersearchcommandlin": [27, 79, 80], "primersearchoutputrecord": 82, "primit": [158, 183], "prin": 123, "princip": [2, 73], "principl": 23, "print": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 56, 59, 60, 62, 66, 67, 68, 69, 71, 76, 80, 83, 85, 90, 92, 104, 110, 112, 113, 114, 116, 122, 123, 129, 134, 135, 137, 154, 156, 157, 158, 168, 169, 176, 182, 183, 195, 199, 206, 207, 216, 217, 236, 237, 238, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 253, 256, 260, 261, 263, 264, 265, 269, 270, 272, 274, 277, 278, 279, 280, 281, 283, 288, 289, 291, 292, 295, 297, 298, 299], "print_a": [206, 207], "print_info_cont": [27, 30, 31], "print_matrix": [27, 297], "print_opt": [192, 195], "print_site_lnl": [181, 182], "print_that": [206, 207], "print_trac": [181, 182], "printabl": 158, "printer": 158, "printformat": [27, 206], "printlist": 207, "printnod": [30, 32], "printout": [14, 297], "prior": [6, 7, 9, 12, 21, 23, 99, 108, 109, 127, 237, 265, 270, 297], "pritchard": [2, 7, 8, 9], "pritchard2006": [2, 8, 9], "privat": [67, 71, 76, 89, 91, 94, 129, 169, 197, 202, 237, 252], "pro": [6, 13, 15, 30, 69, 169, 241, 260], "pro1": [13, 279], "pro2": [13, 279], "pro3": 13, "pro_align": 279, "prob": [0, 202], "probab": 0, "probabilist": [2, 32, 270], "probabl": [3, 4, 6, 8, 9, 11, 12, 13, 15, 21, 23, 32, 53, 62, 66, 107, 108, 109, 120, 122, 127, 169, 202, 203, 238, 251, 253, 260, 270, 282, 283, 290, 305], "probal": 251, "probcon": [0, 32], "probcons_clin": 32, "probconscommandlin": [30, 32], "probe": [7, 20, 80, 157, 238, 264], "probe_radiu": 157, "probe_s": 145, "problem": [1, 3, 5, 6, 7, 8, 9, 11, 12, 20, 21, 22, 23, 27, 92, 99, 107, 108, 136, 143, 144, 151, 158, 160, 169, 182, 198, 221, 226, 251, 278], "problemat": [21, 278], "proc": [83, 264], "proce": [7, 15, 182, 270], "procedur": [4, 15, 20, 32, 129], "proceed": [0, 2, 13, 32], "process": [0, 2, 4, 5, 6, 7, 9, 13, 15, 22, 53, 56, 67, 84, 89, 95, 99, 136, 145, 158, 169, 182, 190, 238, 258, 272], "process_asa_data": [27, 133, 145], "process_clad": [181, 185, 190], "process_rsa_data": [27, 133, 145], "processor": 32, "prodoc": [25, 27, 85], "produc": [3, 4, 8, 12, 15, 16, 17, 20, 22, 48, 59, 63, 69, 80, 94, 99, 103, 158, 183, 186, 222, 229, 238, 251, 253, 272], "product": [7, 8, 12, 13, 15, 16, 21, 27, 73, 80, 81, 94, 99, 113, 115, 117, 158, 176, 177, 264, 277], "product_id": 117, "prof": [17, 123], "profil": [2, 4, 11, 25, 30, 32, 74, 90, 229, 231, 265, 287, 288], "profile1": [30, 32], "profile2": [30, 32], "program": [0, 1, 2, 3, 4, 6, 7, 9, 11, 12, 13, 15, 17, 19, 20, 22, 23, 30, 32, 36, 37, 44, 55, 59, 65, 67, 68, 69, 70, 73, 74, 79, 80, 81, 82, 83, 107, 109, 137, 145, 153, 156, 158, 169, 182, 183, 199, 202, 203, 217, 218, 221, 222, 226, 229, 234, 238, 252, 254, 259, 262, 268, 269, 270, 283, 291, 292, 294, 296, 297], "programm": [7, 19, 20], "programmat": [7, 25, 89], "progress": [4, 32, 79, 80, 182], "progressivemauv": [0, 47, 56, 62], "prohibit": 4, "project": [5, 6, 7, 9, 15, 17, 21, 24, 27, 93, 94, 158, 169, 174, 176, 250], "projects_home_pag": 32, "prokaryot": [6, 8], "prolin": [15, 152], "proma": 2, "promot": [6, 23, 27, 260, 272], "prompt": [3, 12, 19, 80, 260, 297], "proof": [15, 169], "prop": [7, 134, 197], "prop_invar": [181, 182], "propag": [0, 12, 21, 30], "propagate_chang": [133, 169], "propep": 272, "propeptid": 272, "proper": [107, 251, 270], "properli": [4, 5, 129, 149, 182, 183, 237, 270], "properti": [0, 3, 8, 11, 12, 13, 17, 20, 21, 22, 27, 30, 32, 54, 67, 68, 69, 80, 84, 100, 104, 117, 134, 137, 139, 145, 169, 181, 182, 183, 193, 195, 196, 197, 198, 221, 222, 236, 237, 252, 256, 260, 265, 270, 283, 287, 290, 296, 302], "property_1": 134, "property_2": 134, "property_dict": 134, "property_kei": 134, "property_list": 134, "prophag": 8, "proport": [8, 104, 182], "proportoin": 80, "propos": [19, 265, 300], "proprietari": [3, 16], "prorul": 88, "prosit": [9, 27, 85, 86, 87, 89], "prosite_ref": 87, "prot": [0, 2, 9, 19, 23, 26, 32, 69, 86, 88, 89, 137, 197, 238, 255, 307], "prot_guidelin": 25, "prot_sequ": 265, "protcat_gammaimatrixnam": 182, "protcat_gammamatrixnam": 182, "protcatmatrixnam": 182, "protcatwag": 182, "protdist": 80, "proteas": 8, "protect": 25, "protein": [0, 2, 3, 4, 6, 7, 8, 11, 12, 13, 19, 20, 21, 22, 23, 25, 30, 32, 53, 56, 68, 69, 71, 74, 80, 83, 86, 88, 93, 94, 112, 117, 140, 149, 152, 153, 157, 158, 164, 166, 169, 175, 182, 196, 197, 198, 199, 209, 211, 214, 216, 221, 222, 226, 229, 234, 236, 237, 238, 250, 252, 260, 261, 263, 265, 272, 274, 275, 277, 279, 283, 290], "protein2": 25, "protein2dna": [42, 222], "protein2genom": [42, 222], "protein_align": 13, "protein_alphabet": [75, 76], "protein_exist": 272, "protein_id": [7, 21, 94], "protein_letters_3to1_extend": 214, "protein_model": [181, 182, 199], "protein_rec": 260, "protein_record": [13, 260], "protein_scal": [261, 265], "protein_seq": 22, "protein_sequ": 263, "proteinalpabet": 22, "proteinanalysi": [27, 261, 263, 265], "proteinclust": 7, "proteindomain": [27, 181, 197], "proteint": 93, "protgammaimatrixnam": 182, "protgammamatrixnam": 182, "protgi": [7, 275], "protid": [7, 275], "protmix": 182, "protmiximatrixnam": 182, "protmixmatrixnam": 182, "protml": 17, "proton": [152, 169], "prototyp": 177, "protpar": 80, "protparam": [27, 261, 263, 266], "protparamdata": [27, 261, 265], "protscal": 265, "protsim": [7, 275], "protsimlin": [27, 275], "proux": [2, 8], "proux2002": [2, 8], "proux_et_al_2002_figure_6": 8, "prove": [6, 8], "provid": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 20, 21, 23, 24, 25, 27, 30, 36, 37, 38, 42, 45, 53, 56, 60, 61, 65, 66, 67, 68, 70, 73, 80, 83, 91, 93, 94, 95, 99, 100, 104, 109, 119, 126, 130, 132, 137, 143, 148, 149, 150, 151, 152, 157, 158, 169, 182, 186, 197, 199, 204, 205, 209, 214, 215, 217, 218, 221, 222, 226, 229, 236, 237, 238, 246, 251, 253, 261, 268, 272, 274, 275, 278, 287, 288, 294, 297, 298, 299, 300, 303], "provis": [129, 130, 131, 132, 202], "proxi": [16, 149, 237, 260, 274], "proxyhost": 7, "prt": [22, 76, 272], "prune": [17, 128, 132, 181, 182, 183], "ps00001": [25, 85], "ps00004": 25, "ps00005": 25, "ps00387": 88, "ps50948": 25, "psd": 25, "psea": [27, 133], "psea2hec": [27, 133, 153], "pseq": 153, "pseudo": [11, 12, 69, 80, 108, 121, 141, 181, 182, 217], "pseudo_count": [12, 31], "pseudo_emiss": 121, "pseudo_initi": 121, "pseudo_transit": 121, "pseudocount": [11, 13, 27, 68, 69, 108, 182, 283, 287, 290], "pseudogen": 104, "psi": [15, 68, 69, 70, 71, 137, 152, 154, 169], "psiblast": [3, 27, 68, 69, 71], "psipr": 0, "psizeopt": [79, 80], "psl": [13, 20, 27, 30, 38, 45, 217, 221], "psl_34_001": [0, 217], "psl_34_004": 221, "pslayout": [0, 45, 221], "psltobigpsl": 0, "psltochain": 0, "pslx": [217, 221], "pslx_34_004": 221, "psp_test": [11, 283], "pssm": [12, 27, 30, 31, 69, 283, 288, 290, 294, 296], "pssm_reb1": 11, "pst": [30, 32, 123], "psycopg2": 304, "psycopg2_dbutil": [301, 304], "pt": [123, 175], "pthread": 182, "ptm": 272, "ptmlist": 272, "ptmmax": [79, 80], "ptmmin": [79, 80], "ptmopt": [79, 80], "ptr": 6, "pttk": 14, "ptz78488": 23, "pu": 11, "pub": [7, 15, 23, 153, 277], "pubdat": 7, "public": [3, 7, 8, 9, 16, 68, 83, 123, 129, 218, 221, 234, 251, 264, 265], "publicid": 84, "publicli": [8, 253], "publish": [7, 8, 9, 21, 123, 237, 264], "pubm": [9, 11, 19, 83, 123, 182, 237, 274, 288, 295], "pubmed1": 83, "pubmed_id": [7, 21, 93, 237], "pubmed_pmc_ref": 7, "pubmed_pubm": [7, 83], "pubmed_pubmed_alsoview": 7, "pubmed_pubmed_citedin": 7, "pubmed_pubmed_combin": 7, "pubmed_pubmed_f": 7, "pubmed_pubmed_ref": 7, "pubmed_pubmed_review": 7, "pubmed_pubmed_reviews_f": 7, "pubmed_result1": [7, 123], "pubmed_result2": [7, 123], "pubmedarticl": 7, "pubmedcentr": 83, "pull": [0, 5, 6, 12, 25, 131, 260, 274], "punctuat": 129, "pure": 182, "purin": 32, "purl": 185, "purpl": [8, 183], "purpos": [0, 7, 12, 13, 15, 17, 20, 24, 25, 30, 61, 84, 99, 108, 146, 197, 261, 281, 297, 305], "push_back": [229, 230], "put": [6, 7, 9, 12, 15, 23, 24, 31, 68, 70, 84, 104, 149, 163, 169, 175, 216, 277], "pv": [11, 13, 295], "pvalu": [11, 13, 291], "pvcgaael": 0, "pvcgaaelsvnsl": 56, "pvcgaaelsvnslek": 0, "pwdist": [30, 32], "pwdnamatrix": [30, 32], "pwgapext": [30, 32], "pwgapopen": [30, 32], "pwgenom": [30, 32], "pwgenomicdist": [30, 32], "pwm": [11, 27, 283, 288, 290], "pwmatrix": [30, 32], "px": [209, 211, 261], "py": [0, 5, 8, 9, 15, 24, 76, 116, 141, 152, 167, 169, 255, 261], "py38": 24, "py39": 24, "pycog": 17, "pycon": 24, "pyenv": 84, "pygresql": 304, "pyl": 261, "pylab": [6, 17], "pymmlib": 15, "pymol": [15, 141, 166], "pypi": [24, 217, 238], "pyplot": [15, 169], "pyrimidin": 32, "python": [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 32, 35, 39, 46, 51, 52, 61, 67, 68, 69, 80, 83, 84, 86, 89, 90, 123, 131, 158, 166, 172, 174, 175, 182, 183, 185, 197, 200, 218, 221, 236, 237, 238, 253, 260, 261, 270, 273, 274, 278, 284, 295, 297, 299, 303, 306, 307], "python3": [24, 84], "pywivkn": 0, "pywivknswgpqwgmng": 0, "pywivknswgpqwgmngyfliergknmcglaacasypiplv": 0, "pywlikn": 0, "pywliknswgadwgdng": 0, "pywliknswgadwgdngyfkmemgknmcaiatcasypvvaa": 0, "q": [0, 12, 13, 22, 30, 176, 182, 221, 237, 251, 261, 268, 270], "q06000": 25, "q08386": 68, "q29524": 25, "q8jzq5": 23, "q9t0q8": 12, "q9t0q8_bpi": 12, "q9t0q8_bpike": 12, "q9t0q9": 12, "q9t0q9_bpf": 12, "q9t0q9_bpfd": 12, "q9trc7": 23, "q_": [6, 12], "q_end1": [0, 30], "q_end2": [0, 30], "q_endn": [0, 30], "q_handl": 6, "q_i": 270, "q_l": 270, "q_start1": [0, 30], "q_start2": [0, 30], "q_startn": [0, 30], "qa": [13, 27, 268, 269], "qaarflfmknkvrmivdchakhvkvlqdeklpfdltlcgstlraphschlqymanmdsia": 260, "qacc": 218, "qaccver": 218, "qafeyikyng": 0, "qafeyilynk": 0, "qasgpertip": 250, "qatgknisl": 0, "qblast": [3, 9, 27, 68, 70], "qcov_hsp_perc": [68, 69], "qcp": [27, 133, 175], "qcprot": [27, 133], "qcpsuperimpos": [27, 133, 175], "qdfmmyrtgi": 0, "qdfmmyrtgiysstschktpdkvnhavlavgygekngi": 0, "qend": 218, "qend_mark": [218, 220], "qframe": 218, "qgi": 218, "qgkdgy": 0, "qgsgyafphasilsgiamshfyflvlhavk": 6, "qhkamiliv": 237, "qing": 2, "qinter": [202, 203], "qintra": [202, 203], "qkl": 68, "qlen": 218, "qllmspgqststtfpadapageytfycephrgagmvgkitv": 0, "qname": 252, "qncsat": 0, "qpgkaigfvk": 0, "qq": 176, "qquad": 22, "qr": 4, "qresult": [20, 217, 218, 219, 220, 221, 222, 231, 232, 235], "qresult2": 20, "qresult_end": [229, 230, 233], "qresult_start": [229, 230, 233], "qresults2": 20, "qrf": [13, 14], "qseq": 218, "qseqid": [69, 218], "qstart": [0, 218, 221], "qstart_id": 220, "qstart_mark": [218, 220], "qt": 182, "qtcsatlagn": 0, "qual": [23, 238, 240, 249, 251, 253, 260], "qual_digit": [268, 270], "qual_sourc": 251, "qualifi": [3, 7, 8, 21, 27, 68, 80, 92, 93, 94, 99, 104, 164, 237, 245, 260, 272, 275], "qualifier_ind": [238, 245], "qualifier_indent_str": [238, 245], "qualifier_indent_tmp": [238, 245], "qualiti": [0, 2, 13, 17, 21, 23, 32, 52, 182, 238, 240, 249, 251, 253, 260, 268, 269, 270, 302], "qualityio": [6, 23, 27, 238], "qualphrediter": [27, 238, 251], "qualphredwrit": [27, 238, 251], "qualtityio": 251, "quantiti": 6, "quartil": [98, 104], "quaternion": 175, "queri": [0, 3, 5, 12, 13, 20, 25, 27, 30, 38, 44, 45, 51, 52, 59, 61, 68, 69, 70, 71, 74, 83, 89, 119, 146, 169, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 229, 230, 231, 232, 233, 234, 260, 270, 274, 276, 299], "query_1": [68, 218], "query_128889": 3, "query_2": [68, 218], "query_3": 68, "query_4": 68, "query_5": 68, "query_69183": 3, "query_78041": 68, "query_al": 20, "query_believe_deflin": [68, 70], "query_coverag": [27, 74], "query_descript": 20, "query_end": [71, 218, 221, 222, 226, 229, 234], "query_end_extend_gap_scor": 13, "query_end_gap_scor": [13, 30], "query_end_open_gap_scor": 13, "query_endtyp": 229, "query_extend_gap_scor": 13, "query_fil": [68, 70], "query_fram": [218, 222], "query_frame_al": 222, "query_from": [3, 68, 70], "query_gap": [30, 55], "query_gap_num": 221, "query_gap_scor": 13, "query_gapopen_num": 221, "query_gencod": [68, 69], "query_id": [3, 20, 71], "query_inter_rang": 222, "query_internal_extend_gap_scor": 13, "query_internal_gap_scor": 13, "query_internal_open_gap_scor": 13, "query_is_protein": 221, "query_kei": 7, "query_left_extend_gap_scor": 13, "query_left_gap_scor": 13, "query_left_open_gap_scor": 13, "query_len": 3, "query_length": 71, "query_lett": 71, "query_loc": [68, 69], "query_mask": 3, "query_nam": 0, "query_open_gap_scor": 13, "query_rang": 20, "query_right_extend_gap_scor": 13, "query_right_gap_scor": 13, "query_right_open_gap_scor": 13, "query_span": 20, "query_span_al": 221, "query_split_codon": 222, "query_start": [20, 71, 218, 221, 222, 226, 229, 234], "query_start_al": 221, "query_strand": [221, 222, 226, 229], "query_to": [68, 70], "querya": 0, "queryb": 0, "queryc": 0, "querykei": 7, "queryresult": [217, 218, 219, 221, 222, 224, 225, 226, 229, 231, 232, 234], "querytransl": [7, 83], "question": [1, 5, 19, 20, 84, 182, 279], "queue": 169, "quick": [3, 7, 15, 20, 21, 23, 26, 31, 83, 132, 149, 152, 168, 169, 177, 217, 260, 307], "quickaln": 32, "quicker": [23, 209], "quickli": [0, 7, 13, 15, 17, 19, 21, 30, 152], "quicktre": [30, 32], "quiet": [30, 32, 143, 151, 157, 181, 182], "quikchang": 264, "quinoa": 3, "quirk": [7, 23], "quit": [0, 1, 3, 6, 8, 11, 12, 15, 19, 20, 21, 23, 222, 251], "quot": [32, 67, 94, 129, 181, 182], "quotestrip": [27, 128, 129], "quri": [27, 181, 185, 188], "r": [0, 1, 2, 4, 6, 7, 11, 12, 13, 15, 22, 23, 30, 32, 36, 37, 53, 59, 60, 67, 68, 74, 80, 91, 100, 116, 139, 140, 146, 149, 152, 157, 159, 168, 169, 172, 176, 177, 182, 183, 237, 238, 246, 253, 261, 268, 270, 277, 278, 279, 283, 299], "r1": 169, "r126": 0, "r1_cbeta_coord": 169, "r1_cbeta_index": 169, "r1chi2": 169, "r1chi2_index": 169, "r1chi2_kei": 169, "r1chi2_obj": 169, "r1chi2_valu": 169, "r2": 15, "r2_cbeta_coord": 15, "r2_cbeta_index": 15, "r2cacb": 15, "r2chi1": 15, "r2chi1_index": 15, "r2chi1_kei": 15, "r2chi1_object": 15, "r2ic": 15, "r2tau": 15, "r_": 4, "r_dna_nn1": 264, "r_free": 172, "r_method": [268, 270], "r_seed": [181, 182], "r_work": 172, "ra": [0, 11, 12, 53, 295], "rabgltr": 0, "rabgstb": 0, "rad": 176, "radial": 8, "radian": [169, 176], "radiat": 275, "radii": [157, 158, 169], "radii_dict": 157, "radiu": [4, 15, 104, 135, 141, 146, 154, 157, 162], "raf": [27, 209], "rai": [25, 144], "rainbow_color": 102, "rais": [3, 4, 7, 8, 11, 12, 13, 14, 17, 21, 22, 23, 25, 27, 30, 31, 56, 67, 68, 83, 84, 85, 89, 102, 108, 113, 136, 144, 152, 155, 160, 168, 169, 183, 188, 190, 198, 209, 217, 236, 237, 238, 241, 251, 253, 260, 261, 271, 283, 290, 298, 299, 300], "rak": [133, 169], "rak_cach": 169, "raltglsapgirsqtscdrlrelryvpvsl": 6, "ram": [23, 217, 238, 251, 278], "ran": [3, 24, 81, 92], "ranch": 80, "rand": 4, "rand_start": [181, 182], "random": [2, 7, 13, 15, 17, 23, 30, 56, 73, 80, 100, 108, 128, 132, 169, 181, 182, 183, 210, 214, 238, 251, 253, 256, 270, 278], "random_s00": 20, "random_starting_tre": [181, 182], "randomis": 80, "randomli": [4, 6, 108], "randommis": 80, "rang": [0, 2, 3, 6, 7, 11, 12, 13, 15, 18, 20, 21, 30, 32, 61, 69, 80, 88, 98, 99, 100, 102, 103, 104, 119, 169, 182, 236, 237, 251, 264, 265, 270, 274], "rank": [3, 7, 20, 73, 140, 181, 182, 197, 198], "rao": 199, "rapa": 238, "rapid": [175, 182, 210, 214], "rapid_bootstrap_se": [181, 182], "rapidli": [4, 11], "rare": [6, 17, 23], "rarer": 19, "rasmu": 2, "rasrksmraacsrsag": 0, "rasrksmraacsrsagsrpnrfaptlmsscitsttg": 0, "rasrksmraacsrsagsrpnrfaptlmsscitsttgppawagdrsh": 0, "rat": [0, 22, 182], "rate": [2, 11, 13, 32, 34, 79, 80, 83, 100, 182, 196, 270, 294], "rate_proport": 294, "rateancestor": 17, "rather": [6, 7, 12, 13, 15, 17, 21, 23, 24, 27, 32, 34, 62, 65, 66, 83, 84, 92, 197, 217, 237, 238, 251, 255, 269, 270, 278, 280, 303, 305], "ratio": [4, 11, 13, 32, 34, 80, 182, 194, 261, 281, 290], "ravier": 263, "raw": [4, 6, 7, 12, 15, 25, 59, 69, 84, 85, 92, 102, 128, 131, 218, 219, 220, 221, 224, 225, 226, 232, 238, 251, 253, 278], "rawdata": 54, "rawdist": [181, 182], "raxml": [17, 65, 182], "raxml_bipartitionfrequ": 182, "raxml_clin": 182, "raxml_reducedlist": 182, "raxmlcommandlin": [181, 182], "raxmlhpc": 182, "razip": 270, "rb": [3, 7, 23, 29, 68, 83, 247, 253, 278], "rbase": [15, 169], "rbg": 100, "rc": [21, 169, 250, 260], "rc_": 23, "rc_align": [0, 30], "rc_plasmid": 260, "rc_record": 260, "rcst": [15, 169], "rd": [15, 27, 156, 268, 269], "rd_of_read4": 269, "rdf": [185, 274], "rdrsdqhiqlqlsaesvgevyikstetgqylamdtsgllygsqtpseec": 265, "re": [3, 5, 6, 7, 8, 10, 12, 15, 17, 19, 20, 21, 23, 25, 27, 32, 68, 99, 111, 115, 119, 132, 134, 140, 143, 168, 169, 197, 204, 205, 209, 214, 221, 238, 251, 261, 270], "re_class": 169, "re_cod": [181, 197], "re_doi": [181, 197], "re_ref": [181, 197], "re_symbol": [181, 197], "re_valu": [181, 197], "reach": [0, 11, 12, 31, 100, 108, 129, 180, 183, 252, 270, 290], "reachabl": 108, "reactant": [117, 177], "reactant_id": [115, 117], "reaction": [27, 111, 113, 115, 116, 117, 118, 177, 274], "reaction_entri": [115, 117], "read": [1, 3, 4, 5, 7, 8, 9, 10, 14, 16, 17, 18, 19, 21, 22, 24, 25, 27, 28, 29, 30, 32, 41, 45, 50, 52, 54, 55, 56, 58, 59, 61, 65, 66, 68, 71, 73, 74, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 104, 111, 113, 115, 116, 123, 128, 129, 132, 149, 152, 169, 181, 182, 183, 192, 193, 195, 196, 198, 199, 200, 201, 204, 205, 217, 218, 221, 222, 230, 236, 237, 238, 240, 244, 247, 248, 249, 250, 251, 252, 253, 256, 257, 260, 268, 269, 270, 271, 272, 275, 277, 278, 281, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 298, 299], "read4": 269, "read_1": 270, "read_2": 270, "read_cal": [268, 270], "read_colorschem": [98, 104], "read_ctl_fil": [192, 193, 195, 196], "read_fil": [268, 270], "read_file1": [268, 270], "read_file2": [268, 270], "read_group": 270, "read_next": [229, 230], "read_pic": [15, 27, 133, 152, 168, 169], "read_pic_seq": [15, 27, 133, 152, 169], "reada": 0, "readabl": [0, 7, 11, 12, 13, 21, 22, 23, 25, 30, 45, 56, 59, 68, 80, 86, 90, 117, 197, 260, 280, 297, 299], "readb": 0, "readc": 0, "reader": [198, 278], "readfil": [268, 270], "readgroup": 270, "readi": [3, 5, 6, 12, 19, 117, 299], "readili": 20, "readjust": 129, "readlin": [1, 3, 27, 83, 278], "readm": [9, 149, 277], "readrochexmlmanifest": [27, 238, 253], "real": [0, 6, 12, 15, 17, 19, 21, 31, 69, 73, 100, 110, 141, 217, 222, 229, 251, 278], "real_stat": 110, "real_titl": 110, "realbranch": [30, 32], "realign": 270, "realis": 278, "realist": [2, 8, 10, 15], "realiti": 104, "realiz": [14, 15, 20], "realli": [1, 3, 5, 6, 7, 8, 11, 12, 15, 20, 21, 22, 23, 99, 149, 182, 236, 288, 305], "realproxi": 149, "reanchor": 221, "reappear": [0, 4], "rearrang": [2, 79, 80, 181, 182], "reason": [3, 6, 7, 9, 15, 21, 23, 27, 119, 178, 238, 251, 274], "reassign": 4, "reb1": 11, "rebas": 208, "rebuild": [168, 169], "rebuilt": 169, "rec": [6, 18, 21, 23, 238, 251, 260, 277], "rec1": 23, "rec2": 23, "rec3": 23, "rec_i": 8, "rec_loci": 18, "rec_on": 6, "rec_pop": 18, "rec_two": 6, "rec_x": 8, "recal": [3, 8, 20, 23], "recalcul": [0, 11, 21, 265], "recapitul": 11, "receiv": [3, 7, 27, 56, 89, 252], "recent": [0, 3, 4, 6, 7, 12, 13, 14, 17, 19, 21, 22, 23, 30, 32, 45, 56, 67, 68, 80, 85, 137, 149, 183, 217, 236, 237, 238, 241, 251, 260, 264, 278, 283, 298], "recent_orchid_pap": 7, "receptor": 15, "recnam": [23, 25], "recogn": [20, 23, 25, 226], "recognit": 8, "recommend": [2, 3, 4, 7, 9, 11, 12, 15, 23, 24, 30, 32, 56, 60, 67, 69, 80, 83, 86, 99, 152, 182, 197, 201, 217, 218, 251, 260, 264, 270, 278, 285], "recompil": 145, "reconsid": 7, "reconstruct": [0, 4, 15, 201, 204], "record": [0, 1, 4, 6, 8, 9, 11, 12, 13, 15, 16, 18, 19, 21, 22, 27, 28, 29, 30, 37, 46, 50, 52, 53, 56, 59, 60, 61, 62, 65, 66, 68, 69, 71, 73, 74, 79, 81, 82, 83, 85, 86, 87, 88, 89, 90, 92, 94, 96, 111, 112, 113, 114, 123, 145, 148, 152, 169, 177, 197, 200, 201, 204, 205, 209, 210, 211, 212, 213, 214, 215, 217, 220, 226, 237, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 259, 260, 268, 269, 270, 271, 272, 273, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 299, 302, 303, 305], "record1": 21, "record2": [21, 251], "record2titl": [241, 250, 251], "record_complete_ancestri": 185, "record_dict": 238, "record_ha": [27, 276, 277], "record_index": 6, "record_iter": [6, 23, 251, 303], "record_start": [92, 94], "recordpars": [27, 92], "recov": [169, 297], "recreat": [4, 30, 68, 73, 305], "rectangl": [4, 117], "rectangular": [4, 73], "recurs": [17, 80, 107, 139, 152, 183, 185, 197, 198, 263], "red": [0, 4, 8, 17, 104, 122, 181, 183, 198], "reddi": 265, "redefin": [45, 60, 246], "redirect": [12, 69], "redistribut": 3, "redland": 185, "redmin": 5, "reduc": [4, 7, 8, 21, 23, 32, 169, 182, 265, 270, 278], "reducedbi": 182, "reduct": [16, 36, 182], "reductas": 113, "redund": [3, 158, 169, 251, 270], "reestim": 32, "ref": [0, 3, 7, 20, 21, 25, 27, 152, 197, 218, 237, 238, 256, 268, 270, 272], "ref_db": [21, 27, 237], "ref_list": 270, "ref_locu": 7, "ref_rec": 56, "refer": [0, 3, 4, 6, 7, 8, 9, 12, 13, 15, 17, 23, 24, 25, 27, 30, 32, 36, 39, 52, 53, 59, 61, 68, 71, 84, 85, 87, 88, 90, 92, 93, 109, 111, 115, 117, 119, 123, 132, 133, 135, 140, 152, 157, 169, 175, 177, 181, 182, 190, 197, 198, 201, 209, 216, 218, 222, 248, 252, 260, 263, 267, 268, 270, 272, 275, 283, 295, 302], "referenc": [7, 15, 21, 169, 197, 214], "reference_annot": 66, "reference_coord": [175, 216], "reference_fasta": 270, "reference_genom": 270, "reference_kei": [283, 295], "refin": [7, 30, 32, 182, 276], "refinew": [30, 32], "refinewindow": [30, 32], "reflect": [7, 8, 15, 21, 169, 217, 238], "reflist": 270, "refmat": [15, 27, 133, 176], "refresh": [181, 182], "refseq": 93, "refseq_rna": [3, 20], "reg": [229, 270], "regard": [4, 5, 6, 12, 14, 20, 24, 30, 84, 140, 177, 264], "regardless": [11, 25, 217, 226, 236, 237, 256], "regener": [0, 15, 169], "regex": [17, 169], "region": [0, 3, 6, 8, 12, 15, 20, 21, 30, 31, 32, 35, 36, 38, 39, 46, 51, 59, 61, 68, 80, 88, 102, 103, 104, 158, 197, 217, 222, 226, 236, 237, 248, 251, 253, 257, 268, 270, 272, 275, 297], "region1": 270, "region_num": 229, "regist": [0, 236], "register_ncbi_t": [27, 75, 76], "registri": 123, "regraft": 182, "regress": [5, 24, 120], "regul": [2, 3, 104, 260], "regular": [0, 3, 4, 6, 11, 17, 20, 79, 80, 99, 104, 143, 169, 182, 183, 217], "regularli": [1, 19], "regulatori": [8, 296], "rehead": 270, "reheader_cmd": 270, "reinhardt": 0, "reinsch": 2, "reinstal": 7, "reinvent": 178, "reject": 148, "rel": [0, 2, 4, 7, 12, 13, 15, 23, 24, 30, 31, 36, 104, 132, 137, 152, 169, 182, 193, 195, 237, 261, 265, 278, 283], "rel_scor": 11, "relat": [1, 3, 4, 5, 8, 10, 11, 12, 13, 20, 21, 22, 23, 28, 69, 73, 83, 93, 99, 111, 115, 117, 119, 146, 154, 169, 176, 197, 209, 251, 260, 270, 288, 301, 303, 305], "relationship": [0, 99, 117, 197, 198, 214], "relative_entropi": [11, 27, 283], "relax": [12, 17, 56, 65, 129, 182, 186, 241], "relaxedphylipiter": [27, 56, 65], "relaxedphylipwrit": [27, 56, 65], "reldat": 7, "releas": [0, 3, 5, 8, 9, 11, 12, 14, 17, 19, 22, 23, 25, 27, 67, 69, 86, 87, 88, 90, 92, 105, 117, 137, 149, 172, 209, 210, 211, 212, 213, 214, 234, 252, 272, 297, 303], "release_d": [15, 172, 174], "relev": [0, 7, 9, 10, 11, 15, 18, 21, 22, 24, 83, 117, 132, 158, 169, 214, 238, 260, 273, 298], "reli": [0, 15, 17], "reliabl": [0, 15, 104, 251, 275], "relink": [17, 130, 183], "reload": [23, 217, 238], "remain": [3, 4, 17, 20, 23, 30, 32, 68, 107, 132, 169, 183, 217, 236, 238, 250, 265, 298], "remaind": 104, "remark": [15, 25, 93], "rememb": [3, 6, 7, 9, 12, 15, 18, 20, 22, 23, 30, 66, 237], "remmert": 32, "remot": [1, 2, 3, 7, 68, 69, 83, 218, 274], "remov": [3, 6, 9, 12, 13, 15, 18, 21, 22, 23, 24, 27, 30, 32, 65, 67, 69, 80, 85, 91, 94, 99, 104, 117, 129, 130, 135, 138, 139, 148, 155, 158, 169, 170, 173, 177, 179, 180, 182, 190, 201, 204, 209, 217, 221, 230, 236, 239, 241, 248, 250, 251, 253, 261, 264, 270, 285, 301, 303, 305], "remove_compon": [115, 117], "remove_edg": [178, 179, 180], "remove_entri": [115, 117], "remove_graph": [115, 117], "remove_loci_by_nam": [201, 204], "remove_loci_by_posit": [201, 204], "remove_locus_by_nam": [18, 200, 201, 204], "remove_locus_by_posit": [18, 200, 201, 204], "remove_nod": [178, 179, 180], "remove_popul": [18, 200, 201, 204], "remove_react": [27, 115, 117, 177], "remove_rel": [115, 117], "remove_succ": [128, 130], "removeprefix": [27, 236], "removesuffix": [27, 236], "renam": [3, 15, 20, 137], "render": [8, 15, 158, 183], "renderpm": [99, 104], "renumb": 104, "renumber_track": [98, 104], "reorder": [4, 13, 30, 32], "rep": [0, 27, 32, 79, 80, 177, 221, 229], "rep_record": 31, "repair": 10, "repair_gen": 10, "repair_pathwai": 10, "repeat": [0, 3, 4, 7, 8, 12, 20, 23, 24, 30, 38, 51, 53, 56, 68, 69, 80, 84, 152, 209, 221, 237, 246, 251, 268, 270, 272], "repeat_9606": 68, "repeat_unit": 53, "repeated_tag": 84, "repeatedli": [7, 11, 209], "repetit": [9, 19, 53, 73, 88, 203, 251, 272], "replac": [0, 3, 4, 5, 7, 10, 11, 13, 15, 22, 23, 27, 30, 31, 32, 60, 63, 65, 69, 80, 83, 93, 126, 129, 135, 157, 218, 236, 238, 251, 258, 260, 264, 270, 278, 304], "replace_entri": [27, 124, 126], "replacement_dictionari": [30, 31], "repli": 7, "replic": [80, 182, 186], "repmatch": [0, 30, 38, 51, 221], "report": [0, 3, 11, 12, 14, 22, 30, 32, 38, 42, 51, 71, 80, 123, 126, 130, 168, 169, 182, 218, 222, 226, 264, 268, 270, 272, 297], "report_": [27, 133, 168], "report_fil": 0, "reportdict": 168, "reportlab": [8, 24, 98, 99, 100, 102, 103, 104, 105], "repositori": [7, 24, 25, 27, 227], "repr": [0, 19, 23, 54, 68, 169, 183, 260], "repres": [0, 3, 6, 7, 8, 11, 12, 13, 15, 17, 19, 20, 21, 22, 25, 30, 31, 33, 43, 45, 61, 67, 68, 73, 76, 81, 82, 83, 84, 89, 99, 100, 102, 104, 108, 117, 122, 127, 129, 130, 131, 132, 135, 139, 140, 144, 148, 155, 156, 158, 160, 169, 176, 177, 183, 197, 199, 209, 210, 211, 212, 213, 214, 215, 217, 222, 236, 237, 238, 240, 247, 253, 256, 260, 264, 272, 275, 278, 283, 287, 288, 294, 299, 303], "represent": [0, 17, 20, 21, 30, 36, 54, 61, 67, 68, 76, 84, 86, 90, 92, 93, 95, 99, 102, 104, 105, 108, 112, 113, 114, 117, 121, 150, 154, 177, 179, 180, 183, 197, 201, 204, 207, 209, 222, 237, 247, 260, 283, 286, 287, 288, 293, 295, 296, 297, 299], "reproduc": [23, 169, 182], "republish": 123, "reqflag": 270, "request": [0, 3, 4, 6, 7, 8, 10, 11, 15, 25, 32, 68, 69, 83, 90, 104, 149, 177, 217, 236, 257, 260, 274, 278], "requir": [0, 3, 4, 6, 7, 8, 11, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 31, 32, 36, 56, 65, 67, 69, 72, 80, 83, 99, 104, 109, 119, 122, 158, 167, 169, 177, 182, 183, 185, 193, 195, 197, 217, 236, 237, 238, 241, 246, 252, 253, 260, 261, 270, 274, 278, 280, 283, 288, 290, 297], "require_multipl": 31, "reroot": [17, 183, 197], "rerun": 23, "res10": 15, "res152": [140, 156], "res157": 140, "res_": 168, "res_id": [134, 137], "res_list": 15, "resampl": [12, 80, 182], "resav": 4, "rescal": [107, 182], "rescu": [3, 20, 270], "resdict": 126, "research": [2, 7, 9, 15, 19, 32, 238, 250, 251, 253, 261, 283], "resembl": [11, 16], "reserv": [0, 7, 36, 207], "reset": [0, 3, 11, 13, 68, 71, 108, 197], "resetatom": 169, "resetloc": 169, "reshap": [13, 169], "resid": [137, 214], "residu": [12, 13, 14, 20, 21, 27, 31, 32, 68, 70, 71, 80, 93, 108, 125, 126, 133, 134, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 146, 148, 151, 152, 153, 154, 156, 157, 158, 159, 160, 161, 162, 167, 168, 169, 170, 172, 173, 209, 210, 212, 214, 221, 229, 248, 265, 272, 297], "residue1": 15, "residue2": 15, "residue_count_nam": [12, 31], "residue_d": 126, "residue_depth": [15, 27, 133, 156], "residue_dict": [124, 126], "residue_frequ": [12, 13], "residue_id": [15, 134], "residue_list": 15, "residue_typ": 93, "residuedepth": [15, 27, 133], "residuenumb": [30, 32], "resiz": 32, "resnam": [15, 140, 155, 162, 169], "resnamendx": [15, 169], "resolut": [15, 104, 157, 172, 174], "resolv": [25, 129, 185], "reson": 158, "resort": 3, "resourc": [3, 7, 9, 10, 85, 170, 197, 198, 238, 250], "respect": [0, 4, 11, 12, 13, 15, 17, 20, 21, 22, 30, 32, 45, 68, 83, 92, 122, 166, 182, 183, 209, 217, 238, 264, 265, 270, 290], "respiratori": 272, "respo": 169, "respons": [7, 104, 280, 303], "resseq": 162, "rest": [8, 10, 17, 20, 23, 27, 63, 94, 111, 128, 129, 274, 278], "restart": [69, 182], "restor": [15, 169, 217, 297], "restr_expr": [7, 275], "restrict": [6, 7, 8, 11, 15, 21, 27, 30, 65, 69, 108, 117, 119, 132, 169, 197, 217, 251, 260, 278], "restriction_batch": 207, "restriction_dictionari": [27, 206], "restrictionbatch": 207, "restructur": 21, "result": [0, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 34, 51, 59, 61, 68, 69, 71, 73, 80, 83, 84, 88, 89, 108, 119, 122, 127, 132, 157, 168, 169, 177, 182, 183, 186, 193, 195, 196, 202, 206, 207, 209, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 230, 232, 233, 238, 239, 247, 253, 267, 270, 274, 276, 277, 280, 289, 290, 291, 292, 297], "result_handl": 3, "result_iter": 25, "result_stream": 3, "resultdict": [15, 169], "results2": 7, "results_fil": [68, 70, 193, 195, 196], "retain": [3, 4, 6, 83, 169, 183, 270], "retmax": [7, 83], "retmod": [7, 9, 23, 83], "retrac": 4, "retract": 123, "retre": [30, 32], "retri": 83, "retriev": [3, 6, 11, 16, 20, 23, 45, 71, 83, 102, 104, 119, 149, 217, 270, 276, 288, 292, 301, 302, 303, 305], "retrieve_assembly_fil": [133, 149], "retrieve_pdb_fil": [15, 133, 149], "retstart": 7, "retsult": 81, "rettyp": [7, 23, 83], "return": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 59, 60, 61, 64, 65, 66, 67, 68, 70, 71, 73, 74, 76, 80, 83, 84, 85, 86, 89, 90, 91, 92, 93, 94, 95, 96, 97, 99, 100, 102, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 119, 120, 121, 122, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 137, 139, 140, 141, 142, 143, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 159, 160, 161, 162, 164, 165, 166, 168, 169, 170, 171, 173, 174, 175, 176, 177, 179, 180, 182, 183, 185, 188, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 207, 209, 210, 214, 217, 219, 220, 221, 223, 224, 225, 226, 230, 231, 232, 236, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 269, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 286, 287, 288, 289, 290, 291, 292, 293, 295, 296, 297, 298, 299, 300, 303, 304], "return_r": 294, "return_raw_com": 258, "returncod": [12, 67], "returnlin": 125, "reus": [3, 6, 23, 71, 253], "reusabl": 19, "reused_seq": 71, "reuter": 2, "rev": [176, 264], "rev_align": 30, "rev_comp": 23, "revcomp": 11, "reveal": [2, 11, 12, 13], "revers": [3, 6, 8, 15, 17, 20, 27, 30, 68, 69, 79, 80, 104, 117, 169, 176, 177, 182, 183, 217, 236, 237, 253, 260, 270, 283, 290], "reverse_compl": [0, 6, 8, 11, 13, 19, 21, 22, 23, 27, 30, 236, 260, 283, 290], "reverse_complement_rna": [27, 236], "reverse_gc": 81, "reverse_length": 81, "reverse_seq": 81, "reverse_start": 81, "reverse_tm": 81, "reverseinput": [79, 80], "review": [2, 7, 24, 25, 276], "revis": [6, 123], "revolut": 100, "revolv": 100, "reward": [68, 69], "rewind": [27, 30, 45], "rewound": [36, 44, 45], "rewrit": 218, "rewriteformat": [79, 80], "rewritten": [4, 69, 73], "rf": [53, 66, 123], "rf_tabl": 281, "rfc": 7, "rfeifksnlg": 0, "rfind": [22, 27, 236], "rformat": [79, 80], "rfrifsesl": 0, "rg": [0, 270], "rgb": [0, 17, 100, 104, 105, 117, 183], "rgb2003": 124, "rgfile": 270, "rgifmsdtmvvngsggvpaflfsgstlssi": 6, "rgipp": 56, "rgippeeq": 0, "rh": [202, 203], "rhemac10": 0, "rhemac3": 22, "rhemac8": 0, "rhemac8torhemac10": 0, "rho": [30, 32], "rhodopsin": 250, "rhpanel": 275, "ribbon": 158, "ribosom": [13, 15, 23, 272], "ric": [15, 169], "ric0": 169, "rice": [2, 251], "rice2000": [0, 2], "rich": [12, 169, 260], "richard": [2, 16, 27, 52, 298, 299, 300], "richardson1981": 169, "richli": [21, 56], "rid": [3, 12, 68, 69, 218], "ride": [104, 207], "ridicul": 7, "right": [0, 3, 4, 5, 6, 8, 11, 12, 13, 15, 19, 21, 22, 30, 68, 71, 73, 99, 104, 135, 138, 139, 175, 216, 237, 238, 260, 269], "right_extend_gap_scor": 13, "right_gap_scor": 13, "right_multipli": [133, 176], "right_open_gap_scor": 13, "rightarrow": 22, "rightcount": 0, "rightstatu": 0, "rikyilrlscartlarkhkstvrtfmrrlgsglleeffmee": 7, "rin": 123, "rindex": [22, 27, 236], "ring": 158, "rise": 11, "risk": [3, 15, 119, 169, 274], "risler": 199, "rkglpyrlgi": 0, "rkglpyrlginrfsdmswe": 0, "rkglpyrlginrfsdmsweefqatrl": 0, "rl": [0, 11, 53, 250, 295], "rl1_ecoli": 272, "rll": 13, "rlqtfasnwr": 0, "rlt": 0, "rm": [0, 15, 53, 216], "rmdup": 270, "rmdup_cmd": 270, "rmflsf": [13, 14], "rmsd": [15, 140, 163, 166, 175, 216], "rn": [0, 11, 53, 123, 238, 278, 295], "rn3": 0, "rn5": 22, "rn6": 0, "rn6torn7": 0, "rn7": 0, "rna": [0, 13, 22, 23, 30, 32, 53, 56, 76, 93, 104, 154, 197, 236, 237, 238, 250, 252, 260, 261, 264], "rna1": [13, 260], "rna2": [13, 260], "rna3": 13, "rna_de1": 264, "rna_el": 53, "rna_ligand_adocbl": 53, "rna_ligand_aqcbl": 53, "rna_ligand_fmn": 53, "rna_ligand_guanidinium": 53, "rna_ligand_preq1": 53, "rna_ligand_sam": 53, "rna_ligand_thf_1": 53, "rna_ligand_thf_2": 53, "rna_ligand_tpp": 53, "rna_motif_k_turn": 53, "rna_nn1": 264, "rna_nn2": 264, "rna_nn3": 264, "rna_structural_el": 53, "rnaseq": 0, "rnext": [52, 169], "roa1_human": 303, "rob": [2, 133], "robert": 32, "robertson": [202, 203], "robin": 2, "robust": 4, "roch": [6, 21, 238, 251, 253], "rodger": 149, "rodrigu": [133, 166], "rof": 123, "role": 114, "roll": [157, 303], "rollback": [301, 303], "room": 99, "root": [13, 17, 32, 79, 80, 84, 132, 175, 180, 181, 183, 184, 185, 187, 188, 189, 190, 197, 198, 199, 209, 216, 252, 287, 303], "root1": [30, 32], "root2": [30, 32], "root_at_midpoint": [17, 181, 183], "root_with_outgroup": [17, 128, 132, 181, 183], "rooted": 17, "rose": 265, "roseman": 265, "rosemari": 69, "rosetta": 105, "rost": 137, "rot": [15, 135, 139, 216], "rotat": [8, 15, 104, 135, 139, 152, 158, 163, 166, 169, 175, 176, 216], "rotaxi": [15, 27, 133, 176], "rotaxis2m": [27, 133, 176], "rotein": 80, "rotert": 2, "rother": [15, 133, 174], "rotmat": [15, 27, 133, 135, 139, 176], "rotran": 15, "rough": 264, "roughli": [11, 15, 16, 157], "round": [3, 7, 15, 27, 32, 68, 71, 119, 157, 168, 182, 251, 253, 260], "roundoff": 24, "roundrectangl": 117, "rout": 117, "routin": [4, 15, 73, 158, 169, 287, 293], "row": [0, 3, 4, 7, 12, 13, 16, 20, 22, 30, 56, 62, 66, 68, 73, 83, 126, 176, 199, 221, 229, 238, 277, 279, 280, 283, 299, 303], "rpf": 123, "rpi": 123, "rpl16": [7, 23], "rpm": 5, "rprev": 169, "rpsblast": [3, 68, 69, 70], "rpsblastcommandlin": 69, "rpsdb": [68, 69], "rpsppg": 0, "rpsppgprrptgrpccsaaprrpqat": 0, "rpsppgprrptgrpccsaaprrpqatggwktcsgtc": 0, "rpsppgprrptgrpccsaaprrpqatggwktcsgtcttststrhrgrsgw": 0, "rpssm": 11, "rpstblastn": 69, "rpvsvafqvi": 0, "rpwm": 11, "rrgcsaqnpk": 0, "rrkehvskkrrpqkrprrrrffhrlrppd": 6, "rrna": [2, 19, 23], "rrpffpfhsp": 250, "rrplfswlap": 250, "rrrctaqnpk": 0, "rsa": 145, "rsa_data": 145, "rslt": 169, "rspfdypqyi": 250, "rsplit": [27, 236], "rspyeypqyi": 250, "rst": 9, "rst301": 11, "rstrip": [6, 10, 27, 230, 236, 278], "rsync": 23, "rt": [0, 1, 4, 11, 23, 25, 27, 53, 240, 268, 269, 278, 295], "rtllmagvshdlrtpltrirlatemmseqd": 260, "rtoe": 68, "rtol": 168, "rtrev": 182, "rtype": 149, "ru": 88, "ruan": 2, "rule": [0, 4, 7, 10, 11, 88, 122, 127, 132, 186, 251, 264, 280, 283], "run": [0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 23, 25, 27, 32, 55, 67, 68, 69, 73, 80, 81, 83, 133, 137, 145, 153, 169, 175, 182, 192, 193, 195, 196, 216, 217, 218, 237, 238, 247, 251, 270, 274, 289, 291, 292], "run_id": [181, 182], "run_naccess": [27, 133, 145], "run_psea": [27, 133, 153], "run_test": 24, "rundat": 0, "runner": 24, "runtim": [17, 136, 144, 160, 169], "runtimeerror": [7, 83], "runx1": 11, "ruplei": 157, "rusa": 8, "ruzzo": [2, 4], "rw": 149, "rx": [11, 90, 295], "rxpected_frequ": 13, "rxxxxx": 118, "s0022": 2, "s0108767305015266": 175, "s0168": 2, "s0q9zdocveec": 23, "s1": [0, 13, 177, 207], "s10482": 2, "s12859": 2, "s1jjn5": 238, "s2": [13, 25, 177], "s27231": 250, "sa": [53, 66, 270], "sa_con": 53, "saaqtllpdsegaidghlrevgltfhllkdvpgliskniekslveafqplgisdwnslfw": 23, "sab_sab1c": 244, "sabzaa4v2ele9": 238, "sacc": 218, "sacc_ver": 218, "sadreyev": 74, "safe": [3, 15, 17, 169, 183, 238, 278], "safenam": [27, 128, 129], "safer": [7, 83], "sai": [6, 8, 12, 15, 21, 22, 24, 25, 31, 65, 217, 251, 270], "sai_fil": [268, 270], "sai_file1": [268, 270], "sai_file2": [268, 270], "saira": 2, "sakai": 25, "sake": [6, 11], "salc": 264, "saldanha": [2, 4], "saldanha2004": [2, 4], "sallgi": 218, "sallseqid": 218, "salmon": [17, 183], "salt": [80, 264], "salt_correct": [27, 261, 264], "saltconc": [79, 80], "saltcorr": 264, "sam": [27, 30, 33, 53, 55, 270, 278], "sam1": [0, 278], "sam_fil": [268, 270], "sam_or_bam_fil": 270, "sambam": 278, "same": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 30, 31, 32, 43, 45, 54, 56, 65, 66, 68, 69, 71, 73, 84, 90, 94, 99, 102, 104, 119, 120, 126, 127, 129, 132, 135, 155, 169, 182, 183, 197, 199, 202, 209, 214, 216, 217, 221, 222, 226, 234, 237, 238, 241, 244, 248, 251, 260, 261, 264, 265, 267, 270, 277, 278, 280, 282, 283, 287, 288, 290, 297, 299], "samipf": [241, 260], "samp": 270, "sampe_cmd": 270, "sampl": [0, 4, 13, 73, 80, 90, 100, 104, 112, 113, 114, 169, 202, 251, 270, 280, 299], "sams": 270, "samse_cmd": 270, "samtool": [2, 23, 270, 278], "samtools_cat_cmd": 270, "samtools_faidx_cmd": 270, "samtools_idxstats_cmd": 270, "samtools_index_cmd": 270, "samtools_mpileup_cmd": 270, "samtools_phase_cmd": 270, "samtools_sort_cmd": 270, "samtools_targetcut_cmd": 270, "samtools_view_cmd": 270, "samtoolscalmdcommandlin": [268, 270], "samtoolscatcommandlin": [268, 270], "samtoolsfaidxcommandlin": [268, 270], "samtoolsfixmatecommandlin": [268, 270], "samtoolsidxstatscommandlin": [268, 270], "samtoolsindexcommandlin": [268, 270], "samtoolsmergecommandlin": [268, 270], "samtoolsmpileupcommandlin": [268, 270], "samtoolsphasecommandlin": [268, 270], "samtoolsreheadercommandlin": [268, 270], "samtoolsrmdupcommandlin": [268, 270], "samtoolssortcommandlin": [268, 270], "samtoolstargetcutcommandlin": [268, 270], "samtoolsversion0xsortcommandlin": [268, 270], "samtoolsversion1xsortcommandlin": [268, 270], "samtoolsviewcommandlin": [268, 270], "san": 83, "sanchez": 263, "sander": 137, "sanger": [2, 6, 7, 8, 12, 52, 104, 238, 251, 253], "sanger_fak": 251, "saniti": 15, "sanitis": 65, "sanitize_nam": [27, 56, 65], "sanjeev": 2, "sankoff": 199, "sanner": [15, 156], "santalucia": 264, "sapien": [3, 20, 68, 90, 93], "saqai": 206, "saqi": 7, "sas_con": 53, "sasa": [27, 133, 145], "sasano": 25, "satisfi": [4, 11, 169, 237], "sativu": [21, 23], "sato": 25, "satoru": 2, "sav": 13, "save": [6, 7, 10, 11, 12, 13, 15, 17, 19, 20, 23, 25, 27, 32, 69, 71, 73, 80, 84, 99, 121, 133, 148, 149, 169, 170, 171, 173, 182, 183, 222, 238, 249, 251, 260, 270, 283, 298], "save_ascii_pssm": 69, "save_dtd_fil": [83, 84], "save_each_pssm": [68, 69], "save_pssm": 69, "save_pssm_after_last_round": [68, 69], "save_xsd_fil": [83, 84], "savefig": 6, "savefil": 149, "saw": [6, 17, 20], "saxel": 2, "sb": 123, "sbc": [53, 66], "sbjct": [3, 71], "sbjct_end": 71, "sbjct_start": 71, "sc": [3, 15, 68, 169], "sc_match": [3, 71], "sc_mismatch": [3, 71], "sca": 169, "scad": [15, 169], "scadio": [15, 27, 133, 169], "scaffold": [0, 36], "scaffold_114895": 0, "scaffold_288249": 0, "scaffold_334": 0, "scaffold_75566": 0, "scalabl": 32, "scalar": 176, "scale": [2, 4, 7, 8, 10, 15, 32, 99, 102, 104, 107, 109, 122, 127, 158, 169, 176, 182, 202, 203, 222, 251, 263, 265, 270], "scale_color": 104, "scale_colour": 104, "scale_font": 104, "scale_fontangl": 104, "scale_fonts": 104, "scale_format": 104, "scale_largetick": 104, "scale_largetick_interv": 104, "scale_largetick_label": 104, "scale_num": [8, 99], "scale_segment_valu": [98, 102], "scale_smalltick": 104, "scale_smalltick_interv": 104, "scale_smalltick_label": 104, "scale_tick": 104, "scale_valu": 102, "scale_width": 283, "scalebranch": [30, 32], "scaleddpalgorithm": [27, 106, 107, 109], "scan": [6, 11, 23, 27, 85, 89, 214, 238, 253, 270, 296], "scanner": [27, 92], "scanprosit": [25, 27, 85], "scanprosite_doc": 89, "scatter": [4, 6, 101], "scatterplot": 4, "scc": [209, 210, 211], "sccs1": 209, "sccs2": 209, "scer_cad1": 0, "scer_s288c": 0, "scertf": [11, 283], "sch": 3, "scheer": 2, "schema": [3, 6, 9, 11, 84, 185, 303], "schemahandl": [83, 84], "scheme": [0, 6, 8, 13, 15, 30, 32, 102, 104, 137, 229, 237, 251, 278], "scheme_color": [98, 104], "schi": 206, "schiestl": 7, "schildkraut": 264, "schmeiser": [2, 4], "schmidt": [32, 65], "schmitt": [238, 252], "schneider": [2, 13, 199], "schneider1986": [2, 11], "schneider2005": [2, 13], "schutz": 121, "schwartz": 2, "sch\u00e4ffer": [3, 68], "sci": [53, 83, 264], "scienc": [2, 32, 253], "scientif": [9, 23, 197, 252], "scientific_nam": [181, 183, 197, 198], "scientificnam": 7, "scikit": [120, 282], "scinam": 3, "scipi": [16, 299, 300], "sco": [17, 182], "scop": [0, 7, 9, 15, 19, 27, 123], "scope": [11, 16, 217], "scopseq": 209, "score": [0, 2, 3, 8, 14, 20, 21, 23, 25, 27, 30, 31, 32, 35, 36, 37, 39, 42, 46, 51, 53, 68, 69, 71, 80, 83, 121, 182, 199, 217, 218, 221, 222, 226, 229, 234, 238, 240, 249, 251, 253, 260, 265, 270, 275, 283, 290, 294, 297, 302], "score_dict": 297, "score_onli": [14, 297], "scorecon": 53, "scorecons_70": 53, "scorecons_80": 53, "scorecons_90": 53, "scoredistribut": [27, 283, 294], "scorefil": [30, 32], "scorer": [27, 181, 199], "scoreread1": 270, "scoreread2": 270, "scoring_matrix": 13, "scount": [7, 275], "scratch": [0, 12, 17, 20], "screen": [12, 19, 30, 280], "scripp": [15, 156, 263], "script": [0, 3, 5, 6, 7, 8, 9, 17, 19, 23, 24, 25, 68, 76, 85, 141, 158, 209, 253], "scriptcentr": 5, "scrub": 303, "sd": 169, "sd_rslt": 169, "sdfgatfmtl": 250, "sdvpersipi": 250, "se": [0, 53, 66, 202], "sea": [6, 30, 153, 197], "seamless": 217, "sean": 2, "search": [0, 2, 3, 6, 8, 9, 12, 15, 19, 22, 26, 27, 30, 36, 37, 53, 56, 61, 68, 69, 70, 71, 80, 83, 89, 119, 133, 146, 180, 181, 182, 183, 186, 199, 207, 209, 217, 218, 221, 226, 229, 234, 260, 261, 270, 274, 276, 283, 289, 290, 307], "search_al": [133, 146], "search_author": 7, "search_count": [27, 274], "search_dict": 217, "search_idx": 217, "search_it": [27, 274], "search_result": 7, "search_target": 3, "search_taxon": [128, 132], "searchabl": 7, "searched_hmm": 0, "searcher": 199, "searchindex": [219, 220, 221, 226, 232], "searchio": [3, 27, 91], "searchsp": [68, 69], "searchsp_eff": [68, 70], "sebastian": 262, "sec_struc": 265, "second": [0, 2, 3, 4, 6, 7, 9, 11, 12, 13, 14, 15, 17, 18, 20, 22, 23, 24, 25, 30, 31, 32, 73, 80, 83, 117, 119, 169, 172, 181, 182, 197, 205, 207, 222, 241, 250, 251, 256, 260, 261, 265, 269, 270, 274, 278, 297, 299], "second_lin": 1, "second_primer_seq": 82, "second_record": 23, "second_seq": 12, "secondari": [0, 2, 11, 12, 21, 30, 32, 53, 66, 90, 104, 123, 137, 140, 152, 153, 169, 172, 260, 265, 270, 272, 295], "secondary_structur": [66, 260], "secondary_structure_fract": [261, 265], "secondary_structure_typ": 172, "secondli": [3, 6, 8, 10, 12, 21, 251], "secstrout": [30, 32], "sect3": 248, "section": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 30, 62, 71, 94, 109, 158, 169, 236, 237, 238, 245, 255], "section_dict": 6, "secundu": 56, "see": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 35, 36, 37, 38, 39, 46, 49, 50, 51, 52, 53, 56, 59, 61, 64, 65, 66, 67, 68, 69, 73, 83, 84, 85, 86, 87, 88, 89, 90, 92, 94, 97, 99, 104, 108, 109, 119, 129, 135, 137, 145, 150, 152, 153, 156, 158, 164, 165, 168, 169, 170, 181, 182, 184, 185, 187, 188, 189, 190, 199, 201, 202, 204, 209, 210, 212, 214, 217, 221, 222, 226, 229, 236, 237, 238, 240, 245, 247, 248, 249, 251, 252, 253, 255, 258, 260, 261, 262, 264, 265, 269, 270, 272, 273, 274, 275, 276, 278, 283, 295, 297, 301], "seed": [0, 4, 12, 30, 32, 53, 79, 80, 181, 182, 270], "seek": [0, 27, 204, 253, 278], "seek_posit": [201, 204], "seekabl": [27, 278], "seem": [3, 5, 7, 15, 20, 22, 30, 83, 299], "seen": [20, 21, 22, 23, 56, 71], "sefgpifmtv": 250, "seg": [68, 69], "segid": [15, 155, 162], "segmask": 69, "segment": [0, 3, 13, 15, 22, 30, 32, 39, 61, 68, 93, 99, 102, 103, 155, 158, 169, 236, 238, 243, 269], "segment_nam": 102, "seguid": [27, 238, 261, 262], "seguid_dict": [23, 238], "seiya": 2, "sel": 261, "select": [0, 8, 12, 13, 17, 23, 27, 30, 31, 32, 54, 59, 100, 106, 133, 135, 138, 139, 148, 149, 158, 169, 170, 173, 182, 183, 253, 288, 294, 299, 303], "selected_align": 0, "selector": [15, 169], "selenipedium": [7, 19], "selenomethionin": [15, 154], "selex": [11, 32, 288], "self": [0, 2, 8, 11, 15, 17, 23, 24, 30, 31, 36, 45, 54, 67, 68, 73, 80, 104, 125, 126, 132, 169, 176, 177, 183, 185, 197, 214, 236, 260, 261, 264, 265, 275, 283, 288, 290, 297, 299], "selfcomp": 264, "semant": [15, 137], "semi": [4, 104, 129, 244, 250], "send": [67, 83, 218], "sens": [3, 8, 12, 13, 15, 21, 32, 65, 99, 150, 169, 260, 278], "sensibl": [6, 7, 8, 21], "sensibli": [104, 251], "sensit": [32, 270], "sent": [7, 67], "sep": [7, 11, 15, 149, 152, 169, 236], "separ": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 20, 23, 32, 36, 65, 69, 80, 104, 108, 158, 169, 182, 183, 207, 210, 211, 212, 217, 218, 221, 226, 230, 237, 238, 250, 251, 256, 274, 297], "septemb": 7, "seq": [0, 3, 6, 7, 8, 9, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 27, 30, 31, 36, 37, 38, 53, 59, 60, 66, 68, 80, 88, 89, 91, 92, 94, 108, 109, 154, 169, 197, 206, 207, 209, 237, 238, 240, 241, 246, 247, 249, 251, 253, 256, 260, 261, 262, 263, 264, 265, 267, 279, 280, 281, 283, 288, 291, 297, 301, 302, 303, 304], "seq0": 12, "seq1": [0, 9, 12, 13, 14, 22, 27, 30, 261, 279], "seq11111": 23, "seq2": [0, 9, 12, 13, 14, 22, 30, 279], "seq222": 23, "seq3": [12, 27, 30, 261], "seq3333": 23, "seq4": [12, 23, 30], "seq5": 12, "seq555": 23, "seq6": [12, 23], "seq_con": [0, 12, 53], "seq_count": [12, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66], "seq_fil": 32, "seq_len": [6, 20, 218, 221, 226, 229], "seq_lett": 108, "seq_on": 6, "seq_rec": 303, "seq_record": [19, 23], "seq_stat": 108, "seq_two": 6, "seq_typ": [30, 32, 261], "seqa": [0, 14, 27, 30, 68, 297], "seqadv": 248, "seqal": [79, 80], "seqb": [0, 14, 27, 30, 68, 297], "seqboot": [12, 56, 80, 182], "seqc": [0, 30, 68], "seqfeatur": [3, 7, 27, 68, 92, 94, 99, 104, 197, 260, 272], "seqid": [3, 7, 68, 69, 303], "seqidlist": [68, 69], "seqinfo": [25, 272], "seqio": [0, 1, 3, 6, 7, 8, 9, 12, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 27, 40, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 80, 91, 92, 94, 217, 236, 237, 260, 271, 274, 276, 278, 279, 303], "seqmap": [27, 209, 214], "seqmapindex": [27, 209, 214], "seqmatchal": 80, "seqmatchallcommandlin": [27, 79, 80], "seqno": [30, 32], "seqno_rang": [30, 32], "seqnum": 214, "seqr": [214, 238, 248], "seqrec": 152, "seqrecord": [0, 3, 6, 7, 8, 9, 12, 13, 15, 19, 20, 22, 25, 27, 30, 36, 37, 38, 49, 61, 64, 66, 68, 92, 94, 152, 169, 197, 217, 222, 236, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 261, 271, 279, 280, 281, 302, 303, 305], "seqret": [80, 250], "seqretcommandlin": [27, 79, 80], "seqtyp": [0, 7, 17, 30, 32, 79, 80, 275], "sequenc": [1, 2, 3, 8, 9, 10, 14, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 76, 79, 80, 81, 83, 86, 89, 93, 94, 104, 107, 108, 109, 110, 121, 129, 136, 138, 139, 149, 152, 154, 161, 162, 169, 172, 181, 182, 186, 193, 196, 197, 198, 199, 206, 207, 209, 213, 214, 215, 218, 221, 222, 226, 229, 234, 236, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 259, 260, 261, 262, 263, 264, 265, 267, 272, 274, 275, 276, 278, 279, 280, 281, 283, 287, 289, 290, 291, 295, 297, 298, 301, 303, 307], "sequence1": 13, "sequence1entri": [0, 62], "sequence1fil": [0, 62], "sequence1format": [0, 62], "sequence2": 13, "sequence2entri": [0, 62], "sequence2fil": [0, 62], "sequence2format": [0, 62], "sequence3entri": [0, 62], "sequence3fil": [0, 62], "sequence3format": [0, 62], "sequence_0": [0, 11, 291], "sequence_1": [0, 11, 291], "sequence_15": 11, "sequence_2": [0, 11, 291], "sequence_3": [11, 291], "sequence_4": [11, 291], "sequence_5": [11, 291], "sequence_6": [11, 291], "sequence_ac": [25, 89], "sequence_db": 89, "sequence_format": [92, 93], "sequence_head": [92, 94], "sequence_id": [11, 89, 291], "sequence_ind": [238, 245], "sequence_index": 172, "sequence_length": [25, 272], "sequence_nam": [11, 291], "sequence_numb": [12, 31], "sequence_rel": [181, 197, 198], "sequence_upd": [25, 272], "sequence_vers": [21, 23], "sequencea": [14, 297], "sequenceb": [14, 297], "sequencedataabstractbaseclass": [27, 236], "sequencefilenam": 182, "sequenceid": 69, "sequenceiter": [27, 238, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259], "sequencelin": [27, 275], "sequencerel": [27, 181, 197], "sequences1": 0, "sequences2": 0, "sequencewrit": [27, 238, 241, 246, 247, 249, 250, 251, 252, 253, 256, 259], "sequenti": [0, 23, 32, 50, 56, 65, 169, 181, 182, 238, 241, 246, 250, 278], "sequentialalignmentwrit": [27, 56, 57, 60, 61, 62, 65, 66], "sequentialphylipiter": [27, 56, 65], "sequentialphylipwrit": [27, 56, 65], "sequtil": [0, 6, 8, 22, 23, 27, 30, 238], "seqxml": [238, 252], "seqxmlio": [27, 238], "seqxmliter": [27, 238, 252], "seqxmlwrit": [27, 238, 252], "ser": [13, 15, 155], "seri": [0, 7, 13, 16, 35, 36, 39, 46, 51, 52, 55, 61, 93, 186], "serial": [135, 136, 158, 169, 172, 183, 185, 191, 198, 259, 299], "serial_num": [144, 162], "serial_numb": [135, 152, 162, 172], "serialclon": 238, "serin": 14, "serpina3": 7, "serv": [214, 278], "server": [0, 3, 7, 15, 68, 70, 149, 152, 169, 283, 288, 303, 305], "servic": [3, 9, 18, 68, 70, 119, 221, 274, 283], "session": [7, 217, 306], "session_cooki": 7, "set": [0, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 23, 24, 25, 27, 29, 30, 31, 32, 54, 56, 67, 68, 69, 70, 71, 72, 73, 80, 81, 83, 84, 92, 94, 99, 101, 102, 103, 104, 107, 108, 117, 119, 120, 122, 127, 128, 129, 130, 132, 133, 135, 139, 145, 149, 151, 152, 153, 155, 158, 162, 163, 166, 168, 169, 170, 172, 175, 177, 179, 180, 182, 183, 186, 195, 197, 199, 204, 209, 216, 217, 218, 221, 222, 229, 236, 237, 238, 247, 252, 261, 264, 265, 270, 272, 274, 277, 281, 282, 286, 288, 297, 298, 303, 304], "set_accuracy_95": [27, 133, 169], "set_all_featur": [98, 104], "set_all_track": [98, 104], "set_altloc": [133, 135], "set_angl": [15, 133, 169], "set_anis": [133, 135, 162], "set_atom": [15, 133, 163, 175], "set_atom_info": [171, 172], "set_bfactor": [133, 135], "set_bio_assembly_tran": [171, 172], "set_chain_info": [171, 172], "set_charg": [133, 135], "set_color": [98, 104], "set_colour": [98, 104], "set_coord": [15, 133, 135], "set_data": [98, 104, 128, 130], "set_dict": [15, 133, 170], "set_emission_pseudocount": [106, 108], "set_emission_scor": [106, 108], "set_entity_info": [171, 172], "set_equal_prob": [106, 108], "set_featur": [98, 104], "set_flex": [133, 158, 169], "set_group_bond": [171, 172], "set_group_info": [171, 172], "set_handl": [92, 94], "set_hbond": [133, 158, 169], "set_head": [133, 162], "set_header_info": [171, 172], "set_hit_access": [68, 71], "set_hit_def": [68, 71], "set_hit_id": [68, 71], "set_hit_len": [68, 71], "set_homog_trans_mtx": [27, 133, 176], "set_id": [104, 128, 130], "set_initial_prob": [106, 108], "set_inter_group_bond": [171, 172], "set_length": [15, 133, 169], "set_line_count": [133, 162], "set_model_info": [171, 172], "set_occup": [133, 135], "set_opt": 17, "set_par": [133, 135, 139], "set_paramet": [27, 67], "set_prev": [128, 130], "set_printopt": [0, 30, 216], "set_radiu": [133, 135], "set_random_emission_prob": [106, 108], "set_random_initial_prob": [106, 108], "set_random_prob": [106, 108], "set_random_transition_prob": [106, 108], "set_refer": [133, 166], "set_scal": [98, 102], "set_serial_numb": [133, 135], "set_sigatm": [133, 135, 162], "set_siguij": [133, 135, 162], "set_structur": [15, 133, 148, 169, 170, 173], "set_subtre": [128, 132], "set_succ": [128, 130], "set_symmetri": [133, 162], "set_transition_pseudocount": [106, 108], "set_transition_scor": [106, 108], "set_x_homog_rot_mtx": [27, 133, 176], "set_xtal_info": [171, 172], "set_y_homog_rot_mtx": [27, 133, 176], "set_z_homog_rot_mtx": [27, 133, 176], "setattr": 30, "setcas": [11, 290], "setter": 169, "settl": 20, "setup": [3, 5, 24], "seven": [3, 6, 12], "seventh": [0, 154], "sever": [0, 3, 4, 6, 7, 8, 11, 12, 15, 16, 20, 21, 22, 23, 25, 42, 53, 76, 98, 136, 217, 222, 237, 238, 251, 264, 265, 274, 278, 287], "sex": [7, 90], "sexual": 7, "sf": [126, 209, 211], "sff": [238, 251, 253], "sff_extract": 253, "sffinfo": [6, 251], "sffio": [6, 27, 238], "sffiter": [27, 238, 253], "sffwriter": [27, 238, 253], "sfi21": 2, "sfm": 123, "sformat": [79, 80], "sframe": 218, "sg": 169, "sgastskt": 250, "sgc0": [22, 76], "sgc1": 22, "sgi": 218, "sgqdryttevvvnvggtmqmlggrqgggapaggnigggqpqggwgq": 260, "sgsakslrmg": 0, "sgtartklllllaalcaaggal": 13, "sgtsrtkrllllaalgaaggal": 13, "sh": 182, "shade": 8, "shaft": [8, 104], "shall": 182, "shallow": 3, "shallowest": [17, 183], "shape": [8, 12, 27, 29, 30, 53, 54, 68, 100, 117, 175, 182], "share": [0, 6, 7, 12, 15, 30, 32, 94, 132, 169, 221], "sharma": 2, "sharp": 261, "she": 0, "sheer": 6, "sheet": 265, "sheeyl": 0, "sheeylerfeifksnlgkieelnliainhkadtkfgvnkfadlssd": 0, "sheeylerfeifksnlgkieelnliainhkadtkfgvnkfadlssdefknyylnnkeaiftddlpvadylddefinsiptafdwrtrg": 0, "shell": [3, 12, 17], "shibasaka": 25, "shield": 274, "shift": [13, 21, 30, 69, 71, 222, 237, 260, 264], "shimanouchi": 149, "shimodaira": 182, "shindyalov": 166, "short": [0, 6, 8, 9, 11, 12, 14, 15, 20, 21, 22, 23, 30, 68, 69, 70, 83, 104, 132, 169, 197, 237, 249, 251, 256, 260, 265, 269, 270, 272, 295, 303], "short_list": 6, "short_queri": [68, 70], "shortcut": [15, 20, 21, 217, 237, 260], "shorten": [12, 17], "shorter": [6, 14, 17, 19, 21, 22, 23, 30, 32, 238, 270], "shortest": 4, "shorthand": [15, 21, 169, 237, 260], "shortnam": [30, 32], "should": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 36, 38, 42, 43, 45, 51, 56, 59, 60, 61, 64, 66, 67, 69, 71, 72, 73, 83, 84, 92, 94, 95, 99, 101, 102, 103, 104, 107, 108, 109, 116, 120, 121, 126, 127, 148, 162, 169, 170, 173, 177, 182, 183, 197, 199, 202, 203, 204, 207, 217, 218, 221, 222, 230, 236, 237, 238, 246, 247, 248, 251, 253, 256, 258, 259, 260, 261, 264, 270, 277, 278, 280, 281, 282, 297, 298, 299, 303], "shouldn": [3, 5, 12, 16, 24, 67, 198, 305], "show": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 67, 68, 69, 70, 72, 73, 80, 89, 99, 103, 104, 169, 182, 183, 197, 249, 251, 253, 260, 261, 278, 297], "show_compound": 105, "show_domain_hit": [68, 69], "show_end": 283, "show_errorbar": 283, "show_fineprint": 283, "show_gen": 105, "show_gi": [68, 69], "show_map": 105, "show_ortholog": 105, "show_overview": [68, 70], "show_reaction_entri": 105, "show_xaxi": 283, "show_yaxi": 283, "showalign": 0, "showalignemnt": 222, "showcigar": 0, "shown": [0, 3, 4, 6, 7, 8, 12, 13, 14, 15, 16, 17, 20, 22, 23, 24, 30, 33, 59, 66, 68, 71, 104, 143, 151, 154, 236, 237, 238, 250, 251, 253, 260, 280, 283, 297, 298, 299], "showtre": [30, 32], "showvulgar": 0, "showxml": [30, 32], "shrake": 157, "shrakeruplei": [27, 133, 157], "shtml": [226, 270], "shuffl": [4, 6, 73, 79, 80], "shuffled_rec": 6, "si": [104, 123, 161], "sibson": 2, "sibson1973": [2, 4], "sid": [209, 210, 211, 212], "side": [2, 6, 8, 12, 13, 15, 22, 23, 30, 84, 158, 183, 265], "sidechain": [15, 152, 167, 169], "siegffatlg": 250, "siever": 32, "sigatm": 15, "sigatm_arrai": [135, 162], "sigbio": 2, "sigil": 104, "sigma_i": 4, "sigma_x": 4, "sigmoid": [16, 299, 300], "sign": [5, 6, 7, 15, 52, 63, 83, 119, 169, 241, 251], "signal": [4, 16, 94, 272, 275, 299], "signatur": 234, "signature_ac": [25, 89], "signifi": 21, "signific": [7, 20, 74, 166], "significantli": [4, 14, 270], "siguij": 15, "siguij_arrai": [135, 162], "silenc": [17, 27], "silent": [18, 23, 24, 67, 152, 238, 298], "silico": 61, "silurian": 197, "silver": 183, "simeq": 11, "similar": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 19, 20, 21, 24, 32, 56, 67, 69, 71, 79, 80, 93, 97, 103, 119, 121, 158, 166, 182, 197, 209, 217, 221, 222, 226, 229, 260, 261, 265, 270, 274, 275, 290, 299], "similarli": [0, 3, 4, 7, 11, 12, 14, 15, 20, 21, 23, 25, 30, 67, 185, 217, 236, 237, 251, 256, 270], "simpl": [0, 2, 3, 4, 7, 9, 10, 11, 12, 13, 15, 17, 20, 21, 22, 23, 24, 30, 41, 51, 56, 58, 66, 67, 68, 76, 82, 104, 119, 136, 139, 154, 182, 191, 198, 203, 217, 222, 236, 237, 238, 251, 256, 260, 264, 265, 274, 278, 283, 299], "simple_chrom": 8, "simple_seq": 21, "simple_seq_r": 21, "simple_short": 62, "simplefastapars": [6, 23, 27, 238, 241], "simplefilt": 27, "simpleloc": [8, 27, 68, 237, 260, 272], "simpler": [66, 251, 274], "simplest": [11, 17], "simpli": [3, 7, 8, 11, 12, 13, 15, 17, 20, 21, 60, 68, 83, 149, 154, 183, 217, 238, 249, 260, 265, 290], "simplic": [6, 7, 15, 270], "simplifi": [11, 17, 45, 60, 69, 158, 246], "simplist": 6, "simul": [22, 182], "simulan": 13, "sinc": [1, 3, 5, 6, 7, 8, 9, 11, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 67, 84, 88, 95, 166, 182, 217, 221, 234, 236, 237, 238, 249, 251, 259, 260, 269, 270, 278, 297, 303, 305], "sincri": 153, "sinderen": 2, "singl": [0, 2, 3, 4, 6, 7, 8, 9, 11, 13, 15, 17, 18, 20, 21, 22, 23, 25, 27, 30, 31, 33, 35, 36, 39, 40, 44, 45, 46, 47, 49, 50, 51, 52, 53, 56, 57, 60, 61, 62, 65, 66, 68, 71, 73, 76, 80, 81, 82, 83, 92, 99, 102, 103, 104, 116, 119, 123, 126, 129, 130, 137, 144, 149, 158, 159, 169, 172, 176, 182, 183, 198, 201, 202, 209, 214, 215, 217, 221, 222, 226, 234, 236, 237, 240, 241, 242, 244, 245, 246, 247, 249, 250, 251, 253, 254, 255, 256, 259, 260, 261, 270, 271, 274, 275, 277, 278, 280, 283, 288, 290, 299, 303], "single_cov2": 0, "single_letter_cod": 172, "singleton": 270, "singular": [2, 3, 4, 15, 176, 216], "sink": [27, 177], "sink_interact": [27, 177], "sint": 104, "siphovirida": 2, "sister": [6, 21, 251], "site": [2, 3, 6, 7, 8, 9, 10, 14, 15, 19, 21, 23, 25, 34, 53, 68, 71, 80, 84, 88, 129, 182, 195, 206, 207, 221, 256, 260, 270, 272, 273, 274, 280, 283, 288, 295], "situ": 6, "situat": [3, 4, 5, 7, 12, 15, 23, 183], "six": [0, 3, 4, 6, 12, 15, 25, 169, 182, 261], "six_frame_transl": [27, 261], "sixmerpair": [30, 32], "sixth": [126, 154], "size": [0, 6, 7, 8, 13, 15, 22, 23, 25, 30, 32, 35, 36, 39, 46, 51, 61, 68, 69, 70, 71, 80, 81, 93, 99, 102, 104, 121, 135, 139, 146, 166, 169, 182, 198, 202, 203, 207, 221, 236, 248, 261, 265, 267, 270, 278], "sj": 161, "sj\u00f6lander": 2, "sk": 206, "ska": 12, "skew": 261, "skip": [0, 4, 7, 8, 13, 17, 21, 24, 27, 32, 83, 84, 94, 129, 143, 168, 204, 258, 270], "skip_char": 31, "skip_head": [201, 204], "skip_lett": 199, "skip_n": 129, "skip_parsing_error": 258, "skip_popul": [201, 204], "skip_whitespac": [128, 129], "skipcharacterdatahandl": [83, 84], "skipflag": 270, "skipin": [30, 32], "skiplist": 129, "skptcreggr": 0, "skptcreggrsgsakslrmgrrgcsaqnpkdshdppphl": 0, "skptcreggrsgsakslrmgrrgcsaqnpkrlt": 0, "skptcreggrsgsakslrmgrrrctaqnpkrlt": 0, "slash": [10, 260], "slater": 2, "slater2005": [0, 2], "sleep": 83, "sleep_between_tri": 83, "sleev": 23, "slen": 218, "slice": [3, 6, 8, 16, 20, 25, 30, 35, 45, 46, 51, 53, 61, 66, 104, 183, 197, 214, 217, 236, 251, 253, 260, 281, 299], "sliced_hit": 20, "slicer": 158, "slide": [6, 32, 267], "slightli": [0, 7, 11, 13, 20, 23, 32, 251], "slink": [2, 4], "slipper": [7, 19], "slonim": 2, "slope": [4, 16, 299], "slow": [3, 6, 12, 23, 30, 32, 157, 158, 181, 182, 278, 297], "slowdefault": 32, "slower": [6, 23, 32, 169, 182, 204, 253, 270], "slowest": [182, 270], "slownni": [181, 182], "slvmavvvndsdedgdsrdavlpqkkkrlwglvvchnttprfv": 260, "slxa": 251, "slxa_0001_1_0001_01": [251, 260], "slxa_0001_1_0001_01_rc": 260, "slxfq": 270, "sm": [0, 53, 270], "smai": 8, "small": [3, 4, 6, 7, 8, 12, 19, 23, 30, 104, 140, 158, 168, 169, 199, 238, 260, 278], "smaller": [4, 8, 13, 73, 99, 108, 217, 237, 270], "smallest": [4, 11, 73], "smart": 53, "smcra": [15, 143, 151], "smin": [30, 32], "smith": [0, 12, 13, 14, 30, 32, 69], "smooth": [17, 32], "smoother": 6, "smoothscoreceil": [30, 32], "smoothwindow": [30, 32], "smprint": [128, 129], "sn": [0, 169], "snake": 9, "snapgen": [238, 254], "snapgeneio": [27, 238], "snapgeneiter": [27, 238, 254], "snapshot": 9, "sndiyfnfqrfnetnlilqrdasvsssgqlrltnln": 15, "snedecor": [2, 4], "snedecor1989": [2, 4], "snfgpvfmtv": 250, "snippet": [8, 18, 19, 20, 22, 23, 24], "snoop": 19, "snp": [7, 21, 237, 260, 270, 274], "snucleotid": [79, 80], "so": [0, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 53, 54, 56, 62, 66, 68, 79, 80, 83, 84, 90, 93, 99, 101, 104, 107, 108, 109, 117, 123, 155, 158, 169, 182, 183, 197, 209, 217, 218, 229, 237, 238, 242, 251, 254, 260, 277, 278, 288, 289, 291, 294, 297], "soap": 274, "soapi": 274, "soappi": 274, "soc": 129, "social": 83, "sodium": 264, "soe": 221, "soedinglab": 227, "soft": [0, 7, 32, 69, 247], "soft_mask": [68, 69], "softwar": [0, 2, 7, 9, 11, 12, 15, 16, 17, 18, 32, 33, 69, 123, 129, 132, 153, 158, 169, 177, 182, 229, 238, 242, 251, 294], "software_commun": 239, "sole": [61, 177, 270], "solexa": [2, 6, 238, 251, 260], "solexa_exampl": 251, "solexa_fak": [251, 260], "solexa_qu": [251, 260], "solexa_quality_from_phr": [27, 238, 251], "solid": 15, "solut": [2, 6, 15, 21, 23, 73, 84], "solv": [6, 15], "solvent": [2, 15, 145, 156, 157], "som": [4, 73], "somclust": [4, 27, 73], "some": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 56, 66, 67, 68, 69, 70, 80, 84, 92, 99, 102, 103, 104, 107, 109, 110, 117, 121, 122, 127, 132, 134, 136, 144, 147, 149, 151, 152, 169, 177, 182, 186, 202, 207, 217, 218, 222, 226, 236, 237, 238, 251, 253, 260, 261, 278, 297, 299], "some_db": 270, "some_residu": 15, "some_seq": 270, "somehow": [12, 93], "someth": [3, 5, 6, 7, 8, 9, 11, 12, 15, 19, 20, 21, 22, 23, 24, 60, 93, 139, 149, 205, 269, 271, 288, 303], "sometim": [3, 6, 8, 15, 20, 21, 22, 23, 56, 65, 66, 182, 218, 226, 251, 264], "somewhat": [11, 119, 274], "somewher": [21, 237], "son": 130, "sonnhamm": [53, 66], "soon": [3, 15], "sorri": 19, "sort": [4, 12, 15, 17, 20, 23, 27, 30, 66, 73, 76, 104, 126, 133, 135, 155, 169, 183, 217, 237, 238, 268, 269, 270], "sort_kei": [3, 20], "sorted_orchid": 6, "sorted_qresult": 20, "sound": 20, "sourc": [0, 1, 2, 3, 4, 5, 7, 8, 9, 12, 16, 17, 19, 20, 21, 23, 24, 27, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 61, 68, 83, 84, 93, 101, 108, 119, 123, 150, 165, 166, 177, 179, 180, 183, 197, 217, 221, 229, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 269, 271, 272, 277, 287, 306], "source_db": 119, "source_db_or_dbentri": 119, "source_interact": [27, 177], "source_vers": 252, "sourceforg": [4, 15, 32, 270, 274, 278], "sp": [30, 32, 68, 209, 211], "spa": 250, "space": [3, 4, 8, 11, 15, 23, 25, 32, 51, 65, 67, 68, 69, 71, 79, 80, 94, 95, 99, 100, 104, 123, 126, 129, 135, 158, 162, 169, 172, 176, 182, 207, 218, 236, 250, 251, 256, 270, 278, 282, 297], "space_equals_underscor": 132, "space_group": 172, "spacegroup": 162, "spacer": [22, 99], "spacerseg": [27, 98, 99], "span": [0, 3, 8, 20, 30, 158, 169, 237, 299], "spare": 25, "spatial": 202, "speak": [5, 11, 71], "spearman": 73, "spec": [170, 243, 270], "speci": [0, 7, 11, 13, 17, 23, 27, 34, 61, 90, 92, 93, 177, 183, 197, 209, 211, 252, 275, 280, 287, 288, 295], "special": [0, 4, 11, 13, 15, 17, 19, 23, 24, 30, 32, 38, 56, 65, 95, 99, 149, 177, 237, 241, 251, 260, 278], "specialis": [237, 278], "speciat": [17, 132, 181, 183, 197, 198], "speciation_or_dupl": 197, "speciesord": 0, "specif": [0, 3, 5, 7, 8, 9, 13, 17, 19, 20, 21, 23, 24, 25, 30, 31, 32, 37, 46, 53, 56, 66, 67, 68, 69, 76, 83, 92, 93, 99, 102, 105, 117, 139, 147, 152, 158, 165, 169, 172, 177, 182, 183, 197, 198, 217, 222, 229, 237, 238, 239, 248, 257, 260, 265, 270, 272, 274, 278, 283, 288, 290, 291, 298, 299], "specifi": [0, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 21, 22, 24, 27, 29, 30, 31, 32, 34, 36, 38, 51, 54, 56, 59, 65, 67, 68, 69, 70, 73, 80, 84, 92, 93, 95, 99, 102, 103, 104, 105, 108, 109, 117, 119, 127, 131, 135, 139, 149, 151, 158, 162, 164, 169, 176, 182, 183, 193, 195, 196, 197, 207, 212, 217, 218, 221, 229, 236, 238, 252, 259, 260, 261, 270, 274, 281, 282, 283, 288, 297, 298, 299, 303], "specificti": 288, "specimen_vouch": 7, "spectroscopi": 25, "speed": [6, 11, 14, 23, 32, 146, 182, 267, 270, 278], "spell": [8, 83, 104], "spellman": 2, "spent": [1, 270], "spermatophyta": [7, 25], "sphegod": 7, "sphere": [141, 157, 158, 169], "spheric": 176, "sphinx": 306, "spid": 0, "spider": 7, "spifrmpswl": 250, "spin": 123, "spiral": 100, "spit": 92, "spite": 0, "splice": [21, 22, 61, 79, 80, 237, 272], "spliceosom": 30, "splicepenalti": [79, 80], "split": [3, 6, 8, 9, 10, 15, 17, 18, 20, 23, 27, 65, 83, 128, 132, 181, 182, 183, 201, 217, 222, 236, 237, 238, 251, 260, 270, 278, 287], "split_akl": [133, 169], "split_in_loci": [18, 200, 201], "split_in_pop": [18, 200, 201], "split_jaspar_id": [283, 287], "split_virtual_offset": [27, 278], "spn": [30, 32], "sport": 122, "spot": [7, 278], "spr": [181, 182], "spread": 221, "springer": 2, "sprlength": [181, 182], "sprot": 85, "sprotein": [79, 80], "sprotxx": 272, "spscore": [30, 32], "spslspflmr": 250, "sq": [0, 53, 66, 94, 270], "sqflefqdkfnkki": 0, "sql": [11, 209, 303, 304], "sql_file": 303, "sqlite": [20, 217, 238, 304], "sqlite3": [6, 9, 23, 61, 304], "sqlite_dbutil": [301, 304], "sqlite_fil": 61, "sqrt": [4, 11, 182, 270], "squar": [2, 4, 13, 80, 175, 176, 194, 216, 287], "sr": 157, "sra": [6, 12], "sracaggtgkyg": 11, "srand": 4, "src": 221, "srebnik": 265, "srf": [11, 283], "sri": 2, "srifdqifg": 250, "srlfdqffge": 250, "srpnrfaptlmsscitsttgppawagdrsh": 0, "srr001": 6, "srr001666": 6, "srr001666_": 6, "srr001666_1": 6, "srr001666_2": 6, "srr014849": 6, "srr020": 6, "srr020192": 6, "srs004476": 6, "srspair": [0, 41], "srt": 270, "srv": 32, "ss": [0, 12, 53, 66, 93, 137, 270], "ss_con": [0, 12, 53, 66], "ss_dssp": 0, "ss_pred": 0, "ss_seq": 153, "ss_to_index": [27, 133, 137], "ssac": [21, 23], "sscssccbcbgggttbccgggceecttsbeebshhhhsttccbsscssccccbtttttbccsttceecttsceebshhhh": 0, "ssdna": 260, "ssearch": 226, "sseq": 218, "sseqid": [69, 218], "ssfinfo": 253, "sspd5i": 206, "sssseeeeeeettt": 0, "sssssshhhhhttthhhhhhhhhhhhhhhhhhhhhhthhhhhhhhhhhhhhhhhhhhhtt": 260, "sstart": 218, "st": [2, 7, 18, 32, 68, 90, 238, 275], "sta": 32, "stabil": [183, 265], "stabl": [3, 27, 30, 32, 104, 265, 272], "stack": [8, 104], "stack_width": 283, "stackexchang": [15, 169], "stackoverflow": 169, "stacks_per_lin": 283, "stage": [32, 69, 275], "stai": [3, 5, 7, 15, 17, 183], "stal": 32, "stamataki": 182, "stand": [4, 8, 11, 14, 99, 175, 216, 247, 278], "standad": 83, "standalon": [0, 5, 8, 9, 84, 221], "standard": [0, 1, 3, 4, 6, 7, 9, 11, 12, 13, 15, 17, 18, 22, 23, 24, 27, 30, 32, 65, 66, 67, 76, 80, 92, 104, 129, 131, 135, 143, 151, 152, 154, 162, 169, 182, 183, 197, 203, 204, 205, 214, 217, 222, 236, 237, 238, 251, 253, 260, 261, 264, 265, 270, 272, 278, 290, 300, 303], "standard_dna_t": [76, 261], "standard_t": 22, "standarddata": [27, 128], "standardis": 169, "stanford": [4, 32, 209, 214], "stannard": 300, "star": [30, 32], "start": [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 39, 43, 46, 51, 52, 53, 56, 61, 62, 65, 66, 69, 71, 72, 73, 80, 84, 89, 90, 93, 94, 99, 100, 104, 108, 129, 130, 136, 138, 139, 152, 154, 158, 169, 182, 183, 197, 199, 204, 215, 216, 217, 219, 221, 222, 226, 229, 232, 234, 236, 237, 238, 241, 242, 244, 245, 246, 247, 250, 251, 252, 253, 254, 256, 257, 259, 260, 270, 273, 274, 278, 279, 283, 295, 297, 299, 303, 307], "start1": 236, "start2": 236, "start_codon": [22, 75, 76], "start_i": 103, "start_offset": [220, 237], "start_po": 21, "start_read": [201, 204], "start_x": 103, "start_x_posit": 99, "start_y_posit": 99, "starta": [98, 104], "startb": [98, 104], "startdbrefel": [238, 252], "startdescriptionel": [238, 252], "startdocu": [238, 252], "startel": [85, 89], "startelementhandl": [83, 84], "startentryel": [238, 252], "startentryfieldel": [238, 252], "startentryfieldelementversion01": [238, 252], "starting_tre": [181, 182, 199], "startnamespacedeclhandl": [83, 84], "startpropertyel": [238, 252], "startrawelementhandl": [83, 84], "startresid": 215, "startsequenceel": [238, 252], "startseqxmlel": [238, 252], "startskipelementhandl": [83, 84], "startspeciesel": [238, 252], "startswith": [6, 27, 104, 236, 253], "stat": [0, 3, 7, 17, 20, 30, 32, 68, 123, 126, 194, 202, 203, 270], "stat_db_len": 218, "stat_db_num": 218, "stat_eff_spac": 218, "stat_entropi": 218, "stat_hsp_len": 218, "stat_kappa": 218, "stat_lambda": 218, "state": [0, 2, 3, 4, 11, 13, 15, 16, 20, 27, 30, 54, 55, 107, 108, 109, 110, 121, 122, 158, 176, 197, 218, 245, 251], "state_alphabet": 108, "state_lat": 108, "state_lett": 108, "state_path": 109, "statement": [6, 8, 23, 278, 303, 304], "static": [30, 36, 54, 84, 149, 169, 171, 197, 237, 297], "statist": [2, 3, 6, 11, 18, 20, 32, 68, 69, 74, 80, 119, 129, 166, 169, 182, 194, 202, 203, 217, 221, 251, 295], "statistics_db": 218, "statistics_eff": 218, "statistics_entropi": 218, "statistics_hsp": 218, "statistics_kappa": 218, "statistics_lambda": 218, "statu": [0, 7, 30, 32, 67, 123, 149, 168], "status_charact": [30, 46], "std": [11, 131, 152, 169, 218, 283, 290], "std_output": 67, "stddev": 169, "stderr": [12, 17, 32, 67, 182, 270], "stdev": [29, 98, 104], "stdfq": 270, "stdin": [0, 3, 4, 12, 67], "stdo": [30, 32], "stdout": [0, 12, 17, 24, 32, 67, 79, 80, 199, 217, 270], "steeyhh": 0, "steeyhhrlqtfasnwrkinahn": 0, "steinegg": 2, "steinegger2019": [0, 2], "step": [3, 4, 6, 7, 8, 10, 11, 12, 13, 15, 20, 21, 22, 23, 30, 32, 104, 107, 169, 177, 202, 299], "stephan": 2, "stephen": [2, 3, 68], "stepmatrix": [27, 128, 129], "stepwis": 182, "steve": 32, "steven": 2, "sth": [12, 53, 66], "stick": [22, 24, 237], "still": [1, 6, 7, 8, 9, 12, 17, 19, 20, 21, 23, 25, 68, 70, 107, 129, 166, 183, 218, 251, 276], "stl": [15, 158], "stm_stm": 244, "stmt": 185, "stoch": 177, "stochiometr": 177, "stochiometri": [27, 177], "stockholm": [12, 21, 27, 30, 56, 66, 238], "stockholm_format": [53, 66], "stockholm_multiple_alignment_format": 66, "stockholmio": [27, 56], "stockholmiter": [27, 56, 66], "stockholmwrit": [27, 56, 66], "stoichiometri": 177, "stone": 105, "stop": [0, 4, 6, 7, 9, 13, 22, 25, 36, 69, 76, 89, 109, 236, 270], "stop_codon": [22, 75, 76], "stop_symbol": [22, 236, 237, 260, 281], "stopiter": [0, 3, 23, 30, 68], "stopping_criteria": 109, "storag": [139, 185, 305], "store": [0, 1, 3, 4, 7, 12, 13, 14, 15, 20, 21, 23, 24, 25, 29, 30, 32, 35, 36, 37, 38, 39, 42, 45, 46, 51, 52, 53, 54, 56, 59, 61, 67, 68, 69, 71, 73, 76, 83, 84, 89, 93, 104, 123, 129, 130, 132, 135, 136, 149, 155, 164, 169, 171, 185, 197, 198, 217, 222, 234, 238, 239, 240, 247, 251, 257, 269, 272, 273, 275, 278, 280, 286, 287, 288, 293, 295, 296, 299, 301, 302, 305], "stormo": [2, 11, 294], "str": [0, 8, 9, 11, 12, 13, 21, 22, 31, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 62, 64, 67, 68, 71, 76, 84, 90, 91, 94, 125, 126, 131, 135, 139, 149, 150, 152, 158, 162, 164, 165, 168, 169, 176, 183, 185, 188, 190, 197, 199, 215, 236, 238, 241, 245, 246, 249, 251, 256, 260, 261, 262, 270, 276, 283, 299, 302], "straddl": 8, "strai": 17, "straight": [4, 6, 7, 12, 23, 31, 251], "straightforward": [3, 4, 7, 23, 93, 97, 107, 169, 183], "strain": 13, "strand": [0, 3, 6, 8, 11, 15, 20, 21, 22, 27, 30, 32, 36, 46, 61, 62, 68, 69, 71, 80, 99, 104, 137, 221, 222, 226, 229, 236, 237, 260, 261, 264, 269, 270, 272, 290, 291, 295], "strandendin": [30, 32], "strandendout": [30, 32], "strandgap": [30, 32], "strandless": 8, "strang": [17, 183, 278], "stranger": 12, "strategi": [6, 7, 32, 69, 83], "stream": [0, 3, 7, 27, 33, 35, 36, 37, 38, 40, 42, 45, 46, 47, 49, 51, 52, 68, 83, 90, 185, 188, 190, 198, 199, 220, 241, 246, 247, 248, 249, 251, 252, 253, 257, 259, 277], "stream_or_path": 252, "streammodeerror": 27, "strength": 182, "strenm": 45, "streptophyta": [7, 23, 25], "streptophytina": 7, "stretch": [22, 253], "stretcher": [41, 80], "stretchercommandlin": [27, 79, 80], "strict": [11, 12, 15, 132, 135, 139, 155, 186, 241, 261, 264, 283, 295], "strict_consensu": [27, 181, 186], "strict_pars": 15, "stricter": [9, 238], "strictli": [3, 11, 12, 17, 65, 71, 132, 135, 139, 143, 155, 183, 283], "strictly_equ": [133, 135, 139, 155], "stride": [22, 260], "strider": [238, 259, 261], "string": [0, 3, 4, 6, 7, 9, 11, 13, 15, 17, 19, 20, 21, 25, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 43, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 61, 66, 67, 68, 69, 71, 73, 76, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 93, 94, 95, 97, 99, 104, 112, 113, 114, 116, 117, 119, 121, 126, 129, 131, 135, 136, 137, 140, 141, 143, 148, 149, 151, 153, 154, 155, 162, 168, 169, 170, 172, 173, 177, 179, 180, 182, 183, 185, 190, 191, 193, 195, 196, 197, 207, 209, 210, 211, 212, 213, 214, 215, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 229, 232, 234, 236, 237, 238, 241, 244, 248, 251, 253, 256, 260, 261, 262, 263, 264, 265, 267, 270, 272, 274, 275, 276, 278, 280, 283, 286, 287, 288, 290, 293, 295, 296, 297, 298, 299, 303], "stringel": [27, 83, 84], "stringio": [0, 1, 12, 17, 23, 32, 56, 168, 188, 199, 238, 253], "strip": [6, 10, 15, 27, 83, 135, 162, 236, 270], "strive": 93, "strong": [238, 240], "strongli": [24, 182, 201, 251, 260], "struct": [112, 113, 157], "struct_ref_seq": 248, "structur": [0, 2, 4, 7, 9, 11, 12, 21, 23, 25, 27, 30, 31, 32, 53, 66, 78, 83, 84, 99, 108, 112, 113, 116, 123, 132, 133, 135, 136, 137, 138, 139, 140, 143, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 161, 162, 163, 164, 165, 166, 168, 169, 170, 171, 172, 173, 175, 183, 185, 202, 209, 215, 216, 238, 248, 260, 265, 270, 272, 278], "structure_build": [143, 151], "structure_id": [15, 143, 162, 172], "structure_method": [15, 174], "structure_rebuild_test": [15, 27, 133, 168, 169], "structure_refer": [15, 174], "structurealign": [15, 27, 133], "structurebuild": [27, 133, 143, 151], "structured_comment_delim": [92, 94, 238, 245], "structured_comment_end": [92, 94, 238, 245], "structured_comment_start": [92, 94, 238, 245], "structuredecod": [133, 171, 172], "structureio": [27, 133, 148, 170, 173], "struggl": 9, "sts_d11570": 68, "sts_d11734": 238, "stsline": [27, 275], "stslspfylr": 250, "sttccbsscc": 0, "studi": 19, "stuff": [5, 7, 15, 26, 99, 237, 307], "stumbl": [42, 218, 222], "style": [0, 3, 5, 6, 8, 9, 15, 17, 20, 22, 23, 24, 27, 32, 38, 68, 79, 80, 104, 119, 149, 183, 197, 238, 240, 251, 253, 278, 281, 283, 298, 303], "su": [3, 20, 53, 66], "suarez": 2, "sub": [6, 7, 17, 19, 21, 22, 24, 27, 30, 32, 66, 80, 94, 99, 183, 184, 187, 189, 197, 236, 237, 238, 253, 260, 270, 299, 303], "sub_align": 30, "sub_featur": [21, 237, 272], "sub_plat": 299, "sub_rec": 251, "sub_record": [21, 66, 251, 260], "subalign": [30, 68, 182], "subclad": [17, 132, 183], "subclass": [3, 9, 13, 15, 17, 21, 27, 30, 45, 54, 60, 67, 68, 99, 130, 139, 148, 170, 173, 197, 199, 236, 246, 272, 284, 287, 291], "subcohort": 197, "subcompon": 99, "subcomponent_s": [98, 99], "subdirectori": [0, 4, 8, 12, 13, 15, 24], "subdivis": 197, "subel": [84, 117], "subfamili": [11, 19, 197, 295], "subfeatur": [104, 237], "subfigur": 6, "subform": 197, "subgenu": 197, "subject": [0, 7, 68, 69, 71, 123, 237], "subject_loc": [68, 69], "subkingdom": 197, "sublegion": 197, "submiss": [7, 93, 182], "submit": [3, 5, 7, 19, 218, 237], "submodul": [13, 20, 177, 200], "subnam": 25, "subnod": [4, 73, 130, 198], "suboptim": 270, "subord": 197, "subphylum": 197, "subplat": 299, "subplot": 6, "subprocess": [3, 9, 12, 17, 32, 67, 69, 80, 137, 156, 182, 270, 285], "subprogram": 217, "subregion": [80, 136, 169], "subscrib": 27, "subscript": [7, 12], "subsect": [0, 3, 11, 236], "subseq": 261, "subsequ": [0, 2, 4, 7, 13, 21, 27, 30, 83, 158, 182, 236, 260, 265, 270, 297], "subset": [6, 15, 23, 24, 54, 123, 148, 214, 299], "subsp": 23, "subspeci": 197, "substanc": 123, "substitut": [2, 9, 11, 22, 27, 30, 31, 32, 54, 80, 182, 195, 196, 199, 251, 288, 290, 304], "substitution_matric": [13, 14, 27, 30, 290, 297], "substitution_matrix": [11, 12, 13, 30, 290], "substr": [236, 303], "substrat": [113, 115, 117, 177], "substrate_id": 117, "subtili": 13, "subtl": 21, "subtleti": 19, "subtract": [4, 15, 139, 237, 278, 299], "subtract_control": [16, 298, 299], "subtre": [132, 182], "subtrib": 197, "subtyp": 117, "subulata": 7, "subunit": [4, 15, 169], "subvarieti": 197, "success": 12, "successfulli": [15, 19, 299], "successor": [3, 130, 132, 149], "suddenli": 19, "sueff": [30, 32], "suffici": [3, 15, 167, 169], "suffix": [17, 21, 183, 236, 260, 270], "suggest": [1, 4, 8, 12, 13, 17, 21, 23, 83, 158], "sugimoto": 264, "suit": [2, 3, 7, 8, 12, 14, 15, 17, 20, 24, 44, 56, 69, 112, 113, 114, 126, 218, 226, 227, 229, 238, 269], "suitabl": [4, 5, 6, 13, 15, 23, 46, 61, 80, 83, 100, 125, 158, 183, 238, 251, 274, 278], "suite3": 2, "sulfid": 25, "sulfido": 25, "sulfolobu": 0, "sulfur": 25, "sum": [0, 4, 11, 12, 13, 17, 21, 23, 30, 31, 32, 69, 73, 107, 108, 109, 128, 129, 132, 157, 183, 237, 265, 299], "sum_": [4, 11, 12, 270], "sum_branchlength": [128, 132], "sum_prob": 0, "sum_stat": [68, 69], "sum_statist": [68, 69], "summar": [3, 12, 31, 82, 129], "summari": [0, 3, 11, 16, 23, 30, 31, 68, 83, 84, 117, 123, 182, 183, 260, 280, 299, 303], "summaris": 207, "summary_align": 12, "summary_info": 31, "summaryinfo": [12, 27, 30, 31], "summat": 4, "summer": 17, "sunid": [209, 210, 211, 213], "sup": [15, 216], "supardii": 23, "super": [54, 236], "super_orthologi": 197, "superclass": 197, "supercohort": 197, "superdivis": 197, "superfamili": [11, 15, 197, 209, 211, 295], "supergroup": [11, 288], "superimpos": [8, 27, 133, 166, 169, 175, 216], "superlegion": 197, "superord": 197, "superphylum": 197, "superposit": 216, "superscript": 7, "superset": 278, "superspeci": 197, "supertrib": 197, "supervis": [127, 282], "supplement": 2, "suppli": [0, 3, 4, 7, 8, 12, 14, 15, 18, 19, 20, 21, 23, 30, 32, 108, 109, 152, 158, 169, 217, 218, 237, 260, 261, 278, 297], "support": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 70, 80, 84, 104, 132, 140, 149, 154, 158, 169, 171, 177, 178, 182, 183, 186, 191, 192, 193, 195, 196, 197, 199, 227, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 269, 270, 274, 276, 278, 283, 289, 290, 291, 292, 299, 302], "support_as_branchlength": 132, "suppos": [0, 1, 6, 7, 11, 12, 13, 14, 15, 19, 21, 22, 23, 108, 252, 278], "suppress": [15, 32, 51, 143, 151], "sure": [4, 5, 7, 15, 22, 23, 24, 56, 73, 117, 149, 182, 237, 238, 298], "surfac": [12, 15, 20, 53, 104, 137, 156, 157], "surface_access": 66, "surpris": [12, 20, 237], "surprisingli": 21, "surround": [32, 282], "suspect": 15, "sustain": 16, "sutisak": 2, "suv": 122, "suzuki": 2, "sv": [30, 32], "svd": [4, 216], "svdsuperimpos": [15, 27], "svg": [8, 99, 104], "sw": [126, 270], "sw_score": 226, "swap": [0, 30], "sweet": [8, 265], "sweetpea": [238, 260], "swgadwgdng": 0, "swgadwgeqg": 0, "swgpqwgmng": 0, "swift": [15, 137], "swiss": [0, 9, 19, 23, 26, 86, 88, 89, 197, 238, 255, 258, 276, 307], "swissio": [27, 238, 276], "swissiter": [27, 238, 255], "swissport": 23, "swissprot": [6, 9, 25, 27, 53, 85, 88, 238, 255, 258, 276], "swissprotid": 0, "swissprotparsererror": [27, 272], "switch": [4, 8, 12, 22, 30, 32, 68, 69, 73, 80, 99, 137, 169, 182, 202, 236, 260, 270], "swofford": [2, 129], "swshvsslvsasluiklfkkfsska": 12, "swtaadkaaq": 0, "sx": 90, "sy": [12, 17, 24, 25, 90, 199, 273], "syesaaevrr": 0, "syk_syk": 244, "sylvrnqelr": 0, "symbol": [0, 7, 10, 11, 13, 19, 21, 22, 123, 129, 137, 149, 181, 197, 198, 236, 260, 275, 297], "symbols0": 283, "symbols1": 283, "symbols2": 283, "symbols3": 283, "symbols4": 283, "symmetr": [0, 13, 30, 182, 297], "symmetri": 162, "synonym": [2, 90, 181, 196, 197, 198, 272, 273, 277], "syntax": [7, 9, 15, 16, 30, 170, 182, 185, 198, 237, 276, 299], "synthas": [21, 23, 25], "sysadmin": 149, "sysbio": 2, "sysnam": 113, "syst": [7, 129], "system": [0, 2, 3, 4, 5, 6, 7, 10, 12, 15, 19, 24, 27, 32, 33, 61, 67, 99, 169, 177, 182, 221, 241, 250, 251, 253, 278, 299], "systemat": [2, 19, 113, 129, 182], "systemid": 84, "syteni": 99, "szege": 122, "s\u00f6ding": [2, 32], "t": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 45, 46, 48, 56, 61, 63, 65, 66, 67, 69, 71, 76, 80, 99, 100, 102, 104, 108, 119, 122, 129, 131, 137, 143, 149, 152, 176, 182, 183, 191, 197, 198, 221, 222, 236, 237, 246, 247, 251, 260, 261, 264, 265, 268, 269, 270, 275, 278, 288, 292, 296, 297, 302, 305], "t0": [0, 13, 30], "t01001": 119, "t1": [0, 13, 30, 183, 264], "t100": 0, "t11": [0, 13, 30], "t134": 0, "t137": 0, "t1575": 0, "t2": [0, 13, 30, 183], "t265_11027": 3, "t3": 183, "t30": [0, 13, 30], "t35": 0, "t35m": 0, "t4": [0, 13, 30], "t40": [0, 13, 30], "t73": 0, "t8": [0, 13, 30], "t99": 0, "t_coffe": 32, "t_coffee_home_pag": 32, "t_end1": [0, 30], "t_end2": [0, 30], "t_endn": [0, 30], "t_start1": [0, 30], "t_start2": [0, 30], "t_startn": [0, 30], "ta": [13, 30, 32, 123, 236], "taa": [22, 76, 281], "taaaatatat": 7, "taaaga": 0, "taaattag": 0, "taagccctcctagcacacacccggagtggcc": 0, "taagcgtgcacgcgcaacacgtgcatta": 11, "taagga": 0, "taatgattct": 7, "tab": [4, 11, 12, 20, 23, 51, 104, 210, 211, 212, 217, 219, 226, 232, 236, 238, 256, 270], "tab_2226_tblastn_001": [20, 217], "tab_2226_tblastn_002": 217, "tab_2226_tblastn_003": 20, "tab_2226_tblastn_004": 218, "tab_2226_tblastn_005": 20, "tab_2226_tblastn_007": 20, "tab_2226_tblastn_008": 218, "tab_2226_tblastn_009": 218, "tabacum": 23, "tabb": 263, "tabio": [27, 238], "tabiter": [27, 238, 256], "tabix": 23, "tabl": [0, 3, 4, 6, 7, 11, 13, 15, 20, 21, 31, 32, 34, 36, 69, 76, 79, 80, 93, 94, 107, 126, 167, 202, 209, 217, 226, 229, 230, 231, 232, 236, 237, 238, 260, 261, 264, 280, 286, 293, 295, 296, 303, 304], "table_row": 97, "tabular": [3, 6, 20, 27, 30, 68, 69, 217, 218, 219, 226], "tabwrit": [27, 238, 256], "tac": [22, 76], "tacaa": 11, "tacaataattg": 0, "tacac": 11, "tacactgcattacaacccaagcatta": 11, "tacagatgtgaaactttcaagagatttactgactttcctagaatagtttctctactggaa": 238, "taccc": 11, "taccg": 30, "taccggtaacattacccggcgactttcccacgggctatc": 22, "tacg": 264, "tacgagaataatttctcatcatccagctttaacacaaaattcgca": 23, "tacgagaataatttctcatcatccagctttaacacaaaattcgcacagttttcgttaaga": 23, "tacgc": 11, "tacgcacttt": 7, "tacgt": 30, "tackl": [6, 8], "tacnc": 11, "tacqg": 154, "tactgtattg": 7, "tacttcaaag": 7, "tacttgttgatattggatcgaacaaactggagaaccaacatgctcacgtcacttttagtcccttacatattcctc": 3, "tacttgttggtgttggatcgaaccaattggaagacgaatatgctcacatcacttctcattccttacatcttcttc": 3, "tad": 20, "taetgtqcnf": 0, "tag": [0, 7, 8, 15, 22, 24, 30, 52, 68, 71, 76, 80, 83, 84, 197, 240, 252, 260, 269, 270], "tagaaaatca": 7, "tagcatacttgcnatcctttanccatgcttatcatangtaccatttgaggaattgntttg": 238, "tagctaagac": 22, "tagctcagg": 12, "taggcatacgtg": 30, "taggggtgcagagccgagtcacggggttgccagcac": 0, "tags2id": 94, "taii": 206, "tail": 275, "taipal": 288, "takashi": 2, "take": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 56, 83, 99, 104, 105, 120, 121, 122, 169, 182, 204, 217, 237, 238, 251, 260, 265, 270, 274, 278, 282, 288, 297, 298], "taken": [0, 4, 8, 10, 20, 30, 32, 80, 109, 182, 214, 240, 251, 256, 263, 270], "tale": 288, "talevich": [2, 9, 17, 26, 133], "talevich2012": [2, 9, 17], "talk": [7, 12, 21, 22, 23, 274], "tamayo": [2, 4], "tamayo1999": [2, 4], "tamo": 11, "tan": [183, 236], "tanaka": 25, "tanford": 265, "taq": 0, "tar": [76, 149], "target": [0, 3, 7, 12, 13, 15, 17, 20, 27, 30, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 46, 47, 49, 50, 51, 52, 53, 68, 69, 71, 79, 80, 81, 119, 129, 158, 169, 183, 186, 218, 222, 226, 229, 234, 241, 245, 246, 247, 251, 252, 253, 256, 259, 264, 270], "target1": [0, 183], "target2": [0, 183], "target_db": 119, "target_end_extend_gap_scor": 13, "target_end_gap_scor": [13, 30], "target_end_open_gap_scor": 13, "target_extend_gap_scor": 13, "target_gap": [30, 55], "target_gap_scor": 13, "target_internal_extend_gap_scor": 13, "target_internal_gap_scor": 13, "target_internal_open_gap_scor": 13, "target_left_extend_gap_scor": 13, "target_left_gap_scor": 13, "target_left_open_gap_scor": 13, "target_level": 159, "target_open_gap_scor": 13, "target_right_extend_gap_scor": 13, "target_right_gap_scor": 13, "target_right_open_gap_scor": 13, "target_seqnam": 61, "target_tre": 186, "targetcut": 270, "task": [6, 9, 12, 19, 23, 68, 69, 79, 80, 99, 108, 177, 182], "tast": [3, 20], "tasumi": 149, "tat": [22, 30, 76], "tat_mase_nuc": 244, "tataataattgtatatgtcacagaaaaaaatgaattttcaat": 0, "tatacataaa": 30, "tatacataaaagaag": 0, "tatacataaaagaagggggatgcggataaatggaaaggcgaaag": [12, 30], "tatacataaaagaagggggatgcggataaatggaaaggcgaaagaaagaa": 0, "tatacataaaagaagggggatgcggataaatggaaaggcgaaagaaagaaaaaaatgaat": 0, "tatacataaagtgtaccaga": 30, "tatacatt": 0, "tatacattaa": 30, "tatacattaaagaagggggatgcggataaatggaaaggcgaaag": [12, 30], "tatacattaaagaagggggatgcggataaatggaaaggcgaaagaaagaa": 0, "tatacattaaagaagggggatgcggataaatggaaaggcgaaagaaagaaaaaaatgaat": 0, "tatacattaaaggagggggatgcggataaatggaaaggcgaaag": [12, 30], "tatacattaaaggagggggatgcggataaatggaaaggcgaaagaaagaa": 0, "tatacattaaaggagggggatgcggataaatggaaaggcgaaagaaagaaaaaaatgaat": 0, "tatacattaagtataccaga": 30, "tatacattaagtgtaccaga": 30, "tatcacagcg": 7, "tatgaatggcgaggcaatcgctggcacctacacggaccgccgccaccgccgcgccaccat": 22, "tatgacaata": 7, "tatgcgaaga": 7, "tatgtagaaa": 7, "tatgtatatg": 7, "tatgtcatagaaaaaaatgaattttcaat": 0, "tatgtcattc": 278, "tatgtgtcag": 7, "tattctgatg": 7, "tattggatca": 7, "tau": [15, 73, 152, 154, 169], "tau_": 4, "tax": 17, "tax_group": [11, 287, 288], "taxa": [129, 132, 182, 183], "taxacea": 17, "taxid": [3, 7, 68, 69], "taxid_map": [68, 69], "taxlabel": 132, "taxon": [7, 11, 17, 21, 32, 80, 129, 132, 182, 183, 197, 277, 295], "taxon_id": 277, "taxon_list": 132, "taxonom": [11, 69, 88, 93, 197, 288, 295, 303], "taxonomi": [2, 7, 11, 21, 22, 23, 27, 69, 93, 181, 183, 197, 198, 252, 272, 274, 288, 303], "taxonomy_id": [25, 272], "taxonomyid": 69, "taylor": 182, "tba": 0, "tblast": 3, "tblastn": [68, 69, 70, 71, 218], "tblastx": [3, 68, 69, 70, 71, 218], "tc": [0, 53], "tca": 22, "tcaaatcctt": 7, "tcaacatctt": 7, "tcaaggatgt": 7, "tcaagtgtac": 7, "tcacggtggcctgttgaggcaggggctcacgctgacctctctcggcgtgggaggggccgg": 0, "tcacggtggcctgttgaggcaggggctcacgctgacctctctcggcgtgggaggggccggtgtgaggcaagggctcacgctgacctctctcggcgtgggag": 0, "tcacggtggcctgttgaggcagggggtcacgctgacctctgtccgcgtgggaggggccgg": 0, "tcag": [22, 253], "tcagaaagaagtaaggtaaa": 253, "tcagaaagacaagtggtatc": 253, "tcagaagcagtggtatcaac": 253, "tcagaatcat": 253, "tcagaatcatccacttttta": 253, "tcagactttcttctttaccg": 253, "tcagcggccgggcctctcat": 253, "tcagctccgtaagaaggtgc": 253, "tcagggactgcgagaaccaagcta": 13, "tcagggactgcgagaaccaagctactgctgctgctggctgcgctctgcgccgcaggtggg": 13, "tcagggactgcgagaaccaagctactgctgctgctggctgcgctctgcgccgcaggtggggcgctggag": 13, "tcagggacttcgagaaccaagcgc": 13, "tcagggacttcgagaaccaagcgcctcctgctgctggctgcgctcggcgccgcaggtggagcactggag": 13, "tcagggacttcgagaaccaagcgctcctgctgctggctgcgctcggcgccgcaggtggagcactggag": 13, "tcagggtctacatgttggtt": 253, "tcagggtctacatgttggttaacccgtactgatt": 253, "tcagtggtaatggggggaaa": 253, "tcagttttttttggaaagga": 253, "tcatattactntaagttctatagcatacttgcnatcctttanccatgcttatcatangtaccatttgagg": 238, "tcatgtgacca": 19, "tcattggttatggcagtggtcgtcaatgacagcgatgaagatggagatagccgtgacgca": 260, "tcc": [22, 76], "tccttctttg": 7, "tcctttcatg": 7, "tcg": [22, 30, 236, 280], "tcgacgtcg": 236, "tcgt": 260, "tcgtgtgcta": 7, "tchr1": 0, "tcoffe": 32, "tcoffee_clin": 32, "tcoffeecommandlin": [30, 32], "tct": [22, 76], "tctacgattgag": 283, "tctattccag": 7, "tctcctc": 12, "tctcgacgtcg": 236, "tctcttttct": 7, "tctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcg": 0, "tcttgagcga": 7, "tcttgatcga": 7, "tctttgtcgt": 7, "teach": 122, "teal": [8, 183], "team": [5, 234], "teamdslktq": 12, "teamnslktq": 12, "teardown": 24, "teas56_57": 0, "teassvsssq": 250, "teatsvstsq": 250, "techfak": 32, "technic": [22, 23, 25, 27], "techniqu": [4, 8, 107], "technologi": [10, 16, 158, 270], "tediou": 19, "tell": [4, 7, 11, 12, 22, 23, 27, 80, 217, 251, 253, 278], "telomer": [8, 99], "telomere_length": 8, "telomereseg": [8, 27, 98, 99, 102], "temp": [6, 251], "temp_filt": 253, "temp_path": 145, "temp_wat": 67, "temperatur": [80, 135, 172, 264], "temperature_factor": 172, "templat": [0, 15, 22, 24, 52, 69, 99, 191, 236, 264, 275], "template_dna": 22, "template_length": [68, 69, 70], "template_typ": [68, 69, 70], "temporari": [12, 17, 24, 105, 190, 251, 270], "ten": [4, 6, 12, 16, 23, 30, 217, 250, 251, 260], "tend": [4, 24, 73, 265], "ter": 261, "terl": 8, "term": [0, 4, 6, 8, 11, 13, 17, 18, 19, 20, 25, 30, 32, 35, 39, 46, 51, 52, 61, 83, 113, 119, 123, 169, 209, 213, 229, 252, 264, 274, 278], "termgap": [30, 32], "termin": [3, 4, 15, 17, 32, 90, 129, 132, 153, 169, 182, 183, 236, 245, 250, 255, 261, 264, 272], "terminal_gap_to_miss": [128, 129], "terminalgap": [30, 32], "termini": [32, 80], "terminologi": [17, 21, 22, 121], "terminu": [80, 275], "ters": 21, "test": [0, 3, 4, 6, 7, 8, 11, 14, 16, 17, 18, 20, 25, 26, 27, 34, 42, 71, 74, 79, 80, 86, 87, 88, 90, 91, 112, 113, 114, 126, 135, 139, 156, 168, 169, 182, 183, 194, 202, 203, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 241, 249, 251, 260, 265, 275, 280, 281, 305, 307], "test1": 104, "test_": 24, "test_ac": 24, "test_addition1": 24, "test_addition2": 24, "test_align_bigb": 0, "test_alignio": 24, "test_biospam": 24, "test_biospammymodul": 24, "test_biosql": [24, 305], "test_biosql_seqio": 24, "test_cap": 24, "test_clustalw": 24, "test_division1": 24, "test_division2": 24, "test_even_bigendian": 247, "test_genic_diff_al": [201, 202], "test_genic_diff_pair": [201, 202], "test_genotypic_diff_al": [201, 202], "test_genotypic_diff_pair": [201, 202], "test_global_hz_defici": [201, 202], "test_global_hz_excess": [201, 202], "test_hw_glob": [201, 203], "test_hw_pop": [201, 203], "test_ld": [201, 202], "test_ld_all_pair": [201, 203], "test_pop_hz_defici": [201, 202], "test_pop_hz_excess": [201, 202], "test_pop_hz_prob": [201, 202], "test_seq": 11, "test_seqio": 24, "test_tutori": 24, "test_typ": 203, "test_xxx": 24, "testaddit": 24, "testcas": 24, "testdivis": 24, "testenv": 24, "testload": 24, "testrunn": 24, "testsuit": 24, "tetllvqnanpdcktilkalgpgatle": 154, "tetrachloroethen": 197, "tetrahedr": [15, 169], "tetrahedron": 169, "tetrazolium": 16, "teuvo": 2, "text": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 17, 19, 22, 23, 25, 27, 42, 45, 60, 67, 68, 69, 70, 71, 76, 83, 84, 85, 87, 89, 93, 94, 97, 99, 143, 185, 188, 190, 197, 199, 209, 217, 224, 228, 230, 233, 237, 238, 241, 244, 245, 246, 248, 249, 250, 251, 256, 258, 260, 271, 272, 274, 275, 276, 291, 292], "textco": 242, "textio": [150, 152], "textiowrapp": [4, 90], "textrm": [4, 6, 11, 13], "textstream": 90, "texttestrunn": 24, "texttt": 22, "textual": [21, 32, 201, 204], "textw": 229, "tf": [11, 288], "tf0000003": 11, "tf0000070": 288, "tf_class": [11, 287, 288], "tf_famili": [11, 287, 288], "tf_name": 288, "tfastx": 226, "tfb": 288, "tfbss": 11, "tfiiic": 4, "tg": [0, 11, 30, 222], "tga": [22, 76, 236], "tgaactagaatctcagaggatg": 0, "tgacctagaatctcagaggatg": 0, "tgactaagaa": 7, "tgatctccccatcctgccctg": 0, "tgatgccctcaccccctccgtgca": 0, "tgc": [22, 76], "tgca": 264, "tgcaaggcttctacacccgtactcgaatgc": 264, "tgcaatgcaaxrzxrz": 236, "tgccgttaccat": 222, "tgctagagaa": 7, "tgeglewgvlfgfgpgltvetvvlhsvat": 23, "tgg": [22, 76], "tggacgcgggg": 283, "tggcaatctt": 7, "tgggaggttttatgtgga": 251, "tgggaggttttatgtggaaagcagcaatgtacaaga": 251, "tgggtttaa": 281, "tggtaatggggggaaattta": 253, "tgkqnscqmsaiwqlrqntatktrqnrari": 6, "tgt": [22, 76], "tgtaacgaacggtgcaatagtgatccacacccaacgcctgaaatcagatccagg": 21, "tgtaacgaacggtgcaatagtgatccacacccaacgcctgaaatcagatccagggggtaatctgctctcc": 21, "tgtgaatttt": 7, "tgtgaggcaagggctcacactgacctctctcagcgtgggag": 0, "tgtgaggcaagggctcacgctgacctctctcggcgtgggag": 0, "tgttctgaaggaaggtgtgcgtgcgtgtgtgtgtgt": 251, "th": [11, 12, 104, 297], "th0": 0, "th1": 0, "thaimgvaft": 250, "thale": 23, "thaliana": [3, 8, 23, 238, 278], "than": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 17, 19, 20, 21, 23, 24, 25, 27, 30, 31, 32, 34, 35, 46, 49, 51, 56, 61, 62, 64, 65, 66, 68, 69, 71, 83, 88, 92, 113, 135, 136, 139, 152, 166, 169, 182, 197, 198, 203, 207, 209, 217, 222, 237, 238, 240, 241, 251, 255, 260, 265, 269, 270, 271, 275, 280, 283, 288, 290, 297, 298, 303], "thank": [5, 15, 71], "thei": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 32, 35, 36, 37, 38, 39, 41, 51, 52, 58, 67, 68, 70, 71, 88, 94, 107, 108, 121, 143, 151, 152, 155, 164, 169, 178, 182, 183, 214, 217, 221, 222, 226, 237, 251, 260, 264, 270, 278, 297, 303], "thein": 264, "them": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 45, 56, 66, 67, 68, 84, 92, 103, 104, 108, 136, 139, 149, 169, 182, 183, 185, 191, 217, 218, 221, 222, 229, 237, 238, 249, 251, 260, 270, 278, 280, 282, 303, 305], "themselv": [0, 4, 12, 15, 17, 20, 21, 66, 222, 251], "theobald": 175, "theoret": [4, 25, 177, 263], "theori": [6, 12, 217], "thereaft": 182, "therebi": 3, "therefor": [0, 3, 4, 6, 7, 11, 12, 15, 16, 21, 23, 30, 32, 35, 46, 51, 61, 68, 69, 73, 83, 99, 209, 234, 238, 240, 251, 278, 288], "thereof": 291, "thermodynam": 264, "thermophil": 0, "theta": [12, 154, 176], "thf": 53, "thi": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 80, 81, 82, 83, 84, 85, 86, 88, 89, 90, 92, 93, 94, 95, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 112, 113, 114, 116, 117, 119, 120, 124, 125, 126, 127, 128, 129, 132, 134, 135, 136, 137, 138, 139, 140, 143, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 162, 165, 167, 169, 172, 175, 177, 179, 180, 182, 183, 185, 186, 188, 190, 191, 197, 198, 199, 202, 203, 204, 205, 207, 209, 210, 212, 213, 214, 215, 216, 217, 218, 221, 222, 226, 227, 229, 234, 236, 237, 238, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 263, 264, 265, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 279, 280, 281, 282, 283, 285, 288, 290, 291, 292, 295, 296, 297, 298, 299, 300, 302, 303, 305, 306, 307], "thick": [0, 8, 36, 104], "thickend": [0, 36], "thickstart": [0, 36], "thiel": 2, "thin": 8, "thing": [1, 3, 5, 7, 9, 11, 12, 15, 17, 19, 20, 21, 23, 25, 26, 27, 30, 31, 45, 60, 80, 92, 95, 99, 158, 169, 216, 237, 246, 251, 260, 297, 307], "thingivers": [15, 158, 169], "think": [1, 5, 11, 13, 15, 17, 19, 20, 21, 30, 102, 237, 264], "thiomac": 11, "third": [0, 3, 4, 6, 7, 8, 12, 13, 15, 17, 21, 22, 30, 169, 222, 251, 261], "thirdli": 251, "thirteenth": 21, "thoma": [2, 3, 9, 26, 68, 133, 296], "thompson": 32, "thornton": 265, "thorough": [79, 80, 182], "thorton": 182, "those": [3, 4, 6, 8, 9, 10, 12, 16, 17, 22, 23, 24, 27, 76, 83, 84, 94, 102, 105, 157, 182, 191, 207, 251, 253, 260, 261, 283, 288, 297], "though": [3, 9, 11, 12, 13, 17, 20, 21, 23, 30, 183, 197, 237, 270, 303], "thought": [237, 264], "thousand": [3, 20, 182, 204, 217, 251], "thr": [13, 15, 30, 32], "thread": [30, 32, 69, 149, 181, 182, 270], "three": [0, 3, 4, 6, 7, 8, 11, 12, 13, 15, 16, 17, 20, 22, 23, 25, 30, 62, 73, 83, 94, 104, 119, 141, 149, 154, 169, 205, 209, 222, 236, 248, 251, 261, 264, 265, 272, 274, 278, 281, 299], "three_to_index": [27, 133, 154], "threepluson": 283, "thresh": [79, 80], "threshold": [0, 3, 6, 9, 12, 27, 30, 31, 32, 68, 69, 70, 71, 79, 80, 109, 132, 182, 229, 268, 270, 283, 290], "threshold_balanc": [11, 283, 294], "threshold_fnr": [11, 283, 294], "threshold_fpr": [11, 283, 294], "threshold_pats": [11, 283, 294], "through": [0, 3, 5, 6, 7, 10, 11, 16, 17, 19, 20, 21, 23, 25, 30, 31, 62, 71, 84, 92, 100, 104, 107, 135, 152, 169, 183, 191, 197, 203, 215, 218, 226, 227, 229, 234, 236, 238, 278], "throughout": [1, 11, 15, 21, 270], "throughput": [7, 10, 16, 23, 32], "throw": [76, 236], "thrust": 12, "thu": [4, 5, 8, 13, 14, 15, 18, 19, 20, 21, 22, 64, 68, 70, 71, 76, 99, 127, 132, 169, 182, 237, 251, 253, 264, 269, 270, 278, 282], "thumb": [4, 264], "thylakoid": 272, "thymidin": 209, "ti": [7, 20, 123], "tiago": [2, 26], "tick": [8, 104], "tid": 270, "tidi": [24, 85, 91, 148, 170, 173, 251], "tien": 137, "tiff": 104, "tiffin": [11, 283], "tightest": 0, "tightli": [19, 217], "tild": [63, 251], "tim": 2, "time": [0, 1, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 25, 32, 56, 68, 69, 73, 80, 83, 84, 92, 99, 109, 169, 182, 186, 197, 209, 222, 238, 251, 253, 258, 265, 267, 270, 274, 288, 294, 299], "timothi": 2, "tini": 23, "tip": [5, 6, 17, 19, 69], "tissu": [7, 275], "titl": [3, 6, 7, 11, 21, 23, 25, 53, 68, 69, 71, 83, 93, 99, 101, 103, 117, 123, 129, 152, 168, 172, 207, 237, 241, 250, 251, 272, 275, 295], "title_s": 99, "titlemainlist": 7, "titsslsldg": 250, "tj": 32, "tkk": 68, "tl": [94, 182], "tlen": 52, "tln": 0, "tlr": 182, "tm": [30, 32, 53, 66, 264], "tm_con": 53, "tm_gc": [27, 261, 264], "tm_nn": [27, 261, 264], "tm_wallac": [27, 261, 264], "tmf": 0, "tmm_tabl": 264, "tmp": [145, 270], "tmp_directori": 145, "tn93": 182, "tn_x": 8, "tn_y": 8, "tname": [301, 304], "tnm": 0, "tny": 12, "to_align": [181, 197], "to_dict": [23, 27, 217, 238, 251, 283, 287], "to_gener": [68, 71], "to_hex": [181, 183], "to_level": 104, "to_networkx": 17, "to_phylogeni": [181, 197], "to_phyloxml_contain": [181, 197], "to_process": 95, "to_rgb": [181, 183], "to_seqfeatur": [181, 197], "to_seqrecord": [181, 197], "to_stat": 108, "to_stop": [6, 22, 236, 237, 260], "to_str": [98, 104, 128, 132, 181, 185, 188, 190], "toclarecord": [27, 209], "todai": 19, "todd": 2, "todesrecord": [27, 209], "todo": 7, "togeth": [0, 6, 7, 8, 9, 11, 12, 13, 14, 21, 22, 23, 30, 61, 62, 66, 71, 83, 130, 169, 214, 217, 218, 238, 243, 251, 260, 278, 297], "togow": [24, 27, 119], "toh": 32, "tohierecord": [27, 209], "token": [197, 272], "told": 12, "tom": 12, "tomultipleseqalign": [279, 280], "ton": [13, 31], "tonsist": 13, "too": [3, 6, 7, 8, 12, 15, 17, 20, 21, 22, 23, 24, 30, 56, 108, 237, 238, 251, 278], "took": [6, 23, 56, 108, 238, 253, 298], "tool": [0, 2, 3, 5, 6, 7, 9, 11, 14, 15, 17, 19, 23, 26, 27, 30, 32, 40, 41, 42, 48, 50, 55, 56, 57, 58, 59, 63, 65, 66, 67, 68, 69, 70, 74, 80, 83, 126, 156, 182, 217, 218, 221, 222, 226, 250, 251, 253, 264, 278, 283, 285, 289, 290, 307], "toolkit": [2, 7, 123, 218], "top": [0, 2, 3, 4, 11, 12, 15, 20, 21, 23, 24, 84, 99, 101, 104, 139, 158, 163, 175, 181, 182, 198, 216, 241, 251, 256, 278, 302], "topdiag": [30, 32], "topic": [5, 6, 7, 22], "topm": [181, 182], "topo_dom": 272, "topolog": [7, 182, 272], "topologi": [4, 17, 21, 182, 183, 197], "toresnum": 125, "torrent": 253, "torsion": 154, "toseq": [279, 281], "tossgap": [30, 32], "total": [0, 4, 7, 11, 12, 13, 17, 23, 25, 30, 71, 108, 109, 183, 197, 202, 203, 221, 261, 264, 270, 275, 287, 290], "total_branch_length": [17, 181, 183], "total_len": 23, "total_num_atom": 172, "total_num_bond": 172, "total_num_chain": 172, "total_num_group": 172, "total_num_model": 172, "toth": [2, 7, 8], "toth2006": [2, 8], "touch": [7, 8, 32], "toward": [8, 12, 237, 261, 270], "toxic": 260, "tp": [0, 13, 53], "tpc": 2, "tpda": 13, "tpp": 53, "tpr": 53, "tqueri": [0, 13, 30], "tr": 278, "tra": 76, "trace": [7, 17, 55, 128, 130, 169, 181, 183, 238, 251, 253, 275], "traceback": [0, 3, 4, 7, 13, 21, 22, 23, 30, 45, 56, 67, 68, 69, 80, 85, 217, 236, 237, 238, 241, 251, 260, 264, 278, 283, 298], "tracheophyta": [7, 25], "track": [0, 4, 6, 7, 10, 20, 22, 23, 98, 104, 158, 162, 169, 251, 270], "track_geneid": 7, "track_i": 8, "track_level": 104, "track_siz": 104, "track_statu": 7, "track_x": 8, "tracker": [5, 226], "tracklin": 104, "trackscale_fonts": 104, "trade": [23, 169, 270], "tradeoff": 264, "tradit": [101, 278], "traffic": 15, "trail": [0, 6, 12, 15, 94, 135, 207, 230, 236, 260, 297], "trailer": [15, 151], "train": [11, 27, 30, 32, 106, 107, 109, 120, 121, 122, 127, 282], "train_bw": [27, 121], "train_vis": [27, 121], "trainer": [27, 106], "training_data": 121, "training_seq": 109, "training_seq_prob": 109, "training_set": [122, 127], "trainingsequ": [27, 106, 107, 109], "tran": [6, 13, 21, 112, 135, 139, 199, 216], "tranalign": 80, "tranaligncommandlin": [27, 79, 80], "trans_": 6, "trans_len": 6, "trans_tabl": 6, "transact": [7, 303], "transcrib": [22, 27, 236], "transcript": [0, 2, 7, 9, 11, 13, 21, 30, 35, 36, 51, 68, 275], "transcriptom": 7, "transfac": [2, 27, 283], "transfer": [6, 17, 21, 104, 113, 197, 270], "transferas": [10, 23], "transform": [4, 6, 15, 23, 32, 102, 107, 128, 129, 133, 135, 139, 158, 166, 169, 172, 175, 176, 177, 216, 222, 238, 251, 278], "transgen": 261, "transient": [7, 83, 269], "transit": [13, 32, 34, 80, 108, 109, 182, 272, 281], "transition_count": 109, "transition_prob": 108, "transition_pseudo": 108, "transitions_from": [106, 108], "transitions_to": [106, 108], "transl_tabl": [7, 21, 94, 237], "translat": [2, 3, 4, 7, 9, 12, 13, 15, 21, 23, 27, 30, 32, 34, 42, 68, 69, 76, 83, 94, 95, 98, 104, 135, 136, 139, 153, 159, 162, 163, 166, 175, 176, 216, 222, 236, 237, 245, 260, 261, 279, 280, 281, 283], "translationerror": [27, 75, 76, 236], "translationset": 7, "transliter": 123, "transloc": 113, "translocas": 272, "transmem": 272, "transmembran": [32, 53, 66, 272], "transpar": 8, "transport": 272, "transpos": [0, 4, 13, 15, 30, 54, 73, 169], "transvers": [13, 32, 34, 79, 80, 182, 281], "transweight": [30, 32], "tranvers": 80, "travers": [183, 185], "trbg361": 260, "tre": 199, "treat": [4, 5, 7, 11, 12, 15, 17, 23, 30, 31, 32, 65, 67, 69, 80, 83, 182, 197, 222, 236, 251, 260, 261, 270], "tree": [2, 4, 12, 13, 15, 27, 30, 32, 36, 37, 56, 73, 80, 128, 130, 146, 149, 176, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 193, 195, 197, 198, 199, 209, 252, 264, 280], "tree1": [17, 30, 32], "tree2": [30, 32, 132], "tree_constructor": 186, "tree_method": 280, "tree_puzzl": 65, "tree_uri": 185, "treeclust": [4, 27, 73], "treeconstruct": [13, 24, 27, 181], "treeconstructor": [27, 181, 186, 199], "treedist": 80, "treeelement": [17, 27, 181, 183, 197], "treeerror": [27, 128, 132], "treekpaiag": 250, "treemixin": [17, 27, 181, 183], "treeout": [30, 32], "treeprint": [79, 80], "treesearch": [27, 181, 199], "treetext": [185, 188, 190], "treetyp": [79, 80], "treeview": [2, 73], "trembl": [25, 89, 255], "trend": [2, 53], "tri": [1, 3, 5, 6, 12, 15, 16, 21, 23, 83, 182, 237, 264], "triacylglycerol": 25, "triangl": [4, 8, 15, 80], "triangular": 73, "tribe": 197, "trick": [6, 12, 19, 22, 23, 253], "tricki": [6, 14, 251], "trifurc": [17, 183], "trigger": [13, 27, 69, 222, 226, 251, 252, 270], "trim": [21, 238, 239, 251, 253, 268, 270, 277], "trim_adaptor": 6, "trim_prim": 6, "trimmed_primer_read": 6, "trimmed_read": 6, "trip": 19, "tripabl": 23, "tripl": [17, 119, 185, 202, 203], "triplet": 222, "triticea": 25, "triticum": 0, "trivial": [6, 7, 12, 13, 22, 23, 158], "trmviimvif": 250, "trmvvimvvf": 250, "trmvvlmvig": 250, "trna": [2, 8, 237, 250], "trna_chrom": 8, "troglodyt": [3, 20], "troubl": 24, "trout": [79, 80], "trp": [13, 265], "trr": 76, "tru1i": 206, "tru9i": 206, "true": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 17, 20, 21, 22, 24, 25, 29, 30, 31, 32, 36, 37, 38, 49, 51, 52, 64, 67, 68, 69, 70, 73, 76, 80, 83, 88, 91, 94, 104, 105, 117, 125, 127, 129, 132, 135, 139, 140, 143, 148, 149, 151, 152, 153, 154, 158, 166, 168, 169, 176, 177, 179, 180, 183, 188, 190, 193, 195, 196, 197, 198, 199, 202, 203, 204, 209, 217, 218, 220, 221, 230, 231, 236, 237, 238, 251, 253, 258, 260, 261, 264, 265, 276, 277, 278, 281, 283, 287, 290, 295, 297, 299, 303, 304], "truncat": [12, 20, 30, 32, 65, 68, 129, 251, 260, 268, 270, 278, 280, 299], "trust": [52, 53, 251, 253], "trustabl": 201, "truth": 183, "try": [3, 5, 6, 7, 8, 9, 11, 12, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 60, 84, 108, 149, 169, 217, 218, 236, 238, 246, 251, 253, 260, 270, 305], "trypsin": 112, "tryptophan": 288, "ts_tv_ratio": [181, 182], "tsa": 94, "tsm": 270, "tsn": 0, "tso": 0, "tspasirppagpssr": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqat": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqatggwk": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqatggwktcsgtc": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqatggwktcsgtcttststrhrgrsgwsartttaaclrasrksmraacsrsagsrpnrfaptlmsscitsttgppawagdrsh": 0, "tspasirppagpssrrpsppgprrptgrpccsaaprrpqatggwktcsgtctt": 0, "tsq": 12, "tstart": [0, 221], "tsv": 256, "tsy": 12, "tt": [0, 21, 30, 123, 264], "tta": [13, 21, 22], "ttaa": [30, 68], "ttaaact": 0, "ttaaccccatttg": [30, 68], "ttaagaaactggaaatgagggttgaatgacaaactt": 22, "ttactcgaat": 7, "ttactctttcatctgataccttgttcagatttcaaaatagttgtagccttatcctggttt": 238, "ttaggttcgg": 7, "ttagtaaacc": 7, "ttarget": [0, 13, 30], "ttatgctttaattcaaaac": 0, "ttatttacga": 7, "ttatttctct": 7, "ttc": [22, 76], "ttcaaggcttctacacccgtactcgaatgc": 264, "ttcatataaa": 7, "ttcatttata": 7, "ttcc": 0, "ttccattgcactgcgggagggttgacccctgcgatttccccaaatgtgggaaactcgact": 30, "ttcggtaccctccatgacccacg": 62, "ttcggtaccctccatgacccacgaaatgagggcccagggtatgctt": 62, "ttctcaaatg": 7, "ttctcaagga": 7, "ttctggcgtg": 251, "tte": 68, "ttg": [13, 22], "ttgaaaa": 22, "ttgaaaaactgattattagagtcaattaaggatagt": 22, "ttgaaaacctgaatgtgagagtcactcaaggatagt": 22, "ttgaaaacctgaatgtgagagtcagtcaaggatagt": 22, "ttgacwcytgcycwg": 291, "ttgaleaayt": 0, "ttgaleaaytqatgknislseqqlvdcaggfnnf": 0, "ttgalesaia": 0, "ttgalesaiaiatgkmlslaeqqlvdcaqdfnni": 0, "ttgatcggtgacaaattttttacaaagaactgtaggacttgctacttctccctc": 23, "ttgca": 22, "ttggcaggccaaggccgatggatca": [238, 251], "ttggtctcaa": 7, "ttgnvegqhf": 0, "ttgnvegqhfisqnklvslseqnlvdcdhecmeyegeeacdegcngglqpnaynyiikng": 0, "ttgta": 11, "ttgtatcgta": 7, "ttgtcgaaag": 7, "ttgtggtgggaat": 0, "ttk": 13, "ttl": 274, "ttratio": [79, 80], "ttststrhrgrsgw": 0, "ttststrhrgrsgwsartttaaclrasrksmraacsrsagsrpnrfaptlmsscitsttg": 0, "ttt": [0, 12, 13, 21, 22, 30, 68, 76, 236], "tttaaa": 30, "tttaaaaaa": 30, "tttaaaaaaaaa": 30, "tttaaaaaaaaaaattt": 30, "tttaaacacctttttggatg": 62, "tttaaacatccctcggcccgtcgcccttttataatagcagtacg": 62, "tttaaacatccctcggcccgtcgcccttttataatagcagtacgtgagaggagcgccctaagctttgggaaattcaagc": 62, "tttc": 30, "tttcctatagctataggaccaatccacttaccatacgcccggcgtcgcccagtccggttcggtaccctccatgacccacg": 62, "tttccttttc": 0, "tttcttcggt": 7, "tttcttcgta": 7, "tttcttgcccccatagactgagaccttccctaaata": 251, "tttggtagta": 7, "tttggttact": 7, "tttggttagaa": 0, "tttt": 0, "ttttaa": 281, "ttttcagagg": 7, "ttttgccgga": 7, "ttttgtttgaatcctaaac": 0, "ttttgttttaatcctaaac": 0, "tttttagaag": 7, "tttttttctt": 7, "ttttttttggaaaggaaaac": 253, "ttwsxo45s3zcliby4x": 238, "tty": 278, "tuc2009": 8, "tuc2009_01": 8, "tuc2009_03": 8, "tuc2009_05": 8, "tuc2009_06": 8, "tuc2009_07": 8, "tuc2009_08": 8, "tuc2009_09": 8, "tuc2009_10": 8, "tuc2009_11": 8, "tuc2009_12": 8, "tuc2009_13": 8, "tuc2009_14": 8, "tuc2009_15": 8, "tuc2009_17": 8, "tuc2009_18": 8, "tuc2009_19": 8, "tuc2009_20": 8, "tuc2009_22": 8, "tuc2009_23": 8, "tuc2009_24": 8, "tuc2009_26": 8, "tuc2009_46": 8, "tuc2009_48": 8, "tuc2009_49": 8, "tuc2009_52": 8, "tumor": 7, "tune": [8, 15, 270], "tupbel1": 0, "tupl": [0, 4, 6, 8, 13, 14, 15, 16, 20, 21, 23, 30, 36, 54, 71, 73, 87, 88, 94, 99, 101, 102, 104, 105, 108, 109, 112, 113, 114, 117, 121, 134, 135, 137, 139, 149, 169, 176, 177, 183, 202, 205, 209, 210, 215, 217, 222, 231, 232, 236, 238, 241, 251, 260, 261, 264, 265, 272, 278, 297, 299, 303], "tuq": 0, "turn": [0, 1, 6, 7, 8, 9, 11, 12, 15, 17, 20, 23, 30, 32, 53, 56, 67, 68, 69, 70, 76, 80, 100, 137, 142, 182, 217, 238, 241, 251, 260, 265, 270, 272, 295, 298], "turner": 264, "turtl": [119, 185, 274], "tutori": [3, 5, 6, 9, 19, 22, 32, 56, 69, 80, 83, 92, 169, 182, 236, 238, 270, 307], "tv": 80, "tvkfkykgeekqvdiskikkvwrvgkmisftydegggktgrgavsekdapkellqmlek": 0, "tvmagyivst": 0, "tvn": 0, "tweak": [9, 83], "twelfth": 21, "twelv": 13, "twenti": 16, "twice": [30, 32, 90, 205], "two": [0, 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, 30, 32, 34, 56, 61, 67, 68, 73, 76, 80, 81, 92, 94, 99, 101, 102, 108, 109, 117, 130, 132, 135, 139, 140, 146, 155, 161, 163, 166, 169, 175, 176, 177, 182, 183, 197, 198, 209, 216, 217, 222, 226, 237, 238, 241, 244, 247, 250, 251, 252, 256, 257, 260, 261, 263, 265, 269, 270, 278, 280, 281, 282, 295, 297, 299, 300], "two_motif": 11, "twobit": [0, 23, 238, 257], "twobitio": [27, 236, 238], "twobititer": [27, 238, 257], "txid158330": 7, "txmap": 275, "txt": [0, 4, 6, 7, 10, 11, 12, 17, 20, 25, 56, 67, 80, 85, 90, 93, 104, 123, 149, 182, 217, 218, 244, 270, 272, 273, 289], "txt_1": [210, 211], "ty": [0, 11, 13, 14, 295], "type": [0, 3, 7, 8, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 38, 45, 53, 54, 56, 68, 69, 73, 76, 80, 83, 84, 88, 93, 101, 104, 107, 116, 117, 122, 123, 125, 127, 131, 134, 135, 136, 137, 139, 140, 149, 150, 151, 154, 155, 164, 165, 172, 176, 177, 181, 182, 183, 197, 198, 209, 211, 214, 217, 225, 229, 234, 236, 237, 238, 246, 250, 252, 260, 261, 262, 263, 264, 265, 272, 275, 276, 278, 288, 294, 295, 297], "typecod": [120, 127, 282], "typeerror": [0, 22, 236], "typic": [0, 3, 4, 7, 8, 11, 12, 13, 15, 16, 17, 21, 22, 23, 24, 25, 27, 30, 32, 34, 35, 36, 39, 45, 51, 52, 56, 67, 69, 80, 83, 112, 113, 114, 117, 123, 126, 137, 148, 149, 156, 170, 173, 182, 195, 209, 214, 236, 238, 245, 248, 250, 251, 260, 264, 270, 271, 277, 278, 298], "typvnt": 68, "tyr": [13, 154, 265], "u": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 17, 19, 21, 22, 23, 25, 32, 73, 76, 80, 83, 122, 182, 236, 237, 260, 261, 268, 269, 270, 278, 300], "u1": [0, 30], "u78617": [238, 260], "uab": [34, 280], "uac": 76, "uaccgguaacauuacccggcgacu": 261, "uaccuagcuacgaaaagaaugcaguuaaugu": 66, "uag": 76, "uau": 76, "ubiquinon": [113, 272], "ubiquit": 23, "ucaacacucu": 66, "ucaauaugg": 66, "ucc": 76, "ucg": 236, "ucl": 17, "ucsc": [13, 35, 36, 37, 38, 39, 46, 51, 61, 221, 238, 247, 257], "ucsc_mm9_chr10": 0, "ucsc_test": 0, "ucsf": 15, "ucu": 76, "udf1": 122, "udf2": 122, "udf3": 122, "ufunc": 54, "uga": 76, "ugc": 76, "ugcaaggcuucuacacccguacucgaaugc": 264, "ugcaaugcaaxrzxrz": 236, "ugg": 66, "ugu": [66, 76], "ui": [7, 83], "uid": [7, 83], "uin": 123, "uint": [0, 36], "uiuc": 15, "uk": [0, 2, 6, 8, 15, 17, 32, 104, 145, 209, 210, 211, 212, 222, 234, 245, 250, 277], "ultim": [3, 19], "ultra_paralogi": 197, "umcn": [15, 137], "umist": 145, "uml": [3, 15], "un": [230, 297], "unaffect": 15, "unalign": [12, 32], "unambigu": [15, 76, 236, 261, 264, 267], "unambiguous_dna_by_id": 22, "unambiguous_dna_by_nam": 22, "unannot": 8, "unassign": 197, "unavoid": 251, "uncaught": [15, 139], "uncent": 73, "uncer": 131, "uncertain": [131, 237], "uncertainposit": [27, 237], "uncertainti": 272, "unchang": [23, 260], "uncharacter": [94, 277], "unclear": [11, 21], "uncom": 218, "uncompl": 269, "uncompress": [23, 25, 270, 278], "uncondition": 69, "unconvert": [268, 270], "undecaprenyl": 112, "undef_cod": 261, "undefin": [0, 11, 22, 36, 37, 38, 236, 251, 290], "undefined_seq": 22, "undefinedsequenceerror": [22, 27, 236], "under": [0, 2, 4, 5, 6, 7, 8, 9, 11, 12, 13, 16, 17, 19, 20, 21, 23, 24, 37, 39, 46, 67, 68, 93, 104, 109, 123, 182, 183, 217, 236, 240, 244, 247, 249, 251, 253, 300], "underflow": 107, "undergon": 14, "underli": [4, 7, 11, 13, 15, 20, 25, 67, 73, 198, 222, 238, 249, 251, 295], "underlin": 4, "underscor": [9, 214], "understand": [8, 10, 12, 19, 21, 169], "understood": 66, "undervalu": 24, "undisord": 136, "unequ": [11, 297], "unexpect": [13, 23], "unexplain": 4, "unfold": 159, "unfold_ent": [15, 27, 133, 159], "unfortun": [3, 7, 14, 23, 251], "ungap": [0, 11, 42, 68, 69, 222, 279, 281], "ungap_seq": 281, "ungapped_align": [0, 68, 70], "uni": [32, 130], "unic": 287, "unicod": [0, 13, 68, 83, 278], "unicorn_gen": 3, "unifi": [2, 11, 20], "uniform": [4, 5, 11, 23, 79, 80, 100, 182, 197, 270, 290], "unigen": [9, 27], "unigenerecord": 7, "union": [21, 150, 164, 169, 236, 237, 260], "uniparc": 274, "uniprot": [21, 23, 27, 85, 164, 197, 237, 238, 250, 252, 255, 258, 272, 273, 274], "uniprot_sprot": [23, 25], "uniprotio": [27, 238, 255], "uniprotiter": [27, 238, 258], "uniprotkb": [89, 197, 255], "uniqid": [4, 73], "uniqu": [0, 4, 6, 7, 10, 11, 12, 15, 20, 23, 69, 73, 76, 104, 108, 123, 135, 139, 159, 172, 177, 179, 180, 182, 197, 209, 210, 211, 213, 217, 234, 238, 260, 262, 270, 272, 275, 288], "unique_speci": 13, "uniqueifi": [27, 133, 159], "uniref100": 274, "uniref50": 274, "uniref90": 274, "unist": [7, 275], "unit": [6, 8, 11, 13, 16, 21, 24, 27, 53, 99, 104, 158, 172, 182, 197, 249], "unit_branch_length": [17, 183], "unit_cel": 172, "unit_nam": 283, "unittest_suit": 24, "univers": [0, 2, 3, 4, 7, 216, 253, 278], "unix": [5, 32, 67, 149, 238, 278], "unk": [15, 21, 169, 260], "unknown": [0, 3, 4, 13, 17, 20, 21, 23, 30, 68, 71, 94, 104, 109, 135, 197, 205, 214, 236, 237, 247, 250, 260, 261, 272, 279], "unknown_seq": 22, "unknownposit": [21, 27, 237], "unless": [7, 15, 21, 23, 30, 45, 60, 99, 149, 152, 153, 183, 197, 238, 246, 260, 270, 278, 288, 299], "unlik": [4, 11, 15, 20, 83, 119, 169, 182, 207, 236, 238, 260, 265, 274, 278, 288], "unlink": [128, 130], "unlov": 19, "unmap": 0, "unmodifi": [3, 21], "unnam": 215, "unnecessari": [20, 270], "unnorm": 122, "unp": 248, "unpack": [15, 136, 155], "unpair": 270, "unpars": [42, 218, 222], "unpickl": [54, 237], "unpublish": 3, "unreach": 108, "unrealist": 15, "unrecognis": 248, "unroot": [17, 128, 132], "unsign": 278, "unsignedbyt": 197, "unsignedint": 197, "unsignedlong": 197, "unsignedshort": 197, "unsort": [3, 20], "unspecifi": 15, "unstabl": 265, "unstructur": 21, "unsuit": 217, "unsur": 272, "unsurprisingli": 15, "until": [0, 3, 4, 7, 9, 23, 25, 31, 68, 84, 94, 129, 169, 198, 237, 260, 269, 270], "untitl": 0, "untransform": [175, 216], "untrim": 6, "unus": [151, 253], "unweight": [182, 199], "unwrap": 104, "unzip": [6, 278], "uof": 123, "uoffset": 278, "up": [0, 1, 3, 4, 5, 6, 7, 9, 11, 12, 14, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 59, 66, 67, 73, 83, 84, 85, 91, 93, 94, 95, 99, 104, 108, 119, 125, 132, 133, 138, 148, 169, 170, 173, 182, 183, 209, 214, 237, 238, 241, 242, 245, 251, 255, 260, 278, 299], "updat": [0, 3, 7, 8, 9, 11, 12, 24, 30, 32, 54, 76, 83, 88, 123, 136, 144, 149, 160, 169, 176, 182, 264, 295, 299], "update_dcoordspac": [133, 169], "update_emiss": [106, 109], "update_fn": [120, 121, 122], "update_ncbi_codon_t": 76, "update_pdb": [15, 133, 149], "update_transit": [106, 109], "updated": 7, "upgma": [13, 32, 80, 181, 199, 280], "upgmatre": 199, "upgmb": 32, "upgrad": 9, "upon": [15, 42, 61, 129, 218, 222, 265], "upper": [0, 11, 20, 21, 22, 27, 30, 32, 33, 38, 51, 80, 104, 162, 197, 236, 237, 241, 251, 253, 260, 274, 290], "uppercas": [16, 135, 169, 214, 236, 260, 262, 264], "upperq": 104, "uq": 0, "ura": 76, "uri": [27, 84, 181, 185, 188, 197, 198], "url": [3, 4, 7, 10, 25, 68, 70, 83, 84, 90, 105, 111, 115, 117, 119, 149, 171, 197, 198, 274], "url_bas": [3, 68, 70], "urlapi": [68, 70], "urlerror": 83, "urllib": [4, 7, 25, 83, 90], "urlopen": [4, 25, 90], "us": [0, 2, 3, 4, 5, 6, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 76, 78, 79, 80, 81, 83, 84, 89, 90, 91, 92, 93, 94, 95, 98, 99, 100, 101, 102, 103, 104, 107, 108, 109, 110, 112, 113, 114, 116, 117, 118, 119, 121, 122, 125, 126, 127, 129, 130, 131, 132, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 146, 148, 149, 151, 152, 153, 154, 155, 156, 157, 158, 162, 164, 166, 168, 169, 172, 175, 176, 177, 178, 182, 183, 186, 189, 191, 193, 195, 196, 197, 198, 199, 202, 204, 207, 208, 209, 210, 214, 216, 217, 218, 221, 222, 226, 229, 231, 236, 237, 238, 239, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 269, 270, 271, 272, 274, 275, 276, 277, 278, 280, 281, 282, 283, 287, 288, 290, 291, 294, 295, 296, 297, 298, 299, 302, 303, 304, 305, 306, 307], "usa": [2, 7, 80, 264], "usabl": [17, 217], "usag": [0, 1, 7, 10, 12, 17, 21, 23, 24, 25, 27, 29, 30, 45, 60, 67, 69, 83, 107, 119, 123, 133, 152, 169, 182, 199, 217, 238, 240, 246, 269, 271, 272, 274, 298], "use_fuzzi": 92, "use_index": [68, 69], "use_model_flag": 148, "use_raw_hit_id": [218, 220], "use_raw_query_id": [218, 220], "use_sw_tback": [68, 69], "usehistori": 7, "usekimura": [30, 32], "uselog": [30, 32], "user": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 24, 30, 31, 32, 45, 56, 67, 83, 104, 143, 148, 151, 157, 169, 182, 193, 195, 196, 199, 217, 218, 221, 226, 229, 236, 246, 274, 280, 281, 288, 299, 303, 305], "user_funct": 122, "userguid": [8, 229], "userlist": [15, 68], "userman": 272, "userman_doc": 245, "usernam": [68, 70, 303], "userseq1": 25, "userset": 264, "usetre": [30, 32], "usetree1": [30, 32], "usetree2": [30, 32], "usual": [0, 3, 4, 6, 8, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 30, 68, 158, 169, 183, 197, 236, 237, 238, 251, 253, 260, 269, 270], "utf": [7, 90, 236, 278], "util": [7, 10, 15, 18, 22, 27, 83, 84, 92, 106, 222, 238, 247, 265, 268, 274, 294, 304], "utiliz": 9, "utsugi": 25, "uuaaucgagcucaacacucuucguauauccuc": 66, "uuc": 76, "uucuacaaggug": 66, "uuu": 76, "uv": 25, "uveyeaqsv5edqonfoemmvea": 238, "uw": 11, "v": [0, 2, 4, 8, 11, 13, 15, 16, 22, 27, 30, 32, 73, 76, 80, 100, 152, 169, 182, 261, 265, 268, 270, 300], "v0": [105, 117], "v1": [0, 176, 265], "v2": [176, 229], "v3": [32, 176, 229], "v4": [0, 176], "v5": 0, "v6": 32, "v7": [0, 32], "v8": 0, "v_final": [98, 100], "v_init": [98, 100], "vaa": 56, "vafyifthqg": 250, "vagvan": 13, "vaivmgr": 236, "vaivmgrwkgar": 236, "val": [13, 169, 197, 202], "val1": 277, "val2": 277, "valentin": 32, "valid": [4, 6, 7, 10, 13, 15, 20, 22, 27, 32, 67, 68, 70, 71, 83, 84, 117, 119, 136, 169, 176, 182, 186, 191, 198, 207, 236, 237, 251, 252, 264, 270], "validationerror": [7, 27, 83, 84], "valin": [22, 236], "valiv": 237, "valu": [0, 2, 3, 6, 7, 8, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 23, 27, 30, 31, 32, 34, 35, 36, 37, 38, 42, 51, 53, 54, 55, 65, 67, 68, 69, 70, 71, 73, 76, 80, 82, 83, 84, 92, 93, 94, 95, 99, 100, 102, 103, 104, 105, 107, 108, 117, 119, 121, 122, 126, 127, 129, 132, 137, 141, 145, 152, 157, 158, 169, 176, 177, 181, 182, 183, 184, 186, 194, 197, 198, 199, 210, 216, 218, 221, 222, 226, 229, 230, 236, 237, 238, 241, 251, 253, 260, 261, 263, 264, 265, 267, 270, 272, 275, 277, 278, 280, 283, 286, 288, 290, 292, 295, 296, 297, 299, 300, 301, 303], "valuea": 251, "valueerror": [4, 11, 13, 17, 22, 23, 25, 27, 29, 30, 31, 56, 67, 68, 80, 84, 85, 92, 183, 217, 236, 237, 238, 241, 251, 253, 260, 261, 264, 271, 272, 278, 283, 290, 298], "valueexcept": 25, "values_are_confid": [188, 190], "values_are_support": 132, "valueset": 264, "van": [2, 8, 15, 216], "vanderauwera2009": [2, 8], "var_seq": 272, "vari": [7, 11, 16, 21, 152, 168, 238], "variabl": [3, 4, 7, 11, 12, 14, 15, 21, 23, 67, 68, 70, 73, 83, 101, 107, 109, 126, 149, 169, 175, 229, 278, 304], "varianc": 4, "variant": [2, 4, 5, 6, 12, 20, 23, 68, 104, 169, 217, 218, 238, 245, 251, 260, 264, 270, 272, 278], "variat": [2, 4, 8, 80, 168, 268, 270], "varieti": [5, 17, 197], "variou": [3, 9, 12, 15, 20, 75, 80, 158, 199, 217, 268, 278, 283, 290, 293], "vassssfad": 0, "vcnhfmvlcg": 250, "vd": 0, "vdpv": 13, "ve": [3, 5, 6, 7, 8, 12, 15, 16, 17, 19, 20, 21, 23, 24], "vecscreen": 69, "vector": [4, 8, 9, 15, 27, 34, 73, 122, 127, 133, 135, 139, 141, 169, 175, 281], "vector1": 15, "vector2": 15, "vector3": 15, "vector4": 15, "vector_to_axi": [27, 133, 176], "vectoris": 169, "vectorxscalar": 176, "vectorxvector": 176, "vendor": 298, "ver_agm3": 244, "verb": 4, "verbos": [0, 15, 17, 24, 30, 32, 42, 79, 80, 104, 136, 144, 149, 152, 153, 160, 168, 169, 193, 195, 196, 270], "veri": [0, 5, 6, 7, 8, 9, 12, 13, 15, 19, 20, 21, 22, 23, 25, 30, 32, 56, 94, 149, 158, 169, 177, 182, 209, 238, 240, 251, 253, 260, 264, 278], "verifi": [0, 4, 13, 138, 152, 169], "verlag": 2, "versa": 27, "version": [0, 1, 6, 7, 8, 9, 11, 12, 14, 15, 17, 20, 21, 23, 24, 25, 27, 29, 30, 32, 42, 45, 51, 54, 56, 65, 68, 69, 70, 71, 76, 80, 83, 84, 88, 90, 93, 132, 133, 137, 158, 169, 181, 182, 208, 209, 210, 214, 217, 218, 221, 222, 226, 227, 228, 229, 234, 236, 238, 240, 243, 251, 252, 253, 267, 269, 270, 277, 278, 283, 287, 288, 295, 298, 303], "version1": 170, "version_6": 32, "version_str": 137, "versu": 183, "vertebr": [2, 11, 22, 283, 288], "vertex": 156, "vertic": [4, 8, 23, 73, 99, 156, 197, 236], "vertre": 166, "vesca": 23, "vestergaard": 9, "vev": 0, "vg": 14, "vgmnipydga": 0, "vgmnipyhga": 0, "vh": 13, "vhmlnkgkdgamvfepaslkvapgdtvtfiptdk": 0, "vhmlnkgkdgamvfepaslkvapgdtvtfiptdkghnvetikgmipdgaeafk": 0, "vi": [7, 123, 182], "via": [3, 5, 7, 9, 12, 13, 14, 15, 17, 19, 21, 23, 24, 27, 30, 32, 35, 36, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 69, 71, 80, 99, 117, 119, 169, 182, 197, 218, 226, 229, 234, 236, 237, 238, 240, 241, 244, 245, 247, 248, 249, 250, 251, 252, 253, 255, 256, 270, 278, 285, 297, 303, 305], "vice": 27, "victor": 2, "vie": 32, "view": [2, 6, 7, 15, 21, 54, 69, 73, 100, 169, 177, 193, 195, 196, 265, 270, 278, 306], "viewer": 17, "viewpoint": 4, "vihinen": 265, "viklfkkfv": 12, "violat": 182, "viral": 23, "virginia": [59, 226], "viridiplanta": [7, 23, 25], "virlfkkfss": 12, "virtual": [15, 207, 278], "virtual_offset": 278, "viru": [6, 23, 272], "virus": [6, 23], "visibl": [0, 121, 182], "visit": [4, 239], "visual": [2, 4, 6, 7, 15, 17, 22, 30, 72, 117, 123, 141, 183], "visualis": 105, "viterbi": [30, 32, 106, 108], "viverrini": 3, "vk": 13, "vkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg": 12, "vkhfspeelk": 250, "vkkilyikalflctviklrrfifsvnnmkf": 6, "vkkmqsivlalslvlvapmaaqaaeitlvpsvklqigdrdnrgyywdgghwrdh": 22, "vklgadsgalefvpktltiksgetvnfvnnagfphnivfdedaipsg": 0, "vklgadsgalefvpktltiksgetvnfvnnagfphnivfdedaipsgvnadai": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpak": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlak": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlakslshk": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlakslshkqllmspgqststtfpadapageytfycephrgagmvgkit": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlakslshkqllmspgqststtfpadapageytfycephrgagmvgkitv": 0, "vkr": 6, "vkvlgdviev": 250, "vldl": 25, "vllganggvlvfepndfsvkagetitfknnagyphnvvfdedavpsg": 0, "vltvsaprkq": 250, "vmd": 15, "vn": 0, "vnslek": 0, "vntifkei": 260, "vocabulari": 272, "vol": 126, "vol1": 6, "volum": [2, 3, 15, 83, 123, 156, 169], "volunt": [5, 9], "von": 264, "vorata": 2, "voucher": 7, "vpag": 0, "vpfsnktgla": 250, "vpmsnktgvv": 250, "vpnwikaarfeec": 53, "vqikmgtdkyaplyepkalsisagdtvefvmnkvgphnvifdk": 0, "vqikmgtdkyaplyepkalsisagdtvefvmnkvgphnvifdkvpagesap": 0, "vrl": 23, "vskisq": 0, "vskisqeeyltapgetfsvtltv": 0, "vspa": 250, "vss": 0, "vstv": 13, "vt": 182, "vtiqhkklrt": 250, "vtltdnvsd": 237, "vtml240": 32, "vtnalvfeivmtfglvytvyataidpkkgslgtiapiaigfivgani": 260, "vtv": 0, "vtvqhkklrt": 250, "vulgar": [0, 42, 217, 225], "vulgari": 183, "vv": [11, 295], "vvaa": 0, "vvtsvavagl": 12, "vvttvvvagl": 12, "v\u00f6hringer": 2, "w": [0, 2, 3, 4, 6, 7, 10, 11, 12, 13, 15, 22, 23, 25, 32, 40, 45, 53, 56, 57, 59, 80, 85, 91, 126, 145, 162, 169, 182, 183, 226, 236, 238, 241, 245, 246, 250, 251, 256, 261, 264, 265, 268, 270, 278, 281, 298, 299], "w3": 185, "w33": 32, "w36": 32, "w7079": 90, "w_i": 4, "w_ij": 261, "w_prot": 0, "wa": [0, 3, 4, 6, 7, 8, 9, 11, 13, 14, 15, 17, 19, 20, 21, 22, 23, 25, 27, 42, 48, 63, 65, 67, 68, 69, 71, 73, 80, 84, 88, 100, 102, 103, 108, 134, 137, 183, 185, 188, 190, 217, 218, 221, 222, 226, 229, 234, 237, 238, 240, 250, 251, 253, 260, 261, 268, 269, 278, 283, 296, 299, 303], "wacnc": 11, "wacvc": 11, "wag": [32, 181, 182], "wai": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 30, 34, 56, 65, 73, 92, 93, 99, 102, 135, 163, 169, 175, 177, 182, 183, 191, 207, 222, 229, 236, 237, 238, 260, 269, 281, 303], "wait": [7, 12, 67], "walk": 4, "wallac": [7, 32, 264], "walter": 2, "wang": [152, 169], "want": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 30, 32, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 92, 99, 102, 108, 149, 151, 154, 169, 182, 183, 205, 207, 218, 221, 237, 238, 241, 251, 253, 260, 278, 281, 283, 297, 298, 303], "warn": [6, 7, 8, 12, 15, 23, 25, 27, 32, 56, 79, 80, 83, 89, 108, 143, 151, 169, 197, 237, 238, 251, 260, 261, 270, 288, 300], "warren": 2, "washington": [3, 50, 65, 190, 199], "wasn": [19, 71], "wast": [3, 6, 67], "watch": [12, 23], "water": [0, 14, 41, 58, 67, 80, 138, 139, 143, 152, 157, 162, 169, 172], "water_cmd": 67, "watercommandlin": [27, 67, 79, 80], "waterloo": 0, "waterman": [0, 2, 12, 13, 14, 30, 32, 69], "waterman1987": [2, 13], "watkin": 264, "watson": [22, 32], "wayn": 2, "wb": [3, 6, 23, 36, 45], "wbiom": [201, 204], "wc": 202, "wcor413": 3, "wdvktvtgvlhhpfhltfslcpegatqsgr": 6, "we": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 35, 45, 46, 51, 59, 61, 64, 66, 67, 68, 69, 80, 84, 90, 91, 92, 93, 94, 95, 99, 100, 101, 102, 105, 107, 108, 109, 117, 166, 169, 182, 183, 191, 199, 217, 222, 236, 237, 238, 240, 241, 243, 247, 249, 251, 253, 255, 260, 265, 270, 278, 285, 287, 288, 290, 298, 302], "web": [0, 3, 7, 9, 10, 12, 15, 18, 19, 25, 68, 83, 90, 182, 218, 221, 229, 234, 272, 274], "webb": [2, 3, 68], "weblogo": [11, 27, 283], "webpag": 7, "websevic": 274, "websit": [0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 19, 21, 59, 85, 164, 197, 226, 272, 274, 283], "wed": 0, "week": 15, "weekdai": 3, "weekend": [3, 7], "weekli": [15, 149], "weight": [0, 9, 17, 30, 31, 32, 73, 79, 80, 112, 119, 120, 122, 128, 129, 132, 182, 184, 187, 189, 199, 261, 265, 272, 282, 283, 290, 296], "weight1": [30, 32], "weight2": [30, 32], "weight_filenam": [181, 182], "weight_fn": 282, "weighted_stepmatrix": [128, 129], "weighti": [30, 32], "weinberg": [18, 202, 203], "weir": [202, 203], "weird": 22, "welch": [109, 121], "welcom": [11, 20, 32, 177], "well": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 19, 20, 21, 22, 23, 25, 27, 30, 45, 53, 55, 60, 73, 116, 127, 169, 182, 183, 207, 209, 217, 218, 237, 246, 251, 253, 257, 278, 283, 295, 298, 299], "well1": 299, "well2": 299, "wellcom": [52, 251, 253], "wellid": 299, "wellrecord": [16, 27, 298, 299], "wen": 2, "wenglab": 286, "went": 67, "were": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 17, 20, 22, 23, 30, 42, 63, 71, 94, 169, 219, 222, 231, 232, 237, 251, 260, 278], "western": 278, "wet": 21, "wetmur": 264, "wg": 94, "wgklqviglsmwmvlfsqrfddwlneqeda": 6, "wgkv": 13, "wgkvgahag": 14, "wgs84": 197, "whale": 272, "what": [2, 3, 4, 5, 6, 7, 8, 11, 12, 15, 20, 21, 22, 23, 24, 25, 26, 41, 58, 67, 80, 83, 99, 108, 109, 130, 146, 148, 169, 183, 199, 207, 217, 229, 236, 237, 238, 251, 260, 275, 278, 307], "whatev": [3, 8, 169], "wheel": [5, 8, 178], "wheeler": [129, 270], "whelan": 182, "when": [0, 1, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 34, 45, 55, 56, 59, 60, 61, 65, 66, 67, 68, 69, 70, 71, 73, 80, 81, 83, 84, 91, 93, 97, 99, 102, 104, 108, 109, 117, 132, 149, 152, 166, 169, 182, 183, 186, 188, 190, 198, 209, 214, 217, 218, 221, 222, 229, 236, 237, 238, 246, 251, 252, 253, 256, 260, 261, 263, 269, 270, 281, 282, 290, 295, 297, 298, 302, 303], "whenev": [13, 197, 221], "where": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 36, 56, 59, 65, 67, 72, 82, 83, 84, 92, 93, 94, 99, 100, 103, 104, 108, 118, 121, 125, 126, 127, 129, 139, 140, 149, 154, 156, 169, 176, 177, 182, 183, 201, 202, 203, 212, 217, 221, 222, 236, 237, 238, 248, 251, 256, 260, 263, 269, 270, 272, 278, 288, 295, 297, 300, 303, 307], "wherea": [0, 4, 7, 15, 63, 83, 237], "whether": [0, 3, 4, 11, 15, 16, 17, 20, 30, 68, 70, 71, 73, 84, 92, 95, 99, 104, 127, 135, 139, 155, 168, 169, 183, 221, 222, 229, 261, 270, 279, 297, 303], "which": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 35, 37, 39, 42, 43, 45, 46, 49, 51, 52, 53, 56, 59, 63, 64, 66, 67, 68, 69, 70, 71, 73, 76, 80, 83, 84, 91, 92, 93, 94, 96, 99, 100, 101, 102, 104, 107, 108, 109, 110, 119, 120, 125, 126, 129, 132, 134, 135, 143, 148, 149, 152, 157, 166, 169, 170, 173, 175, 177, 182, 186, 197, 199, 206, 207, 209, 210, 216, 217, 229, 231, 236, 237, 238, 240, 244, 246, 248, 250, 251, 252, 253, 255, 257, 260, 261, 263, 264, 265, 268, 269, 270, 271, 272, 273, 274, 277, 278, 283, 288, 290, 294, 295, 297, 298, 299, 303], "whichcod": [79, 80], "while": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 30, 32, 45, 56, 73, 83, 90, 94, 122, 149, 153, 158, 169, 217, 218, 229, 238, 251, 257, 260, 264, 265, 272, 278, 298], "white": [2, 6, 7, 8, 23, 95, 183], "whitehead": 253, "whitelist": 67, "whitespac": [65, 94, 129, 169, 182, 230, 236, 241, 251, 264], "whitten": 7, "who": [5, 7, 11, 12, 21, 22, 30, 299], "whole": [0, 3, 6, 7, 8, 13, 15, 17, 21, 22, 23, 30, 46, 56, 61, 183, 197, 204, 205, 209, 217, 222, 238, 260, 269, 270, 297], "whose": [6, 16, 25, 30, 119, 236, 253, 260, 274, 288], "why": [6, 7, 8, 9, 12, 19, 20, 23, 30, 229, 251, 260], "wiaf": 7, "wid": 299, "wide": [2, 4, 5, 6, 9, 12, 18, 61, 251, 274, 278], "wider": 80, "width": [11, 17, 65, 79, 80, 115, 117, 129, 181, 183, 197, 198, 207, 229, 270, 278], "wiki": [5, 6, 9, 12, 17, 19, 21, 23, 53, 56, 66, 181, 227, 234, 236, 263, 301], "wikipedia": [11, 53, 66, 263], "wilczy\u0144ski": [2, 26], "wild": 15, "wildcard": [0, 11, 13, 30, 38, 51], "wildli": 20, "wilk": 137, "wilkinson": 2, "william": [0, 2, 7, 55, 149], "willing": 5, "wilm": 32, "wilson": 265, "wimalacaap": 250, "wimalacavp": 250, "wimalscaap": 250, "win32": 12, "window": [5, 6, 12, 30, 32, 61, 67, 69, 71, 182, 238, 261, 265, 267, 278], "window_masker_db": [68, 69], "window_masker_taxid": [68, 69], "window_s": [68, 69, 71, 166], "windowmask": 69, "windows": 265, "wing": 11, "wingend": 2, "wingless": 68, "wise": [0, 4, 13, 30, 182], "wish": [11, 21, 27, 45, 60, 61, 158, 182, 246, 248, 260], "with_assembli": 149, "with_prim": 6, "with_primer_trim": 6, "within": [2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 15, 19, 20, 21, 23, 24, 31, 56, 73, 80, 99, 107, 108, 146, 156, 169, 172, 182, 183, 197, 209, 217, 236, 237, 252, 253, 256, 260, 269, 270, 274, 278, 281, 288, 303, 306], "within_block_offset": 278, "withinposit": [21, 27, 237], "without": [0, 3, 4, 6, 7, 11, 12, 13, 15, 17, 21, 22, 23, 30, 56, 67, 71, 73, 80, 83, 99, 105, 113, 129, 130, 135, 166, 167, 169, 177, 182, 183, 199, 207, 214, 217, 218, 219, 221, 229, 238, 241, 251, 253, 260, 261, 270, 272, 278, 281], "wittmann": 0, "wjc39": 238, "wk": 53, "wnt": [68, 217], "wnt2": 68, "wnt3a": 68, "wnt4": 68, "wnt5a": 68, "wnt6": 68, "wolf": 145, "won": [0, 5, 6, 7, 8, 9, 12, 18, 20, 21, 23, 61, 65, 66, 149, 251, 292], "wonder": [3, 8, 19], "wong": 100, "word": [6, 7, 9, 11, 15, 20, 21, 23, 32, 68, 69, 70, 80, 129, 132, 237, 241], "word_siz": [68, 69, 70], "wordfind": 69, "wordsiz": [79, 80], "work": [0, 3, 5, 7, 8, 9, 11, 12, 14, 15, 16, 17, 20, 21, 23, 24, 30, 32, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 70, 71, 76, 87, 92, 93, 103, 107, 109, 110, 111, 112, 113, 114, 115, 119, 123, 124, 127, 137, 149, 158, 164, 169, 172, 181, 182, 193, 195, 196, 201, 205, 215, 217, 236, 237, 238, 240, 248, 249, 251, 260, 267, 270, 272, 274, 278, 298, 299], "workabl": 5, "workaround": 67, "workflow": [12, 17, 20, 222], "workhors": 23, "working_dir": [17, 181, 182, 193, 195, 196], "workselector": 169, "world": [3, 12, 19, 169], "worldwid": [9, 15], "worri": [6, 7, 17, 20, 21, 22, 23], "wors": [238, 251], "worth": 20, "would": [0, 1, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 35, 46, 51, 56, 61, 62, 63, 66, 67, 68, 69, 80, 94, 125, 149, 152, 182, 217, 236, 237, 238, 250, 251, 253, 260, 264, 270, 274, 278, 283, 298, 303], "wouldn": [6, 12, 20, 302], "wprintgc": 22, "wqfyiggv": 0, "wqfyiggvf": 0, "wqvmrl87qwcm9llo4": 238, "wr": [27, 240, 268, 269], "wrap": [9, 15, 17, 22, 23, 30, 32, 53, 66, 104, 129, 237, 238, 241, 250, 251, 303], "wrap_cursor": 303, "wrapper": [1, 3, 9, 10, 17, 30, 32, 67, 69, 80, 104, 139, 153, 155, 177, 182, 185, 188, 190, 191, 238, 270, 274, 277, 285, 303], "wright": 2, "writabl": 217, "write": [1, 4, 5, 6, 7, 8, 9, 10, 13, 17, 19, 21, 22, 25, 27, 30, 32, 33, 36, 37, 38, 40, 42, 45, 46, 47, 49, 51, 52, 56, 57, 60, 61, 62, 63, 64, 65, 66, 68, 80, 82, 85, 91, 98, 99, 101, 103, 104, 126, 129, 132, 138, 141, 148, 152, 153, 158, 164, 168, 169, 170, 173, 181, 182, 183, 185, 188, 190, 191, 198, 199, 209, 217, 218, 219, 220, 221, 229, 231, 232, 237, 238, 241, 244, 245, 246, 247, 249, 250, 251, 252, 253, 256, 259, 260, 270, 274, 277, 278, 283, 286, 287, 293, 295, 298, 299], "write_align": [30, 33, 36, 45, 49, 56, 57, 60, 61, 62, 64, 65, 66], "write_c": [268, 270], "write_cla": [27, 209], "write_cla_sql": [27, 209], "write_ctl_fil": [192, 193, 195, 196], "write_d": [27, 209], "write_des_sql": [27, 209], "write_end": 148, "write_fil": [30, 36, 37, 38, 45, 47, 49, 56, 60, 64, 217, 218, 219, 220, 221, 229, 231, 232, 238, 241, 246, 247, 250, 253, 259], "write_foot": [30, 42, 45, 56, 60, 238, 241, 246, 250, 252], "write_head": [30, 40, 42, 45, 46, 47, 51, 52, 56, 60, 61, 124, 126, 238, 241, 246, 247, 250, 252, 253], "write_hi": [27, 209], "write_hie_sql": [27, 209], "write_multiple_align": [30, 45], "write_nexus_data": [128, 129], "write_nexus_data_partit": [128, 129], "write_p": [15, 27, 133, 152, 168, 169], "write_pdb": [15, 27, 133, 168, 169], "write_record": [238, 241, 245, 246, 247, 249, 250, 251, 252, 253, 256], "write_scad": [15, 27, 133, 158, 169], "write_single_align": [30, 45], "write_to_str": [98, 104], "write_xxx_sql": 209, "writeabl": 199, "writeanc": [30, 32], "writebyproteinrec": [27, 276, 277], "writer": [0, 10, 27, 30, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 47, 49, 50, 51, 52, 53, 57, 60, 62, 64, 65, 66, 148, 181, 185, 188, 190, 191, 198, 217, 218, 219, 220, 221, 229, 231, 232, 241, 245, 246, 247, 250, 251, 253, 259, 299], "writerec": [27, 276, 277], "writetosql": [27, 209], "written": [0, 1, 3, 4, 8, 9, 12, 14, 15, 16, 17, 19, 20, 23, 30, 32, 47, 56, 65, 68, 69, 73, 80, 84, 99, 104, 129, 148, 149, 158, 166, 169, 170, 173, 182, 185, 188, 190, 193, 195, 196, 214, 217, 218, 219, 221, 222, 229, 231, 232, 238, 269, 270, 277, 286, 298], "wrong": [6, 9, 15, 21, 67, 149, 251], "wrongli": [251, 265], "wrote": [5, 12, 23, 24, 25], "wsize": 267, "wt": 14, "wu": [2, 3, 32], "wunsch": [12, 13, 30, 32], "ww": [90, 273], "wwpdb": [15, 78, 149, 150, 248], "www": [0, 5, 6, 7, 9, 10, 12, 15, 17, 19, 22, 25, 32, 52, 68, 70, 71, 83, 85, 86, 87, 88, 94, 96, 97, 99, 104, 105, 111, 115, 116, 117, 119, 122, 149, 158, 167, 170, 174, 182, 185, 188, 209, 218, 221, 222, 234, 237, 245, 248, 250, 252, 253, 258, 265, 270, 272, 273, 279, 299, 301], "www2": 15, "www6": 239, "wysok": 2, "x": [0, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 25, 30, 31, 32, 36, 56, 68, 69, 71, 73, 80, 99, 104, 115, 117, 118, 120, 127, 129, 133, 135, 136, 144, 149, 160, 169, 172, 176, 182, 185, 209, 214, 216, 221, 229, 236, 238, 243, 248, 260, 261, 264, 265, 270, 277, 279, 282, 286, 290, 297, 300], "x0": 0, "x03": 3, "x04": 3, "x1": 0, "x1e": 264, "x2": 176, "x3": 176, "x3x3": 176, "x55053": [238, 245], "x57361": 13, "x57362": 13, "x57363": 13, "x57364": 13, "x57365": 13, "x57366": 13, "x57367": 13, "x57368": 13, "x57369": 13, "x57370": 13, "x57371": 13, "x57372": 13, "x57373": 13, "x57374": 13, "x57375": 13, "x57376": 13, "x62281": [238, 245], "x77802": 303, "x92856": 21, "x_coord_list": 15, "x_i": 4, "x_posit": 99, "x_vs_y": 8, "xa": 270, "xaa": 261, "xaxis_label": 283, "xbbtool": 261, "xc": 122, "xcar": 122, "xctxctx": 12, "xcxxxxccxxxxxcxxxxxxcxxxcxxxxcxxxxxcxxx": 0, "xdna": [238, 259], "xdnaio": [27, 238], "xdnaiter": [27, 238, 259], "xdnawrit": [27, 238, 259], "xdrop_gap": [68, 69], "xdrop_gap_fin": [68, 69], "xdrop_ungap": [68, 69], "xe": 122, "xenologi": 197, "xfam": 12, "xfr": [30, 32], "xg": 0, "xgc_skew": [27, 261], "xhhhhhhhhhhhhhhhchhhhhhhhchhhhhhhhhhhhhhhhhhhhhhhc": 12, "xia": 264, "xke": 68, "xl": 104, "xlabel": 6, "xle": 261, "xlim": 6, "xm": [0, 27, 283], "xm_002875188": [3, 20], "xm_003527287": [3, 20], "xm_003539954": [3, 20], "xm_003723358": [3, 20], "xm_003827011": [3, 20], "xm_021875076": 3, "xm_776818": [3, 20], "xmax": 117, "xmfa": [47, 62], "xmin": 117, "xml": [3, 9, 11, 17, 20, 25, 32, 68, 69, 70, 71, 83, 84, 89, 105, 116, 117, 149, 150, 183, 197, 198, 217, 220, 235, 237, 238, 252, 253, 255, 258, 274, 276, 283, 289, 291, 296], "xml2": [3, 68], "xml_21500_blastn_001": 68, "xml_2212l_blastx_001": 68, "xml_2218_blastp_002": 68, "xml_2222_blastx_001": 3, "xml_2226_blastp_004": 217, "xml_2900_blastx_001_v2": 3, "xmldeclhandl": [83, 84], "xmsscanner": [27, 283, 296], "xo": 0, "xp_001487907": 7, "xp_009175831": 3, "xp_519631": 7, "xpk": [125, 126], "xpkentri": [27, 124, 126], "xpkheadlin": 126, "xpktool": [27, 124, 125], "xprtool": 125, "xr": 104, "xref": 234, "xrh_class": 169, "xsd": [84, 197, 234], "xt": 0, "xv": 122, "xx": [0, 11, 12, 14, 94, 209, 250, 295, 297], "xxmotif": 11, "xxx": [12, 24, 71, 85, 94, 107, 278], "xxxcxxxxccxxxxxcxxxxxxcxxx": 0, "xxxcxxxxccxxxxxcxxxxxxcxxxcxxxxcxxxxxcx": 0, "xxxx": [169, 273], "xxxxx": 169, "xyz": [15, 152, 168, 169, 176], "xz": [15, 169, 176], "y": [4, 6, 7, 8, 11, 12, 13, 14, 15, 22, 36, 68, 73, 76, 80, 99, 104, 115, 117, 120, 122, 129, 135, 136, 144, 145, 154, 160, 169, 172, 176, 182, 183, 216, 261, 265, 282, 297, 300, 303, 304], "y0": [16, 300], "y_": [16, 99], "y_i": 4, "y_list": 15, "y_on_x1": 216, "y_on_x2": 216, "ya19a_yeast": 277, "yaax": 22, "yakuba": 13, "yal001c": 4, "yal002w": 4, "yal003w": 4, "yal004c": 4, "yal005c": 4, "yal010c": 4, "yal019w": 277, "yal068c": 23, "yamamoto": 25, "yang": [2, 13, 34, 196, 281], "yang2000": [2, 13], "yaxis_label": 283, "yaxis_scal": 283, "yaxis_tic_interv": 283, "yb": 104, "ycar": 122, "ycf1": 7, "ycf2": 238, "ycm": [15, 169], "ydpwnlrfqskyksrda": 95, "ye": [0, 7, 69, 80, 122], "year": [6, 7, 8, 83, 197], "yeast": [4, 11, 277], "yee": 2, "yellow": [9, 122, 183], "yersinia": [6, 8, 21, 238], "yet": [4, 8, 11, 14, 17, 19, 23, 24, 30, 36, 44, 45, 80, 88, 107, 130, 132, 191, 230, 253, 274, 290], "yetfasco": [11, 283], "yeung": [2, 4], "yeung2001": [2, 4], "yfegffatlg": 250, "yfkmemgknm": 0, "yfkmemgknmcaiatcasypvvaa": 0, "yfliergknm": 0, "yfliergknmcglaacasypiplv": 0, "yiegffatlg": 250, "yield": [4, 6, 7, 11, 20, 30, 61, 64, 96, 185, 217, 219, 220, 221, 222, 226, 230, 232, 233, 241, 247, 250, 251, 253, 270, 271, 272, 273], "yiylrrgknt": 0, "yiylrrgkntcgvsnfvstsii": 0, "ykri": 206, "ylabel": 6, "ylim": 6, "ylr": 260, "ymax": 117, "ymetric": 80, "ymin": 117, "yn00": [13, 17, 34, 181, 192, 280, 281], "yn00error": [181, 192, 196], "ynpviyilmn": 250, "ynpviyimln": 250, "ynpviyivln": 250, "yongchao": 32, "yorf": 4, "york": 2, "you": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 38, 39, 40, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 80, 81, 83, 90, 92, 93, 94, 95, 97, 99, 101, 102, 108, 109, 110, 119, 121, 123, 137, 140, 143, 146, 149, 151, 154, 157, 158, 159, 169, 176, 182, 183, 186, 197, 205, 207, 209, 214, 217, 218, 221, 222, 226, 229, 236, 237, 238, 240, 241, 244, 245, 246, 247, 249, 250, 251, 253, 255, 256, 260, 261, 264, 265, 269, 270, 274, 278, 281, 283, 288, 289, 290, 291, 292, 297, 298, 299, 302, 303, 305, 306, 307], "your": [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 13, 14, 17, 19, 20, 21, 22, 24, 30, 32, 56, 67, 69, 71, 80, 83, 125, 137, 149, 152, 158, 167, 169, 178, 182, 217, 218, 221, 222, 238, 251, 260, 264, 265, 270, 276, 278, 285, 288, 297, 298], "your_name_her": 129, "your_pssm": [12, 31], "yourdatabas": 11, "yourhostnam": 11, "yourpassword": 11, "yourself": [3, 5, 12, 23, 251, 260, 278, 302, 303], "yourusernam": 11, "yp_025292": 260, "yp_ppcp05": 21, "ypdyyfritnrehkaelkekfqrmcdksmikkrymylteeilkenpsmceymapsldarq": 23, "yppsvdwrkk": 0, "yqkv": 13, "yr": 14, "yrf": 6, "yripadvdpl": 250, "ysstschktp": 0, "yt": 104, "ytsdhcgttp": 0, "yukako": 2, "yv": 122, "yy": 152, "yyh": 6, "yyi": 12, "yytlkpevnn": 250, "yytlnpnfnn": 250, "yyyi": [88, 152], "yyyyyyyyywyyyywwyyywywyww": 251, "yyyyyyyyyywyyyywywwuwwwqq": 251, "yyyyyyyyyyyyywyywyysyyysi": 251, "yyyyyyyyyyyyyyyyyywwwwywi": 251, "yyyyyyyyyyyyyyyyyywywyysu": 251, "z": [0, 13, 15, 53, 135, 136, 144, 160, 169, 172, 176, 182, 197, 214, 268, 270], "z0": [169, 197], "z5100": 10, "z54145": 21, "z78439": [19, 23], "z78442": 23, "z78453": 23, "z78455": 23, "z78458": 23, "z78464": 23, "z78471": 23, "z78475": 23, "z78484": 23, "z78488": 23, "z78521": 23, "z78527": 23, "z78529": 23, "z78530": 23, "z78531": 23, "z78532": 23, "z78533": [19, 23], "z_score": 226, "z_slice": 145, "za": [169, 197], "zero": [3, 4, 7, 11, 12, 13, 14, 15, 20, 21, 22, 23, 30, 31, 35, 39, 45, 46, 51, 52, 61, 67, 68, 69, 73, 169, 199, 217, 221, 236, 237, 240, 241, 248, 250, 251, 253, 260, 261, 264, 270, 290, 297, 300], "zeta": 12, "zf": 11, "zfp": 11, "zhang": [3, 68], "zheng": [3, 68], "zhu": 2, "ziheng": 2, "ziliani": 262, "zimmerman": 265, "zinc": [11, 272, 283], "zip": [3, 8, 23, 122, 260, 278], "zipfil": 3, "zipper": 11, "zlib": [0, 36, 37, 38, 270, 278], "zmasek": 197, "zn_fing": 272, "zoom": 261, "zoop": [11, 283], "zrxzrxaacgtaacgt": 236, "zrxzrxaacguaacgu": 236, "zwieter": [299, 300], "zyxwvutsrqponmlkjhgfecb": 251, "zyxwvutsrqponmlkjihgfedcba": 251, "zzz": 12, "zzzzzzzzzzzxzvzzmvzrxrrrr": 251, "\u00e5": 15}, "titles": ["Sequence alignments", "Appendix: Useful stuff about Python", "Bibliography", "BLAST (new)", "Cluster analysis", "Where to go from here \u2013 contributing to Biopython", "Cookbook \u2013 Cool things to do with it", "Accessing NCBI\u2019s Entrez databases", "Graphics including GenomeDiagram", "Introduction", "KEGG", "Sequence motif analysis using Bio.motifs", "Multiple Sequence Alignment objects", "Pairwise sequence alignment", "Pairwise alignments using pairwise2", "Going 3D: The PDB module", "Bio.phenotype: analyze phenotypic data", "Phylogenetics with Bio.Phylo", "Bio.PopGen: Population genetics", "Quick Start \u2013 What can you do with Biopython?", "BLAST and other sequence search tools", "Sequence annotation objects", "Sequence objects", "Sequence Input/Output", "The Biopython testing framework", "Swiss-Prot and ExPASy", "Biopython Tutorial & Cookbook", "Bio package", "Bio.Affy package", "Bio.Affy.CelFile module", "Bio.Align package", "Bio.Align.AlignInfo module", "Bio.Align.Applications package", "Bio.Align.a2m module", "Bio.Align.analysis module", "Bio.Align.bed module", "Bio.Align.bigbed module", "Bio.Align.bigmaf module", "Bio.Align.bigpsl module", "Bio.Align.chain module", "Bio.Align.clustal module", "Bio.Align.emboss module", "Bio.Align.exonerate module", "Bio.Align.fasta module", "Bio.Align.hhr module", "Bio.Align.interfaces module", "Bio.Align.maf module", "Bio.Align.mauve module", "Bio.Align.msf module", "Bio.Align.nexus module", "Bio.Align.phylip module", "Bio.Align.psl module", "Bio.Align.sam module", "Bio.Align.stockholm module", "Bio.Align.substitution_matrices package", "Bio.Align.tabular module", "Bio.AlignIO package", "Bio.AlignIO.ClustalIO module", "Bio.AlignIO.EmbossIO module", "Bio.AlignIO.FastaIO module", "Bio.AlignIO.Interfaces module", "Bio.AlignIO.MafIO module", "Bio.AlignIO.MauveIO module", "Bio.AlignIO.MsfIO module", "Bio.AlignIO.NexusIO module", "Bio.AlignIO.PhylipIO module", "Bio.AlignIO.StockholmIO module", "Bio.Application package", "Bio.Blast package", "Bio.Blast.Applications module", "Bio.Blast.NCBIWWW module", "Bio.Blast.NCBIXML module", "Bio.CAPS package", "Bio.Cluster package", "Bio.Compass package", "Bio.Data package", "Bio.Data.CodonTable module", "Bio.Data.IUPACData module", "Bio.Data.PDBData module", "Bio.Emboss package", "Bio.Emboss.Applications module", "Bio.Emboss.Primer3 module", "Bio.Emboss.PrimerSearch module", "Bio.Entrez package", "Bio.Entrez.Parser module", "Bio.ExPASy package", "Bio.ExPASy.Enzyme module", "Bio.ExPASy.Prodoc module", "Bio.ExPASy.Prosite module", "Bio.ExPASy.ScanProsite module", "Bio.ExPASy.cellosaurus module", "Bio.File module", "Bio.GenBank package", "Bio.GenBank.Record module", "Bio.GenBank.Scanner module", "Bio.GenBank.utils module", "Bio.Geo package", "Bio.Geo.Record module", "Bio.Graphics package", "Bio.Graphics.BasicChromosome module", "Bio.Graphics.ColorSpiral module", "Bio.Graphics.Comparative module", "Bio.Graphics.DisplayRepresentation module", "Bio.Graphics.Distribution module", "Bio.Graphics.GenomeDiagram package", "Bio.Graphics.KGML_vis module", "Bio.HMM package", "Bio.HMM.DynamicProgramming module", "Bio.HMM.MarkovModel module", "Bio.HMM.Trainer module", "Bio.HMM.Utilities module", "Bio.KEGG package", "Bio.KEGG.Compound package", "Bio.KEGG.Enzyme package", "Bio.KEGG.Gene package", "Bio.KEGG.KGML package", "Bio.KEGG.KGML.KGML_parser module", "Bio.KEGG.KGML.KGML_pathway module", "Bio.KEGG.Map package", "Bio.KEGG.REST module", "Bio.LogisticRegression module", "Bio.MarkovModel module", "Bio.MaxEntropy module", "Bio.Medline package", "Bio.NMR package", "Bio.NMR.NOEtools module", "Bio.NMR.xpktools module", "Bio.NaiveBayes module", "Bio.Nexus package", "Bio.Nexus.Nexus module", "Bio.Nexus.Nodes module", "Bio.Nexus.StandardData module", "Bio.Nexus.Trees module", "Bio.PDB package", "Bio.PDB.AbstractPropertyMap module", "Bio.PDB.Atom module", "Bio.PDB.Chain module", "Bio.PDB.DSSP module", "Bio.PDB.Dice module", "Bio.PDB.Entity module", "Bio.PDB.FragmentMapper module", "Bio.PDB.HSExposure module", "Bio.PDB.MMCIF2Dict module", "Bio.PDB.MMCIFParser module", "Bio.PDB.Model module", "Bio.PDB.NACCESS module", "Bio.PDB.NeighborSearch module", "Bio.PDB.PDBExceptions module", "Bio.PDB.PDBIO module", "Bio.PDB.PDBList module", "Bio.PDB.PDBMLParser module", "Bio.PDB.PDBParser module", "Bio.PDB.PICIO module", "Bio.PDB.PSEA module", "Bio.PDB.Polypeptide module", "Bio.PDB.Residue module", "Bio.PDB.ResidueDepth module", "Bio.PDB.SASA module", "Bio.PDB.SCADIO module", "Bio.PDB.Selection module", "Bio.PDB.Structure module", "Bio.PDB.StructureAlignment module", "Bio.PDB.StructureBuilder module", "Bio.PDB.Superimposer module", "Bio.PDB.alphafold_db module", "Bio.PDB.binary_cif module", "Bio.PDB.cealign module", "Bio.PDB.ic_data module", "Bio.PDB.ic_rebuild module", "Bio.PDB.internal_coords module", "Bio.PDB.mmcifio module", "Bio.PDB.mmtf package", "Bio.PDB.mmtf.DefaultParser module", "Bio.PDB.mmtf.mmtfio module", "Bio.PDB.parse_pdb_header module", "Bio.PDB.qcprot module", "Bio.PDB.vectors module", "Bio.Pathway package", "Bio.Pathway.Rep package", "Bio.Pathway.Rep.Graph module", "Bio.Pathway.Rep.MultiGraph module", "Bio.Phylo package", "Bio.Phylo.Applications package", "Bio.Phylo.BaseTree module", "Bio.Phylo.CDAO module", "Bio.Phylo.CDAOIO module", "Bio.Phylo.Consensus module", "Bio.Phylo.NeXML module", "Bio.Phylo.NeXMLIO module", "Bio.Phylo.Newick module", "Bio.Phylo.NewickIO module", "Bio.Phylo.NexusIO module", "Bio.Phylo.PAML package", "Bio.Phylo.PAML.baseml module", "Bio.Phylo.PAML.chi2 module", "Bio.Phylo.PAML.codeml module", "Bio.Phylo.PAML.yn00 module", "Bio.Phylo.PhyloXML module", "Bio.Phylo.PhyloXMLIO module", "Bio.Phylo.TreeConstruction module", "Bio.PopGen package", "Bio.PopGen.GenePop package", "Bio.PopGen.GenePop.Controller module", "Bio.PopGen.GenePop.EasyController module", "Bio.PopGen.GenePop.FileParser module", "Bio.PopGen.GenePop.LargeFileParser module", "Bio.Restriction package", "Bio.Restriction.PrintFormat module", "Bio.Restriction.Restriction_Dictionary module", "Bio.SCOP package", "Bio.SCOP.Cla module", "Bio.SCOP.Des module", "Bio.SCOP.Dom module", "Bio.SCOP.Hie module", "Bio.SCOP.Raf module", "Bio.SCOP.Residues module", "Bio.SVDSuperimposer package", "Bio.SearchIO package", "Bio.SearchIO.BlastIO package", "Bio.SearchIO.BlastIO.blast_tab module", "Bio.SearchIO.BlastIO.blast_xml module", "Bio.SearchIO.BlatIO module", "Bio.SearchIO.ExonerateIO package", "Bio.SearchIO.ExonerateIO.exonerate_cigar module", "Bio.SearchIO.ExonerateIO.exonerate_text module", "Bio.SearchIO.ExonerateIO.exonerate_vulgar module", "Bio.SearchIO.FastaIO module", "Bio.SearchIO.HHsuiteIO package", "Bio.SearchIO.HHsuiteIO.hhsuite2_text module", "Bio.SearchIO.HmmerIO package", "Bio.SearchIO.HmmerIO.hmmer2_text module", "Bio.SearchIO.HmmerIO.hmmer3_domtab module", "Bio.SearchIO.HmmerIO.hmmer3_tab module", "Bio.SearchIO.HmmerIO.hmmer3_text module", "Bio.SearchIO.InterproscanIO package", "Bio.SearchIO.InterproscanIO.interproscan_xml module", "Bio.Seq module", "Bio.SeqFeature module", "Bio.SeqIO package", "Bio.SeqIO.AbiIO module", "Bio.SeqIO.AceIO module", "Bio.SeqIO.FastaIO module", "Bio.SeqIO.GckIO module", "Bio.SeqIO.GfaIO module", "Bio.SeqIO.IgIO module", "Bio.SeqIO.InsdcIO module", "Bio.SeqIO.Interfaces module", "Bio.SeqIO.NibIO module", "Bio.SeqIO.PdbIO module", "Bio.SeqIO.PhdIO module", "Bio.SeqIO.PirIO module", "Bio.SeqIO.QualityIO module", "Bio.SeqIO.SeqXmlIO module", "Bio.SeqIO.SffIO module", "Bio.SeqIO.SnapGeneIO module", "Bio.SeqIO.SwissIO module", "Bio.SeqIO.TabIO module", "Bio.SeqIO.TwoBitIO module", "Bio.SeqIO.UniprotIO module", "Bio.SeqIO.XdnaIO module", "Bio.SeqRecord module", "Bio.SeqUtils package", "Bio.SeqUtils.CheckSum module", "Bio.SeqUtils.IsoelectricPoint module", "Bio.SeqUtils.MeltingTemp module", "Bio.SeqUtils.ProtParam module", "Bio.SeqUtils.ProtParamData module", "Bio.SeqUtils.lcc module", "Bio.Sequencing package", "Bio.Sequencing.Ace module", "Bio.Sequencing.Applications package", "Bio.Sequencing.Phd module", "Bio.SwissProt package", "Bio.SwissProt.KeyWList module", "Bio.TogoWS package", "Bio.UniGene package", "Bio.UniProt package", "Bio.UniProt.GOA module", "Bio.bgzf module", "Bio.codonalign package", "Bio.codonalign.codonalignment module", "Bio.codonalign.codonseq module", "Bio.kNN module", "Bio.motifs package", "Bio.motifs.alignace module", "Bio.motifs.applications package", "Bio.motifs.clusterbuster module", "Bio.motifs.jaspar package", "Bio.motifs.jaspar.db module", "Bio.motifs.mast module", "Bio.motifs.matrix module", "Bio.motifs.meme module", "Bio.motifs.minimal module", "Bio.motifs.pfm module", "Bio.motifs.thresholds module", "Bio.motifs.transfac module", "Bio.motifs.xms module", "Bio.pairwise2 module", "Bio.phenotype package", "Bio.phenotype.phen_micro module", "Bio.phenotype.pm_fitting module", "BioSQL package", "BioSQL.BioSeq module", "BioSQL.BioSeqDatabase module", "BioSQL.DBUtils module", "BioSQL.Loader module", "API documentation", "Biopython Documentation"], "titleterms": {"": [4, 7, 15, 17], "10": 15, "3d": 15, "50": 15, "A": [8, 15, 19, 20], "In": 23, "The": [0, 3, 4, 7, 11, 13, 15, 20, 21, 24], "a2m": [0, 33], "abiio": 239, "about": [0, 1, 7, 19, 20, 237, 278], "absolut": 4, "abstract": 7, "abstractpropertymap": 134, "ac": 269, "access": [7, 11, 15, 16, 25], "aceio": 240, "acid": 13, "act": 22, "ad": [0, 21, 22], "adaptor": 6, "advanc": 238, "affi": [28, 29], "affin": 13, "aim": 278, "algorithm": 4, "align": [0, 12, 13, 14, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 238], "alignac": 284, "aligninfo": 31, "alignio": [56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66], "all": 15, "alphabet": 13, "alphafold_db": 164, "also": 197, "altloc": 15, "ambigu": 12, "amino": 13, "an": [0, 7, 11, 13, 15], "analysi": [4, 11, 34], "analyz": [13, 15, 16], "angl": [4, 15], "annot": [8, 21], "api": [10, 306], "appendix": 1, "applic": [17, 32, 67, 69, 80, 182, 270, 285], "approach": 15, "ar": 7, "argument": 3, "arrai": [0, 12, 13], "arrow": 8, "ask": 9, "associ": [7, 11, 15], "atom": [15, 135], "atomarrai": 15, "attribut": [0, 13, 15], "automat": 15, "b": 15, "bank": 15, "base": 237, "baseml": 193, "basetre": 183, "basic": 13, "basicchromosom": 99, "bed": [0, 35], "between": [4, 8, 12, 23], "bgzf": 278, "bibliographi": 2, "bigb": [0, 36], "bigmaf": [0, 37], "bigpsl": [0, 38], "binary_cif": 165, "binarycif": 15, "bio": [11, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300], "biolog": 19, "biopython": [5, 9, 19, 24, 26, 307], "bioseq": 302, "bioseqdatabas": 303, "biosql": [6, 301, 302, 303, 304, 305], "blank": 15, "blast": [0, 3, 20, 68, 69, 70, 71, 218], "blast_tab": 219, "blast_xml": 220, "blastio": [218, 219, 220], "blatio": 221, "block": 4, "bond": 15, "bottom": 8, "branch": 17, "broken": 15, "browser": 0, "bug": 5, "build": 15, "ca": 15, "calcul": [4, 12, 13, 15], "can": [9, 19], "cap": 72, "caption": 8, "case": [6, 15, 22], "categori": 25, "cd": 6, "cdao": 184, "cdaoio": 185, "cealign": 166, "celfil": 29, "cellosauru": 90, "centroid": 4, "chain": [0, 15, 39, 136], "chang": 22, "charact": 7, "checksum": [23, 262], "chi2": 194, "chromosom": 8, "cigar": 222, "citat": 7, "citi": 4, "cla": 210, "clade": 17, "class": [0, 3, 237], "clustal": 40, "clustalio": 57, "clustalw": [0, 12], "cluster": [4, 73], "clusterbust": 286, "code": [5, 8, 15], "codeml": 195, "codon": 13, "codonalign": [13, 279, 280, 281], "codonseq": 281, "codont": 76, "coeffici": 4, "color": 17, "colorspir": 100, "column": 11, "common": [0, 15], "commonli": 11, "compar": [0, 11, 22, 101], "comparison": 21, "compass": 74, "compat": 11, "complement": [0, 11, 21, 22, 23], "complet": 15, "compon": 4, "compound": 112, "compoundloc": 21, "compress": 23, "concaten": 22, "connect": 19, "consensu": [11, 12, 186], "contact": 15, "contain": [7, 15], "content": [12, 22, 26, 27, 28, 30, 32, 54, 56, 67, 68, 72, 73, 74, 75, 79, 83, 85, 92, 96, 98, 104, 106, 111, 112, 113, 114, 115, 118, 123, 124, 128, 133, 171, 177, 178, 181, 182, 192, 200, 201, 206, 209, 216, 217, 218, 222, 227, 229, 234, 238, 261, 268, 270, 272, 274, 275, 276, 279, 283, 285, 287, 298, 301, 306, 307], "contribut": 5, "control": [15, 16, 202], "convent": [20, 217], "convers": [56, 217, 238], "convert": [6, 8, 12, 20, 23], "cookbook": [5, 6, 26], "cool": 6, "coordin": [0, 15, 217], "copi": 15, "correct": 15, "correl": 4, "corrupt": 7, "cosin": 4, "count": [0, 7, 12], "creat": [0, 1, 11, 21], "cross": 8, "crystal": 15, "data": [0, 4, 6, 15, 16, 23, 75, 76, 77, 78], "databas": [6, 7, 11, 19, 23, 25], "date": 15, "db": 288, "dbutil": 304, "de": [11, 211], "deal": [3, 20], "default": 15, "defaultpars": 172, "defin": [13, 22], "demo": 17, "depth": 15, "describ": 21, "determin": 15, "diagram": 8, "dice": 138, "dictionari": 23, "dihedr": 15, "directli": 22, "discuss": 23, "disord": 15, "displayrepresent": 102, "distanc": [4, 15], "distribut": [5, 103], "do": [6, 19], "doctest": 24, "document": [5, 25, 306, 307], "dom": 212, "domtab": 229, "don": 19, "dot": 6, "down": 8, "download": [7, 15], "dssp": [15, 137], "dtd": 7, "duplic": 15, "dynamicprogram": 107, "e": 15, "each": [11, 15], "easycontrol": 203, "efetch": 7, "egqueri": 7, "einfo": 7, "elink": 7, "emboss": [0, 12, 41, 79, 80, 81, 82], "embossio": 58, "end": 7, "entir": 15, "entiti": 139, "entrez": [7, 83, 84], "entri": 6, "entropi": 11, "enzym": [25, 86, 113], "epost": 7, "error": [7, 15], "escap": 7, "esearch": 7, "espel": 7, "esummari": 7, "etc": 15, "euclidean": 4, "exact": 11, "exampl": [4, 5, 7, 8, 13, 15, 19, 90, 137, 206, 265, 278], "exoner": [0, 42, 222], "exonerate_cigar": 223, "exonerate_text": 224, "exonerate_vulgar": 225, "exonerateio": [222, 223, 224, 225], "expasi": [25, 85, 86, 87, 88, 89, 90], "export": 17, "exposur": 15, "extend": 0, "extens": 0, "extern": 17, "extract": [15, 16, 23], "factor": 15, "faq": 9, "fast": 15, "fasta": [0, 6, 19, 21, 23, 43, 226], "fastaio": [59, 226, 241], "fastq": [6, 23], "fatal": 15, "featur": [5, 8, 17, 21, 237], "field": 11, "file": [0, 4, 6, 7, 11, 12, 13, 15, 19, 20, 21, 23, 25, 56, 91, 238, 298], "filepars": 204, "filter": [3, 6], "find": [0, 7, 9, 11, 22], "format": [0, 3, 11, 12, 15, 19, 21, 23, 56, 217, 218, 221, 222, 226, 229, 234, 238, 298], "found": 11, "four": 11, "fragmentmapp": 140, "frame": [6, 217], "framework": 24, "frequenc": 0, "frequent": 9, "from": [0, 1, 5, 7, 11, 12, 13, 15, 21, 23], "full": 7, "function": [4, 17], "further": 8, "futur": 17, "fuzzi": 21, "g": 15, "gap": [0, 13], "gc": 6, "gcg": 0, "gckio": 242, "genbank": [7, 19, 21, 23, 92, 93, 94, 95], "gene": 114, "genepop": [18, 201, 202, 203, 204, 205], "gener": [4, 11, 13, 15, 19], "genet": 18, "genom": 6, "genomediagram": [8, 104], "geo": [7, 96, 97], "get": [0, 12, 23], "gfaio": 243, "glc": 15, "global": 7, "glucos": 15, "go": [5, 15], "goa": 277, "graph": 179, "graphic": [8, 15, 98, 99, 100, 101, 102, 103, 104, 105], "guidelin": 7, "ha": 11, "half": 15, "handl": [1, 4, 7], "heck": 1, "help": 5, "here": 5, "hetero": 15, "hh": 0, "hhr": 44, "hhsuite2_text": 228, "hhsuiteio": [227, 228], "hie": 213, "hierarch": 4, "histogram": 6, "histori": 7, "hit": [3, 20], "hmm": [106, 107, 108, 109, 110], "hmmer2": 229, "hmmer2_text": 230, "hmmer3": 229, "hmmer3_domtab": 231, "hmmer3_tab": 232, "hmmer3_text": 233, "hmmerio": [229, 230, 231, 232, 233], "hold": 237, "how": 15, "hsexposur": 141, "hsp": [3, 20], "hspfragment": 20, "html": 7, "huge": 7, "i": [1, 7, 9, 15, 17, 19], "ic_data": 167, "ic_rebuild": 168, "id": 7, "ident": 0, "identifi": [6, 7], "igio": 244, "includ": 8, "index": [0, 6, 20, 23], "indic": 0, "inform": [0, 7, 12, 17, 237], "input": [23, 56, 217, 238, 298], "insdcio": 245, "instal": 9, "instanc": 11, "integ": 13, "integr": 17, "interfac": [45, 60, 246], "intern": 15, "internal_coord": [15, 169], "internet": 3, "interpol": 16, "interproscan": 234, "interproscan_xml": 235, "interproscanio": [234, 235], "introduct": [3, 8, 9, 278], "isoelectricpoint": 263, "item": 7, "iter": [13, 15, 23], "iupacdata": 77, "jaspar": [11, 287, 288], "k": 4, "keep": 15, "kegg": [10, 111, 112, 113, 114, 115, 116, 117, 118, 119], "kei": 23, "kendal": 4, "keywlist": 273, "keyword": 25, "kgml": [115, 116, 117], "kgml_parser": 116, "kgml_pathwai": 117, "kgml_vi": 105, "knn": 282, "kreitman": 13, "larg": 20, "largefilepars": 205, "layout": 0, "lcc": 267, "length": [6, 15], "letter": 0, "level": 23, "like": 22, "lineag": 7, "link": [8, 11], "list": [5, 7, 23, 25], "load": 13, "loader": 305, "local": [3, 15], "locat": [21, 237], "logisticregress": 120, "logo": 11, "loop": 15, "love": 19, "low": 23, "m10": 226, "maf": [0, 46], "mafio": 61, "mail": 5, "maintain": 5, "make": 6, "manipul": [12, 16], "map": [0, 4, 15, 118], "markovmodel": [108, 121], "mast": [11, 289], "match": [11, 13], "matric": [11, 12, 13], "matrix": [4, 11, 12, 13, 290], "mauv": [0, 47], "mauveio": 62, "maxentropi": 122, "mcdonald": 13, "mean": 4, "measur": 15, "median": 4, "medlin": [7, 123], "medoid": 4, "meltingtemp": 264, "meme": [11, 291], "memori": 23, "messag": 7, "meta": 13, "method": [17, 21], "microarrai": 16, "minim": 292, "mismatch": [0, 13], "miss": [4, 7], "mmcif": 15, "mmcif2dict": 142, "mmcifio": 170, "mmcifpars": 143, "mmtf": [15, 171, 172, 173], "mmtfio": 173, "mode": 278, "model": [15, 20, 144], "modif": 17, "modifi": [15, 23], "modul": [11, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305], "moieti": 15, "molecular": 15, "motif": [11, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296], "msf": [0, 48], "msfio": 63, "multi": 0, "multigraph": 180, "multipl": [0, 8, 12, 13, 238], "muscl": 12, "mutableseq": 22, "mutat": 15, "naccess": 145, "naivebay": 127, "namespac": 278, "navig": 15, "ncbi": [3, 7], "ncbiwww": 70, "ncbixml": 71, "needl": 12, "neighborhood": 15, "neighborsearch": 146, "net": 23, "new": [3, 12], "newcom": 5, "newick": 189, "newickio": 190, "nexml": 187, "nexmlio": 188, "next": 19, "nexu": [0, 49, 128, 129, 130, 131, 132], "nexusio": [64, 191], "nibio": 247, "nice": 8, "nmr": [124, 125, 126], "node": 130, "noetool": 125, "nonsynonym": 13, "note": [20, 65], "novo": 11, "nucleotid": [6, 7, 13, 22], "number": [4, 13], "o": 17, "object": [0, 11, 12, 13, 15, 17, 20, 21, 22, 23], "obtain": [3, 7, 11, 15], "off": 6, "old": [3, 8], "onto": 15, "open": 6, "oper": 0, "option": 8, "order": 217, "organ": [4, 7], "other": [3, 15, 20], "otherwis": 7, "out": 15, "output": [0, 3, 20, 23, 56, 217, 238, 298], "over": [3, 13, 15, 23], "overview": 19, "packag": [9, 27, 28, 30, 32, 54, 56, 67, 68, 72, 73, 74, 75, 79, 83, 85, 92, 96, 98, 104, 106, 111, 112, 113, 114, 115, 118, 123, 124, 128, 133, 171, 177, 178, 181, 182, 192, 200, 201, 206, 209, 216, 217, 218, 222, 227, 229, 234, 238, 261, 268, 270, 272, 274, 275, 276, 279, 283, 285, 287, 298, 301], "pairwis": [0, 13, 14], "pairwise2": [14, 297], "paml": [17, 192, 193, 194, 195, 196], "paramet": 16, "pars": [3, 6, 7, 10, 12, 15, 16, 19, 23, 25], "parse_pdb_head": 174, "parser": [7, 23, 84], "partial": 22, "partit": 4, "pathwai": [177, 178, 179, 180], "pattern": 0, "pdb": [15, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176], "pdbdata": 78, "pdbexcept": 147, "pdbio": [148, 248], "pdblist": 149, "pdbml": 15, "pdbmlparser": 150, "pdbparser": 151, "pearson": 4, "per": 13, "perform": [4, 13], "perl": 11, "pfm": [11, 293], "phd": 271, "phdio": 249, "phen_micro": 299, "phenotyp": [16, 298, 299, 300], "phylip": [0, 50], "phylipio": 65, "phylo": [17, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199], "phylogenet": 17, "phyloxml": [17, 197], "phyloxmlio": 198, "pic": 15, "picio": 152, "pirio": 250, "plan": 17, "platform": 5, "pleas": 19, "plot": [6, 15], "plu": 6, "pm_fit": 300, "point": 15, "polypeptid": [15, 154], "popgen": [18, 200, 201, 202, 203, 204, 205], "popul": 18, "posit": [11, 12, 21], "pqr": 15, "pre": 13, "predefin": 13, "prematur": 7, "present": 15, "primari": 7, "primer": 6, "primer3": 81, "primersearch": 82, "princip": 4, "print": [0, 15], "printformat": 207, "problem": 15, "prodoc": 87, "produc": 6, "properti": 4, "prosit": [25, 88], "prot": 25, "protein": 15, "protparam": 265, "protparamdata": 266, "provid": 19, "proxi": 7, "psea": 153, "psi": 3, "psl": [0, 51], "pssm": 11, "pubm": 7, "python": [1, 217], "qcprot": 175, "qual": 6, "qualiti": 6, "qualityio": 251, "queri": [7, 10], "queryresult": 20, "question": [9, 15], "quick": [12, 19], "raf": 214, "random": [4, 6], "rank": 4, "raw": [16, 23], "read": [0, 6, 11, 12, 13, 15, 20, 23], "rebuild": 15, "record": [3, 7, 10, 23, 25, 93, 97, 238, 298], "refer": [11, 21, 166, 237], "rel": 11, "relat": [6, 7, 15], "rep": [178, 179, 180], "report": 5, "repres": 4, "represent": [4, 15], "request": 5, "residu": [15, 155, 215], "residuedepth": 156, "resseq": 15, "rest": 119, "restrict": [206, 207, 208], "restriction_dictionari": 208, "result": [3, 4], "retriev": [7, 25], "revers": [0, 11, 13, 21, 22, 23], "round": 23, "row": 11, "rp": 3, "run": [3, 17, 24], "sam": [0, 52], "sasa": 157, "save": [3, 4], "scadio": 158, "scan": 25, "scanner": 94, "scanprosit": 89, "scop": [209, 210, 211, 212, 213, 214, 215], "score": [6, 11, 12, 13], "scratch": 21, "search": [7, 11, 17, 20, 25], "searchio": [20, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235], "secondari": 15, "see": 197, "seguid": 23, "select": [11, 15, 159], "self": 4, "seq": [22, 236], "seqfeatur": [8, 21, 237], "seqio": [238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259], "seqrecord": [21, 23, 260], "sequenc": [0, 6, 7, 11, 12, 13, 15, 19, 20, 21, 22, 23, 217, 237, 268, 269, 270, 271], "sequtil": [261, 262, 263, 264, 265, 266, 267], "seqxmlio": 252, "server": 25, "set": 8, "sff": 6, "sffio": 253, "shape": 0, "sigil": 8, "simpl": [6, 8, 19], "simpleloc": 21, "singl": [12, 238, 298], "site": [11, 13], "slice": [0, 11, 12, 21, 22], "snapgeneio": 254, "solut": 4, "some": 15, "sort": [0, 3, 6], "space": 0, "spearman": 4, "special": 7, "specif": [11, 12, 15], "specifi": [23, 237], "spell": 7, "sphere": 15, "standalon": 3, "standard": 20, "standarddata": 131, "start": 19, "stockholm": [0, 53], "stockholmio": 66, "stop": 19, "store": [6, 11], "strand": [13, 217], "string": [1, 12, 22, 23], "structur": [15, 160], "structurealign": 161, "structurebuild": 162, "stuff": 1, "style": [12, 217], "submodul": [27, 28, 30, 56, 68, 75, 79, 83, 85, 92, 96, 98, 106, 111, 115, 124, 128, 133, 171, 178, 181, 192, 201, 206, 209, 217, 218, 222, 227, 229, 234, 238, 261, 268, 272, 276, 279, 283, 287, 298, 301], "subpackag": [27, 30, 98, 111, 133, 177, 181, 200, 217, 268, 283], "subsequ": 22, "substitut": [0, 12, 13], "substitution_matric": 54, "subtract": 16, "suggest": 7, "suit": 0, "summari": [7, 12], "superimpos": [15, 163], "support": [15, 217, 218, 221, 222, 226, 229, 234], "svdsuperimpos": 216, "swiss": 25, "swissio": 255, "swissprot": [23, 272, 273], "synonym": 13, "t": 19, "tab": [218, 229], "tabio": 256, "tabl": [22, 26, 307], "tabular": [0, 55], "talk": 19, "tau": 4, "technic": 278, "term": 7, "test": [5, 13, 15, 21, 24], "text": [222, 229, 278], "tfb": 11, "thi": 278, "thing": 6, "threshold": [11, 294], "through": 15, "todo": 169, "togow": 274, "tool": [12, 20], "top": 8, "torsion": 15, "tox": 24, "track": 8, "trainer": 109, "transcript": 22, "transfac": [11, 295], "translat": [6, 22], "travers": 17, "tree": [17, 132], "treeconstruct": 199, "treeview": 4, "trim": 6, "trip": 23, "turn": 22, "tutori": [24, 26], "two": 15, "twobitio": 257, "type": 4, "ucsc": 0, "uncent": 4, "unigen": [7, 275], "uniprot": [25, 276, 277], "uniprotio": 258, "unit": 5, "unittest": 24, "unknown": 22, "up": [8, 15], "upload": 7, "upper": 6, "us": [1, 7, 11, 13, 14, 15, 17, 23, 24], "usag": [13, 19, 137], "util": [95, 110], "valu": [4, 15, 217], "vector": 176, "version": 3, "view": 17, "vulgar": 222, "warn": 278, "water": [12, 15], "webenv": 7, "weight": [4, 11], "well": [15, 16], "what": [1, 9, 17, 19], "where": 5, "who": 15, "within": 17, "without": 8, "work": [6, 19, 22], "write": [0, 3, 11, 12, 15, 16, 20, 23, 24], "xdnaio": 259, "xm": 296, "xmfa": 0, "xml": [7, 15, 218, 234], "xpktool": 126, "yn00": 196, "you": 19, "your": [12, 23]}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"3D printing protein structures": [[15, "d-printing-protein-structures"]], "A blank altloc for a disordered atom": [[15, "a-blank-altloc-for-a-disordered-atom"]], "A bottom up example": [[8, "a-bottom-up-example"]], "A nice example": [[8, "a-nice-example"]], "A note about standards and conventions": [[20, "a-note-about-standards-and-conventions"]], "A top down example": [[8, "a-top-down-example"]], "A usage example": [[19, "a-usage-example"]], "A2M": [[0, "a2m"]], "API Contents:": [[306, null]], "API documentation": [[306, "api-documentation"]], "Absolute Pearson correlation": [[4, "absolute-pearson-correlation"]], "Absolute uncentered correlation": [[4, "absolute-uncentered-correlation"]], "Accessing NCBI\u2019s Entrez databases": [[7, "accessing-ncbis-entrez-databases"]], "Accessing dihedrals, angles and bond lengths": [[15, "accessing-dihedrals-angles-and-bond-lengths"]], "Accessing interpolated data": [[16, "accessing-interpolated-data"]], "Accessing raw data": [[16, "accessing-raw-data"]], "Accessing the ExPASy server": [[25, "accessing-the-expasy-server"]], "Accessing the JASPAR database": [[11, "accessing-the-jaspar-database"]], "Accessing the Protein Data Bank": [[15, "accessing-the-protein-data-bank"]], "Accessing the all-atom AtomArray": [[15, "accessing-the-all-atom-atomarray"]], "Adding SeqRecord objects": [[21, "adding-seqrecord-objects"]], "Adding alignments": [[0, "adding-alignments"]], "Affine gap scores": [[13, "affine-gap-scores"]], "Aim of this module": [[278, "aim-of-this-module"]], "Aligned FASTA": [[0, "aligned-fasta"]], "Aligning a nucleotide sequence to an amino acid sequence": [[13, "aligning-a-nucleotide-sequence-to-an-amino-acid-sequence"]], "Aligning to the reverse strand": [[13, "aligning-to-the-reverse-strand"]], "Alignment Tools": [[12, "alignment-tools"]], "Alignment file formats": [[0, "alignment-file-formats"]], "Alignment objects": [[0, "alignment-objects"]], "Alignment shape": [[0, "alignment-shape"]], "Alignments as arrays": [[0, "alignments-as-arrays"], [12, "alignments-as-arrays"]], "Ambiguous Alignments": [[12, "ambiguous-alignments"]], "Analyzing a codon alignment": [[13, "analyzing-a-codon-alignment"]], "Analyzing structures": [[15, "analyzing-structures"]], "Annotated Chromosomes": [[8, "annotated-chromosomes"]], "Appendix: Useful stuff about Python": [[1, "appendix-useful-stuff-about-python"]], "Array objects": [[13, "array-objects"]], "Arrow sigils": [[8, "arrow-sigils"]], "Associated problems": [[15, "associated-problems"]], "Atom": [[15, "atom"]], "Automatic correction": [[15, "automatic-correction"]], "BLAST (new)": [[3, "blast-new"]], "BLAST (old)": [[3, "blast-old"]], "BLAST and other sequence search tools": [[20, "blast-and-other-sequence-search-tools"]], "BLAST arguments": [[3, "blast-arguments"]], "Base class to hold a Feature": [[237, "base-class-to-hold-a-feature"]], "Basic usage": [[13, "basic-usage"]], "Bibliography": [[2, "bibliography"]], "Bio package": [[27, "bio-package"]], "Bio.Affy package": [[28, "bio-affy-package"]], "Bio.Affy.CelFile module": [[29, "module-Bio.Affy.CelFile"]], "Bio.Align package": [[30, "bio-align-package"]], "Bio.Align.AlignInfo module": [[31, "module-Bio.Align.AlignInfo"]], "Bio.Align.Applications package": [[32, "bio-align-applications-package"]], "Bio.Align.a2m module": [[33, "module-Bio.Align.a2m"]], "Bio.Align.analysis module": [[34, "module-Bio.Align.analysis"]], "Bio.Align.bed module": [[35, "module-Bio.Align.bed"]], "Bio.Align.bigbed module": [[36, "module-Bio.Align.bigbed"]], "Bio.Align.bigmaf module": [[37, "module-Bio.Align.bigmaf"]], "Bio.Align.bigpsl module": [[38, "module-Bio.Align.bigpsl"]], "Bio.Align.chain module": [[39, "module-Bio.Align.chain"]], "Bio.Align.clustal module": [[40, "module-Bio.Align.clustal"]], "Bio.Align.emboss module": [[41, "module-Bio.Align.emboss"]], "Bio.Align.exonerate module": [[42, "module-Bio.Align.exonerate"]], "Bio.Align.fasta module": [[43, "module-Bio.Align.fasta"]], "Bio.Align.hhr module": [[44, "module-Bio.Align.hhr"]], "Bio.Align.interfaces module": [[45, "module-Bio.Align.interfaces"]], "Bio.Align.maf module": [[46, "module-Bio.Align.maf"]], "Bio.Align.mauve module": [[47, "module-Bio.Align.mauve"]], "Bio.Align.msf module": [[48, "module-Bio.Align.msf"]], "Bio.Align.nexus module": [[49, "module-Bio.Align.nexus"]], "Bio.Align.phylip module": [[50, "module-Bio.Align.phylip"]], "Bio.Align.psl module": [[51, "module-Bio.Align.psl"]], "Bio.Align.sam module": [[52, "module-Bio.Align.sam"]], "Bio.Align.stockholm module": [[53, "module-Bio.Align.stockholm"]], "Bio.Align.substitution_matrices package": [[54, "bio-align-substitution-matrices-package"]], "Bio.Align.tabular module": [[55, "module-Bio.Align.tabular"]], "Bio.AlignIO package": [[56, "bio-alignio-package"]], "Bio.AlignIO.ClustalIO module": [[57, "module-Bio.AlignIO.ClustalIO"]], "Bio.AlignIO.EmbossIO module": [[58, "module-Bio.AlignIO.EmbossIO"]], "Bio.AlignIO.FastaIO module": [[59, "module-Bio.AlignIO.FastaIO"]], "Bio.AlignIO.Interfaces module": [[60, "module-Bio.AlignIO.Interfaces"]], "Bio.AlignIO.MafIO module": [[61, "module-Bio.AlignIO.MafIO"]], "Bio.AlignIO.MauveIO module": [[62, "module-Bio.AlignIO.MauveIO"]], "Bio.AlignIO.MsfIO module": [[63, "module-Bio.AlignIO.MsfIO"]], "Bio.AlignIO.NexusIO module": [[64, "module-Bio.AlignIO.NexusIO"]], "Bio.AlignIO.PhylipIO module": [[65, "module-Bio.AlignIO.PhylipIO"]], "Bio.AlignIO.StockholmIO module": [[66, "module-Bio.AlignIO.StockholmIO"]], "Bio.Application package": [[67, "bio-application-package"]], "Bio.Blast package": [[68, "bio-blast-package"]], "Bio.Blast.Applications module": [[69, "module-Bio.Blast.Applications"]], "Bio.Blast.NCBIWWW module": [[70, "module-Bio.Blast.NCBIWWW"]], "Bio.Blast.NCBIXML module": [[71, "module-Bio.Blast.NCBIXML"]], "Bio.CAPS package": [[72, "bio-caps-package"]], "Bio.Cluster package": [[73, "bio-cluster-package"]], "Bio.Compass package": [[74, "bio-compass-package"]], "Bio.Data package": [[75, "bio-data-package"]], "Bio.Data.CodonTable module": [[76, "module-Bio.Data.CodonTable"]], "Bio.Data.IUPACData module": [[77, "module-Bio.Data.IUPACData"]], "Bio.Data.PDBData module": [[78, "module-Bio.Data.PDBData"]], "Bio.Emboss package": [[79, "bio-emboss-package"]], "Bio.Emboss.Applications module": [[80, "module-Bio.Emboss.Applications"]], "Bio.Emboss.Primer3 module": [[81, "module-Bio.Emboss.Primer3"]], "Bio.Emboss.PrimerSearch module": [[82, "module-Bio.Emboss.PrimerSearch"]], "Bio.Entrez package": [[83, "bio-entrez-package"]], "Bio.Entrez.Parser module": [[84, "module-Bio.Entrez.Parser"]], "Bio.ExPASy package": [[85, "bio-expasy-package"]], "Bio.ExPASy.Enzyme module": [[86, "module-Bio.ExPASy.Enzyme"]], "Bio.ExPASy.Prodoc module": [[87, "module-Bio.ExPASy.Prodoc"]], "Bio.ExPASy.Prosite module": [[88, "module-Bio.ExPASy.Prosite"]], "Bio.ExPASy.ScanProsite module": [[89, "module-Bio.ExPASy.ScanProsite"]], "Bio.ExPASy.cellosaurus module": [[90, "module-Bio.ExPASy.cellosaurus"]], "Bio.File module": [[91, "module-Bio.File"]], "Bio.GenBank package": [[92, "bio-genbank-package"]], "Bio.GenBank.Record module": [[93, "module-Bio.GenBank.Record"]], "Bio.GenBank.Scanner module": [[94, "module-Bio.GenBank.Scanner"]], "Bio.GenBank.utils module": [[95, "module-Bio.GenBank.utils"]], "Bio.Geo package": [[96, "bio-geo-package"]], "Bio.Geo.Record module": [[97, "module-Bio.Geo.Record"]], "Bio.Graphics package": [[98, "bio-graphics-package"]], "Bio.Graphics.BasicChromosome module": [[99, "module-Bio.Graphics.BasicChromosome"]], "Bio.Graphics.ColorSpiral module": [[100, "module-Bio.Graphics.ColorSpiral"]], "Bio.Graphics.Comparative module": [[101, "module-Bio.Graphics.Comparative"]], "Bio.Graphics.DisplayRepresentation module": [[102, "module-Bio.Graphics.DisplayRepresentation"]], "Bio.Graphics.Distribution module": [[103, "module-Bio.Graphics.Distribution"]], "Bio.Graphics.GenomeDiagram package": [[104, "bio-graphics-genomediagram-package"]], "Bio.Graphics.KGML_vis module": [[105, "module-Bio.Graphics.KGML_vis"]], "Bio.HMM package": [[106, "bio-hmm-package"]], "Bio.HMM.DynamicProgramming module": [[107, "module-Bio.HMM.DynamicProgramming"]], "Bio.HMM.MarkovModel module": [[108, "module-Bio.HMM.MarkovModel"]], "Bio.HMM.Trainer module": [[109, "module-Bio.HMM.Trainer"]], "Bio.HMM.Utilities module": [[110, "module-Bio.HMM.Utilities"]], "Bio.KEGG package": [[111, "bio-kegg-package"]], "Bio.KEGG.Compound package": [[112, "bio-kegg-compound-package"]], "Bio.KEGG.Enzyme package": [[113, "bio-kegg-enzyme-package"]], "Bio.KEGG.Gene package": [[114, "bio-kegg-gene-package"]], "Bio.KEGG.KGML package": [[115, "bio-kegg-kgml-package"]], "Bio.KEGG.KGML.KGML_parser module": [[116, "module-Bio.KEGG.KGML.KGML_parser"]], "Bio.KEGG.KGML.KGML_pathway module": [[117, "module-Bio.KEGG.KGML.KGML_pathway"]], "Bio.KEGG.Map package": [[118, "bio-kegg-map-package"]], "Bio.KEGG.REST module": [[119, "module-Bio.KEGG.REST"]], "Bio.LogisticRegression module": [[120, "module-Bio.LogisticRegression"]], "Bio.MarkovModel module": [[121, "module-Bio.MarkovModel"]], "Bio.MaxEntropy module": [[122, "module-Bio.MaxEntropy"]], "Bio.Medline package": [[123, "bio-medline-package"]], "Bio.NMR package": [[124, "bio-nmr-package"]], "Bio.NMR.NOEtools module": [[125, "module-Bio.NMR.NOEtools"]], "Bio.NMR.xpktools module": [[126, "module-Bio.NMR.xpktools"]], "Bio.NaiveBayes module": [[127, "module-Bio.NaiveBayes"]], "Bio.Nexus package": [[128, "bio-nexus-package"]], "Bio.Nexus.Nexus module": [[129, "module-Bio.Nexus.Nexus"]], "Bio.Nexus.Nodes module": [[130, "module-Bio.Nexus.Nodes"]], "Bio.Nexus.StandardData module": [[131, "module-Bio.Nexus.StandardData"]], "Bio.Nexus.Trees module": [[132, "module-Bio.Nexus.Trees"]], "Bio.PDB package": [[133, "bio-pdb-package"]], "Bio.PDB.AbstractPropertyMap module": [[134, "module-Bio.PDB.AbstractPropertyMap"]], "Bio.PDB.Atom module": [[135, "module-Bio.PDB.Atom"]], "Bio.PDB.Chain module": [[136, "module-Bio.PDB.Chain"]], "Bio.PDB.DSSP module": [[137, "module-Bio.PDB.DSSP"]], "Bio.PDB.Dice module": [[138, "module-Bio.PDB.Dice"]], "Bio.PDB.Entity module": [[139, "module-Bio.PDB.Entity"]], "Bio.PDB.FragmentMapper module": [[140, "module-Bio.PDB.FragmentMapper"]], "Bio.PDB.HSExposure module": [[141, "module-Bio.PDB.HSExposure"]], "Bio.PDB.MMCIF2Dict module": [[142, "module-Bio.PDB.MMCIF2Dict"]], "Bio.PDB.MMCIFParser module": [[143, "module-Bio.PDB.MMCIFParser"]], "Bio.PDB.Model module": [[144, "module-Bio.PDB.Model"]], "Bio.PDB.NACCESS module": [[145, "module-Bio.PDB.NACCESS"]], "Bio.PDB.NeighborSearch module": [[146, "module-Bio.PDB.NeighborSearch"]], "Bio.PDB.PDBExceptions module": [[147, "module-Bio.PDB.PDBExceptions"]], "Bio.PDB.PDBIO module": [[148, "module-Bio.PDB.PDBIO"]], "Bio.PDB.PDBList module": [[149, "module-Bio.PDB.PDBList"]], "Bio.PDB.PDBMLParser module": [[150, "module-Bio.PDB.PDBMLParser"]], "Bio.PDB.PDBParser module": [[151, "module-Bio.PDB.PDBParser"]], "Bio.PDB.PICIO module": [[152, "module-Bio.PDB.PICIO"]], "Bio.PDB.PSEA module": [[153, "module-Bio.PDB.PSEA"]], "Bio.PDB.Polypeptide module": [[154, "module-Bio.PDB.Polypeptide"]], "Bio.PDB.Residue module": [[155, "module-Bio.PDB.Residue"]], "Bio.PDB.ResidueDepth module": [[156, "module-Bio.PDB.ResidueDepth"]], "Bio.PDB.SASA module": [[157, "module-Bio.PDB.SASA"]], "Bio.PDB.SCADIO module": [[158, "module-Bio.PDB.SCADIO"]], "Bio.PDB.Selection module": [[159, "module-Bio.PDB.Selection"]], "Bio.PDB.Structure module": [[160, "module-Bio.PDB.Structure"]], "Bio.PDB.StructureAlignment module": [[161, "module-Bio.PDB.StructureAlignment"]], "Bio.PDB.StructureBuilder module": [[162, "module-Bio.PDB.StructureBuilder"]], "Bio.PDB.Superimposer module": [[163, "module-Bio.PDB.Superimposer"]], "Bio.PDB.alphafold_db module": [[164, "module-Bio.PDB.alphafold_db"]], "Bio.PDB.binary_cif module": [[165, "module-Bio.PDB.binary_cif"]], "Bio.PDB.cealign module": [[166, "module-Bio.PDB.cealign"]], "Bio.PDB.ic_data module": [[167, "module-Bio.PDB.ic_data"]], "Bio.PDB.ic_rebuild module": [[168, "module-Bio.PDB.ic_rebuild"]], "Bio.PDB.internal_coords module": [[169, "module-Bio.PDB.internal_coords"]], "Bio.PDB.mmcifio module": [[170, "module-Bio.PDB.mmcifio"]], "Bio.PDB.mmtf package": [[171, "bio-pdb-mmtf-package"]], "Bio.PDB.mmtf.DefaultParser module": [[172, "module-Bio.PDB.mmtf.DefaultParser"]], "Bio.PDB.mmtf.mmtfio module": [[173, "module-Bio.PDB.mmtf.mmtfio"]], "Bio.PDB.parse_pdb_header module": [[174, "module-Bio.PDB.parse_pdb_header"]], "Bio.PDB.qcprot module": [[175, "module-Bio.PDB.qcprot"]], "Bio.PDB.vectors module": [[176, "module-Bio.PDB.vectors"]], "Bio.Pathway package": [[177, "bio-pathway-package"]], "Bio.Pathway.Rep package": [[178, "bio-pathway-rep-package"]], "Bio.Pathway.Rep.Graph module": [[179, "module-Bio.Pathway.Rep.Graph"]], "Bio.Pathway.Rep.MultiGraph module": [[180, "module-Bio.Pathway.Rep.MultiGraph"]], "Bio.Phylo package": [[181, "bio-phylo-package"]], "Bio.Phylo.Applications package": [[182, "bio-phylo-applications-package"]], "Bio.Phylo.BaseTree module": [[183, "module-Bio.Phylo.BaseTree"]], "Bio.Phylo.CDAO module": [[184, "module-Bio.Phylo.CDAO"]], "Bio.Phylo.CDAOIO module": [[185, "module-Bio.Phylo.CDAOIO"]], "Bio.Phylo.Consensus module": [[186, "module-Bio.Phylo.Consensus"]], "Bio.Phylo.NeXML module": [[187, "module-Bio.Phylo.NeXML"]], "Bio.Phylo.NeXMLIO module": [[188, "module-Bio.Phylo.NeXMLIO"]], "Bio.Phylo.Newick module": [[189, "module-Bio.Phylo.Newick"]], "Bio.Phylo.NewickIO module": [[190, "module-Bio.Phylo.NewickIO"]], "Bio.Phylo.NexusIO module": [[191, "module-Bio.Phylo.NexusIO"]], "Bio.Phylo.PAML package": [[192, "bio-phylo-paml-package"]], "Bio.Phylo.PAML.baseml module": [[193, "module-Bio.Phylo.PAML.baseml"]], "Bio.Phylo.PAML.chi2 module": [[194, "module-Bio.Phylo.PAML.chi2"]], "Bio.Phylo.PAML.codeml module": [[195, "module-Bio.Phylo.PAML.codeml"]], "Bio.Phylo.PAML.yn00 module": [[196, "module-Bio.Phylo.PAML.yn00"]], "Bio.Phylo.PhyloXML module": [[197, "module-Bio.Phylo.PhyloXML"]], "Bio.Phylo.PhyloXMLIO module": [[198, "module-Bio.Phylo.PhyloXMLIO"]], "Bio.Phylo.TreeConstruction module": [[199, "module-Bio.Phylo.TreeConstruction"]], "Bio.PopGen package": [[200, "bio-popgen-package"]], "Bio.PopGen.GenePop package": [[201, "bio-popgen-genepop-package"]], "Bio.PopGen.GenePop.Controller module": [[202, "module-Bio.PopGen.GenePop.Controller"]], "Bio.PopGen.GenePop.EasyController module": [[203, "module-Bio.PopGen.GenePop.EasyController"]], "Bio.PopGen.GenePop.FileParser module": [[204, "module-Bio.PopGen.GenePop.FileParser"]], "Bio.PopGen.GenePop.LargeFileParser module": [[205, "module-Bio.PopGen.GenePop.LargeFileParser"]], "Bio.PopGen: Population genetics": [[18, "bio-popgen-population-genetics"]], "Bio.Restriction package": [[206, "bio-restriction-package"]], "Bio.Restriction.PrintFormat module": [[207, "module-Bio.Restriction.PrintFormat"]], "Bio.Restriction.Restriction_Dictionary module": [[208, "module-Bio.Restriction.Restriction_Dictionary"]], "Bio.SCOP package": [[209, "bio-scop-package"]], "Bio.SCOP.Cla module": [[210, "module-Bio.SCOP.Cla"]], "Bio.SCOP.Des module": [[211, "module-Bio.SCOP.Des"]], "Bio.SCOP.Dom module": [[212, "module-Bio.SCOP.Dom"]], "Bio.SCOP.Hie module": [[213, "module-Bio.SCOP.Hie"]], "Bio.SCOP.Raf module": [[214, "module-Bio.SCOP.Raf"]], "Bio.SCOP.Residues module": [[215, "module-Bio.SCOP.Residues"]], "Bio.SVDSuperimposer package": [[216, "bio-svdsuperimposer-package"]], "Bio.SearchIO package": [[217, "bio-searchio-package"]], "Bio.SearchIO.BlastIO package": [[218, "bio-searchio-blastio-package"]], "Bio.SearchIO.BlastIO.blast_tab module": [[219, "module-Bio.SearchIO.BlastIO.blast_tab"]], "Bio.SearchIO.BlastIO.blast_xml module": [[220, "module-Bio.SearchIO.BlastIO.blast_xml"]], "Bio.SearchIO.BlatIO module": [[221, "module-Bio.SearchIO.BlatIO"]], "Bio.SearchIO.ExonerateIO package": [[222, "bio-searchio-exonerateio-package"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar module": [[223, "module-Bio.SearchIO.ExonerateIO.exonerate_cigar"]], "Bio.SearchIO.ExonerateIO.exonerate_text module": [[224, "module-Bio.SearchIO.ExonerateIO.exonerate_text"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar module": [[225, "module-Bio.SearchIO.ExonerateIO.exonerate_vulgar"]], "Bio.SearchIO.FastaIO module": [[226, "module-Bio.SearchIO.FastaIO"]], "Bio.SearchIO.HHsuiteIO package": [[227, "bio-searchio-hhsuiteio-package"]], "Bio.SearchIO.HHsuiteIO.hhsuite2_text module": [[228, "module-Bio.SearchIO.HHsuiteIO.hhsuite2_text"]], "Bio.SearchIO.HmmerIO package": [[229, "bio-searchio-hmmerio-package"]], "Bio.SearchIO.HmmerIO.hmmer2_text module": [[230, "module-Bio.SearchIO.HmmerIO.hmmer2_text"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab module": [[231, "module-Bio.SearchIO.HmmerIO.hmmer3_domtab"]], "Bio.SearchIO.HmmerIO.hmmer3_tab module": [[232, "module-Bio.SearchIO.HmmerIO.hmmer3_tab"]], "Bio.SearchIO.HmmerIO.hmmer3_text module": [[233, "module-Bio.SearchIO.HmmerIO.hmmer3_text"]], "Bio.SearchIO.InterproscanIO package": [[234, "bio-searchio-interproscanio-package"]], "Bio.SearchIO.InterproscanIO.interproscan_xml module": [[235, "module-Bio.SearchIO.InterproscanIO.interproscan_xml"]], "Bio.Seq module": [[236, "module-Bio.Seq"]], "Bio.SeqFeature module": [[237, "module-Bio.SeqFeature"]], "Bio.SeqIO package": [[238, "bio-seqio-package"]], "Bio.SeqIO.AbiIO module": [[239, "module-Bio.SeqIO.AbiIO"]], "Bio.SeqIO.AceIO module": [[240, "module-Bio.SeqIO.AceIO"]], "Bio.SeqIO.FastaIO module": [[241, "module-Bio.SeqIO.FastaIO"]], "Bio.SeqIO.GckIO module": [[242, "module-Bio.SeqIO.GckIO"]], "Bio.SeqIO.GfaIO module": [[243, "module-Bio.SeqIO.GfaIO"]], "Bio.SeqIO.IgIO module": [[244, "module-Bio.SeqIO.IgIO"]], "Bio.SeqIO.InsdcIO module": [[245, "module-Bio.SeqIO.InsdcIO"]], "Bio.SeqIO.Interfaces module": [[246, "module-Bio.SeqIO.Interfaces"]], "Bio.SeqIO.NibIO module": [[247, "module-Bio.SeqIO.NibIO"]], "Bio.SeqIO.PdbIO module": [[248, "module-Bio.SeqIO.PdbIO"]], "Bio.SeqIO.PhdIO module": [[249, "module-Bio.SeqIO.PhdIO"]], "Bio.SeqIO.PirIO module": [[250, "module-Bio.SeqIO.PirIO"]], "Bio.SeqIO.QualityIO module": [[251, "module-Bio.SeqIO.QualityIO"]], "Bio.SeqIO.SeqXmlIO module": [[252, "module-Bio.SeqIO.SeqXmlIO"]], "Bio.SeqIO.SffIO module": [[253, "module-Bio.SeqIO.SffIO"]], "Bio.SeqIO.SnapGeneIO module": [[254, "module-Bio.SeqIO.SnapGeneIO"]], "Bio.SeqIO.SwissIO module": [[255, "module-Bio.SeqIO.SwissIO"]], "Bio.SeqIO.TabIO module": [[256, "module-Bio.SeqIO.TabIO"]], "Bio.SeqIO.TwoBitIO module": [[257, "module-Bio.SeqIO.TwoBitIO"]], "Bio.SeqIO.UniprotIO module": [[258, "module-Bio.SeqIO.UniprotIO"]], "Bio.SeqIO.XdnaIO module": [[259, "module-Bio.SeqIO.XdnaIO"]], "Bio.SeqRecord module": [[260, "module-Bio.SeqRecord"]], "Bio.SeqUtils package": [[261, "bio-sequtils-package"]], "Bio.SeqUtils.CheckSum module": [[262, "module-Bio.SeqUtils.CheckSum"]], "Bio.SeqUtils.IsoelectricPoint module": [[263, "module-Bio.SeqUtils.IsoelectricPoint"]], "Bio.SeqUtils.MeltingTemp module": [[264, "module-Bio.SeqUtils.MeltingTemp"]], "Bio.SeqUtils.ProtParam module": [[265, "module-Bio.SeqUtils.ProtParam"]], "Bio.SeqUtils.ProtParamData module": [[266, "module-Bio.SeqUtils.ProtParamData"]], "Bio.SeqUtils.lcc module": [[267, "module-Bio.SeqUtils.lcc"]], "Bio.Sequencing package": [[268, "bio-sequencing-package"]], "Bio.Sequencing.Ace module": [[269, "module-Bio.Sequencing.Ace"]], "Bio.Sequencing.Applications package": [[270, "bio-sequencing-applications-package"]], "Bio.Sequencing.Phd module": [[271, "module-Bio.Sequencing.Phd"]], "Bio.SwissProt package": [[272, "bio-swissprot-package"]], "Bio.SwissProt.KeyWList module": [[273, "module-Bio.SwissProt.KeyWList"]], "Bio.TogoWS package": [[274, "bio-togows-package"]], "Bio.UniGene package": [[275, "bio-unigene-package"]], "Bio.UniProt package": [[276, "bio-uniprot-package"]], "Bio.UniProt.GOA module": [[277, "module-Bio.UniProt.GOA"]], "Bio.bgzf module": [[278, "module-Bio.bgzf"]], "Bio.codonalign package": [[279, "bio-codonalign-package"]], "Bio.codonalign.codonalignment module": [[280, "module-Bio.codonalign.codonalignment"]], "Bio.codonalign.codonseq module": [[281, "module-Bio.codonalign.codonseq"]], "Bio.kNN module": [[282, "module-Bio.kNN"]], "Bio.motifs package": [[283, "bio-motifs-package"]], "Bio.motifs.alignace module": [[284, "module-Bio.motifs.alignace"]], "Bio.motifs.applications package": [[285, "bio-motifs-applications-package"]], "Bio.motifs.clusterbuster module": [[286, "module-Bio.motifs.clusterbuster"]], "Bio.motifs.jaspar package": [[287, "bio-motifs-jaspar-package"]], "Bio.motifs.jaspar.db module": [[288, "module-Bio.motifs.jaspar.db"]], "Bio.motifs.mast module": [[289, "module-Bio.motifs.mast"]], "Bio.motifs.matrix module": [[290, "module-Bio.motifs.matrix"]], "Bio.motifs.meme module": [[291, "module-Bio.motifs.meme"]], "Bio.motifs.minimal module": [[292, "module-Bio.motifs.minimal"]], "Bio.motifs.pfm module": [[293, "module-Bio.motifs.pfm"]], "Bio.motifs.thresholds module": [[294, "module-Bio.motifs.thresholds"]], "Bio.motifs.transfac module": [[295, "module-Bio.motifs.transfac"]], "Bio.motifs.xms module": [[296, "module-Bio.motifs.xms"]], "Bio.pairwise2 module": [[297, "module-Bio.pairwise2"]], "Bio.phenotype package": [[298, "bio-phenotype-package"]], "Bio.phenotype.phen_micro module": [[299, "module-Bio.phenotype.phen_micro"]], "Bio.phenotype.pm_fitting module": [[300, "module-Bio.phenotype.pm_fitting"]], "Bio.phenotype: analyze phenotypic data": [[16, "bio-phenotype-analyze-phenotypic-data"]], "BioSQL package": [[301, "biosql-package"]], "BioSQL \u2013 storing sequences in a relational database": [[6, "biosql-storing-sequences-in-a-relational-database"]], "BioSQL.BioSeq module": [[302, "module-BioSQL.BioSeq"]], "BioSQL.BioSeqDatabase module": [[303, "module-BioSQL.BioSeqDatabase"]], "BioSQL.DBUtils module": [[304, "module-BioSQL.DBUtils"]], "BioSQL.Loader module": [[305, "module-BioSQL.Loader"]], "Biopython Documentation": [[307, "biopython-documentation"]], "Biopython Tutorial & Cookbook": [[26, "biopython-tutorial-cookbook"]], "Broken chains": [[15, "broken-chains"]], "Browser Extensible Data (BED)": [[0, "browser-extensible-data-bed"]], "Bug Reports + Feature Requests": [[5, "bug-reports-feature-requests"]], "Building a structure from a distance plot": [[15, "building-a-structure-from-a-distance-plot"]], "Calculating a Self-Organizing Map": [[4, "calculating-a-self-organizing-map"]], "Calculating a quick consensus sequence": [[12, "calculating-a-quick-consensus-sequence"]], "Calculating a substitution matrix from a multiple sequence alignment": [[12, "calculating-a-substitution-matrix-from-a-multiple-sequence-alignment"], [13, "calculating-a-substitution-matrix-from-a-multiple-sequence-alignment"]], "Calculating a substitution matrix from a pairwise sequence alignment": [[13, "calculating-a-substitution-matrix-from-a-pairwise-sequence-alignment"]], "Calculating cluster properties": [[4, "calculating-cluster-properties"]], "Calculating summary information": [[12, "calculating-summary-information"]], "Calculating the Half Sphere Exposure": [[15, "calculating-the-half-sphere-exposure"]], "Calculating the cluster centroids": [[4, "calculating-the-cluster-centroids"], [4, "id13"]], "Calculating the distance between clusters": [[4, "calculating-the-distance-between-clusters"], [4, "calculating-the-distance-between-clusters-1"]], "Calculating the distance matrix": [[4, "calculating-the-distance-matrix"], [4, "id12"]], "Calculating the number of nonsynonymous and synonymous substitutions per site": [[13, "calculating-the-number-of-nonsynonymous-and-synonymous-substitutions-per-site"]], "Calculating the residue depth": [[15, "calculating-the-residue-depth"]], "Chain": [[15, "chain"]], "Changing case": [[22, "changing-case"]], "Chromosomes": [[8, "chromosomes"]], "City-block distance": [[4, "city-block-distance"]], "ClustalW": [[0, "clustalw"], [12, "clustalw"]], "Cluster analysis": [[4, "cluster-analysis"]], "Codon alignments": [[13, "codon-alignments"]], "Coloring branches within a tree": [[17, "coloring-branches-within-a-tree"]], "Common alignment attributes": [[0, "common-alignment-attributes"]], "Common case": [[15, "common-case"]], "Common problems in PDB files": [[15, "common-problems-in-pdb-files"]], "Comparing Seq objects": [[22, "comparing-seq-objects"]], "Comparing alignments": [[0, "comparing-alignments"]], "Comparing motifs": [[11, "comparing-motifs"]], "Comparison": [[21, "comparison"]], "Compatibility with Perl TFBS modules": [[11, "compatibility-with-perl-tfbs-modules"]], "CompoundLocation object": [[21, "compoundlocation-object"]], "Concatenating or adding sequences": [[22, "concatenating-or-adding-sequences"]], "Connecting with biological databases": [[19, "connecting-with-biological-databases"]], "Contributing Code": [[5, "contributing-code"]], "Contributing Documentation": [[5, "contributing-documentation"]], "Contributing Unit Tests": [[5, "contributing-unit-tests"]], "Contributing cookbook examples": [[5, "contributing-cookbook-examples"]], "Control attributes in Bio.PDB.internal_coords.": [[15, "table-ic-attribs"]], "Control well subtraction": [[16, "control-well-subtraction"]], "Conventions": [[217, "conventions"]], "Conversion": [[56, "conversion"], [217, "conversion"], [238, "conversion"]], "Converting FASTA and QUAL files into FASTQ files": [[6, "converting-fasta-and-qual-files-into-fastq-files"]], "Converting FASTQ files": [[6, "converting-fastq-files"]], "Converting SFF files": [[6, "converting-sff-files"]], "Converting a file of sequences to their reverse complements": [[23, "converting-a-file-of-sequences-to-their-reverse-complements"]], "Converting between sequence alignment file formats": [[12, "converting-between-sequence-alignment-file-formats"]], "Converting between sequence file formats": [[23, "converting-between-sequence-file-formats"]], "Converting old code": [[8, "converting-old-code"]], "Cookbook \u2013 Cool things to do with it": [[6, "cookbook-cool-things-to-do-with-it"]], "Counting identities, mismatches, and gaps": [[0, "counting-identities-mismatches-and-gaps"]], "Counting substitutions": [[12, "counting-substitutions"]], "Creating a SeqRecord": [[21, "creating-a-seqrecord"]], "Creating a handle from a string": [[1, "creating-a-handle-from-a-string"]], "Creating a motif from instances": [[11, "creating-a-motif-from-instances"]], "Creating a sequence logo": [[11, "creating-a-sequence-logo"]], "Creating an Alignment object from aligned sequences": [[0, "creating-an-alignment-object-from-aligned-sequences"]], "Creating an Alignment object from sequences and coordinates": [[0, "creating-an-alignment-object-from-sequences-and-coordinates"]], "Cross-Links between tracks": [[8, "cross-links-between-tracks"]], "DSSP codes in Bio.PDB.": [[15, "table-dssp-codes"]], "Data representation": [[4, "data-representation"]], "De novo motif finding": [[11, "de-novo-motif-finding"]], "Dealing with PSI-BLAST": [[3, "dealing-with-psi-blast"], [3, "dealing-with-psi-blast-1"]], "Dealing with RPS-BLAST": [[3, "dealing-with-rps-blast"], [3, "dealing-with-rps-blast-1"]], "Dealing with large search output files with indexing": [[20, "dealing-with-large-search-output-files-with-indexing"]], "Demo: What\u2019s in a Tree?": [[17, "demo-whats-in-a-tree"]], "Determining atom-atom contacts": [[15, "determining-atom-atom-contacts"]], "Determining the secondary structure": [[15, "determining-the-secondary-structure"]], "Diagrams, tracks, feature-sets and features": [[8, "diagrams-tracks-feature-sets-and-features"]], "Discussion": [[23, "discussion"]], "Disorder": [[15, "disorder"]], "Disordered atoms": [[15, "disordered-atoms"]], "Disordered residues": [[15, "disordered-residues"]], "Distance Plots": [[15, "distance-plots"]], "Distance functions": [[4, "distance-functions"]], "Downloading structures from the Protein Data Bank": [[15, "downloading-structures-from-the-protein-data-bank"]], "Downloading the entire PDB": [[15, "downloading-the-entire-pdb"]], "Duplicate atoms": [[15, "duplicate-atoms"], [15, "duplicate-atoms-1"]], "Duplicate residues": [[15, "duplicate-residues"], [15, "duplicate-residues-1"]], "EFetch: Downloading full records from Entrez": [[7, "efetch-downloading-full-records-from-entrez"]], "EGQuery: Global Query - counts for search terms": [[7, "egquery-global-query-counts-for-search-terms"]], "EInfo: Obtaining information about the Entrez databases": [[7, "einfo-obtaining-information-about-the-entrez-databases"]], "ELink: Searching for related items in NCBI Entrez": [[7, "elink-searching-for-related-items-in-ncbi-entrez"]], "EMBOSS": [[0, "emboss"]], "EMBOSS needle and water": [[12, "emboss-needle-and-water"]], "EPost: Uploading a list of identifiers": [[7, "epost-uploading-a-list-of-identifiers"]], "ESearch: Searching the Entrez databases": [[7, "esearch-searching-the-entrez-databases"]], "ESpell: Obtaining spelling suggestions": [[7, "espell-obtaining-spelling-suggestions"]], "ESummary: Retrieving summaries from primary IDs": [[7, "esummary-retrieving-summaries-from-primary-ids"]], "Each motif object has an associated Position-Specific Scoring Matrix": [[11, "each-motif-object-has-an-associated-position-specific-scoring-matrix"]], "Entrez Guidelines": [[7, "entrez-guidelines"]], "Euclidean distance": [[4, "euclidean-distance"]], "Example calculation": [[4, "example-calculation"]], "Examples": [[7, "examples"], [13, "examples"], [15, "examples"], [90, "examples"], [137, "examples"], [206, "examples"], [265, "examples"], [278, "examples"]], "Exonerate": [[0, "exonerate"]], "Extract hetero residue from chain (e.g. glucose (GLC) moiety with resseq 10)": [[15, "extract-hetero-residue-from-chain-e-g-glucose-glc-moiety-with-resseq-10"]], "Extracting a specific Atom/Residue/Chain/Model from a Structure": [[15, "extracting-a-specific-atom-residue-chain-model-from-a-structure"]], "Extracting data": [[23, "extracting-data"]], "Extracting polypeptides from a Structure object": [[15, "extracting-polypeptides-from-a-structure-object"]], "Fatal errors": [[15, "fatal-errors"]], "Feature captions": [[8, "feature-captions"]], "Feature sigils": [[8, "feature-sigils"]], "Feature, location and position objects": [[21, "feature-location-and-position-objects"]], "Features of PhyloXML trees": [[17, "features-of-phyloxml-trees"]], "Features without a SeqFeature": [[8, "features-without-a-seqfeature"]], "Fields commonly found in TRANSFAC files": [[11, "table-transfaccodes"]], "Fields used to store references in TRANSFAC files": [[11, "id8"]], "File Formats": [[56, "file-formats"], [238, "file-formats"], [298, "file-formats"]], "Filtering a sequence file": [[6, "filtering-a-sequence-file"]], "Finding subsequences": [[22, "finding-subsequences"]], "Finding the indices of aligned sequences": [[0, "finding-the-indices-of-aligned-sequences"]], "Finding the lineage of an organism": [[7, "finding-the-lineage-of-an-organism"]], "Frames and strand values": [[217, "frames-and-strand-values"]], "Frequently Asked Questions (FAQ)": [[9, "frequently-asked-questions-faq"]], "Further options": [[8, "further-options"]], "Future plans": [[17, "future-plans"]], "Fuzzy Positions": [[21, "fuzzy-positions"]], "GCG Multiple Sequence Format (MSF)": [[0, "gcg-multiple-sequence-format-msf"]], "GenePop": [[18, "genepop"]], "General approach": [[15, "general-approach"]], "General gap scores": [[13, "general-gap-scores"]], "General overview of what Biopython provides": [[19, "general-overview-of-what-biopython-provides"]], "General questions": [[15, "general-questions"]], "Generalized pairwise alignments": [[13, "generalized-pairwise-alignments"]], "Generalized pairwise alignments using a substitution matrix and alphabet": [[13, "generalized-pairwise-alignments-using-a-substitution-matrix-and-alphabet"]], "Generalized pairwise alignments using a substitution matrix and integer sequences": [[13, "generalized-pairwise-alignments-using-a-substitution-matrix-and-integer-sequences"]], "Generalized pairwise alignments using match/mismatch scores and an alphabet": [[13, "generalized-pairwise-alignments-using-match-mismatch-scores-and-an-alphabet"]], "Generalized pairwise alignments using match/mismatch scores and integer sequences": [[13, "generalized-pairwise-alignments-using-match-mismatch-scores-and-integer-sequences"]], "Generating a multiple sequence alignment of codon sequences": [[13, "generating-a-multiple-sequence-alignment-of-codon-sequences"]], "GenomeDiagram": [[8, "genomediagram"]], "Getting a list of the records in a sequence file": [[23, "getting-a-list-of-the-records-in-a-sequence-file"]], "Getting a new-style Alignment object": [[12, "getting-a-new-style-alignment-object"]], "Getting information about the alignment": [[0, "getting-information-about-the-alignment"]], "Getting the raw data for a record": [[23, "getting-the-raw-data-for-a-record"], [23, "id2"]], "Getting your SeqRecord objects as formatted strings": [[23, "getting-your-seqrecord-objects-as-formatted-strings"]], "Getting your alignment objects as formatted strings": [[12, "getting-your-alignment-objects-as-formatted-strings"]], "Going 3D: The PDB module": [[15, "going-3d-the-pdb-module"]], "Graphics including GenomeDiagram": [[8, "graphics-including-genomediagram"]], "HH-suite output files": [[0, "hh-suite-output-files"]], "HSP": [[20, "hsp"]], "HSPFragment": [[20, "hspfragment"]], "HTML escape characters": [[7, "html-escape-characters"]], "Handling Cluster/TreeView-type files": [[4, "handling-cluster-treeview-type-files"]], "Handling errors": [[7, "handling-errors"]], "Hetero residues": [[15, "hetero-residues"]], "Hierarchical clustering": [[4, "hierarchical-clustering"]], "Histogram of sequence lengths": [[6, "histogram-of-sequence-lengths"]], "Hit": [[20, "hit"]], "Hold information about a Reference": [[237, "hold-information-about-a-reference"]], "How fast is it?": [[15, "how-fast-is-it"]], "How well tested is Bio.PDB?": [[15, "how-well-tested-is-bio-pdb"]], "I love parsing \u2013 please don\u2019t stop talking about it!": [[19, "i-love-parsing-please-dont-stop-talking-about-it"]], "I/O functions": [[17, "i-o-functions"]], "Identifying open reading frames": [[6, "identifying-open-reading-frames"]], "Indexing a FASTQ file": [[6, "indexing-a-fastq-file"]], "Indexing a dictionary using the SEGUID checksum": [[23, "indexing-a-dictionary-using-the-seguid-checksum"]], "Indexing compressed files": [[23, "indexing-compressed-files"]], "Information Content": [[12, "information-content"]], "Information methods": [[17, "information-methods"]], "Input": [[56, "input"], [217, "input"], [238, "input"], [298, "input"]], "Input - Alignments": [[238, "input-alignments"]], "Input - Multiple Records": [[238, "input-multiple-records"]], "Input - Single Records": [[238, "input-single-records"], [298, "input-single-records"]], "Installing Biopython": [[9, "installing-biopython"]], "Internal coordinates - distances, angles, torsion angles, distance plots, etc": [[15, "internal-coordinates-distances-angles-torsion-angles-distance-plots-etc"]], "Introduction": [[3, "introduction"], [3, "introduction-1"], [8, "introduction"], [9, "introduction"]], "Is there support for molecular graphics?": [[15, "is-there-support-for-molecular-graphics"]], "Iterating over alignments": [[13, "iterating-over-alignments"]], "Iterating over all residues of a model": [[15, "iterating-over-all-residues-of-a-model"]], "Iterating over the records in a sequence file": [[23, "iterating-over-the-records-in-a-sequence-file"]], "Iterating through all atoms of a structure": [[15, "iterating-through-all-atoms-of-a-structure"]], "JASPAR": [[11, "jaspar"]], "KEGG": [[10, "kegg"]], "Keeping a local copy of the PDB up to date": [[15, "keeping-a-local-copy-of-the-pdb-up-to-date"]], "Kendall\u2019s \\tau": [[4, "kendalls-tau"]], "Letter frequencies": [[0, "letter-frequencies"]], "Loading predefined substitution matrices": [[13, "loading-predefined-substitution-matrices"]], "Location testing": [[21, "location-testing"]], "Loop over all disordered atoms, and select all atoms with altloc A (if present)": [[15, "loop-over-all-disordered-atoms-and-select-all-atoms-with-altloc-a-if-present"]], "Low level FASTA and FASTQ parsers": [[23, "low-level-fasta-and-fastq-parsers"]], "MAST": [[11, "mast"]], "MEME": [[11, "meme"], [11, "sec-meme"]], "MUSCLE": [[12, "muscle"]], "Mailing lists and helping newcomers": [[5, "mailing-lists-and-helping-newcomers"]], "Maintaining a distribution for a platform": [[5, "maintaining-a-distribution-for-a-platform"]], "Making the sequences in a FASTA file upper case": [[6, "making-the-sequences-in-a-fasta-file-upper-case"]], "Manipulating Alignments": [[12, "manipulating-alignments"]], "Manipulating Phenotype Microarray data": [[16, "manipulating-phenotype-microarray-data"]], "Mapping a multiple sequence alignment": [[0, "mapping-a-multiple-sequence-alignment"]], "Mapping a pairwise sequence alignment": [[0, "mapping-a-pairwise-sequence-alignment"]], "Mapping the residues of two related structures onto each other": [[15, "mapping-the-residues-of-two-related-structures-onto-each-other"]], "Mauve eXtended Multi-FastA (xmfa) format": [[0, "mauve-extended-multi-fasta-xmfa-format"]], "Measuring angles": [[15, "measuring-angles"]], "Measuring distances": [[15, "measuring-distances"]], "Measuring torsion angles": [[15, "measuring-torsion-angles"]], "Meta-attributes of CodonAligner objects.": [[13, "table-codonalign-meta-attributes"]], "Meta-attributes of the pairwise aligner objects.": [[13, "table-align-meta-attributes"]], "Missing values": [[4, "missing-values"]], "Model": [[15, "model"]], "Modification methods": [[17, "modification-methods"]], "Modifying and rebuilding structures": [[15, "modifying-and-rebuilding-structures"]], "Modifying data": [[23, "modifying-data"]], "Module contents": [[27, "module-Bio"], [28, "module-Bio.Affy"], [30, "module-Bio.Align"], [32, "module-Bio.Align.Applications"], [54, "module-Bio.Align.substitution_matrices"], [56, "module-Bio.AlignIO"], [67, "module-Bio.Application"], [68, "module-Bio.Blast"], [72, "module-Bio.CAPS"], [73, "module-Bio.Cluster"], [74, "module-Bio.Compass"], [75, "module-Bio.Data"], [79, "module-Bio.Emboss"], [83, "module-Bio.Entrez"], [85, "module-Bio.ExPASy"], [92, "module-Bio.GenBank"], [96, "module-Bio.Geo"], [98, "module-Bio.Graphics"], [104, "module-Bio.Graphics.GenomeDiagram"], [106, "module-Bio.HMM"], [111, "module-Bio.KEGG"], [112, "module-Bio.KEGG.Compound"], [113, "module-Bio.KEGG.Enzyme"], [114, "module-Bio.KEGG.Gene"], [115, "module-Bio.KEGG.KGML"], [118, "module-Bio.KEGG.Map"], [123, "module-Bio.Medline"], [124, "module-Bio.NMR"], [128, "module-Bio.Nexus"], [133, "module-Bio.PDB"], [171, "module-Bio.PDB.mmtf"], [177, "module-Bio.Pathway"], [178, "module-Bio.Pathway.Rep"], [181, "module-Bio.Phylo"], [182, "module-Bio.Phylo.Applications"], [192, "module-Bio.Phylo.PAML"], [200, "module-Bio.PopGen"], [201, "module-Bio.PopGen.GenePop"], [206, "module-Bio.Restriction"], [209, "module-Bio.SCOP"], [216, "module-Bio.SVDSuperimposer"], [217, "module-Bio.SearchIO"], [218, "module-Bio.SearchIO.BlastIO"], [222, "module-Bio.SearchIO.ExonerateIO"], [227, "module-Bio.SearchIO.HHsuiteIO"], [229, "module-Bio.SearchIO.HmmerIO"], [234, "module-Bio.SearchIO.InterproscanIO"], [238, "module-Bio.SeqIO"], [261, "module-Bio.SeqUtils"], [268, "module-Bio.Sequencing"], [270, "module-Bio.Sequencing.Applications"], [272, "module-Bio.SwissProt"], [274, "module-Bio.TogoWS"], [275, "module-Bio.UniGene"], [276, "module-Bio.UniProt"], [279, "module-Bio.codonalign"], [283, "module-Bio.motifs"], [285, "module-Bio.motifs.applications"], [287, "module-Bio.motifs.jaspar"], [298, "module-Bio.phenotype"], [301, "module-BioSQL"]], "Motif objects": [[11, "motif-objects"]], "Multiple Alignment Format (MAF)": [[0, "multiple-alignment-format-maf"]], "Multiple Alignments": [[12, "multiple-alignments"]], "Multiple Sequence Alignment objects": [[12, "multiple-sequence-alignment-objects"]], "Multiple tracks": [[8, "multiple-tracks"]], "MutableSeq objects": [[22, "mutableseq-objects"]], "NEXUS": [[0, "nexus"]], "Navigating through a Structure object": [[15, "navigating-through-a-structure-object"]], "Note": [[65, "note"]], "Nucleotide dot plots": [[6, "nucleotide-dot-plots"]], "Nucleotide sequences and (reverse) complements": [[22, "nucleotide-sequences-and-reverse-complements"]], "Obtaining BLAST output in other formats": [[3, "obtaining-blast-output-in-other-formats"]], "Obtaining a consensus sequence": [[11, "obtaining-a-consensus-sequence"]], "Obtaining the sequence of a structure": [[15, "obtaining-the-sequence-of-a-structure"]], "Operations on an alignment": [[0, "operations-on-an-alignment"]], "Other hetero residues": [[15, "other-hetero-residues"]], "Other versions of BLAST": [[3, "other-versions-of-blast"], [3, "id5"]], "Output": [[56, "output"], [217, "output"], [238, "output"], [298, "output"]], "Output - Advanced": [[238, "output-advanced"]], "PAML integration": [[17, "paml-integration"]], "PHYLIP output files": [[0, "phylip-output-files"]], "Pairwise alignments using pairwise2": [[14, "pairwise-alignments-using-pairwise2"]], "Pairwise sequence alignment": [[13, "pairwise-sequence-alignment"]], "Parameters extraction": [[16, "parameters-extraction"]], "Parse a PDB file, and extract some Model, Chain, Residue and Atom objects": [[15, "parse-a-pdb-file-and-extract-some-model-chain-residue-and-atom-objects"]], "Parsing BLAST output": [[3, "parsing-blast-output"], [3, "id6"]], "Parsing Enzyme records": [[25, "parsing-enzyme-records"]], "Parsing GEO records": [[7, "parsing-geo-records"]], "Parsing GenBank records from the net": [[23, "parsing-genbank-records-from-the-net"]], "Parsing KEGG records": [[10, "parsing-kegg-records"]], "Parsing Medline records": [[7, "parsing-medline-records"]], "Parsing Phenotype Microarray data": [[16, "parsing-phenotype-microarray-data"]], "Parsing Prosite documentation records": [[25, "parsing-prosite-documentation-records"]], "Parsing Prosite records": [[25, "parsing-prosite-records"]], "Parsing Swiss-Prot files": [[25, "parsing-swiss-prot-files"]], "Parsing Swiss-Prot records": [[25, "parsing-swiss-prot-records"]], "Parsing SwissProt sequences from the net": [[23, "parsing-swissprot-sequences-from-the-net"]], "Parsing UniGene records": [[7, "parsing-unigene-records"]], "Parsing huge Entrez XML files": [[7, "parsing-huge-entrez-xml-files"]], "Parsing or Reading Sequence Alignments": [[12, "parsing-or-reading-sequence-alignments"]], "Parsing or Reading Sequences": [[23, "parsing-or-reading-sequences"]], "Parsing sequence file formats": [[19, "parsing-sequence-file-formats"]], "Parsing sequences from compressed files": [[23, "parsing-sequences-from-compressed-files"]], "Parsing sequences from the net": [[23, "parsing-sequences-from-the-net"]], "Parsing the Swiss-Prot keyword and category list": [[25, "parsing-the-swiss-prot-keyword-and-category-list"]], "Partitioning algorithms": [[4, "partitioning-algorithms"]], "Pattern Space Layout (PSL)": [[0, "pattern-space-layout-psl"]], "Performing hierarchical clustering": [[4, "performing-hierarchical-clustering"], [4, "performing-hierarchical-clustering-1"]], "Performing k-means or k-medians clustering": [[4, "performing-k-means-or-k-medians-clustering"]], "Performing the McDonald-Kreitman test": [[13, "performing-the-mcdonald-kreitman-test"]], "Phenotype Microarrays": [[16, "phenotype-microarrays"]], "Phylogenetics with Bio.Phylo": [[17, "phylogenetics-with-bio-phylo"]], "Plot of sequence GC%": [[6, "plot-of-sequence-gc"]], "Plotting the quality scores of sequencing read data": [[6, "plotting-the-quality-scores-of-sequencing-read-data"]], "Point mutations": [[15, "point-mutations"]], "Position Specific Score Matrices": [[12, "position-specific-score-matrices"]], "Position-Specific Scoring Matrices": [[11, "position-specific-scoring-matrices"]], "Position-Weight Matrices": [[11, "position-weight-matrices"]], "Positions and locations": [[21, "positions-and-locations"]], "Principal Component Analysis": [[4, "principal-component-analysis"]], "Print all hetero residues in chain": [[15, "print-all-hetero-residues-in-chain"]], "Print out all the residues that contain disordered atoms": [[15, "print-out-all-the-residues-that-contain-disordered-atoms"]], "Print out coordinates of all CA atoms in structure with B factor over 50": [[15, "print-out-coordinates-of-all-ca-atoms-in-structure-with-b-factor-over-50"]], "Printing alignments": [[0, "printing-alignments"]], "Producing randomized genomes": [[6, "producing-randomized-genomes"]], "Protein Internal Coordinate (.pic) files and default values": [[15, "protein-internal-coordinate-pic-files-and-default-values"]], "PubMed and Medline": [[7, "pubmed-and-medline"]], "Python-style sequence coordinates": [[217, "python-style-sequence-coordinates"]], "QueryResult": [[20, "queryresult"]], "Querying the KEGG API": [[10, "querying-the-kegg-api"]], "Quick Start \u2013 What can you do with Biopython?": [[19, "quick-start-what-can-you-do-with-biopython"]], "Random number generator": [[4, "random-number-generator"]], "Reading Array objects from file": [[13, "reading-array-objects-from-file"]], "Reading Sequence Files": [[23, "reading-sequence-files"]], "Reading a BinaryCIF file": [[15, "reading-a-binarycif-file"]], "Reading a PDB file": [[15, "reading-a-pdb-file"]], "Reading a PDBML (PDB XML) file": [[15, "reading-a-pdbml-pdb-xml-file"]], "Reading a PQR file": [[15, "reading-a-pqr-file"]], "Reading alignments": [[0, "reading-alignments"]], "Reading an mmCIF file": [[15, "reading-an-mmcif-file"]], "Reading and writing alignments": [[0, "reading-and-writing-alignments"]], "Reading and writing crystal structure files": [[15, "reading-and-writing-crystal-structure-files"]], "Reading files in the MMTF format": [[15, "reading-files-in-the-mmtf-format"]], "Reading motifs": [[11, "reading-motifs"]], "Reading search output files": [[20, "reading-search-output-files"]], "Reference": [[166, "reference"]], "References": [[21, "references"]], "Relative entropy": [[11, "relative-entropy"]], "Representing a hierarchical clustering solution": [[4, "representing-a-hierarchical-clustering-solution"]], "Residue": [[15, "residue"]], "Retrieving Prosite and Prosite documentation records": [[25, "retrieving-prosite-and-prosite-documentation-records"]], "Retrieving a Swiss-Prot record": [[25, "retrieving-a-swiss-prot-record"]], "Reverse-complementing SeqRecord objects": [[21, "reverse-complementing-seqrecord-objects"]], "Reverse-complementing a motif": [[11, "reverse-complementing-a-motif"]], "Reverse-complementing the alignment": [[0, "reverse-complementing-the-alignment"]], "Round trips": [[23, "round-trips"]], "Running BLAST locally": [[3, "running-blast-locally"], [3, "id2"]], "Running BLAST over the Internet": [[3, "running-blast-over-the-internet"], [3, "id1"]], "Running external applications": [[17, "running-external-applications"]], "Running the tests": [[24, "running-the-tests"]], "Running the tests using Tox": [[24, "running-the-tests-using-tox"]], "Saving BLAST results": [[3, "saving-blast-results"]], "Saving the clustering result": [[4, "saving-the-clustering-result"]], "Scanning the Prosite database": [[25, "scanning-the-prosite-database"]], "Search and traversal methods": [[17, "search-and-traversal-methods"]], "Searching for and downloading abstracts using the history": [[7, "searching-for-and-downloading-abstracts-using-the-history"]], "Searching for and downloading sequences using the history": [[7, "searching-for-and-downloading-sequences-using-the-history"]], "Searching for citations": [[7, "searching-for-citations"]], "Searching for exact matches": [[11, "searching-for-exact-matches"]], "Searching for instances": [[11, "searching-for-instances"]], "Searching for matches using the PSSM score": [[11, "searching-for-matches-using-the-pssm-score"]], "Searching with UniProt": [[25, "searching-with-uniprot"]], "Searching, downloading, and parsing Entrez Nucleotide records": [[7, "searching-downloading-and-parsing-entrez-nucleotide-records"]], "Searching, downloading, and parsing GenBank records": [[7, "searching-downloading-and-parsing-genbank-records"]], "See Also": [[197, "see-also"]], "Selecting a score threshold": [[11, "selecting-a-score-threshold"]], "Self-Organizing Maps": [[4, "self-organizing-maps"]], "SeqFeature objects": [[21, "seqfeature-objects"]], "SeqRecord objects from FASTA files": [[21, "seqrecord-objects-from-fasta-files"]], "SeqRecord objects from GenBank files": [[21, "seqrecord-objects-from-genbank-files"]], "SeqRecord objects from scratch": [[21, "seqrecord-objects-from-scratch"]], "Sequence Alignment/Map (SAM)": [[0, "sequence-alignment-map-sam"]], "Sequence Input/Output": [[23, "sequence-input-output"]], "Sequence alignments": [[0, "sequence-alignments"]], "Sequence annotation objects": [[21, "sequence-annotation-objects"]], "Sequence coordinate order": [[217, "sequence-coordinate-order"]], "Sequence described by a feature or location": [[21, "sequence-described-by-a-feature-or-location"]], "Sequence files as Dictionaries": [[23, "sequence-files-as-dictionaries"]], "Sequence files as Dictionaries \u2013 Database indexed files": [[23, "sequence-files-as-dictionaries-database-indexed-files"]], "Sequence files as Dictionaries \u2013 In memory": [[23, "sequence-files-as-dictionaries-in-memory"]], "Sequence files as Dictionaries \u2013 Indexed files": [[23, "sequence-files-as-dictionaries-indexed-files"]], "Sequence motif analysis using Bio.motifs": [[11, "sequence-motif-analysis-using-bio-motifs"]], "Sequence objects": [[22, "sequence-objects"]], "Sequence parsing plus simple plots": [[6, "sequence-parsing-plus-simple-plots"]], "Sequences act like strings": [[22, "sequences-act-like-strings"]], "Sequences with partially defined sequence contents": [[22, "sequences-with-partially-defined-sequence-contents"]], "Sequences with unknown sequence contents": [[22, "sequences-with-unknown-sequence-contents"]], "Simple Chromosomes": [[8, "simple-chromosomes"]], "Simple FASTA parsing example": [[19, "simple-fasta-parsing-example"]], "Simple GenBank parsing example": [[19, "simple-genbank-parsing-example"]], "Simple quality filtering for FASTQ files": [[6, "simple-quality-filtering-for-fastq-files"]], "SimpleLocation object": [[21, "simplelocation-object"]], "Single Alignments": [[12, "single-alignments"]], "Slicing a SeqRecord": [[21, "slicing-a-seqrecord"]], "Slicing a motif": [[11, "slicing-a-motif"]], "Slicing a sequence": [[22, "slicing-a-sequence"]], "Slicing alignments": [[12, "slicing-alignments"]], "Slicing and indexing an alignment": [[0, "slicing-and-indexing-an-alignment"]], "Sorting a sequence file": [[6, "sorting-a-sequence-file"]], "Sorting an alignment": [[0, "sorting-an-alignment"]], "Sorting and filtering BLAST output": [[3, "sorting-and-filtering-blast-output"]], "Spearman rank correlation": [[4, "spearman-rank-correlation"]], "Specialized parsers": [[7, "specialized-parsers"]], "Specify locations of a feature on a Sequence": [[237, "specify-locations-of-a-feature-on-a-sequence"]], "Specifying the dictionary keys": [[23, "specifying-the-dictionary-keys"], [23, "sec-seqio-index-functionkey"]], "Standalone NCBI BLAST+": [[3, "standalone-ncbi-blast"], [3, "standalone-ncbi-blast-1"]], "Stockholm": [[0, "stockholm"]], "Structure": [[15, "structure"]], "Structure representation": [[15, "structure-representation"]], "Submodules": [[27, "submodules"], [28, "submodules"], [30, "submodules"], [56, "submodules"], [68, "submodules"], [75, "submodules"], [79, "submodules"], [83, "submodules"], [85, "submodules"], [92, "submodules"], [96, "submodules"], [98, "submodules"], [106, "submodules"], [111, "submodules"], [115, "submodules"], [124, "submodules"], [128, "submodules"], [133, "submodules"], [171, "submodules"], [178, "submodules"], [181, "submodules"], [192, "submodules"], [201, "submodules"], [206, "submodules"], [209, "submodules"], [217, "submodules"], [218, "submodules"], [222, "submodules"], [227, "submodules"], [229, "submodules"], [234, "submodules"], [238, "submodules"], [261, "submodules"], [268, "submodules"], [272, "submodules"], [276, "submodules"], [279, "submodules"], [283, "submodules"], [287, "submodules"], [298, "submodules"], [301, "submodules"]], "Subpackages": [[27, "subpackages"], [30, "subpackages"], [98, "subpackages"], [111, "subpackages"], [133, "subpackages"], [177, "subpackages"], [181, "subpackages"], [200, "subpackages"], [217, "subpackages"], [268, "subpackages"], [283, "subpackages"]], "Substitution matrices": [[13, "substitution-matrices"]], "Substitution scores": [[13, "substitution-scores"]], "Substitutions": [[0, "substitutions"]], "Superimposing residues and their neighborhoods": [[15, "superimposing-residues-and-their-neighborhoods"]], "Superimposing two structures": [[15, "superimposing-two-structures"]], "Supported Formats": [[217, "supported-formats"], [218, "supported-formats"], [221, "supported-formats"], [222, "supported-formats"], [226, "supported-formats"]], "Supported format": [[234, "supported-format"]], "Supported formats": [[229, "supported-formats"]], "Swiss-Prot and ExPASy": [[25, "swiss-prot-and-expasy"]], "TRANSFAC": [[11, "transfac"]], "Table of contents": [[307, null]], "Table of contents:": [[26, null]], "Tabular output from BLAST or FASTA": [[0, "tabular-output-from-blast-or-fasta"]], "Technical Introduction to BGZF": [[278, "technical-introduction-to-bgzf"]], "Testing structures for completeness": [[15, "testing-structures-for-completeness"]], "Text Mode": [[278, "text-mode"]], "The Alignments class": [[0, "the-alignments-class"]], "The BLAST HSP class": [[3, "the-blast-hsp-class"]], "The BLAST Hit class": [[3, "the-blast-hit-class"]], "The BLAST Record class": [[3, "the-blast-record-class"]], "The BLAST Records class": [[3, "the-blast-records-class"]], "The BLAST Records, Record, and Hit classes": [[3, "the-blast-records-record-and-hit-classes"]], "The BLAST record class": [[3, "id7"]], "The Biopython testing framework": [[24, "the-biopython-testing-framework"]], "The JASPAR format jaspar": [[11, "the-jaspar-format-jaspar"]], "The JASPAR pfm format": [[11, "the-jaspar-pfm-format"]], "The JASPAR sites format": [[11, "the-jaspar-sites-format"]], "The Pearson correlation coefficient": [[4, "the-pearson-correlation-coefficient"]], "The SearchIO object model": [[20, "the-searchio-object-model"]], "The SeqRecord object": [[21, "the-seqrecord-object"]], "The file contains an error message": [[7, "the-file-contains-an-error-message"]], "The file contains items that are missing from the associated DTD": [[7, "the-file-contains-items-that-are-missing-from-the-associated-dtd"]], "The file ends prematurely or is otherwise corrupted": [[7, "the-file-ends-prematurely-or-is-otherwise-corrupted"]], "The file is not an XML file": [[7, "the-file-is-not-an-xml-file"]], "The format method": [[21, "the-format-method"]], "The generic pfm-four-columns format": [[11, "the-generic-pfm-four-columns-format"]], "The generic pfm-four-rows format": [[11, "the-generic-pfm-four-rows-format"]], "The pairwise aligner object": [[13, "the-pairwise-aligner-object"]], "Todo": [[169, "id1"]], "Transcription": [[22, "transcription"]], "Translating a FASTA file of CDS entries": [[6, "translating-a-fasta-file-of-cds-entries"]], "Translation": [[22, "translation"]], "Translation Tables": [[22, "translation-tables"]], "Trimming off adaptor sequences": [[6, "trimming-off-adaptor-sequences"]], "Trimming off primer sequences": [[6, "trimming-off-primer-sequences"]], "Turning Seq objects into strings": [[22, "turning-seq-objects-into-strings"]], "UCSC chain file format": [[0, "ucsc-chain-file-format"]], "Uncentered correlation (cosine of the angle)": [[4, "uncentered-correlation-cosine-of-the-angle"]], "Usage": [[137, "usage"]], "Useful links": [[11, "useful-links"]], "Using Tree and Clade objects": [[17, "using-tree-and-clade-objects"]], "Using a pre-defined substitution matrix and gap scores": [[13, "using-a-pre-defined-substitution-matrix-and-gap-scores"]], "Using a proxy": [[7, "using-a-proxy"]], "Using the history and WebEnv": [[7, "using-the-history-and-webenv"]], "View and export trees": [[17, "view-and-export-trees"]], "Warning about namespaces": [[278, "warning-about-namespaces"]], "Water residues": [[15, "water-residues"]], "Weighting": [[4, "weighting"]], "What can I find in the Biopython package": [[9, "what-can-i-find-in-the-biopython-package"]], "What is Biopython?": [[9, "what-is-biopython"]], "What the heck is a handle?": [[1, "what-the-heck-is-a-handle"]], "What to do next": [[19, "what-to-do-next"]], "Where to go from here \u2013 contributing to Biopython": [[5, "where-to-go-from-here-contributing-to-biopython"]], "Who\u2019s using Bio.PDB?": [[15, "whos-using-bio-pdb"]], "Working with sequence files": [[6, "working-with-sequence-files"]], "Working with sequences": [[19, "working-with-sequences"]], "Working with strings directly": [[22, "working-with-strings-directly"]], "Writing Alignments": [[12, "writing-alignments"]], "Writing BLAST records": [[3, "writing-blast-records"]], "Writing MMTF files": [[15, "writing-mmtf-files"]], "Writing PDB files": [[15, "writing-pdb-files"]], "Writing PQR files": [[15, "writing-pqr-files"]], "Writing Phenotype Microarray data": [[16, "writing-phenotype-microarray-data"]], "Writing Sequence Files": [[23, "writing-sequence-files"]], "Writing a test using unittest": [[24, "writing-a-test-using-unittest"]], "Writing alignments": [[0, "writing-alignments"]], "Writing and converting search output files": [[20, "writing-and-converting-search-output-files"]], "Writing doctests": [[24, "writing-doctests"]], "Writing doctests in the Tutorial": [[24, "writing-doctests-in-the-tutorial"]], "Writing mmCIF files": [[15, "writing-mmcif-files"]], "Writing motifs": [[11, "writing-motifs"]], "Writing tests": [[24, "writing-tests"]], "bigBed": [[0, "bigbed"]], "bigMaf": [[0, "bigmaf"]], "bigPsl": [[0, "bigpsl"]], "blast-tab": [[218, "blast-tab"]], "blast-xml": [[218, "blast-xml"]], "exonerate-cigar": [[222, "exonerate-cigar"]], "exonerate-text": [[222, "exonerate-text"]], "exonerate-vulgar": [[222, "exonerate-vulgar"]], "fasta-m10": [[226, "fasta-m10"]], "hmmer2-text and hmmer3-text": [[229, "hmmer2-text-and-hmmer3-text"]], "hmmer3-domtab": [[229, "hmmer3-domtab"]], "hmmer3-tab": [[229, "hmmer3-tab"]], "internal_coords control attributes": [[15, "internal-coords-control-attributes"]], "interproscan-xml": [[234, "interproscan-xml"]], "k-means and k-medians": [[4, "k-means-and-k-medians"]], "k-medoids clustering": [[4, "k-medoids-clustering"]]}, "docnames": ["Tutorial/chapter_align", "Tutorial/chapter_appendix", "Tutorial/chapter_bibliography", "Tutorial/chapter_blast", "Tutorial/chapter_cluster", "Tutorial/chapter_contributing", "Tutorial/chapter_cookbook", "Tutorial/chapter_entrez", "Tutorial/chapter_graphics", "Tutorial/chapter_introduction", "Tutorial/chapter_kegg", "Tutorial/chapter_motifs", "Tutorial/chapter_msa", "Tutorial/chapter_pairwise", "Tutorial/chapter_pairwise2", "Tutorial/chapter_pdb", "Tutorial/chapter_phenotype", "Tutorial/chapter_phylo", "Tutorial/chapter_popgen", "Tutorial/chapter_quick_start", "Tutorial/chapter_searchio", "Tutorial/chapter_seq_annot", "Tutorial/chapter_seq_objects", "Tutorial/chapter_seqio", "Tutorial/chapter_testing", "Tutorial/chapter_uniprot", "Tutorial/index", "api/Bio", "api/Bio.Affy", "api/Bio.Affy.CelFile", "api/Bio.Align", "api/Bio.Align.AlignInfo", "api/Bio.Align.Applications", "api/Bio.Align.a2m", "api/Bio.Align.analysis", "api/Bio.Align.bed", "api/Bio.Align.bigbed", "api/Bio.Align.bigmaf", "api/Bio.Align.bigpsl", "api/Bio.Align.chain", "api/Bio.Align.clustal", "api/Bio.Align.emboss", "api/Bio.Align.exonerate", "api/Bio.Align.fasta", "api/Bio.Align.hhr", "api/Bio.Align.interfaces", "api/Bio.Align.maf", "api/Bio.Align.mauve", "api/Bio.Align.msf", "api/Bio.Align.nexus", "api/Bio.Align.phylip", "api/Bio.Align.psl", "api/Bio.Align.sam", "api/Bio.Align.stockholm", "api/Bio.Align.substitution_matrices", "api/Bio.Align.tabular", "api/Bio.AlignIO", "api/Bio.AlignIO.ClustalIO", "api/Bio.AlignIO.EmbossIO", "api/Bio.AlignIO.FastaIO", "api/Bio.AlignIO.Interfaces", "api/Bio.AlignIO.MafIO", "api/Bio.AlignIO.MauveIO", "api/Bio.AlignIO.MsfIO", "api/Bio.AlignIO.NexusIO", "api/Bio.AlignIO.PhylipIO", "api/Bio.AlignIO.StockholmIO", "api/Bio.Application", "api/Bio.Blast", "api/Bio.Blast.Applications", "api/Bio.Blast.NCBIWWW", "api/Bio.Blast.NCBIXML", "api/Bio.CAPS", "api/Bio.Cluster", "api/Bio.Compass", "api/Bio.Data", "api/Bio.Data.CodonTable", "api/Bio.Data.IUPACData", "api/Bio.Data.PDBData", "api/Bio.Emboss", "api/Bio.Emboss.Applications", "api/Bio.Emboss.Primer3", "api/Bio.Emboss.PrimerSearch", "api/Bio.Entrez", "api/Bio.Entrez.Parser", "api/Bio.ExPASy", "api/Bio.ExPASy.Enzyme", "api/Bio.ExPASy.Prodoc", "api/Bio.ExPASy.Prosite", "api/Bio.ExPASy.ScanProsite", "api/Bio.ExPASy.cellosaurus", "api/Bio.File", "api/Bio.GenBank", "api/Bio.GenBank.Record", "api/Bio.GenBank.Scanner", "api/Bio.GenBank.utils", "api/Bio.Geo", "api/Bio.Geo.Record", "api/Bio.Graphics", "api/Bio.Graphics.BasicChromosome", "api/Bio.Graphics.ColorSpiral", "api/Bio.Graphics.Comparative", "api/Bio.Graphics.DisplayRepresentation", "api/Bio.Graphics.Distribution", "api/Bio.Graphics.GenomeDiagram", "api/Bio.Graphics.KGML_vis", "api/Bio.HMM", "api/Bio.HMM.DynamicProgramming", "api/Bio.HMM.MarkovModel", "api/Bio.HMM.Trainer", "api/Bio.HMM.Utilities", "api/Bio.KEGG", "api/Bio.KEGG.Compound", "api/Bio.KEGG.Enzyme", "api/Bio.KEGG.Gene", "api/Bio.KEGG.KGML", "api/Bio.KEGG.KGML.KGML_parser", "api/Bio.KEGG.KGML.KGML_pathway", "api/Bio.KEGG.Map", "api/Bio.KEGG.REST", "api/Bio.LogisticRegression", "api/Bio.MarkovModel", "api/Bio.MaxEntropy", "api/Bio.Medline", "api/Bio.NMR", "api/Bio.NMR.NOEtools", "api/Bio.NMR.xpktools", "api/Bio.NaiveBayes", "api/Bio.Nexus", "api/Bio.Nexus.Nexus", "api/Bio.Nexus.Nodes", "api/Bio.Nexus.StandardData", "api/Bio.Nexus.Trees", "api/Bio.PDB", "api/Bio.PDB.AbstractPropertyMap", "api/Bio.PDB.Atom", "api/Bio.PDB.Chain", "api/Bio.PDB.DSSP", "api/Bio.PDB.Dice", "api/Bio.PDB.Entity", "api/Bio.PDB.FragmentMapper", "api/Bio.PDB.HSExposure", "api/Bio.PDB.MMCIF2Dict", "api/Bio.PDB.MMCIFParser", "api/Bio.PDB.Model", "api/Bio.PDB.NACCESS", "api/Bio.PDB.NeighborSearch", "api/Bio.PDB.PDBExceptions", "api/Bio.PDB.PDBIO", "api/Bio.PDB.PDBList", "api/Bio.PDB.PDBMLParser", "api/Bio.PDB.PDBParser", "api/Bio.PDB.PICIO", "api/Bio.PDB.PSEA", "api/Bio.PDB.Polypeptide", "api/Bio.PDB.Residue", "api/Bio.PDB.ResidueDepth", "api/Bio.PDB.SASA", "api/Bio.PDB.SCADIO", "api/Bio.PDB.Selection", "api/Bio.PDB.Structure", "api/Bio.PDB.StructureAlignment", "api/Bio.PDB.StructureBuilder", "api/Bio.PDB.Superimposer", "api/Bio.PDB.alphafold_db", "api/Bio.PDB.binary_cif", "api/Bio.PDB.cealign", "api/Bio.PDB.ic_data", "api/Bio.PDB.ic_rebuild", "api/Bio.PDB.internal_coords", "api/Bio.PDB.mmcifio", "api/Bio.PDB.mmtf", "api/Bio.PDB.mmtf.DefaultParser", "api/Bio.PDB.mmtf.mmtfio", "api/Bio.PDB.parse_pdb_header", "api/Bio.PDB.qcprot", "api/Bio.PDB.vectors", "api/Bio.Pathway", "api/Bio.Pathway.Rep", "api/Bio.Pathway.Rep.Graph", "api/Bio.Pathway.Rep.MultiGraph", "api/Bio.Phylo", "api/Bio.Phylo.Applications", "api/Bio.Phylo.BaseTree", "api/Bio.Phylo.CDAO", "api/Bio.Phylo.CDAOIO", "api/Bio.Phylo.Consensus", "api/Bio.Phylo.NeXML", "api/Bio.Phylo.NeXMLIO", "api/Bio.Phylo.Newick", "api/Bio.Phylo.NewickIO", "api/Bio.Phylo.NexusIO", "api/Bio.Phylo.PAML", "api/Bio.Phylo.PAML.baseml", "api/Bio.Phylo.PAML.chi2", "api/Bio.Phylo.PAML.codeml", "api/Bio.Phylo.PAML.yn00", "api/Bio.Phylo.PhyloXML", "api/Bio.Phylo.PhyloXMLIO", "api/Bio.Phylo.TreeConstruction", "api/Bio.PopGen", "api/Bio.PopGen.GenePop", "api/Bio.PopGen.GenePop.Controller", "api/Bio.PopGen.GenePop.EasyController", "api/Bio.PopGen.GenePop.FileParser", "api/Bio.PopGen.GenePop.LargeFileParser", "api/Bio.Restriction", "api/Bio.Restriction.PrintFormat", "api/Bio.Restriction.Restriction_Dictionary", "api/Bio.SCOP", "api/Bio.SCOP.Cla", "api/Bio.SCOP.Des", "api/Bio.SCOP.Dom", "api/Bio.SCOP.Hie", "api/Bio.SCOP.Raf", "api/Bio.SCOP.Residues", "api/Bio.SVDSuperimposer", "api/Bio.SearchIO", "api/Bio.SearchIO.BlastIO", "api/Bio.SearchIO.BlastIO.blast_tab", "api/Bio.SearchIO.BlastIO.blast_xml", "api/Bio.SearchIO.BlatIO", "api/Bio.SearchIO.ExonerateIO", "api/Bio.SearchIO.ExonerateIO.exonerate_cigar", "api/Bio.SearchIO.ExonerateIO.exonerate_text", "api/Bio.SearchIO.ExonerateIO.exonerate_vulgar", "api/Bio.SearchIO.FastaIO", "api/Bio.SearchIO.HHsuiteIO", "api/Bio.SearchIO.HHsuiteIO.hhsuite2_text", "api/Bio.SearchIO.HmmerIO", "api/Bio.SearchIO.HmmerIO.hmmer2_text", "api/Bio.SearchIO.HmmerIO.hmmer3_domtab", "api/Bio.SearchIO.HmmerIO.hmmer3_tab", "api/Bio.SearchIO.HmmerIO.hmmer3_text", "api/Bio.SearchIO.InterproscanIO", "api/Bio.SearchIO.InterproscanIO.interproscan_xml", "api/Bio.Seq", "api/Bio.SeqFeature", "api/Bio.SeqIO", "api/Bio.SeqIO.AbiIO", "api/Bio.SeqIO.AceIO", "api/Bio.SeqIO.FastaIO", "api/Bio.SeqIO.GckIO", "api/Bio.SeqIO.GfaIO", "api/Bio.SeqIO.IgIO", "api/Bio.SeqIO.InsdcIO", "api/Bio.SeqIO.Interfaces", "api/Bio.SeqIO.NibIO", "api/Bio.SeqIO.PdbIO", "api/Bio.SeqIO.PhdIO", "api/Bio.SeqIO.PirIO", "api/Bio.SeqIO.QualityIO", "api/Bio.SeqIO.SeqXmlIO", "api/Bio.SeqIO.SffIO", "api/Bio.SeqIO.SnapGeneIO", "api/Bio.SeqIO.SwissIO", "api/Bio.SeqIO.TabIO", "api/Bio.SeqIO.TwoBitIO", "api/Bio.SeqIO.UniprotIO", "api/Bio.SeqIO.XdnaIO", "api/Bio.SeqRecord", "api/Bio.SeqUtils", "api/Bio.SeqUtils.CheckSum", "api/Bio.SeqUtils.IsoelectricPoint", "api/Bio.SeqUtils.MeltingTemp", "api/Bio.SeqUtils.ProtParam", "api/Bio.SeqUtils.ProtParamData", "api/Bio.SeqUtils.lcc", "api/Bio.Sequencing", "api/Bio.Sequencing.Ace", "api/Bio.Sequencing.Applications", "api/Bio.Sequencing.Phd", "api/Bio.SwissProt", "api/Bio.SwissProt.KeyWList", "api/Bio.TogoWS", "api/Bio.UniGene", "api/Bio.UniProt", "api/Bio.UniProt.GOA", "api/Bio.bgzf", "api/Bio.codonalign", "api/Bio.codonalign.codonalignment", "api/Bio.codonalign.codonseq", "api/Bio.kNN", "api/Bio.motifs", "api/Bio.motifs.alignace", "api/Bio.motifs.applications", "api/Bio.motifs.clusterbuster", "api/Bio.motifs.jaspar", "api/Bio.motifs.jaspar.db", "api/Bio.motifs.mast", "api/Bio.motifs.matrix", "api/Bio.motifs.meme", "api/Bio.motifs.minimal", "api/Bio.motifs.pfm", "api/Bio.motifs.thresholds", "api/Bio.motifs.transfac", "api/Bio.motifs.xms", "api/Bio.pairwise2", "api/Bio.phenotype", "api/Bio.phenotype.phen_micro", "api/Bio.phenotype.pm_fitting", "api/BioSQL", "api/BioSQL.BioSeq", "api/BioSQL.BioSeqDatabase", "api/BioSQL.DBUtils", "api/BioSQL.Loader", "api/index", "index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2}, "filenames": ["Tutorial/chapter_align.rst", "Tutorial/chapter_appendix.rst", "Tutorial/chapter_bibliography.rst", "Tutorial/chapter_blast.rst", "Tutorial/chapter_cluster.rst", "Tutorial/chapter_contributing.rst", "Tutorial/chapter_cookbook.rst", "Tutorial/chapter_entrez.rst", "Tutorial/chapter_graphics.rst", "Tutorial/chapter_introduction.rst", "Tutorial/chapter_kegg.rst", "Tutorial/chapter_motifs.rst", "Tutorial/chapter_msa.rst", "Tutorial/chapter_pairwise.rst", "Tutorial/chapter_pairwise2.rst", "Tutorial/chapter_pdb.rst", "Tutorial/chapter_phenotype.rst", "Tutorial/chapter_phylo.rst", "Tutorial/chapter_popgen.rst", "Tutorial/chapter_quick_start.rst", "Tutorial/chapter_searchio.rst", "Tutorial/chapter_seq_annot.rst", "Tutorial/chapter_seq_objects.rst", "Tutorial/chapter_seqio.rst", "Tutorial/chapter_testing.rst", "Tutorial/chapter_uniprot.rst", "Tutorial/index.rst", "api/Bio.rst", "api/Bio.Affy.rst", "api/Bio.Affy.CelFile.rst", "api/Bio.Align.rst", "api/Bio.Align.AlignInfo.rst", "api/Bio.Align.Applications.rst", "api/Bio.Align.a2m.rst", "api/Bio.Align.analysis.rst", "api/Bio.Align.bed.rst", "api/Bio.Align.bigbed.rst", "api/Bio.Align.bigmaf.rst", "api/Bio.Align.bigpsl.rst", "api/Bio.Align.chain.rst", "api/Bio.Align.clustal.rst", "api/Bio.Align.emboss.rst", "api/Bio.Align.exonerate.rst", "api/Bio.Align.fasta.rst", "api/Bio.Align.hhr.rst", "api/Bio.Align.interfaces.rst", "api/Bio.Align.maf.rst", "api/Bio.Align.mauve.rst", "api/Bio.Align.msf.rst", "api/Bio.Align.nexus.rst", "api/Bio.Align.phylip.rst", "api/Bio.Align.psl.rst", "api/Bio.Align.sam.rst", "api/Bio.Align.stockholm.rst", "api/Bio.Align.substitution_matrices.rst", "api/Bio.Align.tabular.rst", "api/Bio.AlignIO.rst", "api/Bio.AlignIO.ClustalIO.rst", "api/Bio.AlignIO.EmbossIO.rst", "api/Bio.AlignIO.FastaIO.rst", "api/Bio.AlignIO.Interfaces.rst", "api/Bio.AlignIO.MafIO.rst", "api/Bio.AlignIO.MauveIO.rst", "api/Bio.AlignIO.MsfIO.rst", "api/Bio.AlignIO.NexusIO.rst", "api/Bio.AlignIO.PhylipIO.rst", "api/Bio.AlignIO.StockholmIO.rst", "api/Bio.Application.rst", "api/Bio.Blast.rst", "api/Bio.Blast.Applications.rst", "api/Bio.Blast.NCBIWWW.rst", "api/Bio.Blast.NCBIXML.rst", "api/Bio.CAPS.rst", "api/Bio.Cluster.rst", "api/Bio.Compass.rst", "api/Bio.Data.rst", "api/Bio.Data.CodonTable.rst", "api/Bio.Data.IUPACData.rst", "api/Bio.Data.PDBData.rst", "api/Bio.Emboss.rst", "api/Bio.Emboss.Applications.rst", "api/Bio.Emboss.Primer3.rst", "api/Bio.Emboss.PrimerSearch.rst", "api/Bio.Entrez.rst", "api/Bio.Entrez.Parser.rst", "api/Bio.ExPASy.rst", "api/Bio.ExPASy.Enzyme.rst", "api/Bio.ExPASy.Prodoc.rst", "api/Bio.ExPASy.Prosite.rst", "api/Bio.ExPASy.ScanProsite.rst", "api/Bio.ExPASy.cellosaurus.rst", "api/Bio.File.rst", "api/Bio.GenBank.rst", "api/Bio.GenBank.Record.rst", "api/Bio.GenBank.Scanner.rst", "api/Bio.GenBank.utils.rst", "api/Bio.Geo.rst", "api/Bio.Geo.Record.rst", "api/Bio.Graphics.rst", "api/Bio.Graphics.BasicChromosome.rst", "api/Bio.Graphics.ColorSpiral.rst", "api/Bio.Graphics.Comparative.rst", "api/Bio.Graphics.DisplayRepresentation.rst", "api/Bio.Graphics.Distribution.rst", "api/Bio.Graphics.GenomeDiagram.rst", "api/Bio.Graphics.KGML_vis.rst", "api/Bio.HMM.rst", "api/Bio.HMM.DynamicProgramming.rst", "api/Bio.HMM.MarkovModel.rst", "api/Bio.HMM.Trainer.rst", "api/Bio.HMM.Utilities.rst", "api/Bio.KEGG.rst", "api/Bio.KEGG.Compound.rst", "api/Bio.KEGG.Enzyme.rst", "api/Bio.KEGG.Gene.rst", "api/Bio.KEGG.KGML.rst", "api/Bio.KEGG.KGML.KGML_parser.rst", "api/Bio.KEGG.KGML.KGML_pathway.rst", "api/Bio.KEGG.Map.rst", "api/Bio.KEGG.REST.rst", "api/Bio.LogisticRegression.rst", "api/Bio.MarkovModel.rst", "api/Bio.MaxEntropy.rst", "api/Bio.Medline.rst", "api/Bio.NMR.rst", "api/Bio.NMR.NOEtools.rst", "api/Bio.NMR.xpktools.rst", "api/Bio.NaiveBayes.rst", "api/Bio.Nexus.rst", "api/Bio.Nexus.Nexus.rst", "api/Bio.Nexus.Nodes.rst", "api/Bio.Nexus.StandardData.rst", "api/Bio.Nexus.Trees.rst", "api/Bio.PDB.rst", "api/Bio.PDB.AbstractPropertyMap.rst", "api/Bio.PDB.Atom.rst", "api/Bio.PDB.Chain.rst", "api/Bio.PDB.DSSP.rst", "api/Bio.PDB.Dice.rst", "api/Bio.PDB.Entity.rst", "api/Bio.PDB.FragmentMapper.rst", "api/Bio.PDB.HSExposure.rst", "api/Bio.PDB.MMCIF2Dict.rst", "api/Bio.PDB.MMCIFParser.rst", "api/Bio.PDB.Model.rst", "api/Bio.PDB.NACCESS.rst", "api/Bio.PDB.NeighborSearch.rst", "api/Bio.PDB.PDBExceptions.rst", "api/Bio.PDB.PDBIO.rst", "api/Bio.PDB.PDBList.rst", "api/Bio.PDB.PDBMLParser.rst", "api/Bio.PDB.PDBParser.rst", "api/Bio.PDB.PICIO.rst", "api/Bio.PDB.PSEA.rst", "api/Bio.PDB.Polypeptide.rst", "api/Bio.PDB.Residue.rst", "api/Bio.PDB.ResidueDepth.rst", "api/Bio.PDB.SASA.rst", "api/Bio.PDB.SCADIO.rst", "api/Bio.PDB.Selection.rst", "api/Bio.PDB.Structure.rst", "api/Bio.PDB.StructureAlignment.rst", "api/Bio.PDB.StructureBuilder.rst", "api/Bio.PDB.Superimposer.rst", "api/Bio.PDB.alphafold_db.rst", "api/Bio.PDB.binary_cif.rst", "api/Bio.PDB.cealign.rst", "api/Bio.PDB.ic_data.rst", "api/Bio.PDB.ic_rebuild.rst", "api/Bio.PDB.internal_coords.rst", "api/Bio.PDB.mmcifio.rst", "api/Bio.PDB.mmtf.rst", "api/Bio.PDB.mmtf.DefaultParser.rst", "api/Bio.PDB.mmtf.mmtfio.rst", "api/Bio.PDB.parse_pdb_header.rst", "api/Bio.PDB.qcprot.rst", "api/Bio.PDB.vectors.rst", "api/Bio.Pathway.rst", "api/Bio.Pathway.Rep.rst", "api/Bio.Pathway.Rep.Graph.rst", "api/Bio.Pathway.Rep.MultiGraph.rst", "api/Bio.Phylo.rst", "api/Bio.Phylo.Applications.rst", "api/Bio.Phylo.BaseTree.rst", "api/Bio.Phylo.CDAO.rst", "api/Bio.Phylo.CDAOIO.rst", "api/Bio.Phylo.Consensus.rst", "api/Bio.Phylo.NeXML.rst", "api/Bio.Phylo.NeXMLIO.rst", "api/Bio.Phylo.Newick.rst", "api/Bio.Phylo.NewickIO.rst", "api/Bio.Phylo.NexusIO.rst", "api/Bio.Phylo.PAML.rst", "api/Bio.Phylo.PAML.baseml.rst", "api/Bio.Phylo.PAML.chi2.rst", "api/Bio.Phylo.PAML.codeml.rst", "api/Bio.Phylo.PAML.yn00.rst", "api/Bio.Phylo.PhyloXML.rst", "api/Bio.Phylo.PhyloXMLIO.rst", "api/Bio.Phylo.TreeConstruction.rst", "api/Bio.PopGen.rst", "api/Bio.PopGen.GenePop.rst", "api/Bio.PopGen.GenePop.Controller.rst", "api/Bio.PopGen.GenePop.EasyController.rst", "api/Bio.PopGen.GenePop.FileParser.rst", "api/Bio.PopGen.GenePop.LargeFileParser.rst", "api/Bio.Restriction.rst", "api/Bio.Restriction.PrintFormat.rst", "api/Bio.Restriction.Restriction_Dictionary.rst", "api/Bio.SCOP.rst", "api/Bio.SCOP.Cla.rst", "api/Bio.SCOP.Des.rst", "api/Bio.SCOP.Dom.rst", "api/Bio.SCOP.Hie.rst", "api/Bio.SCOP.Raf.rst", "api/Bio.SCOP.Residues.rst", "api/Bio.SVDSuperimposer.rst", "api/Bio.SearchIO.rst", "api/Bio.SearchIO.BlastIO.rst", "api/Bio.SearchIO.BlastIO.blast_tab.rst", "api/Bio.SearchIO.BlastIO.blast_xml.rst", "api/Bio.SearchIO.BlatIO.rst", "api/Bio.SearchIO.ExonerateIO.rst", "api/Bio.SearchIO.ExonerateIO.exonerate_cigar.rst", "api/Bio.SearchIO.ExonerateIO.exonerate_text.rst", "api/Bio.SearchIO.ExonerateIO.exonerate_vulgar.rst", "api/Bio.SearchIO.FastaIO.rst", "api/Bio.SearchIO.HHsuiteIO.rst", "api/Bio.SearchIO.HHsuiteIO.hhsuite2_text.rst", "api/Bio.SearchIO.HmmerIO.rst", "api/Bio.SearchIO.HmmerIO.hmmer2_text.rst", "api/Bio.SearchIO.HmmerIO.hmmer3_domtab.rst", "api/Bio.SearchIO.HmmerIO.hmmer3_tab.rst", "api/Bio.SearchIO.HmmerIO.hmmer3_text.rst", "api/Bio.SearchIO.InterproscanIO.rst", "api/Bio.SearchIO.InterproscanIO.interproscan_xml.rst", "api/Bio.Seq.rst", "api/Bio.SeqFeature.rst", "api/Bio.SeqIO.rst", "api/Bio.SeqIO.AbiIO.rst", "api/Bio.SeqIO.AceIO.rst", "api/Bio.SeqIO.FastaIO.rst", "api/Bio.SeqIO.GckIO.rst", "api/Bio.SeqIO.GfaIO.rst", "api/Bio.SeqIO.IgIO.rst", "api/Bio.SeqIO.InsdcIO.rst", "api/Bio.SeqIO.Interfaces.rst", "api/Bio.SeqIO.NibIO.rst", "api/Bio.SeqIO.PdbIO.rst", "api/Bio.SeqIO.PhdIO.rst", "api/Bio.SeqIO.PirIO.rst", "api/Bio.SeqIO.QualityIO.rst", "api/Bio.SeqIO.SeqXmlIO.rst", "api/Bio.SeqIO.SffIO.rst", "api/Bio.SeqIO.SnapGeneIO.rst", "api/Bio.SeqIO.SwissIO.rst", "api/Bio.SeqIO.TabIO.rst", "api/Bio.SeqIO.TwoBitIO.rst", "api/Bio.SeqIO.UniprotIO.rst", "api/Bio.SeqIO.XdnaIO.rst", "api/Bio.SeqRecord.rst", "api/Bio.SeqUtils.rst", "api/Bio.SeqUtils.CheckSum.rst", "api/Bio.SeqUtils.IsoelectricPoint.rst", "api/Bio.SeqUtils.MeltingTemp.rst", "api/Bio.SeqUtils.ProtParam.rst", "api/Bio.SeqUtils.ProtParamData.rst", "api/Bio.SeqUtils.lcc.rst", "api/Bio.Sequencing.rst", "api/Bio.Sequencing.Ace.rst", "api/Bio.Sequencing.Applications.rst", "api/Bio.Sequencing.Phd.rst", "api/Bio.SwissProt.rst", "api/Bio.SwissProt.KeyWList.rst", "api/Bio.TogoWS.rst", "api/Bio.UniGene.rst", "api/Bio.UniProt.rst", "api/Bio.UniProt.GOA.rst", "api/Bio.bgzf.rst", "api/Bio.codonalign.rst", "api/Bio.codonalign.codonalignment.rst", "api/Bio.codonalign.codonseq.rst", "api/Bio.kNN.rst", "api/Bio.motifs.rst", "api/Bio.motifs.alignace.rst", "api/Bio.motifs.applications.rst", "api/Bio.motifs.clusterbuster.rst", "api/Bio.motifs.jaspar.rst", "api/Bio.motifs.jaspar.db.rst", "api/Bio.motifs.mast.rst", "api/Bio.motifs.matrix.rst", "api/Bio.motifs.meme.rst", "api/Bio.motifs.minimal.rst", "api/Bio.motifs.pfm.rst", "api/Bio.motifs.thresholds.rst", "api/Bio.motifs.transfac.rst", "api/Bio.motifs.xms.rst", "api/Bio.pairwise2.rst", "api/Bio.phenotype.rst", "api/Bio.phenotype.phen_micro.rst", "api/Bio.phenotype.pm_fitting.rst", "api/BioSQL.rst", "api/BioSQL.BioSeq.rst", "api/BioSQL.BioSeqDatabase.rst", "api/BioSQL.DBUtils.rst", "api/BioSQL.Loader.rst", "api/index.rst", "index.rst"], "indexentries": {"__abstractmethods__ (bio.align.a2m.alignmentiterator attribute)": [[33, "Bio.Align.a2m.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.a2m.alignmentwriter attribute)": [[33, "Bio.Align.a2m.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.alignments attribute)": [[30, "Bio.Align.Alignments.__abstractmethods__", false]], "__abstractmethods__ (bio.align.alignmentsabstractbaseclass attribute)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bed.alignmentiterator attribute)": [[35, "Bio.Align.bed.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bed.alignmentwriter attribute)": [[35, "Bio.Align.bed.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigbed.alignmentiterator attribute)": [[36, "Bio.Align.bigbed.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigbed.alignmentwriter attribute)": [[36, "Bio.Align.bigbed.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigmaf.alignmentiterator attribute)": [[37, "Bio.Align.bigmaf.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigmaf.alignmentwriter attribute)": [[37, "Bio.Align.bigmaf.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigpsl.alignmentiterator attribute)": [[38, "Bio.Align.bigpsl.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.bigpsl.alignmentwriter attribute)": [[38, "Bio.Align.bigpsl.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.chain.alignmentiterator attribute)": [[39, "Bio.Align.chain.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.chain.alignmentwriter attribute)": [[39, "Bio.Align.chain.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.clustal.alignmentiterator attribute)": [[40, "Bio.Align.clustal.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.clustal.alignmentwriter attribute)": [[40, "Bio.Align.clustal.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.emboss.alignmentiterator attribute)": [[41, "Bio.Align.emboss.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.exonerate.alignmentiterator attribute)": [[42, "Bio.Align.exonerate.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.exonerate.alignmentwriter attribute)": [[42, "Bio.Align.exonerate.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.fasta.alignmentiterator attribute)": [[43, "Bio.Align.fasta.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.fasta.alignmentwriter attribute)": [[43, "Bio.Align.fasta.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.hhr.alignmentiterator attribute)": [[44, "Bio.Align.hhr.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.maf.alignmentwriter attribute)": [[46, "Bio.Align.maf.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.mauve.alignmentiterator attribute)": [[47, "Bio.Align.mauve.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.mauve.alignmentwriter attribute)": [[47, "Bio.Align.mauve.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.msf.alignmentiterator attribute)": [[48, "Bio.Align.msf.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.nexus.alignmentiterator attribute)": [[49, "Bio.Align.nexus.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.nexus.alignmentwriter attribute)": [[49, "Bio.Align.nexus.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.pairwisealignments attribute)": [[30, "Bio.Align.PairwiseAlignments.__abstractmethods__", false]], "__abstractmethods__ (bio.align.phylip.alignmentiterator attribute)": [[50, "Bio.Align.phylip.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.phylip.alignmentwriter attribute)": [[50, "Bio.Align.phylip.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.psl.alignmentiterator attribute)": [[51, "Bio.Align.psl.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.psl.alignmentwriter attribute)": [[51, "Bio.Align.psl.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.sam.alignmentiterator attribute)": [[52, "Bio.Align.sam.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.sam.alignmentwriter attribute)": [[52, "Bio.Align.sam.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.__abstractmethods__", false]], "__abstractmethods__ (bio.align.tabular.alignmentiterator attribute)": [[55, "Bio.Align.tabular.AlignmentIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.blast.hit attribute)": [[68, "Bio.Blast.Hit.__abstractmethods__", false]], "__abstractmethods__ (bio.blast.records attribute)": [[68, "Bio.Blast.Records.__abstractmethods__", false]], "__abstractmethods__ (bio.codonalign.codonseq.codonseq attribute)": [[281, "Bio.codonalign.codonseq.CodonSeq.__abstractmethods__", false]], "__abstractmethods__ (bio.motifs.meme.instance attribute)": [[291, "Bio.motifs.meme.Instance.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.blastio.blast_tab.blasttabindexer attribute)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.blatio.blatpslindexer attribute)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarindexer attribute)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarparser attribute)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_text.exoneratetextindexer attribute)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_text.exoneratetextparser attribute)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer attribute)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarparser attribute)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.fastaio.fastam10indexer attribute)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer attribute)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitindexer attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmqueryindexer attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabindexer attribute)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer attribute)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.__abstractmethods__", false]], "__abstractmethods__ (bio.seq.mutableseq attribute)": [[236, "Bio.Seq.MutableSeq.__abstractmethods__", false]], "__abstractmethods__ (bio.seq.seq attribute)": [[236, "Bio.Seq.Seq.__abstractmethods__", false]], "__abstractmethods__ (bio.seq.sequencedataabstractbaseclass attribute)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.afterposition attribute)": [[237, "Bio.SeqFeature.AfterPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.beforeposition attribute)": [[237, "Bio.SeqFeature.BeforePosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.betweenposition attribute)": [[237, "Bio.SeqFeature.BetweenPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.compoundlocation attribute)": [[237, "Bio.SeqFeature.CompoundLocation.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.exactposition attribute)": [[237, "Bio.SeqFeature.ExactPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.location attribute)": [[237, "Bio.SeqFeature.Location.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.oneofposition attribute)": [[237, "Bio.SeqFeature.OneOfPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.position attribute)": [[237, "Bio.SeqFeature.Position.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.simplelocation attribute)": [[237, "Bio.SeqFeature.SimpleLocation.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.uncertainposition attribute)": [[237, "Bio.SeqFeature.UncertainPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.unknownposition attribute)": [[237, "Bio.SeqFeature.UnknownPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqfeature.withinposition attribute)": [[237, "Bio.SeqFeature.WithinPosition.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.abiio.abiiterator attribute)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.fastaio.fastaiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.fastaio.fastatwolineiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.gckio.gckiterator attribute)": [[242, "Bio.SeqIO.GckIO.GckIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.igio.igiterator attribute)": [[244, "Bio.SeqIO.IgIO.IgIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.emblcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.embliterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.genbankcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.genbankiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.insdcio.imgtiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.interfaces.sequenceiterator attribute)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.nibio.nibiterator attribute)": [[247, "Bio.SeqIO.NibIO.NibIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.pdbio.pdbseqresiterator attribute)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.pirio.piriterator attribute)": [[250, "Bio.SeqIO.PirIO.PirIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.qualityio.fastqphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.qualityio.qualphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.seqxmlio.seqxmliterator attribute)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.sffio.sffiterator attribute)": [[253, "Bio.SeqIO.SffIO.SffIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.snapgeneio.snapgeneiterator attribute)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.tabio.tabiterator attribute)": [[256, "Bio.SeqIO.TabIO.TabIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.twobitio.twobititerator attribute)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__abstractmethods__", false]], "__abstractmethods__ (bio.seqio.xdnaio.xdnaiterator attribute)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.__abstractmethods__", false]], "__add__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__add__", false]], "__add__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__add__", false]], "__add__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__add__", false]], "__add__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__add__", false]], "__add__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__add__", false]], "__add__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__add__", false]], "__add__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__add__", false]], "__add__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__add__", false]], "__add__() (bio.seqfeature.afterposition method)": [[237, "Bio.SeqFeature.AfterPosition.__add__", false]], "__add__() (bio.seqfeature.beforeposition method)": [[237, "Bio.SeqFeature.BeforePosition.__add__", false]], "__add__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__add__", false]], "__add__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__add__", false]], "__add__() (bio.seqfeature.exactposition method)": [[237, "Bio.SeqFeature.ExactPosition.__add__", false]], "__add__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__add__", false]], "__add__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__add__", false]], "__add__() (bio.seqfeature.unknownposition method)": [[237, "Bio.SeqFeature.UnknownPosition.__add__", false]], "__add__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__add__", false]], "__add__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__add__", false]], "__annotations__ (bio.align.bigbed.autosqltable attribute)": [[36, "Bio.Align.bigbed.AutoSQLTable.__annotations__", false]], "__annotations__ (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.__annotations__", false]], "__annotations__ (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.__annotations__", false]], "__annotations__ (bio.alignio.mauveio.mauveiterator attribute)": [[62, "Bio.AlignIO.MauveIO.MauveIterator.__annotations__", false]], "__annotations__ (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.__annotations__", false]], "__annotations__ (bio.data.codontable.ncbicodontable attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTable.__annotations__", false]], "__annotations__ (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.__annotations__", false]], "__annotations__ (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.__annotations__", false]], "__annotations__ (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.__annotations__", false]], "__annotations__ (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.__annotations__", false]], "__annotations__ (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer attribute)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.__annotations__", false]], "__annotations__ (bio.seq.seq attribute)": [[236, "Bio.Seq.Seq.__annotations__", false]], "__annotations__ (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.__annotations__", false]], "__array__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__array__", false]], "__array_finalize__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_finalize__", false]], "__array_prepare__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_prepare__", false]], "__array_ufunc__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_ufunc__", false]], "__array_wrap__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__array_wrap__", false]], "__bool__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__bool__", false]], "__bool__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__bool__", false]], "__bool__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__bool__", false]], "__bytes__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__bytes__", false]], "__bytes__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__bytes__", false]], "__bytes__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__bytes__", false]], "__call__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__call__", false]], "__call__() (bio.pairwise2.affine_penalty method)": [[297, "Bio.pairwise2.affine_penalty.__call__", false]], "__call__() (bio.pairwise2.dictionary_match method)": [[297, "Bio.pairwise2.dictionary_match.__call__", false]], "__call__() (bio.pairwise2.identity_match method)": [[297, "Bio.pairwise2.identity_match.__call__", false]], "__contains__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__contains__", false]], "__contains__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__contains__", false]], "__contains__() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.__contains__", false]], "__contains__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__contains__", false]], "__contains__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__contains__", false]], "__contains__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__contains__", false]], "__contains__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__contains__", false]], "__contains__() (bio.pdb.fragmentmapper.fragmentmapper method)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper.__contains__", false]], "__contains__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__contains__", false]], "__contains__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__contains__", false]], "__contains__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__contains__", false]], "__contains__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__contains__", false]], "__contains__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__contains__", false]], "__contains__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__contains__", false]], "__contains__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__contains__", false]], "__contains__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__contains__", false]], "__contains__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__contains__", false]], "__contains__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__contains__", false]], "__contains__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__contains__", false]], "__contains__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__contains__", false]], "__deepcopy__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__deepcopy__", false]], "__deepcopy__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__deepcopy__", false]], "__deepcopy__() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.__deepcopy__", false]], "__deepcopy__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__deepcopy__", false]], "__delitem__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__delitem__", false]], "__delitem__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__delitem__", false]], "__delitem__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__delitem__", false]], "__delitem__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__delitem__", false]], "__delitem__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__delitem__", false]], "__delitem__() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.__delitem__", false]], "__delitem__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__delitem__", false]], "__delitem__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__delitem__", false]], "__enter__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__enter__", false]], "__enter__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__enter__", false]], "__enter__() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.__enter__", false]], "__enter__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__enter__", false]], "__eq__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__eq__", false]], "__eq__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__eq__", false]], "__eq__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__eq__", false]], "__eq__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__eq__", false]], "__eq__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__eq__", false]], "__eq__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__eq__", false]], "__eq__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__eq__", false]], "__eq__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__eq__", false]], "__eq__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__eq__", false]], "__eq__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__eq__", false]], "__eq__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__eq__", false]], "__eq__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__eq__", false]], "__eq__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__eq__", false]], "__eq__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__eq__", false]], "__eq__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__eq__", false]], "__eq__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__eq__", false]], "__eq__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__eq__", false]], "__eq__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__eq__", false]], "__exit__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__exit__", false]], "__exit__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__exit__", false]], "__exit__() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.__exit__", false]], "__exit__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__exit__", false]], "__format__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__format__", false]], "__format__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__format__", false]], "__format__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__format__", false]], "__format__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__format__", false]], "__format__() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.__format__", false]], "__format__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__format__", false]], "__ge__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__ge__", false]], "__ge__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__ge__", false]], "__ge__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__ge__", false]], "__ge__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__ge__", false]], "__ge__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__ge__", false]], "__ge__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__ge__", false]], "__ge__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__ge__", false]], "__ge__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__ge__", false]], "__ge__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__ge__", false]], "__getattr__() (bio.data.codontable.ambiguouscodontable method)": [[76, "Bio.Data.CodonTable.AmbiguousCodonTable.__getattr__", false]], "__getattr__() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.__getattr__", false]], "__getattr__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__getattr__", false]], "__getitem__() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.__getitem__", false]], "__getitem__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__getitem__", false]], "__getitem__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__getitem__", false]], "__getitem__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__getitem__", false]], "__getitem__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__getitem__", false]], "__getitem__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__getitem__", false]], "__getitem__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__getitem__", false]], "__getitem__() (bio.blast.hit method)": [[68, "Bio.Blast.Hit.__getitem__", false]], "__getitem__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__getitem__", false]], "__getitem__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__getitem__", false]], "__getitem__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__getitem__", false]], "__getitem__() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__getitem__", false]], "__getitem__() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.__getitem__", false]], "__getitem__() (bio.motifs.mast.record method)": [[289, "Bio.motifs.mast.Record.__getitem__", false]], "__getitem__() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.__getitem__", false]], "__getitem__() (bio.motifs.meme.record method)": [[291, "Bio.motifs.meme.Record.__getitem__", false]], "__getitem__() (bio.motifs.minimal.record method)": [[292, "Bio.motifs.minimal.Record.__getitem__", false]], "__getitem__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__getitem__", false]], "__getitem__() (bio.motifs.transfac.motif method)": [[295, "Bio.motifs.transfac.Motif.__getitem__", false]], "__getitem__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__getitem__", false]], "__getitem__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__", false]], "__getitem__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__getitem__", false]], "__getitem__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__getitem__", false]], "__getitem__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__getitem__", false]], "__getitem__() (bio.pdb.fragmentmapper.fragmentmapper method)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper.__getitem__", false]], "__getitem__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__getitem__", false]], "__getitem__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__getitem__", false]], "__getitem__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__getitem__", false]], "__getitem__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__getitem__", false]], "__getitem__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__getitem__", false]], "__getitem__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__getitem__", false]], "__getitem__() (bio.scop.cla.index method)": [[210, "Bio.SCOP.Cla.Index.__getitem__", false]], "__getitem__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__getitem__", false]], "__getitem__() (bio.scop.raf.seqmapindex method)": [[214, "Bio.SCOP.Raf.SeqMapIndex.__getitem__", false]], "__getitem__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__getitem__", false]], "__getitem__() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__getitem__", false]], "__getitem__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__getitem__", false]], "__getitem__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__", false]], "__getitem__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__getitem__", false]], "__getnewargs__() (bio.align.alignmentcounts method)": [[30, "Bio.Align.AlignmentCounts.__getnewargs__", false]], "__getnewargs__() (bio.align.bigbed.field method)": [[36, "Bio.Align.bigbed.Field.__getnewargs__", false]], "__getnewargs__() (bio.pairwise2.alignment method)": [[297, "Bio.pairwise2.Alignment.__getnewargs__", false]], "__getnewargs__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__getnewargs__", false]], "__getnewargs__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__getnewargs__", false]], "__getnewargs__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__getnewargs__", false]], "__getstate__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__getstate__", false]], "__gt__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__gt__", false]], "__gt__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__gt__", false]], "__gt__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__gt__", false]], "__gt__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__gt__", false]], "__gt__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__gt__", false]], "__gt__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__gt__", false]], "__gt__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__gt__", false]], "__gt__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__gt__", false]], "__gt__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__gt__", false]], "__hash__ (bio.align.alignment attribute)": [[30, "Bio.Align.Alignment.__hash__", false]], "__hash__ (bio.entrez.parser.noneelement attribute)": [[84, "Bio.Entrez.Parser.NoneElement.__hash__", false]], "__hash__ (bio.pathway.rep.graph.graph attribute)": [[179, "Bio.Pathway.Rep.Graph.Graph.__hash__", false]], "__hash__ (bio.pathway.rep.multigraph.multigraph attribute)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__hash__", false]], "__hash__ (bio.phenotype.phen_micro.platerecord attribute)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__hash__", false]], "__hash__ (bio.phenotype.phen_micro.wellrecord attribute)": [[299, "Bio.phenotype.phen_micro.WellRecord.__hash__", false]], "__hash__ (bio.seqfeature.compoundlocation attribute)": [[237, "Bio.SeqFeature.CompoundLocation.__hash__", false]], "__hash__ (bio.seqfeature.reference attribute)": [[237, "Bio.SeqFeature.Reference.__hash__", false]], "__hash__ (bio.seqfeature.seqfeature attribute)": [[237, "Bio.SeqFeature.SeqFeature.__hash__", false]], "__hash__ (bio.seqfeature.simplelocation attribute)": [[237, "Bio.SeqFeature.SimpleLocation.__hash__", false]], "__hash__ (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.__hash__", false]], "__hash__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__hash__", false]], "__hash__() (bio.pathway.interaction method)": [[177, "Bio.Pathway.Interaction.__hash__", false]], "__hash__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__hash__", false]], "__hash__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__hash__", false]], "__hash__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__hash__", false]], "__hash__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__hash__", false]], "__hash__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__hash__", false]], "__hash__() (bio.seq.seq method)": [[236, "Bio.Seq.Seq.__hash__", false]], "__hash__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__hash__", false]], "__hash__() (bio.seqfeature.unknownposition method)": [[237, "Bio.SeqFeature.UnknownPosition.__hash__", false]], "__iadd__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__iadd__", false]], "__init__() (bio.affy.celfile.parsererror method)": [[29, "Bio.Affy.CelFile.ParserError.__init__", false]], "__init__() (bio.affy.celfile.record method)": [[29, "Bio.Affy.CelFile.Record.__init__", false]], "__init__() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.__init__", false]], "__init__() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.__init__", false]], "__init__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__init__", false]], "__init__() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.__init__", false]], "__init__() (bio.align.applications.clustalomegacommandline method)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.__init__", false]], "__init__() (bio.align.applications.clustalwcommandline method)": [[32, "Bio.Align.Applications.ClustalwCommandline.__init__", false]], "__init__() (bio.align.applications.dialigncommandline method)": [[32, "Bio.Align.Applications.DialignCommandline.__init__", false]], "__init__() (bio.align.applications.mafftcommandline method)": [[32, "Bio.Align.Applications.MafftCommandline.__init__", false]], "__init__() (bio.align.applications.msaprobscommandline method)": [[32, "Bio.Align.Applications.MSAProbsCommandline.__init__", false]], "__init__() (bio.align.applications.musclecommandline method)": [[32, "Bio.Align.Applications.MuscleCommandline.__init__", false]], "__init__() (bio.align.applications.prankcommandline method)": [[32, "Bio.Align.Applications.PrankCommandline.__init__", false]], "__init__() (bio.align.applications.probconscommandline method)": [[32, "Bio.Align.Applications.ProbconsCommandline.__init__", false]], "__init__() (bio.align.applications.tcoffeecommandline method)": [[32, "Bio.Align.Applications.TCoffeeCommandline.__init__", false]], "__init__() (bio.align.bed.alignmentwriter method)": [[35, "Bio.Align.bed.AlignmentWriter.__init__", false]], "__init__() (bio.align.bigbed.alignmentwriter method)": [[36, "Bio.Align.bigbed.AlignmentWriter.__init__", false]], "__init__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__init__", false]], "__init__() (bio.align.bigmaf.alignmentiterator method)": [[37, "Bio.Align.bigmaf.AlignmentIterator.__init__", false]], "__init__() (bio.align.bigmaf.alignmentwriter method)": [[37, "Bio.Align.bigmaf.AlignmentWriter.__init__", false]], "__init__() (bio.align.bigpsl.alignmentwriter method)": [[38, "Bio.Align.bigpsl.AlignmentWriter.__init__", false]], "__init__() (bio.align.codonaligner method)": [[30, "Bio.Align.CodonAligner.__init__", false]], "__init__() (bio.align.exonerate.alignmentwriter method)": [[42, "Bio.Align.exonerate.AlignmentWriter.__init__", false]], "__init__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__init__", false]], "__init__() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.__init__", false]], "__init__() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.__init__", false]], "__init__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__init__", false]], "__init__() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.__init__", false]], "__init__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__init__", false]], "__init__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__init__", false]], "__init__() (bio.align.psl.alignmentwriter method)": [[51, "Bio.Align.psl.AlignmentWriter.__init__", false]], "__init__() (bio.align.sam.alignmentwriter method)": [[52, "Bio.Align.sam.AlignmentWriter.__init__", false]], "__init__() (bio.alignio.interfaces.alignmentiterator method)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator.__init__", false]], "__init__() (bio.alignio.interfaces.alignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter.__init__", false]], "__init__() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__", false]], "__init__() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.__init__", false]], "__init__() (bio.alignio.mauveio.mauvewriter method)": [[62, "Bio.AlignIO.MauveIO.MauveWriter.__init__", false]], "__init__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__init__", false]], "__init__() (bio.application.applicationerror method)": [[67, "Bio.Application.ApplicationError.__init__", false]], "__init__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__init__", false]], "__init__() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.__init__", false]], "__init__() (bio.blast.applications.ncbiblastformattercommandline method)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbiblastncommandline method)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbiblastpcommandline method)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbiblastxcommandline method)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbideltablastcommandline method)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbimakeblastdbcommandline method)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbipsiblastcommandline method)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbirpsblastcommandline method)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbirpstblastncommandline method)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbitblastncommandline method)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.__init__", false]], "__init__() (bio.blast.applications.ncbitblastxcommandline method)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.__init__", false]], "__init__() (bio.blast.corruptedxmlerror method)": [[68, "Bio.Blast.CorruptedXMLError.__init__", false]], "__init__() (bio.blast.ncbixml.alignment method)": [[71, "Bio.Blast.NCBIXML.Alignment.__init__", false]], "__init__() (bio.blast.ncbixml.blast method)": [[71, "Bio.Blast.NCBIXML.Blast.__init__", false]], "__init__() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.__init__", false]], "__init__() (bio.blast.ncbixml.databasereport method)": [[71, "Bio.Blast.NCBIXML.DatabaseReport.__init__", false]], "__init__() (bio.blast.ncbixml.description method)": [[71, "Bio.Blast.NCBIXML.Description.__init__", false]], "__init__() (bio.blast.ncbixml.descriptionext method)": [[71, "Bio.Blast.NCBIXML.DescriptionExt.__init__", false]], "__init__() (bio.blast.ncbixml.descriptionextitem method)": [[71, "Bio.Blast.NCBIXML.DescriptionExtItem.__init__", false]], "__init__() (bio.blast.ncbixml.header method)": [[71, "Bio.Blast.NCBIXML.Header.__init__", false]], "__init__() (bio.blast.ncbixml.hsp method)": [[71, "Bio.Blast.NCBIXML.HSP.__init__", false]], "__init__() (bio.blast.ncbixml.multiplealignment method)": [[71, "Bio.Blast.NCBIXML.MultipleAlignment.__init__", false]], "__init__() (bio.blast.ncbixml.parameters method)": [[71, "Bio.Blast.NCBIXML.Parameters.__init__", false]], "__init__() (bio.blast.ncbixml.psiblast method)": [[71, "Bio.Blast.NCBIXML.PSIBlast.__init__", false]], "__init__() (bio.blast.ncbixml.round method)": [[71, "Bio.Blast.NCBIXML.Round.__init__", false]], "__init__() (bio.blast.notxmlerror method)": [[68, "Bio.Blast.NotXMLError.__init__", false]], "__init__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__init__", false]], "__init__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__init__", false]], "__init__() (bio.caps.capsmap method)": [[72, "Bio.CAPS.CAPSMap.__init__", false]], "__init__() (bio.caps.differentialcutsite method)": [[72, "Bio.CAPS.DifferentialCutsite.__init__", false]], "__init__() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.__init__", false]], "__init__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__init__", false]], "__init__() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.__init__", false]], "__init__() (bio.compass.record method)": [[74, "Bio.Compass.Record.__init__", false]], "__init__() (bio.data.codontable.ambiguouscodontable method)": [[76, "Bio.Data.CodonTable.AmbiguousCodonTable.__init__", false]], "__init__() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.__init__", false]], "__init__() (bio.data.codontable.codontable method)": [[76, "Bio.Data.CodonTable.CodonTable.__init__", false]], "__init__() (bio.data.codontable.ncbicodontable method)": [[76, "Bio.Data.CodonTable.NCBICodonTable.__init__", false]], "__init__() (bio.emboss.applications.diffseqcommandline method)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.__init__", false]], "__init__() (bio.emboss.applications.einvertedcommandline method)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.__init__", false]], "__init__() (bio.emboss.applications.est2genomecommandline method)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.__init__", false]], "__init__() (bio.emboss.applications.etandemcommandline method)": [[80, "Bio.Emboss.Applications.ETandemCommandline.__init__", false]], "__init__() (bio.emboss.applications.fconsensecommandline method)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.__init__", false]], "__init__() (bio.emboss.applications.fdnadistcommandline method)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.__init__", false]], "__init__() (bio.emboss.applications.fdnaparscommandline method)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.__init__", false]], "__init__() (bio.emboss.applications.fneighborcommandline method)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.__init__", false]], "__init__() (bio.emboss.applications.fprotdistcommandline method)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.__init__", false]], "__init__() (bio.emboss.applications.fprotparscommandline method)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.__init__", false]], "__init__() (bio.emboss.applications.fseqbootcommandline method)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.__init__", false]], "__init__() (bio.emboss.applications.ftreedistcommandline method)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.__init__", false]], "__init__() (bio.emboss.applications.fuzznuccommandline method)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.__init__", false]], "__init__() (bio.emboss.applications.fuzzprocommandline method)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.__init__", false]], "__init__() (bio.emboss.applications.iepcommandline method)": [[80, "Bio.Emboss.Applications.IepCommandline.__init__", false]], "__init__() (bio.emboss.applications.needleallcommandline method)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.__init__", false]], "__init__() (bio.emboss.applications.needlecommandline method)": [[80, "Bio.Emboss.Applications.NeedleCommandline.__init__", false]], "__init__() (bio.emboss.applications.palindromecommandline method)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.__init__", false]], "__init__() (bio.emboss.applications.primer3commandline method)": [[80, "Bio.Emboss.Applications.Primer3Commandline.__init__", false]], "__init__() (bio.emboss.applications.primersearchcommandline method)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.__init__", false]], "__init__() (bio.emboss.applications.seqmatchallcommandline method)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.__init__", false]], "__init__() (bio.emboss.applications.seqretcommandline method)": [[80, "Bio.Emboss.Applications.SeqretCommandline.__init__", false]], "__init__() (bio.emboss.applications.stretchercommandline method)": [[80, "Bio.Emboss.Applications.StretcherCommandline.__init__", false]], "__init__() (bio.emboss.applications.tranaligncommandline method)": [[80, "Bio.Emboss.Applications.TranalignCommandline.__init__", false]], "__init__() (bio.emboss.applications.watercommandline method)": [[80, "Bio.Emboss.Applications.WaterCommandline.__init__", false]], "__init__() (bio.emboss.primer3.primers method)": [[81, "Bio.Emboss.Primer3.Primers.__init__", false]], "__init__() (bio.emboss.primer3.record method)": [[81, "Bio.Emboss.Primer3.Record.__init__", false]], "__init__() (bio.emboss.primersearch.amplifier method)": [[82, "Bio.Emboss.PrimerSearch.Amplifier.__init__", false]], "__init__() (bio.emboss.primersearch.inputrecord method)": [[82, "Bio.Emboss.PrimerSearch.InputRecord.__init__", false]], "__init__() (bio.emboss.primersearch.outputrecord method)": [[82, "Bio.Emboss.PrimerSearch.OutputRecord.__init__", false]], "__init__() (bio.entrez.parser.corruptedxmlerror method)": [[84, "Bio.Entrez.Parser.CorruptedXMLError.__init__", false]], "__init__() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.__init__", false]], "__init__() (bio.entrez.parser.datahandlermeta method)": [[84, "Bio.Entrez.Parser.DataHandlerMeta.__init__", false]], "__init__() (bio.entrez.parser.dictionaryelement method)": [[84, "Bio.Entrez.Parser.DictionaryElement.__init__", false]], "__init__() (bio.entrez.parser.errorelement method)": [[84, "Bio.Entrez.Parser.ErrorElement.__init__", false]], "__init__() (bio.entrez.parser.integerelement method)": [[84, "Bio.Entrez.Parser.IntegerElement.__init__", false]], "__init__() (bio.entrez.parser.listelement method)": [[84, "Bio.Entrez.Parser.ListElement.__init__", false]], "__init__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__init__", false]], "__init__() (bio.entrez.parser.notxmlerror method)": [[84, "Bio.Entrez.Parser.NotXMLError.__init__", false]], "__init__() (bio.entrez.parser.orderedlistelement method)": [[84, "Bio.Entrez.Parser.OrderedListElement.__init__", false]], "__init__() (bio.entrez.parser.stringelement method)": [[84, "Bio.Entrez.Parser.StringElement.__init__", false]], "__init__() (bio.entrez.parser.validationerror method)": [[84, "Bio.Entrez.Parser.ValidationError.__init__", false]], "__init__() (bio.expasy.cellosaurus.record method)": [[90, "Bio.ExPASy.cellosaurus.Record.__init__", false]], "__init__() (bio.expasy.enzyme.record method)": [[86, "Bio.ExPASy.Enzyme.Record.__init__", false]], "__init__() (bio.expasy.prodoc.record method)": [[87, "Bio.ExPASy.Prodoc.Record.__init__", false]], "__init__() (bio.expasy.prodoc.reference method)": [[87, "Bio.ExPASy.Prodoc.Reference.__init__", false]], "__init__() (bio.expasy.prosite.record method)": [[88, "Bio.ExPASy.Prosite.Record.__init__", false]], "__init__() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.__init__", false]], "__init__() (bio.expasy.scanprosite.parser method)": [[89, "Bio.ExPASy.ScanProsite.Parser.__init__", false]], "__init__() (bio.expasy.scanprosite.record method)": [[89, "Bio.ExPASy.ScanProsite.Record.__init__", false]], "__init__() (bio.genbank.featureparser method)": [[92, "Bio.GenBank.FeatureParser.__init__", false]], "__init__() (bio.genbank.iterator method)": [[92, "Bio.GenBank.Iterator.__init__", false]], "__init__() (bio.genbank.record.feature method)": [[93, "Bio.GenBank.Record.Feature.__init__", false]], "__init__() (bio.genbank.record.qualifier method)": [[93, "Bio.GenBank.Record.Qualifier.__init__", false]], "__init__() (bio.genbank.record.record method)": [[93, "Bio.GenBank.Record.Record.__init__", false]], "__init__() (bio.genbank.record.reference method)": [[93, "Bio.GenBank.Record.Reference.__init__", false]], "__init__() (bio.genbank.recordparser method)": [[92, "Bio.GenBank.RecordParser.__init__", false]], "__init__() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.__init__", false]], "__init__() (bio.genbank.utils.featurevaluecleaner method)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.__init__", false]], "__init__() (bio.geo.record.record method)": [[97, "Bio.Geo.Record.Record.__init__", false]], "__init__() (bio.graphics.basicchromosome.annotatedchromosomesegment method)": [[99, "Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment.__init__", false]], "__init__() (bio.graphics.basicchromosome.chromosome method)": [[99, "Bio.Graphics.BasicChromosome.Chromosome.__init__", false]], "__init__() (bio.graphics.basicchromosome.chromosomesegment method)": [[99, "Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__", false]], "__init__() (bio.graphics.basicchromosome.organism method)": [[99, "Bio.Graphics.BasicChromosome.Organism.__init__", false]], "__init__() (bio.graphics.basicchromosome.telomeresegment method)": [[99, "Bio.Graphics.BasicChromosome.TelomereSegment.__init__", false]], "__init__() (bio.graphics.colorspiral.colorspiral method)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.__init__", false]], "__init__() (bio.graphics.comparative.comparativescatterplot method)": [[101, "Bio.Graphics.Comparative.ComparativeScatterPlot.__init__", false]], "__init__() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__", false]], "__init__() (bio.graphics.distribution.barchartdistribution method)": [[103, "Bio.Graphics.Distribution.BarChartDistribution.__init__", false]], "__init__() (bio.graphics.distribution.distributionpage method)": [[103, "Bio.Graphics.Distribution.DistributionPage.__init__", false]], "__init__() (bio.graphics.distribution.linedistribution method)": [[103, "Bio.Graphics.Distribution.LineDistribution.__init__", false]], "__init__() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.__init__", false]], "__init__() (bio.graphics.genomediagram.crosslink method)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.__init__", false]], "__init__() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.__init__", false]], "__init__() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.__init__", false]], "__init__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__init__", false]], "__init__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__init__", false]], "__init__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__init__", false]], "__init__() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.__init__", false]], "__init__() (bio.graphics.kgml_vis.kgmlcanvas method)": [[105, "Bio.Graphics.KGML_vis.KGMLCanvas.__init__", false]], "__init__() (bio.hmm.dynamicprogramming.abstractdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__", false]], "__init__() (bio.hmm.dynamicprogramming.logdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__", false]], "__init__() (bio.hmm.dynamicprogramming.scaleddpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__", false]], "__init__() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.__init__", false]], "__init__() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.__init__", false]], "__init__() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.__init__", false]], "__init__() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.__init__", false]], "__init__() (bio.hmm.trainer.knownstatetrainer method)": [[109, "Bio.HMM.Trainer.KnownStateTrainer.__init__", false]], "__init__() (bio.hmm.trainer.trainingsequence method)": [[109, "Bio.HMM.Trainer.TrainingSequence.__init__", false]], "__init__() (bio.kegg.compound.record method)": [[112, "Bio.KEGG.Compound.Record.__init__", false]], "__init__() (bio.kegg.enzyme.record method)": [[113, "Bio.KEGG.Enzyme.Record.__init__", false]], "__init__() (bio.kegg.gene.record method)": [[114, "Bio.KEGG.Gene.Record.__init__", false]], "__init__() (bio.kegg.kgml.kgml_parser.kgmlparser method)": [[116, "Bio.KEGG.KGML.KGML_parser.KGMLParser.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.component method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.graphics method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.__init__", false]], "__init__() (bio.kegg.kgml.kgml_pathway.relation method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.__init__", false]], "__init__() (bio.knn.knn method)": [[282, "Bio.kNN.kNN.__init__", false]], "__init__() (bio.logisticregression.logisticregression method)": [[120, "Bio.LogisticRegression.LogisticRegression.__init__", false]], "__init__() (bio.markovmodel.markovmodel method)": [[121, "Bio.MarkovModel.MarkovModel.__init__", false]], "__init__() (bio.maxentropy.maxentropy method)": [[122, "Bio.MaxEntropy.MaxEntropy.__init__", false]], "__init__() (bio.motifs.alignace.record method)": [[284, "Bio.motifs.alignace.Record.__init__", false]], "__init__() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.__init__", false]], "__init__() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.__init__", false]], "__init__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__init__", false]], "__init__() (bio.motifs.jaspar.record method)": [[287, "Bio.motifs.jaspar.Record.__init__", false]], "__init__() (bio.motifs.mast.record method)": [[289, "Bio.motifs.mast.Record.__init__", false]], "__init__() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.__init__", false]], "__init__() (bio.motifs.matrix.positionweightmatrix method)": [[290, "Bio.motifs.matrix.PositionWeightMatrix.__init__", false]], "__init__() (bio.motifs.meme.instance method)": [[291, "Bio.motifs.meme.Instance.__init__", false]], "__init__() (bio.motifs.meme.motif method)": [[291, "Bio.motifs.meme.Motif.__init__", false]], "__init__() (bio.motifs.meme.record method)": [[291, "Bio.motifs.meme.Record.__init__", false]], "__init__() (bio.motifs.minimal.record method)": [[292, "Bio.motifs.minimal.Record.__init__", false]], "__init__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__init__", false]], "__init__() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.__init__", false]], "__init__() (bio.motifs.transfac.record method)": [[295, "Bio.motifs.transfac.Record.__init__", false]], "__init__() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.__init__", false]], "__init__() (bio.naivebayes.naivebayes method)": [[127, "Bio.NaiveBayes.NaiveBayes.__init__", false]], "__init__() (bio.nexus.nexus.block method)": [[129, "Bio.Nexus.Nexus.Block.__init__", false]], "__init__() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.__init__", false]], "__init__() (bio.nexus.nexus.commandline method)": [[129, "Bio.Nexus.Nexus.Commandline.__init__", false]], "__init__() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.__init__", false]], "__init__() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.__init__", false]], "__init__() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.__init__", false]], "__init__() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.__init__", false]], "__init__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__init__", false]], "__init__() (bio.nexus.trees.nodedata method)": [[132, "Bio.Nexus.Trees.NodeData.__init__", false]], "__init__() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.__init__", false]], "__init__() (bio.nmr.xpktools.peaklist method)": [[126, "Bio.NMR.xpktools.Peaklist.__init__", false]], "__init__() (bio.nmr.xpktools.xpkentry method)": [[126, "Bio.NMR.xpktools.XpkEntry.__init__", false]], "__init__() (bio.pairwise2.affine_penalty method)": [[297, "Bio.pairwise2.affine_penalty.__init__", false]], "__init__() (bio.pairwise2.dictionary_match method)": [[297, "Bio.pairwise2.dictionary_match.__init__", false]], "__init__() (bio.pairwise2.identity_match method)": [[297, "Bio.pairwise2.identity_match.__init__", false]], "__init__() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.__init__", false]], "__init__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__init__", false]], "__init__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__init__", false]], "__init__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__", false]], "__init__() (bio.pathway.system method)": [[177, "Bio.Pathway.System.__init__", false]], "__init__() (bio.pdb.abstractpropertymap.abstractatompropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__", false]], "__init__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__", false]], "__init__() (bio.pdb.abstractpropertymap.abstractresiduepropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__", false]], "__init__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__init__", false]], "__init__() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.__init__", false]], "__init__() (bio.pdb.binary_cif.binarycifparser method)": [[165, "Bio.PDB.binary_cif.BinaryCIFParser.__init__", false]], "__init__() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.__init__", false]], "__init__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__init__", false]], "__init__() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.__init__", false]], "__init__() (bio.pdb.dssp.dssp method)": [[137, "Bio.PDB.DSSP.DSSP.__init__", false]], "__init__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__init__", false]], "__init__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__init__", false]], "__init__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__init__", false]], "__init__() (bio.pdb.fragmentmapper.fragmentmapper method)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper.__init__", false]], "__init__() (bio.pdb.hsexposure.exposurecn method)": [[141, "Bio.PDB.HSExposure.ExposureCN.__init__", false]], "__init__() (bio.pdb.hsexposure.hsexposureca method)": [[141, "Bio.PDB.HSExposure.HSExposureCA.__init__", false]], "__init__() (bio.pdb.hsexposure.hsexposurecb method)": [[141, "Bio.PDB.HSExposure.HSExposureCB.__init__", false]], "__init__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__init__", false]], "__init__() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.__init__", false]], "__init__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__init__", false]], "__init__() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.__init__", false]], "__init__() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.__init__", false]], "__init__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__init__", false]], "__init__() (bio.pdb.mmcif2dict.mmcif2dict method)": [[142, "Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__", false]], "__init__() (bio.pdb.mmcifio.mmcifio method)": [[170, "Bio.PDB.mmcifio.MMCIFIO.__init__", false]], "__init__() (bio.pdb.mmcifparser.fastmmcifparser method)": [[143, "Bio.PDB.MMCIFParser.FastMMCIFParser.__init__", false]], "__init__() (bio.pdb.mmcifparser.mmcifparser method)": [[143, "Bio.PDB.MMCIFParser.MMCIFParser.__init__", false]], "__init__() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.__init__", false]], "__init__() (bio.pdb.mmtf.mmtfio.mmtfio method)": [[173, "Bio.PDB.mmtf.mmtfio.MMTFIO.__init__", false]], "__init__() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.__init__", false]], "__init__() (bio.pdb.naccess.naccess method)": [[145, "Bio.PDB.NACCESS.NACCESS.__init__", false]], "__init__() (bio.pdb.naccess.naccess_atomic method)": [[145, "Bio.PDB.NACCESS.NACCESS_atomic.__init__", false]], "__init__() (bio.pdb.neighborsearch.neighborsearch method)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch.__init__", false]], "__init__() (bio.pdb.pdbio.pdbio method)": [[148, "Bio.PDB.PDBIO.PDBIO.__init__", false]], "__init__() (bio.pdb.pdbio.structureio method)": [[148, "Bio.PDB.PDBIO.StructureIO.__init__", false]], "__init__() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.__init__", false]], "__init__() (bio.pdb.pdbmlparser.pdbmlparser method)": [[150, "Bio.PDB.PDBMLParser.PDBMLParser.__init__", false]], "__init__() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.__init__", false]], "__init__() (bio.pdb.polypeptide.cappbuilder method)": [[154, "Bio.PDB.Polypeptide.CaPPBuilder.__init__", false]], "__init__() (bio.pdb.polypeptide.ppbuilder method)": [[154, "Bio.PDB.Polypeptide.PPBuilder.__init__", false]], "__init__() (bio.pdb.psea.psea method)": [[153, "Bio.PDB.PSEA.PSEA.__init__", false]], "__init__() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.__init__", false]], "__init__() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.__init__", false]], "__init__() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.__init__", false]], "__init__() (bio.pdb.residuedepth.residuedepth method)": [[156, "Bio.PDB.ResidueDepth.ResidueDepth.__init__", false]], "__init__() (bio.pdb.sasa.shrakerupley method)": [[157, "Bio.PDB.SASA.ShrakeRupley.__init__", false]], "__init__() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.__init__", false]], "__init__() (bio.pdb.structurealignment.structurealignment method)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment.__init__", false]], "__init__() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.__init__", false]], "__init__() (bio.pdb.superimposer.superimposer method)": [[163, "Bio.PDB.Superimposer.Superimposer.__init__", false]], "__init__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__init__", false]], "__init__() (bio.phenotype.phen_micro.jsonwriter method)": [[299, "Bio.phenotype.phen_micro.JsonWriter.__init__", false]], "__init__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__init__", false]], "__init__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__init__", false]], "__init__() (bio.phylo.applications.fasttreecommandline method)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.__init__", false]], "__init__() (bio.phylo.applications.phymlcommandline method)": [[182, "Bio.Phylo.Applications.PhymlCommandline.__init__", false]], "__init__() (bio.phylo.applications.raxmlcommandline method)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.__init__", false]], "__init__() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.__init__", false]], "__init__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__init__", false]], "__init__() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.__init__", false]], "__init__() (bio.phylo.cdao.clade method)": [[184, "Bio.Phylo.CDAO.Clade.__init__", false]], "__init__() (bio.phylo.cdao.tree method)": [[184, "Bio.Phylo.CDAO.Tree.__init__", false]], "__init__() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.__init__", false]], "__init__() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.__init__", false]], "__init__() (bio.phylo.newick.clade method)": [[189, "Bio.Phylo.Newick.Clade.__init__", false]], "__init__() (bio.phylo.newick.tree method)": [[189, "Bio.Phylo.Newick.Tree.__init__", false]], "__init__() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.__init__", false]], "__init__() (bio.phylo.newickio.writer method)": [[190, "Bio.Phylo.NewickIO.Writer.__init__", false]], "__init__() (bio.phylo.nexml.clade method)": [[187, "Bio.Phylo.NeXML.Clade.__init__", false]], "__init__() (bio.phylo.nexml.tree method)": [[187, "Bio.Phylo.NeXML.Tree.__init__", false]], "__init__() (bio.phylo.nexmlio.parser method)": [[188, "Bio.Phylo.NeXMLIO.Parser.__init__", false]], "__init__() (bio.phylo.nexmlio.writer method)": [[188, "Bio.Phylo.NeXMLIO.Writer.__init__", false]], "__init__() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.__init__", false]], "__init__() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.__init__", false]], "__init__() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.__init__", false]], "__init__() (bio.phylo.phyloxml.accession method)": [[197, "Bio.Phylo.PhyloXML.Accession.__init__", false]], "__init__() (bio.phylo.phyloxml.annotation method)": [[197, "Bio.Phylo.PhyloXML.Annotation.__init__", false]], "__init__() (bio.phylo.phyloxml.binarycharacters method)": [[197, "Bio.Phylo.PhyloXML.BinaryCharacters.__init__", false]], "__init__() (bio.phylo.phyloxml.branchcolor method)": [[197, "Bio.Phylo.PhyloXML.BranchColor.__init__", false]], "__init__() (bio.phylo.phyloxml.clade method)": [[197, "Bio.Phylo.PhyloXML.Clade.__init__", false]], "__init__() (bio.phylo.phyloxml.claderelation method)": [[197, "Bio.Phylo.PhyloXML.CladeRelation.__init__", false]], "__init__() (bio.phylo.phyloxml.date method)": [[197, "Bio.Phylo.PhyloXML.Date.__init__", false]], "__init__() (bio.phylo.phyloxml.distribution method)": [[197, "Bio.Phylo.PhyloXML.Distribution.__init__", false]], "__init__() (bio.phylo.phyloxml.domainarchitecture method)": [[197, "Bio.Phylo.PhyloXML.DomainArchitecture.__init__", false]], "__init__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__init__", false]], "__init__() (bio.phylo.phyloxml.id method)": [[197, "Bio.Phylo.PhyloXML.Id.__init__", false]], "__init__() (bio.phylo.phyloxml.molseq method)": [[197, "Bio.Phylo.PhyloXML.MolSeq.__init__", false]], "__init__() (bio.phylo.phyloxml.other method)": [[197, "Bio.Phylo.PhyloXML.Other.__init__", false]], "__init__() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.__init__", false]], "__init__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__init__", false]], "__init__() (bio.phylo.phyloxml.point method)": [[197, "Bio.Phylo.PhyloXML.Point.__init__", false]], "__init__() (bio.phylo.phyloxml.polygon method)": [[197, "Bio.Phylo.PhyloXML.Polygon.__init__", false]], "__init__() (bio.phylo.phyloxml.property method)": [[197, "Bio.Phylo.PhyloXML.Property.__init__", false]], "__init__() (bio.phylo.phyloxml.proteindomain method)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain.__init__", false]], "__init__() (bio.phylo.phyloxml.reference method)": [[197, "Bio.Phylo.PhyloXML.Reference.__init__", false]], "__init__() (bio.phylo.phyloxml.sequence method)": [[197, "Bio.Phylo.PhyloXML.Sequence.__init__", false]], "__init__() (bio.phylo.phyloxml.sequencerelation method)": [[197, "Bio.Phylo.PhyloXML.SequenceRelation.__init__", false]], "__init__() (bio.phylo.phyloxml.taxonomy method)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.__init__", false]], "__init__() (bio.phylo.phyloxml.uri method)": [[197, "Bio.Phylo.PhyloXML.Uri.__init__", false]], "__init__() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.__init__", false]], "__init__() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.__init__", false]], "__init__() (bio.phylo.treeconstruction.distancecalculator method)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.__init__", false]], "__init__() (bio.phylo.treeconstruction.distancematrix method)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix.__init__", false]], "__init__() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.__init__", false]], "__init__() (bio.phylo.treeconstruction.nnitreesearcher method)": [[199, "Bio.Phylo.TreeConstruction.NNITreeSearcher.__init__", false]], "__init__() (bio.phylo.treeconstruction.parsimonyscorer method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyScorer.__init__", false]], "__init__() (bio.phylo.treeconstruction.parsimonytreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor.__init__", false]], "__init__() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.__init__", false]], "__init__() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.__init__", false]], "__init__() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.__init__", false]], "__init__() (bio.popgen.genepop.largefileparser.record method)": [[205, "Bio.PopGen.GenePop.LargeFileParser.Record.__init__", false]], "__init__() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.__init__", false]], "__init__() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.__init__", false]], "__init__() (bio.scop.cla.index method)": [[210, "Bio.SCOP.Cla.Index.__init__", false]], "__init__() (bio.scop.cla.record method)": [[210, "Bio.SCOP.Cla.Record.__init__", false]], "__init__() (bio.scop.des.record method)": [[211, "Bio.SCOP.Des.Record.__init__", false]], "__init__() (bio.scop.dom.record method)": [[212, "Bio.SCOP.Dom.Record.__init__", false]], "__init__() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.__init__", false]], "__init__() (bio.scop.hie.record method)": [[213, "Bio.SCOP.Hie.Record.__init__", false]], "__init__() (bio.scop.node method)": [[209, "Bio.SCOP.Node.__init__", false]], "__init__() (bio.scop.raf.res method)": [[214, "Bio.SCOP.Raf.Res.__init__", false]], "__init__() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.__init__", false]], "__init__() (bio.scop.raf.seqmapindex method)": [[214, "Bio.SCOP.Raf.SeqMapIndex.__init__", false]], "__init__() (bio.scop.residues.residues method)": [[215, "Bio.SCOP.Residues.Residues.__init__", false]], "__init__() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.__init__", false]], "__init__() (bio.searchio.blastio.blast_tab.blasttabindexer method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__init__", false]], "__init__() (bio.searchio.blastio.blast_tab.blasttabparser method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser.__init__", false]], "__init__() (bio.searchio.blastio.blast_tab.blasttabwriter method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter.__init__", false]], "__init__() (bio.searchio.blastio.blast_xml.blastxmlindexer method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.__init__", false]], "__init__() (bio.searchio.blastio.blast_xml.blastxmlparser method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser.__init__", false]], "__init__() (bio.searchio.blastio.blast_xml.blastxmlwriter method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter.__init__", false]], "__init__() (bio.searchio.blatio.blatpslindexer method)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.__init__", false]], "__init__() (bio.searchio.blatio.blatpslparser method)": [[221, "Bio.SearchIO.BlatIO.BlatPslParser.__init__", false]], "__init__() (bio.searchio.blatio.blatpslwriter method)": [[221, "Bio.SearchIO.BlatIO.BlatPslWriter.__init__", false]], "__init__() (bio.searchio.fastaio.fastam10indexer method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.__init__", false]], "__init__() (bio.searchio.fastaio.fastam10parser method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Parser.__init__", false]], "__init__() (bio.searchio.hhsuiteio.hhsuite2_text.hhsuite2textparser method)": [[228, "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitwriter method)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabparser method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabwriter method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter.__init__", false]], "__init__() (bio.searchio.hmmerio.hmmer3_text.hmmer3textparser method)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser.__init__", false]], "__init__() (bio.searchio.interproscanio.interproscan_xml.interproscanxmlparser method)": [[235, "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser.__init__", false]], "__init__() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.__init__", false]], "__init__() (bio.seq.seq method)": [[236, "Bio.Seq.Seq.__init__", false]], "__init__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__init__", false]], "__init__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__init__", false]], "__init__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__init__", false]], "__init__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__init__", false]], "__init__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__init__", false]], "__init__() (bio.seqio.abiio.abiiterator method)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__init__", false]], "__init__() (bio.seqio.fastaio.fastaiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.__init__", false]], "__init__() (bio.seqio.fastaio.fastatwolineiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.__init__", false]], "__init__() (bio.seqio.fastaio.fastatwolinewriter method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineWriter.__init__", false]], "__init__() (bio.seqio.fastaio.fastawriter method)": [[241, "Bio.SeqIO.FastaIO.FastaWriter.__init__", false]], "__init__() (bio.seqio.gckio.gckiterator method)": [[242, "Bio.SeqIO.GckIO.GckIterator.__init__", false]], "__init__() (bio.seqio.igio.igiterator method)": [[244, "Bio.SeqIO.IgIO.IgIterator.__init__", false]], "__init__() (bio.seqio.insdcio.emblcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.__init__", false]], "__init__() (bio.seqio.insdcio.embliterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.__init__", false]], "__init__() (bio.seqio.insdcio.genbankcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.__init__", false]], "__init__() (bio.seqio.insdcio.genbankiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.__init__", false]], "__init__() (bio.seqio.insdcio.imgtiterator method)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.__init__", false]], "__init__() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__init__", false]], "__init__() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.__init__", false]], "__init__() (bio.seqio.nibio.nibiterator method)": [[247, "Bio.SeqIO.NibIO.NibIterator.__init__", false]], "__init__() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.__init__", false]], "__init__() (bio.seqio.pdbio.pdbseqresiterator method)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__init__", false]], "__init__() (bio.seqio.phdio.phdwriter method)": [[249, "Bio.SeqIO.PhdIO.PhdWriter.__init__", false]], "__init__() (bio.seqio.pirio.piriterator method)": [[250, "Bio.SeqIO.PirIO.PirIterator.__init__", false]], "__init__() (bio.seqio.pirio.pirwriter method)": [[250, "Bio.SeqIO.PirIO.PirWriter.__init__", false]], "__init__() (bio.seqio.qualityio.fastqphrediterator method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__init__", false]], "__init__() (bio.seqio.qualityio.qualphrediterator method)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.__init__", false]], "__init__() (bio.seqio.qualityio.qualphredwriter method)": [[251, "Bio.SeqIO.QualityIO.QualPhredWriter.__init__", false]], "__init__() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.__init__", false]], "__init__() (bio.seqio.seqxmlio.seqxmliterator method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__", false]], "__init__() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__", false]], "__init__() (bio.seqio.sffio.sffiterator method)": [[253, "Bio.SeqIO.SffIO.SffIterator.__init__", false]], "__init__() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.__init__", false]], "__init__() (bio.seqio.snapgeneio.snapgeneiterator method)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__init__", false]], "__init__() (bio.seqio.tabio.tabiterator method)": [[256, "Bio.SeqIO.TabIO.TabIterator.__init__", false]], "__init__() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__init__", false]], "__init__() (bio.seqio.uniprotio.parser method)": [[258, "Bio.SeqIO.UniprotIO.Parser.__init__", false]], "__init__() (bio.seqio.xdnaio.xdnaiterator method)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.__init__", false]], "__init__() (bio.seqio.xdnaio.xdnawriter method)": [[259, "Bio.SeqIO.XdnaIO.XdnaWriter.__init__", false]], "__init__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__init__", false]], "__init__() (bio.sequencing.ace.acefilerecord method)": [[269, "Bio.Sequencing.Ace.ACEFileRecord.__init__", false]], "__init__() (bio.sequencing.ace.af method)": [[269, "Bio.Sequencing.Ace.af.__init__", false]], "__init__() (bio.sequencing.ace.bs method)": [[269, "Bio.Sequencing.Ace.bs.__init__", false]], "__init__() (bio.sequencing.ace.contig method)": [[269, "Bio.Sequencing.Ace.Contig.__init__", false]], "__init__() (bio.sequencing.ace.ct method)": [[269, "Bio.Sequencing.Ace.ct.__init__", false]], "__init__() (bio.sequencing.ace.ds method)": [[269, "Bio.Sequencing.Ace.ds.__init__", false]], "__init__() (bio.sequencing.ace.qa method)": [[269, "Bio.Sequencing.Ace.qa.__init__", false]], "__init__() (bio.sequencing.ace.rd method)": [[269, "Bio.Sequencing.Ace.rd.__init__", false]], "__init__() (bio.sequencing.ace.reads method)": [[269, "Bio.Sequencing.Ace.Reads.__init__", false]], "__init__() (bio.sequencing.ace.rt method)": [[269, "Bio.Sequencing.Ace.rt.__init__", false]], "__init__() (bio.sequencing.ace.wa method)": [[269, "Bio.Sequencing.Ace.wa.__init__", false]], "__init__() (bio.sequencing.ace.wr method)": [[269, "Bio.Sequencing.Ace.wr.__init__", false]], "__init__() (bio.sequencing.applications.bwaaligncommandline method)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwabwaswcommandline method)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwaindexcommandline method)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwamemcommandline method)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwasampecommandline method)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.__init__", false]], "__init__() (bio.sequencing.applications.bwasamsecommandline method)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.__init__", false]], "__init__() (bio.sequencing.applications.novoaligncommandline method)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolscalmdcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolscatcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsfaidxcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsFaidxCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsfixmatecommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsidxstatscommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsindexcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsIndexCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsmergecommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsmpileupcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsphasecommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsreheadercommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsrmdupcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolstargetcutcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsversion0xsortcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsversion1xsortcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.__init__", false]], "__init__() (bio.sequencing.applications.samtoolsviewcommandline method)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.__init__", false]], "__init__() (bio.sequencing.phd.record method)": [[271, "Bio.Sequencing.Phd.Record.__init__", false]], "__init__() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.__init__", false]], "__init__() (bio.sequtils.isoelectricpoint.isoelectricpoint method)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__", false]], "__init__() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__", false]], "__init__() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.__init__", false]], "__init__() (bio.swissprot.keywlist.record method)": [[273, "Bio.SwissProt.KeyWList.Record.__init__", false]], "__init__() (bio.swissprot.record method)": [[272, "Bio.SwissProt.Record.__init__", false]], "__init__() (bio.swissprot.reference method)": [[272, "Bio.SwissProt.Reference.__init__", false]], "__init__() (bio.swissprot.swissprotparsererror method)": [[272, "Bio.SwissProt.SwissProtParserError.__init__", false]], "__init__() (bio.unigene.protsimline method)": [[275, "Bio.UniGene.ProtsimLine.__init__", false]], "__init__() (bio.unigene.record method)": [[275, "Bio.UniGene.Record.__init__", false]], "__init__() (bio.unigene.sequenceline method)": [[275, "Bio.UniGene.SequenceLine.__init__", false]], "__init__() (bio.unigene.stsline method)": [[275, "Bio.UniGene.STSLine.__init__", false]], "__init__() (biosql.bioseq.dbseqrecord method)": [[302, "BioSQL.BioSeq.DBSeqRecord.__init__", false]], "__init__() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.__init__", false]], "__init__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__init__", false]], "__init__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__init__", false]], "__init__() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.__init__", false]], "__init__() (biosql.loader.databaseloader method)": [[305, "BioSQL.Loader.DatabaseLoader.__init__", false]], "__init__() (biosql.loader.databaseremover method)": [[305, "BioSQL.Loader.DatabaseRemover.__init__", false]], "__iter__() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__iter__", false]], "__iter__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__iter__", false]], "__iter__() (bio.alignio.interfaces.alignmentiterator method)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator.__iter__", false]], "__iter__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__iter__", false]], "__iter__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__iter__", false]], "__iter__() (bio.genbank.iterator method)": [[92, "Bio.GenBank.Iterator.__iter__", false]], "__iter__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__iter__", false]], "__iter__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__iter__", false]], "__iter__() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.__iter__", false]], "__iter__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__iter__", false]], "__iter__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__iter__", false]], "__iter__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__iter__", false]], "__iter__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__iter__", false]], "__iter__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__iter__", false]], "__iter__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__iter__", false]], "__iter__() (bio.phylo.phyloxml.other method)": [[197, "Bio.Phylo.PhyloXML.Other.__iter__", false]], "__iter__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_tab.blasttabindexer method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_tab.blasttabparser method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_xml.blastxmlindexer method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.__iter__", false]], "__iter__() (bio.searchio.blastio.blast_xml.blastxmlparser method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser.__iter__", false]], "__iter__() (bio.searchio.blatio.blatpslindexer method)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.__iter__", false]], "__iter__() (bio.searchio.blatio.blatpslparser method)": [[221, "Bio.SearchIO.BlatIO.BlatPslParser.__iter__", false]], "__iter__() (bio.searchio.fastaio.fastam10indexer method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.__iter__", false]], "__iter__() (bio.searchio.fastaio.fastam10parser method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Parser.__iter__", false]], "__iter__() (bio.searchio.hhsuiteio.hhsuite2_text.hhsuite2textparser method)": [[228, "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabindexer method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabparser method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer method)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.__iter__", false]], "__iter__() (bio.searchio.hmmerio.hmmer3_text.hmmer3textparser method)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser.__iter__", false]], "__iter__() (bio.searchio.interproscanio.interproscan_xml.interproscanxmlparser method)": [[235, "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser.__iter__", false]], "__iter__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__iter__", false]], "__iter__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__iter__", false]], "__iter__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__iter__", false]], "__iter__() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__iter__", false]], "__iter__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__iter__", false]], "__iter__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__iter__", false]], "__iter__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__iter__", false]], "__le__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__le__", false]], "__le__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__le__", false]], "__le__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__le__", false]], "__le__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__le__", false]], "__le__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__le__", false]], "__le__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__le__", false]], "__le__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__le__", false]], "__le__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__le__", false]], "__le__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__le__", false]], "__len__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__len__", false]], "__len__() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.__len__", false]], "__len__() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__len__", false]], "__len__() (bio.align.bigbed.alignmentiterator method)": [[36, "Bio.Align.bigbed.AlignmentIterator.__len__", false]], "__len__() (bio.align.hhr.alignmentiterator method)": [[44, "Bio.Align.hhr.AlignmentIterator.__len__", false]], "__len__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__len__", false]], "__len__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__len__", false]], "__len__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__len__", false]], "__len__() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.__len__", false]], "__len__() (bio.emboss.primer3.primers method)": [[81, "Bio.Emboss.Primer3.Primers.__len__", false]], "__len__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__len__", false]], "__len__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__len__", false]], "__len__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__len__", false]], "__len__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__len__", false]], "__len__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__len__", false]], "__len__() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__len__", false]], "__len__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__len__", false]], "__len__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__len__", false]], "__len__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__len__", false]], "__len__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__len__", false]], "__len__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__len__", false]], "__len__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__len__", false]], "__len__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__len__", false]], "__len__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__len__", false]], "__len__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__len__", false]], "__len__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__len__", false]], "__len__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__len__", false]], "__len__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__len__", false]], "__len__() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__len__", false]], "__len__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__len__", false]], "__len__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__len__", false]], "__len__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__len__", false]], "__lt__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__lt__", false]], "__lt__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__lt__", false]], "__lt__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__lt__", false]], "__lt__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__lt__", false]], "__lt__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__lt__", false]], "__lt__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__lt__", false]], "__lt__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__lt__", false]], "__lt__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__lt__", false]], "__lt__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__lt__", false]], "__mul__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__mul__", false]], "__mul__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__mul__", false]], "__ne__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__ne__", false]], "__ne__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__ne__", false]], "__ne__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__ne__", false]], "__ne__() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.__ne__", false]], "__ne__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__ne__", false]], "__ne__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__ne__", false]], "__ne__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__ne__", false]], "__neg__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__neg__", false]], "__new__() (bio.align.alignmentcounts static method)": [[30, "Bio.Align.AlignmentCounts.__new__", false]], "__new__() (bio.align.bigbed.field static method)": [[36, "Bio.Align.bigbed.Field.__new__", false]], "__new__() (bio.align.substitution_matrices.array static method)": [[54, "Bio.Align.substitution_matrices.Array.__new__", false]], "__new__() (bio.entrez.parser.errorelement static method)": [[84, "Bio.Entrez.Parser.ErrorElement.__new__", false]], "__new__() (bio.entrez.parser.integerelement static method)": [[84, "Bio.Entrez.Parser.IntegerElement.__new__", false]], "__new__() (bio.entrez.parser.stringelement static method)": [[84, "Bio.Entrez.Parser.StringElement.__new__", false]], "__new__() (bio.pairwise2.alignment static method)": [[297, "Bio.pairwise2.Alignment.__new__", false]], "__new__() (bio.phylo.phyloxml.confidence static method)": [[197, "Bio.Phylo.PhyloXML.Confidence.__new__", false]], "__new__() (bio.seqfeature.afterposition static method)": [[237, "Bio.SeqFeature.AfterPosition.__new__", false]], "__new__() (bio.seqfeature.beforeposition static method)": [[237, "Bio.SeqFeature.BeforePosition.__new__", false]], "__new__() (bio.seqfeature.betweenposition static method)": [[237, "Bio.SeqFeature.BetweenPosition.__new__", false]], "__new__() (bio.seqfeature.exactposition static method)": [[237, "Bio.SeqFeature.ExactPosition.__new__", false]], "__new__() (bio.seqfeature.oneofposition static method)": [[237, "Bio.SeqFeature.OneOfPosition.__new__", false]], "__new__() (bio.seqfeature.withinposition static method)": [[237, "Bio.SeqFeature.WithinPosition.__new__", false]], "__next__() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.__next__", false]], "__next__() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.__next__", false]], "__next__() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.__next__", false]], "__next__() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.__next__", false]], "__next__() (bio.alignio.clustalio.clustaliterator method)": [[57, "Bio.AlignIO.ClustalIO.ClustalIterator.__next__", false]], "__next__() (bio.alignio.embossio.embossiterator method)": [[58, "Bio.AlignIO.EmbossIO.EmbossIterator.__next__", false]], "__next__() (bio.alignio.interfaces.alignmentiterator method)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator.__next__", false]], "__next__() (bio.alignio.mauveio.mauveiterator method)": [[62, "Bio.AlignIO.MauveIO.MauveIterator.__next__", false]], "__next__() (bio.alignio.msfio.msfiterator method)": [[63, "Bio.AlignIO.MsfIO.MsfIterator.__next__", false]], "__next__() (bio.alignio.phylipio.phylipiterator method)": [[65, "Bio.AlignIO.PhylipIO.PhylipIterator.__next__", false]], "__next__() (bio.alignio.phylipio.sequentialphylipiterator method)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipIterator.__next__", false]], "__next__() (bio.alignio.stockholmio.stockholmiterator method)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.__next__", false]], "__next__() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.__next__", false]], "__next__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__next__", false]], "__next__() (bio.genbank.iterator method)": [[92, "Bio.GenBank.Iterator.__next__", false]], "__next__() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.__next__", false]], "__next__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__next__", false]], "__next__() (bio.seqio.abiio.abiiterator method)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__next__", false]], "__next__() (bio.seqio.igio.igiterator method)": [[244, "Bio.SeqIO.IgIO.IgIterator.__next__", false]], "__next__() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__next__", false]], "__next__() (bio.seqio.pdbio.pdbseqresiterator method)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__next__", false]], "__next__() (bio.seqio.pirio.piriterator method)": [[250, "Bio.SeqIO.PirIO.PirIterator.__next__", false]], "__next__() (bio.seqio.seqxmlio.seqxmliterator method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__next__", false]], "__nonzero__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__nonzero__", false]], "__nonzero__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__nonzero__", false]], "__orig_bases__ (bio.pdb.chain.chain attribute)": [[136, "Bio.PDB.Chain.Chain.__orig_bases__", false]], "__orig_bases__ (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.__orig_bases__", false]], "__orig_bases__ (bio.pdb.model.model attribute)": [[144, "Bio.PDB.Model.Model.__orig_bases__", false]], "__orig_bases__ (bio.pdb.residue.residue attribute)": [[155, "Bio.PDB.Residue.Residue.__orig_bases__", false]], "__orig_bases__ (bio.pdb.structure.structure attribute)": [[160, "Bio.PDB.Structure.Structure.__orig_bases__", false]], "__orig_bases__ (bio.seqio.interfaces.sequenceiterator attribute)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__orig_bases__", false]], "__orig_bases__ (bio.seqio.qualityio.fastqphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__orig_bases__", false]], "__parameters__ (bio.pdb.chain.chain attribute)": [[136, "Bio.PDB.Chain.Chain.__parameters__", false]], "__parameters__ (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.__parameters__", false]], "__parameters__ (bio.pdb.model.model attribute)": [[144, "Bio.PDB.Model.Model.__parameters__", false]], "__parameters__ (bio.pdb.residue.residue attribute)": [[155, "Bio.PDB.Residue.Residue.__parameters__", false]], "__parameters__ (bio.pdb.structure.structure attribute)": [[160, "Bio.PDB.Structure.Structure.__parameters__", false]], "__parameters__ (bio.seqio.abiio.abiiterator attribute)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.__parameters__", false]], "__parameters__ (bio.seqio.fastaio.fastaiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.__parameters__", false]], "__parameters__ (bio.seqio.fastaio.fastatwolineiterator attribute)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.__parameters__", false]], "__parameters__ (bio.seqio.gckio.gckiterator attribute)": [[242, "Bio.SeqIO.GckIO.GckIterator.__parameters__", false]], "__parameters__ (bio.seqio.igio.igiterator attribute)": [[244, "Bio.SeqIO.IgIO.IgIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.emblcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.embliterator attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.genbankcdsfeatureiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.genbankiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.__parameters__", false]], "__parameters__ (bio.seqio.insdcio.imgtiterator attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.__parameters__", false]], "__parameters__ (bio.seqio.interfaces.sequenceiterator attribute)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.__parameters__", false]], "__parameters__ (bio.seqio.nibio.nibiterator attribute)": [[247, "Bio.SeqIO.NibIO.NibIterator.__parameters__", false]], "__parameters__ (bio.seqio.pdbio.pdbseqresiterator attribute)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.__parameters__", false]], "__parameters__ (bio.seqio.pirio.piriterator attribute)": [[250, "Bio.SeqIO.PirIO.PirIterator.__parameters__", false]], "__parameters__ (bio.seqio.qualityio.fastqphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.__parameters__", false]], "__parameters__ (bio.seqio.qualityio.qualphrediterator attribute)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.__parameters__", false]], "__parameters__ (bio.seqio.seqxmlio.seqxmliterator attribute)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__parameters__", false]], "__parameters__ (bio.seqio.sffio.sffiterator attribute)": [[253, "Bio.SeqIO.SffIO.SffIterator.__parameters__", false]], "__parameters__ (bio.seqio.snapgeneio.snapgeneiterator attribute)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__parameters__", false]], "__parameters__ (bio.seqio.tabio.tabiterator attribute)": [[256, "Bio.SeqIO.TabIO.TabIterator.__parameters__", false]], "__parameters__ (bio.seqio.twobitio.twobititerator attribute)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.__parameters__", false]], "__parameters__ (bio.seqio.xdnaio.xdnaiterator attribute)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.__parameters__", false]], "__pow__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__pow__", false]], "__radd__() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__radd__", false]], "__radd__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__radd__", false]], "__radd__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__radd__", false]], "__radd__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__radd__", false]], "__reduce__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__reduce__", false]], "__repr__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__repr__", false]], "__repr__() (bio.align.alignmentcounts method)": [[30, "Bio.Align.AlignmentCounts.__repr__", false]], "__repr__() (bio.align.bigbed.field method)": [[36, "Bio.Align.bigbed.Field.__repr__", false]], "__repr__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__repr__", false]], "__repr__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__repr__", false]], "__repr__() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.__repr__", false]], "__repr__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__repr__", false]], "__repr__() (bio.application.applicationerror method)": [[67, "Bio.Application.ApplicationError.__repr__", false]], "__repr__() (bio.blast.hit method)": [[68, "Bio.Blast.Hit.__repr__", false]], "__repr__() (bio.blast.hsp method)": [[68, "Bio.Blast.HSP.__repr__", false]], "__repr__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__repr__", false]], "__repr__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__repr__", false]], "__repr__() (bio.data.codontable.ncbicodontable method)": [[76, "Bio.Data.CodonTable.NCBICodonTable.__repr__", false]], "__repr__() (bio.entrez.parser.dictionaryelement method)": [[84, "Bio.Entrez.Parser.DictionaryElement.__repr__", false]], "__repr__() (bio.entrez.parser.errorelement method)": [[84, "Bio.Entrez.Parser.ErrorElement.__repr__", false]], "__repr__() (bio.entrez.parser.integerelement method)": [[84, "Bio.Entrez.Parser.IntegerElement.__repr__", false]], "__repr__() (bio.entrez.parser.listelement method)": [[84, "Bio.Entrez.Parser.ListElement.__repr__", false]], "__repr__() (bio.entrez.parser.noneelement method)": [[84, "Bio.Entrez.Parser.NoneElement.__repr__", false]], "__repr__() (bio.entrez.parser.orderedlistelement method)": [[84, "Bio.Entrez.Parser.OrderedListElement.__repr__", false]], "__repr__() (bio.entrez.parser.stringelement method)": [[84, "Bio.Entrez.Parser.StringElement.__repr__", false]], "__repr__() (bio.expasy.cellosaurus.record method)": [[90, "Bio.ExPASy.cellosaurus.Record.__repr__", false]], "__repr__() (bio.expasy.enzyme.record method)": [[86, "Bio.ExPASy.Enzyme.Record.__repr__", false]], "__repr__() (bio.genbank.record.feature method)": [[93, "Bio.GenBank.Record.Feature.__repr__", false]], "__repr__() (bio.genbank.record.qualifier method)": [[93, "Bio.GenBank.Record.Qualifier.__repr__", false]], "__repr__() (bio.genbank.utils.featurevaluecleaner method)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.__repr__", false]], "__repr__() (bio.pairwise2.alignment method)": [[297, "Bio.pairwise2.Alignment.__repr__", false]], "__repr__() (bio.pathway.interaction method)": [[177, "Bio.Pathway.Interaction.__repr__", false]], "__repr__() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.__repr__", false]], "__repr__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__repr__", false]], "__repr__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__repr__", false]], "__repr__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__repr__", false]], "__repr__() (bio.pathway.system method)": [[177, "Bio.Pathway.System.__repr__", false]], "__repr__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__repr__", false]], "__repr__() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.__repr__", false]], "__repr__() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.__repr__", false]], "__repr__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__repr__", false]], "__repr__() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.__repr__", false]], "__repr__() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.__repr__", false]], "__repr__() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.__repr__", false]], "__repr__() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.__repr__", false]], "__repr__() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.__repr__", false]], "__repr__() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.__repr__", false]], "__repr__() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.__repr__", false]], "__repr__() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.__repr__", false]], "__repr__() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.__repr__", false]], "__repr__() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.__repr__", false]], "__repr__() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.__repr__", false]], "__repr__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__repr__", false]], "__repr__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__repr__", false]], "__repr__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__repr__", false]], "__repr__() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.__repr__", false]], "__repr__() (bio.phylo.basetree.treeelement method)": [[183, "Bio.Phylo.BaseTree.TreeElement.__repr__", false]], "__repr__() (bio.seqfeature.afterposition method)": [[237, "Bio.SeqFeature.AfterPosition.__repr__", false]], "__repr__() (bio.seqfeature.beforeposition method)": [[237, "Bio.SeqFeature.BeforePosition.__repr__", false]], "__repr__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__repr__", false]], "__repr__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__repr__", false]], "__repr__() (bio.seqfeature.exactposition method)": [[237, "Bio.SeqFeature.ExactPosition.__repr__", false]], "__repr__() (bio.seqfeature.location method)": [[237, "Bio.SeqFeature.Location.__repr__", false]], "__repr__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__repr__", false]], "__repr__() (bio.seqfeature.position method)": [[237, "Bio.SeqFeature.Position.__repr__", false]], "__repr__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__repr__", false]], "__repr__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__repr__", false]], "__repr__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__repr__", false]], "__repr__() (bio.seqfeature.unknownposition method)": [[237, "Bio.SeqFeature.UnknownPosition.__repr__", false]], "__repr__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__repr__", false]], "__repr__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__repr__", false]], "__repr__() (bio.unigene.protsimline method)": [[275, "Bio.UniGene.ProtsimLine.__repr__", false]], "__repr__() (bio.unigene.record method)": [[275, "Bio.UniGene.Record.__repr__", false]], "__repr__() (bio.unigene.sequenceline method)": [[275, "Bio.UniGene.SequenceLine.__repr__", false]], "__repr__() (bio.unigene.stsline method)": [[275, "Bio.UniGene.STSLine.__repr__", false]], "__repr__() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.__repr__", false]], "__repr__() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.__repr__", false]], "__setattr__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__setattr__", false]], "__setattr__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__setattr__", false]], "__setitem__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__setitem__", false]], "__setitem__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__", false]], "__setitem__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__setitem__", false]], "__setitem__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__setitem__", false]], "__setitem__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__setitem__", false]], "__setitem__() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.__setitem__", false]], "__setitem__() (bio.phylo.treeconstruction.distancematrix method)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix.__setitem__", false]], "__setitem__() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.__setitem__", false]], "__setstate__() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.__setstate__", false]], "__setstate__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__setstate__", false]], "__slots__ (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.__slots__", false]], "__slots__ (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.__slots__", false]], "__slots__ (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.__slots__", false]], "__slots__ (bio.seq.sequencedataabstractbaseclass attribute)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.__slots__", false]], "__str__() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.__str__", false]], "__str__() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.__str__", false]], "__str__() (bio.align.bigbed.autosqltable method)": [[36, "Bio.Align.bigbed.AutoSQLTable.__str__", false]], "__str__() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.__str__", false]], "__str__() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.__str__", false]], "__str__() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.__str__", false]], "__str__() (bio.application.applicationerror method)": [[67, "Bio.Application.ApplicationError.__str__", false]], "__str__() (bio.blast.corruptedxmlerror method)": [[68, "Bio.Blast.CorruptedXMLError.__str__", false]], "__str__() (bio.blast.hit method)": [[68, "Bio.Blast.Hit.__str__", false]], "__str__() (bio.blast.hsp method)": [[68, "Bio.Blast.HSP.__str__", false]], "__str__() (bio.blast.ncbixml.alignment method)": [[71, "Bio.Blast.NCBIXML.Alignment.__str__", false]], "__str__() (bio.blast.ncbixml.description method)": [[71, "Bio.Blast.NCBIXML.Description.__str__", false]], "__str__() (bio.blast.ncbixml.descriptionextitem method)": [[71, "Bio.Blast.NCBIXML.DescriptionExtItem.__str__", false]], "__str__() (bio.blast.ncbixml.hsp method)": [[71, "Bio.Blast.NCBIXML.HSP.__str__", false]], "__str__() (bio.blast.notxmlerror method)": [[68, "Bio.Blast.NotXMLError.__str__", false]], "__str__() (bio.blast.record method)": [[68, "Bio.Blast.Record.__str__", false]], "__str__() (bio.blast.records method)": [[68, "Bio.Blast.Records.__str__", false]], "__str__() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.__str__", false]], "__str__() (bio.data.codontable.codontable method)": [[76, "Bio.Data.CodonTable.CodonTable.__str__", false]], "__str__() (bio.emboss.primersearch.inputrecord method)": [[82, "Bio.Emboss.PrimerSearch.InputRecord.__str__", false]], "__str__() (bio.entrez.parser.corruptedxmlerror method)": [[84, "Bio.Entrez.Parser.CorruptedXMLError.__str__", false]], "__str__() (bio.entrez.parser.notxmlerror method)": [[84, "Bio.Entrez.Parser.NotXMLError.__str__", false]], "__str__() (bio.entrez.parser.validationerror method)": [[84, "Bio.Entrez.Parser.ValidationError.__str__", false]], "__str__() (bio.expasy.cellosaurus.record method)": [[90, "Bio.ExPASy.cellosaurus.Record.__str__", false]], "__str__() (bio.expasy.enzyme.record method)": [[86, "Bio.ExPASy.Enzyme.Record.__str__", false]], "__str__() (bio.genbank.record.feature method)": [[93, "Bio.GenBank.Record.Feature.__str__", false]], "__str__() (bio.genbank.record.qualifier method)": [[93, "Bio.GenBank.Record.Qualifier.__str__", false]], "__str__() (bio.genbank.record.record method)": [[93, "Bio.GenBank.Record.Record.__str__", false]], "__str__() (bio.genbank.record.reference method)": [[93, "Bio.GenBank.Record.Reference.__str__", false]], "__str__() (bio.geo.record.record method)": [[97, "Bio.Geo.Record.Record.__str__", false]], "__str__() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.__str__", false]], "__str__() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.__str__", false]], "__str__() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.__str__", false]], "__str__() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.__str__", false]], "__str__() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.__str__", false]], "__str__() (bio.kegg.compound.record method)": [[112, "Bio.KEGG.Compound.Record.__str__", false]], "__str__() (bio.kegg.enzyme.record method)": [[113, "Bio.KEGG.Enzyme.Record.__str__", false]], "__str__() (bio.kegg.gene.record method)": [[114, "Bio.KEGG.Gene.Record.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.__str__", false]], "__str__() (bio.kegg.kgml.kgml_pathway.relation method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.__str__", false]], "__str__() (bio.markovmodel.markovmodel method)": [[121, "Bio.MarkovModel.MarkovModel.__str__", false]], "__str__() (bio.motifs.clusterbuster.record method)": [[286, "Bio.motifs.clusterbuster.Record.__str__", false]], "__str__() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.__str__", false]], "__str__() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.__str__", false]], "__str__() (bio.motifs.jaspar.motif method)": [[287, "Bio.motifs.jaspar.Motif.__str__", false]], "__str__() (bio.motifs.jaspar.record method)": [[287, "Bio.motifs.jaspar.Record.__str__", false]], "__str__() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.__str__", false]], "__str__() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.__str__", false]], "__str__() (bio.motifs.pfm.record method)": [[293, "Bio.motifs.pfm.Record.__str__", false]], "__str__() (bio.motifs.transfac.record method)": [[295, "Bio.motifs.transfac.Record.__str__", false]], "__str__() (bio.motifs.xms.record method)": [[296, "Bio.motifs.xms.Record.__str__", false]], "__str__() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.__str__", false]], "__str__() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.__str__", false]], "__str__() (bio.pathway.interaction method)": [[177, "Bio.Pathway.Interaction.__str__", false]], "__str__() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.__str__", false]], "__str__() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.__str__", false]], "__str__() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.__str__", false]], "__str__() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.__str__", false]], "__str__() (bio.pathway.system method)": [[177, "Bio.Pathway.System.__str__", false]], "__str__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__str__", false]], "__str__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__str__", false]], "__str__() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.__str__", false]], "__str__() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.__str__", false]], "__str__() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.__str__", false]], "__str__() (bio.phylo.basetree.treeelement method)": [[183, "Bio.Phylo.BaseTree.TreeElement.__str__", false]], "__str__() (bio.phylo.phyloxml.accession method)": [[197, "Bio.Phylo.PhyloXML.Accession.__str__", false]], "__str__() (bio.phylo.phyloxml.date method)": [[197, "Bio.Phylo.PhyloXML.Date.__str__", false]], "__str__() (bio.phylo.phyloxml.id method)": [[197, "Bio.Phylo.PhyloXML.Id.__str__", false]], "__str__() (bio.phylo.phyloxml.molseq method)": [[197, "Bio.Phylo.PhyloXML.MolSeq.__str__", false]], "__str__() (bio.phylo.phyloxml.phyloxml method)": [[197, "Bio.Phylo.PhyloXML.Phyloxml.__str__", false]], "__str__() (bio.phylo.phyloxml.polygon method)": [[197, "Bio.Phylo.PhyloXML.Polygon.__str__", false]], "__str__() (bio.phylo.phyloxml.taxonomy method)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.__str__", false]], "__str__() (bio.phylo.phyloxml.uri method)": [[197, "Bio.Phylo.PhyloXML.Uri.__str__", false]], "__str__() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.__str__", false]], "__str__() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.__str__", false]], "__str__() (bio.scop.cla.record method)": [[210, "Bio.SCOP.Cla.Record.__str__", false]], "__str__() (bio.scop.des.record method)": [[211, "Bio.SCOP.Des.Record.__str__", false]], "__str__() (bio.scop.dom.record method)": [[212, "Bio.SCOP.Dom.Record.__str__", false]], "__str__() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.__str__", false]], "__str__() (bio.scop.hie.record method)": [[213, "Bio.SCOP.Hie.Record.__str__", false]], "__str__() (bio.scop.node method)": [[209, "Bio.SCOP.Node.__str__", false]], "__str__() (bio.scop.residues.residues method)": [[215, "Bio.SCOP.Residues.Residues.__str__", false]], "__str__() (bio.seqfeature.afterposition method)": [[237, "Bio.SeqFeature.AfterPosition.__str__", false]], "__str__() (bio.seqfeature.beforeposition method)": [[237, "Bio.SeqFeature.BeforePosition.__str__", false]], "__str__() (bio.seqfeature.betweenposition method)": [[237, "Bio.SeqFeature.BetweenPosition.__str__", false]], "__str__() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.__str__", false]], "__str__() (bio.seqfeature.exactposition method)": [[237, "Bio.SeqFeature.ExactPosition.__str__", false]], "__str__() (bio.seqfeature.oneofposition method)": [[237, "Bio.SeqFeature.OneOfPosition.__str__", false]], "__str__() (bio.seqfeature.reference method)": [[237, "Bio.SeqFeature.Reference.__str__", false]], "__str__() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.__str__", false]], "__str__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__str__", false]], "__str__() (bio.seqfeature.withinposition method)": [[237, "Bio.SeqFeature.WithinPosition.__str__", false]], "__str__() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.__str__", false]], "__str__() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.__str__", false]], "__sub__() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.__sub__", false]], "__sub__() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.__sub__", false]], "__sub__() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.__sub__", false]], "__sub__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__sub__", false]], "__sub__() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.__sub__", false]], "__sub__() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.__sub__", false]], "__sub__() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.__sub__", false]], "__truediv__() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.__truediv__", false]], "a (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.a", false]], "a (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.a", false]], "a (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.a", false]], "a (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.A", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.a", false]], "a (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.a", false]], "a (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.A", false]], "a (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.A", false]], "a (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.A", false]], "aacateg (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.aacateg", false]], "aamatrix (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.aamatrix", false]], "aasiz (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.AAsiz", false]], "abiiterator (class in bio.seqio.abiio)": [[239, "Bio.SeqIO.AbiIO.AbiIterator", false]], "abstractatompropertymap (class in bio.pdb.abstractpropertymap)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap", false]], "abstractcommandline (class in bio.application)": [[67, "Bio.Application.AbstractCommandline", false]], "abstractdpalgorithms (class in bio.hmm.dynamicprogramming)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms", false]], "abstractpropertymap (class in bio.pdb.abstractpropertymap)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap", false]], "abstractresiduepropertymap (class in bio.pdb.abstractpropertymap)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap", false]], "abstracttrainer (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.AbstractTrainer", false]], "accept_atom() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_atom", false]], "accept_atom() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_atom", false]], "accept_atoms (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_atoms", false]], "accept_backbone (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_backbone", false]], "accept_chain() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_chain", false]], "accept_chain() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_chain", false]], "accept_deuteriums (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_deuteriums", false]], "accept_hydrogens (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_hydrogens", false]], "accept_mainchain (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_mainchain", false]], "accept_model() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_model", false]], "accept_model() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_model", false]], "accept_residue() (bio.pdb.dice.chainselector method)": [[138, "Bio.PDB.Dice.ChainSelector.accept_residue", false]], "accept_residue() (bio.pdb.pdbio.select method)": [[148, "Bio.PDB.PDBIO.Select.accept_residue", false]], "accept_resnames (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_resnames", false]], "accept_sidechain (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.accept_sidechain", false]], "accession (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Accession", false]], "accession() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.accession", false]], "accession() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.accession", false]], "acefilerecord (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.ACEFileRecord", false]], "aceiterator() (in module bio.seqio.aceio)": [[240, "Bio.SeqIO.AceIO.AceIterator", false]], "adam_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.adam_consensus", false]], "adapter3 (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.adapter3", false]], "adapter5 (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.adapter5", false]], "adaptor (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.Adaptor", false]], "add() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.add", false]], "add() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.add", false]], "add() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.add", false]], "add() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.add", false]], "add() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.add", false]], "add_annotation() (bio.phylo.nexmlio.parser method)": [[188, "Bio.Phylo.NeXMLIO.Parser.add_annotation", false]], "add_component() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.add_component", false]], "add_count() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.add_count", false]], "add_edge() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.add_edge", false]], "add_edge() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.add_edge", false]], "add_entry() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.add_entry", false]], "add_feature() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.add_feature", false]], "add_graphics() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.add_graphics", false]], "add_interaction() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.add_interaction", false]], "add_label() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.add_label", false]], "add_node() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.add_node", false]], "add_node() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.add_node", false]], "add_point() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.add_point", false]], "add_primer_set() (bio.emboss.primersearch.inputrecord method)": [[82, "Bio.Emboss.PrimerSearch.InputRecord.add_primer_set", false]], "add_product() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.add_product", false]], "add_reaction() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.add_reaction", false]], "add_reaction() (bio.pathway.system method)": [[177, "Bio.Pathway.System.add_reaction", false]], "add_relation() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.add_relation", false]], "add_residue() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.add_residue", false]], "add_sequence() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.add_sequence", false]], "add_set() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.add_set", false]], "add_species() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.add_species", false]], "add_stmt_to_handle() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.add_stmt_to_handle", false]], "add_substrate() (bio.kegg.kgml.kgml_pathway.reaction method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.add_substrate", false]], "add_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.add_succ", false]], "add_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.add_track", false]], "adjustdirection (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.adjustdirection", false]], "adjustdirectionaccurately (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.adjustdirectionaccurately", false]], "af (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.af", false]], "afc (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.afc", false]], "afc_v (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.afc_v", false]], "affine_penalty (class in bio.pairwise2)": [[297, "Bio.pairwise2.affine_penalty", false]], "aformat (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.aformat", false]], "aformat (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.aformat", false]], "aformat (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.aformat", false]], "aformat (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.aformat", false]], "aformat (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.aformat", false]], "afterposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.AfterPosition", false]], "algorithm (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.algorithm", false]], "algorithm (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.algorithm", false]], "align (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.align", false]], "align (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.align", false]], "align() (bio.align.codonaligner method)": [[30, "Bio.Align.CodonAligner.align", false]], "align() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.align", false]], "align() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.align", false]], "aligned (bio.align.alignment property)": [[30, "Bio.Align.Alignment.aligned", false]], "alignment (bio.align.multipleseqalignment property)": [[30, "Bio.Align.MultipleSeqAlignment.alignment", false]], "alignment (bio.phylo.phyloxml.phylogeny property)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.alignment", false]], "alignment (class in bio.align)": [[30, "Bio.Align.Alignment", false]], "alignment (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Alignment", false]], "alignment (class in bio.pairwise2)": [[297, "Bio.pairwise2.Alignment", false]], "alignment_order (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.alignment_order", false]], "alignmentcounts (class in bio.align)": [[30, "Bio.Align.AlignmentCounts", false]], "alignmenthasdifferentlengthserror": [[72, "Bio.CAPS.AlignmentHasDifferentLengthsError", false]], "alignmentiterator (class in bio.align.a2m)": [[33, "Bio.Align.a2m.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bed)": [[35, "Bio.Align.bed.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bigmaf)": [[37, "Bio.Align.bigmaf.AlignmentIterator", false]], "alignmentiterator (class in bio.align.bigpsl)": [[38, "Bio.Align.bigpsl.AlignmentIterator", false]], "alignmentiterator (class in bio.align.chain)": [[39, "Bio.Align.chain.AlignmentIterator", false]], "alignmentiterator (class in bio.align.clustal)": [[40, "Bio.Align.clustal.AlignmentIterator", false]], "alignmentiterator (class in bio.align.emboss)": [[41, "Bio.Align.emboss.AlignmentIterator", false]], "alignmentiterator (class in bio.align.exonerate)": [[42, "Bio.Align.exonerate.AlignmentIterator", false]], "alignmentiterator (class in bio.align.fasta)": [[43, "Bio.Align.fasta.AlignmentIterator", false]], "alignmentiterator (class in bio.align.hhr)": [[44, "Bio.Align.hhr.AlignmentIterator", false]], "alignmentiterator (class in bio.align.interfaces)": [[45, "Bio.Align.interfaces.AlignmentIterator", false]], "alignmentiterator (class in bio.align.maf)": [[46, "Bio.Align.maf.AlignmentIterator", false]], "alignmentiterator (class in bio.align.mauve)": [[47, "Bio.Align.mauve.AlignmentIterator", false]], "alignmentiterator (class in bio.align.msf)": [[48, "Bio.Align.msf.AlignmentIterator", false]], "alignmentiterator (class in bio.align.nexus)": [[49, "Bio.Align.nexus.AlignmentIterator", false]], "alignmentiterator (class in bio.align.phylip)": [[50, "Bio.Align.phylip.AlignmentIterator", false]], "alignmentiterator (class in bio.align.psl)": [[51, "Bio.Align.psl.AlignmentIterator", false]], "alignmentiterator (class in bio.align.sam)": [[52, "Bio.Align.sam.AlignmentIterator", false]], "alignmentiterator (class in bio.align.stockholm)": [[53, "Bio.Align.stockholm.AlignmentIterator", false]], "alignmentiterator (class in bio.align.tabular)": [[55, "Bio.Align.tabular.AlignmentIterator", false]], "alignmentiterator (class in bio.alignio.interfaces)": [[60, "Bio.AlignIO.Interfaces.AlignmentIterator", false]], "alignments (class in bio.align)": [[30, "Bio.Align.Alignments", false]], "alignmentsabstractbaseclass (class in bio.align)": [[30, "Bio.Align.AlignmentsAbstractBaseClass", false]], "alignmentwriter (class in bio.align.a2m)": [[33, "Bio.Align.a2m.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bed)": [[35, "Bio.Align.bed.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bigmaf)": [[37, "Bio.Align.bigmaf.AlignmentWriter", false]], "alignmentwriter (class in bio.align.bigpsl)": [[38, "Bio.Align.bigpsl.AlignmentWriter", false]], "alignmentwriter (class in bio.align.chain)": [[39, "Bio.Align.chain.AlignmentWriter", false]], "alignmentwriter (class in bio.align.clustal)": [[40, "Bio.Align.clustal.AlignmentWriter", false]], "alignmentwriter (class in bio.align.exonerate)": [[42, "Bio.Align.exonerate.AlignmentWriter", false]], "alignmentwriter (class in bio.align.fasta)": [[43, "Bio.Align.fasta.AlignmentWriter", false]], "alignmentwriter (class in bio.align.interfaces)": [[45, "Bio.Align.interfaces.AlignmentWriter", false]], "alignmentwriter (class in bio.align.maf)": [[46, "Bio.Align.maf.AlignmentWriter", false]], "alignmentwriter (class in bio.align.mauve)": [[47, "Bio.Align.mauve.AlignmentWriter", false]], "alignmentwriter (class in bio.align.nexus)": [[49, "Bio.Align.nexus.AlignmentWriter", false]], "alignmentwriter (class in bio.align.phylip)": [[50, "Bio.Align.phylip.AlignmentWriter", false]], "alignmentwriter (class in bio.align.psl)": [[51, "Bio.Align.psl.AlignmentWriter", false]], "alignmentwriter (class in bio.align.sam)": [[52, "Bio.Align.sam.AlignmentWriter", false]], "alignmentwriter (class in bio.align.stockholm)": [[53, "Bio.Align.stockholm.AlignmentWriter", false]], "alignmentwriter (class in bio.alignio.interfaces)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter", false]], "all_ids() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.all_ids", false]], "allow_all_transitions() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.allow_all_transitions", false]], "allow_transition() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.allow_transition", false]], "alpha (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.alpha", false]], "alphabet (bio.align.substitution_matrices.array property)": [[54, "Bio.Align.substitution_matrices.Array.alphabet", false]], "alt() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.alt", false]], "altloc_match() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.altloc_match", false]], "ambiguouscodontable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.AmbiguousCodonTable", false]], "ambiguousforwardtable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable", false]], "amino (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.amino", false]], "amino (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.amino", false]], "amino_acids_percent (bio.sequtils.protparam.proteinanalysis property)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.amino_acids_percent", false]], "amplifier (class in bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.Amplifier", false]], "anc (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.anc", false]], "anchors (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.anchors", false]], "anchorspacing (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.anchorspacing", false]], "angle (bio.pdb.internal_coords.dihedron property)": [[169, "Bio.PDB.internal_coords.Dihedron.angle", false]], "angle (bio.pdb.internal_coords.hedron property)": [[169, "Bio.PDB.internal_coords.Hedron.angle", false]], "angle() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.angle", false]], "angle_avg() (bio.pdb.internal_coords.dihedron static method)": [[169, "Bio.PDB.internal_coords.Dihedron.angle_avg", false]], "angle_dif() (bio.pdb.internal_coords.dihedron static method)": [[169, "Bio.PDB.internal_coords.Dihedron.angle_dif", false]], "angle_pop_sd() (bio.pdb.internal_coords.dihedron static method)": [[169, "Bio.PDB.internal_coords.Dihedron.angle_pop_sd", false]], "annot (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.annot", false]], "annot (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.annot", false]], "annotate() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.annotate", false]], "annotatedchromosomesegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment", false]], "annotation (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Annotation", false]], "annotation() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.annotation", false]], "annotation() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.annotation", false]], "annotations (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.annotations", false]], "annotations (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.annotations", false]], "anticonsensus (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.anticonsensus", false]], "anticonsensus (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.anticonsensus", false]], "aoutfeat (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.aoutfeat", false]], "append() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.append", false]], "append() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.append", false]], "append() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.append", false]], "append_item() (bio.blast.ncbixml.descriptionext method)": [[71, "Bio.Blast.NCBIXML.DescriptionExt.append_item", false]], "append_sets() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.append_sets", false]], "applicationerror": [[67, "Bio.Application.ApplicationError", false]], "apply() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.apply", false]], "apply() (bio.pdb.superimposer.superimposer method)": [[163, "Bio.PDB.Superimposer.Superimposer.apply", false]], "applymtx() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.applyMtx", false]], "archive (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.archive", false]], "aromaticity() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.aromaticity", false]], "array (class in bio.align.substitution_matrices)": [[54, "Bio.Align.substitution_matrices.Array", false]], "artemis_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.artemis_color", false]], "as_fasta() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.as_fasta", false]], "as_fasta_2line() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.as_fasta_2line", false]], "as_fastq() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_fastq", false]], "as_fastq_illumina() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_fastq_illumina", false]], "as_fastq_solexa() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_fastq_solexa", false]], "as_handle() (in module bio.file)": [[91, "Bio.File.as_handle", false]], "as_phyloxml() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.as_phyloxml", false]], "as_phyloxml() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.as_phyloxml", false]], "as_qual() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.as_qual", false]], "as_tab() (in module bio.seqio.tabio)": [[256, "Bio.SeqIO.TabIO.as_tab", false]], "as_type (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.as_type", false]], "asequence (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.asequence", false]], "asequence (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.asequence", false]], "asequence (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.asequence", false]], "asequence (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.asequence", false]], "asequence (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.asequence", false]], "asequence (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.asequence", false]], "assemble() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.assemble", false]], "assemble_residues() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.assemble_residues", false]], "assemble_residues_ser() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.assemble_residues_ser", false]], "astral (class in bio.scop)": [[209, "Bio.SCOP.Astral", false]], "atm() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.atm", false]], "atom (class in bio.pdb.atom)": [[135, "Bio.PDB.Atom.Atom", false]], "atom_chain (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.atom_chain", false]], "atom_re (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.atom_re", false]], "atom_sernum (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.atom_sernum", false]], "atom_to_internal_coordinates() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.atom_to_internal_coordinates", false]], "atom_to_internal_coordinates() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.atom_to_internal_coordinates", false]], "atom_to_internal_coordinates() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.atom_to_internal_coordinates", false]], "atom_to_internal_coordinates() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.atom_to_internal_coordinates", false]], "atomarray (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.atomArray", false]], "atomiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.AtomIterator", false]], "atomkey (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.AtomKey", false]], "auto (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.auto", false]], "auto (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.auto", false]], "auto (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.auto", false]], "auto (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.auto", false]], "auto (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.auto", false]], "auto (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.auto", false]], "auto (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.auto", false]], "auto (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.auto", false]], "auto (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.auto", false]], "auto (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.auto", false]], "auto (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.auto", false]], "auto (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.auto", false]], "auto (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.auto", false]], "auto (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.auto", false]], "auto (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.auto", false]], "auto (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.auto", false]], "auto (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.auto", false]], "auto (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.auto", false]], "auto (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.auto", false]], "auto (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.auto", false]], "auto (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.auto", false]], "auto (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.auto", false]], "auto (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.auto", false]], "auto (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.auto", false]], "auto (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.auto", false]], "auto (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.auto", false]], "auto (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.auto", false]], "autocommit() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.autocommit", false]], "autocommit() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.autocommit", false]], "autocommit() (biosql.dbutils.pgdb_dbutils method)": [[304, "BioSQL.DBUtils.Pgdb_dbutils.autocommit", false]], "autocommit() (biosql.dbutils.psycopg2_dbutils method)": [[304, "BioSQL.DBUtils.Psycopg2_dbutils.autocommit", false]], "autosqltable (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.AutoSQLTable", false]], "b (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.b", false]], "b (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.B", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.b", false]], "b (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.b", false]], "b (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.B", false]], "b (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.b", false]], "b (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.B", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.b", false]], "b (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.b", false]], "b (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.b", false]], "b1 (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.b1", false]], "b2 (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.b2", false]], "back_table (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.back_table", false]], "back_transcribe() (in module bio.seq)": [[236, "Bio.Seq.back_transcribe", false]], "background (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.background", false]], "backward_algorithm() (bio.hmm.dynamicprogramming.abstractdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.backward_algorithm", false]], "bam (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.bam", false]], "bam_file (bio.sequencing.applications.samtoolsreheadercommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline.bam_file", false]], "bams (bio.sequencing.applications.samtoolscatcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.bams", false]], "barchartdistribution (class in bio.graphics.distribution)": [[103, "Bio.Graphics.Distribution.BarChartDistribution", false]], "base_feature_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.BASE_FEATURE_FORMAT", false]], "base_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.BASE_FORMAT", false]], "base_id (bio.motifs.jaspar.motif property)": [[287, "Bio.motifs.jaspar.Motif.base_id", false]], "basefreq (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.basefreq", false]], "basefreq (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.basefreq", false]], "baseml (class in bio.phylo.paml.baseml)": [[193, "Bio.Phylo.PAML.baseml.Baseml", false]], "basemlerror": [[193, "Bio.Phylo.PAML.baseml.BasemlError", false]], "baumwelchtrainer (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer", false]], "bc() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.bc", false]], "beforeposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.BeforePosition", false]], "best (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.best", false]], "best_hit_overhang (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.best_hit_overhang", false]], "best_hit_overhang (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.best_hit_overhang", false]], "best_hit_score_edge (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.best_hit_score_edge", false]], "best_hit_score_edge (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.best_hit_score_edge", false]], "betweenposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.BetweenPosition", false]], "bf_search() (in module bio.pathway.rep.multigraph)": [[180, "Bio.Pathway.Rep.MultiGraph.bf_search", false]], "bgcolor (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.bgcolor", false]], "bgzfblocks() (in module bio.bgzf)": [[278, "Bio.bgzf.BgzfBlocks", false]], "bgzfreader (class in bio.bgzf)": [[278, "Bio.bgzf.BgzfReader", false]], "bgzfwriter (class in bio.bgzf)": [[278, "Bio.bgzf.BgzfWriter", false]], "binary_characters() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.binary_characters", false]], "binary_characters() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.binary_characters", false]], "binary_constraint (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.binary_constraint", false]], "binarycharacters (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.BinaryCharacters", false]], "binarycifparser (class in bio.pdb.binary_cif)": [[165, "Bio.PDB.binary_cif.BinaryCIFParser", false]], "bio": [[27, "module-Bio", false]], "bio.affy": [[28, "module-Bio.Affy", false]], "bio.affy.celfile": [[29, "module-Bio.Affy.CelFile", false]], "bio.align": [[30, "module-Bio.Align", false]], "bio.align.a2m": [[33, "module-Bio.Align.a2m", false]], "bio.align.aligninfo": [[31, "module-Bio.Align.AlignInfo", false]], "bio.align.analysis": [[34, "module-Bio.Align.analysis", false]], "bio.align.applications": [[32, "module-Bio.Align.Applications", false]], "bio.align.bed": [[35, "module-Bio.Align.bed", false]], "bio.align.bigbed": [[36, "module-Bio.Align.bigbed", false]], "bio.align.bigmaf": [[37, "module-Bio.Align.bigmaf", false]], "bio.align.bigpsl": [[38, "module-Bio.Align.bigpsl", false]], "bio.align.chain": [[39, "module-Bio.Align.chain", false]], "bio.align.clustal": [[40, "module-Bio.Align.clustal", false]], "bio.align.emboss": [[41, "module-Bio.Align.emboss", false]], "bio.align.exonerate": [[42, "module-Bio.Align.exonerate", false]], "bio.align.fasta": [[43, "module-Bio.Align.fasta", false]], "bio.align.hhr": [[44, "module-Bio.Align.hhr", false]], "bio.align.interfaces": [[45, "module-Bio.Align.interfaces", false]], "bio.align.maf": [[46, "module-Bio.Align.maf", false]], "bio.align.mauve": [[47, "module-Bio.Align.mauve", false]], "bio.align.msf": [[48, "module-Bio.Align.msf", false]], "bio.align.nexus": [[49, "module-Bio.Align.nexus", false]], "bio.align.phylip": [[50, "module-Bio.Align.phylip", false]], "bio.align.psl": [[51, "module-Bio.Align.psl", false]], "bio.align.sam": [[52, "module-Bio.Align.sam", false]], "bio.align.stockholm": [[53, "module-Bio.Align.stockholm", false]], "bio.align.substitution_matrices": [[54, "module-Bio.Align.substitution_matrices", false]], "bio.align.tabular": [[55, "module-Bio.Align.tabular", false]], "bio.alignio": [[56, "module-Bio.AlignIO", false]], "bio.alignio.clustalio": [[57, "module-Bio.AlignIO.ClustalIO", false]], "bio.alignio.embossio": [[58, "module-Bio.AlignIO.EmbossIO", false]], "bio.alignio.fastaio": [[59, "module-Bio.AlignIO.FastaIO", false]], "bio.alignio.interfaces": [[60, "module-Bio.AlignIO.Interfaces", false]], "bio.alignio.mafio": [[61, "module-Bio.AlignIO.MafIO", false]], "bio.alignio.mauveio": [[62, "module-Bio.AlignIO.MauveIO", false]], "bio.alignio.msfio": [[63, "module-Bio.AlignIO.MsfIO", false]], "bio.alignio.nexusio": [[64, "module-Bio.AlignIO.NexusIO", false]], "bio.alignio.phylipio": [[65, "module-Bio.AlignIO.PhylipIO", false]], "bio.alignio.stockholmio": [[66, "module-Bio.AlignIO.StockholmIO", false]], "bio.application": [[67, "module-Bio.Application", false]], "bio.bgzf": [[278, "module-Bio.bgzf", false]], "bio.blast": [[68, "module-Bio.Blast", false]], "bio.blast.applications": [[69, "module-Bio.Blast.Applications", false]], "bio.blast.ncbiwww": [[70, "module-Bio.Blast.NCBIWWW", false]], "bio.blast.ncbixml": [[71, "module-Bio.Blast.NCBIXML", false]], "bio.caps": [[72, "module-Bio.CAPS", false]], "bio.cluster": [[73, "module-Bio.Cluster", false]], "bio.codonalign": [[279, "module-Bio.codonalign", false]], "bio.codonalign.codonalignment": [[280, "module-Bio.codonalign.codonalignment", false]], "bio.codonalign.codonseq": [[281, "module-Bio.codonalign.codonseq", false]], "bio.compass": [[74, "module-Bio.Compass", false]], "bio.data": [[75, "module-Bio.Data", false]], "bio.data.codontable": [[76, "module-Bio.Data.CodonTable", false]], "bio.data.iupacdata": [[77, "module-Bio.Data.IUPACData", false]], "bio.data.pdbdata": [[78, "module-Bio.Data.PDBData", false]], "bio.emboss": [[79, "module-Bio.Emboss", false]], "bio.emboss.applications": [[80, "module-Bio.Emboss.Applications", false]], "bio.emboss.primer3": [[81, "module-Bio.Emboss.Primer3", false]], "bio.emboss.primersearch": [[82, "module-Bio.Emboss.PrimerSearch", false]], "bio.entrez": [[83, "module-Bio.Entrez", false]], "bio.entrez.parser": [[84, "module-Bio.Entrez.Parser", false]], "bio.expasy": [[85, "module-Bio.ExPASy", false]], "bio.expasy.cellosaurus": [[90, "module-Bio.ExPASy.cellosaurus", false]], "bio.expasy.enzyme": [[86, "module-Bio.ExPASy.Enzyme", false]], "bio.expasy.prodoc": [[87, "module-Bio.ExPASy.Prodoc", false]], "bio.expasy.prosite": [[88, "module-Bio.ExPASy.Prosite", false]], "bio.expasy.scanprosite": [[89, "module-Bio.ExPASy.ScanProsite", false]], "bio.file": [[91, "module-Bio.File", false]], "bio.genbank": [[92, "module-Bio.GenBank", false]], "bio.genbank.record": [[93, "module-Bio.GenBank.Record", false]], "bio.genbank.scanner": [[94, "module-Bio.GenBank.Scanner", false]], "bio.genbank.utils": [[95, "module-Bio.GenBank.utils", false]], "bio.geo": [[96, "module-Bio.Geo", false]], "bio.geo.record": [[97, "module-Bio.Geo.Record", false]], "bio.graphics": [[98, "module-Bio.Graphics", false]], "bio.graphics.basicchromosome": [[99, "module-Bio.Graphics.BasicChromosome", false]], "bio.graphics.colorspiral": [[100, "module-Bio.Graphics.ColorSpiral", false]], "bio.graphics.comparative": [[101, "module-Bio.Graphics.Comparative", false]], "bio.graphics.displayrepresentation": [[102, "module-Bio.Graphics.DisplayRepresentation", false]], "bio.graphics.distribution": [[103, "module-Bio.Graphics.Distribution", false]], "bio.graphics.genomediagram": [[104, "module-Bio.Graphics.GenomeDiagram", false]], "bio.graphics.kgml_vis": [[105, "module-Bio.Graphics.KGML_vis", false]], "bio.hmm": [[106, "module-Bio.HMM", false]], "bio.hmm.dynamicprogramming": [[107, "module-Bio.HMM.DynamicProgramming", false]], "bio.hmm.markovmodel": [[108, "module-Bio.HMM.MarkovModel", false]], "bio.hmm.trainer": [[109, "module-Bio.HMM.Trainer", false]], "bio.hmm.utilities": [[110, "module-Bio.HMM.Utilities", false]], "bio.kegg": [[111, "module-Bio.KEGG", false]], "bio.kegg.compound": [[112, "module-Bio.KEGG.Compound", false]], "bio.kegg.enzyme": [[113, "module-Bio.KEGG.Enzyme", false]], "bio.kegg.gene": [[114, "module-Bio.KEGG.Gene", false]], "bio.kegg.kgml": [[115, "module-Bio.KEGG.KGML", false]], "bio.kegg.kgml.kgml_parser": [[116, "module-Bio.KEGG.KGML.KGML_parser", false]], "bio.kegg.kgml.kgml_pathway": [[117, "module-Bio.KEGG.KGML.KGML_pathway", false]], "bio.kegg.map": [[118, "module-Bio.KEGG.Map", false]], "bio.kegg.rest": [[119, "module-Bio.KEGG.REST", false]], "bio.knn": [[282, "module-Bio.kNN", false]], "bio.logisticregression": [[120, "module-Bio.LogisticRegression", false]], "bio.markovmodel": [[121, "module-Bio.MarkovModel", false]], "bio.maxentropy": [[122, "module-Bio.MaxEntropy", false]], "bio.medline": [[123, "module-Bio.Medline", false]], "bio.motifs": [[283, "module-Bio.motifs", false]], "bio.motifs.alignace": [[284, "module-Bio.motifs.alignace", false]], "bio.motifs.applications": [[285, "module-Bio.motifs.applications", false]], "bio.motifs.clusterbuster": [[286, "module-Bio.motifs.clusterbuster", false]], "bio.motifs.jaspar": [[287, "module-Bio.motifs.jaspar", false]], "bio.motifs.jaspar.db": [[288, "module-Bio.motifs.jaspar.db", false]], "bio.motifs.mast": [[289, "module-Bio.motifs.mast", false]], "bio.motifs.matrix": [[290, "module-Bio.motifs.matrix", false]], "bio.motifs.meme": [[291, "module-Bio.motifs.meme", false]], "bio.motifs.minimal": [[292, "module-Bio.motifs.minimal", false]], "bio.motifs.pfm": [[293, "module-Bio.motifs.pfm", false]], "bio.motifs.thresholds": [[294, "module-Bio.motifs.thresholds", false]], "bio.motifs.transfac": [[295, "module-Bio.motifs.transfac", false]], "bio.motifs.xms": [[296, "module-Bio.motifs.xms", false]], "bio.naivebayes": [[127, "module-Bio.NaiveBayes", false]], "bio.nexus": [[128, "module-Bio.Nexus", false]], "bio.nexus.nexus": [[129, "module-Bio.Nexus.Nexus", false]], "bio.nexus.nodes": [[130, "module-Bio.Nexus.Nodes", false]], "bio.nexus.standarddata": [[131, "module-Bio.Nexus.StandardData", false]], "bio.nexus.trees": [[132, "module-Bio.Nexus.Trees", false]], "bio.nmr": [[124, "module-Bio.NMR", false]], "bio.nmr.noetools": [[125, "module-Bio.NMR.NOEtools", false]], "bio.nmr.xpktools": [[126, "module-Bio.NMR.xpktools", false]], "bio.pairwise2": [[297, "module-Bio.pairwise2", false]], "bio.pathway": [[177, "module-Bio.Pathway", false]], "bio.pathway.rep": [[178, "module-Bio.Pathway.Rep", false]], "bio.pathway.rep.graph": [[179, "module-Bio.Pathway.Rep.Graph", false]], "bio.pathway.rep.multigraph": [[180, "module-Bio.Pathway.Rep.MultiGraph", false]], "bio.pdb": [[133, "module-Bio.PDB", false]], "bio.pdb.abstractpropertymap": [[134, "module-Bio.PDB.AbstractPropertyMap", false]], "bio.pdb.alphafold_db": [[164, "module-Bio.PDB.alphafold_db", false]], "bio.pdb.atom": [[135, "module-Bio.PDB.Atom", false]], "bio.pdb.binary_cif": [[165, "module-Bio.PDB.binary_cif", false]], "bio.pdb.cealign": [[166, "module-Bio.PDB.cealign", false]], "bio.pdb.chain": [[136, "module-Bio.PDB.Chain", false]], "bio.pdb.dice": [[138, "module-Bio.PDB.Dice", false]], "bio.pdb.dssp": [[137, "module-Bio.PDB.DSSP", false]], "bio.pdb.entity": [[139, "module-Bio.PDB.Entity", false]], "bio.pdb.fragmentmapper": [[140, "module-Bio.PDB.FragmentMapper", false]], "bio.pdb.hsexposure": [[141, "module-Bio.PDB.HSExposure", false]], "bio.pdb.ic_data": [[167, "module-Bio.PDB.ic_data", false]], "bio.pdb.ic_rebuild": [[168, "module-Bio.PDB.ic_rebuild", false]], "bio.pdb.internal_coords": [[169, "module-Bio.PDB.internal_coords", false]], "bio.pdb.mmcif2dict": [[142, "module-Bio.PDB.MMCIF2Dict", false]], "bio.pdb.mmcifio": [[170, "module-Bio.PDB.mmcifio", false]], "bio.pdb.mmcifparser": [[143, "module-Bio.PDB.MMCIFParser", false]], "bio.pdb.mmtf": [[171, "module-Bio.PDB.mmtf", false]], "bio.pdb.mmtf.defaultparser": [[172, "module-Bio.PDB.mmtf.DefaultParser", false]], "bio.pdb.mmtf.mmtfio": [[173, "module-Bio.PDB.mmtf.mmtfio", false]], "bio.pdb.model": [[144, "module-Bio.PDB.Model", false]], "bio.pdb.naccess": [[145, "module-Bio.PDB.NACCESS", false]], "bio.pdb.neighborsearch": [[146, "module-Bio.PDB.NeighborSearch", false]], "bio.pdb.parse_pdb_header": [[174, "module-Bio.PDB.parse_pdb_header", false]], "bio.pdb.pdbexceptions": [[147, "module-Bio.PDB.PDBExceptions", false]], "bio.pdb.pdbio": [[148, "module-Bio.PDB.PDBIO", false]], "bio.pdb.pdblist": [[149, "module-Bio.PDB.PDBList", false]], "bio.pdb.pdbmlparser": [[150, "module-Bio.PDB.PDBMLParser", false]], "bio.pdb.pdbparser": [[151, "module-Bio.PDB.PDBParser", false]], "bio.pdb.picio": [[152, "module-Bio.PDB.PICIO", false]], "bio.pdb.polypeptide": [[154, "module-Bio.PDB.Polypeptide", false]], "bio.pdb.psea": [[153, "module-Bio.PDB.PSEA", false]], "bio.pdb.qcprot": [[175, "module-Bio.PDB.qcprot", false]], "bio.pdb.residue": [[155, "module-Bio.PDB.Residue", false]], "bio.pdb.residuedepth": [[156, "module-Bio.PDB.ResidueDepth", false]], "bio.pdb.sasa": [[157, "module-Bio.PDB.SASA", false]], "bio.pdb.scadio": [[158, "module-Bio.PDB.SCADIO", false]], "bio.pdb.selection": [[159, "module-Bio.PDB.Selection", false]], "bio.pdb.structure": [[160, "module-Bio.PDB.Structure", false]], "bio.pdb.structurealignment": [[161, "module-Bio.PDB.StructureAlignment", false]], "bio.pdb.structurebuilder": [[162, "module-Bio.PDB.StructureBuilder", false]], "bio.pdb.superimposer": [[163, "module-Bio.PDB.Superimposer", false]], "bio.pdb.vectors": [[176, "module-Bio.PDB.vectors", false]], "bio.phenotype": [[298, "module-Bio.phenotype", false]], "bio.phenotype.phen_micro": [[299, "module-Bio.phenotype.phen_micro", false]], "bio.phenotype.pm_fitting": [[300, "module-Bio.phenotype.pm_fitting", false]], "bio.phylo": [[181, "module-Bio.Phylo", false]], "bio.phylo.applications": [[182, "module-Bio.Phylo.Applications", false]], "bio.phylo.basetree": [[183, "module-Bio.Phylo.BaseTree", false]], "bio.phylo.cdao": [[184, "module-Bio.Phylo.CDAO", false]], "bio.phylo.cdaoio": [[185, "module-Bio.Phylo.CDAOIO", false]], "bio.phylo.consensus": [[186, "module-Bio.Phylo.Consensus", false]], "bio.phylo.newick": [[189, "module-Bio.Phylo.Newick", false]], "bio.phylo.newickio": [[190, "module-Bio.Phylo.NewickIO", false]], "bio.phylo.nexml": [[187, "module-Bio.Phylo.NeXML", false]], "bio.phylo.nexmlio": [[188, "module-Bio.Phylo.NeXMLIO", false]], "bio.phylo.nexusio": [[191, "module-Bio.Phylo.NexusIO", false]], "bio.phylo.paml": [[192, "module-Bio.Phylo.PAML", false]], "bio.phylo.paml.baseml": [[193, "module-Bio.Phylo.PAML.baseml", false]], "bio.phylo.paml.chi2": [[194, "module-Bio.Phylo.PAML.chi2", false]], "bio.phylo.paml.codeml": [[195, "module-Bio.Phylo.PAML.codeml", false]], "bio.phylo.paml.yn00": [[196, "module-Bio.Phylo.PAML.yn00", false]], "bio.phylo.phyloxml": [[197, "module-Bio.Phylo.PhyloXML", false]], "bio.phylo.phyloxmlio": [[198, "module-Bio.Phylo.PhyloXMLIO", false]], "bio.phylo.treeconstruction": [[199, "module-Bio.Phylo.TreeConstruction", false]], "bio.popgen": [[200, "module-Bio.PopGen", false]], "bio.popgen.genepop": [[201, "module-Bio.PopGen.GenePop", false]], "bio.popgen.genepop.controller": [[202, "module-Bio.PopGen.GenePop.Controller", false]], "bio.popgen.genepop.easycontroller": [[203, "module-Bio.PopGen.GenePop.EasyController", false]], "bio.popgen.genepop.fileparser": [[204, "module-Bio.PopGen.GenePop.FileParser", false]], "bio.popgen.genepop.largefileparser": [[205, "module-Bio.PopGen.GenePop.LargeFileParser", false]], "bio.restriction": [[206, "module-Bio.Restriction", false]], "bio.restriction.printformat": [[207, "module-Bio.Restriction.PrintFormat", false]], "bio.restriction.restriction_dictionary": [[208, "module-Bio.Restriction.Restriction_Dictionary", false]], "bio.scop": [[209, "module-Bio.SCOP", false]], "bio.scop.cla": [[210, "module-Bio.SCOP.Cla", false]], "bio.scop.des": [[211, "module-Bio.SCOP.Des", false]], "bio.scop.dom": [[212, "module-Bio.SCOP.Dom", false]], "bio.scop.hie": [[213, "module-Bio.SCOP.Hie", false]], "bio.scop.raf": [[214, "module-Bio.SCOP.Raf", false]], "bio.scop.residues": [[215, "module-Bio.SCOP.Residues", false]], "bio.searchio": [[217, "module-Bio.SearchIO", false]], "bio.searchio.blastio": [[218, "module-Bio.SearchIO.BlastIO", false]], "bio.searchio.blastio.blast_tab": [[219, "module-Bio.SearchIO.BlastIO.blast_tab", false]], "bio.searchio.blastio.blast_xml": [[220, "module-Bio.SearchIO.BlastIO.blast_xml", false]], "bio.searchio.blatio": [[221, "module-Bio.SearchIO.BlatIO", false]], "bio.searchio.exonerateio": [[222, "module-Bio.SearchIO.ExonerateIO", false]], "bio.searchio.exonerateio.exonerate_cigar": [[223, "module-Bio.SearchIO.ExonerateIO.exonerate_cigar", false]], "bio.searchio.exonerateio.exonerate_text": [[224, "module-Bio.SearchIO.ExonerateIO.exonerate_text", false]], "bio.searchio.exonerateio.exonerate_vulgar": [[225, "module-Bio.SearchIO.ExonerateIO.exonerate_vulgar", false]], "bio.searchio.fastaio": [[226, "module-Bio.SearchIO.FastaIO", false]], "bio.searchio.hhsuiteio": [[227, "module-Bio.SearchIO.HHsuiteIO", false]], "bio.searchio.hhsuiteio.hhsuite2_text": [[228, "module-Bio.SearchIO.HHsuiteIO.hhsuite2_text", false]], "bio.searchio.hmmerio": [[229, "module-Bio.SearchIO.HmmerIO", false]], "bio.searchio.hmmerio.hmmer2_text": [[230, "module-Bio.SearchIO.HmmerIO.hmmer2_text", false]], "bio.searchio.hmmerio.hmmer3_domtab": [[231, "module-Bio.SearchIO.HmmerIO.hmmer3_domtab", false]], "bio.searchio.hmmerio.hmmer3_tab": [[232, "module-Bio.SearchIO.HmmerIO.hmmer3_tab", false]], "bio.searchio.hmmerio.hmmer3_text": [[233, "module-Bio.SearchIO.HmmerIO.hmmer3_text", false]], "bio.searchio.interproscanio": [[234, "module-Bio.SearchIO.InterproscanIO", false]], "bio.searchio.interproscanio.interproscan_xml": [[235, "module-Bio.SearchIO.InterproscanIO.interproscan_xml", false]], "bio.seq": [[236, "module-Bio.Seq", false]], "bio.seqfeature": [[237, "module-Bio.SeqFeature", false]], "bio.seqio": [[238, "module-Bio.SeqIO", false]], "bio.seqio.abiio": [[239, "module-Bio.SeqIO.AbiIO", false]], "bio.seqio.aceio": [[240, "module-Bio.SeqIO.AceIO", false]], "bio.seqio.fastaio": [[241, "module-Bio.SeqIO.FastaIO", false]], "bio.seqio.gckio": [[242, "module-Bio.SeqIO.GckIO", false]], "bio.seqio.gfaio": [[243, "module-Bio.SeqIO.GfaIO", false]], "bio.seqio.igio": [[244, "module-Bio.SeqIO.IgIO", false]], "bio.seqio.insdcio": [[245, "module-Bio.SeqIO.InsdcIO", false]], "bio.seqio.interfaces": [[246, "module-Bio.SeqIO.Interfaces", false]], "bio.seqio.nibio": [[247, "module-Bio.SeqIO.NibIO", false]], "bio.seqio.pdbio": [[248, "module-Bio.SeqIO.PdbIO", false]], "bio.seqio.phdio": [[249, "module-Bio.SeqIO.PhdIO", false]], "bio.seqio.pirio": [[250, "module-Bio.SeqIO.PirIO", false]], "bio.seqio.qualityio": [[251, "module-Bio.SeqIO.QualityIO", false]], "bio.seqio.seqxmlio": [[252, "module-Bio.SeqIO.SeqXmlIO", false]], "bio.seqio.sffio": [[253, "module-Bio.SeqIO.SffIO", false]], "bio.seqio.snapgeneio": [[254, "module-Bio.SeqIO.SnapGeneIO", false]], "bio.seqio.swissio": [[255, "module-Bio.SeqIO.SwissIO", false]], "bio.seqio.tabio": [[256, "module-Bio.SeqIO.TabIO", false]], "bio.seqio.twobitio": [[257, "module-Bio.SeqIO.TwoBitIO", false]], "bio.seqio.uniprotio": [[258, "module-Bio.SeqIO.UniprotIO", false]], "bio.seqio.xdnaio": [[259, "module-Bio.SeqIO.XdnaIO", false]], "bio.seqrecord": [[260, "module-Bio.SeqRecord", false]], "bio.sequencing": [[268, "module-Bio.Sequencing", false]], "bio.sequencing.ace": [[269, "module-Bio.Sequencing.Ace", false]], "bio.sequencing.applications": [[270, "module-Bio.Sequencing.Applications", false]], "bio.sequencing.phd": [[271, "module-Bio.Sequencing.Phd", false]], "bio.sequtils": [[261, "module-Bio.SeqUtils", false]], "bio.sequtils.checksum": [[262, "module-Bio.SeqUtils.CheckSum", false]], "bio.sequtils.isoelectricpoint": [[263, "module-Bio.SeqUtils.IsoelectricPoint", false]], "bio.sequtils.lcc": [[267, "module-Bio.SeqUtils.lcc", false]], "bio.sequtils.meltingtemp": [[264, "module-Bio.SeqUtils.MeltingTemp", false]], "bio.sequtils.protparam": [[265, "module-Bio.SeqUtils.ProtParam", false]], "bio.sequtils.protparamdata": [[266, "module-Bio.SeqUtils.ProtParamData", false]], "bio.svdsuperimposer": [[216, "module-Bio.SVDSuperimposer", false]], "bio.swissprot": [[272, "module-Bio.SwissProt", false]], "bio.swissprot.keywlist": [[273, "module-Bio.SwissProt.KeyWList", false]], "bio.togows": [[274, "module-Bio.TogoWS", false]], "bio.unigene": [[275, "module-Bio.UniGene", false]], "bio.uniprot": [[276, "module-Bio.UniProt", false]], "bio.uniprot.goa": [[277, "module-Bio.UniProt.GOA", false]], "bionj (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.bionj", false]], "biopythondeprecationwarning": [[27, "Bio.BiopythonDeprecationWarning", false]], "biopythonexperimentalwarning": [[27, "Bio.BiopythonExperimentalWarning", false]], "biopythonparserwarning": [[27, "Bio.BiopythonParserWarning", false]], "biopythonwarning": [[27, "Bio.BiopythonWarning", false]], "bioseqdatabase (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase", false]], "biosql": [[301, "module-BioSQL", false]], "biosql.bioseq": [[302, "module-BioSQL.BioSeq", false]], "biosql.bioseqdatabase": [[303, "module-BioSQL.BioSeqDatabase", false]], "biosql.dbutils": [[304, "module-BioSQL.DBUtils", false]], "biosql.loader": [[305, "module-BioSQL.Loader", false]], "bipartition_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.bipartition_filename", false]], "bits() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.bits", false]], "bl (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.bl", false]], "blast (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Blast", false]], "blastdb_version (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.blastdb_version", false]], "blastparser (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.BlastParser", false]], "blasttabindexer (class in bio.searchio.blastio.blast_tab)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer", false]], "blasttabparser (class in bio.searchio.blastio.blast_tab)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser", false]], "blasttabwriter (class in bio.searchio.blastio.blast_tab)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter", false]], "blastxmlindexer (class in bio.searchio.blastio.blast_xml)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer", false]], "blastxmlparser (class in bio.searchio.blastio.blast_xml)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser", false]], "blastxmlwriter (class in bio.searchio.blastio.blast_xml)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter", false]], "blatpslindexer (class in bio.searchio.blatio)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer", false]], "blatpslparser (class in bio.searchio.blatio)": [[221, "Bio.SearchIO.BlatIO.BlatPslParser", false]], "blatpslwriter (class in bio.searchio.blatio)": [[221, "Bio.SearchIO.BlatIO.BlatPslWriter", false]], "block (bio.seqio.seqxmlio.seqxmliterator attribute)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.BLOCK", false]], "block (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.Block", false]], "block_size (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.block_size", false]], "blocks_per_line (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.BLOCKS_PER_LINE", false]], "blocksize (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.blocksize", false]], "blue() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.blue", false]], "bond_rotate() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.bond_rotate", false]], "bond_set() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.bond_set", false]], "boot (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.boot", false]], "bootlabels (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.bootlabels", false]], "bootstrap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.bootstrap", false]], "bootstrap (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.bootstrap", false]], "bootstrap() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.bootstrap", false]], "bootstrap() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.bootstrap", false]], "bootstrap_branch_lengths (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.bootstrap_branch_lengths", false]], "bootstrap_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.bootstrap_consensus", false]], "bootstrap_seed (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.bootstrap_seed", false]], "bootstrap_trees() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.bootstrap_trees", false]], "bounds (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.bounds", false]], "bounds (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.bounds", false]], "bounds (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.bounds", false]], "boutfeat (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.boutfeat", false]], "branch_length() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.branch_length", false]], "branchcolor (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.BranchColor", false]], "branchcolor (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.BranchColor", false]], "branchlength2support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.branchlength2support", false]], "brenner (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.brenner", false]], "brief (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.brief", false]], "brief (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.brief", false]], "brief (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.brief", false]], "bs (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.bs", false]], "bsequence (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.bsequence", false]], "bsequence (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.bsequence", false]], "bsequence (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.bsequence", false]], "bsequence (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.bsequence", false]], "bsequence (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.bsequence", false]], "bsequence (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.bsequence", false]], "build() (in module bio.codonalign)": [[279, "Bio.codonalign.build", false]], "build_atomarray() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.build_atomArray", false]], "build_edraarrays() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.build_edraArrays", false]], "build_tree() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.build_tree", false]], "build_tree() (bio.phylo.treeconstruction.parsimonytreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor.build_tree", false]], "build_tree() (bio.phylo.treeconstruction.treeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.TreeConstructor.build_tree", false]], "bwaaligncommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline", false]], "bwabwaswcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline", false]], "bwaindexcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline", false]], "bwamemcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline", false]], "bwasampecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline", false]], "bwasamsecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline", false]], "c (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.c", false]], "c (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.c", false]], "c (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.c", false]], "c (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.C", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.c", false]], "c (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.C", false]], "c (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.C", false]], "c (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.c", false]], "ca_depth() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.ca_depth", false]], "cal_dn_ds() (in module bio.codonalign.codonseq)": [[281, "Bio.codonalign.codonseq.cal_dn_ds", false]], "calc_affine_penalty() (in module bio.pairwise2)": [[297, "Bio.pairwise2.calc_affine_penalty", false]], "calc_allele_genotype_freqs() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_allele_genotype_freqs", false]], "calc_angle() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.calc_angle", false]], "calc_dihedral() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.calc_dihedral", false]], "calc_diversities_fis_with_identity() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_diversities_fis_with_identity", false]], "calc_diversities_fis_with_size() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_diversities_fis_with_size", false]], "calc_fst_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_fst_all", false]], "calc_fst_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_fst_pair", false]], "calc_ibd() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.calc_ibd", false]], "calc_ibd_diplo() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_ibd_diplo", false]], "calc_ibd_haplo() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_ibd_haplo", false]], "calc_rho_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_rho_all", false]], "calc_rho_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.calc_rho_pair", false]], "calculate() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.calculate", false]], "calculate() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.calculate", false]], "calculate() (in module bio.knn)": [[282, "Bio.kNN.calculate", false]], "calculate() (in module bio.logisticregression)": [[120, "Bio.LogisticRegression.calculate", false]], "calculate() (in module bio.maxentropy)": [[122, "Bio.MaxEntropy.calculate", false]], "calculate() (in module bio.naivebayes)": [[127, "Bio.NaiveBayes.calculate", false]], "calculate_consensus() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.calculate_consensus", false]], "calculate_dn_ds() (in module bio.align.analysis)": [[34, "Bio.Align.analysis.calculate_dn_ds", false]], "calculate_dn_ds_matrix() (in module bio.align.analysis)": [[34, "Bio.Align.analysis.calculate_dn_ds_matrix", false]], "calculate_pseudocounts() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.calculate_pseudocounts", false]], "cappbuilder (class in bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.CaPPBuilder", false]], "capsmap (class in bio.caps)": [[72, "Bio.CAPS.CAPSMap", false]], "carboxyl (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.carboxyl", false]], "case (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.case", false]], "cat (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.cat", false]], "categories (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.categories", false]], "catergories (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.catergories", false]], "catergories (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.catergories", false]], "cdao_to_obo() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.cdao_to_obo", false]], "cdf_chi2() (in module bio.phylo.paml.chi2)": [[194, "Bio.Phylo.PAML.chi2.cdf_chi2", false]], "cealigner (class in bio.pdb.cealign)": [[166, "Bio.PDB.cealign.CEAligner", false]], "center (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.center", false]], "center_of_mass() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.center_of_mass", false]], "center_of_mass() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.center_of_mass", false]], "centre (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.centre", false]], "chain (class in bio.nexus.nodes)": [[130, "Bio.Nexus.Nodes.Chain", false]], "chain (class in bio.pdb.chain)": [[136, "Bio.PDB.Chain.Chain", false]], "chainexception": [[130, "Bio.Nexus.Nodes.ChainException", false]], "chainselector (class in bio.pdb.dice)": [[138, "Bio.PDB.Dice.ChainSelector", false]], "characterdatahandlerescape() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.characterDataHandlerEscape", false]], "characterdatahandlerraw() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.characterDataHandlerRaw", false]], "characters() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.characters", false]], "characters() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.characters", false]], "charbuffer (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.CharBuffer", false]], "charge_at_ph() (bio.sequtils.isoelectricpoint.isoelectricpoint method)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.charge_at_pH", false]], "charge_at_ph() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.charge_at_pH", false]], "check (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.check", false]], "checkpoints (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.checkpoints", false]], "chem_correction() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.chem_correction", false]], "child_dict (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.child_dict", false]], "child_edges() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.child_edges", false]], "child_edges() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.child_edges", false]], "child_list (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.child_list", false]], "children() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.children", false]], "children() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.children", false]], "chromosome (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.Chromosome", false]], "chromosomecounts (class in bio.graphics.displayrepresentation)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts", false]], "chromosomesegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.ChromosomeSegment", false]], "cifatomiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.CifAtomIterator", false]], "cifseqresiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.CifSeqresIterator", false]], "clade (bio.phylo.basetree.tree property)": [[183, "Bio.Phylo.BaseTree.Tree.clade", false]], "clade (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.Clade", false]], "clade (class in bio.phylo.cdao)": [[184, "Bio.Phylo.CDAO.Clade", false]], "clade (class in bio.phylo.newick)": [[189, "Bio.Phylo.Newick.Clade", false]], "clade (class in bio.phylo.nexml)": [[187, "Bio.Phylo.NeXML.Clade", false]], "clade (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Clade", false]], "clade() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.clade", false]], "clade_relation() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.clade_relation", false]], "clade_relation() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.clade_relation", false]], "claderelation (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.CladeRelation", false]], "classify() (in module bio.knn)": [[282, "Bio.kNN.classify", false]], "classify() (in module bio.logisticregression)": [[120, "Bio.LogisticRegression.classify", false]], "classify() (in module bio.maxentropy)": [[122, "Bio.MaxEntropy.classify", false]], "classify() (in module bio.naivebayes)": [[127, "Bio.NaiveBayes.classify", false]], "clean() (bio.alignio.interfaces.alignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter.clean", false]], "clean() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.clean", false]], "clean_value() (bio.genbank.utils.featurevaluecleaner method)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.clean_value", false]], "clear_ic() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.clear_ic", false]], "clear_transforms() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.clear_transforms", false]], "close (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.close", false]], "close() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.close", false]], "close() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.close", false]], "close() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.close", false]], "close() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.close", false]], "close() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.close", false]], "clustaliterator (class in bio.alignio.clustalio)": [[57, "Bio.AlignIO.ClustalIO.ClustalIterator", false]], "clustalomegacommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline", false]], "clustalout (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.clustalout", false]], "clustalw (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.clustalw", false]], "clustalw (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.clustalw", false]], "clustalwcommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.ClustalwCommandline", false]], "clustalwriter (class in bio.alignio.clustalio)": [[57, "Bio.AlignIO.ClustalIO.ClustalWriter", false]], "cluster (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.cluster", false]], "cluster1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.cluster1", false]], "cluster2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.cluster2", false]], "cluster_threshold (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.cluster_threshold", false]], "cluster_threshold_fast (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.cluster_threshold_fast", false]], "clustercentroids() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.clustercentroids", false]], "clustercentroids() (in module bio.cluster)": [[73, "Bio.Cluster.clustercentroids", false]], "clusterdistance() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.clusterdistance", false]], "clusterdistance() (in module bio.cluster)": [[73, "Bio.Cluster.clusterdistance", false]], "clustering (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.clustering", false]], "clusteringout (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.clusteringout", false]], "clustersize (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.clustersize", false]], "clw (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clw", false]], "clwout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clwout", false]], "clwstrict (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clwstrict", false]], "clwstrictout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.clwstrictout", false]], "cmodulo (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.Cmodulo", false]], "cmp_sccs() (in module bio.scop)": [[209, "Bio.SCOP.cmp_sccs", false]], "code() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.code", false]], "codeml (class in bio.phylo.paml.codeml)": [[195, "Bio.Phylo.PAML.codeml.Codeml", false]], "codemlerror": [[195, "Bio.Phylo.PAML.codeml.CodemlError", false]], "codon (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.codon", false]], "codonadaptationindex (class in bio.sequtils)": [[261, "Bio.SeqUtils.CodonAdaptationIndex", false]], "codonaligner (class in bio.align)": [[30, "Bio.Align.CodonAligner", false]], "codonalignment (class in bio.codonalign.codonalignment)": [[280, "Bio.codonalign.codonalignment.CodonAlignment", false]], "codonseq (class in bio.codonalign.codonseq)": [[281, "Bio.codonalign.codonseq.CodonSeq", false]], "codontable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.CodonTable", false]], "collapse() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.collapse", false]], "collapse() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.collapse", false]], "collapse_all() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.collapse_all", false]], "collapse_genera() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.collapse_genera", false]], "color (bio.phylo.basetree.clade property)": [[183, "Bio.Phylo.BaseTree.Clade.color", false]], "color() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.color", false]], "color() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.color", false]], "color_names (bio.phylo.basetree.branchcolor attribute)": [[183, "Bio.Phylo.BaseTree.BranchColor.color_names", false]], "color_to_reportlab() (in module bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.color_to_reportlab", false]], "colorspiral (class in bio.graphics.colorspiral)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral", false]], "colortranslator (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator", false]], "column_annotations (bio.align.multipleseqalignment property)": [[30, "Bio.Align.MultipleSeqAlignment.column_annotations", false]], "combine() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.combine", false]], "commandline (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.Commandline", false]], "comment (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.comment", false]], "commit() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.commit", false]], "commit() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.commit", false]], "common_ancestor() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.common_ancestor", false]], "common_ancestor() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.common_ancestor", false]], "common_name() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.common_name", false]], "comp_based_stats (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.comp_based_stats", false]], "comp_based_stats (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.comp_based_stats", false]], "comparativescatterplot (class in bio.graphics.comparative)": [[101, "Bio.Graphics.Comparative.ComparativeScatterPlot", false]], "compare_residues() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.compare_residues", false]], "complement (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.complement", false]], "complement() (in module bio.seq)": [[236, "Bio.Seq.complement", false]], "complement_rna() (in module bio.seq)": [[236, "Bio.Seq.complement_rna", false]], "component (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component", false]], "compoundlocation (class in bio.seqfeature)": [[237, "Bio.SeqFeature.CompoundLocation", false]], "compounds (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.compounds", false]], "compute() (bio.pdb.sasa.shrakerupley method)": [[157, "Bio.PDB.SASA.ShrakeRupley.compute", false]], "confidence (bio.phylo.phyloxml.clade property)": [[197, "Bio.Phylo.PhyloXML.Clade.confidence", false]], "confidence (bio.phylo.phyloxml.phylogeny property)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.confidence", false]], "confidence (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Confidence", false]], "confidence() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.confidence", false]], "confidence() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.confidence", false]], "consensus (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.consensus", false]], "consensus (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.consensus", false]], "consensus() (in module bio.nexus.trees)": [[132, "Bio.Nexus.Trees.consensus", false]], "consistency (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.consistency", false]], "consistency (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.consistency", false]], "consolewidth (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth", false]], "constant() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.constant", false]], "constraints (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.constraints", false]], "constraintweight (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.constraintWeight", false]], "contenthandler (class in bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler", false]], "contenthandler (class in bio.seqio.seqxmlio)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler", false]], "contig (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.Contig", false]], "convert (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.convert", false]], "convert (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.convert", false]], "convert (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.convert", false]], "convert() (in module bio.alignio)": [[56, "Bio.AlignIO.convert", false]], "convert() (in module bio.searchio)": [[217, "Bio.SearchIO.convert", false]], "convert() (in module bio.seqio)": [[238, "Bio.SeqIO.convert", false]], "convert() (in module bio.togows)": [[274, "Bio.TogoWS.convert", false]], "convert_absolute_support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.convert_absolute_support", false]], "coord_space() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.coord_space", false]], "coords (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.coords", false]], "copy() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.copy", false]], "copy() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.copy", false]], "copy() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.copy", false]], "copy() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.copy", false]], "copy() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.copy", false]], "copy_initncacs() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.copy_initNCaCs", false]], "core (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.core", false]], "cores (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.cores", false]], "corruptedxmlerror": [[68, "Bio.Blast.CorruptedXMLError", false], [84, "Bio.Entrez.Parser.CorruptedXMLError", false]], "count() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.count", false]], "count() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.count", false]], "count() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.count", false]], "count_amino_acids() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.count_amino_acids", false]], "count_terminals() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.count_terminals", false]], "count_terminals() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.count_terminals", false]], "counts() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.counts", false]], "cr_class() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.cr_class", false]], "crc32() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.crc32", false]], "crc64() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.crc64", false]], "create() (in module bio.motifs)": [[283, "Bio.motifs.create", false]], "create_contingency_tables() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.create_contingency_tables", false]], "crop_matrix() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.crop_matrix", false]], "crosslink (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink", false]], "cs (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.cs", false]], "cstatus() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.cstatus", false]], "csviterator() (in module bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.CsvIterator", false]], "ct (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.ct", false]], "culling_limit (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.culling_limit", false]], "culling_limit (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.culling_limit", false]], "cut() (bio.cluster.tree method)": [[73, "Bio.Cluster.Tree.cut", false]], "cw (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.cw", false]], "d (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.d", false]], "d (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.d", false]], "d (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.d", false]], "d (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.D", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.d", false]], "d2h (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.d2h", false]], "darken() (in module bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.darken", false]], "data (bio.blast.records property)": [[68, "Bio.Blast.Records.data", false]], "data_generator() (bio.popgen.genepop.largefileparser.record method)": [[205, "Bio.PopGen.GenePop.LargeFileParser.Record.data_generator", false]], "data_quartiles() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.data_quartiles", false]], "data_table() (in module bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.data_table", false]], "database (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.database", false]], "databaseloader (class in biosql.loader)": [[305, "BioSQL.Loader.DatabaseLoader", false]], "databaseremover (class in biosql.loader)": [[305, "BioSQL.Loader.DatabaseRemover", false]], "databasereport (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.DatabaseReport", false]], "datafile (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.datafile", false]], "datafile (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.datafile", false]], "datafile (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.datafile", false]], "datafile (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.datafile", false]], "datafile (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.datafile", false]], "datahandler (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.DataHandler", false]], "datahandlermeta (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.DataHandlerMeta", false]], "datatype (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.datatype", false]], "date (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Date", false]], "date() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.date", false]], "date() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.date", false]], "db (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.db", false]], "db (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.db", false]], "db (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.db", false]], "db (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.db", false]], "db (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.db", false]], "db (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.db", false]], "db (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.db", false]], "db (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db", false]], "db (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db", false]], "db_gencode (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db_gencode", false]], "db_gencode (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db_gencode", false]], "db_hard_mask (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db_hard_mask", false]], "db_hard_mask (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db_hard_mask", false]], "db_soft_mask (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.db_soft_mask", false]], "db_soft_mask (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.db_soft_mask", false]], "dbseqrecord (class in biosql.bioseq)": [[302, "BioSQL.BioSeq.DBSeqRecord", false]], "dbserver (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.DBServer", false]], "dbsize (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.dbsize", false]], "dbsize (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.dbsize", false]], "dbtype (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.dbtype", false]], "dbxrefs (bio.seqrecord.seqrecord attribute)": [[260, "Bio.SeqRecord.SeqRecord.dbxrefs", false]], "dbxrefs (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.dbxrefs", false]], "dcoordspace (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.dCoordSpace", false]], "dcsvalid (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.dcsValid", false]], "dealign (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.dealign", false]], "debug (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.debug", false]], "debug (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.debug", false]], "debug (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.debug", false]], "debug (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.debug", false]], "debug (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.debug", false]], "debug (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.debug", false]], "debug (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.debug", false]], "debug (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.debug", false]], "debug (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.debug", false]], "debug (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.debug", false]], "debug (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.debug", false]], "debug (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.debug", false]], "debug (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.debug", false]], "debug (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.debug", false]], "debug (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.debug", false]], "debug (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.debug", false]], "debug (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.debug", false]], "debug (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.debug", false]], "debug (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.debug", false]], "debug (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.debug", false]], "debug (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.debug", false]], "debug (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.debug", false]], "debug (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.debug", false]], "debug (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.debug", false]], "debug (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.debug", false]], "decode() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.decode", false]], "default (bio.align.bigbed.autosqltable attribute)": [[36, "Bio.Align.bigbed.AutoSQLTable.default", false]], "default_pseudo (bio.hmm.markovmodel.markovmodelbuilder attribute)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.DEFAULT_PSEUDO", false]], "defined (bio.seq.sequencedataabstractbaseclass property)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.defined", false]], "defined_ranges (bio.seq.sequencedataabstractbaseclass property)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.defined_ranges", false]], "degenerate_consensus (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.degenerate_consensus", false]], "degenerate_consensus (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.degenerate_consensus", false]], "del_feature() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.del_feature", false]], "del_graph() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.del_graph", false]], "del_set() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.del_set", false]], "del_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.del_track", false]], "depths() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.depths", false]], "desc() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.desc", false]], "description (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Description", false]], "description() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.description", false]], "descriptionext (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.DescriptionExt", false]], "descriptionextitem (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.DescriptionExtItem", false]], "destroy_transition() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.destroy_transition", false]], "detach_child() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.detach_child", false]], "detach_parent() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.detach_parent", false]], "detach_parent() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.detach_parent", false]], "detach_parent() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.detach_parent", false]], "df_search() (in module bio.pathway.rep.multigraph)": [[180, "Bio.Pathway.Rep.MultiGraph.df_search", false]], "diagbreak (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diagbreak", false]], "diaglength (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diaglength", false]], "diagmargin (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diagmargin", false]], "diagram (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.Diagram", false]], "diags (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.diags", false]], "dialigncommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.DialignCommandline", false]], "dictionary_match (class in bio.pairwise2)": [[297, "Bio.pairwise2.dictionary_match", false]], "dictionaryelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.DictionaryElement", false]], "die (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.die", false]], "die (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.die", false]], "die (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.die", false]], "die (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.die", false]], "die (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.die", false]], "die (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.die", false]], "die (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.die", false]], "die (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.die", false]], "die (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.die", false]], "die (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.die", false]], "die (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.die", false]], "die (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.die", false]], "die (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.die", false]], "die (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.die", false]], "die (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.die", false]], "die (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.die", false]], "die (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.die", false]], "die (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.die", false]], "die (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.die", false]], "die (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.die", false]], "die (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.die", false]], "die (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.die", false]], "die (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.die", false]], "die (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.die", false]], "die (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.die", false]], "difference() (bio.pdb.internal_coords.dihedron method)": [[169, "Bio.PDB.internal_coords.Dihedron.difference", false]], "differentialcutsite (class in bio.caps)": [[72, "Bio.CAPS.DifferentialCutsite", false]], "diffseqcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.DiffseqCommandline", false]], "dihedral_signs() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.dihedral_signs", false]], "dihedron (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.Dihedron", false]], "dimer (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.dimer", false]], "directory (bio.entrez.parser.datahandlermeta property)": [[84, "Bio.Entrez.Parser.DataHandlerMeta.directory", false]], "disordered_add() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.disordered_add", false]], "disordered_add() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add", false]], "disordered_add() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.disordered_add", false]], "disordered_get() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get", false]], "disordered_get_id_list() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_id_list", false]], "disordered_get_list() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.disordered_get_list", false]], "disordered_get_list() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list", false]], "disordered_has_id() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_has_id", false]], "disordered_remove() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.disordered_remove", false]], "disordered_remove() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_remove", false]], "disordered_remove() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.disordered_remove", false]], "disordered_select() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select", false]], "disorderedatom (class in bio.pdb.atom)": [[135, "Bio.PDB.Atom.DisorderedAtom", false]], "disorderedentitywrapper (class in bio.pdb.entity)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper", false]], "disorderedresidue (class in bio.pdb.residue)": [[155, "Bio.PDB.Residue.DisorderedResidue", false]], "display() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.display", false]], "dist_pearson() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.dist_pearson", false]], "dist_pearson_at() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.dist_pearson_at", false]], "distance() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.distance", false]], "distance() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.distance", false]], "distance1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.distance1", false]], "distance2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.distance2", false]], "distance_plot() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.distance_plot", false]], "distance_to_internal_coordinates() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.distance_to_internal_coordinates", false]], "distancecalculator (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator", false]], "distancematrix (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix", false]], "distancematrix() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.distancematrix", false]], "distancematrix() (in module bio.cluster)": [[73, "Bio.Cluster.distancematrix", false]], "distancetreeconstructor (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor", false]], "distmat_full (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_full", false]], "distmat_full_iter (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_full_iter", false]], "distmat_in (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_in", false]], "distmat_out (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.distmat_out", false]], "distplot_to_dh_arrays() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.distplot_to_dh_arrays", false]], "distribution (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Distribution", false]], "distribution() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.distribution", false]], "distribution() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.distribution", false]], "distribution() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.distribution", false]], "distributionpage (class in bio.graphics.distribution)": [[103, "Bio.Graphics.Distribution.DistributionPage", false]], "disulphides (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.disulphides", false]], "dna_models (bio.phylo.treeconstruction.distancecalculator attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.dna_models", false]], "dnaconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.dnaconc", false]], "dnafreqs (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.dnafreqs", false]], "dnamatrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.dnamatrix", false]], "domain (class in bio.scop)": [[209, "Bio.SCOP.Domain", false]], "domain() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.domain", false]], "domain() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.domain", false]], "domain_architecture() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.domain_architecture", false]], "domain_architecture() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.domain_architecture", false]], "domain_inclusion_ethresh (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.domain_inclusion_ethresh", false]], "domainarchitecture (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.DomainArchitecture", false]], "domainsclusteredbyev() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.domainsClusteredByEv", false]], "domainsclusteredbyid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.domainsClusteredById", false]], "dotdiff (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.dotdiff", false]], "dotdiff (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.dotdiff", false]], "dotdiff (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.dotdiff", false]], "dots (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.dots", false]], "download_all_assemblies() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_all_assemblies", false]], "download_cif_for() (in module bio.pdb.alphafold_db)": [[164, "Bio.PDB.alphafold_db.download_cif_for", false]], "download_entire_pdb() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_entire_pdb", false]], "download_obsolete_entries() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_obsolete_entries", false]], "download_pdb_files() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.download_pdb_files", false]], "dpparttree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.dpparttree", false]], "draw() (bio.graphics.basicchromosome.chromosome method)": [[99, "Bio.Graphics.BasicChromosome.Chromosome.draw", false]], "draw() (bio.graphics.basicchromosome.chromosomesegment method)": [[99, "Bio.Graphics.BasicChromosome.ChromosomeSegment.draw", false]], "draw() (bio.graphics.basicchromosome.organism method)": [[99, "Bio.Graphics.BasicChromosome.Organism.draw", false]], "draw() (bio.graphics.basicchromosome.spacersegment method)": [[99, "Bio.Graphics.BasicChromosome.SpacerSegment.draw", false]], "draw() (bio.graphics.distribution.barchartdistribution method)": [[103, "Bio.Graphics.Distribution.BarChartDistribution.draw", false]], "draw() (bio.graphics.distribution.distributionpage method)": [[103, "Bio.Graphics.Distribution.DistributionPage.draw", false]], "draw() (bio.graphics.distribution.linedistribution method)": [[103, "Bio.Graphics.Distribution.LineDistribution.draw", false]], "draw() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.draw", false]], "draw() (bio.graphics.kgml_vis.kgmlcanvas method)": [[105, "Bio.Graphics.KGML_vis.KGMLCanvas.draw", false]], "draw_to_file() (bio.graphics.comparative.comparativescatterplot method)": [[101, "Bio.Graphics.Comparative.ComparativeScatterPlot.draw_to_file", false]], "ds (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ds", false]], "ds (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.ds", false]], "dssp (class in bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.DSSP", false]], "dssp_dict_from_pdb_file() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.dssp_dict_from_pdb_file", false]], "dtype (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.dtype", false]], "dumb_consensus() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.dumb_consensus", false]], "duplications() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.duplications", false]], "dust (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.dust", false]], "e (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.E", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.e", false]], "e (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.E", false]], "e (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.E", false], [270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.e", false]], "e (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.E", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.e", false]], "ease (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.ease", false]], "easycontroller (class in bio.popgen.genepop.easycontroller)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController", false]], "ecitmatch() (in module bio.entrez)": [[83, "Bio.Entrez.ecitmatch", false]], "edges() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.edges", false]], "edges() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.edges", false]], "edron (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.Edron", false]], "edron_re (bio.pdb.internal_coords.edron attribute)": [[169, "Bio.PDB.internal_coords.Edron.edron_re", false]], "efetch() (in module bio.entrez)": [[83, "Bio.Entrez.efetch", false]], "egquery() (in module bio.entrez)": [[83, "Bio.Entrez.egquery", false]], "einfo() (in module bio.entrez)": [[83, "Bio.Entrez.einfo", false]], "einvertedcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.EInvertedCommandline", false]], "element (bio.kegg.kgml.kgml_pathway.component property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component.element", false]], "element (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.element", false]], "element (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.element", false]], "element (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.element", false]], "element (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.element", false]], "element (bio.kegg.kgml.kgml_pathway.relation property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.element", false]], "elementdecl() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.elementDecl", false]], "elink() (in module bio.entrez)": [[83, "Bio.Entrez.elink", false]], "em0 (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.em0", false]], "em1 (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.em1", false]], "em2 (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.em2", false]], "embl_indent (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.EMBL_INDENT", false]], "embl_spacer (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.EMBL_SPACER", false]], "emblcdsfeatureiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator", false]], "embliterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator", false]], "emblscanner (class in bio.genbank.scanner)": [[94, "Bio.GenBank.Scanner.EmblScanner", false]], "emblwriter (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter", false]], "embossiterator (class in bio.alignio.embossio)": [[58, "Bio.AlignIO.EmbossIO.EmbossIterator", false]], "emissions (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.emissions", false]], "empty_status_characters (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.empty_status_characters", false]], "end (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.end", false]], "end (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.end", false]], "end (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.end", false]], "enda (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.endA", false]], "endb (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.endB", false]], "enddbrefelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endDBRefElement", false]], "enddescriptionelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endDescriptionElement", false]], "endelement() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.endElement", false]], "endelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endElementHandler", false]], "endentryelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endEntryElement", false]], "enderrorelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endErrorElementHandler", false]], "endextend (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.endextend", false]], "endextend (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.endextend", false]], "endgaps (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.endgaps", false]], "endintegerelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endIntegerElementHandler", false]], "endnamespacedeclhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endNamespaceDeclHandler", false]], "endopen (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.endopen", false]], "endopen (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.endopen", false]], "endpropertyelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endPropertyElement", false]], "endrawelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endRawElementHandler", false]], "endsequenceelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endSequenceElement", false]], "endseqxmlelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endSeqXMLElement", false]], "endskipelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endSkipElementHandler", false]], "endspecieselement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.endSpeciesElement", false]], "endstringelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.endStringElementHandler", false]], "endswith() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.endswith", false]], "endweight (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.endweight", false]], "endweight (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.endweight", false]], "entity (class in bio.pdb.entity)": [[139, "Bio.PDB.Entity.Entity", false]], "entrez_query (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.entrez_query", false]], "entrez_query (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.entrez_query", false]], "entry (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.entry", false]], "entry (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry", false]], "entry() (in module bio.togows)": [[274, "Bio.TogoWS.entry", false]], "entry1 (bio.kegg.kgml.kgml_pathway.relation property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.entry1", false]], "entry2 (bio.kegg.kgml.kgml_pathway.relation property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation.entry2", false]], "enumerate_atoms() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.enumerate_atoms", false]], "ep (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.ep", false]], "epost() (in module bio.entrez)": [[83, "Bio.Entrez.epost", false]], "epsilon (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.epsilon", false]], "equal_weight() (in module bio.knn)": [[282, "Bio.kNN.equal_weight", false]], "error (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.error", false]], "error (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.error", false]], "error (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.error", false]], "error (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.error", false]], "error (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.error", false]], "error (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.error", false]], "error (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.error", false]], "error (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.error", false]], "error (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.error", false]], "error (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.error", false]], "error (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.error", false]], "error (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.error", false]], "error (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.error", false]], "error (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.error", false]], "error (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.error", false]], "error (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.error", false]], "error (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.error", false]], "error (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.error", false]], "error (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.error", false]], "error (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.error", false]], "error (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.error", false]], "error (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.error", false]], "error (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.error", false]], "error (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.error", false]], "error (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.error", false]], "errorelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.ErrorElement", false]], "errorfile (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.errorfile", false]], "esearch() (in module bio.entrez)": [[83, "Bio.Entrez.esearch", false]], "espell() (in module bio.entrez)": [[83, "Bio.Entrez.espell", false]], "est (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.est", false]], "est2genomecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline", false]], "estimate_nm() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.estimate_nm", false]], "estimate_nm() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.estimate_nm", false]], "estimate_params() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.estimate_params", false]], "esummary() (in module bio.entrez)": [[83, "Bio.Entrez.esummary", false]], "etandemcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.ETandemCommandline", false]], "evalue (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.evalue", false]], "evalue (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.evalue", false]], "evalue (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.evalue", false]], "evalue (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.evalue", false]], "evalue (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.evalue", false]], "evalue (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.evalue", false]], "evalue (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.evalue", false]], "evalue (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.evalue", false]], "evalue (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.evalue", false]], "events (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Events", false]], "events() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.events", false]], "events() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.events", false]], "exactposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.ExactPosition", false]], "exclude_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.exclude_filename", false]], "excludedregion (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.excludedregion", false]], "execute() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute", false]], "execute() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.execute", false]], "execute() (biosql.dbutils.sqlite_dbutils method)": [[304, "BioSQL.DBUtils.Sqlite_dbutils.execute", false]], "execute_and_fetch_col0() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0", false]], "execute_and_fetch_col0() (biosql.bioseqdatabase.mysqlconnectoradaptor method)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor.execute_and_fetch_col0", false]], "execute_and_fetchall() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall", false]], "execute_and_fetchall() (biosql.bioseqdatabase.mysqlconnectoradaptor method)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor.execute_and_fetchall", false]], "execute_one() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.execute_one", false]], "execute_one() (biosql.bioseqdatabase.mysqlconnectoradaptor method)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor.execute_one", false]], "executemany() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.executemany", false]], "executemany() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.executemany", false]], "executemany() (biosql.dbutils.sqlite_dbutils method)": [[304, "BioSQL.DBUtils.Sqlite_dbutils.executemany", false]], "exoneratecigarindexer (class in bio.searchio.exonerateio.exonerate_cigar)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer", false]], "exoneratecigarparser (class in bio.searchio.exonerateio.exonerate_cigar)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser", false]], "exoneratetextindexer (class in bio.searchio.exonerateio.exonerate_text)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer", false]], "exoneratetextparser (class in bio.searchio.exonerateio.exonerate_text)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser", false]], "exoneratevulgarindexer (class in bio.searchio.exonerateio.exonerate_vulgar)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer", false]], "exoneratevulgarparser (class in bio.searchio.exonerateio.exonerate_vulgar)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser", false]], "expert (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.expert", false]], "explainflag (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.explainflag", false]], "export_fasta() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.export_fasta", false]], "export_phylip() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.export_phylip", false]], "export_search_strategy (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.export_search_strategy", false]], "export_search_strategy (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.export_search_strategy", false]], "exposurecn (class in bio.pdb.hsexposure)": [[141, "Bio.PDB.HSExposure.ExposureCN", false]], "extend() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.extend", false]], "extend() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.extend", false]], "extend() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.extend", false]], "externalentityrefhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.externalEntityRefHandler", false]], "extract() (bio.seqfeature.compoundlocation method)": [[237, "Bio.SeqFeature.CompoundLocation.extract", false]], "extract() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.extract", false]], "extract() (bio.seqfeature.simplelocation method)": [[237, "Bio.SeqFeature.SimpleLocation.extract", false]], "extract() (in module bio.pdb.dice)": [[138, "Bio.PDB.Dice.extract", false]], "f (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.F", false], [32, "Bio.Align.Applications.PrankCommandline.f", false]], "f (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.f", false]], "f (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.f", false]], "f (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.F", false]], "f (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.f", false]], "f (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.F", false], [270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.f", false]], "fa (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fa", false]], "fast_bam (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.fast_bam", false]], "fast_bam (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.fast_bam", false]], "fasta (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.fasta", false]], "fastaiterator (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaIterator", false]], "fastam10indexer (class in bio.searchio.fastaio)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer", false]], "fastam10iterator() (in module bio.alignio.fastaio)": [[59, "Bio.AlignIO.FastaIO.FastaM10Iterator", false]], "fastam10parser (class in bio.searchio.fastaio)": [[226, "Bio.SearchIO.FastaIO.FastaM10Parser", false]], "fastaout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.fastaout", false]], "fastapair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fastapair", false]], "fastaparttree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fastaparttree", false]], "fastatwolineiterator (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator", false]], "fastatwolineparser() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineParser", false]], "fastatwolinewriter (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineWriter", false]], "fastawriter (class in bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.FastaWriter", false]], "fastest (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.fastest", false]], "fastmmcifparser (class in bio.pdb.mmcifparser)": [[143, "Bio.PDB.MMCIFParser.FastMMCIFParser", false]], "fastqgeneraliterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqGeneralIterator", false]], "fastqilluminaiterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqIlluminaIterator", false]], "fastqilluminawriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqIlluminaWriter", false]], "fastqphrediterator (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator", false]], "fastqphredwriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqPhredWriter", false]], "fastqsolexaiterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqSolexaIterator", false]], "fastqsolexawriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.FastqSolexaWriter", false]], "fasttreecommandline (class in bio.phylo.applications)": [[182, "Bio.Phylo.Applications.FastTreeCommandline", false]], "fconsensecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FConsenseCommandline", false]], "fdnadistcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FDNADistCommandline", false]], "fdnaparscommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline", false]], "feature (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Feature", false]], "feature (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.Feature", false]], "feature_end_markers (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_END_MARKERS", false]], "feature_end_markers (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_END_MARKERS", false]], "feature_end_markers (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_END_MARKERS", false]], "feature_header (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.FEATURE_HEADER", false]], "feature_header (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.FEATURE_HEADER", false]], "feature_qualifier_indent (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_QUALIFIER_INDENT", false]], "feature_qualifier_indent (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_QUALIFIER_INDENT", false]], "feature_qualifier_indent (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_QUALIFIER_INDENT", false]], "feature_qualifier_spacer (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_QUALIFIER_SPACER", false]], "feature_qualifier_spacer (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_QUALIFIER_SPACER", false]], "feature_qualifier_spacer (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_QUALIFIER_SPACER", false]], "feature_start_markers (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.FEATURE_START_MARKERS", false]], "feature_start_markers (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.FEATURE_START_MARKERS", false]], "feature_start_markers (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.FEATURE_START_MARKERS", false]], "featurelocation (in module bio.seqfeature)": [[237, "Bio.SeqFeature.FeatureLocation", false]], "featureparser (class in bio.genbank)": [[92, "Bio.GenBank.FeatureParser", false]], "features (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.features", false]], "featureset (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet", false]], "featuretable (class in bio.swissprot)": [[272, "Bio.SwissProt.FeatureTable", false]], "featurevaluecleaner (class in bio.genbank.utils)": [[95, "Bio.GenBank.utils.FeatureValueCleaner", false]], "feed() (bio.expasy.scanprosite.parser method)": [[89, "Bio.ExPASy.ScanProsite.Parser.feed", false]], "feed() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.feed", false]], "fetch_dbid_by_dbname() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_dbid_by_dbname", false]], "fetch_motif_by_id() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.fetch_motif_by_id", false]], "fetch_motifs() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.fetch_motifs", false]], "fetch_motifs_by_name() (bio.motifs.jaspar.db.jaspar5 method)": [[288, "Bio.motifs.jaspar.db.JASPAR5.fetch_motifs_by_name", false]], "fetch_seqid_by_accession() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_accession", false]], "fetch_seqid_by_display_id() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_display_id", false]], "fetch_seqid_by_identifier() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_identifier", false]], "fetch_seqid_by_version() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_version", false]], "fetch_seqids_by_accession() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.fetch_seqids_by_accession", false]], "ff (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ff", false]], "fft (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fft", false]], "fgcolor (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.fgcolor", false]], "field (class in bio.align.bigbed)": [[36, "Bio.Align.bigbed.Field", false]], "fieldnames (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.fieldNames", false]], "fields (bio.pdb.internal_coords.atomkey attribute)": [[169, "Bio.PDB.internal_coords.AtomKey.fields", false]], "fileno() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.fileno", false]], "fileno() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.fileno", false]], "filerecord (class in bio.popgen.genepop.fileparser)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord", false]], "fill_chromosome() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.fill_chromosome", false]], "filter (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.filter", false]], "filter (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.filter", false]], "filter (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.filter", false]], "filter (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.filter", false]], "filter (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.filter", false]], "filter (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.filter", false]], "filter (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.filter", false]], "filter (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.filter", false]], "filter (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.filter", false]], "filter (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.filter", false]], "filter (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.filter", false]], "filter (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.filter", false]], "filter (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.filter", false]], "filter (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.filter", false]], "filter (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.filter", false]], "filter (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.filter", false]], "filter (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.filter", false]], "filter (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.filter", false]], "filter (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.filter", false]], "filter (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.filter", false]], "filter (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.filter", false]], "filter (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.filter", false]], "filter (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.filter", false]], "filter (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.filter", false]], "filter (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.filter", false]], "filtering_db (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.filtering_db", false]], "finalize_structure() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.finalize_structure", false]], "find() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.find", false]], "find_any() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.find_any", false]], "find_clades() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.find_clades", false]], "find_elements() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.find_elements", false]], "find_start() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.find_start", false]], "find_states() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.find_states", false]], "fit() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.fit", false]], "fit() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.fit", false]], "fixedbranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.fixedbranches", false]], "flag_disorder() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.flag_disorder", false]], "flag_disordered() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.flag_disordered", false]], "flexibility() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.flexibility", false]], "float1_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.float1_color", false]], "flush() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.flush", false]], "fmodel (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.fmodel", false]], "fmt (bio.align.a2m.alignmentiterator attribute)": [[33, "Bio.Align.a2m.AlignmentIterator.fmt", false]], "fmt (bio.align.a2m.alignmentwriter attribute)": [[33, "Bio.Align.a2m.AlignmentWriter.fmt", false]], "fmt (bio.align.bed.alignmentiterator attribute)": [[35, "Bio.Align.bed.AlignmentIterator.fmt", false]], "fmt (bio.align.bigbed.alignmentiterator attribute)": [[36, "Bio.Align.bigbed.AlignmentIterator.fmt", false]], "fmt (bio.align.bigbed.alignmentwriter attribute)": [[36, "Bio.Align.bigbed.AlignmentWriter.fmt", false]], "fmt (bio.align.bigmaf.alignmentiterator attribute)": [[37, "Bio.Align.bigmaf.AlignmentIterator.fmt", false]], "fmt (bio.align.bigmaf.alignmentwriter attribute)": [[37, "Bio.Align.bigmaf.AlignmentWriter.fmt", false]], "fmt (bio.align.bigpsl.alignmentiterator attribute)": [[38, "Bio.Align.bigpsl.AlignmentIterator.fmt", false]], "fmt (bio.align.bigpsl.alignmentwriter attribute)": [[38, "Bio.Align.bigpsl.AlignmentWriter.fmt", false]], "fmt (bio.align.chain.alignmentiterator attribute)": [[39, "Bio.Align.chain.AlignmentIterator.fmt", false]], "fmt (bio.align.chain.alignmentwriter attribute)": [[39, "Bio.Align.chain.AlignmentWriter.fmt", false]], "fmt (bio.align.clustal.alignmentiterator attribute)": [[40, "Bio.Align.clustal.AlignmentIterator.fmt", false]], "fmt (bio.align.clustal.alignmentwriter attribute)": [[40, "Bio.Align.clustal.AlignmentWriter.fmt", false]], "fmt (bio.align.emboss.alignmentiterator attribute)": [[41, "Bio.Align.emboss.AlignmentIterator.fmt", false]], "fmt (bio.align.exonerate.alignmentiterator attribute)": [[42, "Bio.Align.exonerate.AlignmentIterator.fmt", false]], "fmt (bio.align.exonerate.alignmentwriter attribute)": [[42, "Bio.Align.exonerate.AlignmentWriter.fmt", false]], "fmt (bio.align.fasta.alignmentiterator attribute)": [[43, "Bio.Align.fasta.AlignmentIterator.fmt", false]], "fmt (bio.align.fasta.alignmentwriter attribute)": [[43, "Bio.Align.fasta.AlignmentWriter.fmt", false]], "fmt (bio.align.hhr.alignmentiterator attribute)": [[44, "Bio.Align.hhr.AlignmentIterator.fmt", false]], "fmt (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.fmt", false]], "fmt (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.fmt", false]], "fmt (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.fmt", false]], "fmt (bio.align.maf.alignmentwriter attribute)": [[46, "Bio.Align.maf.AlignmentWriter.fmt", false]], "fmt (bio.align.mauve.alignmentiterator attribute)": [[47, "Bio.Align.mauve.AlignmentIterator.fmt", false]], "fmt (bio.align.mauve.alignmentwriter attribute)": [[47, "Bio.Align.mauve.AlignmentWriter.fmt", false]], "fmt (bio.align.msf.alignmentiterator attribute)": [[48, "Bio.Align.msf.AlignmentIterator.fmt", false]], "fmt (bio.align.nexus.alignmentiterator attribute)": [[49, "Bio.Align.nexus.AlignmentIterator.fmt", false]], "fmt (bio.align.nexus.alignmentwriter attribute)": [[49, "Bio.Align.nexus.AlignmentWriter.fmt", false]], "fmt (bio.align.phylip.alignmentiterator attribute)": [[50, "Bio.Align.phylip.AlignmentIterator.fmt", false]], "fmt (bio.align.phylip.alignmentwriter attribute)": [[50, "Bio.Align.phylip.AlignmentWriter.fmt", false]], "fmt (bio.align.psl.alignmentiterator attribute)": [[51, "Bio.Align.psl.AlignmentIterator.fmt", false]], "fmt (bio.align.psl.alignmentwriter attribute)": [[51, "Bio.Align.psl.AlignmentWriter.fmt", false]], "fmt (bio.align.sam.alignmentiterator attribute)": [[52, "Bio.Align.sam.AlignmentIterator.fmt", false]], "fmt (bio.align.sam.alignmentwriter attribute)": [[52, "Bio.Align.sam.AlignmentWriter.fmt", false]], "fmt (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.fmt", false]], "fmt (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.fmt", false]], "fmt (bio.align.tabular.alignmentiterator attribute)": [[55, "Bio.Align.tabular.AlignmentIterator.fmt", false]], "fmt_() (in module bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.fmt_", false]], "fn (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fn", false]], "fneighborcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FNeighborCommandline", false]], "fop (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fop", false]], "force (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.force", false]], "format (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.format", false]], "format() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.format", false]], "format() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.format", false]], "format() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.format", false]], "format() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.format", false]], "format() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.format", false]], "format_alignment() (bio.align.a2m.alignmentwriter method)": [[33, "Bio.Align.a2m.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.bed.alignmentwriter method)": [[35, "Bio.Align.bed.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.chain.alignmentwriter method)": [[39, "Bio.Align.chain.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.clustal.alignmentwriter method)": [[40, "Bio.Align.clustal.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.fasta.alignmentwriter method)": [[43, "Bio.Align.fasta.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.maf.alignmentwriter method)": [[46, "Bio.Align.maf.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.phylip.alignmentwriter method)": [[50, "Bio.Align.phylip.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.psl.alignmentwriter method)": [[51, "Bio.Align.psl.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.sam.alignmentwriter method)": [[52, "Bio.Align.sam.AlignmentWriter.format_alignment", false]], "format_alignment() (bio.align.stockholm.alignmentwriter method)": [[53, "Bio.Align.stockholm.AlignmentWriter.format_alignment", false]], "format_alignment() (in module bio.pairwise2)": [[297, "Bio.pairwise2.format_alignment", false]], "format_label() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.format_label", false]], "format_output() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.format_output", false]], "format_phylip() (bio.phylo.treeconstruction.distancematrix method)": [[199, "Bio.Phylo.TreeConstruction.DistanceMatrix.format_phylip", false]], "forward_algorithm() (bio.hmm.dynamicprogramming.abstractdpalgorithms method)": [[107, "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.forward_algorithm", false]], "forward_table (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.forward_table", false]], "forwardinput (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.forwardinput", false]], "fprotdistcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FProtDistCommandline", false]], "fprotparscommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FProtParsCommandline", false]], "fracsample (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.fracsample", false]], "fragment (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.fragment", false]], "fragment (class in bio.pdb.fragmentmapper)": [[140, "Bio.PDB.FragmentMapper.Fragment", false]], "fragmentmapper (class in bio.pdb.fragmentmapper)": [[140, "Bio.PDB.FragmentMapper.FragmentMapper", false]], "frame_shift_penalty (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.frame_shift_penalty", false]], "frame_shift_penalty (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.frame_shift_penalty", false]], "freqsfrom (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.freqsfrom", false]], "frequencies (bio.align.alignment property)": [[30, "Bio.Align.Alignment.frequencies", false]], "frequencies (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.frequencies", false]], "frequencypositionmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.FrequencyPositionMatrix", false]], "from_bytes() (bio.align.bigbed.autosqltable class method)": [[36, "Bio.Align.bigbed.AutoSQLTable.from_bytes", false]], "from_clade() (bio.phylo.basetree.tree class method)": [[183, "Bio.Phylo.BaseTree.Tree.from_clade", false]], "from_clade() (bio.phylo.phyloxml.clade class method)": [[197, "Bio.Phylo.PhyloXML.Clade.from_clade", false]], "from_clade() (bio.phylo.phyloxml.phylogeny class method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.from_clade", false]], "from_hex() (bio.phylo.basetree.branchcolor class method)": [[183, "Bio.Phylo.BaseTree.BranchColor.from_hex", false]], "from_msa() (bio.codonalign.codonalignment.codonalignment class method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.from_msa", false]], "from_name() (bio.phylo.basetree.branchcolor class method)": [[183, "Bio.Phylo.BaseTree.BranchColor.from_name", false]], "from_seq() (bio.codonalign.codonseq.codonseq class method)": [[281, "Bio.codonalign.codonseq.CodonSeq.from_seq", false]], "from_seqfeature() (bio.phylo.phyloxml.proteindomain class method)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain.from_seqfeature", false]], "from_seqrecord() (bio.phylo.phyloxml.sequence class method)": [[197, "Bio.Phylo.PhyloXML.Sequence.from_seqrecord", false]], "from_string() (bio.align.bigbed.autosqltable class method)": [[36, "Bio.Align.bigbed.AutoSQLTable.from_string", false]], "from_string() (bio.phylo.cdaoio.parser class method)": [[185, "Bio.Phylo.CDAOIO.Parser.from_string", false]], "from_string() (bio.phylo.newickio.parser class method)": [[190, "Bio.Phylo.NewickIO.Parser.from_string", false]], "from_string() (bio.phylo.nexmlio.parser class method)": [[188, "Bio.Phylo.NeXMLIO.Parser.from_string", false]], "from_tree() (bio.phylo.phyloxml.phylogeny class method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.from_tree", false]], "fromstring() (bio.seqfeature.location method)": [[237, "Bio.SeqFeature.Location.fromstring", false]], "fromstring() (bio.seqfeature.position static method)": [[237, "Bio.SeqFeature.Position.fromstring", false]], "fromstring() (bio.seqfeature.simplelocation static method)": [[237, "Bio.SeqFeature.SimpleLocation.fromstring", false]], "fseqbootcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline", false]], "fsm (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.fsm", false]], "ftreedistcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline", false]], "full_translate() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.full_translate", false]], "fullhelp (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.fullhelp", false]], "fuzznuccommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FuzznucCommandline", false]], "fuzzprocommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.FuzzproCommandline", false]], "g (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.g", false]], "gafbyproteiniterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gafbyproteiniterator", false]], "gafiterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gafiterator", false]], "gamma (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.gamma", false]], "gamma (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.gamma", false]], "gamma (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gamma", false]], "gammacoefficient (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.gammacoefficient", false]], "gammacoefficient (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.gammacoefficient", false]], "gap (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.gap", false]], "gap_consensus() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.gap_consensus", false]], "gap_extend (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.gap_extend", false]], "gap_open (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.gap_open", false]], "gap_trigger (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gap_trigger", false]], "gap_trigger (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gap_trigger", false]], "gapdist (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.gapdist", false]], "gapext (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.gapext", false]], "gapext (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.gapext", false]], "gapext (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.gapext", false]], "gapextend (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.gapextend", false]], "gapextend (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.gapextend", false]], "gapextend (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.gapextend", false]], "gapextend (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.gapextend", false]], "gapextend (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.gapextend", false]], "gapextend (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.gapextend", false]], "gaplimit (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.gaplimit", false]], "gaponly() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.gaponly", false]], "gapopen (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.gapopen", false]], "gapopen (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.gapopen", false]], "gapopen (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.gapopen", false]], "gapopen (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.gapopen", false]], "gapopen (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.gapopen", false]], "gapopen (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.gapopen", false]], "gapopen (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.gapopen", false]], "gapopen (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.gapopen", false]], "gappenalty (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.gappenalty", false]], "gaprate (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.gaprate", false]], "gaps (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.gaps", false]], "gb_base_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_BASE_INDENT", false]], "gb_feature_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_FEATURE_INDENT", false]], "gb_feature_internal_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_FEATURE_INTERNAL_INDENT", false]], "gb_internal_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_INTERNAL_INDENT", false]], "gb_line_length (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_LINE_LENGTH", false]], "gb_other_internal_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_OTHER_INTERNAL_INDENT", false]], "gb_sequence_indent (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.GB_SEQUENCE_INDENT", false]], "gc123() (in module bio.sequtils)": [[261, "Bio.SeqUtils.GC123", false]], "gc_content (bio.motifs.matrix.genericpositionmatrix property)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.gc_content", false]], "gc_content (bio.motifs.matrix.positionspecificscoringmatrix property)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.gc_content", false]], "gc_fraction() (in module bio.sequtils)": [[261, "Bio.SeqUtils.gc_fraction", false]], "gc_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gc_mapping", false]], "gc_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gc_mapping", false]], "gc_skew() (in module bio.sequtils)": [[261, "Bio.SeqUtils.GC_skew", false]], "gcclamp (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.gcclamp", false]], "gcg() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.gcg", false]], "gckiterator (class in bio.seqio.gckio)": [[242, "Bio.SeqIO.GckIO.GckIterator", false]], "gen_key() (bio.pdb.internal_coords.edron static method)": [[169, "Bio.PDB.internal_coords.Edron.gen_key", false]], "gen_tuple() (bio.pdb.internal_coords.edron static method)": [[169, "Bio.PDB.internal_coords.Edron.gen_tuple", false]], "genafpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.genafpair", false]], "genbank_indent (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.GENBANK_INDENT", false]], "genbank_spacer (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.GENBANK_SPACER", false]], "genbankcdsfeatureiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator", false]], "genbankiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator", false]], "genbankscanner (class in bio.genbank.scanner)": [[94, "Bio.GenBank.Scanner.GenBankScanner", false]], "genbankwriter (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter", false]], "genepopcontroller (class in bio.popgen.genepop.controller)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController", false]], "generic_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Generic_dbutils", false]], "genericpositionmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.GenericPositionMatrix", false]], "genes (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.genes", false]], "genome (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.genome", false]], "get() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.get", false]], "get() (bio.data.codontable.ambiguousforwardtable method)": [[76, "Bio.Data.CodonTable.AmbiguousForwardTable.get", false]], "get_acgt() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.get_acgt", false]], "get_alignment_length() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.get_alignment_length", false]], "get_all_assemblies() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_all_assemblies", false]], "get_all_entries() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_all_entries", false]], "get_all_obsolete() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_all_obsolete", false]], "get_allele_frequency() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_allele_frequency", false]], "get_alleles() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_alleles", false]], "get_alleles_all_pops() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_alleles_all_pops", false]], "get_aln_length() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.get_aln_length", false]], "get_altloc() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_altloc", false]], "get_amino_acids_percent() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent", false]], "get_angle() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.get_angle", false]], "get_anisou() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_anisou", false]], "get_area() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.get_area", false]], "get_array() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.get_array", false]], "get_artemis_colorscheme() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.get_artemis_colorscheme", false]], "get_atoms() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.get_atoms", false]], "get_atoms() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.get_atoms", false]], "get_atoms() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_atoms", false]], "get_atoms() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_atoms", false]], "get_avg_fis() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_avg_fis", false]], "get_avg_fst_pair() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_avg_fst_pair", false]], "get_avg_fst_pair_locus() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_avg_fst_pair_locus", false]], "get_basic_info() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_basic_info", false]], "get_bfactor() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_bfactor", false]], "get_blank_emissions() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.get_blank_emissions", false]], "get_blank_transitions() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.get_blank_transitions", false]], "get_ca_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_ca_list", false]], "get_chains() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.get_chains", false]], "get_chains() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_chains", false]], "get_charge() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_charge", false]], "get_codon() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.get_codon", false]], "get_codon_num() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.get_codon_num", false]], "get_color_dict() (in module bio.graphics.colorspiral)": [[100, "Bio.Graphics.ColorSpiral.get_color_dict", false]], "get_colors() (bio.graphics.colorspiral.colorspiral method)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.get_colors", false]], "get_colors() (in module bio.graphics.colorspiral)": [[100, "Bio.Graphics.ColorSpiral.get_colors", false]], "get_colorscheme() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.get_colorscheme", false]], "get_column() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.get_column", false]], "get_column() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.get_column", false]], "get_coord() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_coord", false]], "get_coords() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.get_coords", false]], "get_data() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.get_data", false]], "get_data() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_data", false]], "get_dbutils() (in module biosql.dbutils)": [[304, "BioSQL.DBUtils.get_dbutils", false]], "get_distance() (bio.phylo.treeconstruction.distancecalculator method)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.get_distance", false]], "get_dn_ds_matrix() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.get_dn_ds_matrix", false]], "get_dn_ds_tree() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.get_dn_ds_tree", false]], "get_drawn_levels() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.get_drawn_levels", false]], "get_f_stats() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_f_stats", false]], "get_feature() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.get_feature", false]], "get_features() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.get_features", false]], "get_fis() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_fis", false]], "get_from_decoded() (in module bio.pdb.mmtf)": [[171, "Bio.PDB.mmtf.get_from_decoded", false]], "get_full_id() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_full_id", false]], "get_full_id() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_full_id", false]], "get_full_rf_table() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.get_full_rf_table", false]], "get_fullname() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_fullname", false]], "get_genotype_count() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_genotype_count", false]], "get_graphs() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.get_graphs", false]], "get_guide_coord_from_structure() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.get_guide_coord_from_structure", false]], "get_header() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.get_header", false]], "get_heterozygosity_info() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_heterozygosity_info", false]], "get_id() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_id", false]], "get_id() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_id", false]], "get_id() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.get_id", false]], "get_id() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_id", false]], "get_id() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.get_id", false]], "get_ids() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.get_ids", false]], "get_ids() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.get_ids", false]], "get_ids() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.get_ids", false]], "get_indiv() (in module bio.popgen.genepop)": [[201, "Bio.PopGen.GenePop.get_indiv", false]], "get_indiv() (in module bio.popgen.genepop.largefileparser)": [[205, "Bio.PopGen.GenePop.LargeFileParser.get_indiv", false]], "get_individual() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.get_individual", false]], "get_init_rms() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_init_rms", false]], "get_init_rms() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_init_rms", false]], "get_iterator() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_iterator", false]], "get_iterator() (bio.pdb.structurealignment.structurealignment method)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment.get_iterator", false]], "get_kgml() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.get_KGML", false]], "get_length() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.get_length", false]], "get_length() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.get_length", false]], "get_level() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_level", false]], "get_level() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_level", false]], "get_levels() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.get_levels", false]], "get_list() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_list", false]], "get_maps() (bio.pdb.structurealignment.structurealignment method)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment.get_maps", false]], "get_markov_model() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.get_markov_model", false]], "get_models() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_models", false]], "get_multilocus_f_stats() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.get_multilocus_f_stats", false]], "get_name() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_name", false]], "get_node_info() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.get_node_info", false]], "get_nonterminals() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.get_nonterminals", false]], "get_occupancy() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_occupancy", false]], "get_parent() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_parent", false]], "get_parent() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.get_parent", false]], "get_parent() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.get_parent", false]], "get_path() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.get_path", false]], "get_phi_psi_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_phi_psi_list", false]], "get_predictions() (in module bio.pdb.alphafold_db)": [[164, "Bio.PDB.alphafold_db.get_predictions", false]], "get_prev() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_prev", false]], "get_prodoc_entry() (in module bio.expasy)": [[85, "Bio.ExPASy.get_prodoc_entry", false]], "get_property_value() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.get_property_value", false]], "get_prosite_entry() (in module bio.expasy)": [[85, "Bio.ExPASy.get_prosite_entry", false]], "get_prosite_raw() (in module bio.expasy)": [[85, "Bio.ExPASy.get_prosite_raw", false]], "get_qresult_id() (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarindexer method)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer.get_qresult_id", false]], "get_qresult_id() (bio.searchio.exonerateio.exonerate_text.exoneratetextindexer method)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer.get_qresult_id", false]], "get_qresult_id() (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer method)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.get_qresult_id", false]], "get_radius() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_radius", false]], "get_raw() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.get_raw", false]], "get_raw() (bio.searchio.blastio.blast_tab.blasttabindexer method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.get_raw", false]], "get_raw() (bio.searchio.blastio.blast_xml.blastxmlindexer method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.get_raw", false]], "get_raw() (bio.searchio.blatio.blatpslindexer method)": [[221, "Bio.SearchIO.BlatIO.BlatPslIndexer.get_raw", false]], "get_raw() (bio.searchio.exonerateio.exonerate_text.exoneratetextindexer method)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer.get_raw", false]], "get_raw() (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarindexer method)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer.get_raw", false]], "get_raw() (bio.searchio.fastaio.fastam10indexer method)": [[226, "Bio.SearchIO.FastaIO.FastaM10Indexer.get_raw", false]], "get_raw() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabindexer method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer.get_raw", false]], "get_recent_changes() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_recent_changes", false]], "get_residue() (bio.align.aligninfo.pssm method)": [[31, "Bio.Align.AlignInfo.PSSM.get_residue", false]], "get_residues() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.get_residues", false]], "get_residues() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.get_residues", false]], "get_residues() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.get_residues", false]], "get_resname() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_resname", false]], "get_resname_list() (bio.pdb.fragmentmapper.fragment method)": [[140, "Bio.PDB.FragmentMapper.Fragment.get_resname_list", false]], "get_rms() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_rms", false]], "get_rms() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_rms", false]], "get_rotran() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_rotran", false]], "get_rotran() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_rotran", false]], "get_row() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.get_row", false]], "get_score() (bio.phylo.treeconstruction.parsimonyscorer method)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyScorer.get_score", false]], "get_score() (bio.phylo.treeconstruction.scorer method)": [[199, "Bio.Phylo.TreeConstruction.Scorer.get_score", false]], "get_segid() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_segid", false]], "get_segment_info() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.get_segment_info", false]], "get_seq() (bio.pdb.psea.psea method)": [[153, "Bio.PDB.PSEA.PSEA.get_seq", false]], "get_seq_by_acc() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_acc", false]], "get_seq_by_id() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_id", false]], "get_seq_by_ver() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_ver", false]], "get_seqres_file() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.get_seqres_file", false]], "get_seqs_by_acc() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seqs_by_acc", false]], "get_sequence() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_sequence", false]], "get_serial_number() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_serial_number", false]], "get_sets() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.get_sets", false]], "get_sigatm() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_sigatm", false]], "get_signals() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.get_signals", false]], "get_siguij() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_siguij", false]], "get_spherical_coordinates() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.get_spherical_coordinates", false]], "get_spliced() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.get_spliced", false]], "get_sprot_raw() (in module bio.expasy)": [[85, "Bio.ExPASy.get_sprot_raw", false]], "get_start_end() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.get_start_end", false]], "get_status_list() (bio.pdb.pdblist.pdblist static method)": [[149, "Bio.PDB.PDBList.PDBList.get_status_list", false]], "get_structural_models_for() (in module bio.pdb.alphafold_db)": [[164, "Bio.PDB.alphafold_db.get_structural_models_for", false]], "get_structure() (bio.pdb.binary_cif.binarycifparser method)": [[165, "Bio.PDB.binary_cif.BinaryCIFParser.get_structure", false]], "get_structure() (bio.pdb.mmcifparser.fastmmcifparser method)": [[143, "Bio.PDB.MMCIFParser.FastMMCIFParser.get_structure", false]], "get_structure() (bio.pdb.mmcifparser.mmcifparser method)": [[143, "Bio.PDB.MMCIFParser.MMCIFParser.get_structure", false]], "get_structure() (bio.pdb.mmtf.mmtfparser static method)": [[171, "Bio.PDB.mmtf.MMTFParser.get_structure", false]], "get_structure() (bio.pdb.pdbmlparser.pdbmlparser method)": [[150, "Bio.PDB.PDBMLParser.PDBMLParser.get_structure", false]], "get_structure() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.get_structure", false]], "get_structure() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.get_structure", false]], "get_structure_from_url() (bio.pdb.mmtf.mmtfparser static method)": [[171, "Bio.PDB.mmtf.MMTFParser.get_structure_from_url", false]], "get_subseq_as_string() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string", false]], "get_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.get_succ", false]], "get_support() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.get_support", false]], "get_surface() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.get_surface", false]], "get_tau_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_tau_list", false]], "get_taxa() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.get_taxa", false]], "get_temp_imagefilename() (in module bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.get_temp_imagefilename", false]], "get_terminals() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.get_terminals", false]], "get_terminals() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.get_terminals", false]], "get_text() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.get_text", false]], "get_theta_list() (bio.pdb.polypeptide.polypeptide method)": [[154, "Bio.PDB.Polypeptide.Polypeptide.get_theta_list", false]], "get_times() (bio.phenotype.phen_micro.wellrecord method)": [[299, "Bio.phenotype.phen_micro.WellRecord.get_times", false]], "get_tracks() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.get_tracks", false]], "get_trailer() (bio.pdb.pdbparser.pdbparser method)": [[151, "Bio.PDB.PDBParser.PDBParser.get_trailer", false]], "get_transformed() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.get_transformed", false]], "get_transformed() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.get_transformed", false]], "get_unique_parents() (in module bio.pdb.selection)": [[159, "Bio.PDB.Selection.get_unique_parents", false]], "get_unpacked_list() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.get_unpacked_list", false]], "get_unpacked_list() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.get_unpacked_list", false]], "get_vector() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.get_vector", false]], "getascendent() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getAscendent", false]], "getascendentfromsql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getAscendentFromSQL", false]], "getastraldomainsfromfile() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getAstralDomainsFromFile", false]], "getastraldomainsfromsql() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getAstralDomainsFromSQL", false]], "getatoms() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.getAtoms", false]], "getchildren() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getChildren", false]], "getdescendents() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getDescendents", false]], "getdescendentsfromsql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDescendentsFromSQL", false]], "getdomainbysid() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDomainBySid", false]], "getdomainfromsql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDomainFromSQL", false]], "getdomains() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getDomains", false]], "getnodebysunid() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getNodeBySunid", false]], "getparent() (bio.scop.node method)": [[209, "Bio.SCOP.Node.getParent", false]], "getroot() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.getRoot", false]], "getseq() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getSeq", false]], "getseqbysid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.getSeqBySid", false]], "getseqmap() (bio.scop.raf.seqmapindex method)": [[214, "Bio.SCOP.Raf.SeqMapIndex.getSeqMap", false]], "gf_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gf_mapping", false]], "gf_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gf_mapping", false]], "gfa1iterator() (in module bio.seqio.gfaio)": [[243, "Bio.SeqIO.GfaIO.Gfa1Iterator", false]], "gfa2iterator() (in module bio.seqio.gfaio)": [[243, "Bio.SeqIO.GfaIO.Gfa2Iterator", false]], "gi_mask (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.gi_mask", false]], "gi_mask_name (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.gi_mask_name", false]], "gilist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.gilist", false]], "gilist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.gilist", false]], "gilist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.gilist", false]], "gilist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.gilist", false]], "gilist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.gilist", false]], "gilist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.gilist", false]], "gilist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.gilist", false]], "gilist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.gilist", false]], "gilist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.gilist", false]], "global_dtd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.global_dtd_dir", false]], "global_xsd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.global_xsd_dir", false]], "globalpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.globalpair", false]], "gly_cbeta (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.gly_Cbeta", false]], "gompertz() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.gompertz", false]], "good_bases (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.good_bases", false]], "gpa_iterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gpa_iterator", false]], "gpi_iterator() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.gpi_iterator", false]], "gr_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gr_mapping", false]], "gr_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gr_mapping", false]], "graph (class in bio.pathway.rep.graph)": [[179, "Bio.Pathway.Rep.Graph.Graph", false]], "graphdata (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.GraphData", false]], "graphics (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics", false]], "graphset (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet", false]], "gravy() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.gravy", false]], "green() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.green", false]], "group (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.group", false]], "grouping_constraint (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.grouping_constraint", false]], "groupsize (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.groupsize", false]], "gs_mapping (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.gs_mapping", false]], "gs_mapping (bio.align.stockholm.alignmentwriter attribute)": [[53, "Bio.Align.stockholm.AlignmentWriter.gs_mapping", false]], "gtr (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gtr", false]], "gtrfreq (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gtrfreq", false]], "gtrrates (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.gtrrates", false]], "guess_lag() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.guess_lag", false]], "guess_plateau() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.guess_plateau", false]], "guidetree_in (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.guidetree_in", false]], "guidetree_out (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.guidetree_out", false]], "h (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.h", false]], "h (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.h", false]], "h (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.h", false]], "h (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.h", false]], "h (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.h", false]], "h (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.h", false]], "h (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.h", false]], "h (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.h", false]], "h (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.h", false]], "h (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.h", false]], "h (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.h", false]], "h (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.H", false]], "h (bio.sequencing.applications.samtoolscatcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.h", false]], "h (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.h", false]], "h (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.h", false]], "h (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.H", false], [270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.h", false]], "handle_motif() (bio.motifs.xms.xmsscanner method)": [[296, "Bio.motifs.xms.XMSScanner.handle_motif", false]], "handlemissingdocumentdefinition() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.handleMissingDocumentDefinition", false]], "has_id() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.has_id", false]], "has_id() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.has_id", false]], "has_support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.has_support", false]], "hash_index (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.hash_index", false]], "hasheddomainsbyev() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.hashedDomainsByEv", false]], "hasheddomainsbyid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.hashedDomainsById", false]], "header (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Header", false]], "header_width (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.HEADER_WIDTH", false]], "header_width (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.HEADER_WIDTH", false]], "header_width (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.HEADER_WIDTH", false]], "header_width (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.HEADER_WIDTH", false]], "header_width (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.HEADER_WIDTH", false]], "header_width (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.HEADER_WIDTH", false]], "hedron (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.Hedron", false]], "hedronmatcherror": [[169, "Bio.PDB.internal_coords.HedronMatchError", false]], "height (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.height", false]], "helixendin (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.helixendin", false]], "helixendout (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.helixendout", false]], "helixgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.helixgap", false]], "help (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.help", false]], "help (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.help", false]], "help (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.help", false]], "help (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.help", false]], "help (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.help", false]], "help (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.help", false]], "help (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.help", false]], "help (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.help", false]], "help (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.help", false]], "help (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.help", false]], "help (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.help", false]], "help (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.help", false]], "help (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.help", false]], "help (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.help", false]], "help (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.help", false]], "help (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.help", false]], "help (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.help", false]], "help (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.help", false]], "help (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.help", false]], "help (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.help", false]], "help (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.help", false]], "help (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.help", false]], "help (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.help", false]], "help (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.help", false]], "help (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.help", false]], "help (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.help", false]], "help (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.help", false]], "help (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.help", false]], "help (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.help", false]], "help (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.help", false]], "help (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.help", false]], "help (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.help", false]], "help (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.help", false]], "help (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.help", false]], "help (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.help", false]], "help (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.help", false]], "help (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.help", false]], "help (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.help", false]], "help (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.help", false]], "hgapresidues (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.hgapresidues", false]], "hhsuite2textparser (class in bio.searchio.hhsuiteio.hhsuite2_text)": [[228, "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser", false]], "hiddenmarkovmodel (class in bio.hmm.markovmodel)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel", false]], "hit (class in bio.blast)": [[68, "Bio.Blast.Hit", false]], "hit_coverage() (bio.compass.record method)": [[74, "Bio.Compass.Record.hit_coverage", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitparser attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser.hmm_as_hit", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitwriter attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter.hmm_as_hit", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmqueryparser attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser.hmm_as_hit", false]], "hmm_as_hit (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmquerywriter attribute)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter.hmm_as_hit", false]], "hmm_input (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.hmm_input", false]], "hmmer2textindexer (class in bio.searchio.hmmerio.hmmer2_text)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer", false]], "hmmer2textparser (class in bio.searchio.hmmerio.hmmer2_text)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser", false]], "hmmer3domtabhmmhitindexer (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer", false]], "hmmer3domtabhmmhitparser (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser", false]], "hmmer3domtabhmmhitwriter (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter", false]], "hmmer3domtabhmmqueryindexer (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer", false]], "hmmer3domtabhmmqueryparser (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser", false]], "hmmer3domtabhmmquerywriter (class in bio.searchio.hmmerio.hmmer3_domtab)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter", false]], "hmmer3tabindexer (class in bio.searchio.hmmerio.hmmer3_tab)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer", false]], "hmmer3tabparser (class in bio.searchio.hmmerio.hmmer3_tab)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser", false]], "hmmer3tabwriter (class in bio.searchio.hmmerio.hmmer3_tab)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter", false]], "hmmer3textindexer (class in bio.searchio.hmmerio.hmmer3_text)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer", false]], "hmmer3textparser (class in bio.searchio.hmmerio.hmmer3_text)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser", false]], "homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.homog_rot_mtx", false]], "homog_scale_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.homog_scale_mtx", false]], "homog_trans_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.homog_trans_mtx", false]], "homopolymer (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.homopolymer", false]], "hsexposureca (class in bio.pdb.hsexposure)": [[141, "Bio.PDB.HSExposure.HSExposureCA", false]], "hsexposurecb (class in bio.pdb.hsexposure)": [[141, "Bio.PDB.HSExposure.HSExposureCB", false]], "hsp (class in bio.blast)": [[68, "Bio.Blast.HSP", false]], "hsp (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.HSP", false]], "html (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.html", false]], "html (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.html", false]], "html (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.html", false]], "html (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.html", false]], "html (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.html", false]], "html (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.html", false]], "html (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.html", false]], "html (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.html", false]], "html (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.html", false]], "html (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.html", false]], "html (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.html", false]], "htmlout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.htmlout", false]], "hybridprobe (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.hybridprobe", false]], "hydro (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.hydro", false]], "hydrofactor (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.hydrofactor", false]], "i (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.I", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.i", false]], "i (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.I", false]], "i (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.i", false]], "i (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.I", false]], "ic_chain (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.IC_Chain", false]], "ic_duplicate() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.IC_duplicate", false]], "ic_residue (class in bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.IC_Residue", false]], "id (bio.kegg.kgml.kgml_pathway.component property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Component.id", false]], "id (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.id", false]], "id (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.id", false]], "id (bio.pdb.entity.entity property)": [[139, "Bio.PDB.Entity.Entity.id", false]], "id (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Id", false]], "id() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.id", false]], "id() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.id", false]], "id_width (bio.alignio.phylipio.phylipiterator attribute)": [[65, "Bio.AlignIO.PhylipIO.PhylipIterator.id_width", false]], "identities (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.identities", false]], "identity_match (class in bio.pairwise2)": [[297, "Bio.pairwise2.identity_match", false]], "iepcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.IepCommandline", false]], "igiterator (class in bio.seqio.igio)": [[244, "Bio.SeqIO.IgIO.IgIterator", false]], "ignore_msa_master (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.ignore_msa_master", false]], "illumina_13 (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.illumina_13", false]], "imgtiterator (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator", false]], "imgtwriter (class in bio.seqio.insdcio)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter", false]], "import_search_strategy (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.import_search_strategy", false]], "import_search_strategy (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.import_search_strategy", false]], "in1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.in1", false]], "in2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.in2", false]], "in_bam (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.in_bam", false]], "in_bam (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.in_bam", false]], "in_msa (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.in_msa", false]], "in_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.in_pssm", false]], "in_pssm (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.in_pssm", false]], "includedregion (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.includedregion", false]], "inclusion_ethresh (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.inclusion_ethresh", false]], "inclusion_ethresh (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.inclusion_ethresh", false]], "indent (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.Indent", false]], "index (class in bio.scop.cla)": [[210, "Bio.SCOP.Cla.Index", false]], "index() (bio.blast.record method)": [[68, "Bio.Blast.Record.index", false]], "index() (bio.scop.raf.seqmap method)": [[214, "Bio.SCOP.Raf.SeqMap.index", false]], "index() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.index", false]], "index() (in module bio.searchio)": [[217, "Bio.SearchIO.index", false]], "index() (in module bio.seqio)": [[238, "Bio.SeqIO.index", false]], "index_db() (in module bio.searchio)": [[217, "Bio.SearchIO.index_db", false]], "index_db() (in module bio.seqio)": [[238, "Bio.SeqIO.index_db", false]], "index_name (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.index_name", false]], "index_to_one() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.index_to_one", false]], "index_to_three() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.index_to_three", false]], "indices (bio.align.alignment property)": [[30, "Bio.Align.Alignment.indices", false]], "infer_coordinates() (bio.align.alignment class method)": [[30, "Bio.Align.Alignment.infer_coordinates", false]], "infile (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.infile", false]], "infile (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.infile", false]], "infile (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.infile", false]], "infile (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.infile", false]], "infile (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.infile", false]], "infile (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.infile", false]], "infmt (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.infmt", false]], "information_content() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.information_content", false]], "init_atom() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_atom", false]], "init_atom_coords() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.init_atom_coords", false]], "init_chain() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_chain", false]], "init_edra() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.init_edra", false]], "init_model() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_model", false]], "init_residue() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_residue", false]], "init_seg() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_seg", false]], "init_structure() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.init_structure", false]], "init_structure() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.init_structure", false]], "input (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.input", false]], "input (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.input", false]], "input (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.input", false]], "input (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.input", false]], "input (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.input", false]], "input (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.input", false]], "input (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.input", false]], "input (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.input", false]], "input1 (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.input1", false]], "input_bam (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.input_bam", false]], "input_bam (bio.sequencing.applications.samtoolsidxstatscommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline.input_bam", false]], "input_bam (bio.sequencing.applications.samtoolsindexcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsIndexCommandline.input_bam", false]], "input_file (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsfixmatecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsrmdupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.input_file", false]], "input_file (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.input_file", false]], "input_tree (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.input_tree", false]], "input_type (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.input_type", false]], "inputorder (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.inputorder", false]], "inputrecord (class in bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.InputRecord", false]], "insdcscanner (class in bio.genbank.scanner)": [[94, "Bio.GenBank.Scanner.InsdcScanner", false]], "insert() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.insert", false]], "insert() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.insert", false]], "insert_gap() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.insert_gap", false]], "instability_index() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.instability_index", false]], "instance (class in bio.motifs.meme)": [[291, "Bio.motifs.meme.Instance", false]], "instances (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.instances", false]], "instances (class in bio.motifs)": [[283, "Bio.motifs.Instances", false]], "int255_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.int255_color", false]], "integerelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.IntegerElement", false]], "integers (bio.expasy.scanprosite.contenthandler attribute)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.integers", false]], "interaction (class in bio.pathway)": [[177, "Bio.Pathway.Interaction", false]], "interactions() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.interactions", false]], "internal_feature_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.INTERNAL_FEATURE_FORMAT", false]], "internal_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.INTERNAL_FORMAT", false]], "internal_to_atom_coordinates() (bio.pdb.chain.chain method)": [[136, "Bio.PDB.Chain.Chain.internal_to_atom_coordinates", false]], "internal_to_atom_coordinates() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.internal_to_atom_coordinates", false]], "internal_to_atom_coordinates() (bio.pdb.model.model method)": [[144, "Bio.PDB.Model.Model.internal_to_atom_coordinates", false]], "internal_to_atom_coordinates() (bio.pdb.structure.structure method)": [[160, "Bio.PDB.Structure.Structure.internal_to_atom_coordinates", false]], "interproscanxmlparser (class in bio.searchio.interproscanio.interproscan_xml)": [[235, "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser", false]], "intree (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.intree", false]], "intree1 (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.intree1", false]], "intreefile (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.intreefile", false]], "intreefile (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.intreefile", false]], "intreefile (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.intreefile", false]], "intreefile (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.intreefile", false]], "intronpenalty (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.intronpenalty", false]], "invarcoefficient (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.invarcoefficient", false]], "invarfrac (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.invarfrac", false]], "inverse_indices (bio.align.alignment property)": [[30, "Bio.Align.Alignment.inverse_indices", false]], "invert() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.invert", false]], "ir (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.ir", false]], "is_aa() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.is_aa", false]], "is_backbone() (bio.pdb.internal_coords.atomkey method)": [[169, "Bio.PDB.internal_coords.AtomKey.is_backbone", false]], "is_backbone() (bio.pdb.internal_coords.edron method)": [[169, "Bio.PDB.internal_coords.Edron.is_backbone", false]], "is_bifurcating() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_bifurcating", false]], "is_bifurcating() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_bifurcating", false]], "is_compatible() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_compatible", false]], "is_disordered() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.is_disordered", false]], "is_disordered() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered", false]], "is_disordered() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.is_disordered", false]], "is_identical() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_identical", false]], "is_internal() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_internal", false]], "is_monophyletic() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_monophyletic", false]], "is_monophyletic() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_monophyletic", false]], "is_nucleic() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.is_nucleic", false]], "is_parent_of() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.is_parent_of", false]], "is_parent_of() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_parent_of", false]], "is_preterminal() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_preterminal", false]], "is_preterminal() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.is_preterminal", false]], "is_reactant (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.is_reactant", false]], "is_terminal() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.is_terminal", false]], "is_terminal() (bio.phylo.basetree.clade method)": [[183, "Bio.Phylo.BaseTree.Clade.is_terminal", false]], "is_terminal() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.is_terminal", false]], "isatty() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.isatty", false]], "isatty() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.isatty", false]], "isdomaininev() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.isDomainInEv", false]], "isdomaininid() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.isDomainInId", false]], "islower() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.islower", false]], "islower() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.islower", false]], "isoelectric_point() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.isoelectric_point", false]], "isoelectricpoint (class in bio.sequtils.isoelectricpoint)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint", false]], "isprofile (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.isprofile", false]], "isupper() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.isupper", false]], "isupper() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.isupper", false]], "itemindex() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.itemindex", false]], "items() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.items", false]], "items() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.items", false]], "items() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.items", false]], "items() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.items", false]], "iterate() (bio.seqio.fastaio.fastaiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.iterate", false]], "iterate() (bio.seqio.fastaio.fastatwolineiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.iterate", false]], "iterate() (bio.seqio.nibio.nibiterator method)": [[247, "Bio.SeqIO.NibIO.NibIterator.iterate", false]], "iterate() (bio.seqio.qualityio.fastqphrediterator method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.iterate", false]], "iterate() (bio.seqio.qualityio.qualphrediterator method)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.iterate", false]], "iterate() (bio.seqio.sffio.sffiterator method)": [[253, "Bio.SeqIO.SffIO.SffIterator.iterate", false]], "iterate() (bio.seqio.snapgeneio.snapgeneiterator method)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.iterate", false]], "iterate() (bio.seqio.tabio.tabiterator method)": [[256, "Bio.SeqIO.TabIO.TabIterator.iterate", false]], "iterate() (bio.seqio.xdnaio.xdnaiterator method)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.iterate", false]], "iteration (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.iteration", false]], "iterations (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.iterations", false]], "iterative_refinement (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.iterative_refinement", false]], "iterator (class in bio.genbank)": [[92, "Bio.GenBank.Iterator", false]], "iw (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.iw", false]], "jaspar5 (class in bio.motifs.jaspar.db)": [[288, "Bio.motifs.jaspar.db.JASPAR5", false]], "jitter (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.jitter", false]], "jsoniterator() (in module bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.JsonIterator", false]], "jsonwriter (class in bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.JsonWriter", false]], "jtt (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.jtt", false]], "jumble (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.jumble", false]], "jusweights (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.jusweights", false]], "k (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.k", false]], "k (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.k", false]], "k (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.k", false]], "kappa (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.kappa", false]], "kcluster() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.kcluster", false]], "kcluster() (in module bio.cluster)": [[73, "Bio.Cluster.kcluster", false]], "kegg_conv() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_conv", false]], "kegg_find() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_find", false]], "kegg_get() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_get", false]], "kegg_info() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_info", false]], "kegg_link() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_link", false]], "kegg_list() (in module bio.kegg.rest)": [[119, "Bio.KEGG.REST.kegg_list", false]], "key (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.key", false]], "keys() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.keys", false]], "keys() (bio.blast.record method)": [[68, "Bio.Blast.Record.keys", false]], "keys() (bio.pdb.abstractpropertymap.abstractpropertymap method)": [[134, "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys", false]], "keys() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.keys", false]], "keys() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.keys", false]], "keys() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.keys", false]], "keys() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.keys", false]], "keys_to_process (bio.genbank.utils.featurevaluecleaner attribute)": [[95, "Bio.GenBank.utils.FeatureValueCleaner.keys_to_process", false]], "keyword (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.keyword", false]], "kgmlcanvas (class in bio.graphics.kgml_vis)": [[105, "Bio.Graphics.KGML_vis.KGMLCanvas", false]], "kgmlparser (class in bio.kegg.kgml.kgml_parser)": [[116, "Bio.KEGG.KGML.KGML_parser.KGMLParser", false]], "kill() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.kill", false]], "kimura (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.kimura", false]], "kmedoids() (in module bio.cluster)": [[73, "Bio.Cluster.kmedoids", false]], "knn (class in bio.knn)": [[282, "Bio.kNN.kNN", false]], "knownstatetrainer (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.KnownStateTrainer", false]], "ktuple (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.ktuple", false]], "l (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.l", false]], "l (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.L", false]], "l (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.L", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.l", false]], "l (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.l", false]], "labels() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.labels", false]], "labels() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.labels", false]], "ladderize() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.ladderize", false]], "last_id() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.last_id", false]], "last_id() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.last_id", false]], "last_id() (biosql.dbutils.mysql_dbutils method)": [[304, "BioSQL.DBUtils.Mysql_dbutils.last_id", false]], "lat() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.lat", false]], "lcase_masking (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.lcase_masking", false]], "lcase_masking (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.lcase_masking", false]], "lcc_mult() (in module bio.sequtils.lcc)": [[267, "Bio.SeqUtils.lcc.lcc_mult", false]], "lcc_simp() (in module bio.sequtils.lcc)": [[267, "Bio.SeqUtils.lcc.lcc_simp", false]], "le (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.le", false]], "left_multiply() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.left_multiply", false]], "len12 (bio.pdb.internal_coords.hedron property)": [[169, "Bio.PDB.internal_coords.Hedron.len12", false]], "len23 (bio.pdb.internal_coords.hedron property)": [[169, "Bio.PDB.internal_coords.Hedron.len23", false]], "length (bio.align.alignment property)": [[30, "Bio.Align.Alignment.length", false]], "lep (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.lep", false]], "letter_annotations (bio.seqrecord.seqrecord property)": [[260, "Bio.SeqRecord.SeqRecord.letter_annotations", false]], "letters_per_block (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.LETTERS_PER_BLOCK", false]], "letters_per_line (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.LETTERS_PER_LINE", false]], "letters_per_line (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.LETTERS_PER_LINE", false]], "level (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.level", false]], "lexp (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.LEXP", false], [32, "Bio.Align.Applications.MafftCommandline.lexp", false]], "lgs (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lgs", false]], "lgs_t (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lgs_t", false]], "line_length (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.line_length", false]], "line_length (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.line_length", false]], "line_length (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.line_length", false]], "line_length (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.line_length", false]], "line_length (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.line_length", false]], "line_length (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.line_length", false]], "line_length (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.line_length", false]], "line_length (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.line_length", false]], "line_length (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.line_length", false]], "line_length (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.line_length", false]], "linedistribution (class in bio.graphics.distribution)": [[103, "Bio.Graphics.Distribution.LineDistribution", false]], "linesize (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.linesize", false]], "link() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.link", false]], "list_ambiguous_codons() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.list_ambiguous_codons", false]], "list_any_ids() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_any_ids", false]], "list_biodatabase_names() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_biodatabase_names", false]], "list_bioentry_display_ids() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_bioentry_display_ids", false]], "list_bioentry_ids() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.list_bioentry_ids", false]], "list_possible_proteins() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.list_possible_proteins", false]], "listelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.ListElement", false]], "lmax (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lmax", false]], "lo (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.lo", false]], "load() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.load", false]], "load() (in module bio.align.substitution_matrices)": [[54, "Bio.Align.substitution_matrices.load", false]], "load() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.load", false]], "load_database_sql() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.load_database_sql", false]], "load_seqrecord() (biosql.loader.databaseloader method)": [[305, "BioSQL.Loader.DatabaseLoader.load_seqrecord", false]], "local_dtd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.local_dtd_dir", false]], "local_xsd_dir (bio.entrez.parser.datahandler attribute)": [[84, "Bio.Entrez.Parser.DataHandler.local_xsd_dir", false]], "localpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.localpair", false]], "location (class in bio.seqfeature)": [[237, "Bio.SeqFeature.Location", false]], "location() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.location", false]], "locationparsererror": [[237, "Bio.SeqFeature.LocationParserError", false]], "log (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.log", false]], "log (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.log", false]], "log (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.log", false]], "log_likelihood() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.log_likelihood", false]], "log_odds() (bio.motifs.matrix.positionweightmatrix method)": [[290, "Bio.motifs.matrix.PositionWeightMatrix.log_odds", false]], "loga (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.loga", false]], "logdpalgorithms (class in bio.hmm.dynamicprogramming)": [[107, "Bio.HMM.DynamicProgramming.LogDPAlgorithms", false]], "logfile (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.logfile", false]], "logistic() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.logistic", false]], "logisticregression (class in bio.logisticregression)": [[120, "Bio.LogisticRegression.LogisticRegression", false]], "long() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.long", false]], "long_version (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.long_version", false]], "longseq (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.longseq", false]], "lookup() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.lookup", false]], "loopgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.loopgap", false]], "lop (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.LOP", false], [32, "Bio.Align.Applications.MafftCommandline.lop", false]], "losses() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.losses", false]], "lower (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.lower", false]], "lower() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.lower", false]], "lower() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.lower", false]], "lstrip() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.lstrip", false]], "lysinemodified (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.lysinemodified", false]], "m (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.m", false]], "m (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.M", false]], "m (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.M", false]], "m (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.M", false]], "m (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.m", false]], "m (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.m", false]], "m2rotaxis() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.m2rotaxis", false]], "ma (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ma", false]], "mafftcommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.MafftCommandline", false]], "mafindex (class in bio.alignio.mafio)": [[61, "Bio.AlignIO.MafIO.MafIndex", false]], "mafiterator() (in module bio.alignio.mafio)": [[61, "Bio.AlignIO.MafIO.MafIterator", false]], "mafwriter (class in bio.alignio.mafio)": [[61, "Bio.AlignIO.MafIO.MafWriter", false]], "majority_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.majority_consensus", false]], "make_back_table() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.make_back_table", false]], "make_dssp_dict() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.make_dssp_dict", false]], "make_extended() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.make_extended", false]], "make_format() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.make_format", false]], "make_table() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.make_table", false]], "make_virtual_offset() (in module bio.bgzf)": [[278, "Bio.bgzf.make_virtual_offset", false]], "makematrix (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.makematrix", false]], "map() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.map", false]], "mapall() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.mapall", false]], "maps (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.maps", false]], "markovmodel (class in bio.markovmodel)": [[121, "Bio.MarkovModel.MarkovModel", false]], "markovmodelbuilder (class in bio.hmm.markovmodel)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder", false]], "mask (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mask", false]], "mask (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.mask", false]], "mask_data (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.mask_data", false]], "mask_desc (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.mask_desc", false]], "mask_id (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.mask_id", false]], "mat (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mat", false]], "mat_thr (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mat_thr", false]], "match (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.MATCH", false]], "match (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.match", false]], "match (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.match", false]], "matches() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.matches", false]], "mate_file (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.mate_file", false]], "matinitsize (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.matinitsize", false]], "matresize (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.matresize", false]], "matrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.matrix", false]], "matrix (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.matrix", false]], "matrix (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.matrix", false]], "matrix (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.matrix", false]], "matrix (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.matrix", false]], "matrix (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.matrix", false]], "matrix (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.matrix", false]], "matrix (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.matrix", false]], "matrix (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.matrix", false]], "matrix (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.matrix", false]], "matrixtype (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.matrixtype", false]], "mauveiterator (class in bio.alignio.mauveio)": [[62, "Bio.AlignIO.MauveIO.MauveIterator", false]], "mauvewriter (class in bio.alignio.mauveio)": [[62, "Bio.AlignIO.MauveIO.MauveWriter", false]], "max (bio.motifs.matrix.positionspecificscoringmatrix property)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.max", false]], "max_file_sz (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.max_file_sz", false]], "max_guidetree_iterations (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.max_guidetree_iterations", false]], "max_hmm_iterations (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.max_hmm_iterations", false]], "max_hsps (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_hsps", false]], "max_hsps (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_hsps", false]], "max_hsps_per_subject (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_hsps_per_subject", false]], "max_hsps_per_subject (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_hsps_per_subject", false]], "max_intron_length (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_intron_length", false]], "max_intron_length (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_intron_length", false]], "max_intron_length (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_intron_length", false]], "max_link (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.max_link", false]], "max_target_seqs (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.max_target_seqs", false]], "max_target_seqs (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.max_target_seqs", false]], "maxbranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.maxbranches", false]], "maxdiagbreak (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxdiagbreak", false]], "maxdifftm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxdifftm", false]], "maxdiv (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.maxdiv", false]], "maxentropy (class in bio.maxentropy)": [[122, "Bio.MaxEntropy.MaxEntropy", false]], "maxgc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxgc", false]], "maxhours (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxhours", false]], "maximum() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.maximum", false]], "maxiterate (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.maxiterate", false]], "maxiters (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxiters", false]], "maxmispriming (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxmispriming", false]], "maxnumseq (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.maxnumseq", false]], "maxpallen (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.maxpallen", false]], "maxpeptidebond (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.MaxPeptideBond", false]], "maxpolyx (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxpolyx", false]], "maxrepeat (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.maxrepeat", false]], "maxrepeat (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.maxrepeat", false]], "maxseqlen (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.maxseqlen", false]], "maxseqlen (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.maxseqlen", false]], "maxsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxsize", false]], "maxsize (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.MaxSize", false]], "maxtm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.maxtm", false]], "maxtrees (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.maxtrees", false]], "maxtrees (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.maxtrees", false]], "mean() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.mean", false]], "mean() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.mean", false]], "memsave (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.memsave", false]], "merge_with_support() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.merge_with_support", false]], "method (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.method", false]], "method (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.method", false]], "method (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.method", false]], "methods (bio.phylo.treeconstruction.distancetreeconstructor attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.methods", false]], "min (bio.motifs.matrix.positionspecificscoringmatrix property)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.min", false]], "min_dist() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.min_dist", false]], "min_link (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.min_link", false]], "min_raw_gapped_score (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.min_raw_gapped_score", false]], "minbestcolscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.minbestcolscore", false]], "mingc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mingc", false]], "minimum() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.minimum", false]], "minpallen (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.minpallen", false]], "minrepeat (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.minrepeat", false]], "minscore (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.minscore", false]], "minscore (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.minscore", false]], "minsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.minsize", false]], "minsmoothscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.minsmoothscore", false]], "mintm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mintm", false]], "mirna (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.miRNA", false]], "mishyblibraryfile (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mishyblibraryfile", false]], "mismatch (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.mismatch", false]], "mismatch (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.mismatch", false]], "mismatch (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.mismatch", false]], "mismatches (bio.align.alignmentcounts attribute)": [[30, "Bio.Align.AlignmentCounts.mismatches", false]], "mismatchpercent (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.mismatchpercent", false]], "mispriminglibraryfile (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.mispriminglibraryfile", false]], "missingatomerror": [[169, "Bio.PDB.internal_coords.MissingAtomError", false]], "missingexternaldependencyerror": [[27, "Bio.MissingExternalDependencyError", false]], "missingpythondependencyerror": [[27, "Bio.MissingPythonDependencyError", false]], "mktest() (in module bio.align.analysis)": [[34, "Bio.Align.analysis.mktest", false]], "mktest() (in module bio.codonalign.codonalignment)": [[280, "Bio.codonalign.codonalignment.mktest", false]], "ml_estimator() (bio.hmm.trainer.abstracttrainer method)": [[109, "Bio.HMM.Trainer.AbstractTrainer.ml_estimator", false]], "mlacc (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.mlacc", false]], "mlfrac (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.mlfrac", false]], "mllen (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.mllen", false]], "mlnni (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.mlnni", false]], "mmcif2dict (class in bio.pdb.mmcif2dict)": [[142, "Bio.PDB.MMCIF2Dict.MMCIF2Dict", false]], "mmcifio (class in bio.pdb.mmcifio)": [[170, "Bio.PDB.mmcifio.MMCIFIO", false]], "mmcifparser (class in bio.pdb.mmcifparser)": [[143, "Bio.PDB.MMCIFParser.MMCIFParser", false]], "mmtfio (class in bio.pdb.mmtf.mmtfio)": [[173, "Bio.PDB.mmtf.mmtfio.MMTFIO", false]], "mmtfparser (class in bio.pdb.mmtf)": [[171, "Bio.PDB.mmtf.MMTFParser", false]], "mode (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.mode", false]], "mode (bio.align.bigbed.alignmentiterator attribute)": [[36, "Bio.Align.bigbed.AlignmentIterator.mode", false]], "mode (bio.align.bigbed.alignmentwriter attribute)": [[36, "Bio.Align.bigbed.AlignmentWriter.mode", false]], "mode (bio.align.bigmaf.alignmentiterator attribute)": [[37, "Bio.Align.bigmaf.AlignmentIterator.mode", false]], "mode (bio.align.interfaces.alignmentiterator attribute)": [[45, "Bio.Align.interfaces.AlignmentIterator.mode", false]], "mode (bio.align.interfaces.alignmentwriter attribute)": [[45, "Bio.Align.interfaces.AlignmentWriter.mode", false]], "mode (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.mode", false]], "model (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.model", false]], "model (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.model", false]], "model (class in bio.pdb.model)": [[144, "Bio.PDB.Model.Model", false]], "models (bio.phylo.treeconstruction.distancecalculator attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.models", false]], "modify() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.modify", false]], "module": [[27, "module-Bio", false], [28, "module-Bio.Affy", false], [29, "module-Bio.Affy.CelFile", false], [30, "module-Bio.Align", false], [31, "module-Bio.Align.AlignInfo", false], [32, "module-Bio.Align.Applications", false], [33, "module-Bio.Align.a2m", false], [34, "module-Bio.Align.analysis", false], [35, "module-Bio.Align.bed", false], [36, "module-Bio.Align.bigbed", false], [37, "module-Bio.Align.bigmaf", false], [38, "module-Bio.Align.bigpsl", false], [39, "module-Bio.Align.chain", false], [40, "module-Bio.Align.clustal", false], [41, "module-Bio.Align.emboss", false], [42, "module-Bio.Align.exonerate", false], [43, "module-Bio.Align.fasta", false], [44, "module-Bio.Align.hhr", false], [45, "module-Bio.Align.interfaces", false], [46, "module-Bio.Align.maf", false], [47, "module-Bio.Align.mauve", false], [48, "module-Bio.Align.msf", false], [49, "module-Bio.Align.nexus", false], [50, "module-Bio.Align.phylip", false], [51, "module-Bio.Align.psl", false], [52, "module-Bio.Align.sam", false], [53, "module-Bio.Align.stockholm", false], [54, "module-Bio.Align.substitution_matrices", false], [55, "module-Bio.Align.tabular", false], [56, "module-Bio.AlignIO", false], [57, "module-Bio.AlignIO.ClustalIO", false], [58, "module-Bio.AlignIO.EmbossIO", false], [59, "module-Bio.AlignIO.FastaIO", false], [60, "module-Bio.AlignIO.Interfaces", false], [61, "module-Bio.AlignIO.MafIO", false], [62, "module-Bio.AlignIO.MauveIO", false], [63, "module-Bio.AlignIO.MsfIO", false], [64, "module-Bio.AlignIO.NexusIO", false], [65, "module-Bio.AlignIO.PhylipIO", false], [66, "module-Bio.AlignIO.StockholmIO", false], [67, "module-Bio.Application", false], [68, "module-Bio.Blast", false], [69, "module-Bio.Blast.Applications", false], [70, "module-Bio.Blast.NCBIWWW", false], [71, "module-Bio.Blast.NCBIXML", false], [72, "module-Bio.CAPS", false], [73, "module-Bio.Cluster", false], [74, "module-Bio.Compass", false], [75, "module-Bio.Data", false], [76, "module-Bio.Data.CodonTable", false], [77, "module-Bio.Data.IUPACData", false], [78, "module-Bio.Data.PDBData", false], [79, "module-Bio.Emboss", false], [80, "module-Bio.Emboss.Applications", false], [81, "module-Bio.Emboss.Primer3", false], [82, "module-Bio.Emboss.PrimerSearch", false], [83, "module-Bio.Entrez", false], [84, "module-Bio.Entrez.Parser", false], [85, "module-Bio.ExPASy", false], [86, "module-Bio.ExPASy.Enzyme", false], [87, "module-Bio.ExPASy.Prodoc", false], [88, "module-Bio.ExPASy.Prosite", false], [89, "module-Bio.ExPASy.ScanProsite", false], [90, "module-Bio.ExPASy.cellosaurus", false], [91, "module-Bio.File", false], [92, "module-Bio.GenBank", false], [93, "module-Bio.GenBank.Record", false], [94, "module-Bio.GenBank.Scanner", false], [95, "module-Bio.GenBank.utils", false], [96, "module-Bio.Geo", false], [97, "module-Bio.Geo.Record", false], [98, "module-Bio.Graphics", false], [99, "module-Bio.Graphics.BasicChromosome", false], [100, "module-Bio.Graphics.ColorSpiral", false], [101, "module-Bio.Graphics.Comparative", false], [102, "module-Bio.Graphics.DisplayRepresentation", false], [103, "module-Bio.Graphics.Distribution", false], [104, "module-Bio.Graphics.GenomeDiagram", false], [105, "module-Bio.Graphics.KGML_vis", false], [106, "module-Bio.HMM", false], [107, "module-Bio.HMM.DynamicProgramming", false], [108, "module-Bio.HMM.MarkovModel", false], [109, "module-Bio.HMM.Trainer", false], [110, "module-Bio.HMM.Utilities", false], [111, "module-Bio.KEGG", false], [112, "module-Bio.KEGG.Compound", false], [113, "module-Bio.KEGG.Enzyme", false], [114, "module-Bio.KEGG.Gene", false], [115, "module-Bio.KEGG.KGML", false], [116, "module-Bio.KEGG.KGML.KGML_parser", false], [117, "module-Bio.KEGG.KGML.KGML_pathway", false], [118, "module-Bio.KEGG.Map", false], [119, "module-Bio.KEGG.REST", false], [120, "module-Bio.LogisticRegression", false], [121, "module-Bio.MarkovModel", false], [122, "module-Bio.MaxEntropy", false], [123, "module-Bio.Medline", false], [124, "module-Bio.NMR", false], [125, "module-Bio.NMR.NOEtools", false], [126, "module-Bio.NMR.xpktools", false], [127, "module-Bio.NaiveBayes", false], [128, "module-Bio.Nexus", false], [129, "module-Bio.Nexus.Nexus", false], [130, "module-Bio.Nexus.Nodes", false], [131, "module-Bio.Nexus.StandardData", false], [132, "module-Bio.Nexus.Trees", false], [133, "module-Bio.PDB", false], [134, "module-Bio.PDB.AbstractPropertyMap", false], [135, "module-Bio.PDB.Atom", false], [136, "module-Bio.PDB.Chain", false], [137, "module-Bio.PDB.DSSP", false], [138, "module-Bio.PDB.Dice", false], [139, "module-Bio.PDB.Entity", false], [140, "module-Bio.PDB.FragmentMapper", false], [141, "module-Bio.PDB.HSExposure", false], [142, "module-Bio.PDB.MMCIF2Dict", false], [143, "module-Bio.PDB.MMCIFParser", false], [144, "module-Bio.PDB.Model", false], [145, "module-Bio.PDB.NACCESS", false], [146, "module-Bio.PDB.NeighborSearch", false], [147, "module-Bio.PDB.PDBExceptions", false], [148, "module-Bio.PDB.PDBIO", false], [149, "module-Bio.PDB.PDBList", false], [150, "module-Bio.PDB.PDBMLParser", false], [151, "module-Bio.PDB.PDBParser", false], [152, "module-Bio.PDB.PICIO", false], [153, "module-Bio.PDB.PSEA", false], [154, "module-Bio.PDB.Polypeptide", false], [155, "module-Bio.PDB.Residue", false], [156, "module-Bio.PDB.ResidueDepth", false], [157, "module-Bio.PDB.SASA", false], [158, "module-Bio.PDB.SCADIO", false], [159, "module-Bio.PDB.Selection", false], [160, "module-Bio.PDB.Structure", false], [161, "module-Bio.PDB.StructureAlignment", false], [162, "module-Bio.PDB.StructureBuilder", false], [163, "module-Bio.PDB.Superimposer", false], [164, "module-Bio.PDB.alphafold_db", false], [165, "module-Bio.PDB.binary_cif", false], [166, "module-Bio.PDB.cealign", false], [167, "module-Bio.PDB.ic_data", false], [168, "module-Bio.PDB.ic_rebuild", false], [169, "module-Bio.PDB.internal_coords", false], [170, "module-Bio.PDB.mmcifio", false], [171, "module-Bio.PDB.mmtf", false], [172, "module-Bio.PDB.mmtf.DefaultParser", false], [173, "module-Bio.PDB.mmtf.mmtfio", false], [174, "module-Bio.PDB.parse_pdb_header", false], [175, "module-Bio.PDB.qcprot", false], [176, "module-Bio.PDB.vectors", false], [177, "module-Bio.Pathway", false], [178, "module-Bio.Pathway.Rep", false], [179, "module-Bio.Pathway.Rep.Graph", false], [180, "module-Bio.Pathway.Rep.MultiGraph", false], [181, "module-Bio.Phylo", false], [182, "module-Bio.Phylo.Applications", false], [183, "module-Bio.Phylo.BaseTree", false], [184, "module-Bio.Phylo.CDAO", false], [185, "module-Bio.Phylo.CDAOIO", false], [186, "module-Bio.Phylo.Consensus", false], [187, "module-Bio.Phylo.NeXML", false], [188, "module-Bio.Phylo.NeXMLIO", false], [189, "module-Bio.Phylo.Newick", false], [190, "module-Bio.Phylo.NewickIO", false], [191, "module-Bio.Phylo.NexusIO", false], [192, "module-Bio.Phylo.PAML", false], [193, "module-Bio.Phylo.PAML.baseml", false], [194, "module-Bio.Phylo.PAML.chi2", false], [195, "module-Bio.Phylo.PAML.codeml", false], [196, "module-Bio.Phylo.PAML.yn00", false], [197, "module-Bio.Phylo.PhyloXML", false], [198, "module-Bio.Phylo.PhyloXMLIO", false], [199, "module-Bio.Phylo.TreeConstruction", false], [200, "module-Bio.PopGen", false], [201, "module-Bio.PopGen.GenePop", false], [202, "module-Bio.PopGen.GenePop.Controller", false], [203, "module-Bio.PopGen.GenePop.EasyController", false], [204, "module-Bio.PopGen.GenePop.FileParser", false], [205, "module-Bio.PopGen.GenePop.LargeFileParser", false], [206, "module-Bio.Restriction", false], [207, "module-Bio.Restriction.PrintFormat", false], [208, "module-Bio.Restriction.Restriction_Dictionary", false], [209, "module-Bio.SCOP", false], [210, "module-Bio.SCOP.Cla", false], [211, "module-Bio.SCOP.Des", false], [212, "module-Bio.SCOP.Dom", false], [213, "module-Bio.SCOP.Hie", false], [214, "module-Bio.SCOP.Raf", false], [215, "module-Bio.SCOP.Residues", false], [216, "module-Bio.SVDSuperimposer", false], [217, "module-Bio.SearchIO", false], [218, "module-Bio.SearchIO.BlastIO", false], [219, "module-Bio.SearchIO.BlastIO.blast_tab", false], [220, "module-Bio.SearchIO.BlastIO.blast_xml", false], [221, "module-Bio.SearchIO.BlatIO", false], [222, "module-Bio.SearchIO.ExonerateIO", false], [223, "module-Bio.SearchIO.ExonerateIO.exonerate_cigar", false], [224, "module-Bio.SearchIO.ExonerateIO.exonerate_text", false], [225, "module-Bio.SearchIO.ExonerateIO.exonerate_vulgar", false], [226, "module-Bio.SearchIO.FastaIO", false], [227, "module-Bio.SearchIO.HHsuiteIO", false], [228, "module-Bio.SearchIO.HHsuiteIO.hhsuite2_text", false], [229, "module-Bio.SearchIO.HmmerIO", false], [230, "module-Bio.SearchIO.HmmerIO.hmmer2_text", false], [231, "module-Bio.SearchIO.HmmerIO.hmmer3_domtab", false], [232, "module-Bio.SearchIO.HmmerIO.hmmer3_tab", false], [233, "module-Bio.SearchIO.HmmerIO.hmmer3_text", false], [234, "module-Bio.SearchIO.InterproscanIO", false], [235, "module-Bio.SearchIO.InterproscanIO.interproscan_xml", false], [236, "module-Bio.Seq", false], [237, "module-Bio.SeqFeature", false], [238, "module-Bio.SeqIO", false], [239, "module-Bio.SeqIO.AbiIO", false], [240, "module-Bio.SeqIO.AceIO", false], [241, "module-Bio.SeqIO.FastaIO", false], [242, "module-Bio.SeqIO.GckIO", false], [243, "module-Bio.SeqIO.GfaIO", false], [244, "module-Bio.SeqIO.IgIO", false], [245, "module-Bio.SeqIO.InsdcIO", false], [246, "module-Bio.SeqIO.Interfaces", false], [247, "module-Bio.SeqIO.NibIO", false], [248, "module-Bio.SeqIO.PdbIO", false], [249, "module-Bio.SeqIO.PhdIO", false], [250, "module-Bio.SeqIO.PirIO", false], [251, "module-Bio.SeqIO.QualityIO", false], [252, "module-Bio.SeqIO.SeqXmlIO", false], [253, "module-Bio.SeqIO.SffIO", false], [254, "module-Bio.SeqIO.SnapGeneIO", false], [255, "module-Bio.SeqIO.SwissIO", false], [256, "module-Bio.SeqIO.TabIO", false], [257, "module-Bio.SeqIO.TwoBitIO", false], [258, "module-Bio.SeqIO.UniprotIO", false], [259, "module-Bio.SeqIO.XdnaIO", false], [260, "module-Bio.SeqRecord", false], [261, "module-Bio.SeqUtils", false], [262, "module-Bio.SeqUtils.CheckSum", false], [263, "module-Bio.SeqUtils.IsoelectricPoint", false], [264, "module-Bio.SeqUtils.MeltingTemp", false], [265, "module-Bio.SeqUtils.ProtParam", false], [266, "module-Bio.SeqUtils.ProtParamData", false], [267, "module-Bio.SeqUtils.lcc", false], [268, "module-Bio.Sequencing", false], [269, "module-Bio.Sequencing.Ace", false], [270, "module-Bio.Sequencing.Applications", false], [271, "module-Bio.Sequencing.Phd", false], [272, "module-Bio.SwissProt", false], [273, "module-Bio.SwissProt.KeyWList", false], [274, "module-Bio.TogoWS", false], [275, "module-Bio.UniGene", false], [276, "module-Bio.UniProt", false], [277, "module-Bio.UniProt.GOA", false], [278, "module-Bio.bgzf", false], [279, "module-Bio.codonalign", false], [280, "module-Bio.codonalign.codonalignment", false], [281, "module-Bio.codonalign.codonseq", false], [282, "module-Bio.kNN", false], [283, "module-Bio.motifs", false], [284, "module-Bio.motifs.alignace", false], [285, "module-Bio.motifs.applications", false], [286, "module-Bio.motifs.clusterbuster", false], [287, "module-Bio.motifs.jaspar", false], [288, "module-Bio.motifs.jaspar.db", false], [289, "module-Bio.motifs.mast", false], [290, "module-Bio.motifs.matrix", false], [291, "module-Bio.motifs.meme", false], [292, "module-Bio.motifs.minimal", false], [293, "module-Bio.motifs.pfm", false], [294, "module-Bio.motifs.thresholds", false], [295, "module-Bio.motifs.transfac", false], [296, "module-Bio.motifs.xms", false], [297, "module-Bio.pairwise2", false], [298, "module-Bio.phenotype", false], [299, "module-Bio.phenotype.phen_micro", false], [300, "module-Bio.phenotype.pm_fitting", false], [301, "module-BioSQL", false], [302, "module-BioSQL.BioSeq", false], [303, "module-BioSQL.BioSeqDatabase", false], [304, "module-BioSQL.DBUtils", false], [305, "module-BioSQL.Loader", false]], "mol_seq() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.mol_seq", false]], "mol_seq() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.mol_seq", false]], "molar_extinction_coefficient() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.molar_extinction_coefficient", false]], "molecular_weight() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.molecular_weight", false]], "molecular_weight() (in module bio.sequtils)": [[261, "Bio.SeqUtils.molecular_weight", false]], "molseq (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.MolSeq", false]], "mot (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.mot", false]], "motif (class in bio.motifs)": [[283, "Bio.motifs.Motif", false]], "motif (class in bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.Motif", false]], "motif (class in bio.motifs.meme)": [[291, "Bio.motifs.meme.Motif", false]], "motif (class in bio.motifs.transfac)": [[295, "Bio.motifs.transfac.Motif", false]], "move_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.move_track", false]], "msa_master_idx (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.msa_master_idx", false]], "msaprobscommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.MSAProbsCommandline", false]], "msf (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.msf", false]], "msf (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.msf", false]], "msfiterator (class in bio.alignio.msfio)": [[63, "Bio.AlignIO.MsfIO.MsfIterator", false]], "msfout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.msfout", false]], "mttranslate (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.mttranslate", false]], "multi_coord_space() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.multi_coord_space", false]], "multi_rot_y() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.multi_rot_Y", false]], "multi_rot_z() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.multi_rot_Z", false]], "multigraph (class in bio.pathway.rep.multigraph)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph", false]], "multiple (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.multiple", false]], "multiple_value_keys (bio.motifs.transfac.motif attribute)": [[295, "Bio.motifs.transfac.Motif.multiple_value_keys", false]], "multiplealignment (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.MultipleAlignment", false]], "multipleseqalignment (class in bio.align)": [[30, "Bio.Align.MultipleSeqAlignment", false]], "musclecommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.MuscleCommandline", false]], "mutableseq (class in bio.seq)": [[236, "Bio.Seq.MutableSeq", false]], "mysql_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Mysql_dbutils", false]], "mysqlconnectoradaptor (class in biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor", false]], "n (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.n", false]], "n (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.n", false]], "n (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.N", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.n", false]], "n (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.N", false]], "n (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.N", false], [270, "Bio.Sequencing.Applications.BwaSampeCommandline.n", false]], "n (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.n", false]], "n (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.n", false]], "n (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.n", false]], "n (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.n", false]], "n_rand_starts (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.n_rand_starts", false]], "naccess (class in bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.NACCESS", false]], "naccess_atomic (class in bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.NACCESS_atomic", false]], "naivebayes (class in bio.naivebayes)": [[127, "Bio.NaiveBayes.NaiveBayes", false]], "name (bio.align.bigbed.field attribute)": [[36, "Bio.Align.bigbed.Field.name", false]], "name (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.name", false]], "name (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.name", false]], "name (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.name", false]], "name (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.name", false]], "name() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.name", false]], "namelength (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.namelength", false]], "namewidth (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.NameWidth", false]], "ncategories (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.ncategories", false]], "ncategories (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.ncategories", false]], "ncbiblastformattercommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline", false]], "ncbiblastncommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline", false]], "ncbiblastpcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline", false]], "ncbiblastxcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline", false]], "ncbicodontable (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.NCBICodonTable", false]], "ncbicodontabledna (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.NCBICodonTableDNA", false]], "ncbicodontablerna (class in bio.data.codontable)": [[76, "Bio.Data.CodonTable.NCBICodonTableRNA", false]], "ncbideltablastcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline", false]], "ncbimakeblastdbcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline", false]], "ncbipsiblastcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline", false]], "ncbirpsblastcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline", false]], "ncbirpstblastncommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline", false]], "ncbitblastncommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline", false]], "ncbitblastxcommandline (class in bio.blast.applications)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline", false]], "nclasses (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.nclasses", false]], "needleallcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.NeedleallCommandline", false]], "needlecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.NeedleCommandline", false]], "negative (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.negative", false]], "negative_gilist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.negative_gilist", false]], "negative_gilist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.negative_gilist", false]], "negative_seqidlist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.negative_seqidlist", false]], "negative_seqidlist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.negative_seqidlist", false]], "neighborsearch (class in bio.pdb.neighborsearch)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch", false]], "network (class in bio.pathway)": [[177, "Bio.Pathway.Network", false]], "new_clade() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.new_clade", false]], "new_clade() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.new_clade", false]], "new_database() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.new_database", false]], "new_graph() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.new_graph", false]], "new_label() (bio.phylo.nexmlio.writer method)": [[188, "Bio.Phylo.NeXMLIO.Writer.new_label", false]], "new_set() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.new_set", false]], "new_track() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.new_track", false]], "newickerror": [[190, "Bio.Phylo.NewickIO.NewickError", false]], "newtree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.newtree", false]], "newtree1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.newtree1", false]], "newtree2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.newtree2", false]], "nexmlerror": [[188, "Bio.Phylo.NeXMLIO.NeXMLError", false]], "next_nonwhitespace() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.next_nonwhitespace", false]], "next_until() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.next_until", false]], "next_word() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.next_word", false]], "nexus (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.Nexus", false]], "nexuserror": [[129, "Bio.Nexus.Nexus.NexusError", false], [131, "Bio.Nexus.StandardData.NexusError", false]], "nexusiterator() (in module bio.alignio.nexusio)": [[64, "Bio.AlignIO.NexusIO.NexusIterator", false]], "nexuswriter (class in bio.alignio.nexusio)": [[64, "Bio.AlignIO.NexusIO.NexusWriter", false]], "nibiterator (class in bio.seqio.nibio)": [[247, "Bio.SeqIO.NibIO.NibIterator", false]], "nibwriter (class in bio.seqio.nibio)": [[247, "Bio.SeqIO.NibIO.NibWriter", false]], "nj (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nj", false]], "nj() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.nj", false]], "njumble (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.njumble", false]], "njumble (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.njumble", false]], "nni (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nni", false]], "nnitreesearcher (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.NNITreeSearcher", false]], "no2nd (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.no2nd", false]], "no_altloc (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.no_altloc", false]], "no_greedy (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.no_greedy", false]], "noanchors (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.noanchors", false]], "nobrief (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.nobrief", false]], "nobrief (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.nobrief", false]], "nobrief (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.nobrief", false]], "nocat (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nocat", false]], "nocore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.nocore", false]], "node (class in bio.cluster)": [[73, "Bio.Cluster.Node", false]], "node (class in bio.nexus.nodes)": [[130, "Bio.Nexus.Nodes.Node", false]], "node (class in bio.scop)": [[209, "Bio.SCOP.Node", false]], "node() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.node", false]], "node_id() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.node_id", false]], "nodedata (class in bio.nexus.trees)": [[132, "Bio.Nexus.Trees.NodeData", false]], "nodeexception": [[130, "Bio.Nexus.Nodes.NodeException", false]], "nodes() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.nodes", false]], "nodes() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes", false]], "nofft (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.nofft", false]], "nohgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nohgap", false]], "nomatrix (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nomatrix", false]], "nome (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nome", false]], "noml (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.noml", false]], "none (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.NONE", false]], "noneelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.NoneElement", false]], "nopgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nopgap", false]], "nopost (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.nopost", false]], "nopr (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nopr", false]], "norm() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.norm", false]], "normalize() (bio.motifs.matrix.frequencypositionmatrix method)": [[290, "Bio.motifs.matrix.FrequencyPositionMatrix.normalize", false]], "normalize() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.normalize", false]], "normalize_letters() (in module bio.scop.raf)": [[214, "Bio.SCOP.Raf.normalize_letters", false]], "normalized() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.normalized", false]], "normsq() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.normsq", false]], "noroot (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.noroot", false]], "noscore (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.noscore", false]], "nosecstr1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nosecstr1", false]], "nosecstr2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.nosecstr2", false]], "nosupport (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nosupport", false]], "notermini (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.notermini", false]], "notop (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.notop", false]], "notree (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.notree", false]], "notxmlerror": [[68, "Bio.Blast.NotXMLError", false], [84, "Bio.Entrez.Parser.NotXMLError", false]], "novoaligncommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline", false]], "noweights (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.noweights", false]], "noxml (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.noxml", false]], "nt (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.nt", false]], "nt (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.nt", false]], "nt_search() (in module bio.sequtils)": [[261, "Bio.SeqUtils.nt_search", false]], "nta (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.nta", false]], "nuc (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.nuc", false]], "nucleotide_alphabet (bio.data.codontable.ncbicodontable attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTable.nucleotide_alphabet", false]], "nucleotide_alphabet (bio.data.codontable.ncbicodontabledna attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTableDNA.nucleotide_alphabet", false]], "nucleotide_alphabet (bio.data.codontable.ncbicodontablerna attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTableRNA.nucleotide_alphabet", false]], "num_alignments (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.num_alignments", false]], "num_alignments (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.num_alignments", false]], "num_bootstrap_searches (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.num_bootstrap_searches", false]], "num_categories (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.num_categories", false]], "num_descriptions (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.num_descriptions", false]], "num_descriptions (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.num_descriptions", false]], "num_iterations (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_iterations", false]], "num_iterations (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_iterations", false]], "num_replicates (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.num_replicates", false]], "num_threads (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.num_threads", false]], "num_threads (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.num_threads", false]], "number (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.number", false]], "numiter (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.numiter", false]], "nummismatches (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.nummismatches", false]], "numreturn (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.numreturn", false]], "numthreads (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.numthreads", false]], "o (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.o", false]], "o (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.o", false]], "o (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.O", false], [270, "Bio.Sequencing.Applications.BwaAlignCommandline.o", false]], "o (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.O", false]], "o (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.o", false]], "o (bio.sequencing.applications.samtoolscatcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline.o", false]], "o (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.o", false]], "o (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.o", false]], "o (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.O", false], [270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.o", false]], "o (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.o", false]], "oanyself (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oanyself", false]], "objscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.objscore", false]], "odnaconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.odnaconc", false]], "oendself (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oendself", false]], "oexcludedregion (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oexcludedregion", false]], "off_diagonal_range (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.off_diagonal_range", false]], "ogcmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcmax", false]], "ogcmin (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcmin", false]], "ogcopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcopt", false]], "ogcpercent (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ogcpercent", false]], "ok_applies_to (bio.phylo.phyloxml.property attribute)": [[197, "Bio.Phylo.PhyloXML.Property.ok_applies_to", false]], "ok_datatype (bio.phylo.phyloxml.property attribute)": [[197, "Bio.Phylo.PhyloXML.Property.ok_datatype", false]], "ok_rank (bio.phylo.phyloxml.taxonomy attribute)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.ok_rank", false]], "ok_type (bio.phylo.phyloxml.events attribute)": [[197, "Bio.Phylo.PhyloXML.Events.ok_type", false]], "ok_type (bio.phylo.phyloxml.sequencerelation attribute)": [[197, "Bio.Phylo.PhyloXML.SequenceRelation.ok_type", false]], "oligoinput (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.oligoinput", false]], "omaxsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.omaxsize", false]], "ominsize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ominsize", false]], "omishybmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.omishybmax", false]], "once (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.once", false]], "one_to_index() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.one_to_index", false]], "oneofposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.OneOfPosition", false]], "op (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.op", false]], "open() (in module bio.bgzf)": [[278, "Bio.bgzf.open", false]], "open_database() (in module biosql.bioseqdatabase)": [[303, "BioSQL.BioSeqDatabase.open_database", false]], "open_dtd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.open_dtd_file", false]], "open_xsd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.open_xsd_file", false]], "opolyxmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.opolyxmax", false]], "optimize (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.optimize", false]], "optimize() (bio.sequtils.codonadaptationindex method)": [[261, "Bio.SeqUtils.CodonAdaptationIndex.optimize", false]], "options (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.options", false]], "options (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.options", false]], "options (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.options", false]], "options (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.options", false]], "options (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.options", false]], "options (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.options", false]], "options (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.options", false]], "options (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.options", false]], "options (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.options", false]], "options (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.options", false]], "options (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.options", false]], "options (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.options", false]], "options (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.options", false]], "options (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.options", false]], "options (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.options", false]], "options (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.options", false]], "options (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.options", false]], "options (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.options", false]], "options (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.options", false]], "options (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.options", false]], "options (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.options", false]], "options (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.options", false]], "options (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.options", false]], "options (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.options", false]], "options (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.options", false]], "options (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.options", false]], "opttm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.opttm", false]], "orderedlistelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.OrderedListElement", false]], "organism (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.Organism", false]], "orthologs (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.orthologs", false]], "osaltconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.osaltconc", false]], "osformat (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.osformat", false]], "osize (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.osize", false]], "osizeopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.osizeopt", false]], "other (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Other", false]], "other() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.other", false]], "other() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.other", false]], "other_internal_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.OTHER_INTERNAL_FORMAT", false]], "otm (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otm", false]], "otmmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otmmax", false]], "otmmin (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otmmin", false]], "otmopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.otmopt", false]], "out (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.out", false]], "out (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.out", false]], "out (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.out", false]], "out (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.out", false]], "out (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.out", false]], "out (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.out", false]], "out (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.out", false]], "out (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.out", false]], "out (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.out", false]], "out (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.out", false]], "out (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.out", false]], "out (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.out", false]], "out (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.out", false]], "out_ascii_pssm (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.out_ascii_pssm", false]], "out_ascii_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.out_ascii_pssm", false]], "out_block() (in module bio.geo.record)": [[97, "Bio.Geo.Record.out_block", false]], "out_prefix (bio.sequencing.applications.samtoolsversion0xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline.out_prefix", false]], "out_pssm (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.out_pssm", false]], "out_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.out_pssm", false]], "outfile (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.outfile", false]], "outfile (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.outfile", false]], "outfile (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.outfile", false]], "outfile (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.outfile", false]], "outfile (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.outfile", false]], "outfile (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.outfile", false]], "outfile (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.outfile", false]], "outfile (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.outfile", false]], "outfile (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.outfile", false]], "outfile (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.outfile", false]], "outfile (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.outfile", false]], "outfile (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.outfile", false]], "outfile (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.outfile", false]], "outfile (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.outfile", false]], "outfile (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.outfile", false]], "outfile (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.outfile", false]], "outfile (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.outfile", false]], "outfile (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.outfile", false]], "outfile (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.outfile", false]], "outfile (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.outfile", false]], "outfile (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.outfile", false]], "outfile (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.outfile", false]], "outfile (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.outfile", false]], "outfile (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.outfile", false]], "outfile (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.outfile", false]], "outfile (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.outfile", false]], "outfile (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.outfile", false]], "outfile (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.outfile", false]], "outfmt (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.outfmt", false]], "outfmt (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.outfmt", false]], "outgrno (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.outgrno", false]], "outgrno (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.outgrno", false]], "outgrno (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.outgrno", false]], "outgrno (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.outgrno", false]], "outgrno (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.outgrno", false]], "outgroup (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.outgroup", false]], "outorder (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.outorder", false]], "outorder (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.outorder", false]], "output (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.output", false]], "output (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.output", false]], "output (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.output", false]], "output_file (bio.sequencing.applications.samtoolsfixmatecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline.output_file", false]], "output_file (bio.sequencing.applications.samtoolsrmdupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.output_file", false]], "outputorder (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.outputorder", false]], "outputrecord (class in bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.OutputRecord", false]], "outputtree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.outputtree", false]], "outseq (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.outseq", false]], "outseq (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.outseq", false]], "outtreefile (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.outtreefile", false]], "outtreefile (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.outtreefile", false]], "outtreefile (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.outtreefile", false]], "outtreefile (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.outtreefile", false]], "overlap (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.overlap", false]], "ow (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ow", false]], "p (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.P", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.p", false]], "p (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.p", false]], "pairedfastaqualiterator() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.PairedFastaQualIterator", false]], "pairgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pairgap", false]], "pairing (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.pairing", false]], "pairs (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.pairs", false]], "pairwisealigner (class in bio.align)": [[30, "Bio.Align.PairwiseAligner", false]], "pairwisealignments (class in bio.align)": [[30, "Bio.Align.PairwiseAlignments", false]], "palindromecommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.PalindromeCommandline", false]], "parallelassembleresidues (bio.pdb.internal_coords.ic_chain attribute)": [[169, "Bio.PDB.internal_coords.IC_Chain.ParallelAssembleResidues", false]], "parameters (bio.application.abstractcommandline attribute)": [[67, "Bio.Application.AbstractCommandline.parameters", false]], "parameters (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Parameters", false]], "paramfile (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.paramfile", false]], "parent (bio.pdb.entity.entity attribute)": [[139, "Bio.PDB.Entity.Entity.parent", false]], "parent_edges() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.parent_edges", false]], "parent_edges() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.parent_edges", false]], "parents() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.parents", false]], "parents() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.parents", false]], "pars (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.pars", false]], "parse() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.parse", false]], "parse() (bio.genbank.featureparser method)": [[92, "Bio.GenBank.FeatureParser.parse", false]], "parse() (bio.genbank.recordparser method)": [[92, "Bio.GenBank.RecordParser.parse", false]], "parse() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse", false]], "parse() (bio.kegg.kgml.kgml_parser.kgmlparser method)": [[116, "Bio.KEGG.KGML.KGML_parser.KGMLParser.parse", false]], "parse() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse", false]], "parse() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.parse", false]], "parse() (bio.phylo.nexmlio.parser method)": [[188, "Bio.Phylo.NeXMLIO.Parser.parse", false]], "parse() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.parse", false]], "parse() (bio.seqio.abiio.abiiterator method)": [[239, "Bio.SeqIO.AbiIO.AbiIterator.parse", false]], "parse() (bio.seqio.fastaio.fastaiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaIterator.parse", false]], "parse() (bio.seqio.fastaio.fastatwolineiterator method)": [[241, "Bio.SeqIO.FastaIO.FastaTwoLineIterator.parse", false]], "parse() (bio.seqio.gckio.gckiterator method)": [[242, "Bio.SeqIO.GckIO.GckIterator.parse", false]], "parse() (bio.seqio.igio.igiterator method)": [[244, "Bio.SeqIO.IgIO.IgIterator.parse", false]], "parse() (bio.seqio.insdcio.emblcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator.parse", false]], "parse() (bio.seqio.insdcio.embliterator method)": [[245, "Bio.SeqIO.InsdcIO.EmblIterator.parse", false]], "parse() (bio.seqio.insdcio.genbankcdsfeatureiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator.parse", false]], "parse() (bio.seqio.insdcio.genbankiterator method)": [[245, "Bio.SeqIO.InsdcIO.GenBankIterator.parse", false]], "parse() (bio.seqio.insdcio.imgtiterator method)": [[245, "Bio.SeqIO.InsdcIO.ImgtIterator.parse", false]], "parse() (bio.seqio.interfaces.sequenceiterator method)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator.parse", false]], "parse() (bio.seqio.nibio.nibiterator method)": [[247, "Bio.SeqIO.NibIO.NibIterator.parse", false]], "parse() (bio.seqio.pdbio.pdbseqresiterator method)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator.parse", false]], "parse() (bio.seqio.pirio.piriterator method)": [[250, "Bio.SeqIO.PirIO.PirIterator.parse", false]], "parse() (bio.seqio.qualityio.fastqphrediterator method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredIterator.parse", false]], "parse() (bio.seqio.qualityio.qualphrediterator method)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator.parse", false]], "parse() (bio.seqio.seqxmlio.seqxmliterator method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator.parse", false]], "parse() (bio.seqio.sffio.sffiterator method)": [[253, "Bio.SeqIO.SffIO.SffIterator.parse", false]], "parse() (bio.seqio.snapgeneio.snapgeneiterator method)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator.parse", false]], "parse() (bio.seqio.tabio.tabiterator method)": [[256, "Bio.SeqIO.TabIO.TabIterator.parse", false]], "parse() (bio.seqio.twobitio.twobititerator method)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator.parse", false]], "parse() (bio.seqio.uniprotio.parser method)": [[258, "Bio.SeqIO.UniprotIO.Parser.parse", false]], "parse() (bio.seqio.xdnaio.xdnaiterator method)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator.parse", false]], "parse() (in module bio.align)": [[30, "Bio.Align.parse", false]], "parse() (in module bio.alignio)": [[56, "Bio.AlignIO.parse", false]], "parse() (in module bio.blast)": [[68, "Bio.Blast.parse", false]], "parse() (in module bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.parse", false]], "parse() (in module bio.compass)": [[74, "Bio.Compass.parse", false]], "parse() (in module bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.parse", false]], "parse() (in module bio.entrez)": [[83, "Bio.Entrez.parse", false]], "parse() (in module bio.expasy.cellosaurus)": [[90, "Bio.ExPASy.cellosaurus.parse", false]], "parse() (in module bio.expasy.enzyme)": [[86, "Bio.ExPASy.Enzyme.parse", false]], "parse() (in module bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.parse", false]], "parse() (in module bio.expasy.prosite)": [[88, "Bio.ExPASy.Prosite.parse", false]], "parse() (in module bio.genbank)": [[92, "Bio.GenBank.parse", false]], "parse() (in module bio.geo)": [[96, "Bio.Geo.parse", false]], "parse() (in module bio.kegg.compound)": [[112, "Bio.KEGG.Compound.parse", false]], "parse() (in module bio.kegg.enzyme)": [[113, "Bio.KEGG.Enzyme.parse", false]], "parse() (in module bio.kegg.gene)": [[114, "Bio.KEGG.Gene.parse", false]], "parse() (in module bio.kegg.kgml.kgml_parser)": [[116, "Bio.KEGG.KGML.KGML_parser.parse", false]], "parse() (in module bio.kegg.map)": [[118, "Bio.KEGG.Map.parse", false]], "parse() (in module bio.medline)": [[123, "Bio.Medline.parse", false]], "parse() (in module bio.motifs)": [[283, "Bio.motifs.parse", false]], "parse() (in module bio.phenotype)": [[298, "Bio.phenotype.parse", false]], "parse() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.parse", false]], "parse() (in module bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.parse", false]], "parse() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.parse", false]], "parse() (in module bio.phylo.nexusio)": [[191, "Bio.Phylo.NexusIO.parse", false]], "parse() (in module bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.parse", false]], "parse() (in module bio.scop.cla)": [[210, "Bio.SCOP.Cla.parse", false]], "parse() (in module bio.scop.des)": [[211, "Bio.SCOP.Des.parse", false]], "parse() (in module bio.scop.dom)": [[212, "Bio.SCOP.Dom.parse", false]], "parse() (in module bio.scop.hie)": [[213, "Bio.SCOP.Hie.parse", false]], "parse() (in module bio.scop.raf)": [[214, "Bio.SCOP.Raf.parse", false]], "parse() (in module bio.searchio)": [[217, "Bio.SearchIO.parse", false]], "parse() (in module bio.seqio)": [[238, "Bio.SeqIO.parse", false]], "parse() (in module bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.parse", false]], "parse() (in module bio.sequencing.phd)": [[271, "Bio.Sequencing.Phd.parse", false]], "parse() (in module bio.swissprot)": [[272, "Bio.SwissProt.parse", false]], "parse() (in module bio.swissprot.keywlist)": [[273, "Bio.SwissProt.KeyWList.parse", false]], "parse() (in module bio.unigene)": [[275, "Bio.UniGene.parse", false]], "parse_alignment_block() (bio.searchio.exonerateio.exonerate_cigar.exoneratecigarparser method)": [[223, "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser.parse_alignment_block", false]], "parse_alignment_block() (bio.searchio.exonerateio.exonerate_text.exoneratetextparser method)": [[224, "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser.parse_alignment_block", false]], "parse_alignment_block() (bio.searchio.exonerateio.exonerate_vulgar.exoneratevulgarparser method)": [[225, "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser.parse_alignment_block", false]], "parse_btop() (bio.align.tabular.alignmentiterator method)": [[55, "Bio.Align.tabular.AlignmentIterator.parse_btop", false]], "parse_cds_features() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_cds_features", false]], "parse_children() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse_children", false]], "parse_cigar() (bio.align.tabular.alignmentiterator method)": [[55, "Bio.Align.tabular.AlignmentIterator.parse_cigar", false]], "parse_deflines (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.parse_deflines", false]], "parse_deflines (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.parse_deflines", false]], "parse_domain() (in module bio.scop)": [[209, "Bio.SCOP.parse_domain", false]], "parse_feature() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_feature", false]], "parse_features() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_features", false]], "parse_footer() (bio.genbank.scanner.emblscanner method)": [[94, "Bio.GenBank.Scanner.EmblScanner.parse_footer", false]], "parse_footer() (bio.genbank.scanner.genbankscanner method)": [[94, "Bio.GenBank.Scanner.GenBankScanner.parse_footer", false]], "parse_footer() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_footer", false]], "parse_graph() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse_graph", false]], "parse_handle_to_graph() (bio.phylo.cdaoio.parser method)": [[185, "Bio.Phylo.CDAOIO.Parser.parse_handle_to_graph", false]], "parse_header() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_header", false]], "parse_hits() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_hits", false]], "parse_hsp_alignments() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_hsp_alignments", false]], "parse_hsps() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_hsps", false]], "parse_key_value() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_key_value", false]], "parse_pdb_header() (in module bio.pdb.parse_pdb_header)": [[174, "Bio.PDB.parse_pdb_header.parse_pdb_header", false]], "parse_preamble() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_preamble", false]], "parse_printed_alignment() (bio.align.alignment class method)": [[30, "Bio.Align.Alignment.parse_printed_alignment", false]], "parse_qresult() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.parse_qresult", false]], "parse_records() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.parse_records", false]], "parse_seqids (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.parse_seqids", false]], "parse_xsd() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.parse_xsd", false]], "parser (class in bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.Parser", false]], "parser (class in bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.Parser", false]], "parser (class in bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.Parser", false]], "parser (class in bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.Parser", false]], "parser (class in bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.Parser", false]], "parser (class in bio.seqio.uniprotio)": [[258, "Bio.SeqIO.UniprotIO.Parser", false]], "parsererror": [[29, "Bio.Affy.CelFile.ParserError", false]], "parserfailureerror": [[92, "Bio.GenBank.ParserFailureError", false]], "parsimony (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.parsimony", false]], "parsimony_seed (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.parsimony_seed", false]], "parsimonyscorer (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyScorer", false]], "parsimonytreeconstructor (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor", false]], "partition_branch_lengths (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.partition_branch_lengths", false]], "partition_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.partition_filename", false]], "parts (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.parts", false]], "partsize (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.partsize", false]], "parttree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.parttree", false]], "pathway (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway", false]], "pattern (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.pattern", false]], "pattern (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.pattern", false]], "pca() (in module bio.cluster)": [[73, "Bio.Cluster.pca", false]], "pcb_vectors_pymol() (bio.pdb.hsexposure.hsexposureca method)": [[141, "Bio.PDB.HSExposure.HSExposureCA.pcb_vectors_pymol", false]], "pdb_date() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.pdb_date", false]], "pdb_ref (bio.pdb.pdblist.pdblist attribute)": [[149, "Bio.PDB.PDBList.PDBList.PDB_REF", false]], "pdb_residue_string() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pdb_residue_string", false]], "pdbatomiterator() (in module bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.PdbAtomIterator", false]], "pdbconstructionexception": [[147, "Bio.PDB.PDBExceptions.PDBConstructionException", false]], "pdbconstructionwarning": [[147, "Bio.PDB.PDBExceptions.PDBConstructionWarning", false]], "pdbexception": [[147, "Bio.PDB.PDBExceptions.PDBException", false]], "pdbio (class in bio.pdb.pdbio)": [[148, "Bio.PDB.PDBIO.PDBIO", false]], "pdbioexception": [[147, "Bio.PDB.PDBExceptions.PDBIOException", false]], "pdblist (class in bio.pdb.pdblist)": [[149, "Bio.PDB.PDBList.PDBList", false]], "pdbmlparser (class in bio.pdb.pdbmlparser)": [[150, "Bio.PDB.PDBMLParser.PDBMLParser", false]], "pdbparser (class in bio.pdb.pdbparser)": [[151, "Bio.PDB.PDBParser.PDBParser", false]], "pdbseqresiterator (class in bio.seqio.pdbio)": [[248, "Bio.SeqIO.PdbIO.PdbSeqresIterator", false]], "peaklist (class in bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.Peaklist", false]], "peek() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.peek", false]], "peek_nonwhitespace() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.peek_nonwhitespace", false]], "peek_word() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.peek_word", false]], "penalty (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.penalty", false]], "perc_identity (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.perc_identity", false]], "percentid (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.percentid", false]], "pfam_gc_mapping (bio.alignio.stockholmio.stockholmiterator attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gc_mapping", false]], "pfam_gc_mapping (bio.alignio.stockholmio.stockholmwriter attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gc_mapping", false]], "pfam_gr_mapping (bio.alignio.stockholmio.stockholmiterator attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping", false]], "pfam_gr_mapping (bio.alignio.stockholmio.stockholmwriter attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping", false]], "pfam_gs_mapping (bio.alignio.stockholmio.stockholmiterator attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping", false]], "pfam_gs_mapping (bio.alignio.stockholmio.stockholmwriter attribute)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping", false]], "pgdb_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Pgdb_dbutils", false]], "phditerator() (in module bio.seqio.phdio)": [[249, "Bio.SeqIO.PhdIO.PhdIterator", false]], "phdwriter (class in bio.seqio.phdio)": [[249, "Bio.SeqIO.PhdIO.PhdWriter", false]], "phi_pattern (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.phi_pattern", false]], "phred_quality_from_solexa() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.phred_quality_from_solexa", false]], "phyi (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.phyi", false]], "phyiout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.phyiout", false]], "phylipiterator (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.PhylipIterator", false]], "phylipout (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.phylipout", false]], "phylipwriter (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.PhylipWriter", false]], "phyloelement (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.PhyloElement", false]], "phylogeny (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Phylogeny", false]], "phylogeny() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.phylogeny", false]], "phyloxml (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Phyloxml", false]], "phyloxml() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.phyloxml", false]], "phyloxmlerror": [[198, "Bio.Phylo.PhyloXMLIO.PhyloXMLError", false]], "phyloxmlwarning": [[197, "Bio.Phylo.PhyloXML.PhyloXMLWarning", false]], "phymlcommandline (class in bio.phylo.applications)": [[182, "Bio.Phylo.Applications.PhymlCommandline", false]], "phys (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.phys", false]], "physout (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.physout", false]], "pi() (bio.sequtils.isoelectricpoint.isoelectricpoint method)": [[263, "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi", false]], "pic_accuracy (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.pic_accuracy", false]], "pic_flags (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.pic_flags", false]], "picflagsdefault (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.picFlagsDefault", false]], "picflagsdict (bio.pdb.internal_coords.ic_residue attribute)": [[169, "Bio.PDB.internal_coords.IC_Residue.picFlagsDict", false]], "pick_angle() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pick_angle", false]], "pick_length() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pick_length", false]], "pim (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pim", false]], "piriterator (class in bio.seqio.pirio)": [[250, "Bio.SeqIO.PirIO.PirIterator", false]], "pirwriter (class in bio.seqio.pirio)": [[250, "Bio.SeqIO.PirIO.PirWriter", false]], "platerecord (class in bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.PlateRecord", false]], "pmismatch (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.pmismatch", false]], "pmismatch (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.pmismatch", false]], "point (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Point", false]], "point() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.point", false]], "point() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.point", false]], "polygon (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Polygon", false]], "polygon() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.polygon", false]], "polygon() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.polygon", false]], "polypeptide (class in bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.Polypeptide", false]], "pop() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.pop", false]], "pos_specific_score_matrix() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.pos_specific_score_matrix", false]], "position (class in bio.seqfeature)": [[237, "Bio.SeqFeature.Position", false]], "position_padding (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.POSITION_PADDING", false]], "positionspecificscoringmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix", false]], "positionweightmatrix (class in bio.motifs.matrix)": [[290, "Bio.motifs.matrix.PositionWeightMatrix", false]], "ppbuilder (class in bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.PPBuilder", false]], "prange (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.prange", false]], "prankcommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.PrankCommandline", false]], "pre (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.pre", false]], "predictnoe() (in module bio.nmr.noetools)": [[125, "Bio.NMR.NOEtools.predictNOE", false]], "prefix (bio.sequencing.applications.bwaindexcommandline property)": [[270, "Bio.Sequencing.Applications.BwaIndexCommandline.prefix", false]], "prefixes (bio.phylo.cdaoio.writer attribute)": [[185, "Bio.Phylo.CDAOIO.Writer.prefixes", false]], "prefwidth (bio.restriction.printformat.printformat attribute)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.PrefWidth", false]], "pretty_print_prediction() (in module bio.hmm.utilities)": [[110, "Bio.HMM.Utilities.pretty_print_prediction", false]], "pretty_str() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.pretty_str", false]], "primer3commandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.Primer3Commandline", false]], "primers (class in bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.Primers", false]], "primersearchcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline", false]], "print_as() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.print_as", false]], "print_info_content() (in module bio.align.aligninfo)": [[31, "Bio.Align.AlignInfo.print_info_content", false]], "print_matrix() (in module bio.pairwise2)": [[297, "Bio.pairwise2.print_matrix", false]], "print_options() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.print_options", false]], "print_site_lnl (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.print_site_lnl", false]], "print_that() (bio.restriction.printformat.printformat method)": [[207, "Bio.Restriction.PrintFormat.PrintFormat.print_that", false]], "print_trace (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.print_trace", false]], "printformat (class in bio.restriction.printformat)": [[207, "Bio.Restriction.PrintFormat.PrintFormat", false]], "printnodes (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.printnodes", false]], "probconscommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.ProbconsCommandline", false]], "process_asa_data() (in module bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.process_asa_data", false]], "process_clade() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.process_clade", false]], "process_clade() (bio.phylo.newickio.parser method)": [[190, "Bio.Phylo.NewickIO.Parser.process_clade", false]], "process_rsa_data() (in module bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.process_rsa_data", false]], "products (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.products", false]], "profile (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.profile", false]], "profile (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.profile", false]], "profile1 (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.profile1", false]], "profile1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.profile1", false]], "profile2 (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.profile2", false]], "profile2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.profile2", false]], "progress (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.progress", false]], "prop_invar (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.prop_invar", false]], "propagate_changes() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.propagate_changes", false]], "property (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Property", false]], "property() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.property", false]], "property() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.property", false]], "protein_alphabet (bio.data.codontable.ncbicodontable attribute)": [[76, "Bio.Data.CodonTable.NCBICodonTable.protein_alphabet", false]], "protein_model (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.protein_model", false]], "protein_models (bio.phylo.treeconstruction.distancecalculator attribute)": [[199, "Bio.Phylo.TreeConstruction.DistanceCalculator.protein_models", false]], "protein_scale() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.protein_scale", false]], "proteinanalysis (class in bio.sequtils.protparam)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis", false]], "proteindomain (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain", false]], "protsimline (class in bio.unigene)": [[275, "Bio.UniGene.ProtsimLine", false]], "prune() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.prune", false]], "prune() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.prune", false]], "psea (class in bio.pdb.psea)": [[153, "Bio.PDB.PSEA.PSEA", false]], "psea() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.psea", false]], "psea2hec() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.psea2HEC", false]], "pseudo (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.pseudo", false]], "pseudocount (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.pseudocount", false]], "pseudocount (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.pseudocount", false]], "pseudocounts (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.pseudocounts", false]], "psiblast (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.PSIBlast", false]], "psizeopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.psizeopt", false]], "pssm (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.pssm", false]], "pssm (class in bio.align.aligninfo)": [[31, "Bio.Align.AlignInfo.PSSM", false]], "pst (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.pst", false]], "psycopg2_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Psycopg2_dbutils", false]], "ptmmax (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ptmmax", false]], "ptmmin (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ptmmin", false]], "ptmopt (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.ptmopt", false]], "push_back() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.push_back", false]], "pwdist (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.pwdist", false]], "pwdnamatrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwdnamatrix", false]], "pwgapext (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwgapext", false]], "pwgapopen (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwgapopen", false]], "pwgenomic (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.pwgenomic", false]], "pwgenomicdist (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.pwgenomicdist", false]], "pwm (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.pwm", false]], "pwmatrix (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.pwmatrix", false]], "q (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.q", false]], "q (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.q", false]], "q (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.Q", false], [270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.q", false]], "q (bio.sequencing.applications.samtoolsphasecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.Q", false], [270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline.q", false]], "q (bio.sequencing.applications.samtoolstargetcutcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline.Q", false]], "q (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.q", false]], "qa (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.qa", false]], "qblast() (in module bio.blast)": [[68, "Bio.Blast.qblast", false]], "qblast() (in module bio.blast.ncbiwww)": [[70, "Bio.Blast.NCBIWWW.qblast", false]], "qcov_hsp_perc (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.qcov_hsp_perc", false]], "qcov_hsp_perc (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.qcov_hsp_perc", false]], "qcp() (in module bio.pdb.qcprot)": [[175, "Bio.PDB.qcprot.qcp", false]], "qcpsuperimposer (class in bio.pdb.qcprot)": [[175, "Bio.PDB.qcprot.QCPSuperimposer", false]], "qend_mark (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.qend_mark", false]], "qresult_end (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer attribute)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.qresult_end", false]], "qresult_end (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer attribute)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.qresult_end", false]], "qresult_start (bio.searchio.hmmerio.hmmer2_text.hmmer2textindexer attribute)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer.qresult_start", false]], "qresult_start (bio.searchio.hmmerio.hmmer3_text.hmmer3textindexer attribute)": [[233, "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer.qresult_start", false]], "qstart_mark (bio.searchio.blastio.blast_xml.blastxmlindexer attribute)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer.qstart_mark", false]], "qual_digits (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.qual_digits", false]], "qualifier (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Qualifier", false]], "qualifier_indent (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.QUALIFIER_INDENT", false]], "qualifier_indent (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.QUALIFIER_INDENT", false]], "qualifier_indent (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.QUALIFIER_INDENT", false]], "qualifier_indent_str (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.QUALIFIER_INDENT_STR", false]], "qualifier_indent_str (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.QUALIFIER_INDENT_STR", false]], "qualifier_indent_tmp (bio.seqio.insdcio.emblwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.QUALIFIER_INDENT_TMP", false]], "qualifier_indent_tmp (bio.seqio.insdcio.imgtwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.ImgtWriter.QUALIFIER_INDENT_TMP", false]], "quality (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.quality", false]], "qualphrediterator (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.QualPhredIterator", false]], "qualphredwriter (class in bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.QualPhredWriter", false]], "quartiles() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.quartiles", false]], "query (bio.align.alignment property)": [[30, "Bio.Align.Alignment.query", false]], "query (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.query", false]], "query (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.query", false]], "query (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.query", false]], "query (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.query", false]], "query (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.query", false]], "query (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.query", false]], "query (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.query", false]], "query (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.query", false]], "query (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.query", false]], "query_coverage() (bio.compass.record method)": [[74, "Bio.Compass.Record.query_coverage", false]], "query_gap (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.QUERY_GAP", false]], "query_gencode (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.query_gencode", false]], "query_gencode (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.query_gencode", false]], "query_gencode (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.query_gencode", false]], "query_loc (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.query_loc", false]], "query_loc (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.query_loc", false]], "quicktree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.quicktree", false]], "quiet (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.quiet", false]], "quiet (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.quiet", false]], "quiet (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.quiet", false]], "quiet (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.quiet", false]], "quiet (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.quiet", false]], "quiet (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.quiet", false]], "quiet (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.quiet", false]], "quote (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.quote", false]], "quotestrip() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.quotestrip", false]], "quri() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.qUri", false]], "quri() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.qUri", false]], "r (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.R", false]], "r (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.r", false]], "r (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.R", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.r", false]], "r (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.r", false]], "r (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.r", false]], "r (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.r", false]], "r (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.R", false], [270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.r", false]], "r (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.r", false]], "r (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.R", false], [270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.r", false]], "r_method (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.r_method", false]], "r_seed (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.r_seed", false]], "rak() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.rak", false]], "rand_start (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.rand_start", false]], "random_starting_tree (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.random_starting_tree", false]], "randomize() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.randomize", false]], "randomized() (bio.phylo.basetree.tree class method)": [[183, "Bio.Phylo.BaseTree.Tree.randomized", false]], "range (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.range", false]], "range() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.range", false]], "range() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.range", false]], "range() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.range", false]], "range() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.range", false]], "range() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.range", false]], "rank() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.rank", false]], "rapid_bootstrap_seed (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.rapid_bootstrap_seed", false]], "rate (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.rate", false]], "rate (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.rate", false]], "raw() (bio.nexus.standarddata.standarddata method)": [[131, "Bio.Nexus.StandardData.StandardData.raw", false]], "rawdist (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.rawdist", false]], "raxmlcommandline (class in bio.phylo.applications)": [[182, "Bio.Phylo.Applications.RaxmlCommandline", false]], "rd (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.rd", false]], "re_code (bio.phylo.phyloxml.taxonomy attribute)": [[197, "Bio.Phylo.PhyloXML.Taxonomy.re_code", false]], "re_doi (bio.phylo.phyloxml.reference attribute)": [[197, "Bio.Phylo.PhyloXML.Reference.re_doi", false]], "re_ref (bio.phylo.phyloxml.annotation attribute)": [[197, "Bio.Phylo.PhyloXML.Annotation.re_ref", false]], "re_ref (bio.phylo.phyloxml.property attribute)": [[197, "Bio.Phylo.PhyloXML.Property.re_ref", false]], "re_symbol (bio.phylo.phyloxml.sequence attribute)": [[197, "Bio.Phylo.PhyloXML.Sequence.re_symbol", false]], "re_value (bio.phylo.phyloxml.molseq attribute)": [[197, "Bio.Phylo.PhyloXML.MolSeq.re_value", false]], "reactant_ids (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.reactant_ids", false]], "reaction (bio.kegg.kgml.kgml_pathway.entry property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.reaction", false]], "reaction (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction", false]], "reaction (class in bio.pathway)": [[177, "Bio.Pathway.Reaction", false]], "reaction_entries (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.reaction_entries", false]], "reactions (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.reactions", false]], "reactions() (bio.pathway.system method)": [[177, "Bio.Pathway.System.reactions", false]], "read() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.read", false]], "read() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.read", false]], "read() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.read", false]], "read() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.read", false]], "read() (in module bio.affy.celfile)": [[29, "Bio.Affy.CelFile.read", false]], "read() (in module bio.align)": [[30, "Bio.Align.read", false]], "read() (in module bio.align.substitution_matrices)": [[54, "Bio.Align.substitution_matrices.read", false]], "read() (in module bio.alignio)": [[56, "Bio.AlignIO.read", false]], "read() (in module bio.blast)": [[68, "Bio.Blast.read", false]], "read() (in module bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.read", false]], "read() (in module bio.cluster)": [[73, "Bio.Cluster.read", false]], "read() (in module bio.compass)": [[74, "Bio.Compass.read", false]], "read() (in module bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.read", false]], "read() (in module bio.emboss.primersearch)": [[82, "Bio.Emboss.PrimerSearch.read", false]], "read() (in module bio.entrez)": [[83, "Bio.Entrez.read", false]], "read() (in module bio.expasy.cellosaurus)": [[90, "Bio.ExPASy.cellosaurus.read", false]], "read() (in module bio.expasy.enzyme)": [[86, "Bio.ExPASy.Enzyme.read", false]], "read() (in module bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.read", false]], "read() (in module bio.expasy.prosite)": [[88, "Bio.ExPASy.Prosite.read", false]], "read() (in module bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.read", false]], "read() (in module bio.genbank)": [[92, "Bio.GenBank.read", false]], "read() (in module bio.kegg.enzyme)": [[113, "Bio.KEGG.Enzyme.read", false]], "read() (in module bio.kegg.kgml.kgml_parser)": [[116, "Bio.KEGG.KGML.KGML_parser.read", false]], "read() (in module bio.medline)": [[123, "Bio.Medline.read", false]], "read() (in module bio.motifs)": [[283, "Bio.motifs.read", false]], "read() (in module bio.motifs.alignace)": [[284, "Bio.motifs.alignace.read", false]], "read() (in module bio.motifs.clusterbuster)": [[286, "Bio.motifs.clusterbuster.read", false]], "read() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.read", false]], "read() (in module bio.motifs.mast)": [[289, "Bio.motifs.mast.read", false]], "read() (in module bio.motifs.meme)": [[291, "Bio.motifs.meme.read", false]], "read() (in module bio.motifs.minimal)": [[292, "Bio.motifs.minimal.read", false]], "read() (in module bio.motifs.pfm)": [[293, "Bio.motifs.pfm.read", false]], "read() (in module bio.motifs.transfac)": [[295, "Bio.motifs.transfac.read", false]], "read() (in module bio.motifs.xms)": [[296, "Bio.motifs.xms.read", false]], "read() (in module bio.phenotype)": [[298, "Bio.phenotype.read", false]], "read() (in module bio.phylo.paml.baseml)": [[193, "Bio.Phylo.PAML.baseml.read", false]], "read() (in module bio.phylo.paml.codeml)": [[195, "Bio.Phylo.PAML.codeml.read", false]], "read() (in module bio.phylo.paml.yn00)": [[196, "Bio.Phylo.PAML.yn00.read", false]], "read() (in module bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.read", false]], "read() (in module bio.popgen.genepop)": [[201, "Bio.PopGen.GenePop.read", false]], "read() (in module bio.popgen.genepop.fileparser)": [[204, "Bio.PopGen.GenePop.FileParser.read", false]], "read() (in module bio.popgen.genepop.largefileparser)": [[205, "Bio.PopGen.GenePop.LargeFileParser.read", false]], "read() (in module bio.searchio)": [[217, "Bio.SearchIO.read", false]], "read() (in module bio.seqio)": [[238, "Bio.SeqIO.read", false]], "read() (in module bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.read", false]], "read() (in module bio.sequencing.phd)": [[271, "Bio.Sequencing.Phd.read", false]], "read() (in module bio.swissprot)": [[272, "Bio.SwissProt.read", false]], "read() (in module bio.unigene)": [[275, "Bio.UniGene.read", false]], "read_cal (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.read_cal", false]], "read_colorscheme() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.read_colorscheme", false]], "read_ctl_file() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.read_ctl_file", false]], "read_ctl_file() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.read_ctl_file", false]], "read_ctl_file() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.read_ctl_file", false]], "read_file (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.read_file", false]], "read_file (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.read_file", false]], "read_file (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.read_file", false]], "read_file1 (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.read_file1", false]], "read_file1 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.read_file1", false]], "read_file2 (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.read_file2", false]], "read_file2 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.read_file2", false]], "read_next() (bio.searchio.hmmerio.hmmer2_text.hmmer2textparser method)": [[230, "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.read_next", false]], "read_pic() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.read_PIC", false]], "read_pic_seq() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.read_PIC_seq", false]], "readfile (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.readfile", false]], "readline() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.readline", false]], "readrochexmlmanifest() (in module bio.seqio.sffio)": [[253, "Bio.SeqIO.SffIO.ReadRocheXmlManifest", false]], "reads (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.Reads", false]], "realbranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.realbranches", false]], "rearrange (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.rearrange", false]], "rearrangements (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.rearrangements", false]], "record (class in bio.affy.celfile)": [[29, "Bio.Affy.CelFile.Record", false]], "record (class in bio.blast)": [[68, "Bio.Blast.Record", false]], "record (class in bio.cluster)": [[73, "Bio.Cluster.Record", false]], "record (class in bio.compass)": [[74, "Bio.Compass.Record", false]], "record (class in bio.emboss.primer3)": [[81, "Bio.Emboss.Primer3.Record", false]], "record (class in bio.expasy.cellosaurus)": [[90, "Bio.ExPASy.cellosaurus.Record", false]], "record (class in bio.expasy.enzyme)": [[86, "Bio.ExPASy.Enzyme.Record", false]], "record (class in bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.Record", false]], "record (class in bio.expasy.prosite)": [[88, "Bio.ExPASy.Prosite.Record", false]], "record (class in bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.Record", false]], "record (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Record", false]], "record (class in bio.geo.record)": [[97, "Bio.Geo.Record.Record", false]], "record (class in bio.kegg.compound)": [[112, "Bio.KEGG.Compound.Record", false]], "record (class in bio.kegg.enzyme)": [[113, "Bio.KEGG.Enzyme.Record", false]], "record (class in bio.kegg.gene)": [[114, "Bio.KEGG.Gene.Record", false]], "record (class in bio.medline)": [[123, "Bio.Medline.Record", false]], "record (class in bio.motifs.alignace)": [[284, "Bio.motifs.alignace.Record", false]], "record (class in bio.motifs.clusterbuster)": [[286, "Bio.motifs.clusterbuster.Record", false]], "record (class in bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.Record", false]], "record (class in bio.motifs.mast)": [[289, "Bio.motifs.mast.Record", false]], "record (class in bio.motifs.meme)": [[291, "Bio.motifs.meme.Record", false]], "record (class in bio.motifs.minimal)": [[292, "Bio.motifs.minimal.Record", false]], "record (class in bio.motifs.pfm)": [[293, "Bio.motifs.pfm.Record", false]], "record (class in bio.motifs.transfac)": [[295, "Bio.motifs.transfac.Record", false]], "record (class in bio.motifs.xms)": [[296, "Bio.motifs.xms.Record", false]], "record (class in bio.popgen.genepop)": [[201, "Bio.PopGen.GenePop.Record", false]], "record (class in bio.popgen.genepop.largefileparser)": [[205, "Bio.PopGen.GenePop.LargeFileParser.Record", false]], "record (class in bio.scop.cla)": [[210, "Bio.SCOP.Cla.Record", false]], "record (class in bio.scop.des)": [[211, "Bio.SCOP.Des.Record", false]], "record (class in bio.scop.dom)": [[212, "Bio.SCOP.Dom.Record", false]], "record (class in bio.scop.hie)": [[213, "Bio.SCOP.Hie.Record", false]], "record (class in bio.sequencing.phd)": [[271, "Bio.Sequencing.Phd.Record", false]], "record (class in bio.swissprot)": [[272, "Bio.SwissProt.Record", false]], "record (class in bio.swissprot.keywlist)": [[273, "Bio.SwissProt.KeyWList.Record", false]], "record (class in bio.unigene)": [[275, "Bio.UniGene.Record", false]], "record_has() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.record_has", false]], "record_start (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.RECORD_START", false]], "record_start (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.RECORD_START", false]], "record_start (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.RECORD_START", false]], "recorded (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.recorded", false]], "recordparser (class in bio.genbank)": [[92, "Bio.GenBank.RecordParser", false]], "records (class in bio.blast)": [[68, "Bio.Blast.Records", false]], "red() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.red", false]], "ref (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.ref", false]], "ref (bio.seqfeature.seqfeature property)": [[237, "Bio.SeqFeature.SeqFeature.ref", false]], "ref (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.ref", false]], "ref (bio.sequencing.applications.samtoolsfaidxcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsFaidxCommandline.ref", false]], "ref_db (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.ref_db", false]], "ref_db (bio.seqfeature.seqfeature property)": [[237, "Bio.SeqFeature.SeqFeature.ref_db", false]], "reference (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.reference", false]], "reference (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.reference", false]], "reference (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.reference", false]], "reference (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.reference", false]], "reference (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.reference", false]], "reference (class in bio.expasy.prodoc)": [[87, "Bio.ExPASy.Prodoc.Reference", false]], "reference (class in bio.genbank.record)": [[93, "Bio.GenBank.Record.Reference", false]], "reference (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Reference", false]], "reference (class in bio.seqfeature)": [[237, "Bio.SeqFeature.Reference", false]], "reference (class in bio.swissprot)": [[272, "Bio.SwissProt.Reference", false]], "reference() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.reference", false]], "reference() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.reference", false]], "reference_keys (bio.motifs.transfac.motif attribute)": [[295, "Bio.motifs.transfac.Motif.reference_keys", false]], "refine (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.refine", false]], "refinew (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.refinew", false]], "refinewindow (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.refinewindow", false]], "refmat() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.refmat", false]], "refresh (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.refresh", false]], "region (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.region", false]], "register_ncbi_table() (in module bio.data.codontable)": [[76, "Bio.Data.CodonTable.register_ncbi_table", false]], "regular (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.regular", false]], "relation (class in bio.kegg.kgml.kgml_pathway)": [[117, "Bio.KEGG.KGML.KGML_pathway.Relation", false]], "relations (bio.kegg.kgml.kgml_pathway.pathway property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.relations", false]], "relative_entropy (bio.motifs.motif property)": [[283, "Bio.motifs.Motif.relative_entropy", false]], "relaxedphylipiterator (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.RelaxedPhylipIterator", false]], "relaxedphylipwriter (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.RelaxedPhylipWriter", false]], "remote (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.remote", false]], "remote (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.remote", false]], "remote (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.remote", false]], "remote (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.remote", false]], "remote (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.remote", false]], "remote (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.remote", false]], "remote (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.remote", false]], "remote (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.remote", false]], "remote (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.remote", false]], "remove() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.remove", false]], "remove() (biosql.loader.databaseremover method)": [[305, "BioSQL.Loader.DatabaseRemover.remove", false]], "remove_component() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.remove_component", false]], "remove_edge() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.remove_edge", false]], "remove_edge() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.remove_edge", false]], "remove_entry() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.remove_entry", false]], "remove_graphics() (bio.kegg.kgml.kgml_pathway.entry method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Entry.remove_graphics", false]], "remove_loci_by_name() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_loci_by_name", false]], "remove_loci_by_position() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_loci_by_position", false]], "remove_locus_by_name() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_locus_by_name", false]], "remove_locus_by_name() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.remove_locus_by_name", false]], "remove_locus_by_position() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_locus_by_position", false]], "remove_locus_by_position() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.remove_locus_by_position", false]], "remove_node() (bio.pathway.rep.graph.graph method)": [[179, "Bio.Pathway.Rep.Graph.Graph.remove_node", false]], "remove_node() (bio.pathway.rep.multigraph.multigraph method)": [[180, "Bio.Pathway.Rep.MultiGraph.MultiGraph.remove_node", false]], "remove_population() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.remove_population", false]], "remove_population() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.remove_population", false]], "remove_reaction() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.remove_reaction", false]], "remove_reaction() (bio.pathway.system method)": [[177, "Bio.Pathway.System.remove_reaction", false]], "remove_relation() (bio.kegg.kgml.kgml_pathway.pathway method)": [[117, "Bio.KEGG.KGML.KGML_pathway.Pathway.remove_relation", false]], "remove_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.remove_succ", false]], "removeprefix() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.removeprefix", false]], "removesuffix() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.removesuffix", false]], "renumber_tracks() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.renumber_tracks", false]], "reorder (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.reorder", false]], "repeats (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.repeats", false]], "replace() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.replace", false]], "replace_entry() (in module bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.replace_entry", false]], "replacement_dictionary() (bio.align.aligninfo.summaryinfo method)": [[31, "Bio.Align.AlignInfo.SummaryInfo.replacement_dictionary", false]], "report (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.report", false]], "report_ic() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.report_IC", false]], "reps (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.reps", false]], "res (class in bio.scop.raf)": [[214, "Bio.SCOP.Raf.Res", false]], "reset() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.reset", false]], "residue (class in bio.pdb.residue)": [[155, "Bio.PDB.Residue.Residue", false]], "residue_depth() (in module bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.residue_depth", false]], "residue_dict() (bio.nmr.xpktools.peaklist method)": [[126, "Bio.NMR.xpktools.Peaklist.residue_dict", false]], "residuedepth (class in bio.pdb.residuedepth)": [[156, "Bio.PDB.ResidueDepth.ResidueDepth", false]], "residuenumber (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.residuenumber", false]], "residues (class in bio.scop.residues)": [[215, "Bio.SCOP.Residues.Residues", false]], "rest() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.rest", false]], "retree (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.retree", false]], "retrieve_assembly_file() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.retrieve_assembly_file", false]], "retrieve_pdb_file() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.retrieve_pdb_file", false]], "reverse (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.reverse", false]], "reverse() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.reverse", false]], "reverse() (bio.seq.mutableseq method)": [[236, "Bio.Seq.MutableSeq.reverse", false]], "reverse_complement() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.reverse_complement", false]], "reverse_complement() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.reverse_complement", false]], "reverse_complement() (bio.motifs.matrix.genericpositionmatrix method)": [[290, "Bio.motifs.matrix.GenericPositionMatrix.reverse_complement", false]], "reverse_complement() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.reverse_complement", false]], "reverse_complement() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.reverse_complement", false]], "reverse_complement() (in module bio.seq)": [[236, "Bio.Seq.reverse_complement", false]], "reverse_complement_rna() (in module bio.seq)": [[236, "Bio.Seq.reverse_complement_rna", false]], "reverseinput (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.reverseinput", false]], "reward (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.reward", false]], "rewind() (bio.align.alignments method)": [[30, "Bio.Align.Alignments.rewind", false]], "rewind() (bio.align.alignmentsabstractbaseclass method)": [[30, "Bio.Align.AlignmentsAbstractBaseClass.rewind", false]], "rewind() (bio.align.interfaces.alignmentiterator method)": [[45, "Bio.Align.interfaces.AlignmentIterator.rewind", false]], "rewind() (bio.align.pairwisealignments method)": [[30, "Bio.Align.PairwiseAlignments.rewind", false]], "rewriteformat (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.rewriteformat", false]], "rfind() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rfind", false]], "rformat (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.rformat", false]], "rformat (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.rformat", false]], "rformat (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.rformat", false]], "rformat (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.rformat", false]], "rho (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.rho", false]], "richards() (in module bio.phenotype.pm_fitting)": [[300, "Bio.phenotype.pm_fitting.richards", false]], "rid (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.rid", false]], "right_multiply() (bio.pdb.vectors.vector method)": [[176, "Bio.PDB.vectors.Vector.right_multiply", false]], "rindex() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rindex", false]], "rollback() (biosql.bioseqdatabase.adaptor method)": [[303, "BioSQL.BioSeqDatabase.Adaptor.rollback", false]], "rollback() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.rollback", false]], "root (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.root", false]], "root (bio.phylo.basetree.clade property)": [[183, "Bio.Phylo.BaseTree.Clade.root", false]], "root1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.root1", false]], "root2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.root2", false]], "root_at_midpoint() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.root_at_midpoint", false]], "root_with_outgroup() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.root_with_outgroup", false]], "root_with_outgroup() (bio.phylo.basetree.tree method)": [[183, "Bio.Phylo.BaseTree.Tree.root_with_outgroup", false]], "rotaxis() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.rotaxis", false]], "rotaxis2m() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.rotaxis2m", false]], "rotmat() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.rotmat", false]], "round (class in bio.blast.ncbixml)": [[71, "Bio.Blast.NCBIXML.Round", false]], "rpsdb (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.rpsdb", false]], "rsplit() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rsplit", false]], "rstrip() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.rstrip", false]], "rt (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.rt", false]], "run() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.run", false]], "run() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.run", false]], "run() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.run", false]], "run() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.run", false]], "run() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.run", false]], "run_id (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.run_id", false]], "run_naccess() (in module bio.pdb.naccess)": [[145, "Bio.PDB.NACCESS.run_naccess", false]], "run_psea() (in module bio.pdb.psea)": [[153, "Bio.PDB.PSEA.run_psea", false]], "s (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.s", false]], "s (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.S", false]], "s (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.S", false]], "s (bio.sequencing.applications.samtoolsrmdupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.S", false], [270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline.s", false]], "s (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.S", false]], "safename() (in module bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.safename", false]], "sai_file (bio.sequencing.applications.bwasamsecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSamseCommandline.sai_file", false]], "sai_file1 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.sai_file1", false]], "sai_file2 (bio.sequencing.applications.bwasampecommandline property)": [[270, "Bio.Sequencing.Applications.BwaSampeCommandline.sai_file2", false]], "salt_correction() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.salt_correction", false]], "saltconc (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.saltconc", false]], "sam_file (bio.sequencing.applications.samtoolsreheadercommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline.sam_file", false]], "samtoolscalmdcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline", false]], "samtoolscatcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsCatCommandline", false]], "samtoolsfaidxcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsFaidxCommandline", false]], "samtoolsfixmatecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsFixmateCommandline", false]], "samtoolsidxstatscommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline", false]], "samtoolsindexcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsIndexCommandline", false]], "samtoolsmergecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline", false]], "samtoolsmpileupcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline", false]], "samtoolsphasecommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsPhaseCommandline", false]], "samtoolsreheadercommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsReheaderCommandline", false]], "samtoolsrmdupcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsRmdupCommandline", false]], "samtoolssortcommandline (in module bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsSortCommandline", false]], "samtoolstargetcutcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline", false]], "samtoolsversion0xsortcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline", false]], "samtoolsversion1xsortcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline", false]], "samtoolsviewcommandline (class in bio.sequencing.applications)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline", false]], "sanitize_name() (in module bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.sanitize_name", false]], "save() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.save", false]], "save() (bio.pdb.mmcifio.mmcifio method)": [[170, "Bio.PDB.mmcifio.MMCIFIO.save", false]], "save() (bio.pdb.mmtf.mmtfio.mmtfio method)": [[173, "Bio.PDB.mmtf.mmtfio.MMTFIO.save", false]], "save() (bio.pdb.pdbio.pdbio method)": [[148, "Bio.PDB.PDBIO.PDBIO.save", false]], "save() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.save", false]], "save_dtd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.save_dtd_file", false]], "save_each_pssm (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.save_each_pssm", false]], "save_each_pssm (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.save_each_pssm", false]], "save_pssm_after_last_round (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.save_pssm_after_last_round", false]], "save_pssm_after_last_round (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.save_pssm_after_last_round", false]], "save_xsd_file() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.save_xsd_file", false]], "scale_segment_value() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.scale_segment_value", false]], "scalebranches (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.scalebranches", false]], "scaleddpalgorithms (class in bio.hmm.dynamicprogramming)": [[107, "Bio.HMM.DynamicProgramming.ScaledDPAlgorithms", false]], "scan() (in module bio.expasy.scanprosite)": [[89, "Bio.ExPASy.ScanProsite.scan", false]], "schemahandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.schemaHandler", false]], "scheme_color() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.scheme_color", false]], "scientific_name() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.scientific_name", false]], "scop (class in bio.scop)": [[209, "Bio.SCOP.Scop", false]], "score (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.score", false]], "score (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.score", false]], "score() (bio.align.codonaligner method)": [[30, "Bio.Align.CodonAligner.score", false]], "score() (bio.align.pairwisealigner method)": [[30, "Bio.Align.PairwiseAligner.score", false]], "scoredistribution (class in bio.motifs.thresholds)": [[294, "Bio.motifs.thresholds.ScoreDistribution", false]], "scorefile (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.scorefile", false]], "scorer (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.Scorer", false]], "search (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.search", false]], "search() (bio.align.bigbed.alignmentiterator method)": [[36, "Bio.Align.bigbed.AlignmentIterator.search", false]], "search() (bio.alignio.mafio.mafindex method)": [[61, "Bio.AlignIO.MafIO.MafIndex.search", false]], "search() (bio.motifs.instances method)": [[283, "Bio.motifs.Instances.search", false]], "search() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.search", false]], "search() (bio.pdb.neighborsearch.neighborsearch method)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch.search", false]], "search() (bio.phylo.treeconstruction.nnitreesearcher method)": [[199, "Bio.Phylo.TreeConstruction.NNITreeSearcher.search", false]], "search() (bio.phylo.treeconstruction.treesearcher method)": [[199, "Bio.Phylo.TreeConstruction.TreeSearcher.search", false]], "search() (in module bio.scop)": [[209, "Bio.SCOP.search", false]], "search() (in module bio.togows)": [[274, "Bio.TogoWS.search", false]], "search() (in module bio.uniprot)": [[276, "Bio.UniProt.search", false]], "search_all() (bio.pdb.neighborsearch.neighborsearch method)": [[146, "Bio.PDB.NeighborSearch.NeighborSearch.search_all", false]], "search_count() (in module bio.togows)": [[274, "Bio.TogoWS.search_count", false]], "search_iter() (in module bio.togows)": [[274, "Bio.TogoWS.search_iter", false]], "search_taxon() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.search_taxon", false]], "searchsp (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.searchsp", false]], "searchsp (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.searchsp", false]], "second (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.second", false]], "secondary_structure_fraction() (bio.sequtils.protparam.proteinanalysis method)": [[265, "Bio.SeqUtils.ProtParam.ProteinAnalysis.secondary_structure_fraction", false]], "secstrout (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.secstrout", false]], "seed (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.seed", false]], "seed (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.seed", false]], "seed (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.seed", false]], "seed (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.seed", false]], "seed (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.seed", false]], "seed (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.seed", false]], "seed (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.seed", false]], "seed (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.seed", false]], "seek() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.seek", false]], "seek_position() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.seek_position", false]], "seekable() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.seekable", false]], "seekable() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.seekable", false]], "seg (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.seg", false]], "seg (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.seg", false]], "seg (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.seg", false]], "seg (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.seg", false]], "seg (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.seg", false]], "seg (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.seg", false]], "seg (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.seg", false]], "seg (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.seg", false]], "seguid() (in module bio.sequtils.checksum)": [[262, "Bio.SeqUtils.CheckSum.seguid", false]], "select (class in bio.pdb.pdbio)": [[148, "Bio.PDB.PDBIO.Select", false]], "select() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.select", false]], "seq (bio.seqrecord.seqrecord property)": [[260, "Bio.SeqRecord.SeqRecord.seq", false]], "seq (biosql.bioseq.dbseqrecord property)": [[302, "BioSQL.BioSeq.DBSeqRecord.seq", false]], "seq (class in bio.seq)": [[236, "Bio.Seq.Seq", false]], "seq1() (in module bio.sequtils)": [[261, "Bio.SeqUtils.seq1", false]], "seq3() (in module bio.sequtils)": [[261, "Bio.SeqUtils.seq3", false]], "seq_types (bio.align.applications.tcoffeecommandline attribute)": [[32, "Bio.Align.Applications.TCoffeeCommandline.SEQ_TYPES", false]], "seqa (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.seqA", false]], "seqall (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.seqall", false]], "seqb (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.seqB", false]], "seqfeature (class in bio.seqfeature)": [[237, "Bio.SeqFeature.SeqFeature", false]], "seqidlist (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.seqidlist", false]], "seqidlist (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.seqidlist", false]], "seqmap (class in bio.scop.raf)": [[214, "Bio.SCOP.Raf.SeqMap", false]], "seqmapindex (class in bio.scop.raf)": [[214, "Bio.SCOP.Raf.SeqMapIndex", false]], "seqmatchallcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline", false]], "seqno_range (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.seqno_range", false]], "seqnos (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.seqnos", false]], "seqrecord (class in bio.seqrecord)": [[260, "Bio.SeqRecord.SeqRecord", false]], "seqretcommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.SeqretCommandline", false]], "seqtype (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.seqtype", false]], "seqtype (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.seqtype", false]], "seqtype (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.seqtype", false]], "sequence (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.sequence", false]], "sequence (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.sequence", false]], "sequence (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.sequence", false]], "sequence (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.sequence", false]], "sequence (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.sequence", false]], "sequence (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.sequence", false]], "sequence (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.sequence", false]], "sequence (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.sequence", false]], "sequence (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.sequence", false]], "sequence (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.sequence", false]], "sequence (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.sequence", false]], "sequence (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.sequence", false]], "sequence (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.sequence", false]], "sequence (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.sequence", false]], "sequence (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Sequence", false]], "sequence() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.sequence", false]], "sequence_format (bio.genbank.record.record attribute)": [[93, "Bio.GenBank.Record.Record.SEQUENCE_FORMAT", false]], "sequence_headers (bio.genbank.scanner.emblscanner attribute)": [[94, "Bio.GenBank.Scanner.EmblScanner.SEQUENCE_HEADERS", false]], "sequence_headers (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.SEQUENCE_HEADERS", false]], "sequence_headers (bio.genbank.scanner.insdcscanner attribute)": [[94, "Bio.GenBank.Scanner.InsdcScanner.SEQUENCE_HEADERS", false]], "sequence_indent (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.SEQUENCE_INDENT", false]], "sequence_relation() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.sequence_relation", false]], "sequence_relation() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.sequence_relation", false]], "sequencedataabstractbaseclass (class in bio.seq)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass", false]], "sequenceiterator (class in bio.seqio.interfaces)": [[246, "Bio.SeqIO.Interfaces.SequenceIterator", false]], "sequenceline (class in bio.unigene)": [[275, "Bio.UniGene.SequenceLine", false]], "sequencerelation (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.SequenceRelation", false]], "sequences (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.sequences", false]], "sequences (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.sequences", false]], "sequencewriter (class in bio.seqio.interfaces)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter", false]], "sequential (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.sequential", false]], "sequentialalignmentwriter (class in bio.alignio.interfaces)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter", false]], "sequentialphylipiterator (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipIterator", false]], "sequentialphylipwriter (class in bio.alignio.phylipio)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipWriter", false]], "seqxmliterator (class in bio.seqio.seqxmlio)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlIterator", false]], "seqxmlwriter (class in bio.seqio.seqxmlio)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter", false]], "set() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.set", false]], "set() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.set", false]], "set() (bio.svdsuperimposer.svdsuperimposer method)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer.set", false]], "set_accuracy_95() (in module bio.pdb.internal_coords)": [[169, "Bio.PDB.internal_coords.set_accuracy_95", false]], "set_all_features() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.set_all_features", false]], "set_all_tracks() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.set_all_tracks", false]], "set_altloc() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_altloc", false]], "set_angle() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_angle", false]], "set_anisou() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_anisou", false]], "set_anisou() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_anisou", false]], "set_atom_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_atom_info", false]], "set_atoms() (bio.pdb.qcprot.qcpsuperimposer method)": [[175, "Bio.PDB.qcprot.QCPSuperimposer.set_atoms", false]], "set_atoms() (bio.pdb.superimposer.superimposer method)": [[163, "Bio.PDB.Superimposer.Superimposer.set_atoms", false]], "set_bfactor() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_bfactor", false]], "set_bio_assembly_trans() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_bio_assembly_trans", false]], "set_chain_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_chain_info", false]], "set_charge() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_charge", false]], "set_color() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.set_color", false]], "set_colour() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.set_colour", false]], "set_coord() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_coord", false]], "set_data() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.set_data", false]], "set_data() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_data", false]], "set_dict() (bio.pdb.mmcifio.mmcifio method)": [[170, "Bio.PDB.mmcifio.MMCIFIO.set_dict", false]], "set_emission_pseudocount() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_emission_pseudocount", false]], "set_emission_score() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_emission_score", false]], "set_entity_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_entity_info", false]], "set_equal_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_equal_probabilities", false]], "set_feature() (bio.graphics.genomediagram.feature method)": [[104, "Bio.Graphics.GenomeDiagram.Feature.set_feature", false]], "set_flexible() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_flexible", false]], "set_group_bond() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_group_bond", false]], "set_group_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_group_info", false]], "set_handle() (bio.genbank.scanner.insdcscanner method)": [[94, "Bio.GenBank.Scanner.InsdcScanner.set_handle", false]], "set_hbond() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_hbond", false]], "set_header() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_header", false]], "set_header_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_header_info", false]], "set_hit_accession() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_accession", false]], "set_hit_def() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_def", false]], "set_hit_id() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_id", false]], "set_hit_len() (bio.blast.ncbixml.blastparser method)": [[71, "Bio.Blast.NCBIXML.BlastParser.set_hit_len", false]], "set_homog_trans_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_homog_trans_mtx", false]], "set_id() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_id", false]], "set_initial_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_initial_probabilities", false]], "set_inter_group_bond() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_inter_group_bond", false]], "set_length() (bio.pdb.internal_coords.hedron method)": [[169, "Bio.PDB.internal_coords.Hedron.set_length", false]], "set_length() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.set_length", false]], "set_line_counter() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_line_counter", false]], "set_model_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_model_info", false]], "set_occupancy() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_occupancy", false]], "set_parameter() (bio.application.abstractcommandline method)": [[67, "Bio.Application.AbstractCommandline.set_parameter", false]], "set_parent() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_parent", false]], "set_parent() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.set_parent", false]], "set_parent() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.set_parent", false]], "set_prev() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_prev", false]], "set_radius() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_radius", false]], "set_random_emission_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_emission_probabilities", false]], "set_random_initial_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_initial_probabilities", false]], "set_random_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_probabilities", false]], "set_random_transition_probabilities() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_random_transition_probabilities", false]], "set_reference() (bio.pdb.cealign.cealigner method)": [[166, "Bio.PDB.cealign.CEAligner.set_reference", false]], "set_scale() (bio.graphics.displayrepresentation.chromosomecounts method)": [[102, "Bio.Graphics.DisplayRepresentation.ChromosomeCounts.set_scale", false]], "set_serial_number() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_serial_number", false]], "set_sigatm() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_sigatm", false]], "set_sigatm() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_sigatm", false]], "set_siguij() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.set_siguij", false]], "set_siguij() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_siguij", false]], "set_structure() (bio.pdb.pdbio.structureio method)": [[148, "Bio.PDB.PDBIO.StructureIO.set_structure", false]], "set_subtree() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.set_subtree", false]], "set_succ() (bio.nexus.nodes.node method)": [[130, "Bio.Nexus.Nodes.Node.set_succ", false]], "set_symmetry() (bio.pdb.structurebuilder.structurebuilder method)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder.set_symmetry", false]], "set_transition_pseudocount() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_transition_pseudocount", false]], "set_transition_score() (bio.hmm.markovmodel.markovmodelbuilder method)": [[108, "Bio.HMM.MarkovModel.MarkovModelBuilder.set_transition_score", false]], "set_x_homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_X_homog_rot_mtx", false]], "set_xtal_info() (bio.pdb.mmtf.defaultparser.structuredecoder method)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder.set_xtal_info", false]], "set_y_homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_Y_homog_rot_mtx", false]], "set_z_homog_rot_mtx() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.set_Z_homog_rot_mtx", false]], "sffiterator (class in bio.seqio.sffio)": [[253, "Bio.SeqIO.SffIO.SffIterator", false]], "sffwriter (class in bio.seqio.sffio)": [[253, "Bio.SeqIO.SffIO.SffWriter", false]], "sformat (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.sformat", false]], "shape (bio.align.alignment property)": [[30, "Bio.Align.Alignment.shape", false]], "shortnames (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.shortnames", false]], "show_domain_hits (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.show_domain_hits", false]], "show_gis (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.show_gis", false]], "show_gis (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.show_gis", false]], "showtree (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.showtree", false]], "showxml (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.showxml", false]], "shrakerupley (class in bio.pdb.sasa)": [[157, "Bio.PDB.SASA.ShrakeRupley", false]], "shuffle (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.shuffle", false]], "similarity (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.similarity", false]], "similarity (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.similarity", false]], "similarity (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.similarity", false]], "simplefastaparser() (in module bio.seqio.fastaio)": [[241, "Bio.SeqIO.FastaIO.SimpleFastaParser", false]], "simplelocation (class in bio.seqfeature)": [[237, "Bio.SeqFeature.SimpleLocation", false]], "sink() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.sink", false]], "sink_interactions() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.sink_interactions", false]], "six_frame_translations() (in module bio.sequtils)": [[261, "Bio.SeqUtils.six_frame_translations", false]], "sixmerpair (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.sixmerpair", false]], "skip_header() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.skip_header", false]], "skip_population() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.skip_population", false]], "skip_whitespace() (bio.nexus.nexus.charbuffer method)": [[129, "Bio.Nexus.Nexus.CharBuffer.skip_whitespace", false]], "skipcharacterdatahandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.skipCharacterDataHandler", false]], "skipins (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.skipins", false]], "slow (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.slow", false]], "slownni (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.slownni", false]], "smin (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.smin", false]], "smoothscoreceil (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.smoothscoreceil", false]], "smoothwindow (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.smoothwindow", false]], "smprint() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.smprint", false]], "snapgeneiterator (class in bio.seqio.snapgeneio)": [[254, "Bio.SeqIO.SnapGeneIO.SnapGeneIterator", false]], "snucleotide (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.snucleotide", false]], "snucleotide (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.snucleotide", false]], "soft_masking (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.soft_masking", false]], "soft_masking (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.soft_masking", false]], "solexa_quality_from_phred() (in module bio.seqio.qualityio)": [[251, "Bio.SeqIO.QualityIO.solexa_quality_from_phred", false]], "somcluster() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.somcluster", false]], "somcluster() (in module bio.cluster)": [[73, "Bio.Cluster.somcluster", false]], "sort() (bio.align.alignment method)": [[30, "Bio.Align.Alignment.sort", false]], "sort() (bio.align.multipleseqalignment method)": [[30, "Bio.Align.MultipleSeqAlignment.sort", false]], "sort() (bio.cluster.tree method)": [[73, "Bio.Cluster.Tree.sort", false]], "sort() (bio.pdb.residue.disorderedresidue method)": [[155, "Bio.PDB.Residue.DisorderedResidue.sort", false]], "sort() (bio.sequencing.ace.acefilerecord method)": [[269, "Bio.Sequencing.Ace.ACEFileRecord.sort", false]], "source() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.source", false]], "source_interactions() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.source_interactions", false]], "sp (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.sp", false]], "space (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.space", false]], "spacersegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.SpacerSegment", false]], "speciations() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.speciations", false]], "species() (bio.pathway.network method)": [[177, "Bio.Pathway.Network.species", false]], "species() (bio.pathway.reaction method)": [[177, "Bio.Pathway.Reaction.species", false]], "species() (bio.pathway.system method)": [[177, "Bio.Pathway.System.species", false]], "splice (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.splice", false]], "splicepenalty (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.splicepenalty", false]], "split() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.split", false]], "split() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.split", false]], "split() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.split", false]], "split_akl() (bio.pdb.internal_coords.ic_residue method)": [[169, "Bio.PDB.internal_coords.IC_Residue.split_akl", false]], "split_in_loci() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.split_in_loci", false]], "split_in_pops() (bio.popgen.genepop.record method)": [[201, "Bio.PopGen.GenePop.Record.split_in_pops", false]], "split_jaspar_id() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.split_jaspar_id", false]], "split_virtual_offset() (in module bio.bgzf)": [[278, "Bio.bgzf.split_virtual_offset", false]], "spn (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.spn", false]], "spr (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.spr", false]], "sprlength (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.sprlength", false]], "sprotein (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.sprotein", false]], "sprotein (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.sprotein", false]], "sprotein (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.sprotein", false]], "sprotein (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.sprotein", false]], "sprotein (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.sprotein", false]], "spscore (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.spscore", false]], "sqlite_dbutils (class in biosql.dbutils)": [[304, "BioSQL.DBUtils.Sqlite_dbutils", false]], "ss_to_index() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.ss_to_index", false]], "stable (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.stable", false]], "standarddata (class in bio.nexus.standarddata)": [[131, "Bio.Nexus.StandardData.StandardData", false]], "stars (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.stars", false]], "start (bio.pairwise2.alignment attribute)": [[297, "Bio.pairwise2.Alignment.start", false]], "start (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.start", false]], "start (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.start", false]], "start_codons (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.start_codons", false]], "start_read() (bio.popgen.genepop.fileparser.filerecord method)": [[204, "Bio.PopGen.GenePop.FileParser.FileRecord.start_read", false]], "starta (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.startA", false]], "startb (bio.graphics.genomediagram.crosslink property)": [[104, "Bio.Graphics.GenomeDiagram.CrossLink.startB", false]], "startdbrefelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startDBRefElement", false]], "startdescriptionelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startDescriptionElement", false]], "startdocument() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startDocument", false]], "startelement() (bio.expasy.scanprosite.contenthandler method)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.startElement", false]], "startelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startElementHandler", false]], "startentryelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startEntryElement", false]], "startentryfieldelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startEntryFieldElement", false]], "startentryfieldelementversion01() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startEntryFieldElementVersion01", false]], "starting_tree (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.starting_tree", false]], "startnamespacedeclhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startNamespaceDeclHandler", false]], "startpropertyelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startPropertyElement", false]], "startrawelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startRawElementHandler", false]], "startsequenceelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startSequenceElement", false]], "startseqxmlelement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startSeqXMLElement", false]], "startskipelementhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.startSkipElementHandler", false]], "startspecieselement() (bio.seqio.seqxmlio.contenthandler method)": [[252, "Bio.SeqIO.SeqXmlIO.ContentHandler.startSpeciesElement", false]], "startswith() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.startswith", false]], "state (class in bio.align.tabular)": [[55, "Bio.Align.tabular.State", false]], "stats (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.stats", false]], "status_characters (bio.align.maf.alignmentiterator attribute)": [[46, "Bio.Align.maf.AlignmentIterator.status_characters", false]], "std() (bio.motifs.matrix.positionspecificscoringmatrix method)": [[290, "Bio.motifs.matrix.PositionSpecificScoringMatrix.std", false]], "stdev() (bio.graphics.genomediagram.graphdata method)": [[104, "Bio.Graphics.GenomeDiagram.GraphData.stdev", false]], "stdo (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.stdo", false]], "stdout (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.stdout", false]], "stdout (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.stdout", false]], "stdout (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.stdout", false]], "stdout (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.stdout", false]], "stdout (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.stdout", false]], "stdout (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.stdout", false]], "stdout (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.stdout", false]], "stdout (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.stdout", false]], "stdout (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.stdout", false]], "stdout (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.stdout", false]], "stdout (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.stdout", false]], "stdout (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.stdout", false]], "stdout (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.stdout", false]], "stdout (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.stdout", false]], "stdout (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.stdout", false]], "stdout (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.stdout", false]], "stdout (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.stdout", false]], "stdout (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.stdout", false]], "stdout (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.stdout", false]], "stdout (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.stdout", false]], "stdout (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.stdout", false]], "stdout (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.stdout", false]], "stdout (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.stdout", false]], "stdout (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.stdout", false]], "stdout (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.stdout", false]], "stepmatrix (class in bio.nexus.nexus)": [[129, "Bio.Nexus.Nexus.StepMatrix", false]], "stochiometry() (bio.pathway.system method)": [[177, "Bio.Pathway.System.stochiometry", false]], "stockholmiterator (class in bio.alignio.stockholmio)": [[66, "Bio.AlignIO.StockholmIO.StockholmIterator", false]], "stockholmwriter (class in bio.alignio.stockholmio)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter", false]], "stop_codons (bio.data.codontable.codontable attribute)": [[76, "Bio.Data.CodonTable.CodonTable.stop_codons", false]], "store() (bio.entrez.parser.dictionaryelement method)": [[84, "Bio.Entrez.Parser.DictionaryElement.store", false]], "store() (bio.entrez.parser.listelement method)": [[84, "Bio.Entrez.Parser.ListElement.store", false]], "store() (bio.entrez.parser.orderedlistelement method)": [[84, "Bio.Entrez.Parser.OrderedListElement.store", false]], "strand (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.strand", false]], "strand (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.strand", false]], "strand (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.strand", false]], "strand (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.strand", false]], "strand (bio.seqfeature.compoundlocation property)": [[237, "Bio.SeqFeature.CompoundLocation.strand", false]], "strand (bio.seqfeature.seqfeature property)": [[237, "Bio.SeqFeature.SeqFeature.strand", false]], "strand (bio.seqfeature.simplelocation property)": [[237, "Bio.SeqFeature.SimpleLocation.strand", false]], "strandendin (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.strandendin", false]], "strandendout (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.strandendout", false]], "strandgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.strandgap", false]], "streammodeerror": [[27, "Bio.StreamModeError", false]], "stretchercommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.StretcherCommandline", false]], "strict_consensus() (in module bio.phylo.consensus)": [[186, "Bio.Phylo.Consensus.strict_consensus", false]], "strictly_equals() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.strictly_equals", false]], "strictly_equals() (bio.pdb.entity.disorderedentitywrapper method)": [[139, "Bio.PDB.Entity.DisorderedEntityWrapper.strictly_equals", false]], "strictly_equals() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.strictly_equals", false]], "strictly_equals() (bio.pdb.residue.residue method)": [[155, "Bio.PDB.Residue.Residue.strictly_equals", false]], "stringelement (class in bio.entrez.parser)": [[84, "Bio.Entrez.Parser.StringElement", false]], "strings (bio.expasy.scanprosite.contenthandler attribute)": [[89, "Bio.ExPASy.ScanProsite.ContentHandler.strings", false]], "strip() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.strip", false]], "structure (class in bio.pdb.structure)": [[160, "Bio.PDB.Structure.Structure", false]], "structure_rebuild_test() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.structure_rebuild_test", false]], "structurealignment (class in bio.pdb.structurealignment)": [[161, "Bio.PDB.StructureAlignment.StructureAlignment", false]], "structurebuilder (class in bio.pdb.structurebuilder)": [[162, "Bio.PDB.StructureBuilder.StructureBuilder", false]], "structured_comment_delim (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.STRUCTURED_COMMENT_DELIM", false]], "structured_comment_delim (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.STRUCTURED_COMMENT_DELIM", false]], "structured_comment_end (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.STRUCTURED_COMMENT_END", false]], "structured_comment_end (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.STRUCTURED_COMMENT_END", false]], "structured_comment_start (bio.genbank.scanner.genbankscanner attribute)": [[94, "Bio.GenBank.Scanner.GenBankScanner.STRUCTURED_COMMENT_START", false]], "structured_comment_start (bio.seqio.insdcio.genbankwriter attribute)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.STRUCTURED_COMMENT_START", false]], "structuredecoder (class in bio.pdb.mmtf.defaultparser)": [[172, "Bio.PDB.mmtf.DefaultParser.StructureDecoder", false]], "structureio (class in bio.pdb.pdbio)": [[148, "Bio.PDB.PDBIO.StructureIO", false]], "stsline (class in bio.unigene)": [[275, "Bio.UniGene.STSLine", false]], "style (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.style", false]], "subcomponent_size() (bio.graphics.basicchromosome.chromosome method)": [[99, "Bio.Graphics.BasicChromosome.Chromosome.subcomponent_size", false]], "subject (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.subject", false]], "subject (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.subject", false]], "subject (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.subject", false]], "subject (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.subject", false]], "subject (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.subject", false]], "subject (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.subject", false]], "subject (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.subject", false]], "subject_loc (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.subject_loc", false]], "subject_loc (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.subject_loc", false]], "substitutions (bio.align.alignment property)": [[30, "Bio.Align.Alignment.substitutions", false]], "substitutions (bio.align.multipleseqalignment property)": [[30, "Bio.Align.MultipleSeqAlignment.substitutions", false]], "substrates (bio.kegg.kgml.kgml_pathway.reaction property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Reaction.substrates", false]], "subtract_control() (bio.phenotype.phen_micro.platerecord method)": [[299, "Bio.phenotype.phen_micro.PlateRecord.subtract_control", false]], "sueff (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.sueff", false]], "sum() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.sum", false]], "sum_branchlength() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.sum_branchlength", false]], "sum_statistics (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.sum_statistics", false]], "sum_statistics (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.sum_statistics", false]], "sum_stats (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.sum_stats", false]], "sum_stats (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.sum_stats", false]], "summaryinfo (class in bio.align.aligninfo)": [[31, "Bio.Align.AlignInfo.SummaryInfo", false]], "superimposer (class in bio.pdb.superimposer)": [[163, "Bio.PDB.Superimposer.Superimposer", false]], "sv (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.sv", false]], "svdsuperimposer (class in bio.svdsuperimposer)": [[216, "Bio.SVDSuperimposer.SVDSuperimposer", false]], "swissiterator() (in module bio.seqio.swissio)": [[255, "Bio.SeqIO.SwissIO.SwissIterator", false]], "swissprotparsererror": [[272, "Bio.SwissProt.SwissProtParserError", false]], "symbol() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.symbol", false]], "synonym() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.synonym", false]], "system (class in bio.pathway)": [[177, "Bio.Pathway.System", false]], "t (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.t", false]], "t (bio.sequencing.applications.bwaaligncommandline property)": [[270, "Bio.Sequencing.Applications.BwaAlignCommandline.t", false]], "t (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.T", false], [270, "Bio.Sequencing.Applications.BwaBwaswCommandline.t", false]], "t (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.T", false], [270, "Bio.Sequencing.Applications.BwaMemCommandline.t", false]], "t (bio.sequencing.applications.samtoolsversion1xsortcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline.T", false]], "t (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.t", false]], "ta (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.ta", false]], "tabiterator (class in bio.seqio.tabio)": [[256, "Bio.SeqIO.TabIO.TabIterator", false]], "table (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.table", false]], "tabwriter (class in bio.seqio.tabio)": [[256, "Bio.SeqIO.TabIO.TabWriter", false]], "target (bio.align.alignment property)": [[30, "Bio.Align.Alignment.target", false]], "target (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.target", false]], "target_gap (bio.align.tabular.state attribute)": [[55, "Bio.Align.tabular.State.TARGET_GAP", false]], "task (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.task", false]], "task (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.task", false]], "task (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.task", false]], "task (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.task", false]], "task (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.task", false]], "taxid (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.taxid", false]], "taxid_map (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.taxid_map", false]], "taxonomy (bio.phylo.phyloxml.clade property)": [[197, "Bio.Phylo.PhyloXML.Clade.taxonomy", false]], "taxonomy (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Taxonomy", false]], "taxonomy() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.taxonomy", false]], "tcoffeecommandline (class in bio.align.applications)": [[32, "Bio.Align.Applications.TCoffeeCommandline", false]], "tell() (bio.bgzf.bgzfreader method)": [[278, "Bio.bgzf.BgzfReader.tell", false]], "tell() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.tell", false]], "telomeresegment (class in bio.graphics.basicchromosome)": [[99, "Bio.Graphics.BasicChromosome.TelomereSegment", false]], "template_length (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.template_length", false]], "template_type (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.template_type", false]], "termgap (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.termgap", false]], "terminal_gap_to_missing() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.terminal_gap_to_missing", false]], "terminalgap (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.terminalgap", false]], "test (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.test", false]], "test_genic_diff_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genic_diff_all", false]], "test_genic_diff_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genic_diff_pair", false]], "test_genotypic_diff_all() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genotypic_diff_all", false]], "test_genotypic_diff_pair() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_genotypic_diff_pair", false]], "test_global_hz_deficiency() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_global_hz_deficiency", false]], "test_global_hz_excess() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_global_hz_excess", false]], "test_hw_global() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.test_hw_global", false]], "test_hw_pop() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.test_hw_pop", false]], "test_ld() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_ld", false]], "test_ld_all_pair() (bio.popgen.genepop.easycontroller.easycontroller method)": [[203, "Bio.PopGen.GenePop.EasyController.EasyController.test_ld_all_pair", false]], "test_pop_hz_deficiency() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_pop_hz_deficiency", false]], "test_pop_hz_excess() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_pop_hz_excess", false]], "test_pop_hz_prob() (bio.popgen.genepop.controller.genepopcontroller method)": [[202, "Bio.PopGen.GenePop.Controller.GenePopController.test_pop_hz_prob", false]], "thorough (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.thorough", false]], "thr (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.thr", false]], "thread (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.thread", false]], "threads (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.threads", false]], "threads (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.threads", false]], "three_to_index() (in module bio.pdb.polypeptide)": [[154, "Bio.PDB.Polypeptide.three_to_index", false]], "thresh (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.thresh", false]], "thresh (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.thresh", false]], "threshold (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.threshold", false]], "threshold (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.threshold", false]], "threshold (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.threshold", false]], "threshold (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.threshold", false]], "threshold (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.threshold", false]], "threshold (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.threshold", false]], "threshold (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.threshold", false]], "threshold (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.threshold", false]], "threshold (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.threshold", false]], "threshold (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.threshold", false]], "threshold (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.threshold", false]], "threshold_balanced() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_balanced", false]], "threshold_fnr() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_fnr", false]], "threshold_fpr() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_fpr", false]], "threshold_patser() (bio.motifs.thresholds.scoredistribution method)": [[294, "Bio.motifs.thresholds.ScoreDistribution.threshold_patser", false]], "title (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.title", false]], "tm (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.tm", false]], "tm_gc() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.Tm_GC", false]], "tm_nn() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.Tm_NN", false]], "tm_wallace() (in module bio.sequtils.meltingtemp)": [[264, "Bio.SeqUtils.MeltingTemp.Tm_Wallace", false]], "tname() (biosql.dbutils.generic_dbutils method)": [[304, "BioSQL.DBUtils.Generic_dbutils.tname", false]], "to_alignment() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.to_alignment", false]], "to_dict() (bio.motifs.jaspar.record method)": [[287, "Bio.motifs.jaspar.Record.to_dict", false]], "to_dict() (in module bio.searchio)": [[217, "Bio.SearchIO.to_dict", false]], "to_dict() (in module bio.seqio)": [[238, "Bio.SeqIO.to_dict", false]], "to_generic() (bio.blast.ncbixml.multiplealignment method)": [[71, "Bio.Blast.NCBIXML.MultipleAlignment.to_generic", false]], "to_hex() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.to_hex", false]], "to_phylogeny() (bio.phylo.phyloxml.clade method)": [[197, "Bio.Phylo.PhyloXML.Clade.to_phylogeny", false]], "to_phyloxml_container() (bio.phylo.phyloxml.phylogeny method)": [[197, "Bio.Phylo.PhyloXML.Phylogeny.to_phyloxml_container", false]], "to_rgb() (bio.phylo.basetree.branchcolor method)": [[183, "Bio.Phylo.BaseTree.BranchColor.to_rgb", false]], "to_seqfeature() (bio.phylo.phyloxml.proteindomain method)": [[197, "Bio.Phylo.PhyloXML.ProteinDomain.to_seqfeature", false]], "to_seqrecord() (bio.phylo.phyloxml.sequence method)": [[197, "Bio.Phylo.PhyloXML.Sequence.to_seqrecord", false]], "to_string() (bio.graphics.genomediagram.featureset method)": [[104, "Bio.Graphics.GenomeDiagram.FeatureSet.to_string", false]], "to_string() (bio.graphics.genomediagram.graphset method)": [[104, "Bio.Graphics.GenomeDiagram.GraphSet.to_string", false]], "to_string() (bio.graphics.genomediagram.track method)": [[104, "Bio.Graphics.GenomeDiagram.Track.to_string", false]], "to_string() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.to_string", false]], "to_strings() (bio.phylo.newickio.writer method)": [[190, "Bio.Phylo.NewickIO.Writer.to_strings", false]], "toclarecord() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.toClaRecord", false]], "todesrecord() (bio.scop.domain method)": [[209, "Bio.SCOP.Domain.toDesRecord", false]], "todesrecord() (bio.scop.node method)": [[209, "Bio.SCOP.Node.toDesRecord", false]], "tohierecord() (bio.scop.node method)": [[209, "Bio.SCOP.Node.toHieRecord", false]], "tomultipleseqalignment() (bio.codonalign.codonalignment.codonalignment method)": [[280, "Bio.codonalign.codonalignment.CodonAlignment.toMultipleSeqAlignment", false]], "top (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.top", false]], "topdiags (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.topdiags", false]], "topm (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.topm", false]], "toseq() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.toSeq", false]], "tossgaps (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.tossgaps", false]], "total_branch_length() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.total_branch_length", false]], "trace() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.trace", false]], "trace() (bio.phylo.basetree.treemixin method)": [[183, "Bio.Phylo.BaseTree.TreeMixin.trace", false]], "track (class in bio.graphics.genomediagram)": [[104, "Bio.Graphics.GenomeDiagram.Track", false]], "train (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.train", false]], "train() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.train", false]], "train() (bio.hmm.trainer.knownstatetrainer method)": [[109, "Bio.HMM.Trainer.KnownStateTrainer.train", false]], "train() (in module bio.knn)": [[282, "Bio.kNN.train", false]], "train() (in module bio.logisticregression)": [[120, "Bio.LogisticRegression.train", false]], "train() (in module bio.maxentropy)": [[122, "Bio.MaxEntropy.train", false]], "train() (in module bio.naivebayes)": [[127, "Bio.NaiveBayes.train", false]], "train_bw() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.train_bw", false]], "train_visible() (in module bio.markovmodel)": [[121, "Bio.MarkovModel.train_visible", false]], "trainingsequence (class in bio.hmm.trainer)": [[109, "Bio.HMM.Trainer.TrainingSequence", false]], "tranaligncommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.TranalignCommandline", false]], "transcribe() (in module bio.seq)": [[236, "Bio.Seq.transcribe", false]], "transform() (bio.pdb.atom.atom method)": [[135, "Bio.PDB.Atom.Atom.transform", false]], "transform() (bio.pdb.atom.disorderedatom method)": [[135, "Bio.PDB.Atom.DisorderedAtom.transform", false]], "transform() (bio.pdb.entity.entity method)": [[139, "Bio.PDB.Entity.Entity.transform", false]], "transformation() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.transformation", false]], "transitions_from() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_from", false]], "transitions_to() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_to", false]], "translate (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.translate", false]], "translate() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.translate", false]], "translate() (bio.graphics.genomediagram.colortranslator method)": [[104, "Bio.Graphics.GenomeDiagram.ColorTranslator.translate", false]], "translate() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.translate", false]], "translate() (bio.seqfeature.seqfeature method)": [[237, "Bio.SeqFeature.SeqFeature.translate", false]], "translate() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.translate", false]], "translate() (in module bio.seq)": [[236, "Bio.Seq.translate", false]], "translationerror": [[76, "Bio.Data.CodonTable.TranslationError", false]], "transpose() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.transpose", false]], "transversion (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.transversion", false]], "transweight (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.transweight", false]], "tree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.tree", false]], "tree (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.tree", false]], "tree (class in bio.cluster)": [[73, "Bio.Cluster.Tree", false]], "tree (class in bio.nexus.trees)": [[132, "Bio.Nexus.Trees.Tree", false]], "tree (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.Tree", false]], "tree (class in bio.phylo.cdao)": [[184, "Bio.Phylo.CDAO.Tree", false]], "tree (class in bio.phylo.newick)": [[189, "Bio.Phylo.Newick.Tree", false]], "tree (class in bio.phylo.nexml)": [[187, "Bio.Phylo.NeXML.Tree", false]], "tree1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.tree1", false]], "tree2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.tree2", false]], "treecluster() (bio.cluster.record method)": [[73, "Bio.Cluster.Record.treecluster", false]], "treecluster() (in module bio.cluster)": [[73, "Bio.Cluster.treecluster", false]], "treeconstructor (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.TreeConstructor", false]], "treeelement (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.TreeElement", false]], "treeerror": [[132, "Bio.Nexus.Trees.TreeError", false]], "treemixin (class in bio.phylo.basetree)": [[183, "Bio.Phylo.BaseTree.TreeMixin", false]], "treeout (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.treeout", false]], "treeprint (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.treeprint", false]], "treesearcher (class in bio.phylo.treeconstruction)": [[199, "Bio.Phylo.TreeConstruction.TreeSearcher", false]], "treetype (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.treetype", false]], "trimming (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.trimming", false]], "trout (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.trout", false]], "trout (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.trout", false]], "trout (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.trout", false]], "trout (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.trout", false]], "truncate (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.truncate", false]], "ts_tv_ratio (bio.phylo.applications.phymlcommandline property)": [[182, "Bio.Phylo.Applications.PhymlCommandline.ts_tv_ratio", false]], "ttratio (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.ttratio", false]], "ttratio (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.ttratio", false]], "twice (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.twice", false]], "twobititerator (class in bio.seqio.twobitio)": [[257, "Bio.SeqIO.TwoBitIO.TwoBitIterator", false]], "type (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.type", false]], "type (bio.align.applications.tcoffeecommandline property)": [[32, "Bio.Align.Applications.TCoffeeCommandline.type", false]], "type() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.type", false]], "types (bio.phylo.phyloxml.sequence attribute)": [[197, "Bio.Phylo.PhyloXML.Sequence.types", false]], "u (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.U", false]], "u (bio.sequencing.applications.samtoolscalmdcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsCalmdCommandline.u", false]], "u (bio.sequencing.applications.samtoolsmergecommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMergeCommandline.u", false]], "u (bio.sequencing.applications.samtoolsmpileupcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsMpileupCommandline.u", false]], "u (bio.sequencing.applications.samtoolsviewcommandline property)": [[270, "Bio.Sequencing.Applications.SamtoolsViewCommandline.u", false]], "uncertainposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.UncertainPosition", false]], "unconverted (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.unconverted", false]], "undefinedsequenceerror": [[236, "Bio.Seq.UndefinedSequenceError", false]], "unfold_entities() (in module bio.pdb.selection)": [[159, "Bio.PDB.Selection.unfold_entities", false]], "ungap() (bio.codonalign.codonseq.codonseq method)": [[281, "Bio.codonalign.codonseq.CodonSeq.ungap", false]], "ungapped (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.ungapped", false]], "ungapped (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.ungapped", false]], "uniform (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.uniform", false]], "uniprotiterator() (in module bio.seqio.uniprotio)": [[258, "Bio.SeqIO.UniprotIO.UniprotIterator", false]], "uniqueify() (in module bio.pdb.selection)": [[159, "Bio.PDB.Selection.uniqueify", false]], "unknownposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.UnknownPosition", false]], "unlink() (bio.nexus.nodes.chain method)": [[130, "Bio.Nexus.Nodes.Chain.unlink", false]], "unroot() (bio.nexus.trees.tree method)": [[132, "Bio.Nexus.Trees.Tree.unroot", false]], "update() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.update", false]], "update_dcoordspace() (bio.pdb.internal_coords.ic_chain method)": [[169, "Bio.PDB.internal_coords.IC_Chain.update_dCoordSpace", false]], "update_emissions() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.update_emissions", false]], "update_pdb() (bio.pdb.pdblist.pdblist method)": [[149, "Bio.PDB.PDBList.PDBList.update_pdb", false]], "update_transitions() (bio.hmm.trainer.baumwelchtrainer method)": [[109, "Bio.HMM.Trainer.BaumWelchTrainer.update_transitions", false]], "upgma() (bio.phylo.treeconstruction.distancetreeconstructor method)": [[199, "Bio.Phylo.TreeConstruction.DistanceTreeConstructor.upgma", false]], "upper() (bio.seq.sequencedataabstractbaseclass method)": [[236, "Bio.Seq.SequenceDataAbstractBaseClass.upper", false]], "upper() (bio.seqrecord.seqrecord method)": [[260, "Bio.SeqRecord.SeqRecord.upper", false]], "uri (class in bio.phylo.phyloxml)": [[197, "Bio.Phylo.PhyloXML.Uri", false]], "uri() (bio.phylo.phyloxmlio.parser method)": [[198, "Bio.Phylo.PhyloXMLIO.Parser.uri", false]], "uri() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.uri", false]], "use_index (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.use_index", false]], "use_sw_tback (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.use_sw_tback", false]], "use_sw_tback (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.use_sw_tback", false]], "usekimura (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.usekimura", false]], "uselogs (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.uselogs", false]], "usetree (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.usetree", false]], "usetree (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.usetree", false]], "usetree1 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.usetree1", false]], "usetree2 (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.usetree2", false]], "v (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.v", false]], "v_final (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.v_final", false]], "v_init (bio.graphics.colorspiral.colorspiral property)": [[100, "Bio.Graphics.ColorSpiral.ColorSpiral.v_init", false]], "validationerror": [[84, "Bio.Entrez.Parser.ValidationError", false]], "value (bio.align.stockholm.alignmentiterator attribute)": [[53, "Bio.Align.stockholm.AlignmentIterator.value", false]], "value (bio.phylo.phyloxml.confidence property)": [[197, "Bio.Phylo.PhyloXML.Confidence.value", false]], "value() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.value", false]], "values() (bio.align.substitution_matrices.array method)": [[54, "Bio.Align.substitution_matrices.Array.values", false]], "values() (bio.phylo.phyloxml.events method)": [[197, "Bio.Phylo.PhyloXML.Events.values", false]], "values() (biosql.bioseqdatabase.bioseqdatabase method)": [[303, "BioSQL.BioSeqDatabase.BioSeqDatabase.values", false]], "values() (biosql.bioseqdatabase.dbserver method)": [[303, "BioSQL.BioSeqDatabase.DBServer.values", false]], "variation (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.variation", false]], "vector (class in bio.pdb.vectors)": [[176, "Bio.PDB.vectors.Vector", false]], "vector_to_axis() (in module bio.pdb.vectors)": [[176, "Bio.PDB.vectors.vector_to_axis", false]], "verbose (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.verbose", false]], "verbose (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.verbose", false]], "verbose (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.verbose", false]], "verbose (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.verbose", false]], "verbose (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.verbose", false]], "verbose (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.verbose", false]], "verbose (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.verbose", false]], "verbose (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.verbose", false]], "verbose (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.verbose", false]], "verbose (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.verbose", false]], "verbose (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.verbose", false]], "verbose (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.verbose", false]], "verbose (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.verbose", false]], "verbose (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.verbose", false]], "verbose (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.verbose", false]], "verbose (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.verbose", false]], "verbose (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.verbose", false]], "verbose (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.verbose", false]], "verbose (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.verbose", false]], "verbose (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.verbose", false]], "verbose (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.verbose", false]], "verbose (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.verbose", false]], "verbose (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.verbose", false]], "verbose (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.verbose", false]], "verbose (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.verbose", false]], "verbose (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.verbose", false]], "verbose (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.verbose", false]], "verbose (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.verbose", false]], "verbose (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.verbose", false]], "version (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.version", false]], "version (bio.align.applications.msaprobscommandline property)": [[32, "Bio.Align.Applications.MSAProbsCommandline.version", false]], "version (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.version", false]], "version (bio.blast.applications.ncbiblastformattercommandline property)": [[69, "Bio.Blast.Applications.NcbiblastformatterCommandline.version", false]], "version (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.version", false]], "version (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.version", false]], "version (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.version", false]], "version (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.version", false]], "version (bio.blast.applications.ncbimakeblastdbcommandline property)": [[69, "Bio.Blast.Applications.NcbimakeblastdbCommandline.version", false]], "version (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.version", false]], "version (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.version", false]], "version (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.version", false]], "version (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.version", false]], "version (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.version", false]], "version (bio.motifs.jaspar.motif property)": [[287, "Bio.motifs.jaspar.Motif.version", false]], "version (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.version", false]], "version() (in module bio.pdb.dssp)": [[137, "Bio.PDB.DSSP.version", false]], "viterbi (bio.align.applications.probconscommandline property)": [[32, "Bio.Align.Applications.ProbconsCommandline.viterbi", false]], "viterbi() (bio.hmm.markovmodel.hiddenmarkovmodel method)": [[108, "Bio.HMM.MarkovModel.HiddenMarkovModel.viterbi", false]], "w (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.w", false]], "w (bio.sequencing.applications.bwamemcommandline property)": [[270, "Bio.Sequencing.Applications.BwaMemCommandline.w", false]], "wa (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.wa", false]], "wag (bio.phylo.applications.fasttreecommandline property)": [[182, "Bio.Phylo.Applications.FastTreeCommandline.wag", false]], "warning (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.warning", false]], "warning (bio.emboss.applications.einvertedcommandline property)": [[80, "Bio.Emboss.Applications.EInvertedCommandline.warning", false]], "warning (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.warning", false]], "warning (bio.emboss.applications.etandemcommandline property)": [[80, "Bio.Emboss.Applications.ETandemCommandline.warning", false]], "warning (bio.emboss.applications.fconsensecommandline property)": [[80, "Bio.Emboss.Applications.FConsenseCommandline.warning", false]], "warning (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.warning", false]], "warning (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.warning", false]], "warning (bio.emboss.applications.fneighborcommandline property)": [[80, "Bio.Emboss.Applications.FNeighborCommandline.warning", false]], "warning (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.warning", false]], "warning (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.warning", false]], "warning (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.warning", false]], "warning (bio.emboss.applications.ftreedistcommandline property)": [[80, "Bio.Emboss.Applications.FTreeDistCommandline.warning", false]], "warning (bio.emboss.applications.fuzznuccommandline property)": [[80, "Bio.Emboss.Applications.FuzznucCommandline.warning", false]], "warning (bio.emboss.applications.fuzzprocommandline property)": [[80, "Bio.Emboss.Applications.FuzzproCommandline.warning", false]], "warning (bio.emboss.applications.iepcommandline property)": [[80, "Bio.Emboss.Applications.IepCommandline.warning", false]], "warning (bio.emboss.applications.needleallcommandline property)": [[80, "Bio.Emboss.Applications.NeedleallCommandline.warning", false]], "warning (bio.emboss.applications.needlecommandline property)": [[80, "Bio.Emboss.Applications.NeedleCommandline.warning", false]], "warning (bio.emboss.applications.palindromecommandline property)": [[80, "Bio.Emboss.Applications.PalindromeCommandline.warning", false]], "warning (bio.emboss.applications.primer3commandline property)": [[80, "Bio.Emboss.Applications.Primer3Commandline.warning", false]], "warning (bio.emboss.applications.primersearchcommandline property)": [[80, "Bio.Emboss.Applications.PrimerSearchCommandline.warning", false]], "warning (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.warning", false]], "warning (bio.emboss.applications.seqretcommandline property)": [[80, "Bio.Emboss.Applications.SeqretCommandline.warning", false]], "warning (bio.emboss.applications.stretchercommandline property)": [[80, "Bio.Emboss.Applications.StretcherCommandline.warning", false]], "warning (bio.emboss.applications.tranaligncommandline property)": [[80, "Bio.Emboss.Applications.TranalignCommandline.warning", false]], "warning (bio.emboss.applications.watercommandline property)": [[80, "Bio.Emboss.Applications.WaterCommandline.warning", false]], "watercommandline (class in bio.emboss.applications)": [[80, "Bio.Emboss.Applications.WaterCommandline", false]], "weblogo() (bio.motifs.motif method)": [[283, "Bio.motifs.Motif.weblogo", false]], "weight1 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.weight1", false]], "weight2 (bio.align.applications.musclecommandline property)": [[32, "Bio.Align.Applications.MuscleCommandline.weight2", false]], "weight_filename (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.weight_filename", false]], "weighted_stepmatrix() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.weighted_stepmatrix", false]], "weighti (bio.align.applications.mafftcommandline property)": [[32, "Bio.Align.Applications.MafftCommandline.weighti", false]], "weighting() (bio.nexus.nexus.stepmatrix method)": [[129, "Bio.Nexus.Nexus.StepMatrix.weighting", false]], "weights (bio.emboss.applications.fdnadistcommandline property)": [[80, "Bio.Emboss.Applications.FDNADistCommandline.weights", false]], "weights (bio.emboss.applications.fdnaparscommandline property)": [[80, "Bio.Emboss.Applications.FDNAParsCommandline.weights", false]], "weights (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.weights", false]], "weights (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.weights", false]], "weights (bio.emboss.applications.fseqbootcommandline property)": [[80, "Bio.Emboss.Applications.FSeqBootCommandline.weights", false]], "wellrecord (class in bio.phenotype.phen_micro)": [[299, "Bio.phenotype.phen_micro.WellRecord", false]], "whichcode (bio.emboss.applications.fprotdistcommandline property)": [[80, "Bio.Emboss.Applications.FProtDistCommandline.whichcode", false]], "whichcode (bio.emboss.applications.fprotparscommandline property)": [[80, "Bio.Emboss.Applications.FProtParsCommandline.whichcode", false]], "width (bio.emboss.applications.est2genomecommandline property)": [[80, "Bio.Emboss.Applications.Est2GenomeCommandline.width", false]], "width (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.width", false]], "width() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.width", false]], "window (bio.align.applications.clustalwcommandline property)": [[32, "Bio.Align.Applications.ClustalwCommandline.window", false]], "window_masker_db (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.window_masker_db", false]], "window_masker_taxid (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.window_masker_taxid", false]], "window_size (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.window_size", false]], "window_size (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.window_size", false]], "window_size (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.window_size", false]], "window_size (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.window_size", false]], "window_size (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.window_size", false]], "window_size (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.window_size", false]], "window_size (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.window_size", false]], "window_size (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.window_size", false]], "window_size (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.window_size", false]], "withinposition (class in bio.seqfeature)": [[237, "Bio.SeqFeature.WithinPosition", false]], "word_size (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.word_size", false]], "word_size (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.word_size", false]], "word_size (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.word_size", false]], "word_size (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.word_size", false]], "word_size (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.word_size", false]], "word_size (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.word_size", false]], "word_size (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.word_size", false]], "word_size (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.word_size", false]], "word_size (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.word_size", false]], "wordsize (bio.emboss.applications.diffseqcommandline property)": [[80, "Bio.Emboss.Applications.DiffseqCommandline.wordsize", false]], "wordsize (bio.emboss.applications.seqmatchallcommandline property)": [[80, "Bio.Emboss.Applications.SeqmatchallCommandline.wordsize", false]], "working_dir (bio.phylo.applications.raxmlcommandline property)": [[182, "Bio.Phylo.Applications.RaxmlCommandline.working_dir", false]], "wr (class in bio.sequencing.ace)": [[269, "Bio.Sequencing.Ace.wr", false]], "wrap (bio.align.applications.clustalomegacommandline property)": [[32, "Bio.Align.Applications.ClustalOmegaCommandline.wrap", false]], "write() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write", false]], "write() (bio.bgzf.bgzfwriter method)": [[278, "Bio.bgzf.BgzfWriter.write", false]], "write() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.write", false]], "write() (bio.phenotype.phen_micro.jsonwriter method)": [[299, "Bio.phenotype.phen_micro.JsonWriter.write", false]], "write() (bio.phylo.cdaoio.writer method)": [[185, "Bio.Phylo.CDAOIO.Writer.write", false]], "write() (bio.phylo.newickio.writer method)": [[190, "Bio.Phylo.NewickIO.Writer.write", false]], "write() (bio.phylo.nexmlio.writer method)": [[188, "Bio.Phylo.NeXMLIO.Writer.write", false]], "write() (bio.phylo.phyloxmlio.writer method)": [[198, "Bio.Phylo.PhyloXMLIO.Writer.write", false]], "write() (in module bio.align)": [[30, "Bio.Align.write", false]], "write() (in module bio.alignio)": [[56, "Bio.AlignIO.write", false]], "write() (in module bio.blast)": [[68, "Bio.Blast.write", false]], "write() (in module bio.motifs)": [[283, "Bio.motifs.write", false]], "write() (in module bio.motifs.clusterbuster)": [[286, "Bio.motifs.clusterbuster.write", false]], "write() (in module bio.motifs.jaspar)": [[287, "Bio.motifs.jaspar.write", false]], "write() (in module bio.motifs.pfm)": [[293, "Bio.motifs.pfm.write", false]], "write() (in module bio.motifs.transfac)": [[295, "Bio.motifs.transfac.write", false]], "write() (in module bio.phenotype)": [[298, "Bio.phenotype.write", false]], "write() (in module bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.write", false]], "write() (in module bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.write", false]], "write() (in module bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.write", false]], "write() (in module bio.phylo.nexusio)": [[191, "Bio.Phylo.NexusIO.write", false]], "write() (in module bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.write", false]], "write() (in module bio.searchio)": [[217, "Bio.SearchIO.write", false]], "write() (in module bio.seqio)": [[238, "Bio.SeqIO.write", false]], "write_alignment() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.write_alignment", false]], "write_alignment() (bio.alignio.clustalio.clustalwriter method)": [[57, "Bio.AlignIO.ClustalIO.ClustalWriter.write_alignment", false]], "write_alignment() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_alignment", false]], "write_alignment() (bio.alignio.mafio.mafwriter method)": [[61, "Bio.AlignIO.MafIO.MafWriter.write_alignment", false]], "write_alignment() (bio.alignio.mauveio.mauvewriter method)": [[62, "Bio.AlignIO.MauveIO.MauveWriter.write_alignment", false]], "write_alignment() (bio.alignio.nexusio.nexuswriter method)": [[64, "Bio.AlignIO.NexusIO.NexusWriter.write_alignment", false]], "write_alignment() (bio.alignio.phylipio.phylipwriter method)": [[65, "Bio.AlignIO.PhylipIO.PhylipWriter.write_alignment", false]], "write_alignment() (bio.alignio.phylipio.relaxedphylipwriter method)": [[65, "Bio.AlignIO.PhylipIO.RelaxedPhylipWriter.write_alignment", false]], "write_alignment() (bio.alignio.phylipio.sequentialphylipwriter method)": [[65, "Bio.AlignIO.PhylipIO.SequentialPhylipWriter.write_alignment", false]], "write_alignment() (bio.alignio.stockholmio.stockholmwriter method)": [[66, "Bio.AlignIO.StockholmIO.StockholmWriter.write_alignment", false]], "write_alignments() (bio.align.a2m.alignmentwriter method)": [[33, "Bio.Align.a2m.AlignmentWriter.write_alignments", false]], "write_alignments() (bio.align.bigbed.alignmentwriter method)": [[36, "Bio.Align.bigbed.AlignmentWriter.write_alignments", false]], "write_alignments() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_alignments", false]], "write_alignments() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.write_alignments", false]], "write_cal (bio.sequencing.applications.novoaligncommandline property)": [[270, "Bio.Sequencing.Applications.NovoalignCommandline.write_cal", false]], "write_cla() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_cla", false]], "write_cla_sql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_cla_sql", false]], "write_ctl_file() (bio.phylo.paml.baseml.baseml method)": [[193, "Bio.Phylo.PAML.baseml.Baseml.write_ctl_file", false]], "write_ctl_file() (bio.phylo.paml.codeml.codeml method)": [[195, "Bio.Phylo.PAML.codeml.Codeml.write_ctl_file", false]], "write_ctl_file() (bio.phylo.paml.yn00.yn00 method)": [[196, "Bio.Phylo.PAML.yn00.Yn00.write_ctl_file", false]], "write_des() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_des", false]], "write_des_sql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_des_sql", false]], "write_file() (bio.align.bigbed.alignmentwriter method)": [[36, "Bio.Align.bigbed.AlignmentWriter.write_file", false]], "write_file() (bio.align.bigmaf.alignmentwriter method)": [[37, "Bio.Align.bigmaf.AlignmentWriter.write_file", false]], "write_file() (bio.align.bigpsl.alignmentwriter method)": [[38, "Bio.Align.bigpsl.AlignmentWriter.write_file", false]], "write_file() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_file", false]], "write_file() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.write_file", false]], "write_file() (bio.align.nexus.alignmentwriter method)": [[49, "Bio.Align.nexus.AlignmentWriter.write_file", false]], "write_file() (bio.alignio.interfaces.alignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.AlignmentWriter.write_file", false]], "write_file() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_file", false]], "write_file() (bio.alignio.nexusio.nexuswriter method)": [[64, "Bio.AlignIO.NexusIO.NexusWriter.write_file", false]], "write_file() (bio.searchio.blastio.blast_tab.blasttabwriter method)": [[219, "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter.write_file", false]], "write_file() (bio.searchio.blastio.blast_xml.blastxmlwriter method)": [[220, "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter.write_file", false]], "write_file() (bio.searchio.blatio.blatpslwriter method)": [[221, "Bio.SearchIO.BlatIO.BlatPslWriter.write_file", false]], "write_file() (bio.searchio.hmmerio.hmmer3_domtab.hmmer3domtabhmmhitwriter method)": [[231, "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter.write_file", false]], "write_file() (bio.searchio.hmmerio.hmmer3_tab.hmmer3tabwriter method)": [[232, "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter.write_file", false]], "write_file() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_file", false]], "write_file() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.write_file", false]], "write_file() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.write_file", false]], "write_file() (bio.seqio.xdnaio.xdnawriter method)": [[259, "Bio.SeqIO.XdnaIO.XdnaWriter.write_file", false]], "write_footer() (bio.align.exonerate.alignmentwriter method)": [[42, "Bio.Align.exonerate.AlignmentWriter.write_footer", false]], "write_footer() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_footer", false]], "write_footer() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_footer", false]], "write_footer() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_footer", false]], "write_footer() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_footer", false]], "write_header() (bio.align.clustal.alignmentwriter method)": [[40, "Bio.Align.clustal.AlignmentWriter.write_header", false]], "write_header() (bio.align.exonerate.alignmentwriter method)": [[42, "Bio.Align.exonerate.AlignmentWriter.write_header", false]], "write_header() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_header", false]], "write_header() (bio.align.maf.alignmentwriter method)": [[46, "Bio.Align.maf.AlignmentWriter.write_header", false]], "write_header() (bio.align.mauve.alignmentwriter method)": [[47, "Bio.Align.mauve.AlignmentWriter.write_header", false]], "write_header() (bio.align.psl.alignmentwriter method)": [[51, "Bio.Align.psl.AlignmentWriter.write_header", false]], "write_header() (bio.align.sam.alignmentwriter method)": [[52, "Bio.Align.sam.AlignmentWriter.write_header", false]], "write_header() (bio.alignio.interfaces.sequentialalignmentwriter method)": [[60, "Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_header", false]], "write_header() (bio.alignio.mafio.mafwriter method)": [[61, "Bio.AlignIO.MafIO.MafWriter.write_header", false]], "write_header() (bio.nmr.xpktools.peaklist method)": [[126, "Bio.NMR.xpktools.Peaklist.write_header", false]], "write_header() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_header", false]], "write_header() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.write_header", false]], "write_header() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_header", false]], "write_header() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.write_header", false]], "write_hie() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_hie", false]], "write_hie_sql() (bio.scop.scop method)": [[209, "Bio.SCOP.Scop.write_hie_sql", false]], "write_multiple_alignments() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_multiple_alignments", false]], "write_nexus_data() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.write_nexus_data", false]], "write_nexus_data_partitions() (bio.nexus.nexus.nexus method)": [[129, "Bio.Nexus.Nexus.Nexus.write_nexus_data_partitions", false]], "write_pdb() (in module bio.pdb.ic_rebuild)": [[168, "Bio.PDB.ic_rebuild.write_PDB", false]], "write_pic() (in module bio.pdb.picio)": [[152, "Bio.PDB.PICIO.write_PIC", false]], "write_record() (bio.seqio.fastaio.fastawriter method)": [[241, "Bio.SeqIO.FastaIO.FastaWriter.write_record", false]], "write_record() (bio.seqio.insdcio.emblwriter method)": [[245, "Bio.SeqIO.InsdcIO.EmblWriter.write_record", false]], "write_record() (bio.seqio.insdcio.genbankwriter method)": [[245, "Bio.SeqIO.InsdcIO.GenBankWriter.write_record", false]], "write_record() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_record", false]], "write_record() (bio.seqio.nibio.nibwriter method)": [[247, "Bio.SeqIO.NibIO.NibWriter.write_record", false]], "write_record() (bio.seqio.phdio.phdwriter method)": [[249, "Bio.SeqIO.PhdIO.PhdWriter.write_record", false]], "write_record() (bio.seqio.pirio.pirwriter method)": [[250, "Bio.SeqIO.PirIO.PirWriter.write_record", false]], "write_record() (bio.seqio.qualityio.fastqilluminawriter method)": [[251, "Bio.SeqIO.QualityIO.FastqIlluminaWriter.write_record", false]], "write_record() (bio.seqio.qualityio.fastqphredwriter method)": [[251, "Bio.SeqIO.QualityIO.FastqPhredWriter.write_record", false]], "write_record() (bio.seqio.qualityio.fastqsolexawriter method)": [[251, "Bio.SeqIO.QualityIO.FastqSolexaWriter.write_record", false]], "write_record() (bio.seqio.qualityio.qualphredwriter method)": [[251, "Bio.SeqIO.QualityIO.QualPhredWriter.write_record", false]], "write_record() (bio.seqio.seqxmlio.seqxmlwriter method)": [[252, "Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_record", false]], "write_record() (bio.seqio.sffio.sffwriter method)": [[253, "Bio.SeqIO.SffIO.SffWriter.write_record", false]], "write_record() (bio.seqio.tabio.tabwriter method)": [[256, "Bio.SeqIO.TabIO.TabWriter.write_record", false]], "write_records() (bio.seqio.interfaces.sequencewriter method)": [[246, "Bio.SeqIO.Interfaces.SequenceWriter.write_records", false]], "write_scad() (in module bio.pdb.scadio)": [[158, "Bio.PDB.SCADIO.write_SCAD", false]], "write_single_alignment() (bio.align.interfaces.alignmentwriter method)": [[45, "Bio.Align.interfaces.AlignmentWriter.write_single_alignment", false]], "write_to_string() (bio.graphics.genomediagram.diagram method)": [[104, "Bio.Graphics.GenomeDiagram.Diagram.write_to_string", false]], "writeanc (bio.align.applications.prankcommandline property)": [[32, "Bio.Align.Applications.PrankCommandline.writeanc", false]], "writebyproteinrec() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.writebyproteinrec", false]], "writer (class in bio.phylo.cdaoio)": [[185, "Bio.Phylo.CDAOIO.Writer", false]], "writer (class in bio.phylo.newickio)": [[190, "Bio.Phylo.NewickIO.Writer", false]], "writer (class in bio.phylo.nexmlio)": [[188, "Bio.Phylo.NeXMLIO.Writer", false]], "writer (class in bio.phylo.phyloxmlio)": [[198, "Bio.Phylo.PhyloXMLIO.Writer", false]], "writerec() (in module bio.uniprot.goa)": [[277, "Bio.UniProt.GOA.writerec", false]], "writetosql() (bio.scop.astral method)": [[209, "Bio.SCOP.Astral.writeToSQL", false]], "x (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.x", false]], "xdnaiterator (class in bio.seqio.xdnaio)": [[259, "Bio.SeqIO.XdnaIO.XdnaIterator", false]], "xdnawriter (class in bio.seqio.xdnaio)": [[259, "Bio.SeqIO.XdnaIO.XdnaWriter", false]], "xdrop_gap (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.xdrop_gap", false]], "xdrop_gap (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.xdrop_gap", false]], "xdrop_gap_final (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.xdrop_gap_final", false]], "xdrop_gap_final (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.xdrop_gap_final", false]], "xdrop_ungap (bio.blast.applications.ncbiblastncommandline property)": [[69, "Bio.Blast.Applications.NcbiblastnCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbiblastpcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastpCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbiblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbiblastxCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbideltablastcommandline property)": [[69, "Bio.Blast.Applications.NcbideltablastCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbipsiblastcommandline property)": [[69, "Bio.Blast.Applications.NcbipsiblastCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbirpsblastcommandline property)": [[69, "Bio.Blast.Applications.NcbirpsblastCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbirpstblastncommandline property)": [[69, "Bio.Blast.Applications.NcbirpstblastnCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbitblastncommandline property)": [[69, "Bio.Blast.Applications.NcbitblastnCommandline.xdrop_ungap", false]], "xdrop_ungap (bio.blast.applications.ncbitblastxcommandline property)": [[69, "Bio.Blast.Applications.NcbitblastxCommandline.xdrop_ungap", false]], "xfr (bio.align.applications.dialigncommandline property)": [[32, "Bio.Align.Applications.DialignCommandline.xfr", false]], "xgc_skew() (in module bio.sequtils)": [[261, "Bio.SeqUtils.xGC_skew", false]], "xmldeclhandler() (bio.entrez.parser.datahandler method)": [[84, "Bio.Entrez.Parser.DataHandler.xmlDeclHandler", false]], "xmsscanner (class in bio.motifs.xms)": [[296, "Bio.motifs.xms.XMSScanner", false]], "xpkentry (class in bio.nmr.xpktools)": [[126, "Bio.NMR.xpktools.XpkEntry", false]], "y (bio.kegg.kgml.kgml_pathway.graphics property)": [[117, "Bio.KEGG.KGML.KGML_pathway.Graphics.y", false]], "yn00 (class in bio.phylo.paml.yn00)": [[196, "Bio.Phylo.PAML.yn00.Yn00", false]], "yn00error": [[196, "Bio.Phylo.PAML.yn00.Yn00Error", false]], "z (bio.sequencing.applications.bwabwaswcommandline property)": [[270, "Bio.Sequencing.Applications.BwaBwaswCommandline.z", false]]}, "objects": {"": [[27, 0, 0, "-", "Bio"], [301, 0, 0, "-", "BioSQL"]], "Bio": [[28, 0, 0, "-", "Affy"], [30, 0, 0, "-", "Align"], [56, 0, 0, "-", "AlignIO"], [67, 0, 0, "-", "Application"], [27, 1, 1, "", "BiopythonDeprecationWarning"], [27, 1, 1, "", "BiopythonExperimentalWarning"], [27, 1, 1, "", "BiopythonParserWarning"], [27, 1, 1, "", "BiopythonWarning"], [68, 0, 0, "-", "Blast"], [72, 0, 0, "-", "CAPS"], [73, 0, 0, "-", "Cluster"], [74, 0, 0, "-", "Compass"], [75, 0, 0, "-", "Data"], [79, 0, 0, "-", "Emboss"], [83, 0, 0, "-", "Entrez"], [85, 0, 0, "-", "ExPASy"], [91, 0, 0, "-", "File"], [92, 0, 0, "-", "GenBank"], [96, 0, 0, "-", "Geo"], [98, 0, 0, "-", "Graphics"], [106, 0, 0, "-", "HMM"], [111, 0, 0, "-", "KEGG"], [120, 0, 0, "-", "LogisticRegression"], [121, 0, 0, "-", "MarkovModel"], [122, 0, 0, "-", "MaxEntropy"], [123, 0, 0, "-", "Medline"], [27, 1, 1, "", "MissingExternalDependencyError"], [27, 1, 1, "", "MissingPythonDependencyError"], [124, 0, 0, "-", "NMR"], [127, 0, 0, "-", "NaiveBayes"], [128, 0, 0, "-", "Nexus"], [133, 0, 0, "-", "PDB"], [177, 0, 0, "-", "Pathway"], [181, 0, 0, "-", "Phylo"], [200, 0, 0, "-", "PopGen"], [206, 0, 0, "-", "Restriction"], [209, 0, 0, "-", "SCOP"], [216, 0, 0, "-", "SVDSuperimposer"], [217, 0, 0, "-", "SearchIO"], [236, 0, 0, "-", "Seq"], [237, 0, 0, "-", "SeqFeature"], [238, 0, 0, "-", "SeqIO"], [260, 0, 0, "-", "SeqRecord"], [261, 0, 0, "-", "SeqUtils"], [268, 0, 0, "-", "Sequencing"], [27, 1, 1, "", "StreamModeError"], [272, 0, 0, "-", "SwissProt"], [274, 0, 0, "-", "TogoWS"], [275, 0, 0, "-", "UniGene"], [276, 0, 0, "-", "UniProt"], [278, 0, 0, "-", "bgzf"], [279, 0, 0, "-", "codonalign"], [282, 0, 0, "-", "kNN"], [283, 0, 0, "-", "motifs"], [297, 0, 0, "-", "pairwise2"], [298, 0, 0, "-", "phenotype"]], "Bio.Affy": [[29, 0, 0, "-", "CelFile"]], "Bio.Affy.CelFile": [[29, 1, 1, "", "ParserError"], [29, 3, 1, "", "Record"], [29, 4, 1, "", "read"]], "Bio.Affy.CelFile.ParserError": [[29, 2, 1, "", "__init__"]], "Bio.Affy.CelFile.Record": [[29, 2, 1, "", "__init__"]], "Bio.Align": [[31, 0, 0, "-", "AlignInfo"], [30, 3, 1, "", "Alignment"], [30, 3, 1, "", "AlignmentCounts"], [30, 3, 1, "", "Alignments"], [30, 3, 1, "", "AlignmentsAbstractBaseClass"], [32, 0, 0, "-", "Applications"], [30, 3, 1, "", "CodonAligner"], [30, 3, 1, "", "MultipleSeqAlignment"], [30, 3, 1, "", "PairwiseAligner"], [30, 3, 1, "", "PairwiseAlignments"], [33, 0, 0, "-", "a2m"], [34, 0, 0, "-", "analysis"], [35, 0, 0, "-", "bed"], [36, 0, 0, "-", "bigbed"], [37, 0, 0, "-", "bigmaf"], [38, 0, 0, "-", "bigpsl"], [39, 0, 0, "-", "chain"], [40, 0, 0, "-", "clustal"], [41, 0, 0, "-", "emboss"], [42, 0, 0, "-", "exonerate"], [43, 0, 0, "-", "fasta"], [44, 0, 0, "-", "hhr"], [45, 0, 0, "-", "interfaces"], [46, 0, 0, "-", "maf"], [47, 0, 0, "-", "mauve"], [48, 0, 0, "-", "msf"], [49, 0, 0, "-", "nexus"], [30, 4, 1, "", "parse"], [50, 0, 0, "-", "phylip"], [51, 0, 0, "-", "psl"], [30, 4, 1, "", "read"], [52, 0, 0, "-", "sam"], [53, 0, 0, "-", "stockholm"], [54, 0, 0, "-", "substitution_matrices"], [55, 0, 0, "-", "tabular"], [30, 4, 1, "", "write"]], "Bio.Align.AlignInfo": [[31, 3, 1, "", "PSSM"], [31, 3, 1, "", "SummaryInfo"], [31, 4, 1, "", "print_info_content"]], "Bio.Align.AlignInfo.PSSM": [[31, 2, 1, "", "__getitem__"], [31, 2, 1, "", "__init__"], [31, 2, 1, "", "__str__"], [31, 2, 1, "", "get_residue"]], "Bio.Align.AlignInfo.SummaryInfo": [[31, 2, 1, "", "__init__"], [31, 2, 1, "", "dumb_consensus"], [31, 2, 1, "", "gap_consensus"], [31, 2, 1, "", "get_column"], [31, 2, 1, "", "information_content"], [31, 2, 1, "", "pos_specific_score_matrix"], [31, 2, 1, "", "replacement_dictionary"]], "Bio.Align.Alignment": [[30, 2, 1, "", "__add__"], [30, 2, 1, "", "__array__"], [30, 2, 1, "", "__eq__"], [30, 2, 1, "", "__format__"], [30, 2, 1, "", "__ge__"], [30, 2, 1, "", "__getitem__"], [30, 2, 1, "", "__gt__"], [30, 5, 1, "", "__hash__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__le__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__lt__"], [30, 2, 1, "", "__ne__"], [30, 2, 1, "", "__repr__"], [30, 2, 1, "", "__str__"], [30, 6, 1, "", "aligned"], [30, 2, 1, "", "counts"], [30, 2, 1, "", "format"], [30, 6, 1, "", "frequencies"], [30, 6, 1, "", "indices"], [30, 2, 1, "", "infer_coordinates"], [30, 6, 1, "", "inverse_indices"], [30, 6, 1, "", "length"], [30, 2, 1, "", "map"], [30, 2, 1, "", "mapall"], [30, 2, 1, "", "parse_printed_alignment"], [30, 6, 1, "", "query"], [30, 2, 1, "", "reverse_complement"], [30, 6, 1, "", "shape"], [30, 2, 1, "", "sort"], [30, 6, 1, "", "substitutions"], [30, 6, 1, "", "target"]], "Bio.Align.AlignmentCounts": [[30, 2, 1, "", "__getnewargs__"], [30, 2, 1, "", "__new__"], [30, 2, 1, "", "__repr__"], [30, 5, 1, "", "__slots__"], [30, 5, 1, "", "gaps"], [30, 5, 1, "", "identities"], [30, 5, 1, "", "mismatches"]], "Bio.Align.Alignments": [[30, 5, 1, "", "__abstractmethods__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__next__"], [30, 2, 1, "", "rewind"]], "Bio.Align.AlignmentsAbstractBaseClass": [[30, 5, 1, "", "__abstractmethods__"], [30, 2, 1, "", "__iter__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__next__"], [30, 2, 1, "", "rewind"]], "Bio.Align.Applications": [[32, 3, 1, "", "ClustalOmegaCommandline"], [32, 3, 1, "", "ClustalwCommandline"], [32, 3, 1, "", "DialignCommandline"], [32, 3, 1, "", "MSAProbsCommandline"], [32, 3, 1, "", "MafftCommandline"], [32, 3, 1, "", "MuscleCommandline"], [32, 3, 1, "", "PrankCommandline"], [32, 3, 1, "", "ProbconsCommandline"], [32, 3, 1, "", "TCoffeeCommandline"]], "Bio.Align.Applications.ClustalOmegaCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "auto"], [32, 6, 1, "", "clusteringout"], [32, 6, 1, "", "clustersize"], [32, 6, 1, "", "dealign"], [32, 6, 1, "", "distmat_full"], [32, 6, 1, "", "distmat_full_iter"], [32, 6, 1, "", "distmat_in"], [32, 6, 1, "", "distmat_out"], [32, 6, 1, "", "force"], [32, 6, 1, "", "guidetree_in"], [32, 6, 1, "", "guidetree_out"], [32, 6, 1, "", "help"], [32, 6, 1, "", "hmm_input"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "infmt"], [32, 6, 1, "", "isprofile"], [32, 6, 1, "", "iterations"], [32, 6, 1, "", "log"], [32, 6, 1, "", "long_version"], [32, 6, 1, "", "max_guidetree_iterations"], [32, 6, 1, "", "max_hmm_iterations"], [32, 6, 1, "", "maxnumseq"], [32, 6, 1, "", "maxseqlen"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "outfmt"], [32, 6, 1, "", "outputorder"], [32, 6, 1, "", "percentid"], [32, 6, 1, "", "profile1"], [32, 6, 1, "", "profile2"], [32, 6, 1, "", "residuenumber"], [32, 6, 1, "", "seqtype"], [32, 6, 1, "", "threads"], [32, 6, 1, "", "usekimura"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "version"], [32, 6, 1, "", "wrap"]], "Bio.Align.Applications.ClustalwCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "align"], [32, 6, 1, "", "bootlabels"], [32, 6, 1, "", "bootstrap"], [32, 6, 1, "", "case"], [32, 6, 1, "", "check"], [32, 6, 1, "", "clustering"], [32, 6, 1, "", "convert"], [32, 6, 1, "", "dnamatrix"], [32, 6, 1, "", "endgaps"], [32, 6, 1, "", "fullhelp"], [32, 6, 1, "", "gapdist"], [32, 6, 1, "", "gapext"], [32, 6, 1, "", "gapopen"], [32, 6, 1, "", "helixendin"], [32, 6, 1, "", "helixendout"], [32, 6, 1, "", "helixgap"], [32, 6, 1, "", "help"], [32, 6, 1, "", "hgapresidues"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "iteration"], [32, 6, 1, "", "kimura"], [32, 6, 1, "", "ktuple"], [32, 6, 1, "", "loopgap"], [32, 6, 1, "", "matrix"], [32, 6, 1, "", "maxdiv"], [32, 6, 1, "", "maxseqlen"], [32, 6, 1, "", "negative"], [32, 6, 1, "", "newtree"], [32, 6, 1, "", "newtree1"], [32, 6, 1, "", "newtree2"], [32, 6, 1, "", "nohgap"], [32, 6, 1, "", "nopgap"], [32, 6, 1, "", "nosecstr1"], [32, 6, 1, "", "nosecstr2"], [32, 6, 1, "", "noweights"], [32, 6, 1, "", "numiter"], [32, 6, 1, "", "options"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "outorder"], [32, 6, 1, "", "output"], [32, 6, 1, "", "outputtree"], [32, 6, 1, "", "pairgap"], [32, 6, 1, "", "pim"], [32, 6, 1, "", "profile"], [32, 6, 1, "", "profile1"], [32, 6, 1, "", "profile2"], [32, 6, 1, "", "pwdnamatrix"], [32, 6, 1, "", "pwgapext"], [32, 6, 1, "", "pwgapopen"], [32, 6, 1, "", "pwmatrix"], [32, 6, 1, "", "quicktree"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "range"], [32, 6, 1, "", "score"], [32, 6, 1, "", "secstrout"], [32, 6, 1, "", "seed"], [32, 6, 1, "", "seqno_range"], [32, 6, 1, "", "seqnos"], [32, 6, 1, "", "sequences"], [32, 6, 1, "", "stats"], [32, 6, 1, "", "strandendin"], [32, 6, 1, "", "strandendout"], [32, 6, 1, "", "strandgap"], [32, 6, 1, "", "terminalgap"], [32, 6, 1, "", "topdiags"], [32, 6, 1, "", "tossgaps"], [32, 6, 1, "", "transweight"], [32, 6, 1, "", "tree"], [32, 6, 1, "", "type"], [32, 6, 1, "", "usetree"], [32, 6, 1, "", "usetree1"], [32, 6, 1, "", "usetree2"], [32, 6, 1, "", "window"]], "Bio.Align.Applications.DialignCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "afc"], [32, 6, 1, "", "afc_v"], [32, 6, 1, "", "anc"], [32, 6, 1, "", "cs"], [32, 6, 1, "", "cw"], [32, 6, 1, "", "ds"], [32, 6, 1, "", "fa"], [32, 6, 1, "", "ff"], [32, 6, 1, "", "fn"], [32, 6, 1, "", "fop"], [32, 6, 1, "", "fsm"], [32, 6, 1, "", "input"], [32, 6, 1, "", "iw"], [32, 6, 1, "", "lgs"], [32, 6, 1, "", "lgs_t"], [32, 6, 1, "", "lmax"], [32, 6, 1, "", "lo"], [32, 6, 1, "", "ma"], [32, 6, 1, "", "mask"], [32, 6, 1, "", "mat"], [32, 6, 1, "", "mat_thr"], [32, 6, 1, "", "max_link"], [32, 6, 1, "", "min_link"], [32, 6, 1, "", "mot"], [32, 6, 1, "", "msf"], [32, 6, 1, "", "n"], [32, 6, 1, "", "nt"], [32, 6, 1, "", "nta"], [32, 6, 1, "", "o"], [32, 6, 1, "", "ow"], [32, 6, 1, "", "pst"], [32, 6, 1, "", "smin"], [32, 6, 1, "", "stars"], [32, 6, 1, "", "stdo"], [32, 6, 1, "", "ta"], [32, 6, 1, "", "thr"], [32, 6, 1, "", "xfr"]], "Bio.Align.Applications.MSAProbsCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "alignment_order"], [32, 6, 1, "", "annot"], [32, 6, 1, "", "clustalw"], [32, 6, 1, "", "consistency"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "iterative_refinement"], [32, 6, 1, "", "numthreads"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "version"]], "Bio.Align.Applications.MafftCommandline": [[32, 6, 1, "", "LEXP"], [32, 6, 1, "", "LOP"], [32, 2, 1, "", "__init__"], [32, 6, 1, "", "aamatrix"], [32, 6, 1, "", "adjustdirection"], [32, 6, 1, "", "adjustdirectionaccurately"], [32, 6, 1, "", "amino"], [32, 6, 1, "", "auto"], [32, 6, 1, "", "bl"], [32, 6, 1, "", "clustalout"], [32, 6, 1, "", "dpparttree"], [32, 6, 1, "", "ep"], [32, 6, 1, "", "fastapair"], [32, 6, 1, "", "fastaparttree"], [32, 6, 1, "", "fft"], [32, 6, 1, "", "fmodel"], [32, 6, 1, "", "genafpair"], [32, 6, 1, "", "globalpair"], [32, 6, 1, "", "groupsize"], [32, 6, 1, "", "input"], [32, 6, 1, "", "input1"], [32, 6, 1, "", "inputorder"], [32, 6, 1, "", "jtt"], [32, 6, 1, "", "lep"], [32, 6, 1, "", "lexp"], [32, 6, 1, "", "localpair"], [32, 6, 1, "", "lop"], [32, 6, 1, "", "maxiterate"], [32, 6, 1, "", "memsave"], [32, 6, 1, "", "namelength"], [32, 6, 1, "", "nofft"], [32, 6, 1, "", "noscore"], [32, 6, 1, "", "nuc"], [32, 6, 1, "", "op"], [32, 6, 1, "", "partsize"], [32, 6, 1, "", "parttree"], [32, 6, 1, "", "phylipout"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "reorder"], [32, 6, 1, "", "retree"], [32, 6, 1, "", "seed"], [32, 6, 1, "", "sixmerpair"], [32, 6, 1, "", "thread"], [32, 6, 1, "", "tm"], [32, 6, 1, "", "treeout"], [32, 6, 1, "", "weighti"]], "Bio.Align.Applications.MuscleCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "anchors"], [32, 6, 1, "", "anchorspacing"], [32, 6, 1, "", "brenner"], [32, 6, 1, "", "center"], [32, 6, 1, "", "cluster"], [32, 6, 1, "", "cluster1"], [32, 6, 1, "", "cluster2"], [32, 6, 1, "", "clw"], [32, 6, 1, "", "clwout"], [32, 6, 1, "", "clwstrict"], [32, 6, 1, "", "clwstrictout"], [32, 6, 1, "", "core"], [32, 6, 1, "", "diagbreak"], [32, 6, 1, "", "diaglength"], [32, 6, 1, "", "diagmargin"], [32, 6, 1, "", "diags"], [32, 6, 1, "", "dimer"], [32, 6, 1, "", "distance1"], [32, 6, 1, "", "distance2"], [32, 6, 1, "", "fasta"], [32, 6, 1, "", "fastaout"], [32, 6, 1, "", "gapextend"], [32, 6, 1, "", "gapopen"], [32, 6, 1, "", "group"], [32, 6, 1, "", "html"], [32, 6, 1, "", "htmlout"], [32, 6, 1, "", "hydro"], [32, 6, 1, "", "hydrofactor"], [32, 6, 1, "", "in1"], [32, 6, 1, "", "in2"], [32, 6, 1, "", "input"], [32, 6, 1, "", "le"], [32, 6, 1, "", "log"], [32, 6, 1, "", "loga"], [32, 6, 1, "", "matrix"], [32, 6, 1, "", "maxdiagbreak"], [32, 6, 1, "", "maxhours"], [32, 6, 1, "", "maxiters"], [32, 6, 1, "", "maxtrees"], [32, 6, 1, "", "minbestcolscore"], [32, 6, 1, "", "minsmoothscore"], [32, 6, 1, "", "msf"], [32, 6, 1, "", "msfout"], [32, 6, 1, "", "noanchors"], [32, 6, 1, "", "nocore"], [32, 6, 1, "", "objscore"], [32, 6, 1, "", "out"], [32, 6, 1, "", "phyi"], [32, 6, 1, "", "phyiout"], [32, 6, 1, "", "phys"], [32, 6, 1, "", "physout"], [32, 6, 1, "", "profile"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "refine"], [32, 6, 1, "", "refinew"], [32, 6, 1, "", "refinewindow"], [32, 6, 1, "", "root1"], [32, 6, 1, "", "root2"], [32, 6, 1, "", "scorefile"], [32, 6, 1, "", "seqtype"], [32, 6, 1, "", "smoothscoreceil"], [32, 6, 1, "", "smoothwindow"], [32, 6, 1, "", "sp"], [32, 6, 1, "", "spn"], [32, 6, 1, "", "spscore"], [32, 6, 1, "", "stable"], [32, 6, 1, "", "sueff"], [32, 6, 1, "", "sv"], [32, 6, 1, "", "tree1"], [32, 6, 1, "", "tree2"], [32, 6, 1, "", "usetree"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "version"], [32, 6, 1, "", "weight1"], [32, 6, 1, "", "weight2"]], "Bio.Align.Applications.PrankCommandline": [[32, 6, 1, "", "F"], [32, 2, 1, "", "__init__"], [32, 6, 1, "", "codon"], [32, 6, 1, "", "convert"], [32, 6, 1, "", "d"], [32, 6, 1, "", "dnafreqs"], [32, 6, 1, "", "dots"], [32, 6, 1, "", "f"], [32, 6, 1, "", "fixedbranches"], [32, 6, 1, "", "gapext"], [32, 6, 1, "", "gaprate"], [32, 6, 1, "", "kappa"], [32, 6, 1, "", "longseq"], [32, 6, 1, "", "m"], [32, 6, 1, "", "matinitsize"], [32, 6, 1, "", "matresize"], [32, 6, 1, "", "maxbranches"], [32, 6, 1, "", "mttranslate"], [32, 6, 1, "", "nopost"], [32, 6, 1, "", "notree"], [32, 6, 1, "", "noxml"], [32, 6, 1, "", "o"], [32, 6, 1, "", "once"], [32, 6, 1, "", "printnodes"], [32, 6, 1, "", "pwdist"], [32, 6, 1, "", "pwgenomic"], [32, 6, 1, "", "pwgenomicdist"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "realbranches"], [32, 6, 1, "", "rho"], [32, 6, 1, "", "scalebranches"], [32, 6, 1, "", "shortnames"], [32, 6, 1, "", "showtree"], [32, 6, 1, "", "showxml"], [32, 6, 1, "", "skipins"], [32, 6, 1, "", "t"], [32, 6, 1, "", "termgap"], [32, 6, 1, "", "translate"], [32, 6, 1, "", "tree"], [32, 6, 1, "", "twice"], [32, 6, 1, "", "uselogs"], [32, 6, 1, "", "writeanc"]], "Bio.Align.Applications.ProbconsCommandline": [[32, 2, 1, "", "__init__"], [32, 6, 1, "", "a"], [32, 6, 1, "", "annot"], [32, 6, 1, "", "clustalw"], [32, 6, 1, "", "consistency"], [32, 6, 1, "", "emissions"], [32, 6, 1, "", "input"], [32, 6, 1, "", "ir"], [32, 6, 1, "", "pairs"], [32, 6, 1, "", "paramfile"], [32, 6, 1, "", "pre"], [32, 6, 1, "", "train"], [32, 6, 1, "", "verbose"], [32, 6, 1, "", "viterbi"]], "Bio.Align.Applications.TCoffeeCommandline": [[32, 5, 1, "", "SEQ_TYPES"], [32, 2, 1, "", "__init__"], [32, 6, 1, "", "convert"], [32, 6, 1, "", "gapext"], [32, 6, 1, "", "gapopen"], [32, 6, 1, "", "infile"], [32, 6, 1, "", "matrix"], [32, 6, 1, "", "mode"], [32, 6, 1, "", "outfile"], [32, 6, 1, "", "outorder"], [32, 6, 1, "", "output"], [32, 6, 1, "", "quiet"], [32, 6, 1, "", "type"]], "Bio.Align.CodonAligner": [[30, 2, 1, "", "__init__"], [30, 2, 1, "", "align"], [30, 2, 1, "", "score"]], "Bio.Align.MultipleSeqAlignment": [[30, 2, 1, "", "__add__"], [30, 2, 1, "", "__delitem__"], [30, 2, 1, "", "__format__"], [30, 2, 1, "", "__getitem__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__iter__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__repr__"], [30, 2, 1, "", "__str__"], [30, 6, 1, "", "alignment"], [30, 2, 1, "", "append"], [30, 6, 1, "", "column_annotations"], [30, 2, 1, "", "extend"], [30, 2, 1, "", "get_alignment_length"], [30, 2, 1, "", "sort"], [30, 6, 1, "", "substitutions"]], "Bio.Align.PairwiseAligner": [[30, 2, 1, "", "__getstate__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__setattr__"], [30, 2, 1, "", "__setstate__"], [30, 2, 1, "", "align"], [30, 2, 1, "", "score"]], "Bio.Align.PairwiseAlignments": [[30, 5, 1, "", "__abstractmethods__"], [30, 2, 1, "", "__getitem__"], [30, 2, 1, "", "__init__"], [30, 2, 1, "", "__len__"], [30, 2, 1, "", "__next__"], [30, 2, 1, "", "rewind"]], "Bio.Align.a2m": [[33, 3, 1, "", "AlignmentIterator"], [33, 3, 1, "", "AlignmentWriter"]], "Bio.Align.a2m.AlignmentIterator": [[33, 5, 1, "", "__abstractmethods__"], [33, 5, 1, "", "fmt"]], "Bio.Align.a2m.AlignmentWriter": [[33, 5, 1, "", "__abstractmethods__"], [33, 5, 1, "", "fmt"], [33, 2, 1, "", "format_alignment"], [33, 2, 1, "", "write_alignments"]], "Bio.Align.analysis": [[34, 4, 1, "", "calculate_dn_ds"], [34, 4, 1, "", "calculate_dn_ds_matrix"], [34, 4, 1, "", "mktest"]], "Bio.Align.bed": [[35, 3, 1, "", "AlignmentIterator"], [35, 3, 1, "", "AlignmentWriter"]], "Bio.Align.bed.AlignmentIterator": [[35, 5, 1, "", "__abstractmethods__"], [35, 5, 1, "", "fmt"]], "Bio.Align.bed.AlignmentWriter": [[35, 5, 1, "", "__abstractmethods__"], [35, 2, 1, "", "__init__"], [35, 2, 1, "", "format_alignment"]], "Bio.Align.bigbed": [[36, 3, 1, "", "AlignmentIterator"], [36, 3, 1, "", "AlignmentWriter"], [36, 3, 1, "", "AutoSQLTable"], [36, 3, 1, "", "Field"]], "Bio.Align.bigbed.AlignmentIterator": [[36, 5, 1, "", "__abstractmethods__"], [36, 2, 1, "", "__len__"], [36, 5, 1, "", "fmt"], [36, 5, 1, "", "mode"], [36, 2, 1, "", "search"]], "Bio.Align.bigbed.AlignmentWriter": [[36, 5, 1, "", "__abstractmethods__"], [36, 2, 1, "", "__init__"], [36, 5, 1, "", "fmt"], [36, 5, 1, "", "mode"], [36, 2, 1, "", "write_alignments"], [36, 2, 1, "", "write_file"]], "Bio.Align.bigbed.AutoSQLTable": [[36, 5, 1, "", "__annotations__"], [36, 2, 1, "", "__bytes__"], [36, 2, 1, "", "__getitem__"], [36, 2, 1, "", "__init__"], [36, 2, 1, "", "__str__"], [36, 5, 1, "", "default"], [36, 2, 1, "", "from_bytes"], [36, 2, 1, "", "from_string"]], "Bio.Align.bigbed.Field": [[36, 2, 1, "", "__getnewargs__"], [36, 2, 1, "", "__new__"], [36, 2, 1, "", "__repr__"], [36, 5, 1, "", "__slots__"], [36, 5, 1, "", "as_type"], [36, 5, 1, "", "comment"], [36, 5, 1, "", "name"]], "Bio.Align.bigmaf": [[37, 3, 1, "", "AlignmentIterator"], [37, 3, 1, "", "AlignmentWriter"]], "Bio.Align.bigmaf.AlignmentIterator": [[37, 5, 1, "", "__abstractmethods__"], [37, 2, 1, "", "__init__"], [37, 5, 1, "", "fmt"], [37, 5, 1, "", "mode"]], "Bio.Align.bigmaf.AlignmentWriter": [[37, 5, 1, "", "__abstractmethods__"], [37, 2, 1, "", "__init__"], [37, 5, 1, "", "fmt"], [37, 2, 1, "", "write_file"]], "Bio.Align.bigpsl": [[38, 3, 1, "", "AlignmentIterator"], [38, 3, 1, "", "AlignmentWriter"]], "Bio.Align.bigpsl.AlignmentIterator": [[38, 5, 1, "", "__abstractmethods__"], [38, 5, 1, "", "fmt"]], "Bio.Align.bigpsl.AlignmentWriter": [[38, 5, 1, "", "__abstractmethods__"], [38, 2, 1, "", "__init__"], [38, 5, 1, "", "fmt"], [38, 2, 1, "", "write_file"]], "Bio.Align.chain": [[39, 3, 1, "", "AlignmentIterator"], [39, 3, 1, "", "AlignmentWriter"]], "Bio.Align.chain.AlignmentIterator": [[39, 5, 1, "", "__abstractmethods__"], [39, 5, 1, "", "fmt"]], "Bio.Align.chain.AlignmentWriter": [[39, 5, 1, "", "__abstractmethods__"], [39, 5, 1, "", "fmt"], [39, 2, 1, "", "format_alignment"]], "Bio.Align.clustal": [[40, 3, 1, "", "AlignmentIterator"], [40, 3, 1, "", "AlignmentWriter"]], "Bio.Align.clustal.AlignmentIterator": [[40, 5, 1, "", "__abstractmethods__"], [40, 5, 1, "", "fmt"]], "Bio.Align.clustal.AlignmentWriter": [[40, 5, 1, "", "__abstractmethods__"], [40, 5, 1, "", "fmt"], [40, 2, 1, "", "format_alignment"], [40, 2, 1, "", "write_header"]], "Bio.Align.emboss": [[41, 3, 1, "", "AlignmentIterator"]], "Bio.Align.emboss.AlignmentIterator": [[41, 5, 1, "", "__abstractmethods__"], [41, 5, 1, "", "fmt"]], "Bio.Align.exonerate": [[42, 3, 1, "", "AlignmentIterator"], [42, 3, 1, "", "AlignmentWriter"]], "Bio.Align.exonerate.AlignmentIterator": [[42, 5, 1, "", "__abstractmethods__"], [42, 5, 1, "", "fmt"]], "Bio.Align.exonerate.AlignmentWriter": [[42, 5, 1, "", "__abstractmethods__"], [42, 2, 1, "", "__init__"], [42, 5, 1, "", "fmt"], [42, 2, 1, "", "write_footer"], [42, 2, 1, "", "write_header"]], "Bio.Align.fasta": [[43, 3, 1, "", "AlignmentIterator"], [43, 3, 1, "", "AlignmentWriter"]], "Bio.Align.fasta.AlignmentIterator": [[43, 5, 1, "", "__abstractmethods__"], [43, 5, 1, "", "fmt"]], "Bio.Align.fasta.AlignmentWriter": [[43, 5, 1, "", "__abstractmethods__"], [43, 5, 1, "", "fmt"], [43, 2, 1, "", "format_alignment"]], "Bio.Align.hhr": [[44, 3, 1, "", "AlignmentIterator"]], "Bio.Align.hhr.AlignmentIterator": [[44, 5, 1, "", "__abstractmethods__"], [44, 2, 1, "", "__len__"], [44, 5, 1, "", "fmt"]], "Bio.Align.interfaces": [[45, 3, 1, "", "AlignmentIterator"], [45, 3, 1, "", "AlignmentWriter"]], "Bio.Align.interfaces.AlignmentIterator": [[45, 5, 1, "", "__abstractmethods__"], [45, 5, 1, "", "__annotations__"], [45, 2, 1, "", "__enter__"], [45, 2, 1, "", "__exit__"], [45, 2, 1, "", "__getitem__"], [45, 2, 1, "", "__init__"], [45, 2, 1, "", "__len__"], [45, 2, 1, "", "__next__"], [45, 5, 1, "", "fmt"], [45, 5, 1, "", "mode"], [45, 2, 1, "", "rewind"]], "Bio.Align.interfaces.AlignmentWriter": [[45, 5, 1, "", "__abstractmethods__"], [45, 5, 1, "", "__annotations__"], [45, 2, 1, "", "__init__"], [45, 5, 1, "", "fmt"], [45, 2, 1, "", "format_alignment"], [45, 5, 1, "", "mode"], [45, 2, 1, "", "write"], [45, 2, 1, "", "write_alignments"], [45, 2, 1, "", "write_file"], [45, 2, 1, "", "write_footer"], [45, 2, 1, "", "write_header"], [45, 2, 1, "", "write_multiple_alignments"], [45, 2, 1, "", "write_single_alignment"]], "Bio.Align.maf": [[46, 3, 1, "", "AlignmentIterator"], [46, 3, 1, "", "AlignmentWriter"]], "Bio.Align.maf.AlignmentIterator": [[46, 5, 1, "", "__abstractmethods__"], [46, 5, 1, "", "empty_status_characters"], [46, 5, 1, "", "fmt"], [46, 5, 1, "", "status_characters"]], "Bio.Align.maf.AlignmentWriter": [[46, 5, 1, "", "__abstractmethods__"], [46, 5, 1, "", "fmt"], [46, 2, 1, "", "format_alignment"], [46, 2, 1, "", "write_header"]], "Bio.Align.mauve": [[47, 3, 1, "", "AlignmentIterator"], [47, 3, 1, "", "AlignmentWriter"]], "Bio.Align.mauve.AlignmentIterator": [[47, 5, 1, "", "__abstractmethods__"], [47, 5, 1, "", "fmt"]], "Bio.Align.mauve.AlignmentWriter": [[47, 5, 1, "", "__abstractmethods__"], [47, 2, 1, "", "__init__"], [47, 5, 1, "", "fmt"], [47, 2, 1, "", "format_alignment"], [47, 2, 1, "", "write_file"], [47, 2, 1, "", "write_header"]], "Bio.Align.msf": [[48, 3, 1, "", "AlignmentIterator"]], "Bio.Align.msf.AlignmentIterator": [[48, 5, 1, "", "__abstractmethods__"], [48, 5, 1, "", "fmt"]], "Bio.Align.nexus": [[49, 3, 1, "", "AlignmentIterator"], [49, 3, 1, "", "AlignmentWriter"]], "Bio.Align.nexus.AlignmentIterator": [[49, 5, 1, "", "__abstractmethods__"], [49, 5, 1, "", "fmt"]], "Bio.Align.nexus.AlignmentWriter": [[49, 5, 1, "", "__abstractmethods__"], [49, 2, 1, "", "__init__"], [49, 5, 1, "", "fmt"], [49, 2, 1, "", "format_alignment"], [49, 2, 1, "", "write_alignment"], [49, 2, 1, "", "write_alignments"], [49, 2, 1, "", "write_file"]], "Bio.Align.phylip": [[50, 3, 1, "", "AlignmentIterator"], [50, 3, 1, "", "AlignmentWriter"]], "Bio.Align.phylip.AlignmentIterator": [[50, 5, 1, "", "__abstractmethods__"], [50, 5, 1, "", "fmt"]], "Bio.Align.phylip.AlignmentWriter": [[50, 5, 1, "", "__abstractmethods__"], [50, 5, 1, "", "fmt"], [50, 2, 1, "", "format_alignment"]], "Bio.Align.psl": [[51, 3, 1, "", "AlignmentIterator"], [51, 3, 1, "", "AlignmentWriter"]], "Bio.Align.psl.AlignmentIterator": [[51, 5, 1, "", "__abstractmethods__"], [51, 5, 1, "", "fmt"]], "Bio.Align.psl.AlignmentWriter": [[51, 5, 1, "", "__abstractmethods__"], [51, 2, 1, "", "__init__"], [51, 5, 1, "", "fmt"], [51, 2, 1, "", "format_alignment"], [51, 2, 1, "", "write_header"]], "Bio.Align.sam": [[52, 3, 1, "", "AlignmentIterator"], [52, 3, 1, "", "AlignmentWriter"]], "Bio.Align.sam.AlignmentIterator": [[52, 5, 1, "", "__abstractmethods__"], [52, 5, 1, "", "fmt"]], "Bio.Align.sam.AlignmentWriter": [[52, 5, 1, "", "__abstractmethods__"], [52, 2, 1, "", "__init__"], [52, 5, 1, "", "fmt"], [52, 2, 1, "", "format_alignment"], [52, 2, 1, "", "write_header"]], "Bio.Align.stockholm": [[53, 3, 1, "", "AlignmentIterator"], [53, 3, 1, "", "AlignmentWriter"]], "Bio.Align.stockholm.AlignmentIterator": [[53, 5, 1, "", "__abstractmethods__"], [53, 5, 1, "", "fmt"], [53, 5, 1, "", "gc_mapping"], [53, 5, 1, "", "gf_mapping"], [53, 5, 1, "", "gr_mapping"], [53, 5, 1, "", "gs_mapping"], [53, 5, 1, "", "key"], [53, 5, 1, "", "keyword"], [53, 5, 1, "", "value"]], "Bio.Align.stockholm.AlignmentWriter": [[53, 5, 1, "", "__abstractmethods__"], [53, 5, 1, "", "fmt"], [53, 2, 1, "", "format_alignment"], [53, 5, 1, "", "gc_mapping"], [53, 5, 1, "", "gf_mapping"], [53, 5, 1, "", "gr_mapping"], [53, 5, 1, "", "gs_mapping"]], "Bio.Align.substitution_matrices": [[54, 3, 1, "", "Array"], [54, 4, 1, "", "load"], [54, 4, 1, "", "read"]], "Bio.Align.substitution_matrices.Array": [[54, 2, 1, "", "__array_finalize__"], [54, 2, 1, "", "__array_prepare__"], [54, 2, 1, "", "__array_ufunc__"], [54, 2, 1, "", "__array_wrap__"], [54, 2, 1, "", "__contains__"], [54, 2, 1, "", "__format__"], [54, 2, 1, "", "__getitem__"], [54, 2, 1, "", "__new__"], [54, 2, 1, "", "__reduce__"], [54, 2, 1, "", "__repr__"], [54, 2, 1, "", "__setitem__"], [54, 2, 1, "", "__setstate__"], [54, 2, 1, "", "__str__"], [54, 6, 1, "", "alphabet"], [54, 2, 1, "", "copy"], [54, 2, 1, "", "format"], [54, 2, 1, "", "get"], [54, 2, 1, "", "items"], [54, 2, 1, "", "keys"], [54, 2, 1, "", "select"], [54, 2, 1, "", "transpose"], [54, 2, 1, "", "update"], [54, 2, 1, "", "values"]], "Bio.Align.tabular": [[55, 3, 1, "", "AlignmentIterator"], [55, 3, 1, "", "State"]], "Bio.Align.tabular.AlignmentIterator": [[55, 5, 1, "", "__abstractmethods__"], [55, 5, 1, "", "fmt"], [55, 2, 1, "", "parse_btop"], [55, 2, 1, "", "parse_cigar"]], "Bio.Align.tabular.State": [[55, 5, 1, "", "MATCH"], [55, 5, 1, "", "NONE"], [55, 5, 1, "", "QUERY_GAP"], [55, 5, 1, "", "TARGET_GAP"]], "Bio.AlignIO": [[57, 0, 0, "-", "ClustalIO"], [58, 0, 0, "-", "EmbossIO"], [59, 0, 0, "-", "FastaIO"], [60, 0, 0, "-", "Interfaces"], [61, 0, 0, "-", "MafIO"], [62, 0, 0, "-", "MauveIO"], [63, 0, 0, "-", "MsfIO"], [64, 0, 0, "-", "NexusIO"], [65, 0, 0, "-", "PhylipIO"], [66, 0, 0, "-", "StockholmIO"], [56, 4, 1, "", "convert"], [56, 4, 1, "", "parse"], [56, 4, 1, "", "read"], [56, 4, 1, "", "write"]], "Bio.AlignIO.ClustalIO": [[57, 3, 1, "", "ClustalIterator"], [57, 3, 1, "", "ClustalWriter"]], "Bio.AlignIO.ClustalIO.ClustalIterator": [[57, 2, 1, "", "__next__"]], "Bio.AlignIO.ClustalIO.ClustalWriter": [[57, 2, 1, "", "write_alignment"]], "Bio.AlignIO.EmbossIO": [[58, 3, 1, "", "EmbossIterator"]], "Bio.AlignIO.EmbossIO.EmbossIterator": [[58, 2, 1, "", "__next__"]], "Bio.AlignIO.FastaIO": [[59, 4, 1, "", "FastaM10Iterator"]], "Bio.AlignIO.Interfaces": [[60, 3, 1, "", "AlignmentIterator"], [60, 3, 1, "", "AlignmentWriter"], [60, 3, 1, "", "SequentialAlignmentWriter"]], "Bio.AlignIO.Interfaces.AlignmentIterator": [[60, 2, 1, "", "__init__"], [60, 2, 1, "", "__iter__"], [60, 2, 1, "", "__next__"]], "Bio.AlignIO.Interfaces.AlignmentWriter": [[60, 2, 1, "", "__init__"], [60, 2, 1, "", "clean"], [60, 2, 1, "", "write_file"]], "Bio.AlignIO.Interfaces.SequentialAlignmentWriter": [[60, 2, 1, "", "__init__"], [60, 2, 1, "", "write_alignment"], [60, 2, 1, "", "write_file"], [60, 2, 1, "", "write_footer"], [60, 2, 1, "", "write_header"]], "Bio.AlignIO.MafIO": [[61, 3, 1, "", "MafIndex"], [61, 4, 1, "", "MafIterator"], [61, 3, 1, "", "MafWriter"]], "Bio.AlignIO.MafIO.MafIndex": [[61, 2, 1, "", "__init__"], [61, 2, 1, "", "__len__"], [61, 2, 1, "", "__repr__"], [61, 2, 1, "", "close"], [61, 2, 1, "", "get_spliced"], [61, 2, 1, "", "search"]], "Bio.AlignIO.MafIO.MafWriter": [[61, 2, 1, "", "write_alignment"], [61, 2, 1, "", "write_header"]], "Bio.AlignIO.MauveIO": [[62, 3, 1, "", "MauveIterator"], [62, 3, 1, "", "MauveWriter"]], "Bio.AlignIO.MauveIO.MauveIterator": [[62, 5, 1, "", "__annotations__"], [62, 2, 1, "", "__next__"]], "Bio.AlignIO.MauveIO.MauveWriter": [[62, 2, 1, "", "__init__"], [62, 2, 1, "", "write_alignment"]], "Bio.AlignIO.MsfIO": [[63, 3, 1, "", "MsfIterator"]], "Bio.AlignIO.MsfIO.MsfIterator": [[63, 2, 1, "", "__next__"]], "Bio.AlignIO.NexusIO": [[64, 4, 1, "", "NexusIterator"], [64, 3, 1, "", "NexusWriter"]], "Bio.AlignIO.NexusIO.NexusWriter": [[64, 2, 1, "", "write_alignment"], [64, 2, 1, "", "write_file"]], "Bio.AlignIO.PhylipIO": [[65, 3, 1, "", "PhylipIterator"], [65, 3, 1, "", "PhylipWriter"], [65, 3, 1, "", "RelaxedPhylipIterator"], [65, 3, 1, "", "RelaxedPhylipWriter"], [65, 3, 1, "", "SequentialPhylipIterator"], [65, 3, 1, "", "SequentialPhylipWriter"], [65, 4, 1, "", "sanitize_name"]], "Bio.AlignIO.PhylipIO.PhylipIterator": [[65, 2, 1, "", "__next__"], [65, 5, 1, "", "id_width"]], "Bio.AlignIO.PhylipIO.PhylipWriter": [[65, 2, 1, "", "write_alignment"]], "Bio.AlignIO.PhylipIO.RelaxedPhylipWriter": [[65, 2, 1, "", "write_alignment"]], "Bio.AlignIO.PhylipIO.SequentialPhylipIterator": [[65, 2, 1, "", "__next__"]], "Bio.AlignIO.PhylipIO.SequentialPhylipWriter": [[65, 2, 1, "", "write_alignment"]], "Bio.AlignIO.StockholmIO": [[66, 3, 1, "", "StockholmIterator"], [66, 3, 1, "", "StockholmWriter"]], "Bio.AlignIO.StockholmIO.StockholmIterator": [[66, 2, 1, "", "__next__"], [66, 5, 1, "", "pfam_gc_mapping"], [66, 5, 1, "", "pfam_gr_mapping"], [66, 5, 1, "", "pfam_gs_mapping"]], "Bio.AlignIO.StockholmIO.StockholmWriter": [[66, 5, 1, "", "pfam_gc_mapping"], [66, 5, 1, "", "pfam_gr_mapping"], [66, 5, 1, "", "pfam_gs_mapping"], [66, 2, 1, "", "write_alignment"]], "Bio.Application": [[67, 3, 1, "", "AbstractCommandline"], [67, 1, 1, "", "ApplicationError"]], "Bio.Application.AbstractCommandline": [[67, 2, 1, "", "__call__"], [67, 2, 1, "", "__init__"], [67, 2, 1, "", "__repr__"], [67, 2, 1, "", "__setattr__"], [67, 2, 1, "", "__str__"], [67, 5, 1, "", "parameters"], [67, 2, 1, "", "set_parameter"]], "Bio.Application.ApplicationError": [[67, 2, 1, "", "__init__"], [67, 2, 1, "", "__repr__"], [67, 2, 1, "", "__str__"]], "Bio.Blast": [[69, 0, 0, "-", "Applications"], [68, 1, 1, "", "CorruptedXMLError"], [68, 3, 1, "", "HSP"], [68, 3, 1, "", "Hit"], [70, 0, 0, "-", "NCBIWWW"], [71, 0, 0, "-", "NCBIXML"], [68, 1, 1, "", "NotXMLError"], [68, 3, 1, "", "Record"], [68, 3, 1, "", "Records"], [68, 4, 1, "", "parse"], [68, 4, 1, "", "qblast"], [68, 4, 1, "", "read"], [68, 4, 1, "", "write"]], "Bio.Blast.Applications": [[69, 3, 1, "", "NcbiblastformatterCommandline"], [69, 3, 1, "", "NcbiblastnCommandline"], [69, 3, 1, "", "NcbiblastpCommandline"], [69, 3, 1, "", "NcbiblastxCommandline"], [69, 3, 1, "", "NcbideltablastCommandline"], [69, 3, 1, "", "NcbimakeblastdbCommandline"], [69, 3, 1, "", "NcbipsiblastCommandline"], [69, 3, 1, "", "NcbirpsblastCommandline"], [69, 3, 1, "", "NcbirpstblastnCommandline"], [69, 3, 1, "", "NcbitblastnCommandline"], [69, 3, 1, "", "NcbitblastxCommandline"]], "Bio.Blast.Applications.NcbiblastformatterCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "archive"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "rid"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "version"]], "Bio.Blast.Applications.NcbiblastnCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "dust"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "filtering_db"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "index_name"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "min_raw_gapped_score"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "no_greedy"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "off_diagonal_range"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "penalty"], [69, 6, 1, "", "perc_identity"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "reward"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "template_length"], [69, 6, 1, "", "template_type"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_index"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_masker_db"], [69, 6, 1, "", "window_masker_taxid"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbiblastpCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbiblastxCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "frame_shift_penalty"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_intron_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_gencode"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbideltablastCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "domain_inclusion_ethresh"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gap_trigger"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "inclusion_ethresh"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_iterations"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "out_ascii_pssm"], [69, 6, 1, "", "out_pssm"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "pseudocount"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "rpsdb"], [69, 6, 1, "", "save_each_pssm"], [69, 6, 1, "", "save_pssm_after_last_round"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_domain_hits"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbimakeblastdbCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "blastdb_version"], [69, 6, 1, "", "dbtype"], [69, 6, 1, "", "gi_mask"], [69, 6, 1, "", "gi_mask_name"], [69, 6, 1, "", "h"], [69, 6, 1, "", "hash_index"], [69, 6, 1, "", "help"], [69, 6, 1, "", "input_file"], [69, 6, 1, "", "input_type"], [69, 6, 1, "", "logfile"], [69, 6, 1, "", "mask_data"], [69, 6, 1, "", "mask_desc"], [69, 6, 1, "", "mask_id"], [69, 6, 1, "", "max_file_sz"], [69, 6, 1, "", "out"], [69, 6, 1, "", "parse_seqids"], [69, 6, 1, "", "taxid"], [69, 6, 1, "", "taxid_map"], [69, 6, 1, "", "title"], [69, 6, 1, "", "version"]], "Bio.Blast.Applications.NcbipsiblastCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gap_trigger"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "ignore_msa_master"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "in_msa"], [69, 6, 1, "", "in_pssm"], [69, 6, 1, "", "inclusion_ethresh"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "msa_master_idx"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_iterations"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "out_ascii_pssm"], [69, 6, 1, "", "out_pssm"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "phi_pattern"], [69, 6, 1, "", "pseudocount"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "save_each_pssm"], [69, 6, 1, "", "save_pssm_after_last_round"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbirpsblastCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbirpstblastnCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "db"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_gencode"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbitblastnCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "comp_based_stats"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_gencode"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "frame_shift_penalty"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "in_pssm"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_intron_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "task"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "ungapped"], [69, 6, 1, "", "use_sw_tback"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.Applications.NcbitblastxCommandline": [[69, 2, 1, "", "__init__"], [69, 6, 1, "", "best_hit_overhang"], [69, 6, 1, "", "best_hit_score_edge"], [69, 6, 1, "", "culling_limit"], [69, 6, 1, "", "db"], [69, 6, 1, "", "db_gencode"], [69, 6, 1, "", "db_hard_mask"], [69, 6, 1, "", "db_soft_mask"], [69, 6, 1, "", "dbsize"], [69, 6, 1, "", "entrez_query"], [69, 6, 1, "", "evalue"], [69, 6, 1, "", "export_search_strategy"], [69, 6, 1, "", "gapextend"], [69, 6, 1, "", "gapopen"], [69, 6, 1, "", "gilist"], [69, 6, 1, "", "h"], [69, 6, 1, "", "help"], [69, 6, 1, "", "html"], [69, 6, 1, "", "import_search_strategy"], [69, 6, 1, "", "lcase_masking"], [69, 6, 1, "", "line_length"], [69, 6, 1, "", "matrix"], [69, 6, 1, "", "max_hsps"], [69, 6, 1, "", "max_hsps_per_subject"], [69, 6, 1, "", "max_intron_length"], [69, 6, 1, "", "max_target_seqs"], [69, 6, 1, "", "negative_gilist"], [69, 6, 1, "", "negative_seqidlist"], [69, 6, 1, "", "num_alignments"], [69, 6, 1, "", "num_descriptions"], [69, 6, 1, "", "num_threads"], [69, 6, 1, "", "out"], [69, 6, 1, "", "outfmt"], [69, 6, 1, "", "parse_deflines"], [69, 6, 1, "", "qcov_hsp_perc"], [69, 6, 1, "", "query"], [69, 6, 1, "", "query_gencode"], [69, 6, 1, "", "query_loc"], [69, 6, 1, "", "remote"], [69, 6, 1, "", "searchsp"], [69, 6, 1, "", "seg"], [69, 6, 1, "", "seqidlist"], [69, 6, 1, "", "show_gis"], [69, 6, 1, "", "soft_masking"], [69, 6, 1, "", "strand"], [69, 6, 1, "", "subject"], [69, 6, 1, "", "subject_loc"], [69, 6, 1, "", "sum_statistics"], [69, 6, 1, "", "sum_stats"], [69, 6, 1, "", "threshold"], [69, 6, 1, "", "version"], [69, 6, 1, "", "window_size"], [69, 6, 1, "", "word_size"], [69, 6, 1, "", "xdrop_gap"], [69, 6, 1, "", "xdrop_gap_final"], [69, 6, 1, "", "xdrop_ungap"]], "Bio.Blast.CorruptedXMLError": [[68, 2, 1, "", "__init__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.HSP": [[68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.Hit": [[68, 5, 1, "", "__abstractmethods__"], [68, 2, 1, "", "__getitem__"], [68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.NCBIWWW": [[70, 4, 1, "", "qblast"]], "Bio.Blast.NCBIXML": [[71, 3, 1, "", "Alignment"], [71, 3, 1, "", "Blast"], [71, 3, 1, "", "BlastParser"], [71, 3, 1, "", "DatabaseReport"], [71, 3, 1, "", "Description"], [71, 3, 1, "", "DescriptionExt"], [71, 3, 1, "", "DescriptionExtItem"], [71, 3, 1, "", "HSP"], [71, 3, 1, "", "Header"], [71, 3, 1, "", "MultipleAlignment"], [71, 3, 1, "", "PSIBlast"], [71, 3, 1, "", "Parameters"], [71, 3, 1, "", "Round"], [71, 4, 1, "", "fmt_"], [71, 4, 1, "", "parse"], [71, 4, 1, "", "read"]], "Bio.Blast.NCBIXML.Alignment": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.Blast": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.BlastParser": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "reset"], [71, 2, 1, "", "set_hit_accession"], [71, 2, 1, "", "set_hit_def"], [71, 2, 1, "", "set_hit_id"], [71, 2, 1, "", "set_hit_len"]], "Bio.Blast.NCBIXML.DatabaseReport": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.Description": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.DescriptionExt": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "append_item"]], "Bio.Blast.NCBIXML.DescriptionExtItem": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.HSP": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "__str__"]], "Bio.Blast.NCBIXML.Header": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.MultipleAlignment": [[71, 2, 1, "", "__init__"], [71, 2, 1, "", "to_generic"]], "Bio.Blast.NCBIXML.PSIBlast": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.Parameters": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NCBIXML.Round": [[71, 2, 1, "", "__init__"]], "Bio.Blast.NotXMLError": [[68, 2, 1, "", "__init__"], [68, 2, 1, "", "__str__"]], "Bio.Blast.Record": [[68, 2, 1, "", "__contains__"], [68, 2, 1, "", "__getitem__"], [68, 2, 1, "", "__init__"], [68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"], [68, 2, 1, "", "index"], [68, 2, 1, "", "keys"]], "Bio.Blast.Records": [[68, 5, 1, "", "__abstractmethods__"], [68, 2, 1, "", "__enter__"], [68, 2, 1, "", "__exit__"], [68, 2, 1, "", "__getitem__"], [68, 2, 1, "", "__init__"], [68, 2, 1, "", "__iter__"], [68, 2, 1, "", "__next__"], [68, 2, 1, "", "__repr__"], [68, 2, 1, "", "__str__"], [68, 6, 1, "", "data"]], "Bio.CAPS": [[72, 1, 1, "", "AlignmentHasDifferentLengthsError"], [72, 3, 1, "", "CAPSMap"], [72, 3, 1, "", "DifferentialCutsite"]], "Bio.CAPS.CAPSMap": [[72, 2, 1, "", "__init__"]], "Bio.CAPS.DifferentialCutsite": [[72, 2, 1, "", "__init__"]], "Bio.Cluster": [[73, 3, 1, "", "Node"], [73, 3, 1, "", "Record"], [73, 3, 1, "", "Tree"], [73, 4, 1, "", "clustercentroids"], [73, 4, 1, "", "clusterdistance"], [73, 4, 1, "", "distancematrix"], [73, 4, 1, "", "kcluster"], [73, 4, 1, "", "kmedoids"], [73, 4, 1, "", "pca"], [73, 4, 1, "", "read"], [73, 4, 1, "", "somcluster"], [73, 4, 1, "", "treecluster"]], "Bio.Cluster.Record": [[73, 2, 1, "", "__init__"], [73, 2, 1, "", "clustercentroids"], [73, 2, 1, "", "clusterdistance"], [73, 2, 1, "", "distancematrix"], [73, 2, 1, "", "kcluster"], [73, 2, 1, "", "save"], [73, 2, 1, "", "somcluster"], [73, 2, 1, "", "treecluster"]], "Bio.Cluster.Tree": [[73, 2, 1, "", "cut"], [73, 2, 1, "", "sort"]], "Bio.Compass": [[74, 3, 1, "", "Record"], [74, 4, 1, "", "parse"], [74, 4, 1, "", "read"]], "Bio.Compass.Record": [[74, 2, 1, "", "__init__"], [74, 2, 1, "", "hit_coverage"], [74, 2, 1, "", "query_coverage"]], "Bio.Data": [[76, 0, 0, "-", "CodonTable"], [77, 0, 0, "-", "IUPACData"], [78, 0, 0, "-", "PDBData"]], "Bio.Data.CodonTable": [[76, 3, 1, "", "AmbiguousCodonTable"], [76, 3, 1, "", "AmbiguousForwardTable"], [76, 3, 1, "", "CodonTable"], [76, 3, 1, "", "NCBICodonTable"], [76, 3, 1, "", "NCBICodonTableDNA"], [76, 3, 1, "", "NCBICodonTableRNA"], [76, 1, 1, "", "TranslationError"], [76, 4, 1, "", "list_ambiguous_codons"], [76, 4, 1, "", "list_possible_proteins"], [76, 4, 1, "", "make_back_table"], [76, 4, 1, "", "register_ncbi_table"]], "Bio.Data.CodonTable.AmbiguousCodonTable": [[76, 2, 1, "", "__getattr__"], [76, 2, 1, "", "__init__"]], "Bio.Data.CodonTable.AmbiguousForwardTable": [[76, 2, 1, "", "__contains__"], [76, 2, 1, "", "__getitem__"], [76, 2, 1, "", "__init__"], [76, 2, 1, "", "get"]], "Bio.Data.CodonTable.CodonTable": [[76, 5, 1, "", "__annotations__"], [76, 2, 1, "", "__init__"], [76, 2, 1, "", "__str__"], [76, 5, 1, "", "back_table"], [76, 5, 1, "", "forward_table"], [76, 5, 1, "", "start_codons"], [76, 5, 1, "", "stop_codons"]], "Bio.Data.CodonTable.NCBICodonTable": [[76, 5, 1, "", "__annotations__"], [76, 2, 1, "", "__init__"], [76, 2, 1, "", "__repr__"], [76, 5, 1, "", "nucleotide_alphabet"], [76, 5, 1, "", "protein_alphabet"]], "Bio.Data.CodonTable.NCBICodonTableDNA": [[76, 5, 1, "", "nucleotide_alphabet"]], "Bio.Data.CodonTable.NCBICodonTableRNA": [[76, 5, 1, "", "nucleotide_alphabet"]], "Bio.Emboss": [[80, 0, 0, "-", "Applications"], [81, 0, 0, "-", "Primer3"], [82, 0, 0, "-", "PrimerSearch"]], "Bio.Emboss.Applications": [[80, 3, 1, "", "DiffseqCommandline"], [80, 3, 1, "", "EInvertedCommandline"], [80, 3, 1, "", "ETandemCommandline"], [80, 3, 1, "", "Est2GenomeCommandline"], [80, 3, 1, "", "FConsenseCommandline"], [80, 3, 1, "", "FDNADistCommandline"], [80, 3, 1, "", "FDNAParsCommandline"], [80, 3, 1, "", "FNeighborCommandline"], [80, 3, 1, "", "FProtDistCommandline"], [80, 3, 1, "", "FProtParsCommandline"], [80, 3, 1, "", "FSeqBootCommandline"], [80, 3, 1, "", "FTreeDistCommandline"], [80, 3, 1, "", "FuzznucCommandline"], [80, 3, 1, "", "FuzzproCommandline"], [80, 3, 1, "", "IepCommandline"], [80, 3, 1, "", "NeedleCommandline"], [80, 3, 1, "", "NeedleallCommandline"], [80, 3, 1, "", "PalindromeCommandline"], [80, 3, 1, "", "Primer3Commandline"], [80, 3, 1, "", "PrimerSearchCommandline"], [80, 3, 1, "", "SeqmatchallCommandline"], [80, 3, 1, "", "SeqretCommandline"], [80, 3, 1, "", "StretcherCommandline"], [80, 3, 1, "", "TranalignCommandline"], [80, 3, 1, "", "WaterCommandline"]], "Bio.Emboss.Applications.DiffseqCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aoutfeat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "boutfeat"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "wordsize"]], "Bio.Emboss.Applications.EInvertedCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gap"], [80, 6, 1, "", "help"], [80, 6, 1, "", "match"], [80, 6, 1, "", "maxrepeat"], [80, 6, 1, "", "mismatch"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.ETandemCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "maxrepeat"], [80, 6, 1, "", "minrepeat"], [80, 6, 1, "", "mismatch"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "uniform"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.Est2GenomeCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "align"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "best"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "est"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gappenalty"], [80, 6, 1, "", "genome"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intronpenalty"], [80, 6, 1, "", "match"], [80, 6, 1, "", "minscore"], [80, 6, 1, "", "mismatch"], [80, 6, 1, "", "mode"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "reverse"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "shuffle"], [80, 6, 1, "", "space"], [80, 6, 1, "", "splice"], [80, 6, 1, "", "splicepenalty"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "width"]], "Bio.Emboss.Applications.FConsenseCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "method"], [80, 6, 1, "", "mlfrac"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "root"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FDNADistCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "basefreq"], [80, 6, 1, "", "categories"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "freqsfrom"], [80, 6, 1, "", "gamma"], [80, 6, 1, "", "gammacoefficient"], [80, 6, 1, "", "help"], [80, 6, 1, "", "invarfrac"], [80, 6, 1, "", "lower"], [80, 6, 1, "", "method"], [80, 6, 1, "", "ncategories"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rate"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "ttratio"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"]], "Bio.Emboss.Applications.FDNAParsCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dotdiff"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "maxtrees"], [80, 6, 1, "", "njumble"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "rearrange"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "thorough"], [80, 6, 1, "", "thresh"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "transversion"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"]], "Bio.Emboss.Applications.FNeighborCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "jumble"], [80, 6, 1, "", "matrixtype"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "progress"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "treeprint"], [80, 6, 1, "", "treetype"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FProtDistCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aacateg"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "basefreq"], [80, 6, 1, "", "catergories"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "ease"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gamma"], [80, 6, 1, "", "gammacoefficient"], [80, 6, 1, "", "help"], [80, 6, 1, "", "invarcoefficient"], [80, 6, 1, "", "method"], [80, 6, 1, "", "ncategories"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "rate"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "ttratio"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"], [80, 6, 1, "", "whichcode"]], "Bio.Emboss.Applications.FProtParsCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dotdiff"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "njumble"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "outtreefile"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "thresh"], [80, 6, 1, "", "threshold"], [80, 6, 1, "", "trout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"], [80, 6, 1, "", "whichcode"]], "Bio.Emboss.Applications.FSeqBootCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "blocksize"], [80, 6, 1, "", "catergories"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dotdiff"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "fracsample"], [80, 6, 1, "", "help"], [80, 6, 1, "", "jusweights"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "regular"], [80, 6, 1, "", "reps"], [80, 6, 1, "", "rewriteformat"], [80, 6, 1, "", "seed"], [80, 6, 1, "", "seqtype"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "test"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "weights"]], "Bio.Emboss.Applications.FTreeDistCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dtype"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "intreefile"], [80, 6, 1, "", "noroot"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outgrno"], [80, 6, 1, "", "pairing"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "style"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FuzznucCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "complement"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "pattern"], [80, 6, 1, "", "pmismatch"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.FuzzproCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "pattern"], [80, 6, 1, "", "pmismatch"], [80, 6, 1, "", "rformat"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.IepCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "amino"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "carboxyl"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "disulphides"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "lysinemodified"], [80, 6, 1, "", "notermini"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.NeedleCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "brief"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "endextend"], [80, 6, 1, "", "endopen"], [80, 6, 1, "", "endweight"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "nobrief"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "similarity"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.NeedleallCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "brief"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "endextend"], [80, 6, 1, "", "endopen"], [80, 6, 1, "", "endweight"], [80, 6, 1, "", "error"], [80, 6, 1, "", "errorfile"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "minscore"], [80, 6, 1, "", "nobrief"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "similarity"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.PalindromeCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gaplimit"], [80, 6, 1, "", "help"], [80, 6, 1, "", "maxpallen"], [80, 6, 1, "", "minpallen"], [80, 6, 1, "", "nummismatches"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "overlap"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.Primer3Commandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "dnaconc"], [80, 6, 1, "", "error"], [80, 6, 1, "", "excludedregion"], [80, 6, 1, "", "explainflag"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "forwardinput"], [80, 6, 1, "", "gcclamp"], [80, 6, 1, "", "help"], [80, 6, 1, "", "hybridprobe"], [80, 6, 1, "", "includedregion"], [80, 6, 1, "", "maxdifftm"], [80, 6, 1, "", "maxgc"], [80, 6, 1, "", "maxmispriming"], [80, 6, 1, "", "maxpolyx"], [80, 6, 1, "", "maxsize"], [80, 6, 1, "", "maxtm"], [80, 6, 1, "", "mingc"], [80, 6, 1, "", "minsize"], [80, 6, 1, "", "mintm"], [80, 6, 1, "", "mishyblibraryfile"], [80, 6, 1, "", "mispriminglibraryfile"], [80, 6, 1, "", "numreturn"], [80, 6, 1, "", "oanyself"], [80, 6, 1, "", "odnaconc"], [80, 6, 1, "", "oendself"], [80, 6, 1, "", "oexcludedregion"], [80, 6, 1, "", "ogcmax"], [80, 6, 1, "", "ogcmin"], [80, 6, 1, "", "ogcopt"], [80, 6, 1, "", "ogcpercent"], [80, 6, 1, "", "oligoinput"], [80, 6, 1, "", "omaxsize"], [80, 6, 1, "", "ominsize"], [80, 6, 1, "", "omishybmax"], [80, 6, 1, "", "opolyxmax"], [80, 6, 1, "", "options"], [80, 6, 1, "", "opttm"], [80, 6, 1, "", "osaltconc"], [80, 6, 1, "", "osize"], [80, 6, 1, "", "osizeopt"], [80, 6, 1, "", "otm"], [80, 6, 1, "", "otmmax"], [80, 6, 1, "", "otmmin"], [80, 6, 1, "", "otmopt"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "prange"], [80, 6, 1, "", "psizeopt"], [80, 6, 1, "", "ptmmax"], [80, 6, 1, "", "ptmmin"], [80, 6, 1, "", "ptmopt"], [80, 6, 1, "", "reverseinput"], [80, 6, 1, "", "saltconc"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "target"], [80, 6, 1, "", "task"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.PrimerSearchCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "infile"], [80, 6, 1, "", "mismatchpercent"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "seqall"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.SeqmatchallCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"], [80, 6, 1, "", "wordsize"]], "Bio.Emboss.Applications.SeqretCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "osformat"], [80, 6, 1, "", "outseq"], [80, 6, 1, "", "sequence"], [80, 6, 1, "", "sformat"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.StretcherCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.TranalignCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "help"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "outseq"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "table"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Applications.WaterCommandline": [[80, 2, 1, "", "__init__"], [80, 6, 1, "", "aformat"], [80, 6, 1, "", "asequence"], [80, 6, 1, "", "auto"], [80, 6, 1, "", "brief"], [80, 6, 1, "", "bsequence"], [80, 6, 1, "", "datafile"], [80, 6, 1, "", "debug"], [80, 6, 1, "", "die"], [80, 6, 1, "", "error"], [80, 6, 1, "", "filter"], [80, 6, 1, "", "gapextend"], [80, 6, 1, "", "gapopen"], [80, 6, 1, "", "help"], [80, 6, 1, "", "nobrief"], [80, 6, 1, "", "options"], [80, 6, 1, "", "outfile"], [80, 6, 1, "", "similarity"], [80, 6, 1, "", "snucleotide"], [80, 6, 1, "", "sprotein"], [80, 6, 1, "", "stdout"], [80, 6, 1, "", "verbose"], [80, 6, 1, "", "warning"]], "Bio.Emboss.Primer3": [[81, 3, 1, "", "Primers"], [81, 3, 1, "", "Record"], [81, 4, 1, "", "parse"], [81, 4, 1, "", "read"]], "Bio.Emboss.Primer3.Primers": [[81, 2, 1, "", "__init__"], [81, 2, 1, "", "__len__"]], "Bio.Emboss.Primer3.Record": [[81, 2, 1, "", "__init__"]], "Bio.Emboss.PrimerSearch": [[82, 3, 1, "", "Amplifier"], [82, 3, 1, "", "InputRecord"], [82, 3, 1, "", "OutputRecord"], [82, 4, 1, "", "read"]], "Bio.Emboss.PrimerSearch.Amplifier": [[82, 2, 1, "", "__init__"]], "Bio.Emboss.PrimerSearch.InputRecord": [[82, 2, 1, "", "__init__"], [82, 2, 1, "", "__str__"], [82, 2, 1, "", "add_primer_set"]], "Bio.Emboss.PrimerSearch.OutputRecord": [[82, 2, 1, "", "__init__"]], "Bio.Entrez": [[84, 0, 0, "-", "Parser"], [83, 4, 1, "", "ecitmatch"], [83, 4, 1, "", "efetch"], [83, 4, 1, "", "egquery"], [83, 4, 1, "", "einfo"], [83, 4, 1, "", "elink"], [83, 4, 1, "", "epost"], [83, 4, 1, "", "esearch"], [83, 4, 1, "", "espell"], [83, 4, 1, "", "esummary"], [83, 4, 1, "", "parse"], [83, 4, 1, "", "read"]], "Bio.Entrez.Parser": [[84, 1, 1, "", "CorruptedXMLError"], [84, 3, 1, "", "DataHandler"], [84, 3, 1, "", "DataHandlerMeta"], [84, 3, 1, "", "DictionaryElement"], [84, 3, 1, "", "ErrorElement"], [84, 3, 1, "", "IntegerElement"], [84, 3, 1, "", "ListElement"], [84, 3, 1, "", "NoneElement"], [84, 1, 1, "", "NotXMLError"], [84, 3, 1, "", "OrderedListElement"], [84, 3, 1, "", "StringElement"], [84, 1, 1, "", "ValidationError"]], "Bio.Entrez.Parser.CorruptedXMLError": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__str__"]], "Bio.Entrez.Parser.DataHandler": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "characterDataHandlerEscape"], [84, 2, 1, "", "characterDataHandlerRaw"], [84, 2, 1, "", "elementDecl"], [84, 2, 1, "", "endElementHandler"], [84, 2, 1, "", "endErrorElementHandler"], [84, 2, 1, "", "endIntegerElementHandler"], [84, 2, 1, "", "endNamespaceDeclHandler"], [84, 2, 1, "", "endRawElementHandler"], [84, 2, 1, "", "endSkipElementHandler"], [84, 2, 1, "", "endStringElementHandler"], [84, 2, 1, "", "externalEntityRefHandler"], [84, 5, 1, "", "global_dtd_dir"], [84, 5, 1, "", "global_xsd_dir"], [84, 2, 1, "", "handleMissingDocumentDefinition"], [84, 5, 1, "", "local_dtd_dir"], [84, 5, 1, "", "local_xsd_dir"], [84, 2, 1, "", "open_dtd_file"], [84, 2, 1, "", "open_xsd_file"], [84, 2, 1, "", "parse"], [84, 2, 1, "", "parse_xsd"], [84, 2, 1, "", "read"], [84, 2, 1, "", "save_dtd_file"], [84, 2, 1, "", "save_xsd_file"], [84, 2, 1, "", "schemaHandler"], [84, 2, 1, "", "skipCharacterDataHandler"], [84, 2, 1, "", "startElementHandler"], [84, 2, 1, "", "startNamespaceDeclHandler"], [84, 2, 1, "", "startRawElementHandler"], [84, 2, 1, "", "startSkipElementHandler"], [84, 2, 1, "", "xmlDeclHandler"]], "Bio.Entrez.Parser.DataHandlerMeta": [[84, 2, 1, "", "__init__"], [84, 6, 1, "", "directory"]], "Bio.Entrez.Parser.DictionaryElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__repr__"], [84, 2, 1, "", "store"]], "Bio.Entrez.Parser.ErrorElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__new__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.IntegerElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__new__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.ListElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__repr__"], [84, 2, 1, "", "store"]], "Bio.Entrez.Parser.NoneElement": [[84, 2, 1, "", "__eq__"], [84, 5, 1, "", "__hash__"], [84, 2, 1, "", "__init__"], [84, 2, 1, "", "__ne__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.NotXMLError": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__str__"]], "Bio.Entrez.Parser.OrderedListElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__repr__"], [84, 2, 1, "", "store"]], "Bio.Entrez.Parser.StringElement": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__new__"], [84, 2, 1, "", "__repr__"]], "Bio.Entrez.Parser.ValidationError": [[84, 2, 1, "", "__init__"], [84, 2, 1, "", "__str__"]], "Bio.ExPASy": [[86, 0, 0, "-", "Enzyme"], [87, 0, 0, "-", "Prodoc"], [88, 0, 0, "-", "Prosite"], [89, 0, 0, "-", "ScanProsite"], [90, 0, 0, "-", "cellosaurus"], [85, 4, 1, "", "get_prodoc_entry"], [85, 4, 1, "", "get_prosite_entry"], [85, 4, 1, "", "get_prosite_raw"], [85, 4, 1, "", "get_sprot_raw"]], "Bio.ExPASy.Enzyme": [[86, 3, 1, "", "Record"], [86, 4, 1, "", "parse"], [86, 4, 1, "", "read"]], "Bio.ExPASy.Enzyme.Record": [[86, 2, 1, "", "__init__"], [86, 2, 1, "", "__repr__"], [86, 2, 1, "", "__str__"]], "Bio.ExPASy.Prodoc": [[87, 3, 1, "", "Record"], [87, 3, 1, "", "Reference"], [87, 4, 1, "", "parse"], [87, 4, 1, "", "read"]], "Bio.ExPASy.Prodoc.Record": [[87, 2, 1, "", "__init__"]], "Bio.ExPASy.Prodoc.Reference": [[87, 2, 1, "", "__init__"]], "Bio.ExPASy.Prosite": [[88, 3, 1, "", "Record"], [88, 4, 1, "", "parse"], [88, 4, 1, "", "read"]], "Bio.ExPASy.Prosite.Record": [[88, 2, 1, "", "__init__"]], "Bio.ExPASy.ScanProsite": [[89, 3, 1, "", "ContentHandler"], [89, 3, 1, "", "Parser"], [89, 3, 1, "", "Record"], [89, 4, 1, "", "read"], [89, 4, 1, "", "scan"]], "Bio.ExPASy.ScanProsite.ContentHandler": [[89, 2, 1, "", "__init__"], [89, 2, 1, "", "characters"], [89, 2, 1, "", "endElement"], [89, 5, 1, "", "integers"], [89, 2, 1, "", "startElement"], [89, 5, 1, "", "strings"]], "Bio.ExPASy.ScanProsite.Parser": [[89, 2, 1, "", "__init__"], [89, 2, 1, "", "feed"]], "Bio.ExPASy.ScanProsite.Record": [[89, 2, 1, "", "__init__"]], "Bio.ExPASy.cellosaurus": [[90, 3, 1, "", "Record"], [90, 4, 1, "", "parse"], [90, 4, 1, "", "read"]], "Bio.ExPASy.cellosaurus.Record": [[90, 2, 1, "", "__init__"], [90, 2, 1, "", "__repr__"], [90, 2, 1, "", "__str__"]], "Bio.File": [[91, 4, 1, "", "as_handle"]], "Bio.GenBank": [[92, 3, 1, "", "FeatureParser"], [92, 3, 1, "", "Iterator"], [92, 1, 1, "", "ParserFailureError"], [93, 0, 0, "-", "Record"], [92, 3, 1, "", "RecordParser"], [94, 0, 0, "-", "Scanner"], [92, 4, 1, "", "parse"], [92, 4, 1, "", "read"], [95, 0, 0, "-", "utils"]], "Bio.GenBank.FeatureParser": [[92, 2, 1, "", "__init__"], [92, 2, 1, "", "parse"]], "Bio.GenBank.Iterator": [[92, 2, 1, "", "__init__"], [92, 2, 1, "", "__iter__"], [92, 2, 1, "", "__next__"]], "Bio.GenBank.Record": [[93, 3, 1, "", "Feature"], [93, 3, 1, "", "Qualifier"], [93, 3, 1, "", "Record"], [93, 3, 1, "", "Reference"]], "Bio.GenBank.Record.Feature": [[93, 2, 1, "", "__init__"], [93, 2, 1, "", "__repr__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.Record.Qualifier": [[93, 2, 1, "", "__init__"], [93, 2, 1, "", "__repr__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.Record.Record": [[93, 5, 1, "", "BASE_FEATURE_FORMAT"], [93, 5, 1, "", "BASE_FORMAT"], [93, 5, 1, "", "GB_BASE_INDENT"], [93, 5, 1, "", "GB_FEATURE_INDENT"], [93, 5, 1, "", "GB_FEATURE_INTERNAL_INDENT"], [93, 5, 1, "", "GB_INTERNAL_INDENT"], [93, 5, 1, "", "GB_LINE_LENGTH"], [93, 5, 1, "", "GB_OTHER_INTERNAL_INDENT"], [93, 5, 1, "", "GB_SEQUENCE_INDENT"], [93, 5, 1, "", "INTERNAL_FEATURE_FORMAT"], [93, 5, 1, "", "INTERNAL_FORMAT"], [93, 5, 1, "", "OTHER_INTERNAL_FORMAT"], [93, 5, 1, "", "SEQUENCE_FORMAT"], [93, 2, 1, "", "__init__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.Record.Reference": [[93, 2, 1, "", "__init__"], [93, 2, 1, "", "__str__"]], "Bio.GenBank.RecordParser": [[92, 2, 1, "", "__init__"], [92, 2, 1, "", "parse"]], "Bio.GenBank.Scanner": [[94, 3, 1, "", "EmblScanner"], [94, 3, 1, "", "GenBankScanner"], [94, 3, 1, "", "InsdcScanner"]], "Bio.GenBank.Scanner.EmblScanner": [[94, 5, 1, "", "EMBL_INDENT"], [94, 5, 1, "", "EMBL_SPACER"], [94, 5, 1, "", "FEATURE_END_MARKERS"], [94, 5, 1, "", "FEATURE_QUALIFIER_INDENT"], [94, 5, 1, "", "FEATURE_QUALIFIER_SPACER"], [94, 5, 1, "", "FEATURE_START_MARKERS"], [94, 5, 1, "", "HEADER_WIDTH"], [94, 5, 1, "", "RECORD_START"], [94, 5, 1, "", "SEQUENCE_HEADERS"], [94, 2, 1, "", "parse_footer"]], "Bio.GenBank.Scanner.GenBankScanner": [[94, 5, 1, "", "FEATURE_END_MARKERS"], [94, 5, 1, "", "FEATURE_QUALIFIER_INDENT"], [94, 5, 1, "", "FEATURE_QUALIFIER_SPACER"], [94, 5, 1, "", "FEATURE_START_MARKERS"], [94, 5, 1, "", "GENBANK_INDENT"], [94, 5, 1, "", "GENBANK_SPACER"], [94, 5, 1, "", "HEADER_WIDTH"], [94, 5, 1, "", "RECORD_START"], [94, 5, 1, "", "SEQUENCE_HEADERS"], [94, 5, 1, "", "STRUCTURED_COMMENT_DELIM"], [94, 5, 1, "", "STRUCTURED_COMMENT_END"], [94, 5, 1, "", "STRUCTURED_COMMENT_START"], [94, 5, 1, "", "__annotations__"], [94, 2, 1, "", "parse_footer"]], "Bio.GenBank.Scanner.InsdcScanner": [[94, 5, 1, "", "FEATURE_END_MARKERS"], [94, 5, 1, "", "FEATURE_QUALIFIER_INDENT"], [94, 5, 1, "", "FEATURE_QUALIFIER_SPACER"], [94, 5, 1, "", "FEATURE_START_MARKERS"], [94, 5, 1, "", "HEADER_WIDTH"], [94, 5, 1, "", "RECORD_START"], [94, 5, 1, "", "SEQUENCE_HEADERS"], [94, 2, 1, "", "__init__"], [94, 2, 1, "", "feed"], [94, 2, 1, "", "find_start"], [94, 2, 1, "", "parse"], [94, 2, 1, "", "parse_cds_features"], [94, 2, 1, "", "parse_feature"], [94, 2, 1, "", "parse_features"], [94, 2, 1, "", "parse_footer"], [94, 2, 1, "", "parse_header"], [94, 2, 1, "", "parse_records"], [94, 2, 1, "", "set_handle"]], "Bio.GenBank.utils": [[95, 3, 1, "", "FeatureValueCleaner"]], "Bio.GenBank.utils.FeatureValueCleaner": [[95, 2, 1, "", "__init__"], [95, 2, 1, "", "__repr__"], [95, 2, 1, "", "clean_value"], [95, 5, 1, "", "keys_to_process"]], "Bio.Geo": [[97, 0, 0, "-", "Record"], [96, 4, 1, "", "parse"]], "Bio.Geo.Record": [[97, 3, 1, "", "Record"], [97, 4, 1, "", "out_block"]], "Bio.Geo.Record.Record": [[97, 2, 1, "", "__init__"], [97, 2, 1, "", "__str__"]], "Bio.Graphics": [[99, 0, 0, "-", "BasicChromosome"], [100, 0, 0, "-", "ColorSpiral"], [101, 0, 0, "-", "Comparative"], [102, 0, 0, "-", "DisplayRepresentation"], [103, 0, 0, "-", "Distribution"], [104, 0, 0, "-", "GenomeDiagram"], [105, 0, 0, "-", "KGML_vis"]], "Bio.Graphics.BasicChromosome": [[99, 3, 1, "", "AnnotatedChromosomeSegment"], [99, 3, 1, "", "Chromosome"], [99, 3, 1, "", "ChromosomeSegment"], [99, 3, 1, "", "Organism"], [99, 3, 1, "", "SpacerSegment"], [99, 3, 1, "", "TelomereSegment"]], "Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment": [[99, 2, 1, "", "__init__"]], "Bio.Graphics.BasicChromosome.Chromosome": [[99, 2, 1, "", "__init__"], [99, 2, 1, "", "draw"], [99, 2, 1, "", "subcomponent_size"]], "Bio.Graphics.BasicChromosome.ChromosomeSegment": [[99, 2, 1, "", "__init__"], [99, 2, 1, "", "draw"]], "Bio.Graphics.BasicChromosome.Organism": [[99, 2, 1, "", "__init__"], [99, 2, 1, "", "draw"]], "Bio.Graphics.BasicChromosome.SpacerSegment": [[99, 2, 1, "", "draw"]], "Bio.Graphics.BasicChromosome.TelomereSegment": [[99, 2, 1, "", "__init__"]], "Bio.Graphics.ColorSpiral": [[100, 3, 1, "", "ColorSpiral"], [100, 4, 1, "", "get_color_dict"], [100, 4, 1, "", "get_colors"]], "Bio.Graphics.ColorSpiral.ColorSpiral": [[100, 2, 1, "", "__init__"], [100, 6, 1, "", "a"], [100, 6, 1, "", "b"], [100, 2, 1, "", "get_colors"], [100, 6, 1, "", "jitter"], [100, 6, 1, "", "v_final"], [100, 6, 1, "", "v_init"]], "Bio.Graphics.Comparative": [[101, 3, 1, "", "ComparativeScatterPlot"]], "Bio.Graphics.Comparative.ComparativeScatterPlot": [[101, 2, 1, "", "__init__"], [101, 2, 1, "", "draw_to_file"]], "Bio.Graphics.DisplayRepresentation": [[102, 3, 1, "", "ChromosomeCounts"]], "Bio.Graphics.DisplayRepresentation.ChromosomeCounts": [[102, 2, 1, "", "__init__"], [102, 2, 1, "", "add_count"], [102, 2, 1, "", "add_label"], [102, 2, 1, "", "fill_chromosome"], [102, 2, 1, "", "get_segment_info"], [102, 2, 1, "", "scale_segment_value"], [102, 2, 1, "", "set_scale"]], "Bio.Graphics.Distribution": [[103, 3, 1, "", "BarChartDistribution"], [103, 3, 1, "", "DistributionPage"], [103, 3, 1, "", "LineDistribution"]], "Bio.Graphics.Distribution.BarChartDistribution": [[103, 2, 1, "", "__init__"], [103, 2, 1, "", "draw"]], "Bio.Graphics.Distribution.DistributionPage": [[103, 2, 1, "", "__init__"], [103, 2, 1, "", "draw"]], "Bio.Graphics.Distribution.LineDistribution": [[103, 2, 1, "", "__init__"], [103, 2, 1, "", "draw"]], "Bio.Graphics.GenomeDiagram": [[104, 3, 1, "", "ColorTranslator"], [104, 3, 1, "", "CrossLink"], [104, 3, 1, "", "Diagram"], [104, 3, 1, "", "Feature"], [104, 3, 1, "", "FeatureSet"], [104, 3, 1, "", "GraphData"], [104, 3, 1, "", "GraphSet"], [104, 3, 1, "", "Track"]], "Bio.Graphics.GenomeDiagram.ColorTranslator": [[104, 2, 1, "", "__init__"], [104, 2, 1, "", "artemis_color"], [104, 2, 1, "", "float1_color"], [104, 2, 1, "", "get_artemis_colorscheme"], [104, 2, 1, "", "get_colorscheme"], [104, 2, 1, "", "int255_color"], [104, 2, 1, "", "read_colorscheme"], [104, 2, 1, "", "scheme_color"], [104, 2, 1, "", "translate"]], "Bio.Graphics.GenomeDiagram.CrossLink": [[104, 2, 1, "", "__init__"], [104, 6, 1, "", "endA"], [104, 6, 1, "", "endB"], [104, 6, 1, "", "startA"], [104, 6, 1, "", "startB"]], "Bio.Graphics.GenomeDiagram.Diagram": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_track"], [104, 2, 1, "", "del_track"], [104, 2, 1, "", "draw"], [104, 2, 1, "", "get_drawn_levels"], [104, 2, 1, "", "get_levels"], [104, 2, 1, "", "get_tracks"], [104, 2, 1, "", "move_track"], [104, 2, 1, "", "new_track"], [104, 2, 1, "", "range"], [104, 2, 1, "", "renumber_tracks"], [104, 2, 1, "", "set_all_tracks"], [104, 2, 1, "", "write"], [104, 2, 1, "", "write_to_string"]], "Bio.Graphics.GenomeDiagram.Feature": [[104, 2, 1, "", "__getattr__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "get_feature"], [104, 2, 1, "", "set_color"], [104, 2, 1, "", "set_colour"], [104, 2, 1, "", "set_feature"]], "Bio.Graphics.GenomeDiagram.FeatureSet": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__len__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_feature"], [104, 2, 1, "", "del_feature"], [104, 2, 1, "", "get_features"], [104, 2, 1, "", "get_ids"], [104, 2, 1, "", "range"], [104, 2, 1, "", "set_all_features"], [104, 2, 1, "", "to_string"]], "Bio.Graphics.GenomeDiagram.GraphData": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__len__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_point"], [104, 2, 1, "", "get_data"], [104, 2, 1, "", "mean"], [104, 2, 1, "", "quartiles"], [104, 2, 1, "", "range"], [104, 2, 1, "", "set_data"], [104, 2, 1, "", "stdev"]], "Bio.Graphics.GenomeDiagram.GraphSet": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__len__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "data_quartiles"], [104, 2, 1, "", "del_graph"], [104, 2, 1, "", "get_graphs"], [104, 2, 1, "", "get_ids"], [104, 2, 1, "", "new_graph"], [104, 2, 1, "", "range"], [104, 2, 1, "", "to_string"]], "Bio.Graphics.GenomeDiagram.Track": [[104, 2, 1, "", "__getitem__"], [104, 2, 1, "", "__init__"], [104, 2, 1, "", "__str__"], [104, 2, 1, "", "add_set"], [104, 2, 1, "", "del_set"], [104, 2, 1, "", "get_ids"], [104, 2, 1, "", "get_sets"], [104, 2, 1, "", "new_set"], [104, 2, 1, "", "range"], [104, 2, 1, "", "to_string"]], "Bio.Graphics.KGML_vis": [[105, 3, 1, "", "KGMLCanvas"], [105, 4, 1, "", "color_to_reportlab"], [105, 4, 1, "", "darken"], [105, 4, 1, "", "get_temp_imagefilename"]], "Bio.Graphics.KGML_vis.KGMLCanvas": [[105, 2, 1, "", "__init__"], [105, 2, 1, "", "draw"]], "Bio.HMM": [[107, 0, 0, "-", "DynamicProgramming"], [108, 0, 0, "-", "MarkovModel"], [109, 0, 0, "-", "Trainer"], [110, 0, 0, "-", "Utilities"]], "Bio.HMM.DynamicProgramming": [[107, 3, 1, "", "AbstractDPAlgorithms"], [107, 3, 1, "", "LogDPAlgorithms"], [107, 3, 1, "", "ScaledDPAlgorithms"]], "Bio.HMM.DynamicProgramming.AbstractDPAlgorithms": [[107, 2, 1, "", "__init__"], [107, 2, 1, "", "backward_algorithm"], [107, 2, 1, "", "forward_algorithm"]], "Bio.HMM.DynamicProgramming.LogDPAlgorithms": [[107, 2, 1, "", "__init__"]], "Bio.HMM.DynamicProgramming.ScaledDPAlgorithms": [[107, 2, 1, "", "__init__"]], "Bio.HMM.MarkovModel": [[108, 3, 1, "", "HiddenMarkovModel"], [108, 3, 1, "", "MarkovModelBuilder"]], "Bio.HMM.MarkovModel.HiddenMarkovModel": [[108, 2, 1, "", "__init__"], [108, 2, 1, "", "get_blank_emissions"], [108, 2, 1, "", "get_blank_transitions"], [108, 2, 1, "", "transitions_from"], [108, 2, 1, "", "transitions_to"], [108, 2, 1, "", "viterbi"]], "Bio.HMM.MarkovModel.MarkovModelBuilder": [[108, 5, 1, "", "DEFAULT_PSEUDO"], [108, 2, 1, "", "__init__"], [108, 2, 1, "", "allow_all_transitions"], [108, 2, 1, "", "allow_transition"], [108, 2, 1, "", "destroy_transition"], [108, 2, 1, "", "get_markov_model"], [108, 2, 1, "", "set_emission_pseudocount"], [108, 2, 1, "", "set_emission_score"], [108, 2, 1, "", "set_equal_probabilities"], [108, 2, 1, "", "set_initial_probabilities"], [108, 2, 1, "", "set_random_emission_probabilities"], [108, 2, 1, "", "set_random_initial_probabilities"], [108, 2, 1, "", "set_random_probabilities"], [108, 2, 1, "", "set_random_transition_probabilities"], [108, 2, 1, "", "set_transition_pseudocount"], [108, 2, 1, "", "set_transition_score"]], "Bio.HMM.Trainer": [[109, 3, 1, "", "AbstractTrainer"], [109, 3, 1, "", "BaumWelchTrainer"], [109, 3, 1, "", "KnownStateTrainer"], [109, 3, 1, "", "TrainingSequence"]], "Bio.HMM.Trainer.AbstractTrainer": [[109, 2, 1, "", "__init__"], [109, 2, 1, "", "estimate_params"], [109, 2, 1, "", "log_likelihood"], [109, 2, 1, "", "ml_estimator"]], "Bio.HMM.Trainer.BaumWelchTrainer": [[109, 2, 1, "", "__init__"], [109, 2, 1, "", "train"], [109, 2, 1, "", "update_emissions"], [109, 2, 1, "", "update_transitions"]], "Bio.HMM.Trainer.KnownStateTrainer": [[109, 2, 1, "", "__init__"], [109, 2, 1, "", "train"]], "Bio.HMM.Trainer.TrainingSequence": [[109, 2, 1, "", "__init__"]], "Bio.HMM.Utilities": [[110, 4, 1, "", "pretty_print_prediction"]], "Bio.KEGG": [[112, 0, 0, "-", "Compound"], [113, 0, 0, "-", "Enzyme"], [114, 0, 0, "-", "Gene"], [115, 0, 0, "-", "KGML"], [118, 0, 0, "-", "Map"], [119, 0, 0, "-", "REST"]], "Bio.KEGG.Compound": [[112, 3, 1, "", "Record"], [112, 4, 1, "", "parse"]], "Bio.KEGG.Compound.Record": [[112, 2, 1, "", "__init__"], [112, 2, 1, "", "__str__"]], "Bio.KEGG.Enzyme": [[113, 3, 1, "", "Record"], [113, 4, 1, "", "parse"], [113, 4, 1, "", "read"]], "Bio.KEGG.Enzyme.Record": [[113, 2, 1, "", "__init__"], [113, 2, 1, "", "__str__"]], "Bio.KEGG.Gene": [[114, 3, 1, "", "Record"], [114, 4, 1, "", "parse"]], "Bio.KEGG.Gene.Record": [[114, 2, 1, "", "__init__"], [114, 2, 1, "", "__str__"]], "Bio.KEGG.KGML": [[116, 0, 0, "-", "KGML_parser"], [117, 0, 0, "-", "KGML_pathway"]], "Bio.KEGG.KGML.KGML_parser": [[116, 3, 1, "", "KGMLParser"], [116, 4, 1, "", "parse"], [116, 4, 1, "", "read"]], "Bio.KEGG.KGML.KGML_parser.KGMLParser": [[116, 2, 1, "", "__init__"], [116, 2, 1, "", "parse"]], "Bio.KEGG.KGML.KGML_pathway": [[117, 3, 1, "", "Component"], [117, 3, 1, "", "Entry"], [117, 3, 1, "", "Graphics"], [117, 3, 1, "", "Pathway"], [117, 3, 1, "", "Reaction"], [117, 3, 1, "", "Relation"]], "Bio.KEGG.KGML.KGML_pathway.Component": [[117, 2, 1, "", "__init__"], [117, 6, 1, "", "element"], [117, 6, 1, "", "id"]], "Bio.KEGG.KGML.KGML_pathway.Entry": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 2, 1, "", "add_component"], [117, 2, 1, "", "add_graphics"], [117, 6, 1, "", "bounds"], [117, 6, 1, "", "element"], [117, 6, 1, "", "id"], [117, 6, 1, "", "is_reactant"], [117, 6, 1, "", "name"], [117, 6, 1, "", "reaction"], [117, 2, 1, "", "remove_component"], [117, 2, 1, "", "remove_graphics"]], "Bio.KEGG.KGML.KGML_pathway.Graphics": [[117, 2, 1, "", "__init__"], [117, 6, 1, "", "bgcolor"], [117, 6, 1, "", "bounds"], [117, 6, 1, "", "centre"], [117, 6, 1, "", "coords"], [117, 6, 1, "", "element"], [117, 6, 1, "", "fgcolor"], [117, 6, 1, "", "height"], [117, 6, 1, "", "width"], [117, 6, 1, "", "x"], [117, 6, 1, "", "y"]], "Bio.KEGG.KGML.KGML_pathway.Pathway": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 2, 1, "", "add_entry"], [117, 2, 1, "", "add_reaction"], [117, 2, 1, "", "add_relation"], [117, 6, 1, "", "bounds"], [117, 6, 1, "", "compounds"], [117, 6, 1, "", "element"], [117, 6, 1, "", "genes"], [117, 2, 1, "", "get_KGML"], [117, 6, 1, "", "maps"], [117, 6, 1, "", "name"], [117, 6, 1, "", "number"], [117, 6, 1, "", "orthologs"], [117, 6, 1, "", "reaction_entries"], [117, 6, 1, "", "reactions"], [117, 6, 1, "", "relations"], [117, 2, 1, "", "remove_entry"], [117, 2, 1, "", "remove_reaction"], [117, 2, 1, "", "remove_relation"]], "Bio.KEGG.KGML.KGML_pathway.Reaction": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 2, 1, "", "add_product"], [117, 2, 1, "", "add_substrate"], [117, 6, 1, "", "element"], [117, 6, 1, "", "entry"], [117, 6, 1, "", "id"], [117, 6, 1, "", "name"], [117, 6, 1, "", "products"], [117, 6, 1, "", "reactant_ids"], [117, 6, 1, "", "substrates"]], "Bio.KEGG.KGML.KGML_pathway.Relation": [[117, 2, 1, "", "__init__"], [117, 2, 1, "", "__str__"], [117, 6, 1, "", "element"], [117, 6, 1, "", "entry1"], [117, 6, 1, "", "entry2"]], "Bio.KEGG.Map": [[118, 4, 1, "", "parse"]], "Bio.KEGG.REST": [[119, 4, 1, "", "kegg_conv"], [119, 4, 1, "", "kegg_find"], [119, 4, 1, "", "kegg_get"], [119, 4, 1, "", "kegg_info"], [119, 4, 1, "", "kegg_link"], [119, 4, 1, "", "kegg_list"]], "Bio.LogisticRegression": [[120, 3, 1, "", "LogisticRegression"], [120, 4, 1, "", "calculate"], [120, 4, 1, "", "classify"], [120, 4, 1, "", "train"]], "Bio.LogisticRegression.LogisticRegression": [[120, 2, 1, "", "__init__"]], "Bio.MarkovModel": [[121, 3, 1, "", "MarkovModel"], [121, 4, 1, "", "find_states"], [121, 4, 1, "", "itemindex"], [121, 4, 1, "", "load"], [121, 4, 1, "", "save"], [121, 4, 1, "", "train_bw"], [121, 4, 1, "", "train_visible"]], "Bio.MarkovModel.MarkovModel": [[121, 2, 1, "", "__init__"], [121, 2, 1, "", "__str__"]], "Bio.MaxEntropy": [[122, 3, 1, "", "MaxEntropy"], [122, 4, 1, "", "calculate"], [122, 4, 1, "", "classify"], [122, 4, 1, "", "train"]], "Bio.MaxEntropy.MaxEntropy": [[122, 2, 1, "", "__init__"]], "Bio.Medline": [[123, 3, 1, "", "Record"], [123, 4, 1, "", "parse"], [123, 4, 1, "", "read"]], "Bio.NMR": [[125, 0, 0, "-", "NOEtools"], [126, 0, 0, "-", "xpktools"]], "Bio.NMR.NOEtools": [[125, 4, 1, "", "predictNOE"]], "Bio.NMR.xpktools": [[126, 3, 1, "", "Peaklist"], [126, 3, 1, "", "XpkEntry"], [126, 4, 1, "", "data_table"], [126, 4, 1, "", "replace_entry"]], "Bio.NMR.xpktools.Peaklist": [[126, 2, 1, "", "__init__"], [126, 2, 1, "", "residue_dict"], [126, 2, 1, "", "write_header"]], "Bio.NMR.xpktools.XpkEntry": [[126, 2, 1, "", "__init__"]], "Bio.NaiveBayes": [[127, 3, 1, "", "NaiveBayes"], [127, 4, 1, "", "calculate"], [127, 4, 1, "", "classify"], [127, 4, 1, "", "train"]], "Bio.NaiveBayes.NaiveBayes": [[127, 2, 1, "", "__init__"]], "Bio.Nexus": [[129, 0, 0, "-", "Nexus"], [130, 0, 0, "-", "Nodes"], [131, 0, 0, "-", "StandardData"], [132, 0, 0, "-", "Trees"]], "Bio.Nexus.Nexus": [[129, 3, 1, "", "Block"], [129, 3, 1, "", "CharBuffer"], [129, 3, 1, "", "Commandline"], [129, 3, 1, "", "Nexus"], [129, 1, 1, "", "NexusError"], [129, 3, 1, "", "StepMatrix"], [129, 4, 1, "", "combine"], [129, 4, 1, "", "get_start_end"], [129, 4, 1, "", "quotestrip"], [129, 4, 1, "", "safename"]], "Bio.Nexus.Nexus.Block": [[129, 2, 1, "", "__init__"]], "Bio.Nexus.Nexus.CharBuffer": [[129, 2, 1, "", "__init__"], [129, 2, 1, "", "__next__"], [129, 2, 1, "", "next_nonwhitespace"], [129, 2, 1, "", "next_until"], [129, 2, 1, "", "next_word"], [129, 2, 1, "", "peek"], [129, 2, 1, "", "peek_nonwhitespace"], [129, 2, 1, "", "peek_word"], [129, 2, 1, "", "rest"], [129, 2, 1, "", "skip_whitespace"]], "Bio.Nexus.Nexus.Commandline": [[129, 2, 1, "", "__init__"]], "Bio.Nexus.Nexus.Nexus": [[129, 2, 1, "", "__init__"], [129, 2, 1, "", "add_sequence"], [129, 2, 1, "", "append_sets"], [129, 2, 1, "", "bootstrap"], [129, 2, 1, "", "constant"], [129, 2, 1, "", "crop_matrix"], [129, 2, 1, "", "cstatus"], [129, 2, 1, "", "export_fasta"], [129, 2, 1, "", "export_phylip"], [129, 2, 1, "", "gaponly"], [129, 2, 1, "", "insert_gap"], [129, 2, 1, "", "invert"], [129, 2, 1, "", "read"], [129, 2, 1, "", "terminal_gap_to_missing"], [129, 2, 1, "", "weighted_stepmatrix"], [129, 2, 1, "", "write_nexus_data"], [129, 2, 1, "", "write_nexus_data_partitions"]], "Bio.Nexus.Nexus.StepMatrix": [[129, 2, 1, "", "__init__"], [129, 2, 1, "", "add"], [129, 2, 1, "", "set"], [129, 2, 1, "", "smprint"], [129, 2, 1, "", "sum"], [129, 2, 1, "", "transformation"], [129, 2, 1, "", "weighting"]], "Bio.Nexus.Nodes": [[130, 3, 1, "", "Chain"], [130, 1, 1, "", "ChainException"], [130, 3, 1, "", "Node"], [130, 1, 1, "", "NodeException"]], "Bio.Nexus.Nodes.Chain": [[130, 2, 1, "", "__init__"], [130, 2, 1, "", "add"], [130, 2, 1, "", "all_ids"], [130, 2, 1, "", "collapse"], [130, 2, 1, "", "is_parent_of"], [130, 2, 1, "", "kill"], [130, 2, 1, "", "link"], [130, 2, 1, "", "trace"], [130, 2, 1, "", "unlink"]], "Bio.Nexus.Nodes.Node": [[130, 2, 1, "", "__init__"], [130, 2, 1, "", "add_succ"], [130, 2, 1, "", "get_data"], [130, 2, 1, "", "get_id"], [130, 2, 1, "", "get_prev"], [130, 2, 1, "", "get_succ"], [130, 2, 1, "", "remove_succ"], [130, 2, 1, "", "set_data"], [130, 2, 1, "", "set_id"], [130, 2, 1, "", "set_prev"], [130, 2, 1, "", "set_succ"]], "Bio.Nexus.StandardData": [[131, 1, 1, "", "NexusError"], [131, 3, 1, "", "StandardData"]], "Bio.Nexus.StandardData.StandardData": [[131, 2, 1, "", "__getitem__"], [131, 2, 1, "", "__init__"], [131, 2, 1, "", "__iter__"], [131, 2, 1, "", "__len__"], [131, 2, 1, "", "__next__"], [131, 2, 1, "", "__str__"], [131, 2, 1, "", "raw"]], "Bio.Nexus.Trees": [[132, 3, 1, "", "NodeData"], [132, 3, 1, "", "Tree"], [132, 1, 1, "", "TreeError"], [132, 4, 1, "", "consensus"]], "Bio.Nexus.Trees.NodeData": [[132, 2, 1, "", "__init__"]], "Bio.Nexus.Trees.Tree": [[132, 2, 1, "", "__init__"], [132, 2, 1, "", "__str__"], [132, 2, 1, "", "branchlength2support"], [132, 2, 1, "", "collapse_genera"], [132, 2, 1, "", "common_ancestor"], [132, 2, 1, "", "convert_absolute_support"], [132, 2, 1, "", "count_terminals"], [132, 2, 1, "", "display"], [132, 2, 1, "", "distance"], [132, 2, 1, "", "get_taxa"], [132, 2, 1, "", "get_terminals"], [132, 2, 1, "", "has_support"], [132, 2, 1, "", "is_bifurcating"], [132, 2, 1, "", "is_compatible"], [132, 2, 1, "", "is_identical"], [132, 2, 1, "", "is_internal"], [132, 2, 1, "", "is_monophyletic"], [132, 2, 1, "", "is_preterminal"], [132, 2, 1, "", "is_terminal"], [132, 2, 1, "", "merge_with_support"], [132, 2, 1, "", "node"], [132, 2, 1, "", "prune"], [132, 2, 1, "", "randomize"], [132, 2, 1, "", "root_with_outgroup"], [132, 2, 1, "", "search_taxon"], [132, 2, 1, "", "set_subtree"], [132, 2, 1, "", "split"], [132, 2, 1, "", "sum_branchlength"], [132, 2, 1, "", "to_string"], [132, 2, 1, "", "unroot"]], "Bio.PDB": [[134, 0, 0, "-", "AbstractPropertyMap"], [135, 0, 0, "-", "Atom"], [136, 0, 0, "-", "Chain"], [137, 0, 0, "-", "DSSP"], [138, 0, 0, "-", "Dice"], [139, 0, 0, "-", "Entity"], [140, 0, 0, "-", "FragmentMapper"], [141, 0, 0, "-", "HSExposure"], [142, 0, 0, "-", "MMCIF2Dict"], [143, 0, 0, "-", "MMCIFParser"], [144, 0, 0, "-", "Model"], [145, 0, 0, "-", "NACCESS"], [146, 0, 0, "-", "NeighborSearch"], [147, 0, 0, "-", "PDBExceptions"], [148, 0, 0, "-", "PDBIO"], [149, 0, 0, "-", "PDBList"], [150, 0, 0, "-", "PDBMLParser"], [151, 0, 0, "-", "PDBParser"], [152, 0, 0, "-", "PICIO"], [153, 0, 0, "-", "PSEA"], [154, 0, 0, "-", "Polypeptide"], [155, 0, 0, "-", "Residue"], [156, 0, 0, "-", "ResidueDepth"], [157, 0, 0, "-", "SASA"], [158, 0, 0, "-", "SCADIO"], [159, 0, 0, "-", "Selection"], [160, 0, 0, "-", "Structure"], [161, 0, 0, "-", "StructureAlignment"], [162, 0, 0, "-", "StructureBuilder"], [163, 0, 0, "-", "Superimposer"], [164, 0, 0, "-", "alphafold_db"], [165, 0, 0, "-", "binary_cif"], [166, 0, 0, "-", "cealign"], [167, 0, 0, "-", "ic_data"], [168, 0, 0, "-", "ic_rebuild"], [169, 0, 0, "-", "internal_coords"], [170, 0, 0, "-", "mmcifio"], [171, 0, 0, "-", "mmtf"], [174, 0, 0, "-", "parse_pdb_header"], [175, 0, 0, "-", "qcprot"], [176, 0, 0, "-", "vectors"]], "Bio.PDB.AbstractPropertyMap": [[134, 3, 1, "", "AbstractAtomPropertyMap"], [134, 3, 1, "", "AbstractPropertyMap"], [134, 3, 1, "", "AbstractResiduePropertyMap"]], "Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap": [[134, 2, 1, "", "__init__"]], "Bio.PDB.AbstractPropertyMap.AbstractPropertyMap": [[134, 2, 1, "", "__contains__"], [134, 2, 1, "", "__getitem__"], [134, 2, 1, "", "__init__"], [134, 2, 1, "", "__iter__"], [134, 2, 1, "", "__len__"], [134, 2, 1, "", "keys"]], "Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap": [[134, 2, 1, "", "__init__"]], "Bio.PDB.Atom": [[135, 3, 1, "", "Atom"], [135, 3, 1, "", "DisorderedAtom"]], "Bio.PDB.Atom.Atom": [[135, 2, 1, "", "__eq__"], [135, 2, 1, "", "__ge__"], [135, 2, 1, "", "__gt__"], [135, 2, 1, "", "__hash__"], [135, 2, 1, "", "__init__"], [135, 2, 1, "", "__le__"], [135, 2, 1, "", "__lt__"], [135, 2, 1, "", "__ne__"], [135, 2, 1, "", "__repr__"], [135, 2, 1, "", "__sub__"], [135, 2, 1, "", "copy"], [135, 2, 1, "", "detach_parent"], [135, 2, 1, "", "flag_disorder"], [135, 2, 1, "", "get_altloc"], [135, 2, 1, "", "get_anisou"], [135, 2, 1, "", "get_bfactor"], [135, 2, 1, "", "get_charge"], [135, 2, 1, "", "get_coord"], [135, 2, 1, "", "get_full_id"], [135, 2, 1, "", "get_fullname"], [135, 2, 1, "", "get_id"], [135, 2, 1, "", "get_level"], [135, 2, 1, "", "get_name"], [135, 2, 1, "", "get_occupancy"], [135, 2, 1, "", "get_parent"], [135, 2, 1, "", "get_radius"], [135, 2, 1, "", "get_serial_number"], [135, 2, 1, "", "get_sigatm"], [135, 2, 1, "", "get_siguij"], [135, 2, 1, "", "get_vector"], [135, 2, 1, "", "is_disordered"], [135, 2, 1, "", "set_altloc"], [135, 2, 1, "", "set_anisou"], [135, 2, 1, "", "set_bfactor"], [135, 2, 1, "", "set_charge"], [135, 2, 1, "", "set_coord"], [135, 2, 1, "", "set_occupancy"], [135, 2, 1, "", "set_parent"], [135, 2, 1, "", "set_radius"], [135, 2, 1, "", "set_serial_number"], [135, 2, 1, "", "set_sigatm"], [135, 2, 1, "", "set_siguij"], [135, 2, 1, "", "strictly_equals"], [135, 2, 1, "", "transform"]], "Bio.PDB.Atom.DisorderedAtom": [[135, 2, 1, "", "__init__"], [135, 2, 1, "", "__iter__"], [135, 2, 1, "", "__repr__"], [135, 2, 1, "", "center_of_mass"], [135, 2, 1, "", "disordered_add"], [135, 2, 1, "", "disordered_get_list"], [135, 2, 1, "", "disordered_remove"], [135, 2, 1, "", "transform"]], "Bio.PDB.Chain": [[136, 3, 1, "", "Chain"]], "Bio.PDB.Chain.Chain": [[136, 2, 1, "", "__contains__"], [136, 2, 1, "", "__delitem__"], [136, 2, 1, "", "__ge__"], [136, 2, 1, "", "__getitem__"], [136, 2, 1, "", "__gt__"], [136, 2, 1, "", "__init__"], [136, 2, 1, "", "__le__"], [136, 2, 1, "", "__lt__"], [136, 5, 1, "", "__orig_bases__"], [136, 5, 1, "", "__parameters__"], [136, 2, 1, "", "__repr__"], [136, 2, 1, "", "atom_to_internal_coordinates"], [136, 2, 1, "", "get_atoms"], [136, 2, 1, "", "get_residues"], [136, 2, 1, "", "get_unpacked_list"], [136, 2, 1, "", "has_id"], [136, 2, 1, "", "internal_to_atom_coordinates"]], "Bio.PDB.DSSP": [[137, 3, 1, "", "DSSP"], [137, 4, 1, "", "dssp_dict_from_pdb_file"], [137, 4, 1, "", "make_dssp_dict"], [137, 4, 1, "", "ss_to_index"], [137, 4, 1, "", "version"]], "Bio.PDB.DSSP.DSSP": [[137, 2, 1, "", "__init__"]], "Bio.PDB.Dice": [[138, 3, 1, "", "ChainSelector"], [138, 4, 1, "", "extract"]], "Bio.PDB.Dice.ChainSelector": [[138, 2, 1, "", "__init__"], [138, 2, 1, "", "accept_atom"], [138, 2, 1, "", "accept_chain"], [138, 2, 1, "", "accept_model"], [138, 2, 1, "", "accept_residue"]], "Bio.PDB.Entity": [[139, 3, 1, "", "DisorderedEntityWrapper"], [139, 3, 1, "", "Entity"]], "Bio.PDB.Entity.DisorderedEntityWrapper": [[139, 2, 1, "", "__contains__"], [139, 2, 1, "", "__ge__"], [139, 2, 1, "", "__getattr__"], [139, 2, 1, "", "__getitem__"], [139, 2, 1, "", "__gt__"], [139, 2, 1, "", "__init__"], [139, 2, 1, "", "__iter__"], [139, 2, 1, "", "__le__"], [139, 2, 1, "", "__len__"], [139, 2, 1, "", "__lt__"], [139, 2, 1, "", "__setitem__"], [139, 2, 1, "", "__sub__"], [139, 2, 1, "", "copy"], [139, 2, 1, "", "detach_parent"], [139, 2, 1, "", "disordered_add"], [139, 2, 1, "", "disordered_get"], [139, 2, 1, "", "disordered_get_id_list"], [139, 2, 1, "", "disordered_get_list"], [139, 2, 1, "", "disordered_has_id"], [139, 2, 1, "", "disordered_remove"], [139, 2, 1, "", "disordered_select"], [139, 2, 1, "", "get_id"], [139, 2, 1, "", "get_parent"], [139, 2, 1, "", "is_disordered"], [139, 2, 1, "", "set_parent"], [139, 2, 1, "", "strictly_equals"]], "Bio.PDB.Entity.Entity": [[139, 5, 1, "", "__annotations__"], [139, 2, 1, "", "__contains__"], [139, 2, 1, "", "__delitem__"], [139, 2, 1, "", "__eq__"], [139, 2, 1, "", "__ge__"], [139, 2, 1, "", "__getitem__"], [139, 2, 1, "", "__gt__"], [139, 2, 1, "", "__hash__"], [139, 2, 1, "", "__init__"], [139, 2, 1, "", "__iter__"], [139, 2, 1, "", "__le__"], [139, 2, 1, "", "__len__"], [139, 2, 1, "", "__lt__"], [139, 2, 1, "", "__ne__"], [139, 5, 1, "", "__orig_bases__"], [139, 5, 1, "", "__parameters__"], [139, 2, 1, "", "add"], [139, 2, 1, "", "center_of_mass"], [139, 5, 1, "", "child_dict"], [139, 5, 1, "", "child_list"], [139, 2, 1, "", "copy"], [139, 2, 1, "", "detach_child"], [139, 2, 1, "", "detach_parent"], [139, 2, 1, "", "get_full_id"], [139, 2, 1, "", "get_id"], [139, 2, 1, "", "get_iterator"], [139, 2, 1, "", "get_level"], [139, 2, 1, "", "get_list"], [139, 2, 1, "", "get_parent"], [139, 2, 1, "", "has_id"], [139, 6, 1, "", "id"], [139, 2, 1, "", "insert"], [139, 5, 1, "", "level"], [139, 5, 1, "", "parent"], [139, 2, 1, "", "set_parent"], [139, 2, 1, "", "strictly_equals"], [139, 2, 1, "", "transform"]], "Bio.PDB.FragmentMapper": [[140, 3, 1, "", "Fragment"], [140, 3, 1, "", "FragmentMapper"]], "Bio.PDB.FragmentMapper.Fragment": [[140, 2, 1, "", "__init__"], [140, 2, 1, "", "__len__"], [140, 2, 1, "", "__repr__"], [140, 2, 1, "", "__sub__"], [140, 2, 1, "", "add_residue"], [140, 2, 1, "", "get_coords"], [140, 2, 1, "", "get_id"], [140, 2, 1, "", "get_resname_list"]], "Bio.PDB.FragmentMapper.FragmentMapper": [[140, 2, 1, "", "__contains__"], [140, 2, 1, "", "__getitem__"], [140, 2, 1, "", "__init__"]], "Bio.PDB.HSExposure": [[141, 3, 1, "", "ExposureCN"], [141, 3, 1, "", "HSExposureCA"], [141, 3, 1, "", "HSExposureCB"]], "Bio.PDB.HSExposure.ExposureCN": [[141, 2, 1, "", "__init__"]], "Bio.PDB.HSExposure.HSExposureCA": [[141, 2, 1, "", "__init__"], [141, 2, 1, "", "pcb_vectors_pymol"]], "Bio.PDB.HSExposure.HSExposureCB": [[141, 2, 1, "", "__init__"]], "Bio.PDB.MMCIF2Dict": [[142, 3, 1, "", "MMCIF2Dict"]], "Bio.PDB.MMCIF2Dict.MMCIF2Dict": [[142, 2, 1, "", "__init__"]], "Bio.PDB.MMCIFParser": [[143, 3, 1, "", "FastMMCIFParser"], [143, 3, 1, "", "MMCIFParser"]], "Bio.PDB.MMCIFParser.FastMMCIFParser": [[143, 2, 1, "", "__init__"], [143, 2, 1, "", "get_structure"]], "Bio.PDB.MMCIFParser.MMCIFParser": [[143, 2, 1, "", "__init__"], [143, 2, 1, "", "get_structure"]], "Bio.PDB.Model": [[144, 3, 1, "", "Model"]], "Bio.PDB.Model.Model": [[144, 2, 1, "", "__init__"], [144, 5, 1, "", "__orig_bases__"], [144, 5, 1, "", "__parameters__"], [144, 2, 1, "", "__repr__"], [144, 2, 1, "", "atom_to_internal_coordinates"], [144, 2, 1, "", "get_atoms"], [144, 2, 1, "", "get_chains"], [144, 2, 1, "", "get_residues"], [144, 2, 1, "", "internal_to_atom_coordinates"]], "Bio.PDB.NACCESS": [[145, 3, 1, "", "NACCESS"], [145, 3, 1, "", "NACCESS_atomic"], [145, 4, 1, "", "process_asa_data"], [145, 4, 1, "", "process_rsa_data"], [145, 4, 1, "", "run_naccess"]], "Bio.PDB.NACCESS.NACCESS": [[145, 2, 1, "", "__init__"]], "Bio.PDB.NACCESS.NACCESS_atomic": [[145, 2, 1, "", "__init__"]], "Bio.PDB.NeighborSearch": [[146, 3, 1, "", "NeighborSearch"]], "Bio.PDB.NeighborSearch.NeighborSearch": [[146, 2, 1, "", "__init__"], [146, 2, 1, "", "search"], [146, 2, 1, "", "search_all"]], "Bio.PDB.PDBExceptions": [[147, 1, 1, "", "PDBConstructionException"], [147, 1, 1, "", "PDBConstructionWarning"], [147, 1, 1, "", "PDBException"], [147, 1, 1, "", "PDBIOException"]], "Bio.PDB.PDBIO": [[148, 3, 1, "", "PDBIO"], [148, 3, 1, "", "Select"], [148, 3, 1, "", "StructureIO"]], "Bio.PDB.PDBIO.PDBIO": [[148, 2, 1, "", "__init__"], [148, 2, 1, "", "save"]], "Bio.PDB.PDBIO.Select": [[148, 2, 1, "", "__repr__"], [148, 2, 1, "", "accept_atom"], [148, 2, 1, "", "accept_chain"], [148, 2, 1, "", "accept_model"], [148, 2, 1, "", "accept_residue"]], "Bio.PDB.PDBIO.StructureIO": [[148, 2, 1, "", "__init__"], [148, 2, 1, "", "set_structure"]], "Bio.PDB.PDBList": [[149, 3, 1, "", "PDBList"]], "Bio.PDB.PDBList.PDBList": [[149, 5, 1, "", "PDB_REF"], [149, 2, 1, "", "__init__"], [149, 2, 1, "", "download_all_assemblies"], [149, 2, 1, "", "download_entire_pdb"], [149, 2, 1, "", "download_obsolete_entries"], [149, 2, 1, "", "download_pdb_files"], [149, 2, 1, "", "get_all_assemblies"], [149, 2, 1, "", "get_all_entries"], [149, 2, 1, "", "get_all_obsolete"], [149, 2, 1, "", "get_recent_changes"], [149, 2, 1, "", "get_seqres_file"], [149, 2, 1, "", "get_status_list"], [149, 2, 1, "", "retrieve_assembly_file"], [149, 2, 1, "", "retrieve_pdb_file"], [149, 2, 1, "", "update_pdb"]], "Bio.PDB.PDBMLParser": [[150, 3, 1, "", "PDBMLParser"]], "Bio.PDB.PDBMLParser.PDBMLParser": [[150, 2, 1, "", "__init__"], [150, 2, 1, "", "get_structure"]], "Bio.PDB.PDBParser": [[151, 3, 1, "", "PDBParser"]], "Bio.PDB.PDBParser.PDBParser": [[151, 2, 1, "", "__init__"], [151, 2, 1, "", "get_header"], [151, 2, 1, "", "get_structure"], [151, 2, 1, "", "get_trailer"]], "Bio.PDB.PICIO": [[152, 4, 1, "", "enumerate_atoms"], [152, 4, 1, "", "pdb_date"], [152, 4, 1, "", "read_PIC"], [152, 4, 1, "", "read_PIC_seq"], [152, 4, 1, "", "write_PIC"]], "Bio.PDB.PSEA": [[153, 3, 1, "", "PSEA"], [153, 4, 1, "", "annotate"], [153, 4, 1, "", "psea"], [153, 4, 1, "", "psea2HEC"], [153, 4, 1, "", "run_psea"]], "Bio.PDB.PSEA.PSEA": [[153, 2, 1, "", "__init__"], [153, 2, 1, "", "get_seq"]], "Bio.PDB.Polypeptide": [[154, 3, 1, "", "CaPPBuilder"], [154, 3, 1, "", "PPBuilder"], [154, 3, 1, "", "Polypeptide"], [154, 4, 1, "", "index_to_one"], [154, 4, 1, "", "index_to_three"], [154, 4, 1, "", "is_aa"], [154, 4, 1, "", "is_nucleic"], [154, 4, 1, "", "one_to_index"], [154, 4, 1, "", "three_to_index"]], "Bio.PDB.Polypeptide.CaPPBuilder": [[154, 2, 1, "", "__init__"]], "Bio.PDB.Polypeptide.PPBuilder": [[154, 2, 1, "", "__init__"]], "Bio.PDB.Polypeptide.Polypeptide": [[154, 2, 1, "", "__repr__"], [154, 2, 1, "", "get_ca_list"], [154, 2, 1, "", "get_phi_psi_list"], [154, 2, 1, "", "get_sequence"], [154, 2, 1, "", "get_tau_list"], [154, 2, 1, "", "get_theta_list"]], "Bio.PDB.Residue": [[155, 3, 1, "", "DisorderedResidue"], [155, 3, 1, "", "Residue"]], "Bio.PDB.Residue.DisorderedResidue": [[155, 2, 1, "", "__init__"], [155, 2, 1, "", "__repr__"], [155, 2, 1, "", "add"], [155, 2, 1, "", "disordered_add"], [155, 2, 1, "", "disordered_remove"], [155, 2, 1, "", "sort"]], "Bio.PDB.Residue.Residue": [[155, 2, 1, "", "__init__"], [155, 5, 1, "", "__orig_bases__"], [155, 5, 1, "", "__parameters__"], [155, 2, 1, "", "__repr__"], [155, 2, 1, "", "add"], [155, 2, 1, "", "flag_disordered"], [155, 2, 1, "", "get_atoms"], [155, 2, 1, "", "get_resname"], [155, 2, 1, "", "get_segid"], [155, 2, 1, "", "get_unpacked_list"], [155, 2, 1, "", "is_disordered"], [155, 2, 1, "", "strictly_equals"]], "Bio.PDB.ResidueDepth": [[156, 3, 1, "", "ResidueDepth"], [156, 4, 1, "", "ca_depth"], [156, 4, 1, "", "get_surface"], [156, 4, 1, "", "min_dist"], [156, 4, 1, "", "residue_depth"]], "Bio.PDB.ResidueDepth.ResidueDepth": [[156, 2, 1, "", "__init__"]], "Bio.PDB.SASA": [[157, 3, 1, "", "ShrakeRupley"]], "Bio.PDB.SASA.ShrakeRupley": [[157, 2, 1, "", "__init__"], [157, 2, 1, "", "compute"]], "Bio.PDB.SCADIO": [[158, 4, 1, "", "write_SCAD"]], "Bio.PDB.Selection": [[159, 4, 1, "", "get_unique_parents"], [159, 4, 1, "", "unfold_entities"], [159, 4, 1, "", "uniqueify"]], "Bio.PDB.Structure": [[160, 3, 1, "", "Structure"]], "Bio.PDB.Structure.Structure": [[160, 2, 1, "", "__init__"], [160, 5, 1, "", "__orig_bases__"], [160, 5, 1, "", "__parameters__"], [160, 2, 1, "", "__repr__"], [160, 2, 1, "", "atom_to_internal_coordinates"], [160, 2, 1, "", "get_atoms"], [160, 2, 1, "", "get_chains"], [160, 2, 1, "", "get_models"], [160, 2, 1, "", "get_residues"], [160, 2, 1, "", "internal_to_atom_coordinates"]], "Bio.PDB.StructureAlignment": [[161, 3, 1, "", "StructureAlignment"]], "Bio.PDB.StructureAlignment.StructureAlignment": [[161, 2, 1, "", "__init__"], [161, 2, 1, "", "get_iterator"], [161, 2, 1, "", "get_maps"]], "Bio.PDB.StructureBuilder": [[162, 3, 1, "", "StructureBuilder"]], "Bio.PDB.StructureBuilder.StructureBuilder": [[162, 2, 1, "", "__init__"], [162, 2, 1, "", "get_structure"], [162, 2, 1, "", "init_atom"], [162, 2, 1, "", "init_chain"], [162, 2, 1, "", "init_model"], [162, 2, 1, "", "init_residue"], [162, 2, 1, "", "init_seg"], [162, 2, 1, "", "init_structure"], [162, 2, 1, "", "set_anisou"], [162, 2, 1, "", "set_header"], [162, 2, 1, "", "set_line_counter"], [162, 2, 1, "", "set_sigatm"], [162, 2, 1, "", "set_siguij"], [162, 2, 1, "", "set_symmetry"]], "Bio.PDB.Superimposer": [[163, 3, 1, "", "Superimposer"]], "Bio.PDB.Superimposer.Superimposer": [[163, 2, 1, "", "__init__"], [163, 2, 1, "", "apply"], [163, 2, 1, "", "set_atoms"]], "Bio.PDB.alphafold_db": [[164, 4, 1, "", "download_cif_for"], [164, 4, 1, "", "get_predictions"], [164, 4, 1, "", "get_structural_models_for"]], "Bio.PDB.binary_cif": [[165, 3, 1, "", "BinaryCIFParser"]], "Bio.PDB.binary_cif.BinaryCIFParser": [[165, 2, 1, "", "__init__"], [165, 2, 1, "", "get_structure"]], "Bio.PDB.cealign": [[166, 3, 1, "", "CEAligner"]], "Bio.PDB.cealign.CEAligner": [[166, 2, 1, "", "__init__"], [166, 2, 1, "", "align"], [166, 2, 1, "", "get_guide_coord_from_structure"], [166, 2, 1, "", "set_reference"]], "Bio.PDB.ic_rebuild": [[168, 4, 1, "", "IC_duplicate"], [168, 4, 1, "", "compare_residues"], [168, 4, 1, "", "report_IC"], [168, 4, 1, "", "structure_rebuild_test"], [168, 4, 1, "", "write_PDB"]], "Bio.PDB.internal_coords": [[169, 3, 1, "", "AtomKey"], [169, 3, 1, "", "Dihedron"], [169, 3, 1, "", "Edron"], [169, 3, 1, "", "Hedron"], [169, 1, 1, "", "HedronMatchError"], [169, 3, 1, "", "IC_Chain"], [169, 3, 1, "", "IC_Residue"], [169, 1, 1, "", "MissingAtomError"], [169, 4, 1, "", "set_accuracy_95"]], "Bio.PDB.internal_coords.AtomKey": [[169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__eq__"], [169, 2, 1, "", "__ge__"], [169, 2, 1, "", "__gt__"], [169, 2, 1, "", "__hash__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "__le__"], [169, 2, 1, "", "__lt__"], [169, 2, 1, "", "__ne__"], [169, 2, 1, "", "__repr__"], [169, 2, 1, "", "altloc_match"], [169, 2, 1, "", "atm"], [169, 5, 1, "", "atom_re"], [169, 2, 1, "", "cr_class"], [169, 5, 1, "", "d2h"], [169, 5, 1, "", "fieldNames"], [169, 5, 1, "", "fields"], [169, 2, 1, "", "is_backbone"]], "Bio.PDB.internal_coords.Dihedron": [[169, 2, 1, "", "__init__"], [169, 2, 1, "", "__repr__"], [169, 6, 1, "", "angle"], [169, 2, 1, "", "angle_avg"], [169, 2, 1, "", "angle_dif"], [169, 2, 1, "", "angle_pop_sd"], [169, 2, 1, "", "bits"], [169, 2, 1, "", "difference"]], "Bio.PDB.internal_coords.Edron": [[169, 2, 1, "", "__contains__"], [169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__eq__"], [169, 2, 1, "", "__ge__"], [169, 2, 1, "", "__gt__"], [169, 2, 1, "", "__hash__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "__le__"], [169, 2, 1, "", "__lt__"], [169, 2, 1, "", "__ne__"], [169, 2, 1, "", "__repr__"], [169, 5, 1, "", "edron_re"], [169, 2, 1, "", "gen_key"], [169, 2, 1, "", "gen_tuple"], [169, 2, 1, "", "is_backbone"]], "Bio.PDB.internal_coords.Hedron": [[169, 2, 1, "", "__init__"], [169, 2, 1, "", "__repr__"], [169, 6, 1, "", "angle"], [169, 2, 1, "", "get_length"], [169, 6, 1, "", "len12"], [169, 6, 1, "", "len23"], [169, 2, 1, "", "set_length"]], "Bio.PDB.internal_coords.IC_Chain": [[169, 5, 1, "", "AAsiz"], [169, 5, 1, "", "MaxPeptideBond"], [169, 5, 1, "", "ParallelAssembleResidues"], [169, 5, 1, "", "__annotations__"], [169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "assemble_residues"], [169, 2, 1, "", "assemble_residues_ser"], [169, 5, 1, "", "atomArray"], [169, 2, 1, "", "atom_to_internal_coordinates"], [169, 2, 1, "", "build_atomArray"], [169, 2, 1, "", "build_edraArrays"], [169, 2, 1, "", "clear_ic"], [169, 2, 1, "", "copy_initNCaCs"], [169, 5, 1, "", "dCoordSpace"], [169, 5, 1, "", "dcsValid"], [169, 2, 1, "", "dihedral_signs"], [169, 2, 1, "", "distance_plot"], [169, 2, 1, "", "distance_to_internal_coordinates"], [169, 2, 1, "", "distplot_to_dh_arrays"], [169, 2, 1, "", "init_atom_coords"], [169, 2, 1, "", "init_edra"], [169, 2, 1, "", "internal_to_atom_coordinates"], [169, 2, 1, "", "make_extended"], [169, 2, 1, "", "propagate_changes"], [169, 2, 1, "", "update_dCoordSpace"]], "Bio.PDB.internal_coords.IC_Residue": [[169, 5, 1, "", "__annotations__"], [169, 2, 1, "", "__contains__"], [169, 2, 1, "", "__deepcopy__"], [169, 2, 1, "", "__init__"], [169, 2, 1, "", "__repr__"], [169, 5, 1, "", "accept_atoms"], [169, 5, 1, "", "accept_backbone"], [169, 5, 1, "", "accept_deuteriums"], [169, 5, 1, "", "accept_hydrogens"], [169, 5, 1, "", "accept_mainchain"], [169, 5, 1, "", "accept_resnames"], [169, 5, 1, "", "accept_sidechain"], [169, 2, 1, "", "applyMtx"], [169, 2, 1, "", "assemble"], [169, 5, 1, "", "atom_chain"], [169, 5, 1, "", "atom_sernum"], [169, 2, 1, "", "bond_rotate"], [169, 2, 1, "", "bond_set"], [169, 2, 1, "", "clear_transforms"], [169, 2, 1, "", "get_angle"], [169, 2, 1, "", "get_length"], [169, 5, 1, "", "gly_Cbeta"], [169, 5, 1, "", "no_altloc"], [169, 2, 1, "", "pdb_residue_string"], [169, 5, 1, "", "picFlagsDefault"], [169, 5, 1, "", "picFlagsDict"], [169, 5, 1, "", "pic_accuracy"], [169, 5, 1, "", "pic_flags"], [169, 2, 1, "", "pick_angle"], [169, 2, 1, "", "pick_length"], [169, 2, 1, "", "pretty_str"], [169, 2, 1, "", "rak"], [169, 2, 1, "", "set_angle"], [169, 2, 1, "", "set_flexible"], [169, 2, 1, "", "set_hbond"], [169, 2, 1, "", "set_length"], [169, 2, 1, "", "split_akl"]], "Bio.PDB.mmcifio": [[170, 3, 1, "", "MMCIFIO"]], "Bio.PDB.mmcifio.MMCIFIO": [[170, 2, 1, "", "__init__"], [170, 2, 1, "", "save"], [170, 2, 1, "", "set_dict"]], "Bio.PDB.mmtf": [[172, 0, 0, "-", "DefaultParser"], [171, 3, 1, "", "MMTFParser"], [171, 4, 1, "", "get_from_decoded"], [173, 0, 0, "-", "mmtfio"]], "Bio.PDB.mmtf.DefaultParser": [[172, 3, 1, "", "StructureDecoder"]], "Bio.PDB.mmtf.DefaultParser.StructureDecoder": [[172, 2, 1, "", "__init__"], [172, 2, 1, "", "finalize_structure"], [172, 2, 1, "", "init_structure"], [172, 2, 1, "", "set_atom_info"], [172, 2, 1, "", "set_bio_assembly_trans"], [172, 2, 1, "", "set_chain_info"], [172, 2, 1, "", "set_entity_info"], [172, 2, 1, "", "set_group_bond"], [172, 2, 1, "", "set_group_info"], [172, 2, 1, "", "set_header_info"], [172, 2, 1, "", "set_inter_group_bond"], [172, 2, 1, "", "set_model_info"], [172, 2, 1, "", "set_xtal_info"]], "Bio.PDB.mmtf.MMTFParser": [[171, 2, 1, "", "get_structure"], [171, 2, 1, "", "get_structure_from_url"]], "Bio.PDB.mmtf.mmtfio": [[173, 3, 1, "", "MMTFIO"]], "Bio.PDB.mmtf.mmtfio.MMTFIO": [[173, 2, 1, "", "__init__"], [173, 2, 1, "", "save"]], "Bio.PDB.parse_pdb_header": [[174, 4, 1, "", "parse_pdb_header"]], "Bio.PDB.qcprot": [[175, 3, 1, "", "QCPSuperimposer"], [175, 4, 1, "", "qcp"]], "Bio.PDB.qcprot.QCPSuperimposer": [[175, 2, 1, "", "__init__"], [175, 2, 1, "", "apply"], [175, 2, 1, "", "get_init_rms"], [175, 2, 1, "", "get_rms"], [175, 2, 1, "", "get_rotran"], [175, 2, 1, "", "get_transformed"], [175, 2, 1, "", "run"], [175, 2, 1, "", "set"], [175, 2, 1, "", "set_atoms"]], "Bio.PDB.vectors": [[176, 3, 1, "", "Vector"], [176, 4, 1, "", "calc_angle"], [176, 4, 1, "", "calc_dihedral"], [176, 4, 1, "", "coord_space"], [176, 4, 1, "", "get_spherical_coordinates"], [176, 4, 1, "", "homog_rot_mtx"], [176, 4, 1, "", "homog_scale_mtx"], [176, 4, 1, "", "homog_trans_mtx"], [176, 4, 1, "", "m2rotaxis"], [176, 4, 1, "", "multi_coord_space"], [176, 4, 1, "", "multi_rot_Y"], [176, 4, 1, "", "multi_rot_Z"], [176, 4, 1, "", "refmat"], [176, 4, 1, "", "rotaxis"], [176, 4, 1, "", "rotaxis2m"], [176, 4, 1, "", "rotmat"], [176, 4, 1, "", "set_X_homog_rot_mtx"], [176, 4, 1, "", "set_Y_homog_rot_mtx"], [176, 4, 1, "", "set_Z_homog_rot_mtx"], [176, 4, 1, "", "set_homog_trans_mtx"], [176, 4, 1, "", "vector_to_axis"]], "Bio.PDB.vectors.Vector": [[176, 2, 1, "", "__add__"], [176, 2, 1, "", "__contains__"], [176, 2, 1, "", "__getitem__"], [176, 2, 1, "", "__init__"], [176, 2, 1, "", "__mul__"], [176, 2, 1, "", "__neg__"], [176, 2, 1, "", "__pow__"], [176, 2, 1, "", "__repr__"], [176, 2, 1, "", "__setitem__"], [176, 2, 1, "", "__sub__"], [176, 2, 1, "", "__truediv__"], [176, 2, 1, "", "angle"], [176, 2, 1, "", "copy"], [176, 2, 1, "", "get_array"], [176, 2, 1, "", "left_multiply"], [176, 2, 1, "", "norm"], [176, 2, 1, "", "normalize"], [176, 2, 1, "", "normalized"], [176, 2, 1, "", "normsq"], [176, 2, 1, "", "right_multiply"]], "Bio.Pathway": [[177, 3, 1, "", "Interaction"], [177, 3, 1, "", "Network"], [177, 3, 1, "", "Reaction"], [178, 0, 0, "-", "Rep"], [177, 3, 1, "", "System"]], "Bio.Pathway.Interaction": [[177, 2, 1, "", "__hash__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"]], "Bio.Pathway.Network": [[177, 2, 1, "", "__init__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"], [177, 2, 1, "", "add_interaction"], [177, 2, 1, "", "add_species"], [177, 2, 1, "", "interactions"], [177, 2, 1, "", "sink"], [177, 2, 1, "", "sink_interactions"], [177, 2, 1, "", "source"], [177, 2, 1, "", "source_interactions"], [177, 2, 1, "", "species"]], "Bio.Pathway.Reaction": [[177, 2, 1, "", "__eq__"], [177, 2, 1, "", "__hash__"], [177, 2, 1, "", "__init__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"], [177, 2, 1, "", "reverse"], [177, 2, 1, "", "species"]], "Bio.Pathway.Rep": [[179, 0, 0, "-", "Graph"], [180, 0, 0, "-", "MultiGraph"]], "Bio.Pathway.Rep.Graph": [[179, 3, 1, "", "Graph"]], "Bio.Pathway.Rep.Graph.Graph": [[179, 2, 1, "", "__eq__"], [179, 5, 1, "", "__hash__"], [179, 2, 1, "", "__init__"], [179, 2, 1, "", "__repr__"], [179, 2, 1, "", "__str__"], [179, 2, 1, "", "add_edge"], [179, 2, 1, "", "add_node"], [179, 2, 1, "", "child_edges"], [179, 2, 1, "", "children"], [179, 2, 1, "", "edges"], [179, 2, 1, "", "labels"], [179, 2, 1, "", "nodes"], [179, 2, 1, "", "parent_edges"], [179, 2, 1, "", "parents"], [179, 2, 1, "", "remove_edge"], [179, 2, 1, "", "remove_node"]], "Bio.Pathway.Rep.MultiGraph": [[180, 3, 1, "", "MultiGraph"], [180, 4, 1, "", "bf_search"], [180, 4, 1, "", "df_search"]], "Bio.Pathway.Rep.MultiGraph.MultiGraph": [[180, 2, 1, "", "__eq__"], [180, 5, 1, "", "__hash__"], [180, 2, 1, "", "__init__"], [180, 2, 1, "", "__repr__"], [180, 2, 1, "", "__str__"], [180, 2, 1, "", "add_edge"], [180, 2, 1, "", "add_node"], [180, 2, 1, "", "child_edges"], [180, 2, 1, "", "children"], [180, 2, 1, "", "edges"], [180, 2, 1, "", "labels"], [180, 2, 1, "", "nodes"], [180, 2, 1, "", "parent_edges"], [180, 2, 1, "", "parents"], [180, 2, 1, "", "remove_edge"], [180, 2, 1, "", "remove_node"]], "Bio.Pathway.System": [[177, 2, 1, "", "__init__"], [177, 2, 1, "", "__repr__"], [177, 2, 1, "", "__str__"], [177, 2, 1, "", "add_reaction"], [177, 2, 1, "", "reactions"], [177, 2, 1, "", "remove_reaction"], [177, 2, 1, "", "species"], [177, 2, 1, "", "stochiometry"]], "Bio.Phylo": [[182, 0, 0, "-", "Applications"], [183, 0, 0, "-", "BaseTree"], [184, 0, 0, "-", "CDAO"], [185, 0, 0, "-", "CDAOIO"], [186, 0, 0, "-", "Consensus"], [187, 0, 0, "-", "NeXML"], [188, 0, 0, "-", "NeXMLIO"], [189, 0, 0, "-", "Newick"], [190, 0, 0, "-", "NewickIO"], [191, 0, 0, "-", "NexusIO"], [192, 0, 0, "-", "PAML"], [197, 0, 0, "-", "PhyloXML"], [198, 0, 0, "-", "PhyloXMLIO"], [199, 0, 0, "-", "TreeConstruction"]], "Bio.Phylo.Applications": [[182, 3, 1, "", "FastTreeCommandline"], [182, 3, 1, "", "PhymlCommandline"], [182, 3, 1, "", "RaxmlCommandline"]], "Bio.Phylo.Applications.FastTreeCommandline": [[182, 2, 1, "", "__init__"], [182, 6, 1, "", "bionj"], [182, 6, 1, "", "boot"], [182, 6, 1, "", "cat"], [182, 6, 1, "", "close"], [182, 6, 1, "", "constraintWeight"], [182, 6, 1, "", "constraints"], [182, 6, 1, "", "expert"], [182, 6, 1, "", "fastest"], [182, 6, 1, "", "gamma"], [182, 6, 1, "", "gtr"], [182, 6, 1, "", "gtrfreq"], [182, 6, 1, "", "gtrrates"], [182, 6, 1, "", "help"], [182, 6, 1, "", "input"], [182, 6, 1, "", "intree"], [182, 6, 1, "", "intree1"], [182, 6, 1, "", "log"], [182, 6, 1, "", "makematrix"], [182, 6, 1, "", "matrix"], [182, 6, 1, "", "mlacc"], [182, 6, 1, "", "mllen"], [182, 6, 1, "", "mlnni"], [182, 6, 1, "", "n"], [182, 6, 1, "", "nj"], [182, 6, 1, "", "nni"], [182, 6, 1, "", "no2nd"], [182, 6, 1, "", "nocat"], [182, 6, 1, "", "nomatrix"], [182, 6, 1, "", "nome"], [182, 6, 1, "", "noml"], [182, 6, 1, "", "nopr"], [182, 6, 1, "", "nosupport"], [182, 6, 1, "", "notop"], [182, 6, 1, "", "nt"], [182, 6, 1, "", "out"], [182, 6, 1, "", "pseudo"], [182, 6, 1, "", "quiet"], [182, 6, 1, "", "quote"], [182, 6, 1, "", "rawdist"], [182, 6, 1, "", "refresh"], [182, 6, 1, "", "second"], [182, 6, 1, "", "seed"], [182, 6, 1, "", "slow"], [182, 6, 1, "", "slownni"], [182, 6, 1, "", "spr"], [182, 6, 1, "", "sprlength"], [182, 6, 1, "", "top"], [182, 6, 1, "", "topm"], [182, 6, 1, "", "wag"]], "Bio.Phylo.Applications.PhymlCommandline": [[182, 2, 1, "", "__init__"], [182, 6, 1, "", "alpha"], [182, 6, 1, "", "bootstrap"], [182, 6, 1, "", "datatype"], [182, 6, 1, "", "frequencies"], [182, 6, 1, "", "input"], [182, 6, 1, "", "input_tree"], [182, 6, 1, "", "model"], [182, 6, 1, "", "multiple"], [182, 6, 1, "", "n_rand_starts"], [182, 6, 1, "", "nclasses"], [182, 6, 1, "", "optimize"], [182, 6, 1, "", "pars"], [182, 6, 1, "", "print_site_lnl"], [182, 6, 1, "", "print_trace"], [182, 6, 1, "", "prop_invar"], [182, 6, 1, "", "quiet"], [182, 6, 1, "", "r_seed"], [182, 6, 1, "", "rand_start"], [182, 6, 1, "", "run_id"], [182, 6, 1, "", "search"], [182, 6, 1, "", "sequential"], [182, 6, 1, "", "ts_tv_ratio"]], "Bio.Phylo.Applications.RaxmlCommandline": [[182, 2, 1, "", "__init__"], [182, 6, 1, "", "algorithm"], [182, 6, 1, "", "binary_constraint"], [182, 6, 1, "", "bipartition_filename"], [182, 6, 1, "", "bootstrap_branch_lengths"], [182, 6, 1, "", "bootstrap_seed"], [182, 6, 1, "", "checkpoints"], [182, 6, 1, "", "cluster_threshold"], [182, 6, 1, "", "cluster_threshold_fast"], [182, 6, 1, "", "epsilon"], [182, 6, 1, "", "exclude_filename"], [182, 6, 1, "", "grouping_constraint"], [182, 6, 1, "", "model"], [182, 6, 1, "", "name"], [182, 6, 1, "", "num_bootstrap_searches"], [182, 6, 1, "", "num_categories"], [182, 6, 1, "", "num_replicates"], [182, 6, 1, "", "outgroup"], [182, 6, 1, "", "parsimony"], [182, 6, 1, "", "parsimony_seed"], [182, 6, 1, "", "partition_branch_lengths"], [182, 6, 1, "", "partition_filename"], [182, 6, 1, "", "protein_model"], [182, 6, 1, "", "random_starting_tree"], [182, 6, 1, "", "rapid_bootstrap_seed"], [182, 6, 1, "", "rearrangements"], [182, 6, 1, "", "sequences"], [182, 6, 1, "", "starting_tree"], [182, 6, 1, "", "threads"], [182, 6, 1, "", "version"], [182, 6, 1, "", "weight_filename"], [182, 6, 1, "", "working_dir"]], "Bio.Phylo.BaseTree": [[183, 3, 1, "", "BranchColor"], [183, 3, 1, "", "Clade"], [183, 3, 1, "", "Tree"], [183, 3, 1, "", "TreeElement"], [183, 3, 1, "", "TreeMixin"]], "Bio.Phylo.BaseTree.BranchColor": [[183, 2, 1, "", "__init__"], [183, 2, 1, "", "__repr__"], [183, 2, 1, "", "__str__"], [183, 5, 1, "", "color_names"], [183, 2, 1, "", "from_hex"], [183, 2, 1, "", "from_name"], [183, 2, 1, "", "to_hex"], [183, 2, 1, "", "to_rgb"]], "Bio.Phylo.BaseTree.Clade": [[183, 2, 1, "", "__bool__"], [183, 2, 1, "", "__getitem__"], [183, 2, 1, "", "__init__"], [183, 2, 1, "", "__iter__"], [183, 2, 1, "", "__len__"], [183, 2, 1, "", "__str__"], [183, 6, 1, "", "color"], [183, 2, 1, "", "is_terminal"], [183, 6, 1, "", "root"]], "Bio.Phylo.BaseTree.Tree": [[183, 2, 1, "", "__format__"], [183, 2, 1, "", "__init__"], [183, 2, 1, "", "__str__"], [183, 2, 1, "", "as_phyloxml"], [183, 6, 1, "", "clade"], [183, 2, 1, "", "format"], [183, 2, 1, "", "from_clade"], [183, 2, 1, "", "is_terminal"], [183, 2, 1, "", "randomized"], [183, 2, 1, "", "root_at_midpoint"], [183, 2, 1, "", "root_with_outgroup"]], "Bio.Phylo.BaseTree.TreeElement": [[183, 2, 1, "", "__repr__"], [183, 2, 1, "", "__str__"]], "Bio.Phylo.BaseTree.TreeMixin": [[183, 2, 1, "", "collapse"], [183, 2, 1, "", "collapse_all"], [183, 2, 1, "", "common_ancestor"], [183, 2, 1, "", "count_terminals"], [183, 2, 1, "", "depths"], [183, 2, 1, "", "distance"], [183, 2, 1, "", "find_any"], [183, 2, 1, "", "find_clades"], [183, 2, 1, "", "find_elements"], [183, 2, 1, "", "get_nonterminals"], [183, 2, 1, "", "get_path"], [183, 2, 1, "", "get_terminals"], [183, 2, 1, "", "is_bifurcating"], [183, 2, 1, "", "is_monophyletic"], [183, 2, 1, "", "is_parent_of"], [183, 2, 1, "", "is_preterminal"], [183, 2, 1, "", "ladderize"], [183, 2, 1, "", "prune"], [183, 2, 1, "", "split"], [183, 2, 1, "", "total_branch_length"], [183, 2, 1, "", "trace"]], "Bio.Phylo.CDAO": [[184, 3, 1, "", "Clade"], [184, 3, 1, "", "Tree"]], "Bio.Phylo.CDAO.Clade": [[184, 2, 1, "", "__init__"]], "Bio.Phylo.CDAO.Tree": [[184, 2, 1, "", "__init__"]], "Bio.Phylo.CDAOIO": [[185, 3, 1, "", "Parser"], [185, 3, 1, "", "Writer"], [185, 4, 1, "", "format_label"], [185, 4, 1, "", "parse"], [185, 4, 1, "", "qUri"], [185, 4, 1, "", "write"]], "Bio.Phylo.CDAOIO.Parser": [[185, 2, 1, "", "__init__"], [185, 2, 1, "", "from_string"], [185, 2, 1, "", "get_node_info"], [185, 2, 1, "", "new_clade"], [185, 2, 1, "", "parse"], [185, 2, 1, "", "parse_children"], [185, 2, 1, "", "parse_graph"], [185, 2, 1, "", "parse_handle_to_graph"]], "Bio.Phylo.CDAOIO.Writer": [[185, 2, 1, "", "__init__"], [185, 2, 1, "", "add_stmt_to_handle"], [185, 5, 1, "", "prefixes"], [185, 2, 1, "", "process_clade"], [185, 2, 1, "", "write"]], "Bio.Phylo.Consensus": [[186, 4, 1, "", "adam_consensus"], [186, 4, 1, "", "bootstrap"], [186, 4, 1, "", "bootstrap_consensus"], [186, 4, 1, "", "bootstrap_trees"], [186, 4, 1, "", "get_support"], [186, 4, 1, "", "majority_consensus"], [186, 4, 1, "", "strict_consensus"]], "Bio.Phylo.NeXML": [[187, 3, 1, "", "Clade"], [187, 3, 1, "", "Tree"]], "Bio.Phylo.NeXML.Clade": [[187, 2, 1, "", "__init__"]], "Bio.Phylo.NeXML.Tree": [[187, 2, 1, "", "__init__"]], "Bio.Phylo.NeXMLIO": [[188, 1, 1, "", "NeXMLError"], [188, 3, 1, "", "Parser"], [188, 3, 1, "", "Writer"], [188, 4, 1, "", "cdao_to_obo"], [188, 4, 1, "", "matches"], [188, 4, 1, "", "parse"], [188, 4, 1, "", "qUri"], [188, 4, 1, "", "write"]], "Bio.Phylo.NeXMLIO.Parser": [[188, 2, 1, "", "__init__"], [188, 2, 1, "", "add_annotation"], [188, 2, 1, "", "from_string"], [188, 2, 1, "", "parse"]], "Bio.Phylo.NeXMLIO.Writer": [[188, 2, 1, "", "__init__"], [188, 2, 1, "", "new_label"], [188, 2, 1, "", "write"]], "Bio.Phylo.Newick": [[189, 3, 1, "", "Clade"], [189, 3, 1, "", "Tree"]], "Bio.Phylo.Newick.Clade": [[189, 2, 1, "", "__init__"]], "Bio.Phylo.Newick.Tree": [[189, 2, 1, "", "__init__"]], "Bio.Phylo.NewickIO": [[190, 1, 1, "", "NewickError"], [190, 3, 1, "", "Parser"], [190, 3, 1, "", "Writer"], [190, 4, 1, "", "parse"], [190, 4, 1, "", "write"]], "Bio.Phylo.NewickIO.Parser": [[190, 2, 1, "", "__init__"], [190, 2, 1, "", "from_string"], [190, 2, 1, "", "new_clade"], [190, 2, 1, "", "parse"], [190, 2, 1, "", "process_clade"]], "Bio.Phylo.NewickIO.Writer": [[190, 2, 1, "", "__init__"], [190, 2, 1, "", "to_strings"], [190, 2, 1, "", "write"]], "Bio.Phylo.NexusIO": [[191, 4, 1, "", "parse"], [191, 4, 1, "", "write"]], "Bio.Phylo.PAML": [[193, 0, 0, "-", "baseml"], [194, 0, 0, "-", "chi2"], [195, 0, 0, "-", "codeml"], [196, 0, 0, "-", "yn00"]], "Bio.Phylo.PAML.baseml": [[193, 3, 1, "", "Baseml"], [193, 1, 1, "", "BasemlError"], [193, 4, 1, "", "read"]], "Bio.Phylo.PAML.baseml.Baseml": [[193, 2, 1, "", "__init__"], [193, 2, 1, "", "read_ctl_file"], [193, 2, 1, "", "run"], [193, 2, 1, "", "write_ctl_file"]], "Bio.Phylo.PAML.chi2": [[194, 4, 1, "", "cdf_chi2"]], "Bio.Phylo.PAML.codeml": [[195, 3, 1, "", "Codeml"], [195, 1, 1, "", "CodemlError"], [195, 4, 1, "", "read"]], "Bio.Phylo.PAML.codeml.Codeml": [[195, 2, 1, "", "__init__"], [195, 2, 1, "", "print_options"], [195, 2, 1, "", "read_ctl_file"], [195, 2, 1, "", "run"], [195, 2, 1, "", "write_ctl_file"]], "Bio.Phylo.PAML.yn00": [[196, 3, 1, "", "Yn00"], [196, 1, 1, "", "Yn00Error"], [196, 4, 1, "", "read"]], "Bio.Phylo.PAML.yn00.Yn00": [[196, 2, 1, "", "__init__"], [196, 2, 1, "", "read_ctl_file"], [196, 2, 1, "", "run"], [196, 2, 1, "", "write_ctl_file"]], "Bio.Phylo.PhyloXML": [[197, 3, 1, "", "Accession"], [197, 3, 1, "", "Annotation"], [197, 3, 1, "", "BinaryCharacters"], [197, 3, 1, "", "BranchColor"], [197, 3, 1, "", "Clade"], [197, 3, 1, "", "CladeRelation"], [197, 3, 1, "", "Confidence"], [197, 3, 1, "", "Date"], [197, 3, 1, "", "Distribution"], [197, 3, 1, "", "DomainArchitecture"], [197, 3, 1, "", "Events"], [197, 3, 1, "", "Id"], [197, 3, 1, "", "MolSeq"], [197, 3, 1, "", "Other"], [197, 3, 1, "", "PhyloElement"], [197, 1, 1, "", "PhyloXMLWarning"], [197, 3, 1, "", "Phylogeny"], [197, 3, 1, "", "Phyloxml"], [197, 3, 1, "", "Point"], [197, 3, 1, "", "Polygon"], [197, 3, 1, "", "Property"], [197, 3, 1, "", "ProteinDomain"], [197, 3, 1, "", "Reference"], [197, 3, 1, "", "Sequence"], [197, 3, 1, "", "SequenceRelation"], [197, 3, 1, "", "Taxonomy"], [197, 3, 1, "", "Uri"]], "Bio.Phylo.PhyloXML.Accession": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Annotation": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "re_ref"]], "Bio.Phylo.PhyloXML.BinaryCharacters": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.BranchColor": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Clade": [[197, 2, 1, "", "__init__"], [197, 6, 1, "", "confidence"], [197, 2, 1, "", "from_clade"], [197, 6, 1, "", "taxonomy"], [197, 2, 1, "", "to_phylogeny"]], "Bio.Phylo.PhyloXML.CladeRelation": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Confidence": [[197, 2, 1, "", "__new__"], [197, 6, 1, "", "value"]], "Bio.Phylo.PhyloXML.Date": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Distribution": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.DomainArchitecture": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Events": [[197, 2, 1, "", "__contains__"], [197, 2, 1, "", "__delitem__"], [197, 2, 1, "", "__getitem__"], [197, 2, 1, "", "__init__"], [197, 2, 1, "", "__iter__"], [197, 2, 1, "", "__len__"], [197, 2, 1, "", "__setitem__"], [197, 2, 1, "", "items"], [197, 2, 1, "", "keys"], [197, 5, 1, "", "ok_type"], [197, 2, 1, "", "values"]], "Bio.Phylo.PhyloXML.Id": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.MolSeq": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"], [197, 5, 1, "", "re_value"]], "Bio.Phylo.PhyloXML.Other": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__iter__"]], "Bio.Phylo.PhyloXML.Phylogeny": [[197, 2, 1, "", "__init__"], [197, 6, 1, "", "alignment"], [197, 2, 1, "", "as_phyloxml"], [197, 6, 1, "", "confidence"], [197, 2, 1, "", "from_clade"], [197, 2, 1, "", "from_tree"], [197, 2, 1, "", "to_alignment"], [197, 2, 1, "", "to_phyloxml_container"]], "Bio.Phylo.PhyloXML.Phyloxml": [[197, 2, 1, "", "__getitem__"], [197, 2, 1, "", "__init__"], [197, 2, 1, "", "__iter__"], [197, 2, 1, "", "__len__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Point": [[197, 2, 1, "", "__init__"]], "Bio.Phylo.PhyloXML.Polygon": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXML.Property": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "ok_applies_to"], [197, 5, 1, "", "ok_datatype"], [197, 5, 1, "", "re_ref"]], "Bio.Phylo.PhyloXML.ProteinDomain": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "from_seqfeature"], [197, 2, 1, "", "to_seqfeature"]], "Bio.Phylo.PhyloXML.Reference": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "re_doi"]], "Bio.Phylo.PhyloXML.Sequence": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "from_seqrecord"], [197, 5, 1, "", "re_symbol"], [197, 2, 1, "", "to_seqrecord"], [197, 5, 1, "", "types"]], "Bio.Phylo.PhyloXML.SequenceRelation": [[197, 2, 1, "", "__init__"], [197, 5, 1, "", "ok_type"]], "Bio.Phylo.PhyloXML.Taxonomy": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"], [197, 5, 1, "", "ok_rank"], [197, 5, 1, "", "re_code"]], "Bio.Phylo.PhyloXML.Uri": [[197, 2, 1, "", "__init__"], [197, 2, 1, "", "__str__"]], "Bio.Phylo.PhyloXMLIO": [[198, 3, 1, "", "Parser"], [198, 1, 1, "", "PhyloXMLError"], [198, 3, 1, "", "Writer"], [198, 4, 1, "", "parse"], [198, 4, 1, "", "read"], [198, 4, 1, "", "write"]], "Bio.Phylo.PhyloXMLIO.Parser": [[198, 2, 1, "", "__init__"], [198, 2, 1, "", "accession"], [198, 2, 1, "", "annotation"], [198, 2, 1, "", "binary_characters"], [198, 2, 1, "", "clade_relation"], [198, 2, 1, "", "color"], [198, 2, 1, "", "confidence"], [198, 2, 1, "", "date"], [198, 2, 1, "", "distribution"], [198, 2, 1, "", "domain"], [198, 2, 1, "", "domain_architecture"], [198, 2, 1, "", "events"], [198, 2, 1, "", "id"], [198, 2, 1, "", "mol_seq"], [198, 2, 1, "", "other"], [198, 2, 1, "", "parse"], [198, 2, 1, "", "point"], [198, 2, 1, "", "polygon"], [198, 2, 1, "", "property"], [198, 2, 1, "", "read"], [198, 2, 1, "", "reference"], [198, 2, 1, "", "sequence_relation"], [198, 2, 1, "", "uri"]], "Bio.Phylo.PhyloXMLIO.Writer": [[198, 2, 1, "", "__init__"], [198, 2, 1, "", "accession"], [198, 2, 1, "", "alt"], [198, 2, 1, "", "annotation"], [198, 2, 1, "", "bc"], [198, 2, 1, "", "binary_characters"], [198, 2, 1, "", "blue"], [198, 2, 1, "", "branch_length"], [198, 2, 1, "", "clade"], [198, 2, 1, "", "clade_relation"], [198, 2, 1, "", "code"], [198, 2, 1, "", "color"], [198, 2, 1, "", "common_name"], [198, 2, 1, "", "confidence"], [198, 2, 1, "", "date"], [198, 2, 1, "", "desc"], [198, 2, 1, "", "description"], [198, 2, 1, "", "distribution"], [198, 2, 1, "", "domain"], [198, 2, 1, "", "domain_architecture"], [198, 2, 1, "", "duplications"], [198, 2, 1, "", "events"], [198, 2, 1, "", "green"], [198, 2, 1, "", "id"], [198, 2, 1, "", "lat"], [198, 2, 1, "", "location"], [198, 2, 1, "", "long"], [198, 2, 1, "", "losses"], [198, 2, 1, "", "maximum"], [198, 2, 1, "", "minimum"], [198, 2, 1, "", "mol_seq"], [198, 2, 1, "", "name"], [198, 2, 1, "", "node_id"], [198, 2, 1, "", "other"], [198, 2, 1, "", "phylogeny"], [198, 2, 1, "", "phyloxml"], [198, 2, 1, "", "point"], [198, 2, 1, "", "polygon"], [198, 2, 1, "", "property"], [198, 2, 1, "", "rank"], [198, 2, 1, "", "red"], [198, 2, 1, "", "reference"], [198, 2, 1, "", "scientific_name"], [198, 2, 1, "", "sequence"], [198, 2, 1, "", "sequence_relation"], [198, 2, 1, "", "speciations"], [198, 2, 1, "", "symbol"], [198, 2, 1, "", "synonym"], [198, 2, 1, "", "taxonomy"], [198, 2, 1, "", "type"], [198, 2, 1, "", "uri"], [198, 2, 1, "", "value"], [198, 2, 1, "", "width"], [198, 2, 1, "", "write"]], "Bio.Phylo.TreeConstruction": [[199, 3, 1, "", "DistanceCalculator"], [199, 3, 1, "", "DistanceMatrix"], [199, 3, 1, "", "DistanceTreeConstructor"], [199, 3, 1, "", "NNITreeSearcher"], [199, 3, 1, "", "ParsimonyScorer"], [199, 3, 1, "", "ParsimonyTreeConstructor"], [199, 3, 1, "", "Scorer"], [199, 3, 1, "", "TreeConstructor"], [199, 3, 1, "", "TreeSearcher"]], "Bio.Phylo.TreeConstruction.DistanceCalculator": [[199, 2, 1, "", "__init__"], [199, 5, 1, "", "dna_models"], [199, 2, 1, "", "get_distance"], [199, 5, 1, "", "models"], [199, 5, 1, "", "protein_models"]], "Bio.Phylo.TreeConstruction.DistanceMatrix": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "__setitem__"], [199, 2, 1, "", "format_phylip"]], "Bio.Phylo.TreeConstruction.DistanceTreeConstructor": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "build_tree"], [199, 5, 1, "", "methods"], [199, 2, 1, "", "nj"], [199, 2, 1, "", "upgma"]], "Bio.Phylo.TreeConstruction.NNITreeSearcher": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "search"]], "Bio.Phylo.TreeConstruction.ParsimonyScorer": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "get_score"]], "Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor": [[199, 2, 1, "", "__init__"], [199, 2, 1, "", "build_tree"]], "Bio.Phylo.TreeConstruction.Scorer": [[199, 2, 1, "", "get_score"]], "Bio.Phylo.TreeConstruction.TreeConstructor": [[199, 2, 1, "", "build_tree"]], "Bio.Phylo.TreeConstruction.TreeSearcher": [[199, 2, 1, "", "search"]], "Bio.PopGen": [[201, 0, 0, "-", "GenePop"]], "Bio.PopGen.GenePop": [[202, 0, 0, "-", "Controller"], [203, 0, 0, "-", "EasyController"], [204, 0, 0, "-", "FileParser"], [205, 0, 0, "-", "LargeFileParser"], [201, 3, 1, "", "Record"], [201, 4, 1, "", "get_indiv"], [201, 4, 1, "", "read"]], "Bio.PopGen.GenePop.Controller": [[202, 3, 1, "", "GenePopController"]], "Bio.PopGen.GenePop.Controller.GenePopController": [[202, 2, 1, "", "__init__"], [202, 2, 1, "", "calc_allele_genotype_freqs"], [202, 2, 1, "", "calc_diversities_fis_with_identity"], [202, 2, 1, "", "calc_diversities_fis_with_size"], [202, 2, 1, "", "calc_fst_all"], [202, 2, 1, "", "calc_fst_pair"], [202, 2, 1, "", "calc_ibd_diplo"], [202, 2, 1, "", "calc_ibd_haplo"], [202, 2, 1, "", "calc_rho_all"], [202, 2, 1, "", "calc_rho_pair"], [202, 2, 1, "", "create_contingency_tables"], [202, 2, 1, "", "estimate_nm"], [202, 2, 1, "", "test_genic_diff_all"], [202, 2, 1, "", "test_genic_diff_pair"], [202, 2, 1, "", "test_genotypic_diff_all"], [202, 2, 1, "", "test_genotypic_diff_pair"], [202, 2, 1, "", "test_global_hz_deficiency"], [202, 2, 1, "", "test_global_hz_excess"], [202, 2, 1, "", "test_ld"], [202, 2, 1, "", "test_pop_hz_deficiency"], [202, 2, 1, "", "test_pop_hz_excess"], [202, 2, 1, "", "test_pop_hz_prob"]], "Bio.PopGen.GenePop.EasyController": [[203, 3, 1, "", "EasyController"]], "Bio.PopGen.GenePop.EasyController.EasyController": [[203, 2, 1, "", "__init__"], [203, 2, 1, "", "calc_ibd"], [203, 2, 1, "", "estimate_nm"], [203, 2, 1, "", "get_allele_frequency"], [203, 2, 1, "", "get_alleles"], [203, 2, 1, "", "get_alleles_all_pops"], [203, 2, 1, "", "get_avg_fis"], [203, 2, 1, "", "get_avg_fst_pair"], [203, 2, 1, "", "get_avg_fst_pair_locus"], [203, 2, 1, "", "get_basic_info"], [203, 2, 1, "", "get_f_stats"], [203, 2, 1, "", "get_fis"], [203, 2, 1, "", "get_genotype_count"], [203, 2, 1, "", "get_heterozygosity_info"], [203, 2, 1, "", "get_multilocus_f_stats"], [203, 2, 1, "", "test_hw_global"], [203, 2, 1, "", "test_hw_pop"], [203, 2, 1, "", "test_ld_all_pair"]], "Bio.PopGen.GenePop.FileParser": [[204, 3, 1, "", "FileRecord"], [204, 4, 1, "", "read"]], "Bio.PopGen.GenePop.FileParser.FileRecord": [[204, 2, 1, "", "__init__"], [204, 2, 1, "", "__str__"], [204, 2, 1, "", "get_individual"], [204, 2, 1, "", "remove_loci_by_name"], [204, 2, 1, "", "remove_loci_by_position"], [204, 2, 1, "", "remove_locus_by_name"], [204, 2, 1, "", "remove_locus_by_position"], [204, 2, 1, "", "remove_population"], [204, 2, 1, "", "seek_position"], [204, 2, 1, "", "skip_header"], [204, 2, 1, "", "skip_population"], [204, 2, 1, "", "start_read"]], "Bio.PopGen.GenePop.LargeFileParser": [[205, 3, 1, "", "Record"], [205, 4, 1, "", "get_indiv"], [205, 4, 1, "", "read"]], "Bio.PopGen.GenePop.LargeFileParser.Record": [[205, 2, 1, "", "__init__"], [205, 2, 1, "", "data_generator"]], "Bio.PopGen.GenePop.Record": [[201, 2, 1, "", "__init__"], [201, 2, 1, "", "__str__"], [201, 2, 1, "", "remove_locus_by_name"], [201, 2, 1, "", "remove_locus_by_position"], [201, 2, 1, "", "remove_population"], [201, 2, 1, "", "split_in_loci"], [201, 2, 1, "", "split_in_pops"]], "Bio.Restriction": [[207, 0, 0, "-", "PrintFormat"], [208, 0, 0, "-", "Restriction_Dictionary"]], "Bio.Restriction.PrintFormat": [[207, 3, 1, "", "PrintFormat"]], "Bio.Restriction.PrintFormat.PrintFormat": [[207, 5, 1, "", "Cmodulo"], [207, 5, 1, "", "ConsoleWidth"], [207, 5, 1, "", "Indent"], [207, 5, 1, "", "MaxSize"], [207, 5, 1, "", "NameWidth"], [207, 5, 1, "", "PrefWidth"], [207, 2, 1, "", "format_output"], [207, 5, 1, "", "linesize"], [207, 2, 1, "", "make_format"], [207, 2, 1, "", "print_as"], [207, 2, 1, "", "print_that"]], "Bio.SCOP": [[209, 3, 1, "", "Astral"], [210, 0, 0, "-", "Cla"], [211, 0, 0, "-", "Des"], [212, 0, 0, "-", "Dom"], [209, 3, 1, "", "Domain"], [213, 0, 0, "-", "Hie"], [209, 3, 1, "", "Node"], [214, 0, 0, "-", "Raf"], [215, 0, 0, "-", "Residues"], [209, 3, 1, "", "Scop"], [209, 4, 1, "", "cmp_sccs"], [209, 4, 1, "", "parse_domain"], [209, 4, 1, "", "search"]], "Bio.SCOP.Astral": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "domainsClusteredByEv"], [209, 2, 1, "", "domainsClusteredById"], [209, 2, 1, "", "getAstralDomainsFromFile"], [209, 2, 1, "", "getAstralDomainsFromSQL"], [209, 2, 1, "", "getSeq"], [209, 2, 1, "", "getSeqBySid"], [209, 2, 1, "", "hashedDomainsByEv"], [209, 2, 1, "", "hashedDomainsById"], [209, 2, 1, "", "isDomainInEv"], [209, 2, 1, "", "isDomainInId"], [209, 2, 1, "", "writeToSQL"]], "Bio.SCOP.Cla": [[210, 3, 1, "", "Index"], [210, 3, 1, "", "Record"], [210, 4, 1, "", "parse"]], "Bio.SCOP.Cla.Index": [[210, 2, 1, "", "__getitem__"], [210, 2, 1, "", "__init__"]], "Bio.SCOP.Cla.Record": [[210, 2, 1, "", "__init__"], [210, 2, 1, "", "__str__"]], "Bio.SCOP.Des": [[211, 3, 1, "", "Record"], [211, 4, 1, "", "parse"]], "Bio.SCOP.Des.Record": [[211, 2, 1, "", "__init__"], [211, 2, 1, "", "__str__"]], "Bio.SCOP.Dom": [[212, 3, 1, "", "Record"], [212, 4, 1, "", "parse"]], "Bio.SCOP.Dom.Record": [[212, 2, 1, "", "__init__"], [212, 2, 1, "", "__str__"]], "Bio.SCOP.Domain": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "__str__"], [209, 2, 1, "", "toClaRecord"], [209, 2, 1, "", "toDesRecord"]], "Bio.SCOP.Hie": [[213, 3, 1, "", "Record"], [213, 4, 1, "", "parse"]], "Bio.SCOP.Hie.Record": [[213, 2, 1, "", "__init__"], [213, 2, 1, "", "__str__"]], "Bio.SCOP.Node": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "__str__"], [209, 2, 1, "", "getAscendent"], [209, 2, 1, "", "getChildren"], [209, 2, 1, "", "getDescendents"], [209, 2, 1, "", "getParent"], [209, 2, 1, "", "toDesRecord"], [209, 2, 1, "", "toHieRecord"]], "Bio.SCOP.Raf": [[214, 3, 1, "", "Res"], [214, 3, 1, "", "SeqMap"], [214, 3, 1, "", "SeqMapIndex"], [214, 4, 1, "", "normalize_letters"], [214, 4, 1, "", "parse"]], "Bio.SCOP.Raf.Res": [[214, 2, 1, "", "__init__"]], "Bio.SCOP.Raf.SeqMap": [[214, 2, 1, "", "__add__"], [214, 2, 1, "", "__getitem__"], [214, 2, 1, "", "__iadd__"], [214, 2, 1, "", "__init__"], [214, 2, 1, "", "append"], [214, 2, 1, "", "extend"], [214, 2, 1, "", "getAtoms"], [214, 2, 1, "", "index"]], "Bio.SCOP.Raf.SeqMapIndex": [[214, 2, 1, "", "__getitem__"], [214, 2, 1, "", "__init__"], [214, 2, 1, "", "getSeqMap"]], "Bio.SCOP.Residues": [[215, 3, 1, "", "Residues"]], "Bio.SCOP.Residues.Residues": [[215, 2, 1, "", "__init__"], [215, 2, 1, "", "__str__"]], "Bio.SCOP.Scop": [[209, 2, 1, "", "__init__"], [209, 2, 1, "", "getAscendentFromSQL"], [209, 2, 1, "", "getDescendentsFromSQL"], [209, 2, 1, "", "getDomainBySid"], [209, 2, 1, "", "getDomainFromSQL"], [209, 2, 1, "", "getDomains"], [209, 2, 1, "", "getNodeBySunid"], [209, 2, 1, "", "getRoot"], [209, 2, 1, "", "write_cla"], [209, 2, 1, "", "write_cla_sql"], [209, 2, 1, "", "write_des"], [209, 2, 1, "", "write_des_sql"], [209, 2, 1, "", "write_hie"], [209, 2, 1, "", "write_hie_sql"]], "Bio.SVDSuperimposer": [[216, 3, 1, "", "SVDSuperimposer"]], "Bio.SVDSuperimposer.SVDSuperimposer": [[216, 2, 1, "", "__init__"], [216, 2, 1, "", "get_init_rms"], [216, 2, 1, "", "get_rms"], [216, 2, 1, "", "get_rotran"], [216, 2, 1, "", "get_transformed"], [216, 2, 1, "", "run"], [216, 2, 1, "", "set"]], "Bio.SearchIO": [[218, 0, 0, "-", "BlastIO"], [221, 0, 0, "-", "BlatIO"], [222, 0, 0, "-", "ExonerateIO"], [226, 0, 0, "-", "FastaIO"], [227, 0, 0, "-", "HHsuiteIO"], [229, 0, 0, "-", "HmmerIO"], [234, 0, 0, "-", "InterproscanIO"], [217, 4, 1, "", "convert"], [217, 4, 1, "", "index"], [217, 4, 1, "", "index_db"], [217, 4, 1, "", "parse"], [217, 4, 1, "", "read"], [217, 4, 1, "", "to_dict"], [217, 4, 1, "", "write"]], "Bio.SearchIO.BlastIO": [[219, 0, 0, "-", "blast_tab"], [220, 0, 0, "-", "blast_xml"]], "Bio.SearchIO.BlastIO.blast_tab": [[219, 3, 1, "", "BlastTabIndexer"], [219, 3, 1, "", "BlastTabParser"], [219, 3, 1, "", "BlastTabWriter"]], "Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer": [[219, 5, 1, "", "__abstractmethods__"], [219, 2, 1, "", "__init__"], [219, 2, 1, "", "__iter__"], [219, 2, 1, "", "get_raw"]], "Bio.SearchIO.BlastIO.blast_tab.BlastTabParser": [[219, 2, 1, "", "__init__"], [219, 2, 1, "", "__iter__"]], "Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter": [[219, 2, 1, "", "__init__"], [219, 2, 1, "", "write_file"]], "Bio.SearchIO.BlastIO.blast_xml": [[220, 3, 1, "", "BlastXmlIndexer"], [220, 3, 1, "", "BlastXmlParser"], [220, 3, 1, "", "BlastXmlWriter"]], "Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer": [[220, 5, 1, "", "__abstractmethods__"], [220, 2, 1, "", "__init__"], [220, 2, 1, "", "__iter__"], [220, 5, 1, "", "block_size"], [220, 2, 1, "", "get_raw"], [220, 5, 1, "", "qend_mark"], [220, 5, 1, "", "qstart_mark"]], "Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser": [[220, 2, 1, "", "__init__"], [220, 2, 1, "", "__iter__"]], "Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter": [[220, 2, 1, "", "__init__"], [220, 2, 1, "", "write_file"]], "Bio.SearchIO.BlatIO": [[221, 3, 1, "", "BlatPslIndexer"], [221, 3, 1, "", "BlatPslParser"], [221, 3, 1, "", "BlatPslWriter"]], "Bio.SearchIO.BlatIO.BlatPslIndexer": [[221, 5, 1, "", "__abstractmethods__"], [221, 2, 1, "", "__init__"], [221, 2, 1, "", "__iter__"], [221, 2, 1, "", "get_raw"]], "Bio.SearchIO.BlatIO.BlatPslParser": [[221, 2, 1, "", "__init__"], [221, 2, 1, "", "__iter__"]], "Bio.SearchIO.BlatIO.BlatPslWriter": [[221, 2, 1, "", "__init__"], [221, 2, 1, "", "write_file"]], "Bio.SearchIO.ExonerateIO": [[223, 0, 0, "-", "exonerate_cigar"], [224, 0, 0, "-", "exonerate_text"], [225, 0, 0, "-", "exonerate_vulgar"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar": [[223, 3, 1, "", "ExonerateCigarIndexer"], [223, 3, 1, "", "ExonerateCigarParser"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer": [[223, 5, 1, "", "__abstractmethods__"], [223, 2, 1, "", "get_qresult_id"]], "Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser": [[223, 5, 1, "", "__abstractmethods__"], [223, 2, 1, "", "parse_alignment_block"]], "Bio.SearchIO.ExonerateIO.exonerate_text": [[224, 3, 1, "", "ExonerateTextIndexer"], [224, 3, 1, "", "ExonerateTextParser"]], "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer": [[224, 5, 1, "", "__abstractmethods__"], [224, 2, 1, "", "get_qresult_id"], [224, 2, 1, "", "get_raw"]], "Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser": [[224, 5, 1, "", "__abstractmethods__"], [224, 2, 1, "", "parse_alignment_block"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar": [[225, 3, 1, "", "ExonerateVulgarIndexer"], [225, 3, 1, "", "ExonerateVulgarParser"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer": [[225, 5, 1, "", "__abstractmethods__"], [225, 5, 1, "", "__annotations__"], [225, 2, 1, "", "get_qresult_id"], [225, 2, 1, "", "get_raw"]], "Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser": [[225, 5, 1, "", "__abstractmethods__"], [225, 2, 1, "", "parse_alignment_block"]], "Bio.SearchIO.FastaIO": [[226, 3, 1, "", "FastaM10Indexer"], [226, 3, 1, "", "FastaM10Parser"]], "Bio.SearchIO.FastaIO.FastaM10Indexer": [[226, 5, 1, "", "__abstractmethods__"], [226, 2, 1, "", "__init__"], [226, 2, 1, "", "__iter__"], [226, 2, 1, "", "get_raw"]], "Bio.SearchIO.FastaIO.FastaM10Parser": [[226, 2, 1, "", "__init__"], [226, 2, 1, "", "__iter__"]], "Bio.SearchIO.HHsuiteIO": [[228, 0, 0, "-", "hhsuite2_text"]], "Bio.SearchIO.HHsuiteIO.hhsuite2_text": [[228, 3, 1, "", "Hhsuite2TextParser"]], "Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser": [[228, 2, 1, "", "__init__"], [228, 2, 1, "", "__iter__"]], "Bio.SearchIO.HmmerIO": [[230, 0, 0, "-", "hmmer2_text"], [231, 0, 0, "-", "hmmer3_domtab"], [232, 0, 0, "-", "hmmer3_tab"], [233, 0, 0, "-", "hmmer3_text"]], "Bio.SearchIO.HmmerIO.hmmer2_text": [[230, 3, 1, "", "Hmmer2TextIndexer"], [230, 3, 1, "", "Hmmer2TextParser"]], "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer": [[230, 5, 1, "", "__abstractmethods__"], [230, 2, 1, "", "__iter__"], [230, 5, 1, "", "qresult_end"], [230, 5, 1, "", "qresult_start"]], "Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser": [[230, 2, 1, "", "__init__"], [230, 2, 1, "", "__iter__"], [230, 2, 1, "", "parse_hits"], [230, 2, 1, "", "parse_hsp_alignments"], [230, 2, 1, "", "parse_hsps"], [230, 2, 1, "", "parse_key_value"], [230, 2, 1, "", "parse_preamble"], [230, 2, 1, "", "parse_qresult"], [230, 2, 1, "", "push_back"], [230, 2, 1, "", "read_next"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab": [[231, 3, 1, "", "Hmmer3DomtabHmmhitIndexer"], [231, 3, 1, "", "Hmmer3DomtabHmmhitParser"], [231, 3, 1, "", "Hmmer3DomtabHmmhitWriter"], [231, 3, 1, "", "Hmmer3DomtabHmmqueryIndexer"], [231, 3, 1, "", "Hmmer3DomtabHmmqueryParser"], [231, 3, 1, "", "Hmmer3DomtabHmmqueryWriter"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer": [[231, 5, 1, "", "__abstractmethods__"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser": [[231, 5, 1, "", "hmm_as_hit"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter": [[231, 2, 1, "", "__init__"], [231, 5, 1, "", "hmm_as_hit"], [231, 2, 1, "", "write_file"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer": [[231, 5, 1, "", "__abstractmethods__"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser": [[231, 5, 1, "", "hmm_as_hit"]], "Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter": [[231, 5, 1, "", "hmm_as_hit"]], "Bio.SearchIO.HmmerIO.hmmer3_tab": [[232, 3, 1, "", "Hmmer3TabIndexer"], [232, 3, 1, "", "Hmmer3TabParser"], [232, 3, 1, "", "Hmmer3TabWriter"]], "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer": [[232, 5, 1, "", "__abstractmethods__"], [232, 2, 1, "", "__iter__"], [232, 2, 1, "", "get_raw"]], "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser": [[232, 2, 1, "", "__init__"], [232, 2, 1, "", "__iter__"]], "Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter": [[232, 2, 1, "", "__init__"], [232, 2, 1, "", "write_file"]], "Bio.SearchIO.HmmerIO.hmmer3_text": [[233, 3, 1, "", "Hmmer3TextIndexer"], [233, 3, 1, "", "Hmmer3TextParser"]], "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer": [[233, 5, 1, "", "__abstractmethods__"], [233, 2, 1, "", "__iter__"], [233, 5, 1, "", "qresult_end"], [233, 5, 1, "", "qresult_start"]], "Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser": [[233, 2, 1, "", "__init__"], [233, 2, 1, "", "__iter__"]], "Bio.SearchIO.InterproscanIO": [[235, 0, 0, "-", "interproscan_xml"]], "Bio.SearchIO.InterproscanIO.interproscan_xml": [[235, 3, 1, "", "InterproscanXmlParser"]], "Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser": [[235, 2, 1, "", "__init__"], [235, 2, 1, "", "__iter__"]], "Bio.Seq": [[236, 3, 1, "", "MutableSeq"], [236, 3, 1, "", "Seq"], [236, 3, 1, "", "SequenceDataAbstractBaseClass"], [236, 1, 1, "", "UndefinedSequenceError"], [236, 4, 1, "", "back_transcribe"], [236, 4, 1, "", "complement"], [236, 4, 1, "", "complement_rna"], [236, 4, 1, "", "reverse_complement"], [236, 4, 1, "", "reverse_complement_rna"], [236, 4, 1, "", "transcribe"], [236, 4, 1, "", "translate"]], "Bio.Seq.MutableSeq": [[236, 5, 1, "", "__abstractmethods__"], [236, 2, 1, "", "__delitem__"], [236, 2, 1, "", "__init__"], [236, 2, 1, "", "__setitem__"], [236, 2, 1, "", "append"], [236, 2, 1, "", "extend"], [236, 2, 1, "", "insert"], [236, 2, 1, "", "pop"], [236, 2, 1, "", "remove"], [236, 2, 1, "", "reverse"]], "Bio.Seq.Seq": [[236, 5, 1, "", "__abstractmethods__"], [236, 5, 1, "", "__annotations__"], [236, 2, 1, "", "__hash__"], [236, 2, 1, "", "__init__"]], "Bio.Seq.SequenceDataAbstractBaseClass": [[236, 5, 1, "", "__abstractmethods__"], [236, 2, 1, "", "__add__"], [236, 2, 1, "", "__bytes__"], [236, 2, 1, "", "__contains__"], [236, 2, 1, "", "__eq__"], [236, 2, 1, "", "__ge__"], [236, 2, 1, "", "__getitem__"], [236, 2, 1, "", "__gt__"], [236, 2, 1, "", "__hash__"], [236, 2, 1, "", "__init__"], [236, 2, 1, "", "__le__"], [236, 2, 1, "", "__len__"], [236, 2, 1, "", "__lt__"], [236, 2, 1, "", "__mul__"], [236, 2, 1, "", "__radd__"], [236, 5, 1, "", "__slots__"], [236, 2, 1, "", "count"], [236, 2, 1, "", "decode"], [236, 6, 1, "", "defined"], [236, 6, 1, "", "defined_ranges"], [236, 2, 1, "", "endswith"], [236, 2, 1, "", "find"], [236, 2, 1, "", "index"], [236, 2, 1, "", "islower"], [236, 2, 1, "", "isupper"], [236, 2, 1, "", "lower"], [236, 2, 1, "", "lstrip"], [236, 2, 1, "", "removeprefix"], [236, 2, 1, "", "removesuffix"], [236, 2, 1, "", "replace"], [236, 2, 1, "", "rfind"], [236, 2, 1, "", "rindex"], [236, 2, 1, "", "rsplit"], [236, 2, 1, "", "rstrip"], [236, 2, 1, "", "split"], [236, 2, 1, "", "startswith"], [236, 2, 1, "", "strip"], [236, 2, 1, "", "translate"], [236, 2, 1, "", "upper"]], "Bio.SeqFeature": [[237, 3, 1, "", "AfterPosition"], [237, 3, 1, "", "BeforePosition"], [237, 3, 1, "", "BetweenPosition"], [237, 3, 1, "", "CompoundLocation"], [237, 3, 1, "", "ExactPosition"], [237, 5, 1, "", "FeatureLocation"], [237, 3, 1, "", "Location"], [237, 1, 1, "", "LocationParserError"], [237, 3, 1, "", "OneOfPosition"], [237, 3, 1, "", "Position"], [237, 3, 1, "", "Reference"], [237, 3, 1, "", "SeqFeature"], [237, 3, 1, "", "SimpleLocation"], [237, 3, 1, "", "UncertainPosition"], [237, 3, 1, "", "UnknownPosition"], [237, 3, 1, "", "WithinPosition"]], "Bio.SeqFeature.AfterPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.BeforePosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.BetweenPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__getnewargs__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.CompoundLocation": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__contains__"], [237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__iter__"], [237, 2, 1, "", "__len__"], [237, 2, 1, "", "__nonzero__"], [237, 2, 1, "", "__radd__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"], [237, 6, 1, "", "end"], [237, 2, 1, "", "extract"], [237, 6, 1, "", "ref"], [237, 6, 1, "", "ref_db"], [237, 6, 1, "", "start"], [237, 6, 1, "", "strand"]], "Bio.SeqFeature.ExactPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.Location": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "fromstring"]], "Bio.SeqFeature.OneOfPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__getnewargs__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.Position": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "fromstring"]], "Bio.SeqFeature.Reference": [[237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqFeature.SeqFeature": [[237, 2, 1, "", "__bool__"], [237, 2, 1, "", "__contains__"], [237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__iter__"], [237, 2, 1, "", "__len__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"], [237, 2, 1, "", "extract"], [237, 6, 1, "", "ref"], [237, 6, 1, "", "ref_db"], [237, 6, 1, "", "strand"], [237, 2, 1, "", "translate"]], "Bio.SeqFeature.SimpleLocation": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__contains__"], [237, 2, 1, "", "__eq__"], [237, 5, 1, "", "__hash__"], [237, 2, 1, "", "__init__"], [237, 2, 1, "", "__iter__"], [237, 2, 1, "", "__len__"], [237, 2, 1, "", "__nonzero__"], [237, 2, 1, "", "__radd__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"], [237, 2, 1, "", "__sub__"], [237, 6, 1, "", "end"], [237, 2, 1, "", "extract"], [237, 2, 1, "", "fromstring"], [237, 6, 1, "", "parts"], [237, 6, 1, "", "start"], [237, 6, 1, "", "strand"]], "Bio.SeqFeature.UncertainPosition": [[237, 5, 1, "", "__abstractmethods__"]], "Bio.SeqFeature.UnknownPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__hash__"], [237, 2, 1, "", "__repr__"]], "Bio.SeqFeature.WithinPosition": [[237, 5, 1, "", "__abstractmethods__"], [237, 2, 1, "", "__add__"], [237, 2, 1, "", "__getnewargs__"], [237, 2, 1, "", "__new__"], [237, 2, 1, "", "__repr__"], [237, 2, 1, "", "__str__"]], "Bio.SeqIO": [[239, 0, 0, "-", "AbiIO"], [240, 0, 0, "-", "AceIO"], [241, 0, 0, "-", "FastaIO"], [242, 0, 0, "-", "GckIO"], [243, 0, 0, "-", "GfaIO"], [244, 0, 0, "-", "IgIO"], [245, 0, 0, "-", "InsdcIO"], [246, 0, 0, "-", "Interfaces"], [247, 0, 0, "-", "NibIO"], [248, 0, 0, "-", "PdbIO"], [249, 0, 0, "-", "PhdIO"], [250, 0, 0, "-", "PirIO"], [251, 0, 0, "-", "QualityIO"], [252, 0, 0, "-", "SeqXmlIO"], [253, 0, 0, "-", "SffIO"], [254, 0, 0, "-", "SnapGeneIO"], [255, 0, 0, "-", "SwissIO"], [256, 0, 0, "-", "TabIO"], [257, 0, 0, "-", "TwoBitIO"], [258, 0, 0, "-", "UniprotIO"], [259, 0, 0, "-", "XdnaIO"], [238, 4, 1, "", "convert"], [238, 4, 1, "", "index"], [238, 4, 1, "", "index_db"], [238, 4, 1, "", "parse"], [238, 4, 1, "", "read"], [238, 4, 1, "", "to_dict"], [238, 4, 1, "", "write"]], "Bio.SeqIO.AbiIO": [[239, 3, 1, "", "AbiIterator"]], "Bio.SeqIO.AbiIO.AbiIterator": [[239, 5, 1, "", "__abstractmethods__"], [239, 2, 1, "", "__init__"], [239, 2, 1, "", "__next__"], [239, 5, 1, "", "__parameters__"], [239, 2, 1, "", "parse"]], "Bio.SeqIO.AceIO": [[240, 4, 1, "", "AceIterator"]], "Bio.SeqIO.FastaIO": [[241, 3, 1, "", "FastaIterator"], [241, 3, 1, "", "FastaTwoLineIterator"], [241, 4, 1, "", "FastaTwoLineParser"], [241, 3, 1, "", "FastaTwoLineWriter"], [241, 3, 1, "", "FastaWriter"], [241, 4, 1, "", "SimpleFastaParser"], [241, 4, 1, "", "as_fasta"], [241, 4, 1, "", "as_fasta_2line"]], "Bio.SeqIO.FastaIO.FastaIterator": [[241, 5, 1, "", "__abstractmethods__"], [241, 2, 1, "", "__init__"], [241, 5, 1, "", "__parameters__"], [241, 2, 1, "", "iterate"], [241, 2, 1, "", "parse"]], "Bio.SeqIO.FastaIO.FastaTwoLineIterator": [[241, 5, 1, "", "__abstractmethods__"], [241, 2, 1, "", "__init__"], [241, 5, 1, "", "__parameters__"], [241, 2, 1, "", "iterate"], [241, 2, 1, "", "parse"]], "Bio.SeqIO.FastaIO.FastaTwoLineWriter": [[241, 2, 1, "", "__init__"]], "Bio.SeqIO.FastaIO.FastaWriter": [[241, 2, 1, "", "__init__"], [241, 2, 1, "", "write_record"]], "Bio.SeqIO.GckIO": [[242, 3, 1, "", "GckIterator"]], "Bio.SeqIO.GckIO.GckIterator": [[242, 5, 1, "", "__abstractmethods__"], [242, 2, 1, "", "__init__"], [242, 5, 1, "", "__parameters__"], [242, 2, 1, "", "parse"]], "Bio.SeqIO.GfaIO": [[243, 4, 1, "", "Gfa1Iterator"], [243, 4, 1, "", "Gfa2Iterator"]], "Bio.SeqIO.IgIO": [[244, 3, 1, "", "IgIterator"]], "Bio.SeqIO.IgIO.IgIterator": [[244, 5, 1, "", "__abstractmethods__"], [244, 2, 1, "", "__init__"], [244, 2, 1, "", "__next__"], [244, 5, 1, "", "__parameters__"], [244, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO": [[245, 3, 1, "", "EmblCdsFeatureIterator"], [245, 3, 1, "", "EmblIterator"], [245, 3, 1, "", "EmblWriter"], [245, 3, 1, "", "GenBankCdsFeatureIterator"], [245, 3, 1, "", "GenBankIterator"], [245, 3, 1, "", "GenBankWriter"], [245, 3, 1, "", "ImgtIterator"], [245, 3, 1, "", "ImgtWriter"]], "Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.EmblIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.EmblWriter": [[245, 5, 1, "", "BLOCKS_PER_LINE"], [245, 5, 1, "", "FEATURE_HEADER"], [245, 5, 1, "", "HEADER_WIDTH"], [245, 5, 1, "", "LETTERS_PER_BLOCK"], [245, 5, 1, "", "LETTERS_PER_LINE"], [245, 5, 1, "", "POSITION_PADDING"], [245, 5, 1, "", "QUALIFIER_INDENT"], [245, 5, 1, "", "QUALIFIER_INDENT_STR"], [245, 5, 1, "", "QUALIFIER_INDENT_TMP"], [245, 2, 1, "", "write_record"]], "Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.GenBankIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.GenBankWriter": [[245, 5, 1, "", "HEADER_WIDTH"], [245, 5, 1, "", "LETTERS_PER_LINE"], [245, 5, 1, "", "QUALIFIER_INDENT"], [245, 5, 1, "", "SEQUENCE_INDENT"], [245, 5, 1, "", "STRUCTURED_COMMENT_DELIM"], [245, 5, 1, "", "STRUCTURED_COMMENT_END"], [245, 5, 1, "", "STRUCTURED_COMMENT_START"], [245, 2, 1, "", "write_record"]], "Bio.SeqIO.InsdcIO.ImgtIterator": [[245, 5, 1, "", "__abstractmethods__"], [245, 2, 1, "", "__init__"], [245, 5, 1, "", "__parameters__"], [245, 2, 1, "", "parse"]], "Bio.SeqIO.InsdcIO.ImgtWriter": [[245, 5, 1, "", "FEATURE_HEADER"], [245, 5, 1, "", "HEADER_WIDTH"], [245, 5, 1, "", "QUALIFIER_INDENT"], [245, 5, 1, "", "QUALIFIER_INDENT_STR"], [245, 5, 1, "", "QUALIFIER_INDENT_TMP"]], "Bio.SeqIO.Interfaces": [[246, 3, 1, "", "SequenceIterator"], [246, 3, 1, "", "SequenceWriter"]], "Bio.SeqIO.Interfaces.SequenceIterator": [[246, 5, 1, "", "__abstractmethods__"], [246, 2, 1, "", "__init__"], [246, 2, 1, "", "__iter__"], [246, 2, 1, "", "__next__"], [246, 5, 1, "", "__orig_bases__"], [246, 5, 1, "", "__parameters__"], [246, 2, 1, "", "parse"]], "Bio.SeqIO.Interfaces.SequenceWriter": [[246, 2, 1, "", "__init__"], [246, 2, 1, "", "clean"], [246, 2, 1, "", "write_file"], [246, 2, 1, "", "write_footer"], [246, 2, 1, "", "write_header"], [246, 2, 1, "", "write_record"], [246, 2, 1, "", "write_records"]], "Bio.SeqIO.NibIO": [[247, 3, 1, "", "NibIterator"], [247, 3, 1, "", "NibWriter"]], "Bio.SeqIO.NibIO.NibIterator": [[247, 5, 1, "", "__abstractmethods__"], [247, 2, 1, "", "__init__"], [247, 5, 1, "", "__parameters__"], [247, 2, 1, "", "iterate"], [247, 2, 1, "", "parse"]], "Bio.SeqIO.NibIO.NibWriter": [[247, 2, 1, "", "__init__"], [247, 2, 1, "", "write_file"], [247, 2, 1, "", "write_header"], [247, 2, 1, "", "write_record"]], "Bio.SeqIO.PdbIO": [[248, 4, 1, "", "AtomIterator"], [248, 4, 1, "", "CifAtomIterator"], [248, 4, 1, "", "CifSeqresIterator"], [248, 4, 1, "", "PdbAtomIterator"], [248, 3, 1, "", "PdbSeqresIterator"]], "Bio.SeqIO.PdbIO.PdbSeqresIterator": [[248, 5, 1, "", "__abstractmethods__"], [248, 2, 1, "", "__init__"], [248, 2, 1, "", "__next__"], [248, 5, 1, "", "__parameters__"], [248, 2, 1, "", "parse"]], "Bio.SeqIO.PhdIO": [[249, 4, 1, "", "PhdIterator"], [249, 3, 1, "", "PhdWriter"]], "Bio.SeqIO.PhdIO.PhdWriter": [[249, 2, 1, "", "__init__"], [249, 2, 1, "", "write_record"]], "Bio.SeqIO.PirIO": [[250, 3, 1, "", "PirIterator"], [250, 3, 1, "", "PirWriter"]], "Bio.SeqIO.PirIO.PirIterator": [[250, 5, 1, "", "__abstractmethods__"], [250, 2, 1, "", "__init__"], [250, 2, 1, "", "__next__"], [250, 5, 1, "", "__parameters__"], [250, 2, 1, "", "parse"]], "Bio.SeqIO.PirIO.PirWriter": [[250, 2, 1, "", "__init__"], [250, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO": [[251, 4, 1, "", "FastqGeneralIterator"], [251, 4, 1, "", "FastqIlluminaIterator"], [251, 3, 1, "", "FastqIlluminaWriter"], [251, 3, 1, "", "FastqPhredIterator"], [251, 3, 1, "", "FastqPhredWriter"], [251, 4, 1, "", "FastqSolexaIterator"], [251, 3, 1, "", "FastqSolexaWriter"], [251, 4, 1, "", "PairedFastaQualIterator"], [251, 3, 1, "", "QualPhredIterator"], [251, 3, 1, "", "QualPhredWriter"], [251, 4, 1, "", "as_fastq"], [251, 4, 1, "", "as_fastq_illumina"], [251, 4, 1, "", "as_fastq_solexa"], [251, 4, 1, "", "as_qual"], [251, 4, 1, "", "phred_quality_from_solexa"], [251, 4, 1, "", "solexa_quality_from_phred"]], "Bio.SeqIO.QualityIO.FastqIlluminaWriter": [[251, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO.FastqPhredIterator": [[251, 5, 1, "", "__abstractmethods__"], [251, 2, 1, "", "__init__"], [251, 5, 1, "", "__orig_bases__"], [251, 5, 1, "", "__parameters__"], [251, 2, 1, "", "iterate"], [251, 2, 1, "", "parse"]], "Bio.SeqIO.QualityIO.FastqPhredWriter": [[251, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO.FastqSolexaWriter": [[251, 2, 1, "", "write_record"]], "Bio.SeqIO.QualityIO.QualPhredIterator": [[251, 5, 1, "", "__abstractmethods__"], [251, 2, 1, "", "__init__"], [251, 5, 1, "", "__parameters__"], [251, 2, 1, "", "iterate"], [251, 2, 1, "", "parse"]], "Bio.SeqIO.QualityIO.QualPhredWriter": [[251, 2, 1, "", "__init__"], [251, 2, 1, "", "write_record"]], "Bio.SeqIO.SeqXmlIO": [[252, 3, 1, "", "ContentHandler"], [252, 3, 1, "", "SeqXmlIterator"], [252, 3, 1, "", "SeqXmlWriter"]], "Bio.SeqIO.SeqXmlIO.ContentHandler": [[252, 2, 1, "", "__init__"], [252, 2, 1, "", "characters"], [252, 2, 1, "", "endDBRefElement"], [252, 2, 1, "", "endDescriptionElement"], [252, 2, 1, "", "endEntryElement"], [252, 2, 1, "", "endPropertyElement"], [252, 2, 1, "", "endSeqXMLElement"], [252, 2, 1, "", "endSequenceElement"], [252, 2, 1, "", "endSpeciesElement"], [252, 2, 1, "", "startDBRefElement"], [252, 2, 1, "", "startDescriptionElement"], [252, 2, 1, "", "startDocument"], [252, 2, 1, "", "startEntryElement"], [252, 2, 1, "", "startEntryFieldElement"], [252, 2, 1, "", "startEntryFieldElementVersion01"], [252, 2, 1, "", "startPropertyElement"], [252, 2, 1, "", "startSeqXMLElement"], [252, 2, 1, "", "startSequenceElement"], [252, 2, 1, "", "startSpeciesElement"]], "Bio.SeqIO.SeqXmlIO.SeqXmlIterator": [[252, 5, 1, "", "BLOCK"], [252, 5, 1, "", "__abstractmethods__"], [252, 2, 1, "", "__init__"], [252, 2, 1, "", "__next__"], [252, 5, 1, "", "__parameters__"], [252, 2, 1, "", "parse"]], "Bio.SeqIO.SeqXmlIO.SeqXmlWriter": [[252, 2, 1, "", "__init__"], [252, 2, 1, "", "write_footer"], [252, 2, 1, "", "write_header"], [252, 2, 1, "", "write_record"]], "Bio.SeqIO.SffIO": [[253, 4, 1, "", "ReadRocheXmlManifest"], [253, 3, 1, "", "SffIterator"], [253, 3, 1, "", "SffWriter"]], "Bio.SeqIO.SffIO.SffIterator": [[253, 5, 1, "", "__abstractmethods__"], [253, 2, 1, "", "__init__"], [253, 5, 1, "", "__parameters__"], [253, 2, 1, "", "iterate"], [253, 2, 1, "", "parse"]], "Bio.SeqIO.SffIO.SffWriter": [[253, 2, 1, "", "__init__"], [253, 2, 1, "", "write_file"], [253, 2, 1, "", "write_header"], [253, 2, 1, "", "write_record"]], "Bio.SeqIO.SnapGeneIO": [[254, 3, 1, "", "SnapGeneIterator"]], "Bio.SeqIO.SnapGeneIO.SnapGeneIterator": [[254, 5, 1, "", "__abstractmethods__"], [254, 2, 1, "", "__init__"], [254, 5, 1, "", "__parameters__"], [254, 2, 1, "", "iterate"], [254, 2, 1, "", "parse"]], "Bio.SeqIO.SwissIO": [[255, 4, 1, "", "SwissIterator"]], "Bio.SeqIO.TabIO": [[256, 3, 1, "", "TabIterator"], [256, 3, 1, "", "TabWriter"], [256, 4, 1, "", "as_tab"]], "Bio.SeqIO.TabIO.TabIterator": [[256, 5, 1, "", "__abstractmethods__"], [256, 2, 1, "", "__init__"], [256, 5, 1, "", "__parameters__"], [256, 2, 1, "", "iterate"], [256, 2, 1, "", "parse"]], "Bio.SeqIO.TabIO.TabWriter": [[256, 2, 1, "", "write_record"]], "Bio.SeqIO.TwoBitIO": [[257, 3, 1, "", "TwoBitIterator"]], "Bio.SeqIO.TwoBitIO.TwoBitIterator": [[257, 5, 1, "", "__abstractmethods__"], [257, 2, 1, "", "__getitem__"], [257, 2, 1, "", "__init__"], [257, 2, 1, "", "__len__"], [257, 5, 1, "", "__parameters__"], [257, 2, 1, "", "keys"], [257, 2, 1, "", "parse"]], "Bio.SeqIO.UniprotIO": [[258, 3, 1, "", "Parser"], [258, 4, 1, "", "UniprotIterator"]], "Bio.SeqIO.UniprotIO.Parser": [[258, 2, 1, "", "__init__"], [258, 2, 1, "", "parse"]], "Bio.SeqIO.XdnaIO": [[259, 3, 1, "", "XdnaIterator"], [259, 3, 1, "", "XdnaWriter"]], "Bio.SeqIO.XdnaIO.XdnaIterator": [[259, 5, 1, "", "__abstractmethods__"], [259, 2, 1, "", "__init__"], [259, 5, 1, "", "__parameters__"], [259, 2, 1, "", "iterate"], [259, 2, 1, "", "parse"]], "Bio.SeqIO.XdnaIO.XdnaWriter": [[259, 2, 1, "", "__init__"], [259, 2, 1, "", "write_file"]], "Bio.SeqRecord": [[260, 3, 1, "", "SeqRecord"]], "Bio.SeqRecord.SeqRecord": [[260, 2, 1, "", "__add__"], [260, 5, 1, "", "__annotations__"], [260, 2, 1, "", "__bool__"], [260, 2, 1, "", "__bytes__"], [260, 2, 1, "", "__contains__"], [260, 2, 1, "", "__eq__"], [260, 2, 1, "", "__format__"], [260, 2, 1, "", "__ge__"], [260, 2, 1, "", "__getitem__"], [260, 2, 1, "", "__gt__"], [260, 5, 1, "", "__hash__"], [260, 2, 1, "", "__init__"], [260, 2, 1, "", "__iter__"], [260, 2, 1, "", "__le__"], [260, 2, 1, "", "__len__"], [260, 2, 1, "", "__lt__"], [260, 2, 1, "", "__ne__"], [260, 2, 1, "", "__radd__"], [260, 2, 1, "", "__repr__"], [260, 2, 1, "", "__str__"], [260, 5, 1, "", "annotations"], [260, 2, 1, "", "count"], [260, 5, 1, "", "dbxrefs"], [260, 2, 1, "", "format"], [260, 2, 1, "", "islower"], [260, 2, 1, "", "isupper"], [260, 6, 1, "", "letter_annotations"], [260, 2, 1, "", "lower"], [260, 2, 1, "", "reverse_complement"], [260, 6, 1, "", "seq"], [260, 2, 1, "", "translate"], [260, 2, 1, "", "upper"]], "Bio.SeqUtils": [[262, 0, 0, "-", "CheckSum"], [261, 3, 1, "", "CodonAdaptationIndex"], [261, 4, 1, "", "GC123"], [261, 4, 1, "", "GC_skew"], [263, 0, 0, "-", "IsoelectricPoint"], [264, 0, 0, "-", "MeltingTemp"], [265, 0, 0, "-", "ProtParam"], [266, 0, 0, "-", "ProtParamData"], [261, 4, 1, "", "gc_fraction"], [267, 0, 0, "-", "lcc"], [261, 4, 1, "", "molecular_weight"], [261, 4, 1, "", "nt_search"], [261, 4, 1, "", "seq1"], [261, 4, 1, "", "seq3"], [261, 4, 1, "", "six_frame_translations"], [261, 4, 1, "", "xGC_skew"]], "Bio.SeqUtils.CheckSum": [[262, 4, 1, "", "crc32"], [262, 4, 1, "", "crc64"], [262, 4, 1, "", "gcg"], [262, 4, 1, "", "seguid"]], "Bio.SeqUtils.CodonAdaptationIndex": [[261, 2, 1, "", "__init__"], [261, 2, 1, "", "__str__"], [261, 2, 1, "", "calculate"], [261, 2, 1, "", "optimize"]], "Bio.SeqUtils.IsoelectricPoint": [[263, 3, 1, "", "IsoelectricPoint"]], "Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint": [[263, 2, 1, "", "__init__"], [263, 2, 1, "", "charge_at_pH"], [263, 2, 1, "", "pi"]], "Bio.SeqUtils.MeltingTemp": [[264, 4, 1, "", "Tm_GC"], [264, 4, 1, "", "Tm_NN"], [264, 4, 1, "", "Tm_Wallace"], [264, 4, 1, "", "chem_correction"], [264, 4, 1, "", "make_table"], [264, 4, 1, "", "salt_correction"]], "Bio.SeqUtils.ProtParam": [[265, 3, 1, "", "ProteinAnalysis"]], "Bio.SeqUtils.ProtParam.ProteinAnalysis": [[265, 2, 1, "", "__init__"], [265, 6, 1, "", "amino_acids_percent"], [265, 2, 1, "", "aromaticity"], [265, 2, 1, "", "charge_at_pH"], [265, 2, 1, "", "count_amino_acids"], [265, 2, 1, "", "flexibility"], [265, 2, 1, "", "get_amino_acids_percent"], [265, 2, 1, "", "gravy"], [265, 2, 1, "", "instability_index"], [265, 2, 1, "", "isoelectric_point"], [265, 2, 1, "", "molar_extinction_coefficient"], [265, 2, 1, "", "molecular_weight"], [265, 2, 1, "", "protein_scale"], [265, 2, 1, "", "secondary_structure_fraction"]], "Bio.SeqUtils.lcc": [[267, 4, 1, "", "lcc_mult"], [267, 4, 1, "", "lcc_simp"]], "Bio.Sequencing": [[269, 0, 0, "-", "Ace"], [270, 0, 0, "-", "Applications"], [271, 0, 0, "-", "Phd"]], "Bio.Sequencing.Ace": [[269, 3, 1, "", "ACEFileRecord"], [269, 3, 1, "", "Contig"], [269, 3, 1, "", "Reads"], [269, 3, 1, "", "af"], [269, 3, 1, "", "bs"], [269, 3, 1, "", "ct"], [269, 3, 1, "", "ds"], [269, 4, 1, "", "parse"], [269, 3, 1, "", "qa"], [269, 3, 1, "", "rd"], [269, 4, 1, "", "read"], [269, 3, 1, "", "rt"], [269, 3, 1, "", "wa"], [269, 3, 1, "", "wr"]], "Bio.Sequencing.Ace.ACEFileRecord": [[269, 2, 1, "", "__init__"], [269, 2, 1, "", "sort"]], "Bio.Sequencing.Ace.Contig": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.Reads": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.af": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.bs": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.ct": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.ds": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.qa": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.rd": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.rt": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.wa": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Ace.wr": [[269, 2, 1, "", "__init__"]], "Bio.Sequencing.Applications": [[270, 3, 1, "", "BwaAlignCommandline"], [270, 3, 1, "", "BwaBwaswCommandline"], [270, 3, 1, "", "BwaIndexCommandline"], [270, 3, 1, "", "BwaMemCommandline"], [270, 3, 1, "", "BwaSampeCommandline"], [270, 3, 1, "", "BwaSamseCommandline"], [270, 3, 1, "", "NovoalignCommandline"], [270, 3, 1, "", "SamtoolsCalmdCommandline"], [270, 3, 1, "", "SamtoolsCatCommandline"], [270, 3, 1, "", "SamtoolsFaidxCommandline"], [270, 3, 1, "", "SamtoolsFixmateCommandline"], [270, 3, 1, "", "SamtoolsIdxstatsCommandline"], [270, 3, 1, "", "SamtoolsIndexCommandline"], [270, 3, 1, "", "SamtoolsMergeCommandline"], [270, 3, 1, "", "SamtoolsMpileupCommandline"], [270, 3, 1, "", "SamtoolsPhaseCommandline"], [270, 3, 1, "", "SamtoolsReheaderCommandline"], [270, 3, 1, "", "SamtoolsRmdupCommandline"], [270, 5, 1, "", "SamtoolsSortCommandline"], [270, 3, 1, "", "SamtoolsTargetcutCommandline"], [270, 3, 1, "", "SamtoolsVersion0xSortCommandline"], [270, 3, 1, "", "SamtoolsVersion1xSortCommandline"], [270, 3, 1, "", "SamtoolsViewCommandline"]], "Bio.Sequencing.Applications.BwaAlignCommandline": [[270, 6, 1, "", "B"], [270, 6, 1, "", "E"], [270, 6, 1, "", "I"], [270, 6, 1, "", "M"], [270, 6, 1, "", "N"], [270, 6, 1, "", "O"], [270, 6, 1, "", "R"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "b1"], [270, 6, 1, "", "b2"], [270, 6, 1, "", "c"], [270, 6, 1, "", "d"], [270, 6, 1, "", "e"], [270, 6, 1, "", "i"], [270, 6, 1, "", "k"], [270, 6, 1, "", "l"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"], [270, 6, 1, "", "q"], [270, 6, 1, "", "read_file"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "t"]], "Bio.Sequencing.Applications.BwaBwaswCommandline": [[270, 6, 1, "", "N"], [270, 6, 1, "", "T"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "a"], [270, 6, 1, "", "b"], [270, 6, 1, "", "c"], [270, 6, 1, "", "mate_file"], [270, 6, 1, "", "q"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "s"], [270, 6, 1, "", "t"], [270, 6, 1, "", "w"], [270, 6, 1, "", "z"]], "Bio.Sequencing.Applications.BwaIndexCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "algorithm"], [270, 6, 1, "", "c"], [270, 6, 1, "", "infile"], [270, 6, 1, "", "prefix"]], "Bio.Sequencing.Applications.BwaMemCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "B"], [270, 6, 1, "", "C"], [270, 6, 1, "", "E"], [270, 6, 1, "", "H"], [270, 6, 1, "", "L"], [270, 6, 1, "", "M"], [270, 6, 1, "", "O"], [270, 6, 1, "", "P"], [270, 6, 1, "", "R"], [270, 6, 1, "", "T"], [270, 6, 1, "", "U"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "a"], [270, 6, 1, "", "c"], [270, 6, 1, "", "d"], [270, 6, 1, "", "k"], [270, 6, 1, "", "p"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file1"], [270, 6, 1, "", "read_file2"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "t"], [270, 6, 1, "", "v"], [270, 6, 1, "", "w"]], "Bio.Sequencing.Applications.BwaSampeCommandline": [[270, 6, 1, "", "N"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "a"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file1"], [270, 6, 1, "", "read_file2"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "sai_file1"], [270, 6, 1, "", "sai_file2"]], "Bio.Sequencing.Applications.BwaSamseCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "n"], [270, 6, 1, "", "r"], [270, 6, 1, "", "read_file"], [270, 6, 1, "", "reference"], [270, 6, 1, "", "sai_file"]], "Bio.Sequencing.Applications.NovoalignCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "adapter3"], [270, 6, 1, "", "adapter5"], [270, 6, 1, "", "cores"], [270, 6, 1, "", "database"], [270, 6, 1, "", "format"], [270, 6, 1, "", "fragment"], [270, 6, 1, "", "gap_extend"], [270, 6, 1, "", "gap_open"], [270, 6, 1, "", "good_bases"], [270, 6, 1, "", "homopolymer"], [270, 6, 1, "", "miRNA"], [270, 6, 1, "", "qual_digits"], [270, 6, 1, "", "quality"], [270, 6, 1, "", "r_method"], [270, 6, 1, "", "read_cal"], [270, 6, 1, "", "readfile"], [270, 6, 1, "", "recorded"], [270, 6, 1, "", "repeats"], [270, 6, 1, "", "report"], [270, 6, 1, "", "threshold"], [270, 6, 1, "", "trimming"], [270, 6, 1, "", "truncate"], [270, 6, 1, "", "unconverted"], [270, 6, 1, "", "variation"], [270, 6, 1, "", "write_cal"]], "Bio.Sequencing.Applications.SamtoolsCalmdCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "C"], [270, 6, 1, "", "E"], [270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "e"], [270, 6, 1, "", "input_bam"], [270, 6, 1, "", "r"], [270, 6, 1, "", "ref"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Applications.SamtoolsCatCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "bams"], [270, 6, 1, "", "h"], [270, 6, 1, "", "o"]], "Bio.Sequencing.Applications.SamtoolsFaidxCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "ref"]], "Bio.Sequencing.Applications.SamtoolsFixmateCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "output_file"]], "Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_bam"]], "Bio.Sequencing.Applications.SamtoolsIndexCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_bam"]], "Bio.Sequencing.Applications.SamtoolsMergeCommandline": [[270, 6, 1, "", "R"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "bam"], [270, 6, 1, "", "f"], [270, 6, 1, "", "fast_bam"], [270, 6, 1, "", "h"], [270, 6, 1, "", "n"], [270, 6, 1, "", "output"], [270, 6, 1, "", "r"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Applications.SamtoolsMpileupCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "B"], [270, 6, 1, "", "C"], [270, 6, 1, "", "D"], [270, 6, 1, "", "E"], [270, 6, 1, "", "I"], [270, 6, 1, "", "L"], [270, 6, 1, "", "M"], [270, 6, 1, "", "Q"], [270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "d"], [270, 6, 1, "", "e"], [270, 6, 1, "", "f"], [270, 6, 1, "", "g"], [270, 6, 1, "", "h"], [270, 6, 1, "", "illumina_13"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "l"], [270, 6, 1, "", "o"], [270, 6, 1, "", "p"], [270, 6, 1, "", "q"], [270, 6, 1, "", "r"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Applications.SamtoolsPhaseCommandline": [[270, 6, 1, "", "A"], [270, 6, 1, "", "F"], [270, 6, 1, "", "Q"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "in_bam"], [270, 6, 1, "", "k"], [270, 6, 1, "", "q"]], "Bio.Sequencing.Applications.SamtoolsReheaderCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "bam_file"], [270, 6, 1, "", "sam_file"]], "Bio.Sequencing.Applications.SamtoolsRmdupCommandline": [[270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "output_file"], [270, 6, 1, "", "s"]], "Bio.Sequencing.Applications.SamtoolsTargetcutCommandline": [[270, 6, 1, "", "Q"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "em0"], [270, 6, 1, "", "em1"], [270, 6, 1, "", "em2"], [270, 6, 1, "", "f"], [270, 6, 1, "", "i"], [270, 6, 1, "", "in_bam"]], "Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline": [[270, 2, 1, "", "__init__"], [270, 6, 1, "", "input"], [270, 6, 1, "", "m"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"], [270, 6, 1, "", "out_prefix"]], "Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline": [[270, 6, 1, "", "I"], [270, 6, 1, "", "O"], [270, 6, 1, "", "T"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "input"], [270, 6, 1, "", "m"], [270, 6, 1, "", "n"], [270, 6, 1, "", "o"]], "Bio.Sequencing.Applications.SamtoolsViewCommandline": [[270, 6, 1, "", "F"], [270, 6, 1, "", "H"], [270, 6, 1, "", "R"], [270, 6, 1, "", "S"], [270, 2, 1, "", "__init__"], [270, 6, 1, "", "b"], [270, 6, 1, "", "c"], [270, 6, 1, "", "f"], [270, 6, 1, "", "fast_bam"], [270, 6, 1, "", "h"], [270, 6, 1, "", "input_file"], [270, 6, 1, "", "l"], [270, 6, 1, "", "o"], [270, 6, 1, "", "q"], [270, 6, 1, "", "r"], [270, 6, 1, "", "region"], [270, 6, 1, "", "t"], [270, 6, 1, "", "u"]], "Bio.Sequencing.Phd": [[271, 3, 1, "", "Record"], [271, 4, 1, "", "parse"], [271, 4, 1, "", "read"]], "Bio.Sequencing.Phd.Record": [[271, 2, 1, "", "__init__"]], "Bio.SwissProt": [[272, 3, 1, "", "FeatureTable"], [273, 0, 0, "-", "KeyWList"], [272, 3, 1, "", "Record"], [272, 3, 1, "", "Reference"], [272, 1, 1, "", "SwissProtParserError"], [272, 4, 1, "", "parse"], [272, 4, 1, "", "read"]], "Bio.SwissProt.KeyWList": [[273, 3, 1, "", "Record"], [273, 4, 1, "", "parse"]], "Bio.SwissProt.KeyWList.Record": [[273, 2, 1, "", "__init__"]], "Bio.SwissProt.Record": [[272, 2, 1, "", "__init__"]], "Bio.SwissProt.Reference": [[272, 2, 1, "", "__init__"]], "Bio.SwissProt.SwissProtParserError": [[272, 2, 1, "", "__init__"]], "Bio.TogoWS": [[274, 4, 1, "", "convert"], [274, 4, 1, "", "entry"], [274, 4, 1, "", "search"], [274, 4, 1, "", "search_count"], [274, 4, 1, "", "search_iter"]], "Bio.UniGene": [[275, 3, 1, "", "ProtsimLine"], [275, 3, 1, "", "Record"], [275, 3, 1, "", "STSLine"], [275, 3, 1, "", "SequenceLine"], [275, 4, 1, "", "parse"], [275, 4, 1, "", "read"]], "Bio.UniGene.ProtsimLine": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniGene.Record": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniGene.STSLine": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniGene.SequenceLine": [[275, 2, 1, "", "__init__"], [275, 2, 1, "", "__repr__"]], "Bio.UniProt": [[277, 0, 0, "-", "GOA"], [276, 4, 1, "", "search"]], "Bio.UniProt.GOA": [[277, 4, 1, "", "gafbyproteiniterator"], [277, 4, 1, "", "gafiterator"], [277, 4, 1, "", "gpa_iterator"], [277, 4, 1, "", "gpi_iterator"], [277, 4, 1, "", "record_has"], [277, 4, 1, "", "writebyproteinrec"], [277, 4, 1, "", "writerec"]], "Bio.bgzf": [[278, 4, 1, "", "BgzfBlocks"], [278, 3, 1, "", "BgzfReader"], [278, 3, 1, "", "BgzfWriter"], [278, 4, 1, "", "make_virtual_offset"], [278, 4, 1, "", "open"], [278, 4, 1, "", "split_virtual_offset"]], "Bio.bgzf.BgzfReader": [[278, 2, 1, "", "__enter__"], [278, 2, 1, "", "__exit__"], [278, 2, 1, "", "__init__"], [278, 2, 1, "", "__iter__"], [278, 2, 1, "", "__next__"], [278, 2, 1, "", "close"], [278, 2, 1, "", "fileno"], [278, 2, 1, "", "isatty"], [278, 2, 1, "", "read"], [278, 2, 1, "", "readline"], [278, 2, 1, "", "seek"], [278, 2, 1, "", "seekable"], [278, 2, 1, "", "tell"]], "Bio.bgzf.BgzfWriter": [[278, 2, 1, "", "__enter__"], [278, 2, 1, "", "__exit__"], [278, 2, 1, "", "__init__"], [278, 2, 1, "", "close"], [278, 2, 1, "", "fileno"], [278, 2, 1, "", "flush"], [278, 2, 1, "", "isatty"], [278, 2, 1, "", "seekable"], [278, 2, 1, "", "tell"], [278, 2, 1, "", "write"]], "Bio.codonalign": [[279, 4, 1, "", "build"], [280, 0, 0, "-", "codonalignment"], [281, 0, 0, "-", "codonseq"]], "Bio.codonalign.codonalignment": [[280, 3, 1, "", "CodonAlignment"], [280, 4, 1, "", "mktest"]], "Bio.codonalign.codonalignment.CodonAlignment": [[280, 2, 1, "", "__add__"], [280, 2, 1, "", "__getitem__"], [280, 2, 1, "", "__init__"], [280, 2, 1, "", "__str__"], [280, 2, 1, "", "from_msa"], [280, 2, 1, "", "get_aln_length"], [280, 2, 1, "", "get_dn_ds_matrix"], [280, 2, 1, "", "get_dn_ds_tree"], [280, 2, 1, "", "toMultipleSeqAlignment"]], "Bio.codonalign.codonseq": [[281, 3, 1, "", "CodonSeq"], [281, 4, 1, "", "cal_dn_ds"]], "Bio.codonalign.codonseq.CodonSeq": [[281, 5, 1, "", "__abstractmethods__"], [281, 2, 1, "", "__init__"], [281, 2, 1, "", "from_seq"], [281, 2, 1, "", "full_translate"], [281, 2, 1, "", "get_codon"], [281, 2, 1, "", "get_codon_num"], [281, 2, 1, "", "get_full_rf_table"], [281, 2, 1, "", "toSeq"], [281, 2, 1, "", "translate"], [281, 2, 1, "", "ungap"]], "Bio.kNN": [[282, 4, 1, "", "calculate"], [282, 4, 1, "", "classify"], [282, 4, 1, "", "equal_weight"], [282, 3, 1, "", "kNN"], [282, 4, 1, "", "train"]], "Bio.kNN.kNN": [[282, 2, 1, "", "__init__"]], "Bio.motifs": [[283, 3, 1, "", "Instances"], [283, 3, 1, "", "Motif"], [284, 0, 0, "-", "alignace"], [285, 0, 0, "-", "applications"], [286, 0, 0, "-", "clusterbuster"], [283, 4, 1, "", "create"], [287, 0, 0, "-", "jaspar"], [289, 0, 0, "-", "mast"], [290, 0, 0, "-", "matrix"], [291, 0, 0, "-", "meme"], [292, 0, 0, "-", "minimal"], [283, 4, 1, "", "parse"], [293, 0, 0, "-", "pfm"], [283, 4, 1, "", "read"], [294, 0, 0, "-", "thresholds"], [295, 0, 0, "-", "transfac"], [283, 4, 1, "", "write"], [296, 0, 0, "-", "xms"]], "Bio.motifs.Instances": [[283, 2, 1, "", "__init__"], [283, 2, 1, "", "__str__"], [283, 2, 1, "", "count"], [283, 2, 1, "", "reverse_complement"], [283, 2, 1, "", "search"]], "Bio.motifs.Motif": [[283, 2, 1, "", "__format__"], [283, 2, 1, "", "__getitem__"], [283, 2, 1, "", "__init__"], [283, 2, 1, "", "__len__"], [283, 2, 1, "", "__str__"], [283, 6, 1, "", "anticonsensus"], [283, 6, 1, "", "background"], [283, 6, 1, "", "consensus"], [283, 6, 1, "", "degenerate_consensus"], [283, 2, 1, "", "format"], [283, 6, 1, "", "instances"], [283, 6, 1, "", "mask"], [283, 6, 1, "", "pseudocounts"], [283, 6, 1, "", "pssm"], [283, 6, 1, "", "pwm"], [283, 6, 1, "", "relative_entropy"], [283, 2, 1, "", "reverse_complement"], [283, 2, 1, "", "weblogo"]], "Bio.motifs.alignace": [[284, 3, 1, "", "Record"], [284, 4, 1, "", "read"]], "Bio.motifs.alignace.Record": [[284, 2, 1, "", "__init__"]], "Bio.motifs.clusterbuster": [[286, 3, 1, "", "Record"], [286, 4, 1, "", "read"], [286, 4, 1, "", "write"]], "Bio.motifs.clusterbuster.Record": [[286, 2, 1, "", "__str__"]], "Bio.motifs.jaspar": [[287, 3, 1, "", "Motif"], [287, 3, 1, "", "Record"], [287, 4, 1, "", "calculate_pseudocounts"], [288, 0, 0, "-", "db"], [287, 4, 1, "", "read"], [287, 4, 1, "", "split_jaspar_id"], [287, 4, 1, "", "write"]], "Bio.motifs.jaspar.Motif": [[287, 2, 1, "", "__eq__"], [287, 2, 1, "", "__hash__"], [287, 2, 1, "", "__init__"], [287, 2, 1, "", "__str__"], [287, 6, 1, "", "base_id"], [287, 6, 1, "", "version"]], "Bio.motifs.jaspar.Record": [[287, 2, 1, "", "__init__"], [287, 2, 1, "", "__str__"], [287, 2, 1, "", "to_dict"]], "Bio.motifs.jaspar.db": [[288, 3, 1, "", "JASPAR5"]], "Bio.motifs.jaspar.db.JASPAR5": [[288, 2, 1, "", "__init__"], [288, 2, 1, "", "__str__"], [288, 2, 1, "", "fetch_motif_by_id"], [288, 2, 1, "", "fetch_motifs"], [288, 2, 1, "", "fetch_motifs_by_name"]], "Bio.motifs.mast": [[289, 3, 1, "", "Record"], [289, 4, 1, "", "read"]], "Bio.motifs.mast.Record": [[289, 2, 1, "", "__getitem__"], [289, 2, 1, "", "__init__"]], "Bio.motifs.matrix": [[290, 3, 1, "", "FrequencyPositionMatrix"], [290, 3, 1, "", "GenericPositionMatrix"], [290, 3, 1, "", "PositionSpecificScoringMatrix"], [290, 3, 1, "", "PositionWeightMatrix"]], "Bio.motifs.matrix.FrequencyPositionMatrix": [[290, 2, 1, "", "normalize"]], "Bio.motifs.matrix.GenericPositionMatrix": [[290, 2, 1, "", "__getitem__"], [290, 2, 1, "", "__init__"], [290, 2, 1, "", "__str__"], [290, 6, 1, "", "anticonsensus"], [290, 2, 1, "", "calculate_consensus"], [290, 6, 1, "", "consensus"], [290, 6, 1, "", "degenerate_consensus"], [290, 6, 1, "", "gc_content"], [290, 2, 1, "", "reverse_complement"]], "Bio.motifs.matrix.PositionSpecificScoringMatrix": [[290, 2, 1, "", "calculate"], [290, 2, 1, "", "dist_pearson"], [290, 2, 1, "", "dist_pearson_at"], [290, 2, 1, "", "distribution"], [290, 6, 1, "", "gc_content"], [290, 6, 1, "", "max"], [290, 2, 1, "", "mean"], [290, 6, 1, "", "min"], [290, 2, 1, "", "search"], [290, 2, 1, "", "std"]], "Bio.motifs.matrix.PositionWeightMatrix": [[290, 2, 1, "", "__init__"], [290, 2, 1, "", "log_odds"]], "Bio.motifs.meme": [[291, 3, 1, "", "Instance"], [291, 3, 1, "", "Motif"], [291, 3, 1, "", "Record"], [291, 4, 1, "", "read"]], "Bio.motifs.meme.Instance": [[291, 5, 1, "", "__abstractmethods__"], [291, 2, 1, "", "__init__"]], "Bio.motifs.meme.Motif": [[291, 2, 1, "", "__init__"]], "Bio.motifs.meme.Record": [[291, 2, 1, "", "__getitem__"], [291, 2, 1, "", "__init__"]], "Bio.motifs.minimal": [[292, 3, 1, "", "Record"], [292, 4, 1, "", "read"]], "Bio.motifs.minimal.Record": [[292, 2, 1, "", "__getitem__"], [292, 2, 1, "", "__init__"]], "Bio.motifs.pfm": [[293, 3, 1, "", "Record"], [293, 4, 1, "", "read"], [293, 4, 1, "", "write"]], "Bio.motifs.pfm.Record": [[293, 2, 1, "", "__str__"]], "Bio.motifs.thresholds": [[294, 3, 1, "", "ScoreDistribution"]], "Bio.motifs.thresholds.ScoreDistribution": [[294, 2, 1, "", "__init__"], [294, 2, 1, "", "modify"], [294, 2, 1, "", "threshold_balanced"], [294, 2, 1, "", "threshold_fnr"], [294, 2, 1, "", "threshold_fpr"], [294, 2, 1, "", "threshold_patser"]], "Bio.motifs.transfac": [[295, 3, 1, "", "Motif"], [295, 3, 1, "", "Record"], [295, 4, 1, "", "read"], [295, 4, 1, "", "write"]], "Bio.motifs.transfac.Motif": [[295, 2, 1, "", "__getitem__"], [295, 5, 1, "", "multiple_value_keys"], [295, 5, 1, "", "reference_keys"]], "Bio.motifs.transfac.Record": [[295, 2, 1, "", "__init__"], [295, 2, 1, "", "__str__"]], "Bio.motifs.xms": [[296, 3, 1, "", "Record"], [296, 3, 1, "", "XMSScanner"], [296, 4, 1, "", "read"]], "Bio.motifs.xms.Record": [[296, 2, 1, "", "__str__"]], "Bio.motifs.xms.XMSScanner": [[296, 2, 1, "", "__init__"], [296, 2, 1, "", "get_acgt"], [296, 2, 1, "", "get_property_value"], [296, 2, 1, "", "get_text"], [296, 2, 1, "", "handle_motif"]], "Bio.pairwise2": [[297, 3, 1, "", "Alignment"], [297, 3, 1, "", "affine_penalty"], [297, 4, 1, "", "calc_affine_penalty"], [297, 3, 1, "", "dictionary_match"], [297, 4, 1, "", "format_alignment"], [297, 3, 1, "", "identity_match"], [297, 4, 1, "", "print_matrix"]], "Bio.pairwise2.Alignment": [[297, 2, 1, "", "__getnewargs__"], [297, 2, 1, "", "__new__"], [297, 2, 1, "", "__repr__"], [297, 5, 1, "", "__slots__"], [297, 5, 1, "", "end"], [297, 5, 1, "", "score"], [297, 5, 1, "", "seqA"], [297, 5, 1, "", "seqB"], [297, 5, 1, "", "start"]], "Bio.pairwise2.affine_penalty": [[297, 2, 1, "", "__call__"], [297, 2, 1, "", "__init__"]], "Bio.pairwise2.dictionary_match": [[297, 2, 1, "", "__call__"], [297, 2, 1, "", "__init__"]], "Bio.pairwise2.identity_match": [[297, 2, 1, "", "__call__"], [297, 2, 1, "", "__init__"]], "Bio.phenotype": [[298, 4, 1, "", "parse"], [299, 0, 0, "-", "phen_micro"], [300, 0, 0, "-", "pm_fitting"], [298, 4, 1, "", "read"], [298, 4, 1, "", "write"]], "Bio.phenotype.phen_micro": [[299, 4, 1, "", "CsvIterator"], [299, 4, 1, "", "JsonIterator"], [299, 3, 1, "", "JsonWriter"], [299, 3, 1, "", "PlateRecord"], [299, 3, 1, "", "WellRecord"]], "Bio.phenotype.phen_micro.JsonWriter": [[299, 2, 1, "", "__init__"], [299, 2, 1, "", "write"]], "Bio.phenotype.phen_micro.PlateRecord": [[299, 2, 1, "", "__add__"], [299, 2, 1, "", "__contains__"], [299, 2, 1, "", "__delitem__"], [299, 2, 1, "", "__eq__"], [299, 2, 1, "", "__getitem__"], [299, 5, 1, "", "__hash__"], [299, 2, 1, "", "__init__"], [299, 2, 1, "", "__iter__"], [299, 2, 1, "", "__len__"], [299, 2, 1, "", "__repr__"], [299, 2, 1, "", "__setitem__"], [299, 2, 1, "", "__str__"], [299, 2, 1, "", "__sub__"], [299, 2, 1, "", "get_column"], [299, 2, 1, "", "get_row"], [299, 2, 1, "", "subtract_control"]], "Bio.phenotype.phen_micro.WellRecord": [[299, 2, 1, "", "__add__"], [299, 2, 1, "", "__eq__"], [299, 2, 1, "", "__getitem__"], [299, 5, 1, "", "__hash__"], [299, 2, 1, "", "__init__"], [299, 2, 1, "", "__iter__"], [299, 2, 1, "", "__len__"], [299, 2, 1, "", "__repr__"], [299, 2, 1, "", "__setitem__"], [299, 2, 1, "", "__str__"], [299, 2, 1, "", "__sub__"], [299, 2, 1, "", "fit"], [299, 2, 1, "", "get_raw"], [299, 2, 1, "", "get_signals"], [299, 2, 1, "", "get_times"]], "Bio.phenotype.pm_fitting": [[300, 4, 1, "", "fit"], [300, 4, 1, "", "get_area"], [300, 4, 1, "", "gompertz"], [300, 4, 1, "", "guess_lag"], [300, 4, 1, "", "guess_plateau"], [300, 4, 1, "", "logistic"], [300, 4, 1, "", "richards"]], "BioSQL": [[302, 0, 0, "-", "BioSeq"], [303, 0, 0, "-", "BioSeqDatabase"], [304, 0, 0, "-", "DBUtils"], [305, 0, 0, "-", "Loader"]], "BioSQL.BioSeq": [[302, 3, 1, "", "DBSeqRecord"]], "BioSQL.BioSeq.DBSeqRecord": [[302, 2, 1, "", "__init__"], [302, 6, 1, "", "annotations"], [302, 6, 1, "", "dbxrefs"], [302, 6, 1, "", "features"], [302, 6, 1, "", "seq"]], "BioSQL.BioSeqDatabase": [[303, 3, 1, "", "Adaptor"], [303, 3, 1, "", "BioSeqDatabase"], [303, 3, 1, "", "DBServer"], [303, 3, 1, "", "MysqlConnectorAdaptor"], [303, 4, 1, "", "open_database"]], "BioSQL.BioSeqDatabase.Adaptor": [[303, 2, 1, "", "__init__"], [303, 2, 1, "", "autocommit"], [303, 2, 1, "", "close"], [303, 2, 1, "", "commit"], [303, 2, 1, "", "execute"], [303, 2, 1, "", "execute_and_fetch_col0"], [303, 2, 1, "", "execute_and_fetchall"], [303, 2, 1, "", "execute_one"], [303, 2, 1, "", "executemany"], [303, 2, 1, "", "fetch_dbid_by_dbname"], [303, 2, 1, "", "fetch_seqid_by_accession"], [303, 2, 1, "", "fetch_seqid_by_display_id"], [303, 2, 1, "", "fetch_seqid_by_identifier"], [303, 2, 1, "", "fetch_seqid_by_version"], [303, 2, 1, "", "fetch_seqids_by_accession"], [303, 2, 1, "", "get_subseq_as_string"], [303, 2, 1, "", "last_id"], [303, 2, 1, "", "list_any_ids"], [303, 2, 1, "", "list_biodatabase_names"], [303, 2, 1, "", "list_bioentry_display_ids"], [303, 2, 1, "", "list_bioentry_ids"], [303, 2, 1, "", "rollback"]], "BioSQL.BioSeqDatabase.BioSeqDatabase": [[303, 2, 1, "", "__contains__"], [303, 2, 1, "", "__delitem__"], [303, 2, 1, "", "__getitem__"], [303, 2, 1, "", "__init__"], [303, 2, 1, "", "__iter__"], [303, 2, 1, "", "__len__"], [303, 2, 1, "", "__repr__"], [303, 2, 1, "", "get_Seq_by_acc"], [303, 2, 1, "", "get_Seq_by_id"], [303, 2, 1, "", "get_Seq_by_ver"], [303, 2, 1, "", "get_Seqs_by_acc"], [303, 2, 1, "", "items"], [303, 2, 1, "", "keys"], [303, 2, 1, "", "load"], [303, 2, 1, "", "lookup"], [303, 2, 1, "", "values"]], "BioSQL.BioSeqDatabase.DBServer": [[303, 2, 1, "", "__contains__"], [303, 2, 1, "", "__delitem__"], [303, 2, 1, "", "__getitem__"], [303, 2, 1, "", "__init__"], [303, 2, 1, "", "__iter__"], [303, 2, 1, "", "__len__"], [303, 2, 1, "", "__repr__"], [303, 2, 1, "", "close"], [303, 2, 1, "", "commit"], [303, 2, 1, "", "items"], [303, 2, 1, "", "keys"], [303, 2, 1, "", "load_database_sql"], [303, 2, 1, "", "new_database"], [303, 2, 1, "", "rollback"], [303, 2, 1, "", "values"]], "BioSQL.BioSeqDatabase.MysqlConnectorAdaptor": [[303, 2, 1, "", "execute_and_fetch_col0"], [303, 2, 1, "", "execute_and_fetchall"], [303, 2, 1, "", "execute_one"]], "BioSQL.DBUtils": [[304, 3, 1, "", "Generic_dbutils"], [304, 3, 1, "", "Mysql_dbutils"], [304, 3, 1, "", "Pgdb_dbutils"], [304, 3, 1, "", "Psycopg2_dbutils"], [304, 3, 1, "", "Sqlite_dbutils"], [304, 4, 1, "", "get_dbutils"]], "BioSQL.DBUtils.Generic_dbutils": [[304, 2, 1, "", "__init__"], [304, 2, 1, "", "autocommit"], [304, 2, 1, "", "execute"], [304, 2, 1, "", "executemany"], [304, 2, 1, "", "last_id"], [304, 2, 1, "", "tname"]], "BioSQL.DBUtils.Mysql_dbutils": [[304, 2, 1, "", "last_id"]], "BioSQL.DBUtils.Pgdb_dbutils": [[304, 2, 1, "", "autocommit"]], "BioSQL.DBUtils.Psycopg2_dbutils": [[304, 2, 1, "", "autocommit"]], "BioSQL.DBUtils.Sqlite_dbutils": [[304, 2, 1, "", "execute"], [304, 2, 1, "", "executemany"]], "BioSQL.Loader": [[305, 3, 1, "", "DatabaseLoader"], [305, 3, 1, "", "DatabaseRemover"]], "BioSQL.Loader.DatabaseLoader": [[305, 2, 1, "", "__init__"], [305, 2, 1, "", "load_seqrecord"]], "BioSQL.Loader.DatabaseRemover": [[305, 2, 1, "", "__init__"], [305, 2, 1, "", "remove"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "exception", "Python exception"], "2": ["py", "method", "Python method"], "3": ["py", "class", "Python class"], "4": ["py", "function", "Python function"], "5": ["py", "attribute", "Python attribute"], "6": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:exception", "2": "py:method", "3": "py:class", "4": "py:function", "5": "py:attribute", "6": "py:property"}, "terms": {"": [0, 2, 3, 5, 6, 8, 9, 10, 11, 12, 13, 14, 16, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 36, 37, 55, 56, 59, 61, 65, 66, 67, 68, 69, 70, 71, 73, 76, 80, 81, 83, 84, 90, 93, 96, 99, 100, 104, 111, 112, 113, 114, 115, 117, 119, 122, 129, 130, 132, 137, 139, 140, 141, 146, 149, 152, 154, 156, 157, 159, 168, 169, 172, 177, 178, 182, 183, 185, 188, 190, 193, 195, 196, 197, 199, 202, 205, 209, 217, 218, 220, 221, 222, 226, 229, 234, 237, 238, 239, 240, 241, 244, 245, 247, 248, 249, 250, 251, 253, 256, 257, 259, 260, 261, 262, 263, 264, 265, 268, 269, 270, 272, 274, 275, 278, 280, 281, 287, 288, 290, 293, 296, 297, 298, 299, 304, 305, 307], "0": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 35, 36, 46, 51, 53, 54, 61, 62, 66, 67, 68, 69, 70, 71, 73, 80, 83, 87, 88, 89, 90, 92, 94, 99, 100, 104, 105, 108, 112, 113, 114, 120, 122, 126, 129, 132, 135, 137, 138, 139, 140, 141, 148, 152, 154, 156, 157, 161, 168, 169, 170, 173, 176, 177, 182, 183, 184, 186, 187, 189, 190, 195, 197, 199, 202, 203, 204, 207, 214, 216, 217, 222, 229, 230, 233, 234, 236, 237, 238, 240, 243, 246, 247, 249, 251, 252, 253, 260, 261, 263, 264, 265, 270, 277, 278, 280, 281, 283, 286, 288, 289, 290, 291, 292, 294, 297, 299, 303], "00": [0, 2, 11, 12, 16, 32, 53, 169, 176, 216, 251, 261, 263, 264, 288, 299], "000": [6, 11, 32, 126, 182, 207, 278], "0000": [0, 11, 13], "000000": [0, 11, 13, 182, 199, 299], "000000001": 251, "00000001": 251, "00001": [6, 202, 203], "0000313": 25, "0000417": 0, "0001": [11, 25], "0001068": 53, "0002": [0, 13, 25], "00029": 0, "0003": 0, "0005260": 267, "0006": 13, "0008270": 197, "0009490": 182, "001": [3, 11, 24, 69, 80, 182], "0012": 13, "0013": 13, "0019": 13, "001991": 11, "002": [11, 69], "00206457": 13, "0021": 13, "0022": [2, 137], "002263": 11, "002387": 11, "002418": 11, "0025": 32, "002613": 11, "002850": 11, "002868": 11, "003": 11, "00332": 11, "003922": 104, "003964": 11, "004030": 11, "004352": 11, "004470": 11, "004653": 11, "005": 11, "0051537": 25, "005737": 11, "006": 11, "006667": 11, "007769": 11, "0080635": 137, "008165": 11, "0089": 13, "009": [0, 2, 11], "0095": [12, 13], "00961538461538462": 11, "00e": 11, "01": [0, 11, 16, 21, 68, 149, 185, 214, 216, 251], "010": [11, 126], "0108695652173913": 11, "0112": 13, "012": [0, 11], "012345": 182, "0132": 13, "013277": 11, "014": 11, "0142": 13, "01421": 199, "014631": 11, "01477186": 11, "016": 11, "0162": 13, "016304347826087": 11, "0166": [12, 13], "017663": 11, "019": 2, "0194": 13, "019497": 11, "0197": [12, 13], "01e": [216, 291], "02": [0, 4, 11, 16, 73, 105, 149, 185, 216, 251, 264], "020": 11, "02024": 2, "020643": 11, "021": 126, "0215": 13, "0217391304347826": 11, "0224": 13, "023": 11, "0230646871686108": 11, "023194": 13, "023344": 11, "024": 32, "025": 32, "025056": 11, "0251": [12, 13], "025231": 11, "025414": 11, "026": 11, "026128": 11, "026652": 11, "026732": 11, "026737": 11, "0268": [12, 13], "026928": 11, "027444": 11, "028": 11, "02832e": 3, "0284994697773065": 11, "0288": [12, 13], "029759": 11, "02e": 216, "03": [0, 7, 11, 32, 86, 149, 168, 176, 216], "0301021": 13, "03370807": 11, "0339342523860021": 11, "034": 3, "0342": [12, 13], "036": 13, "037": 11, "03734159": 11, "037406": 11, "038461538461538464": 199, "038860": 11, "0397": 13, "04": [0, 3, 7, 11, 149, 216, 251, 264, 270, 277], "040264": 11, "0406": [12, 13], "04066086": 11, "040694591728526": 11, "041": 68, "04194000000000003": 199, "043": 11, "0436": [12, 13], "04403040513919": 169, "045": 11, "0461293743372216": 11, "0465": [12, 13], "0466": 13, "047": 11, "047316": 11, "04807692307692307": 199, "049537": 11, "0499": 13, "04e": 216, "05": [0, 2, 7, 11, 12, 69, 100, 104, 263, 270, 280], "050": [0, 11], "0502386002120891": 11, "051282051282051266": 199, "0518": [12, 13], "052017": 11, "053296": 13, "054": 11, "0546": 13, "0553": [12, 13], "056317": 11, "0585": 13, "058787": 11, "059": 24, "05e": 291, "06": [0, 3, 7, 11, 13, 17, 20, 149, 291], "060204": 13, "060312": 11, "06172252": 11, "062": 11, "062462": 11, "0627": 13, "0631": 13, "0660": [12, 13], "067715": 13, "068": 11, "068728": 13, "0691940615058324": 11, "069475": 13, "06e": 216, "07": [0, 11, 185, 216, 291], "0705": [12, 13], "070505": 2, "071113_eas56_0053": 251, "0740": 13, "07477": 199, "0752": [12, 13], "076117": 11, "07692307692307693": 199, "077066": 11, "078208": 11, "07922333291745": 11, "0793": 13, "07e": 216, "08": [11, 149, 291], "081202": 32, "081468": 13, "0833333": 11, "0833333334583333": 11, "08531": 199, "089579": 11, "0896076352067868": 11, "08e": 291, "09": [7, 11, 216, 277], "090": 11, "0939": 13, "0976": [12, 13], "098612": 11, "09919716": 11, "0b100": 0, "0b1000101": 0, "0c": 169, "0cc864": 183, "0e": [3, 11, 122], "0pdb": 158, "0x": [0, 30, 68], "0x10403d850": [30, 68], "0xc356b0": 11, "1": [0, 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 51, 53, 55, 56, 61, 62, 65, 66, 68, 69, 70, 71, 73, 74, 76, 80, 83, 92, 93, 94, 99, 100, 101, 102, 104, 105, 108, 109, 113, 120, 122, 126, 129, 132, 135, 136, 137, 139, 148, 149, 152, 154, 155, 156, 157, 158, 161, 169, 170, 172, 173, 176, 182, 183, 184, 186, 187, 189, 190, 195, 197, 199, 201, 204, 205, 206, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 221, 222, 234, 236, 237, 238, 241, 243, 245, 247, 251, 252, 253, 256, 260, 261, 264, 265, 270, 274, 277, 278, 281, 282, 283, 288, 289, 290, 291, 292, 294, 295, 297, 299, 303, 304, 307], "10": [0, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 16, 17, 20, 22, 23, 24, 30, 31, 32, 50, 53, 56, 59, 65, 66, 67, 68, 69, 70, 73, 80, 83, 87, 88, 91, 93, 100, 104, 119, 122, 125, 126, 137, 139, 140, 146, 169, 175, 182, 197, 202, 206, 207, 215, 217, 218, 221, 222, 226, 236, 237, 238, 240, 245, 249, 251, 252, 253, 260, 262, 264, 265, 267, 270, 272, 274, 276, 278, 279, 290, 291, 294], "100": [0, 3, 4, 6, 7, 8, 11, 15, 20, 21, 22, 23, 25, 32, 61, 69, 80, 122, 157, 182, 183, 207, 217, 237, 238, 253, 261, 264, 265, 270, 274, 278], "1000": [0, 4, 11, 13, 14, 15, 22, 32, 36, 49, 53, 64, 69, 215, 237, 261, 270], "10000": [0, 8, 122, 182, 202, 203, 270], "100000": [270, 278], "1000000": 8, "100000028": 7, "100002": 0, "1002": [2, 13, 137, 149, 262], "100598": 13, "1006": 2, "1007": 2, "10076": 62, "10090": [7, 11], "101": [0, 20, 217, 218], "1010b": 214, "1011": 69, "1011751523": 68, "101564639": 7, "101574747": 7, "101582229": 7, "101585369": 7, "101586429": 7, "101589678": 7, "1016": [2, 137], "101627224": 7, "101639023": 7, "101645372": 7, "101647801": 7, "101647835": 7, "101649614": 7, "101653734": 7, "101657941": 7, "101659814": 7, "101660833": 7, "101661657": 7, "101664671": 7, "101669877": 7, "101671907": 7, "101_9001_1242061629": 7, "101m": 0, "102": [0, 17, 32], "1020": 22, "1021": [7, 169], "1023": 263, "1024": [169, 252], "10256410256410259": 199, "10271783": 0, "10271816": 0, "103": [0, 11, 13, 278], "1030": 6, "1031": 263, "10328": 137, "10338": 2, "1038": [32, 100, 267], "104": [66, 169, 278], "10458": 10, "104968": 11, "105": [68, 217, 237], "105172": 237, "105173": 237, "1055": 0, "10557": 32, "10562": 32, "10574": 0, "106": [0, 11, 206, 253], "10638": 21, "10666704": [34, 281], "107": [2, 6, 11, 24], "107212": 278, "107263": 278, "107264": 278, "1073": 2, "1074592421627525": 11, "108": [2, 68, 217, 237], "1081": [7, 260], "1083": 288, "108462": 237, "109": 264, "10915": 2, "10919": 2, "1093": [2, 73, 251, 252], "1098": 0, "10a": 214, "10mb": 270, "10th": 0, "11": [0, 2, 3, 4, 6, 7, 8, 11, 13, 20, 21, 22, 30, 32, 36, 67, 68, 73, 94, 104, 137, 157, 166, 209, 236, 237, 251, 260, 261, 264, 265, 270, 281, 299], "110": [16, 237], "1101": [0, 2], "1102": 288, "1104": 2, "1105": 2, "11057692307692304": 199, "1107": 175, "1109": 6, "111": [3, 6, 16, 20, 222], "1110": 3, "1111": 3, "111776384": [0, 30], "111776784": [0, 30], "111776785": [0, 30], "111982717": [0, 30], "111982775": [0, 30], "111987921": [0, 30], "111988073": [0, 30], "112": [0, 3, 11, 16, 149], "112009200": [0, 30], "112009302": [0, 30], "112019962": [0, 30], "112019978": [0, 30], "1125": 0, "1128": 2, "113": [13, 15, 16, 32, 156], "114": [6, 16, 183, 222], "1141": 7, "1144": 0, "1145": 2, "1146": 2, "114619004": 7, "11464971": [20, 217, 218], "115": [16, 237], "11538461538461536": 199, "116": [0, 11, 12], "1160": [68, 217], "116576": 7, "1166": [68, 217], "1167": 0, "116834": 0, "116835": 0, "116837": 0, "116856": 0, "116872": 0, "11691a": 11, "116l": 149, "117": [3, 7, 16, 237], "117054": 11, "1173": 3, "117512670": 22, "117512683": 22, "117512690": 22, "117512700": 22, "118": [0, 13, 56, 126, 264], "1186": [2, 69, 197], "119": [6, 13, 56], "119000876": 22, "1190160": 7, "1195311108": 278, "1198066": 0, "11e": 291, "12": [0, 2, 3, 7, 8, 10, 11, 12, 13, 16, 17, 20, 21, 22, 25, 30, 31, 32, 35, 36, 38, 69, 73, 93, 94, 99, 104, 125, 137, 141, 149, 183, 206, 207, 215, 218, 221, 237, 245, 251, 253, 260, 263, 264, 265, 281, 288, 299], "120": [0, 3, 13, 15, 16, 30, 32, 56, 169, 237, 253, 264], "1200": [0, 207], "1200166": 21, "1201": 7, "120217": 11, "1205": [68, 217], "120626": 32, "121": [0, 7], "1219041180": 3, "122": [3, 11, 68, 169, 237], "122114": 0, "122250000": [0, 30], "122250400": [0, 30], "12230038": 7, "1226": 0, "1226m3m1m": 0, "122835789": [0, 30], "122835847": [0, 30], "122840993": [0, 30], "122841145": [0, 30], "1229": 0, "122907212": [0, 30], "122907314": [0, 30], "122909818": [0, 30], "122909819": [0, 30], "122909835": [0, 30], "123": [32, 68, 169, 237, 256], "1230": 0, "12300": 0, "12301": 0, "12318": 0, "1234593": 222, "1234630": 222, "1235": [12, 13], "12368254": 7, "124": [0, 13, 56, 237, 288], "124556": 278, "124602": 278, "124653": 278, "125": [6, 8, 17, 56], "1250": 299, "126": [0, 251, 264, 278], "1261": 7, "12654095": 68, "126722851": 7, "127": [0, 11, 24, 299], "127706": 13, "128": [0, 6, 16, 17, 169, 183, 253], "1281": 261, "129": [0, 11, 16, 222], "1295": 261, "129628": 68, "129993255": 0, "13": [0, 2, 3, 7, 8, 11, 12, 13, 14, 15, 20, 21, 22, 30, 38, 68, 87, 104, 113, 137, 153, 183, 199, 206, 217, 222, 237, 249, 251, 260, 297, 299], "130": [11, 13, 237, 253], "1302": 7, "130382477": 0, "130383872": 0, "130383910": 0, "130383918": 0, "130383920": 0, "130383943": 0, "130383946": 0, "130383958": 0, "130384222": 0, "130388520": 0, "1305": 169, "130607995": 0, "130611000": 0, "130611008": 0, "130611010": 0, "130611033": 0, "130611036": 0, "130611048": 0, "130620657": 0, "130881": 278, "130946": 278, "131": 0, "131007": 11, "131071": 278, "131072": 278, "1313": [68, 217], "1318045": 0, "1318046": 0, "1318075": 0, "1319220": 222, "1319271": 0, "1319274": 0, "1319275": [0, 222], "132": [0, 16], "132427": 11, "1327": 149, "132953340402969": 11, "13298": 260, "133": [0, 68], "133105": 0, "133919957": 0, "133922962": 0, "133922970": 0, "133922972": 0, "133922995": 0, "133922998": 0, "133923010": 0, "133924947": 0, "133926309": 0, "133926312": 0, "133932620": 0, "134": [0, 2, 253], "1347369": 68, "1348912": 238, "1348917": 238, "135": [0, 11], "1353": [2, 283], "136": 16, "1361": [2, 283], "136185": 0, "136186": 0, "1362": 0, "136245": 0, "136286": 0, "13687943": 11, "13691": 199, "137": 0, "1371": [137, 182], "137181": 7, "138": [0, 4, 11, 256], "13813": 3, "13819": 6, "1383": [68, 217], "13919613": 23, "13925890": 23, "1394": 2, "13990994": 238, "13f": 169, "14": [0, 2, 3, 7, 8, 11, 13, 15, 20, 22, 30, 32, 68, 69, 71, 104, 113, 149, 206, 237, 249, 251, 253, 260, 263, 264, 281, 299], "140": [16, 183], "1403": 2, "14098": 169, "141213431": 0, "1415": 157, "14150838": [21, 23], "142": [13, 16], "1422": 2, "1423": 2, "143": [11, 16, 278], "143444": 2, "144": [0, 15], "14423076923076922": 199, "145": [0, 11, 256], "1453": 2, "14530136": 182, "1454": 2, "145469": 13, "145707": 3, "14580": 6, "146": [0, 30], "1460": 264, "14630660": [7, 83], "146364022": 0, "1465": 264, "1467": 7, "147": [13, 25], "1471": [2, 69, 197, 218], "1475": 240, "148": [0, 11, 30], "14863": 2, "14868": 2, "14871861": 7, "1488655": 21, "149": [11, 12, 13, 116], "14918518": 11, "14939": 278, "149736546": 22, "149742490": 7, "14986": 209, "149m1d7m1i17m3d60m5i6m1i13m2i13m4i30m2i6m2d112m": 0, "15": [0, 2, 3, 7, 8, 11, 13, 16, 20, 31, 32, 53, 69, 83, 87, 88, 104, 206, 237, 249, 251, 253, 260, 261, 263, 264, 270, 278, 281, 283, 299], "150": [2, 8, 11, 30, 237, 253], "15000": 0, "1501": 2, "1505": 13, "15073": 278, "151": 2, "151104725": 0, "152": [15, 140, 156], "152_d_c": 15, "152_d_ca": 15, "152_d_cb": 15, "152_d_cg": 15, "152_d_n": 15, "153": [11, 15, 251], "1530": 0, "1531": 2, "15310": 90, "1532": 0, "153846": 199, "15384615384615383": 199, "154478": [237, 278], "155": [68, 265], "155029160": 0, "155029206": 0, "155184381": 0, "155563": 7, "155784573": 0, "155784581": 0, "155784583": 0, "155784606": 0, "155784609": 0, "155784621": 0, "155814782": 0, "155814790": 0, "155814792": 0, "155814815": 0, "155814818": 0, "155814830": 0, "155c_": 214, "156": [0, 30], "1560": 0, "15613794": 11, "156330991": 22, "156354347": 0, "156354348": 0, "156630997": [68, 217], "1567": 0, "156859": 13, "156861": 13, "156863": 13, "156865": 13, "156867": 13, "156869": 13, "156871": 13, "156873": 13, "156875": 13, "156877": 13, "156879": 13, "157": [0, 140], "157128497": 0, "157137496": 0, "1575": 0, "157519211": 0, "157519257": 0, "158": 0, "1580": 288, "158040939": 0, "158048983": 0, "1581": 13, "158330": 7, "1584": 0, "158545518": 0, "15870786": 0, "1589": [152, 169], "159": [0, 237], "1591": [152, 169], "1592936": 238, "159345973": 22, "15973002": 175, "159745316": 0, "15985178": 7, "159862546986584": 11, "15e": 216, "15m2i17m2d11m1i58m1i11m1d7m1d8m": 0, "15n": 126, "15n2": 126, "16": [0, 2, 3, 4, 7, 11, 12, 13, 14, 20, 25, 30, 32, 53, 69, 73, 87, 93, 104, 129, 169, 206, 251, 253, 260, 264, 265, 270, 278, 299], "160": [0, 222], "160039680": 0, "160127253446448": 11, "16080617": [20, 218], "16082683": 21, "161": [0, 222, 265], "16131885": 260, "161576975": 0, "16161448": 0, "161824586": 22, "162": 0, "1620": 0, "163": 0, "1632": 32, "16348228": [299, 300], "16377612": 7, "16384": [169, 220], "16389355": 0, "164": [0, 11, 29, 30], "16403221": 7, "165": [0, 6, 183], "1658": 253, "166": 0, "166667": 11, "1668": 0, "167": 0, "1672": 116, "167234445": 238, "167376": 0, "167877390": 238, "168": 29, "1680": 0, "1688586483": 262, "168904": 0, "169": 0, "1697": [12, 13], "16e": 216, "17": [0, 2, 3, 7, 8, 11, 12, 13, 20, 23, 25, 30, 32, 104, 113, 169, 206, 237, 249, 251, 260, 261, 264, 281], "170": 29, "170899992": 0, "171": 0, "17103": 265, "1711": 0, "17121776": 7, "1716": 237, "1717": 237, "172": [0, 11, 169, 253], "17292": 278, "173": 0, "173163865": 22, "17342": 278, "17353": 278, "17390": 278, "173908612": 0, "174": [2, 29], "17420": 265, "174210431": 0, "174256650": 0, "174256662": 0, "174256685": 0, "174256689": 0, "174256691": 0, "174256699": 0, "174256702": 0, "175": [0, 250], "1750": 237, "1751": 237, "17523": 199, "175231": 0, "175262": 0, "175316": 0, "17545": 265, "176": [0, 6], "1760": 237, "176504": 11, "1767": [2, 251], "17708": 278, "17709": 278, "1771": [2, 251], "17715": 278, "17728": 278, "17762460233298": 11, "177k": 222, "1780": 0, "178247": 0, "17857": 278, "1792": 32, "1795": 13, "17989604": 7, "17beta": 113, "17e": 216, "17m1d6m": 0, "18": [0, 3, 8, 11, 12, 13, 15, 16, 20, 21, 22, 23, 53, 68, 69, 80, 90, 109, 149, 206, 216, 251, 260, 278, 281, 299], "180": [13, 15, 169, 183, 288], "18004": 278, "18017": 278, "181": [0, 7], "181217": 0, "18190": 278, "18195": 278, "182": [29, 251], "18207101": 22, "18223": 278, "18239": 278, "18248": 278, "18269230769230765": 199, "1827": 0, "18299": 278, "183": 129, "183925984": 0, "183925985": 0, "183925990": 0, "183926028": 0, "184": [2, 222], "1848": 13, "185": [0, 53], "18575690": 7, "18575811": 7, "18579475": 7, "18585042": 8, "18589523": 7, "18591784": 7, "18594007": 7, "186": [7, 15], "18606172": 7, "18612381": 7, "18627452": 7, "18627489": 7, "1863": 197, "18661158": 7, "18665331": 7, "18665981": 11, "18680603": 7, "18689808": 7, "187237168": 7, "1873": 0, "187371129": 0, "18749999999999994": 199, "187676": 7, "188": [2, 29, 250], "188111581": 0, "188158351": 0, "188162918": 0, "188162930": 0, "188162953": 0, "188162957": 0, "188162959": 0, "188162967": 0, "188162970": 0, "188171225": 0, "188228261": 0, "188236997": 0, "1888": [6, 237], "18m22": 0, "19": [0, 2, 3, 8, 11, 12, 13, 20, 29, 30, 84, 88, 152, 154, 169, 206, 221, 249, 251, 260, 264, 270, 299], "190": 0, "1901": 237, "190214555": 13, "1904993": [34, 280], "191": [0, 53], "191154276": 0, "19159": 0, "192": [0, 183], "193": [2, 11, 29], "19304878": [7, 83], "193835": 0, "19450287": 7, "1949": 0, "195": [0, 11, 264], "195230749": [68, 217], "1956": 264, "1958": 32, "196": 129, "1960": 260, "1961": 264, "1962": 264, "196364": 278, "1964": 32, "196429": 278, "1965": 264, "196608": 278, "1967": 80, "196734": 278, "19698094": 7, "197": [0, 2], "1970": 288, "19705359": 8, "1971": 2, "1972": 109, "1973": [2, 157], "19732999999999998": 199, "1977": 149, "197793": 11, "1978": 2, "1979": 2, "198": [29, 222], "1980": 21, "1981": 129, "1982": 265, "198295559": [0, 13], "198365852": 22, "1984": 2, "1985": [2, 13, 34, 281], "1986": [2, 13, 34, 264, 281], "1987": [2, 137, 261, 283], "1988": [0, 2, 32, 59, 237], "1989": [2, 216], "1990": [2, 129, 265, 299, 300], "1990656": 13, "1991": [83, 264], "1992": [2, 32, 182], "19923": 83, "1993": [13, 72, 169, 263, 264, 265], "1994": [2, 13, 32, 34, 137, 169, 263, 265, 281], "1995": 264, "199577": 11, "1996": [2, 264], "1997": [2, 3, 4, 68, 129, 153, 264], "1998": [2, 32, 53, 87, 93, 166, 264], "1999": [2, 4, 69, 87, 185, 264, 294], "19mb": 6, "1_k_ca": 169, "1_k_cb": 169, "1_k_cd": 169, "1_k_cg": 169, "1_modifi": 0, "1a": [215, 264], "1a8o": [15, 140, 148, 154, 156, 170, 173, 248], "1a91": 238, "1abc": [15, 139], "1acgt2tgca3atgc4cgta": 264, "1asrukw": 238, "1b4o": 0, "1bba": 215, "1c": 169, "1ca": 169, "1d": [0, 4, 30, 73], "1e": [0, 13, 73, 168, 292], "1e4": 104, "1e6": 104, "1ejg": 15, "1en2": 15, "1f": [6, 30, 54, 251, 264], "1fat": [15, 137], "1ffk": 15, "1fkk": 15, "1g": 11, "1gb": [23, 69], "1gbt": 15, "1hft": 149, "1hfv": 149, "1hg6": 149, "1hhb": 149, "1hid": 149, "1hiu": 149, "1hke": 149, "1ifk": 12, "1ifl": 12, "1jic": 0, "1joi": 260, "1k7t_a": 0, "1k7u_a": 0, "1k7v_a": 0, "1kl12": 0, "1kl120": 0, "1lcd": 157, "1mot": 137, "1n": 169, "1nh4": 12, "1r": 25, "1rnd": [15, 169], "1s6m4i38m1": 0, "1sso": 0, "1st": [126, 169], "1t": 264, "1t0w_a": 0, "1ulk_a": 0, "1uuz": 149, "1wga": 0, "1wgc_a": 0, "1wgt_a": 0, "2": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 36, 42, 45, 53, 55, 56, 59, 62, 66, 68, 69, 71, 73, 80, 83, 93, 101, 104, 108, 112, 113, 114, 117, 118, 122, 132, 137, 139, 140, 149, 157, 168, 169, 176, 182, 183, 195, 197, 201, 202, 204, 205, 206, 209, 210, 211, 216, 217, 218, 222, 227, 228, 230, 234, 236, 237, 238, 241, 243, 247, 251, 252, 253, 260, 264, 265, 269, 270, 277, 278, 279, 287, 288, 291, 297, 299, 303], "20": [0, 2, 3, 6, 7, 8, 11, 12, 13, 15, 20, 21, 22, 25, 30, 32, 53, 66, 67, 69, 80, 87, 88, 109, 113, 140, 154, 169, 182, 183, 202, 203, 206, 215, 216, 236, 237, 247, 251, 253, 260, 264, 270, 272, 280, 299], "200": [18, 21, 23, 32, 69, 80, 83, 182, 183, 201, 204, 205, 237], "2000": [0, 2, 7, 9, 13, 14, 16, 21, 32, 34, 111, 115, 119, 185, 196, 264, 281], "2000000": 237, "200000016": 7, "2001": [2, 4, 69, 149, 182, 211, 213, 237, 264], "20010710": 263, "2002": [0, 2, 7, 8, 32, 140, 185], "20020916": 7, "2003": [2, 9, 15, 65, 74, 122, 137, 152, 169, 182], "20030606": 7, "20031006": 149, "20031013": 149, "2004": [0, 2, 9, 11, 32, 36, 73, 264], "20041117": 7, "20049947": 262, "2005": [2, 32, 69, 175, 264, 267], "2006": [2, 8, 9, 23, 182], "200600032": 262, "2007": [7, 25, 32, 83, 87], "2008": [7, 21, 32, 210, 253, 264], "2009": [2, 3, 7, 8, 9, 17, 20, 23, 25, 32, 69, 86, 87, 88, 93, 197, 278], "201": [0, 18, 53, 201, 204, 205], "2010": [2, 6, 7, 9, 32, 182, 251, 264], "2011": [32, 238, 252], "201197": 13, "201198": 13, "2012": [2, 7, 8, 9, 17, 83, 264], "2013": [11, 32, 137, 288], "2014": 15, "2014248": 83, "2015": [12, 13, 23], "2016": [7, 9, 90, 265, 277], "20161961": 7, "2017": [0, 9, 88], "2017_03": 88, "2019": [0, 2, 15, 76, 152, 169], "202": [0, 2, 11], "2020": 0, "2024": 208, "2026": 13, "203": [0, 31, 183], "20370": 29, "20379": 2, "204": [0, 2, 11], "2048": 169, "205": [11, 32, 237], "20517297": 288, "205754": 13, "206": 0, "20605": 29, "206124072110286": 11, "2073": 25, "207551": 13, "2078": 2, "2079": [2, 12, 13], "208": [0, 264], "208639": 222, "208677": 222, "209": [2, 264], "20945": 29, "20m": 0, "21": [0, 2, 3, 8, 11, 12, 20, 21, 30, 53, 69, 93, 94, 109, 149, 172, 176, 182, 183, 206, 245, 251, 253, 260, 264, 288], "210": [0, 11, 23, 183, 237, 288], "2105": [2, 69, 197, 218], "211": 11, "211387": 11, "212": 32, "2120": 7, "21300": 29, "2134": 0, "214": [0, 11], "21438": 29, "21455": 29, "2146": 0, "215": [0, 2, 183, 237], "216": [0, 2, 11, 15, 53, 68, 217], "2164": 2, "216l": 149, "217": [13, 14, 32, 237], "2170": 23, "218451749734889": 11, "21871": 29, "21883": 29, "219": [244, 253], "21e": [11, 291], "22": [0, 2, 3, 6, 7, 11, 12, 15, 20, 21, 36, 69, 87, 122, 182, 185, 206, 216, 217, 218, 249, 251, 253, 260, 288, 292], "220": [0, 7, 237], "221": 253, "22104": 29, "22144": 278, "22177": 29, "222": [2, 53, 237], "222222": 199, "22230": 278, "223": 13, "223616942": 0, "224": 0, "224244399": [0, 30], "225584828": 0, "227": 264, "228": [0, 13], "228573443": [0, 30], "2289704": 2, "22909249": 7, "229193": 21, "229202": 2, "23": [0, 3, 6, 11, 13, 17, 20, 21, 22, 32, 53, 69, 175, 206, 216, 221, 237, 251, 253, 260, 299], "230": 237, "2300": 0, "2303": 0, "230769": 199, "2308": 2, "231": 11, "2310": 2, "231336967110781": 11, "23181": 6, "23186": 6, "2325": 0, "23262": 0, "233": 53, "23344455555555555555544433": 0, "2337": 13, "234": [11, 29], "234666677777777777766666655544332223333": 0, "23470805": 8, "235": [2, 264], "235949098621421": 11, "236": [0, 251], "2360": [12, 13], "23891310": 0, "23891349": 0, "239": [11, 20, 217], "23927": 199, "239940": 0, "23e": 216, "24": [0, 3, 6, 7, 8, 11, 12, 13, 17, 20, 21, 25, 29, 30, 32, 69, 74, 183, 206, 249, 251, 260, 261], "240": [13, 62, 104], "241": [7, 11, 13, 288], "241163": 0, "242": [0, 30], "242193529": 13, "243199373": 0, "2433": 0, "2434": 253, "2444": [2, 59], "2448": [2, 13, 59], "246": 3, "247": 68, "2475": 7, "2480607": 11, "248343840": 22, "248956422": [0, 13, 36, 37, 38], "249": 261, "249053267": 0, "249182": 0, "249250621": 0, "249999999875": 11, "25": [0, 2, 3, 6, 8, 11, 12, 13, 16, 17, 20, 21, 29, 32, 68, 99, 104, 113, 182, 202, 206, 237, 245, 251, 260, 261, 264, 270, 299], "250": [8, 182, 183, 270], "2500": 207, "250000": [199, 299], "2505": 13, "250645": 11, "2514": 13, "255": [0, 12, 17, 104, 183], "256": [0, 13, 36, 37, 169, 236, 253, 278], "256374": 7, "2569": [12, 13], "2587879": 8, "259": 264, "259112547756697": 11, "25g14g2c34a12a9": 0, "25m": 0, "25mb": 23, "26": [0, 3, 6, 7, 8, 11, 13, 20, 21, 29, 30, 32, 69, 206, 217, 218, 234, 251, 253, 260], "260": [0, 253, 256], "2606": 7, "261": [0, 253], "2611": 29, "261883": 278, "261948": 278, "262144": 278, "262205": 3, "262205281": [3, 20], "262205290": [3, 20], "262205298": [3, 20], "262205302": [3, 20], "262205309": [3, 20], "262205317": [3, 20], "262205330": [3, 20], "262205423": [3, 20], "262205429": [3, 20], "262205445": [3, 20], "262205451": [3, 20], "2625807": 8, "263": [0, 250], "264": 244, "2643": 237, "2644": 237, "26466274": 11, "2647": 13, "265": [0, 253], "26503372": 11, "265207": 13, "26585": [0, 30], "266": [0, 253], "266435125": 0, "2669": 29, "267": [68, 244], "268": 156, "2682512": 7, "2683": 288, "2688": 182, "269": [129, 253], "2690": 182, "2697049": [25, 276], "26992728": 8, "27": [0, 3, 7, 11, 12, 13, 16, 20, 68, 69, 206, 236, 251, 253, 260, 264], "270": [11, 13], "270132717": [3, 20], "270133": 3, "270133242": [3, 20], "270133247": [3, 20], "270133254": [3, 20], "270133306": [3, 20], "2705363": 7, "271": 253, "2715": 11, "272": 0, "272646": 7, "272960": 23, "273": 0, "2732620": 94, "274": 0, "2743": [12, 13], "2744707": 7, "274597": 11, "275": [8, 11, 129], "27578828": 0, "27578829": 0, "27578831": 0, "27578850": 0, "27578866": 0, "2759": 29, "276": 2, "2762": 29, "2765564": 19, "2765583": 23, "2765596": 23, "2765613": 23, "2765646": 23, "2765658": [19, 23], "276694": 11, "2767712": 21, "27699739": 0, "277": [2, 7, 11, 20, 217, 253], "27707221": 0, "278": 253, "2783487": 169, "27884615384615385": 199, "279": 0, "2792": 29, "2795": 29, "28": [0, 2, 3, 7, 8, 11, 20, 22, 30, 93, 111, 113, 115, 119, 149, 217, 249, 251, 253, 260, 278], "280": [0, 13], "281": [0, 253], "2810": 29, "281474976710656": 278, "283": 0, "2830": 6, "2836": [2, 137], "283785": 11, "284": [7, 68, 222, 264], "285": 6, "2852": 0, "286": 32, "2868": 237, "287": [0, 253], "28741140": 0, "28741141": 0, "28741143": 0, "28741162": 0, "28741178": 0, "288": 7, "28862317": 0, "28869787": 0, "289": 0, "29": [0, 2, 3, 8, 11, 13, 20, 22, 29, 69, 111, 115, 119, 149, 222, 251, 260, 261, 264, 265], "290": [11, 264], "2907": 2, "290900": 11, "291": 153, "2912": 2, "2914": 29, "292": [13, 14, 253], "2923": 199, "2931": 0, "2934173": 68, "2936": [3, 20], "294118": 104, "2947": 32, "2948": 32, "295": [153, 253], "296": 7, "296143": 0, "296143771": 0, "2963": 260, "297": [140, 288], "2976": 29, "297814701": [3, 20], "297911": 222, "297993": 222, "298": 32, "299": 253, "2994": 69, "2996219": 21, "299651": 12, "29e": 216, "2_a_c": 169, "2_r1": [15, 152, 169], "2beg": 154, "2bit": [0, 23, 257], "2cp": 12, "2cpb": 12, "2cvr": 0, "2cwg_a": 0, "2d": [0, 2, 4, 11, 12, 13, 15, 30, 73, 101, 169, 177, 303], "2drca": 214, "2e": [0, 291], "2f": [11, 12, 13, 16, 183, 190, 216, 251, 261, 263, 264, 265], "2fe": 25, "2fm5fnyyy07j4": 238, "2gb": 270, "2hft": 149, "2hhb": 149, "2hid": 149, "2hiu": 149, "2j5x": 149, "2l": 25, "2l3j": 53, "2l3j_b_ss": 53, "2line": [238, 241], "2mb": 6, "2nd": [2, 69, 169, 182, 216], "2uvo": 0, "2uvo_a": 0, "2uvo_hhblit": 0, "2uvoah": 0, "2wga": 0, "2wgc_a": 0, "2x3t_a": 0, "2x52_a": 0, "3": [0, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 45, 53, 55, 56, 62, 65, 68, 69, 73, 80, 83, 84, 93, 94, 101, 104, 109, 112, 113, 126, 135, 137, 139, 140, 154, 157, 162, 168, 169, 176, 182, 183, 197, 201, 204, 205, 207, 214, 217, 218, 221, 222, 228, 229, 233, 236, 237, 238, 241, 247, 249, 251, 253, 260, 261, 263, 264, 265, 269, 270, 272, 275, 278, 279, 280, 281, 283, 288, 290, 291, 294, 297, 299], "30": [0, 2, 4, 6, 8, 11, 12, 13, 21, 23, 30, 32, 59, 68, 69, 70, 166, 169, 182, 216, 237, 251, 260, 270], "300": [10, 182, 207, 237, 261], "300256": 11, "3005": 69, "300mb": 25, "301": [7, 68, 217], "301171": 3, "301171146": [3, 20], "301171153": [3, 20], "301171211": [3, 20], "301171259": [3, 20], "301171267": [3, 20], "301171276": [3, 20], "301171311": [3, 20], "301171322": [3, 20], "301171354": [3, 20], "301171394": [3, 20], "301171401": [3, 20], "301171428": [3, 20], "301171437": [3, 20], "301171447": [3, 20], "3014644": 0, "3014689": 0, "3014742": 0, "3014778": 0, "3017743": 0, "3018000": 0, "3018161": 0, "3018230": 0, "3018359": 0, "3018482": 0, "3018644": 0, "3018822": 0, "3018932": 0, "3019": 2, "3019000": 0, "3019271": 0, "3019377": 0, "3019435": 0, "3019465": 0, "302": [7, 32], "3021": 2, "303": 244, "3030": 2, "30367": 7, "30432563": 8, "305": [2, 11], "305622": 278, "3056429": 3, "3059": 32, "306": 244, "3066": 32, "307": [11, 13, 140, 182], "308": [0, 11], "3085": 11, "309": [238, 244, 260], "31": [0, 2, 8, 11, 116, 149, 222, 251, 260, 288], "310": [10, 253], "310520": 11, "3109": 210, "311": 0, "312": 256, "312544902": 22, "31278684": 7, "31298": 20, "3130377": 0, "31359": 20, "314": 11, "315": 6, "3165": 13, "317": 74, "3171620263517245": 11, "317338282078473": 11, "31744": 169, "3176602": [238, 260], "319": [68, 222], "3190": 6, "31_i86win32": 32, "32": [0, 2, 11, 12, 13, 16, 22, 30, 32, 69, 169, 251, 260, 264], "320": 32, "321": 0, "321580063626723": 11, "3218": [12, 13], "323": 140, "324": [126, 238], "3246": 2, "3248": [2, 83], "325053704": [68, 217], "3251": [3, 20], "326": 74, "32611": 7, "326933": 0, "327294": 278, "327359": 278, "327680": 278, "32930": 278, "3298468": [241, 260], "32bp": 270, "33": [0, 6, 8, 11, 16, 32, 53, 100, 169, 238, 251, 260, 261, 264, 265, 270], "330": [32, 244], "330443": 0, "330443520": 0, "330443688": 0, "3305": [12, 13], "331078": 0, "3318709": 238, "33211": 217, "33212": 217, "33213": 217, "333333": 11, "335": [0, 11], "336": [2, 16], "3376": 0, "338": 0, "3389": [3, 68], "34": [0, 2, 11, 13, 25, 29, 111, 115, 119, 221, 251, 260], "340": [32, 256], "3402": [3, 68], "340200303": 137, "341": 126, "341303": 11, "342": 244, "343": 0, "344": [0, 30], "3444411": [34, 281], "344556666666666666566555543333223333321": 0, "345": [2, 68], "3459481": 68, "346": [0, 11], "3470": 6, "348": [7, 238, 244], "34_222_": 249, "35": [0, 11, 16, 30, 32, 156, 226, 251, 260, 264, 270], "350783": 11, "351": 11, "3512": 0, "3512432070271259": 11, "352": 2, "3537": 264, "354": 244, "35483340": 0, "35483510": 0, "355": 6, "35538": 8, "3554": 264, "3555": 264, "355556": 199, "356": [0, 197], "3562": 264, "356517317": [3, 20], "356543101": [3, 20], "357": 256, "358": 222, "35847450464382": 11, "359464": 0, "35m": 0, "36": [0, 2, 11, 13, 22, 74, 216, 226, 251, 253, 260, 299], "360": 169, "36001014": 169, "3601": 0, "3609329790": 278, "361": [6, 7], "361464": 11, "362": [0, 11], "3628": 116, "36438": 278, "364552": 11, "36462": 278, "36489": 278, "365": 7, "365806": 13, "3661": 29, "368": 264, "369048": 199, "37": [0, 3, 11, 13, 16, 20, 183, 249, 251, 260, 265, 270], "371502086": [68, 217], "372": [13, 32], "374": [2, 32], "375": [8, 11], "37613720253387": 11, "3765": 260, "378": 2, "37n": 270, "38": [0, 2, 7, 11, 16, 21, 23, 29, 216, 251, 260, 278], "382": 222, "38240": 6, "38347": 8, "384": [0, 56, 299], "3842": 260, "384615": 199, "3857": 6, "386123": 222, "386207": 222, "387": 244, "388": 222, "39": [0, 3, 11, 13, 20, 30, 104, 237, 251, 260, 264], "390": 244, "390332043": [3, 20], "390332045": [3, 20], "3910647": 12, "3916709": [34, 281], "392760": 278, "392825": 278, "393": 156, "393216": 278, "393333": 251, "394": 23, "39429784": 11, "3957471": [15, 158], "396": [11, 288], "397513516": [3, 20], "397623": 11, "398": 11, "399": [0, 11, 68], "3_p_ca": 169, "3_p_n": 169, "3a": 68, "3c": 118, "3d": [4, 7, 25, 26, 135, 158, 169, 171, 175, 176, 248, 307], "3dcoffe": 32, "3e": [3, 20], "3f": 11, "3fe": 25, "3g": 11, "3hhb": 149, "3j92": 149, "3jb9": 53, "3pbl": 15, "3rd": [169, 253], "3x": 71, "3x3": [135, 139, 176], "3x4": 169, "4": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 22, 23, 24, 25, 29, 30, 31, 32, 45, 53, 55, 68, 69, 73, 76, 80, 101, 104, 113, 126, 129, 137, 149, 154, 158, 169, 175, 176, 182, 201, 204, 206, 207, 209, 214, 216, 217, 218, 221, 222, 237, 238, 247, 251, 253, 260, 263, 264, 265, 270, 272, 278, 283, 288, 290, 297, 299], "40": [0, 7, 8, 11, 21, 32, 56, 157, 206, 216, 237, 251, 260, 261, 265, 270, 283], "400": [3, 8, 10, 182, 207, 253], "4005": 0, "401": [13, 288], "403": 2, "404": [10, 208], "40568": 6, "407": [0, 30], "4079": [3, 20], "408": 0, "4082": [3, 20], "40832722": 11, "409": 15, "409215": 11, "4096": 169, "40a": 0, "40e": 264, "41": [0, 3, 6, 11, 13, 16, 21, 251, 260, 264, 265], "410": 2, "411": [0, 11, 56], "41253757072521": 11, "413": [0, 3, 238], "4145": 0, "415": 2, "41614797": 94, "416667": 11, "418": 2, "41833273": 22, "41892": 6, "419": 11, "42": [0, 8, 11, 21, 183], "420": [182, 244], "421": [7, 69, 218], "42144400": 0, "42144436": 0, "42291": [3, 20], "42322": 222, "42326848": 22, "42372": 2, "42381": 2, "4249": 6, "425": 288, "42530895": 0, "42530922": 0, "42530955": 0, "42530958": 0, "42532020": 0, "42532039": 0, "42532095": 0, "42532515": 0, "42532563": 0, "42532575": 0, "42532606": 0, "425_103_": 249, "425_7_": 249, "426": 2, "4284": 0, "42991": 20, "43": [0, 2, 11, 12, 20, 87, 88, 157, 264], "4300": [0, 21], "4301": 0, "431": 2, "4310": 237, "4311": 237, "43177247": 11, "4320": 0, "433": 0, "4342": 21, "4343": 21, "43458748": 11, "4347": 237, "43478": 278, "435": 3, "4350": 21, "44": [0, 2, 11, 16, 18, 183, 217, 251, 260], "440": 30, "441039751299748": 11, "4414": 16, "44157214": 7, "443": 238, "44334329": 11, "444": 11, "4457": 7, "44576": 7, "447": 238, "449": 222, "45": [0, 6, 7, 8, 9, 11, 13, 15, 30, 104, 207, 264], "4512": 0, "453": 264, "454": [6, 21, 238, 251, 253], "45478711": 21, "45478712": 256, "45478713": 256, "45478714": 256, "45478715": 256, "45478716": [21, 256], "45478717": [238, 256], "45478718": 256, "45478719": 256, "45478720": 256, "45478721": 256, "455": 237, "455991516436904": 11, "456": 237, "456614": 278, "456679": 278, "457": 237, "46": [0, 2, 11, 22, 62, 129, 209, 216], "461538": 199, "4622798": 0, "463": 7, "465": 15, "4660": 0, "46757": 0, "46785": 0, "46845": 0, "46875": 22, "468851": 25, "46m1827n82m3376n76m12h": 0, "47": [0, 3, 11, 20, 30, 216, 264], "470": 0, "47031477": 0, "471": [11, 238], "4722596": 7, "473": [2, 3], "47448759": 0, "4749": 0, "47545159": 0, "47545187": 0, "47545247": 0, "476": 126, "478": 175, "4780": [6, 21], "48": [0, 2, 8, 11, 13, 16, 216, 264, 278], "480": [11, 21, 175], "4800": 21, "48000000": 0, "481": 7, "4814": 6, "482": 3, "48663767": 0, "48663768": 0, "48663795": 0, "48663796": 0, "48663813": 0, "48665640": 0, "48665716": 0, "48665722": 0, "48669098": 0, "48669174": 0, "487327": 222, "487387": 222, "4877": 25, "488": 0, "488889": 199, "49": [0, 4, 8, 11, 12, 15, 22, 29, 73, 216], "4900": 0, "49000000": 0, "490883": 94, "490885": 94, "491": 6, "491055": 11, "4923": 260, "492621": 11, "4927836298652875": 11, "49340": 15, "493976": 199, "49598789": 11, "496": 169, "498070": 11, "49840": 126, "498454": 0, "4990": 0, "4aml_a": 0, "4cup": 15, "4e": 0, "4f": [12, 13, 261], "4gb": 23, "4lgy": 169, "4th": 169, "4x4": [169, 176], "4yyaj7ibmqgnkxdxq": 23, "4z8i_a": 0, "5": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 67, 68, 69, 73, 80, 93, 94, 99, 100, 101, 104, 108, 113, 122, 126, 132, 135, 137, 140, 169, 176, 182, 183, 186, 199, 207, 209, 216, 217, 218, 234, 236, 237, 238, 245, 251, 260, 261, 264, 265, 270, 272, 275, 288, 290, 291, 297, 299], "50": [0, 3, 6, 8, 11, 12, 23, 25, 30, 32, 65, 68, 70, 155, 169, 202, 207, 214, 216, 237, 247, 249, 251, 253, 261, 264, 270, 299], "500": [7, 21, 68, 69, 70, 264, 270, 276], "5000": [0, 202, 203], "500000": 299, "501": 251, "502": 30, "5062": 0, "50977498": 11, "51": [0, 2, 3, 8, 9, 11, 15, 20, 216], "510": 11, "511": [32, 275], "512": [0, 36, 37, 149, 169], "51304566": 0, "51343240527031": 11, "5147": 25, "516": 0, "518": [0, 32], "5199": 169, "519a": 3, "52": [0, 3, 7, 11, 12, 20, 169, 182, 216, 251], "5203": 0, "5204": 0, "5209": 13, "520b": [3, 20], "520c": [3, 20], "521": 11, "525": 169, "528": 264, "529": 263, "52_g_ca": 169, "52_g_ca_0": 169, "52_g_ca_b_0": 169, "52b_g_ca": 169, "53": [9, 11, 13, 15, 32, 104, 263, 264, 278], "530": 68, "53215344": 0, "53215346": 0, "53215347": 0, "53215366": 0, "53215382": 0, "53303881": 0, "5331": 0, "53310102": 0, "5336": 264, "535": 149, "5353": 264, "53575980": 0, "53575997": 0, "53729353": [68, 217], "538462": 199, "539": [32, 263], "54": [0, 1, 6, 8, 9, 11, 17, 207, 216, 240, 251, 261, 264], "540": 238, "54006": 17, "541": 7, "5416": 62, "5417": 62, "54178987": 20, "54179038": 20, "54185425": 20, "54185486": 20, "54189735": 20, "54189795": 20, "54197657": 20, "54197717": 20, "54198476": 20, "54198536": 20, "542": 149, "54201651": 20, "54201712": 20, "54204480": 20, "54204541": 20, "54206009": 20, "54206061": 20, "54210720": 20, "54210780": 20, "54212018": 20, "54212071": 20, "54233104": 20, "54233122": 20, "54234278": 20, "54234321": 20, "54238143": 20, "54238196": 20, "54240175": 20, "54254477": 20, "54255662": 20, "54255723": 20, "54260071": 20, "54264420": 20, "54264463": 20, "54265610": 20, "54265671": 20, "54442": 278, "54479": 278, "54493": 278, "54503e": 3, "5463": 7, "5465132509466635": 11, "54723985087516": 11, "547619": 199, "55": [3, 6, 7, 8, 9, 11, 16, 17, 20, 108, 211, 212, 213, 264], "5500": 15, "55074": 278, "55423": 222, "556": 68, "559292": 277, "56": [0, 11, 17, 222], "5601": 0, "56122354": 238, "56325207": 22, "56422281": 11, "566265": 199, "567": [0, 7], "5688": 262, "5690369": 3, "56e": 291, "57": [0, 9, 11, 21, 23, 108, 240], "57096847": [0, 53], "572": 6, "57240071": 7, "57240072": 7, "573": 100, "5763814": 21, "5781": 11, "579": 11, "58": [0, 11, 13, 16, 17, 65, 107, 216, 264], "58037": 21, "582000": 0, "582060": 0, "582120": 0, "582180": 0, "582228": 0, "583333": 11, "583333333208333": 11, "585366": 199, "585505": 68, "59": [0, 2, 7, 8, 9, 11, 17, 21, 104, 107, 182, 237, 251, 264], "590": [2, 129], "5900": [0, 6], "5901": 0, "590402969247084": 11, "591": 0, "59128983": [0, 20], "592": [6, 19, 23], "5923": 6, "5925": 0, "594": 0, "5960": 0, "5968": 62, "5969": 62, "5974": 6, "599": 126, "59e": 291, "5a": 68, "5alpha": 90, "5e": [0, 3], "5f": [11, 169, 190], "5gb": 25, "5xx": 83, "6": [0, 2, 3, 4, 7, 8, 11, 12, 13, 17, 20, 21, 29, 30, 32, 68, 69, 73, 80, 93, 101, 104, 105, 113, 126, 129, 135, 137, 149, 154, 172, 207, 217, 218, 237, 238, 245, 249, 251, 253, 260, 261, 264, 265, 270, 278, 281, 288, 290, 291, 297, 299], "60": [0, 3, 11, 13, 15, 16, 20, 23, 30, 68, 69, 83, 126, 155, 207, 237, 241, 245, 250, 251, 264, 280], "600": [14, 264, 277], "6000": 0, "6002": [3, 20], "601": [7, 11], "60124254": 11, "6015": 62, "6016975": 11, "6026": 2, "6036": 2, "605": 11, "608": 264, "609": 11, "60966679": 22, "61": [0, 3, 7, 8, 11, 16, 20, 116, 175, 261, 299], "6146": 0, "6150": 30, "615385": 199, "616": 2, "61646095": 0, "61646111": 0, "617": 2, "6182": 0, "62": [3, 7, 13, 21, 29, 32, 113, 149, 251, 264], "620": 11, "621": [2, 129], "622": 11, "62230396": 11, "6228": 0, "625": 3, "627328": 0, "6273284": [0, 7, 12, 30], "6273285": [0, 7, 12, 30], "6273286": [0, 7, 12, 30], "6273287": [0, 7, 12, 30], "6273289": [0, 7, 12, 23, 30], "627329": 0, "6273290": [0, 7, 12, 23, 30], "6273291": [0, 7, 12, 23, 30], "6283": 0, "628313891834571": 11, "62959": 2, "62969": 2, "6298": 6, "62e": 291, "63": [0, 11, 13, 16], "630": 68, "6308": 0, "6311": 0, "633": 238, "63398": 278, "6340": 4, "63459": 3, "63854": 278, "63m1062n75m468n43m": 0, "64": [0, 4, 6, 13, 16, 68, 69, 73, 157, 169, 238, 251, 256, 264, 270, 278], "640": 288, "64000": 15, "641682": 222, "6421": 6, "646": 0, "64668512": 11, "646m": 0, "64bit": 23, "64kb": 278, "65": [0, 9, 11, 22, 104, 216, 234, 236, 264], "650": [207, 264], "6500": 197, "652": 0, "6523201955933": 11, "65409": 278, "65411": 278, "65434": 278, "65466": 278, "65472": 278, "65483": 278, "655": 0, "65519": 278, "65535": 278, "65536": 278, "6553600000": 278, "6553600001": 278, "6553600010": 278, "65537": 278, "65540": 278, "656": [2, 221], "65614533": 11, "656680805938494": 11, "657": 0, "657m": 0, "659": 11, "66": [0, 7, 9, 11, 264], "661": 7, "663": 126, "663044098": 3, "66312982331297": 11, "6636": 0, "664": 2, "664268": 13, "665": 11, "6654": 6, "666667": 11, "6667": 261, "666990": 0, "667": 11, "667050": 0, "667109": 0, "667168": 0, "667216": 0, "66807541": 0, "67": [11, 14, 16, 21, 29, 264], "673143725": 3, "675": 264, "67518": 23, "6754794": 7, "679": 0, "6796999": 11, "68": [9, 11, 13, 113, 216, 240, 264], "682194862932": 169, "684409690": 3, "68521": 278, "69": [0, 9, 11, 13, 65, 238, 264], "694": 0, "69599e": 68, "696": 182, "6979": 13, "6982": 0, "6989": 7, "69e": 291, "6a": 113, "6e": 0, "6mb": 278, "6mer": 32, "6merpair": 32, "7": [0, 2, 3, 4, 6, 7, 8, 11, 12, 13, 17, 20, 27, 29, 30, 31, 32, 55, 69, 73, 74, 101, 104, 105, 113, 116, 117, 126, 137, 140, 154, 169, 206, 207, 217, 236, 237, 238, 249, 251, 253, 260, 263, 264, 265, 288, 291], "70": [9, 11, 12, 53, 129, 183, 207, 209, 237, 264, 270, 278], "700": [6, 11, 23, 207], "70000": 278, "700000": 199, "70143": 278, "7024864140542533": 11, "703928": 11, "704": [6, 182], "7053": 157, "706746561638717": 11, "7087": 0, "709": 6, "7093": 0, "71": [0, 8, 11, 16, 216, 236, 249, 297], "712": [251, 288], "71483e": 3, "71525": [0, 30], "7165707818416": 11, "7168": 169, "71795": 278, "717b": 32, "718": [6, 11], "71821": 278, "71846": 278, "71917": 222, "72": [0, 11, 12, 13, 14, 68, 104, 240, 264, 265], "720": 13, "721": 7, "723": [2, 23], "7235": 23, "7236": 0, "725": 2, "726": 6, "727": 0, "728": 2, "73": [0, 3, 4, 11, 12, 16, 20, 210, 264], "730": 6, "733": 6, "7331": 0, "73414803": 11, "736": 2, "738": 11, "7381525": 11, "739": [11, 166], "74": [0, 7, 23], "740": [6, 19, 23], "74100009": 238, "74196805": 0, "74196831": 0, "742": 2, "744": 6, "747": 166, "748": 6, "749": 2, "74907211028632": 11, "75": [0, 2, 3, 7, 11, 15, 16, 17, 23, 32, 104, 110, 182, 251, 261, 263, 264, 270, 299], "750": 11, "750000": 299, "7525076": 238, "753": 6, "755": 11, "7564": 0, "7592839": 11, "76": [0, 7, 11, 29, 263, 299], "7602": 6, "761": 11, "76216221": 11, "763": 2, "768": 13, "77": [0, 8, 9, 11, 14, 251, 264], "772259": 11, "772949": 11, "77304": 278, "77363485291994": 11, "774": [2, 11], "775": [13, 263], "7788": 6, "78": [3, 9, 11, 21, 68, 104, 107, 238, 264], "780": 11, "78077248": 0, "781": 7, "782996e": 11, "783": [3, 25], "7860": 126, "789": 6, "79": [0, 7, 11, 13, 93, 238, 264], "7902972158110341": 11, "792": 238, "793": 2, "7968486": [34, 281], "797": 3, "797852598091198": 11, "798957": 13, "79999999999999999999999999999999999999999999999999999999999999999999999999999999": 0, "799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998899999999999999999999999999999999999999999999999999999999999999999999999999986": 0, "7a": 0, "7b": 0, "7e": 0, "7kd": 0, "7kd_dna_bind": 0, "7rsa": 169, "7wga_a": 0, "8": [0, 2, 3, 4, 7, 8, 11, 12, 13, 16, 17, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 73, 90, 101, 104, 109, 126, 137, 154, 166, 169, 182, 206, 226, 236, 237, 238, 247, 249, 251, 260, 261, 264, 278, 281, 288, 291, 299], "80": [0, 3, 11, 14, 15, 20, 30, 53, 68, 97, 175, 182, 207, 249, 250, 251, 278], "800": [11, 15], "801": 11, "803": 288, "80360": 2, "8044": 0, "806": 2, "807": 13, "8080": 7, "808080": 17, "8087": 6, "81": [0, 11, 12, 13, 15, 32, 104, 249, 264], "8106085": 72, "8124": 6, "81344243": 0, "81344245": 0, "81344264": 0, "81344267": 0, "81344283": 0, "814": 7, "81444246": 0, "81519121131782": 11, "8192": 169, "82": [0, 11, 176, 238, 265], "8230": 126, "82356262": 11, "827": 6, "83": [11, 12, 32, 251, 253], "831": 11, "832": 0, "8332116": [1, 3], "833333": 11, "84": [0, 7, 11, 149, 253, 264, 265], "841": 7, "84337": 278, "844": 0, "844049228115868": 11, "844718": 278, "8465": 6, "847": 32, "84771": 278, "84962463": 11, "84962511": 11, "85": [0, 2, 3, 11, 20, 26, 59, 100, 216, 238, 240, 264, 307], "85010": 0, "85061": 0, "8526": 7, "853516785566917": 299, "854": 13, "854375": 11, "85454": 278, "85737865": 0, "85737906": 0, "85843": 278, "85e": 291, "86": [2, 3, 11, 15, 20, 24, 206, 264], "8637051322628": 11, "86436": 238, "8660": 4, "87": [0, 2, 8, 11, 137], "870": 11, "870876719950774": 11, "873": 25, "8741": 6, "875": 22, "87558226865211": 11, "87661": 0, "877470982533044": 11, "879": 94, "87e": 291, "88": [0, 8, 11, 29, 83, 216, 251, 264], "8800": 7, "880567338282079": 11, "881": 7, "883079837598544": 11, "8859": 278, "88765292": 0, "88765304": 0, "88765327": 0, "88765331": 0, "88765333": 0, "88765335": 0, "88765343": 0, "88765346": 0, "888": 149, "88857985": 0, "88857997": 0, "88858020": 0, "88858024": 0, "88858026": 0, "88858028": 0, "88858036": 0, "88858039": 0, "89": [0, 2, 206, 288], "892": [7, 83], "893": [7, 264], "894": 7, "895": 7, "89503": 278, "89536": 278, "89554": 278, "896": 7, "89741": 279, "898": 3, "898197242841994": 11, "899": [7, 23], "899024": 11, "8b8": 0, "8cb": [0, 55], "8cc": [0, 55], "8e": 0, "8gb": 23, "8h": 0, "8p22": 7, "9": [0, 2, 3, 4, 7, 8, 11, 12, 13, 16, 20, 21, 22, 24, 29, 30, 32, 73, 80, 84, 93, 104, 113, 126, 137, 156, 157, 166, 169, 206, 207, 217, 237, 245, 247, 249, 251, 253, 260, 263, 264, 265, 270, 279, 280, 281, 288], "90": [0, 6, 7, 8, 11, 17, 30, 53, 169, 206, 216, 240, 251, 256], "900": 0, "90038": 137, "901": 7, "90165": 2, "902": [7, 23, 69], "9044": 6, "90478": 2, "906": 12, "9085": 0, "909": 288, "9097": 13, "9099": 13, "90e": 216, "91": [0, 4, 8, 11], "91001": [21, 238], "9101": 13, "9103": 13, "9106": 0, "911": 69, "91102552": 11, "91307e": [3, 20], "9169": 0, "9183534": 153, "918728": 11, "919596": 11, "92": [11, 32], "9217": 13, "9219": 13, "9221": 13, "9223": 13, "9223372036854775807": [0, 13], "92243": 278, "9225": 13, "9227": 13, "9229": 13, "923": 264, "9231": 13, "9233": 13, "9235": 13, "9237": 13, "9239": 13, "923902": 12, "926": 7, "926202": 11, "9264": 6, "9290": 0, "93": [0, 6, 8, 11, 251], "9316": 2, "9317": 0, "935284": 11, "936213": 11, "9373": 0, "93827754": 11, "939": 11, "94": [0, 6, 8, 11, 19, 23, 149, 250], "940": 11, "9407": 0, "941176": 104, "9428": 62, "9429": 62, "943": 11, "943639": 11, "94630059171354": 299, "94707528": 0, "94708176": 0, "94708178": 0, "94708718": 0, "9475": 62, "9476": 62, "9478129": 53, "9483": 0, "948570": 260, "948639": 11, "949": 261, "94967506": 56, "94e": 216, "95": [0, 2, 8, 11, 15, 217, 238, 240, 261, 264, 265, 299], "95160479": 0, "95160520": 0, "95186205": 0, "95186217": 0, "95186220": 0, "95186243": 0, "95186245": 0, "95186253": 0, "95225": 0, "9525": 2, "95871737667187": 11, "9598": 7, "96": [2, 11, 16, 149, 206, 251, 264, 298, 299], "960": [0, 157], "9606": [68, 288], "9609": [6, 21], "961": 7, "965": 11, "968132": 11, "96820": 0, "97": [3, 8, 11, 20, 32, 149, 264], "970": [11, 13], "971": 13, "971153846153846": 11, "972": [0, 11], "974": 11, "9758318": 0, "9758326": 0, "9758328": 0, "9758351": 0, "9758354": 0, "9758366": 0, "976567": 11, "97769": 222, "978": 0, "9786631": 0, "9787941": 0, "9788508": 0, "9790455": 0, "9790463": 0, "9790465": 0, "9790488": 0, "9790491": 0, "9790503": 0, "9795062": 0, "9795065": 0, "9795737": 0, "9796": 7, "9796821": 166, "97e": 11, "98": [3, 7, 8, 11, 20, 25, 104, 206, 265], "980": 11, "9805": 11, "981": 13, "983797": 11, "984": 11, "9876543210": 251, "987828735": 278, "989200": 11, "99": [0, 3, 8, 11, 16, 20, 116, 207, 216, 256, 264, 270], "990": [13, 251], "997": [11, 261], "9974": 0, "998": 251, "9986": 7, "999": 207, "9997": 0, "9999": 0, "99999": 149, "99999699899": 0, "9999969989999999999999998699989997": 0, "99999999": 7, "99999999986": 0, "99999999999988999999999999999999999999999999999999999999999999999999999999999999": 0, "9999999999999869998": 0, "9999999999999999999": 0, "99999999999999999999999": 0, "9999999999999999999999999999999999999999999999": 0, "9_": 197, "9e": [0, 3, 20], "9wga_a": 0, "A": [0, 1, 2, 3, 4, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 21, 22, 23, 24, 25, 30, 31, 32, 33, 35, 36, 37, 38, 45, 46, 47, 49, 51, 53, 55, 56, 60, 61, 64, 65, 66, 68, 71, 72, 73, 76, 80, 81, 84, 92, 93, 94, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 112, 113, 114, 117, 118, 119, 121, 123, 127, 129, 130, 135, 137, 139, 140, 141, 146, 149, 150, 152, 154, 155, 156, 157, 159, 164, 165, 169, 172, 175, 177, 179, 180, 182, 183, 197, 199, 202, 207, 209, 210, 212, 214, 215, 217, 222, 236, 237, 238, 246, 247, 248, 251, 260, 261, 262, 263, 264, 265, 268, 270, 271, 272, 275, 277, 280, 281, 283, 287, 288, 289, 290, 291, 296, 297, 298, 299, 300, 302, 303], "AND": [7, 25, 149, 251, 276], "AS": [0, 11, 53, 66, 90, 270, 295], "AT": [30, 31, 264], "And": [6, 7, 12, 20, 23, 30, 80, 182, 251, 260], "As": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 38, 39, 45, 46, 51, 61, 68, 73, 81, 169, 217, 222, 236, 238, 247, 250, 251, 253, 270, 275, 278, 283], "At": [3, 7, 8, 11, 15, 20, 24, 25, 30, 68, 260, 270, 274, 277], "But": [0, 3, 7, 15, 17, 20, 23, 217, 222, 237, 251, 305], "By": [0, 3, 4, 6, 7, 8, 11, 12, 13, 15, 17, 20, 22, 23, 24, 25, 30, 32, 54, 67, 69, 83, 92, 99, 102, 108, 109, 127, 135, 149, 182, 183, 217, 237, 241, 250, 251, 260, 261, 265, 270, 274, 278, 286, 290, 297, 299, 303], "For": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 20, 21, 22, 23, 24, 25, 30, 31, 41, 50, 53, 54, 55, 56, 58, 59, 61, 62, 65, 66, 67, 68, 69, 73, 81, 83, 85, 94, 99, 108, 112, 113, 114, 117, 119, 125, 137, 157, 168, 169, 177, 182, 183, 197, 205, 212, 215, 217, 218, 221, 222, 229, 234, 237, 238, 239, 241, 247, 249, 251, 252, 253, 255, 256, 260, 262, 264, 265, 270, 274, 275, 278, 283, 295, 297, 298, 299, 305], "IN": [53, 60, 66, 129, 151], "INS": 32, "IT": 66, "If": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 36, 37, 38, 44, 45, 47, 51, 52, 54, 56, 66, 67, 68, 69, 73, 80, 81, 83, 84, 92, 93, 94, 95, 99, 101, 102, 104, 108, 109, 113, 117, 127, 129, 132, 135, 136, 137, 139, 143, 149, 151, 154, 158, 166, 169, 176, 180, 182, 183, 193, 195, 196, 197, 205, 207, 209, 214, 217, 218, 221, 222, 229, 236, 237, 238, 241, 251, 253, 260, 261, 263, 264, 265, 269, 270, 277, 278, 281, 282, 283, 286, 288, 290, 297, 298, 299, 300], "In": [0, 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 30, 31, 56, 60, 65, 66, 67, 68, 73, 94, 107, 135, 144, 154, 176, 182, 183, 197, 201, 205, 214, 215, 217, 218, 221, 222, 234, 236, 237, 238, 248, 251, 260, 264, 270, 274, 277, 278, 297], "It": [0, 3, 4, 6, 7, 8, 9, 11, 13, 14, 15, 17, 19, 20, 21, 23, 24, 25, 27, 30, 31, 45, 46, 56, 60, 61, 65, 67, 68, 71, 94, 103, 104, 121, 122, 139, 140, 146, 149, 155, 182, 183, 197, 199, 201, 204, 207, 209, 217, 218, 221, 229, 236, 237, 238, 246, 251, 252, 257, 264, 265, 270, 278, 280, 281, 283, 291, 294], "Its": [0, 12, 15, 197, 263], "NO": 182, "NOT": [7, 27, 30, 32, 59, 66, 80, 94, 129, 159, 169, 179, 180, 246, 251, 260, 261], "No": [0, 3, 4, 32, 65, 104, 122, 126, 182, 207, 217, 236, 251, 265, 297, 303], "Not": [3, 15, 17, 20, 23, 25, 31, 69, 71, 132, 182, 183, 237], "OF": [83, 149], "ON": 32, "ONE": [49, 64, 182], "OR": [32, 142, 143, 151, 152, 154], "Of": [6, 7, 15, 19, 68, 251, 253, 278], "On": [1, 3, 15, 23, 222], "One": [1, 6, 7, 8, 9, 11, 12, 13, 14, 15, 19, 21, 23, 25, 30, 32, 56, 119, 135, 154, 197, 211, 217, 251, 278, 303], "Or": [3, 8, 11, 12, 15, 17, 20, 22, 23, 25, 30, 238, 241, 249, 250, 251, 253, 260, 278, 283, 298, 299], "Such": [12, 13, 15, 22, 27, 238], "THAT": 60, "THE": 151, "THESE": 151, "TO": [15, 151, 169], "That": [6, 7, 17, 19, 20, 21, 23, 183, 229], "The": [1, 2, 5, 6, 8, 9, 10, 12, 14, 16, 17, 18, 19, 22, 23, 25, 26, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39, 44, 45, 46, 48, 50, 51, 52, 53, 54, 56, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 80, 83, 84, 85, 88, 89, 92, 93, 94, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 112, 113, 114, 116, 117, 118, 119, 122, 123, 125, 126, 127, 128, 135, 136, 137, 139, 140, 143, 144, 149, 150, 151, 152, 155, 156, 157, 158, 160, 162, 164, 166, 169, 176, 177, 182, 183, 185, 186, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 222, 226, 229, 234, 236, 237, 238, 241, 242, 244, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 263, 264, 265, 267, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 282, 283, 286, 287, 288, 289, 290, 291, 293, 295, 296, 297, 298, 299, 300, 303, 307], "Their": [0, 177], "Then": [3, 7, 8, 15, 17, 23, 25, 94, 251], "There": [0, 3, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 20, 23, 24, 25, 30, 69, 73, 85, 116, 117, 169, 217, 222, 238, 250, 251, 256, 269, 278, 288, 299], "These": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 66, 67, 73, 76, 80, 91, 94, 99, 103, 104, 109, 122, 123, 143, 148, 151, 169, 170, 173, 178, 215, 217, 218, 221, 226, 236, 237, 245, 251, 264, 270, 283, 295], "To": [0, 3, 4, 5, 6, 7, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 61, 84, 92, 108, 119, 146, 149, 156, 169, 176, 182, 183, 198, 204, 209, 221, 229, 236, 239, 244, 248, 250, 251, 252, 260, 264, 274, 278, 288, 297, 299], "WILL": 66, "WITH": 278, "Will": [31, 32, 92, 202, 237, 261, 275], "With": [0, 1, 4, 7, 11, 12, 13, 14, 17, 20, 69, 182, 236, 237, 260, 270, 297], "_": [4, 6, 12, 13, 17, 73, 169, 197, 214, 226, 238, 251], "_7_": 100, "__": [0, 12], "___": 12, "_____": 12, "______": 12, "________": 17, "_________": 17, "__________": [12, 17], "___________": 17, "______________": 17, "_______________": 12, "________________": 17, "_________________": 12, "__________________": 17, "________________________": 17, "__________________________": 12, "___________________________": 17, "___________________________________________": 17, "___________________________________________________________________________": 17, "__abstractmethods__": [27, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 68, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 233, 236, 237, 238, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259, 279, 281, 283, 291], "__add__": [27, 30, 133, 176, 209, 214, 236, 237, 260, 279, 280, 298, 299], "__annotations__": [27, 30, 36, 45, 56, 62, 75, 76, 92, 94, 133, 139, 169, 222, 225, 236, 260], "__array__": [27, 30], "__array_finalize__": [30, 54], "__array_prepare__": [30, 54], "__array_ufunc__": [30, 54], "__array_wrap__": [30, 54], "__bool__": [27, 181, 183, 237, 260], "__bytes__": [27, 30, 36, 236, 260], "__call__": [27, 67, 297], "__contains__": [27, 30, 54, 68, 75, 76, 133, 134, 136, 139, 140, 169, 176, 181, 197, 236, 237, 260, 298, 299, 301, 303], "__deepcopy__": [133, 169], "__delitem__": [27, 30, 133, 136, 139, 181, 197, 236, 298, 299, 301, 303], "__dict__": 20, "__doc__": 25, "__enter__": [27, 30, 45, 68, 278], "__eq__": [27, 30, 83, 84, 133, 135, 139, 169, 177, 178, 179, 180, 236, 237, 260, 283, 287, 298, 299], "__exit__": [27, 30, 45, 68, 278], "__format__": [27, 30, 54, 181, 183, 260, 283], "__ge__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__getattr__": [75, 76, 98, 104, 133, 139], "__getitem__": [27, 30, 31, 36, 45, 54, 68, 75, 76, 98, 104, 128, 131, 133, 134, 136, 139, 140, 176, 181, 183, 197, 209, 210, 214, 236, 238, 257, 260, 279, 280, 283, 289, 290, 291, 292, 295, 298, 299, 301, 303], "__getnewargs__": [27, 30, 36, 237, 297], "__getstate__": [27, 30], "__gt__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__hash__": [27, 30, 83, 84, 133, 135, 139, 169, 177, 178, 179, 180, 236, 237, 260, 283, 287, 298, 299], "__iadd__": [209, 214], "__init__": [9, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 42, 45, 47, 49, 51, 52, 56, 60, 61, 62, 67, 68, 69, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 114, 115, 116, 117, 120, 121, 122, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 148, 149, 150, 151, 153, 154, 155, 156, 157, 160, 161, 162, 163, 165, 166, 169, 170, 171, 172, 173, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 187, 188, 189, 190, 192, 193, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 263, 265, 268, 269, 270, 271, 272, 273, 275, 278, 279, 280, 281, 282, 283, 284, 287, 288, 289, 290, 291, 292, 294, 295, 296, 297, 298, 299, 301, 302, 303, 304, 305], "__iter__": [27, 30, 56, 60, 68, 92, 128, 131, 133, 134, 135, 139, 181, 183, 197, 217, 218, 219, 220, 221, 226, 227, 228, 229, 230, 232, 233, 234, 235, 237, 238, 246, 260, 278, 298, 299, 301, 303], "__le__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__len__": [27, 30, 36, 44, 45, 56, 61, 79, 81, 98, 104, 128, 131, 133, 134, 139, 140, 181, 183, 197, 236, 237, 238, 257, 260, 283, 298, 299, 301, 303], "__lt__": [27, 30, 133, 135, 136, 139, 169, 236, 260], "__main__": 24, "__module__": [25, 278], "__mul__": [27, 133, 176, 236], "__name__": [24, 303], "__ne__": [27, 30, 83, 84, 133, 135, 139, 169, 260], "__neg__": [133, 176], "__new__": [27, 30, 36, 54, 83, 84, 181, 197, 237, 297], "__next__": [27, 30, 45, 56, 57, 58, 60, 62, 63, 65, 66, 68, 92, 128, 129, 131, 238, 239, 244, 246, 248, 250, 252, 278], "__nonzero__": [27, 237], "__orig_bases__": [133, 136, 139, 144, 155, 160, 238, 246, 251], "__parameters__": [133, 136, 139, 144, 155, 160, 238, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259], "__pow__": [133, 176], "__radd__": [27, 236, 237, 260], "__reduce__": [30, 54], "__repr__": [27, 30, 36, 54, 56, 61, 67, 68, 75, 76, 83, 84, 85, 86, 90, 92, 93, 95, 133, 135, 136, 140, 144, 148, 154, 155, 160, 169, 176, 177, 178, 179, 180, 181, 183, 237, 260, 275, 297, 298, 299, 301, 303], "__setattr__": [27, 30, 67], "__setitem__": [27, 30, 54, 133, 139, 176, 181, 197, 199, 236, 298, 299], "__setstate__": [27, 30, 54], "__slots__": [27, 30, 36, 236, 297], "__str__": [27, 30, 31, 36, 54, 67, 68, 71, 75, 76, 79, 82, 83, 84, 85, 86, 90, 92, 93, 96, 97, 98, 104, 111, 112, 113, 114, 115, 117, 121, 128, 131, 132, 177, 178, 179, 180, 181, 183, 197, 200, 201, 204, 209, 210, 211, 212, 213, 215, 237, 260, 261, 279, 280, 283, 286, 287, 288, 290, 293, 295, 296, 298, 299], "__sub__": [27, 133, 135, 139, 140, 176, 237, 298, 299], "__truediv__": [133, 176], "__version__": 9, "_abstracthsexposur": 141, "_all": 20, "_allbond": 169, "_alphabet": 13, "_atom_sit": [15, 248], "_atomt": 135, "_attr_tagnam": 252, "_backward_recurs": 107, "_base": 225, "_baseexonerateindex": [224, 225], "_baseexoneratepars": [223, 224, 225], "_basehmmertextindex": [230, 233], "_bit": 226, "_bitstr": 186, "_calc_ibd": 202, "_child": 139, "_chromosomecompon": 99, "_cl": [30, 36, 297], "_color": 104, "_create_edra": 169, "_data": 236, "_default_field": 219, "_draw_seg": 99, "_elem_tagnam": 252, "_embosscommandlin": 80, "_embossminimalcommandlin": 80, "_end_tag": 71, "_entity_poly_seq": 248, "_expect": 226, "_exptl_cryst": 15, "_fastam10parser__parse_hit_t": 226, "_fasttre": [24, 182], "_featur": 104, "_featureconsum": 94, "_forward_recurs": 107, "_gc_valu": 261, "_grei": 104, "_hedradict2chain": 169, "_id": 62, "_ident": 226, "_init1": 226, "_initn": 226, "_insdcwrit": 245, "_io": 24, "_item": 20, "_make_": 207, "_matric": 11, "_matrix": 199, "_ncbibaseblastcommandlin": 69, "_ncbiblast2seqcommandlin": 69, "_ncbiblastcommandlin": 69, "_ncbiblastmain2seqcommandlin": 69, "_open": [83, 209], "_opt": 226, "_parent": 139, "_parser": 225, "_pdbx_poly_seq": 248, "_pdbx_poly_seq_schem": [238, 248], "_per_letter_annot": 260, "_phylip_id_width": 65, "_phyml_lk": 182, "_phyml_stat": 17, "_phyml_trac": 182, "_phyml_tre": 17, "_posit": 99, "_postgresql_dbutil": 304, "_ppbuilder": 154, "_pseudcount": 11, "_query_mark": 225, "_rc": 260, "_read_next_align": 45, "_recordconsum": 269, "_residuet": 155, "_restricteddict": 260, "_score": 226, "_select": [148, 170, 173], "_self": 139, "_seqabstractbaseclass": 236, "_sim": 226, "_start_tag": 71, "_struct_ref_seq": 248, "_tba_c": 0, "_tba_right": 0, "_toopm": 299, "_translate_id": 136, "_twobitsequencedata": [236, 257], "_uk": 167, "_undefinedsequencedata": 236, "_uniprotsearchresult": 276, "_util": 24, "_xmlparser": 71, "_z": 226, "a0": [17, 176, 183], "a00022": 245, "a00028": 245, "a00031": 245, "a00034": 245, "a00060": 245, "a00071": 245, "a00072": 245, "a00078": 245, "a01": [16, 299], "a02": [16, 299], "a026236": 2, "a03": [16, 249, 299], "a040153": 2, "a040343": 2, "a040410": 2, "a05": 299, "a1": [0, 17, 30, 169, 176, 183, 264], "a12": [16, 299], "a1bg": 7, "a2": [0, 30, 169, 176], "a202": 15, "a203": 15, "a204": 15, "a2d_map": 169, "a2da_map": 169, "a2h_map": 169, "a2ha_map": 169, "a2l": 154, "a2m": [7, 27, 30, 32], "a2mp": 7, "a3": [15, 104, 169, 176], "a3c184c": 30, "a4": [8, 169], "a4yea2": 0, "a_": 109, "a_color": 8, "a_kei": 137, "a_rec": 8, "a_rod": 244, "a_u455": 244, "a_vs_b": 8, "aa": [0, 7, 11, 13, 22, 30, 31, 32, 66, 104, 137, 154, 182, 275], "aa1": 13, "aa2": 13, "aa3": 13, "aa_cont": 263, "aa_end": 6, "aa_multiple_align": 0, "aa_onli": 154, "aa_start": 6, "aaa": [0, 13, 22, 30, 222, 260, 280, 281], "aaaa": 22, "aaaaaaa": 30, "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa": 56, "aaaaaaaaattt": 30, "aaaaaaaacccccccaaaaaaaaaaaggggggaaaaaaaa": [0, 13, 30], "aaaaaaaggggggngaaaaa": 0, "aaaaaatacc": 7, "aaaaaattt": 30, "aaaaac": 12, "aaaaaccg": 0, "aaaaaccgg": 0, "aaaaagaaag": 7, "aaaaaggcattgtggtgggaat": 0, "aaaac": [0, 30], "aaaacaggtt": 7, "aaaacc": 12, "aaaaccc": 13, "aaaacgt": 30, "aaaacgtcg": 280, "aaaacgtt": [0, 30], "aaaag": [0, 30], "aaaagagacagatggtcactaataaaatctgt": 0, "aaaagattcc": 7, "aaaagcaatt": 7, "aaaagg": [0, 30], "aaaaggt": 30, "aaaaggtgg": 280, "aaaagtacag": 7, "aaaatatcag": 7, "aaaauugaauaucguuuuacuuguuuau": 66, "aaac": [0, 13, 30], "aaacaa": 12, "aaacaaa": [0, 13, 30], "aaacatgtgaaggttcttcaagacgaaaaactcccatttgatttgactctgtgcggttcg": 260, "aaacca": 12, "aaaccc": 12, "aaacccccccaaaaaaaaacaaaaaaaaaaaaaaaaaaaa": 56, "aaacct": 0, "aaacgtttaa": 7, "aaag": [0, 13, 30], "aaaga": 253, "aaagaaa": [0, 13, 30], "aaagaagtaaggtaaataac": 253, "aaagacaact": 278, "aaagacaagtggtatcaacg": 253, "aaagannnnn": 253, "aaaggggctt": [30, 68], "aaai": 2, "aaanccagtcacctttctcctaggtaatgagtagtgctgttcatattactntaagttcta": 238, "aaatcttggt": 7, "aaatgagggcccagggtatgctt": 62, "aaatgta": 0, "aaattcattt": 7, "aaattt": 30, "aaatttcccgg": 281, "aaatttcccgggaa": 281, "aaatttgggccaaattt": 281, "aac": [13, 22, 222], "aac62543": 21, "aacaac": 12, "aacagtcttc": 7, "aacateg": [79, 80], "aacc": [13, 22], "aaccaaaaag": 7, "aaccc": 11, "aacccc": 12, "aaccgg": 22, "aacctgtgga": 7, "aacg": 30, "aacgagcgttccg": 222, "aacgcc": [283, 295], "aacgcca": [283, 295], "aacgtacgt": 30, "aacgtg": 11, "aacgtgacagccctcc": 11, "aacgtgcacatcgtcc": 11, "aacgtggccacat": 199, "aacp": 7, "aactattcct": 7, "aactcc": [283, 295], "aactccg": [283, 295], "aactcgacggtcg": 236, "aactcgacgtcg": 236, "aactg": 30, "aactgg": 30, "aactggagttccg": 222, "aactt": 13, "aacttaatagcc": 0, "aadac": 7, "aaf": [15, 169], "aag": [13, 22, 30], "aagaa": 30, "aagaaagctcctcatgatcatcacggcggtcatggtccaggcaaacatcaccgctaa": 22, "aagaaatgga": 7, "aagcagcaatgtacaaga": 251, "aagcagtggtatcaacgcag": 253, "aagcccc": [30, 68], "aagccccttt": [30, 68], "aagccctcctagcacacacccggagtgg": 0, "aagccctgc": 0, "aagctt": 8, "aaggtcgccacac": 199, "aagtacgt": 0, "aagttccctccataattccttcctcccacccccaca": 0, "aah00859": 68, "aai": 15, "aak33142": 23, "aak49457": 23, "aak54648": [21, 23], "aalpetkdwredg": 0, "aamatrix": [30, 32], "aamp": 7, "aanat": 7, "aandx": [15, 169], "aani": 206, "aapkk": 250, "aar": 7, "aaron": 2, "aaseq": [10, 119], "aasiz": [15, 133, 169], "aat": [12, 13, 22], "aataa": 30, "aatatttccc": 7, "aatcatccac": 253, "aatcatccacttttta": 253, "aatcatccactttttaacgt": 253, "aatccggaggaccggtgtactcagctcaccgggggcattgctcccgtggtgaccctgatttgttgttggg": [19, 23], "aatcg": 236, "aatcgtggctattactgggatggaggtcactggcgcgaccacggctggtggaaacaacat": 22, "aatctagttt": 7, "aatg": 30, "aatgc": 11, "aatgcgaata": 7, "aatgggaatgttaagcaaacga": 0, "aatt": 13, "aattgntttgcccttttgggtttnttnttggtaaannnttcccgggtgggggnggtnnngaaa": 238, "aatttacgat": 7, "aatttcatct": 7, "aatttttggt": 7, "aattttttga": 7, "aaucg": 236, "aav74328": 238, "aavs1": 7, "aaymfflilv": 250, "aaymfllil": 250, "aaz99217": 238, "ab": [3, 7, 73, 123, 169, 182], "ab01234": 93, "ab1": 249, "ab811634": 23, "abacu": 17, "abasi": 206, "abbrevi": [0, 7, 12, 119, 123], "abc": [30, 45, 236, 237, 246], "abcd": 13, "abcdefghij": 260, "abcdejt": 251, "abd": 11, "abda_cell_fbgn0000014": 11, "abecasi": 2, "abi": [238, 239], "abif_file_format": 239, "abiio": [27, 238], "abiiter": [27, 238, 239], "abil": [0, 8, 9, 13, 19, 20, 30, 169], "abl": [0, 1, 3, 5, 7, 12, 17, 20, 23, 31, 42, 66, 108, 218, 221, 222, 264], "aboderin": 265, "abort": 56, "about": [3, 5, 6, 8, 9, 11, 12, 15, 17, 21, 22, 23, 25, 26, 27, 30, 31, 32, 59, 67, 71, 73, 77, 83, 84, 93, 99, 100, 102, 104, 117, 132, 149, 183, 185, 198, 214, 218, 222, 227, 234, 243, 246, 251, 253, 260, 262, 264, 269, 270, 273, 289, 307], "abov": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 56, 66, 83, 94, 104, 108, 152, 168, 169, 177, 202, 205, 217, 221, 237, 238, 250, 251, 252, 253, 256, 260, 263, 265, 270, 278, 283, 290, 297, 298], "abrahamleo": 265, "abs_scor": 11, "abs_score_threshold": 11, "absent": [0, 69, 182, 197, 270, 273], "absent_count": 197, "absolut": [11, 13, 15, 32, 73, 80, 100, 132, 193, 195], "abstract": [21, 30, 107, 123, 177, 178, 179, 180, 209, 236, 237, 246], "abstractatompropertymap": [27, 133, 134, 145], "abstractcommandlin": [27, 32, 67, 69, 80, 182, 270], "abstractdpalgorithm": [27, 106, 107], "abstractpropertymap": [24, 27, 133, 141, 156], "abstractresiduepropertymap": [27, 133, 134, 137, 145], "abstracttrain": [27, 106, 109], "abund": [102, 265], "abus": 7, "ac": [0, 6, 11, 12, 13, 14, 15, 17, 25, 27, 30, 32, 53, 66, 68, 90, 104, 129, 145, 169, 176, 182, 209, 210, 211, 212, 222, 234, 238, 240, 245, 250, 268, 273, 277, 295, 297], "ac007323": 238, "ac12345": 21, "aca": [13, 22, 23], "acaaattttt": 7, "acacatttat": 7, "acactacgactacgactcagactacaan": 256, "acad": [83, 264], "academ": [15, 137], "academi": [2, 32], "acagctgaaaata": 0, "acat": 13, "acataaatca": 249, "acataaatcaaattactnaccaacacacaaaccngtctcgcgtagtggag": 249, "acatttgaat": 7, "acc": [7, 11, 13, 22, 23, 83, 229, 275, 287], "acc1": [11, 291], "acc99456": 7, "acc_arrai": 137, "acc_avg": 229, "acc_list": 7, "accaac": 12, "accagtgtact": 19, "accal": 145, "acccaa": 12, "acccagctaatttttgtatttttgttagagacagtg": 251, "acccca": 12, "accccatccc": 7, "accccc": 12, "acccccgt": 297, "acccgagcgcggt": 67, "acccgggcgcggt": 67, "accd": 83, "acceler": [69, 182], "accept": [0, 3, 4, 7, 9, 13, 15, 17, 20, 22, 23, 30, 38, 46, 51, 61, 67, 68, 80, 83, 99, 104, 138, 169, 217, 218, 237, 251, 270, 277, 281, 303], "accept_atom": [15, 133, 138, 148, 152, 168, 169, 170, 173], "accept_backbon": [15, 133, 169], "accept_chain": [15, 133, 138, 148, 170, 173], "accept_deuterium": [133, 169], "accept_hydrogen": [133, 169], "accept_mainchain": [133, 169], "accept_model": [15, 133, 138, 148, 170, 173], "accept_residu": [15, 133, 138, 148, 170, 173], "accept_resnam": [15, 133, 169], "accept_sidechain": [133, 169], "acceptor": 80, "access": [0, 3, 4, 6, 8, 9, 12, 13, 17, 19, 20, 21, 22, 23, 26, 27, 30, 31, 49, 53, 56, 64, 66, 67, 68, 71, 73, 83, 85, 87, 88, 89, 90, 92, 93, 117, 119, 126, 134, 136, 137, 145, 149, 156, 157, 164, 169, 181, 183, 197, 198, 209, 210, 214, 217, 218, 229, 234, 236, 237, 238, 240, 248, 251, 253, 255, 263, 264, 270, 272, 273, 274, 275, 278, 288, 289, 291, 292, 295, 297, 299, 303, 307], "accession_vers": 218, "accg": [0, 30, 297], "accgacggcagctaaaaggg": 283, "accgagacggcaaaggctagcataggtatgagacttccttcctgccagtgctgaggaactgggagcctac": 21, "accgcc": [283, 295], "accgccc": [283, 295], "accgg": 30, "accggatgta": 238, "accggttt": 30, "accgt": [30, 68, 297], "accident": [0, 22, 30], "accii": 206, "acclim": [2, 3], "accomplish": [4, 7, 17, 25], "accord": [0, 15, 17, 32, 47, 59, 65, 99, 102, 129, 149, 158, 169, 172, 183, 217, 236, 263, 264, 265, 270], "accordingli": [4, 11, 50, 66, 169, 229, 260], "account": [6, 11, 12, 15, 30, 31, 32, 104, 182, 237, 270], "acct": 0, "acctgatgcttttataagccattgtgattaggatgactgttacaggcttagctttgtgtg": 238, "accttaagagctccacatagttgccatttgcagtacatggctaacatggattcaattgct": 260, "accumul": [261, 270], "accur": [32, 140, 182], "accuraci": [15, 32, 152, 166, 168, 169, 229, 264, 270], "acdefghiklmnpqrstvwi": 76, "acdq": 13, "acefilerecord": [27, 268, 269], "aceio": [27, 238], "aceiter": [27, 238, 240], "acet": 113, "acetylesteras": 113, "acetyltransferas": 7, "acg": [13, 22, 30, 260, 264, 297], "acga": 260, "acgc": 30, "acgcatacttg": 30, "acgccgct": 30, "acgccttttc": 7, "acgg": 30, "acggaaacat": 7, "acggcggt": 30, "acggcgtt": 30, "acgggtt": 30, "acgt": [11, 12, 13, 21, 22, 24, 30, 68, 236, 260, 264, 283, 287, 295, 297], "acgta": 241, "acgtaaccgg": 22, "acgtaaccggtt": 22, "acgtacct": 0, "acgtacgt": [0, 22, 260], "acgtacgtacgt": 262, "acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtn": 251, "acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtnnnnnn": [251, 260], "acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtnnnnnnact": 260, "acgtcggt": 30, "acgtcgtt": 30, "acgtnnnnnn": 260, "acgtt": 30, "acgttgcaatgccgta": 264, "acgtuacgtuxyzxyz": 236, "acgu": 13, "achiev": [197, 251, 260], "acid": [0, 2, 3, 11, 12, 14, 15, 23, 30, 32, 68, 71, 76, 111, 115, 119, 137, 154, 166, 169, 182, 214, 222, 236, 245, 248, 251, 261, 262, 263, 265, 272, 283, 290, 297], "acidocaldariu": 0, "acii": 206, "acm": 2, "acnq": 13, "aconitas": 83, "acoordmatchcount": 168, "acquaint": 17, "acquir": 6, "acr": 94, "across": [3, 12, 15, 99, 103, 217, 229, 288], "act": [0, 6, 12, 13, 23, 30, 105, 117, 237, 241, 260, 274, 278, 303], "act_sit": 272, "acta": [83, 175], "actaccgctagctcagaag": 12, "actacgac": 12, "actacgactagctcag": 12, "actacgactagctcagg": 12, "actacggcaagcacagg": 12, "actacggctagcacagaag": 12, "actacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtnnnnnn": 260, "actagtacag": 12, "actagtacagct": 12, "actagtacagctg": 12, "actagtta": 0, "actccta": 12, "actcgacgt": 236, "actcgacgtc": 236, "actcgacgtcg": 236, "actcgacgtcga": 236, "actcgacgtcgattt": 236, "actcgnnntcg": 236, "actcgtcgtcg": 236, "actg": [22, 261], "actgctagat": 30, "actgctagatag": 30, "actgctagct": [12, 30], "actgctagctag": [12, 30], "actgctagdt": 12, "actgctagdtag": 12, "actgn": [236, 261], "actgssss": 261, "actgswu": 261, "actgtn": 261, "actin": 197, "action": [12, 20, 71, 169], "activ": [15, 16, 17, 24, 25, 53, 86, 136, 139, 169, 272, 303], "active_sit": 66, "actm": 197, "acttcgactt": 7, "actttcttctttaccgtaac": 253, "actual": [6, 7, 8, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 69, 83, 99, 108, 109, 110, 217, 222, 226, 237, 238, 245, 246, 251, 260, 278, 294], "acugn": 236, "acxq": 13, "acyltransferas": 23, "ad": [4, 6, 8, 11, 12, 13, 15, 17, 23, 24, 30, 31, 32, 67, 69, 73, 76, 80, 99, 102, 111, 115, 117, 123, 132, 149, 155, 177, 182, 183, 209, 211, 237, 256, 260, 265, 269, 277, 280, 290, 303], "adaisrd": 0, "adaisrddylnapgetysvklta": 0, "adam": 186, "adam_consensu": [27, 181, 186], "adapt": [13, 20, 104, 166, 182, 253, 261, 262, 270, 283], "adapter3": [268, 270], "adapter5": [268, 270], "adaptor": [21, 301, 302, 303, 305], "adaptor3": 270, "add": [0, 5, 6, 7, 8, 9, 10, 11, 12, 15, 17, 19, 21, 22, 23, 24, 30, 31, 32, 45, 49, 60, 64, 71, 76, 82, 84, 99, 100, 102, 104, 105, 108, 109, 117, 121, 128, 129, 130, 132, 133, 135, 139, 140, 149, 155, 169, 172, 177, 179, 180, 182, 183, 185, 188, 197, 218, 221, 222, 226, 227, 229, 234, 236, 237, 246, 251, 260, 264, 265, 270, 278, 296, 299, 303], "add_annot": [181, 188], "add_compon": [115, 117], "add_count": [98, 102], "add_edg": [178, 179, 180], "add_entri": [115, 117], "add_featur": [8, 98, 104], "add_graph": [115, 117], "add_interact": [27, 177], "add_label": [98, 102], "add_nod": [178, 179, 180], "add_point": [98, 104], "add_primer_set": [79, 82], "add_product": [115, 117], "add_react": [27, 115, 117, 177], "add_rel": [115, 117], "add_residu": [133, 140], "add_sequ": [128, 129], "add_set": [8, 98, 104], "add_speci": [27, 177], "add_stmt_to_handl": [181, 185], "add_substr": [115, 117], "add_succ": [128, 130], "add_track": [8, 98, 104], "addit": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 35, 36, 38, 45, 60, 62, 66, 68, 69, 73, 80, 97, 99, 158, 166, 169, 177, 182, 183, 185, 198, 209, 211, 214, 215, 217, 221, 237, 246, 248, 253, 260, 264, 269, 270, 272, 278, 287], "addition": [5, 21, 56, 238, 247, 264, 278], "address": [6, 7, 20, 30, 68, 158], "adh": 13, "adh_zinc": 88, "adjac": [15, 169, 226], "adjust": [4, 6, 8, 9, 12, 21, 32, 68, 69, 70, 117, 129, 152, 169, 182, 217, 222, 229, 253, 260, 264, 270], "adjustdirect": [30, 32], "adjustdirectionaccur": [30, 32], "adlakslshkqllmspgqststtfpadapageytfycephrgagmvgkit": 0, "admin": 221, "administr": 3, "adocbl": 53, "adopt": [15, 20, 27], "adrian": 2, "adult": 7, "advanc": [3, 14, 15, 17, 27, 90, 169], "advantag": [3, 7, 8, 20, 22, 23, 237, 253], "advic": 8, "ae": [0, 16], "ae007476": 66, "aegddp": 12, "aegddpakaafdslqasateyigyawamvvvivgatigiklfkkfaska": 12, "aegddpakaafdslqasateyigyawamvvvivgatigiklfkkftska": 12, "aegddpakaafnslqasateyigyawamvvvivgatigiklfkkftska": 12, "aegothel": 0, "aepnaa": 12, "aepnaaateamdslktqaidlisqtwpvvttvvvaglviklfkkfvsra": 12, "aepnaaateamdslktqaidlisqtwpvvttvvvaglvirlfkkfsska": 12, "aepnaatnya": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvikl": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglviklfkkfv": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglviklfkkfvsra": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvirl": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvirlfkkfss": 12, "aepnaatnyateamdslktqaidlisqtwpvvttvvvaglvirlfkkfsska": 12, "aequinoctial": 7, "aerodramu": 0, "aessss": 12, "aestivum": 0, "af": [13, 27, 268, 269, 270], "af053945": 21, "af158246": 3, "af191": [0, 12, 30], "af191658": [0, 7, 12, 30], "af191659": [0, 7, 12, 30], "af191660": [0, 7, 12, 30], "af191661": [0, 7, 12, 30], "af191663": [0, 7, 12, 23, 30], "af191664": [0, 7, 12, 23, 30], "af191665": [0, 7, 12, 23, 30], "af283004": 3, "af297471": [238, 245], "af323668": 8, "af376133_1": [21, 23], "afai": 206, "afc": [30, 32], "afc_v": [30, 32], "affect": [4, 15, 20, 30, 32, 169, 182, 270], "affi": [24, 27], "affili": [7, 123], "affin": [14, 32, 42, 222, 297], "affine_penalti": [27, 297], "affl": 7, "affy_v3_exampl": 29, "affy_v4_exampl": 29, "affymetrix": [28, 29], "aformat": [79, 80], "african": 250, "after": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 17, 19, 20, 21, 22, 23, 24, 30, 56, 68, 69, 83, 93, 126, 169, 182, 183, 198, 202, 204, 222, 237, 238, 251, 253, 260, 269, 270, 278, 298], "afterposit": [21, 27, 237], "afterward": 3, "ag": [0, 7, 12, 30, 90, 182, 222], "aga": [12, 22, 30], "agaaatcaaa": 7, "agaacatctt": 7, "agaact": 14, "agaactc": 13, "agaattcttt": 7, "agagctattt": 278, "agagg": 240, "agagtcagtcaaggatagt": 22, "again": [0, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 18, 20, 21, 22, 23, 25, 30, 68, 71, 217, 218, 221, 237, 241, 251, 264], "against": [0, 3, 4, 6, 11, 12, 13, 17, 20, 24, 25, 30, 32, 68, 69, 70, 83, 168, 183, 218, 270, 290], "agatttc": 0, "agc": [22, 260, 261], "agccccgggc": 240, "agcccgtgggaaagtcgccgggtaatgcaccg": 22, "agcctttgccgtc": 21, "agcgcgcgtg": 283, "ageygyycephqgagmvgkii": 0, "ageygyycephqgagmvgkiiv": 0, "agg": [22, 30], "aggaatcgcgtgc": 11, "aggcatgcatc": 22, "aggctcggtta": 238, "aggctta": 0, "agggaactct": 7, "aggggtgcagagccgagtcacggggttgccagcac": 0, "agglutinin": 0, "aggreg": [15, 143, 151], "aggt": 0, "aggttt": 0, "aggtttgtt": 260, "aggua": 66, "agl3": 11, "agnost": [25, 169], "ago": 197, "agre": [12, 260], "agreement": 9, "agt": 22, "agtaaggtaaataacaaacg": 253, "agtacactggt": [19, 22], "agtacttgtg": 7, "agtatcttct": 7, "agttt": 0, "agtttaa": 0, "agtttatatataaatttcctttttattgga": 23, "ahcgscwtf": 0, "ahead": [3, 19, 278], "ahki": 13, "ahmad": 137, "ahr_si": 11, "ahsen": 264, "aid": [100, 123, 167], "aidlisqtwp": 12, "aiftddlpva": 0, "aik": 6, "aim": [17, 23, 27, 109, 119, 209, 237, 274], "airlfkkfss": 12, "aj237582": [238, 245], "ak": 169, "ak_set": 169, "ak_spec": 169, "ak_tpl": 169, "aka": [22, 238, 241, 250, 255, 278, 304], "akaafdslqasateyigyawamvvvivgatigikl": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkfa": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkfaska": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkft": 12, "akaafdslqasateyigyawamvvvivgatigiklfkkftska": 12, "akaafdsltaqatemsgyawalvvlvvgatvgiklfkkfvsra": 12, "akaafnslqasateyigyawamvvvivgatigikl": 12, "akaafnslqasateyigyawamvvvivgatigiklfkkft": 12, "akaafnslqasateyigyawamvvvivgatigiklfkkftska": 12, "akc": 169, "akl": [15, 169], "akset": 169, "akstr": 169, "aktupl": 169, "al": [0, 4, 6, 7, 8, 9, 13, 17, 32, 34, 65, 69, 73, 107, 108, 109, 137, 140, 238, 252, 264, 265, 281, 299, 300], "al109969": 21, "al391218": 237, "al_con": 226, "ala": [13, 15, 154, 169], "alan": 2, "alanin": 112, "alcohol": 113, "alec": 2, "alejandro": [3, 68], "alert": 27, "aleu_horv": 0, "aleu_horvu": [0, 56], "aleu_horvumaharvlllalavlataavavassssfadsnpirpvtdraastlesavlgalgrtrhalrfarfavrygksyesaaevrrrfrifsesleevrstn": 0, "algebra": [2, 177], "algol": 4, "algorithm": [2, 9, 12, 13, 14, 15, 20, 30, 32, 68, 69, 70, 73, 107, 108, 109, 121, 127, 157, 166, 169, 175, 177, 181, 182, 186, 199, 216, 238, 263, 268, 270, 282, 297], "algotyp": 270, "algrtrhalr": 0, "ali": 229, "ali1": 74, "ali2": 74, "alia": [23, 30, 36, 104, 218, 237, 238, 251, 270, 297], "alias": 0, "alifrom": 229, "alig": 238, "align": [2, 3, 4, 6, 9, 11, 15, 17, 19, 20, 21, 22, 23, 26, 27, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 74, 79, 80, 133, 161, 166, 169, 175, 181, 182, 186, 193, 195, 196, 197, 199, 216, 217, 218, 221, 222, 223, 224, 225, 229, 230, 244, 250, 264, 270, 275, 278, 279, 280, 281, 283, 287, 289, 290, 291, 295, 297, 307], "align1": [12, 30, 297], "align2": [12, 30, 297], "align2model": [0, 33], "align3": 12, "align_arrai": [0, 12], "align_cmd": 270, "align_format": 0, "align_length": 71, "alignac": [11, 27, 283], "aligned_col": 0, "aligned_sequ": 0, "aligninfo": [12, 27, 30], "alignio": [0, 1, 9, 12, 17, 19, 20, 27, 30, 32, 91, 199, 217, 238, 250, 274], "alignment1": [0, 13, 30], "alignment2": [0, 13, 30], "alignment3": [0, 13], "alignment_format": 66, "alignment_iterator1": 0, "alignment_iterator2": 0, "alignment_list": 0, "alignment_n": 32, "alignment_ord": [30, 32], "alignment_view": [68, 70], "alignmentcount": [0, 27, 30], "alignmentfil": 182, "alignmenthasdifferentlengthserror": [27, 72], "alignmentiter": [0, 27, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 60, 62, 63, 65, 66], "alignments1": [13, 30], "alignments2": [13, 30], "alignments3": 13, "alignmentsabstractbaseclass": [0, 27, 30, 45], "alignmentwrit": [27, 30, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 46, 47, 49, 50, 51, 52, 53, 56, 60, 64], "alignmnet": 32, "alignn": [66, 274], "alignret": 58, "alito": 229, "all": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 36, 42, 56, 59, 61, 68, 69, 70, 71, 72, 73, 76, 80, 83, 88, 91, 93, 94, 97, 98, 99, 102, 104, 108, 109, 112, 117, 123, 129, 130, 132, 135, 139, 146, 149, 152, 154, 155, 156, 157, 158, 161, 164, 166, 167, 169, 177, 179, 180, 182, 183, 185, 186, 195, 197, 198, 199, 202, 203, 206, 209, 211, 214, 217, 218, 221, 222, 229, 236, 237, 238, 248, 251, 252, 253, 260, 261, 262, 264, 265, 269, 270, 271, 274, 276, 277, 278, 280, 282, 287, 288, 290, 295, 297, 298, 299, 303], "all_id": [128, 130], "all_qresult": 222, "all_speci": 23, "all_vers": 288, "allawi": 264, "allclos": [15, 168, 169], "allel": [18, 201, 202, 203, 204, 205], "allele1": 202, "allele2": 202, "allenzym": 206, "alloc": [8, 99, 176], "allow": [0, 1, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 27, 30, 31, 32, 42, 45, 56, 61, 65, 66, 68, 69, 71, 80, 83, 84, 99, 102, 103, 104, 105, 107, 108, 117, 119, 121, 123, 139, 182, 183, 197, 207, 217, 222, 236, 237, 238, 246, 251, 253, 257, 258, 261, 264, 269, 270, 274, 278, 280, 281, 288, 297, 302, 303], "allow_all_transit": [106, 108], "allow_transit": [106, 108], "allowed_tag": 84, "almost": [6, 8, 12, 15, 17, 19, 20, 21, 84, 251, 278], "aln": [0, 7, 12, 13, 20, 30, 32, 56, 62, 199, 238, 270, 275, 279], "aln_al": 20, "aln_annot": [218, 222, 226, 229], "aln_bam": 270, "aln_cod": 0, "aln_span": [20, 218, 229, 234], "alok": [2, 4], "alon": [4, 15, 182, 278], "along": [0, 4, 5, 6, 8, 11, 12, 15, 17, 20, 21, 31, 73, 100, 102, 169, 183, 197, 237, 261, 265, 299], "alpha": [0, 3, 8, 12, 13, 14, 15, 27, 30, 105, 113, 122, 137, 140, 154, 166, 169, 172, 181, 182, 199, 238, 241, 250, 260, 272, 280], "alphabet": [0, 11, 12, 30, 54, 76, 77, 78, 94, 108, 121, 135, 207, 214, 238, 241, 246, 251, 253, 258, 283, 287, 290, 291, 295], "alphabet_dna": 283, "alphafold": 164, "alphafold_db": [27, 133], "alphanumer": [4, 253], "alreadi": [3, 4, 7, 12, 15, 17, 19, 20, 22, 23, 24, 30, 67, 94, 108, 117, 169, 199, 217, 238, 297], "alrt": 182, "also": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 49, 52, 56, 59, 64, 65, 66, 68, 69, 71, 72, 73, 76, 83, 89, 94, 99, 100, 103, 104, 119, 135, 149, 150, 154, 169, 176, 181, 182, 183, 185, 189, 209, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 240, 245, 247, 249, 251, 253, 255, 257, 258, 259, 260, 261, 264, 270, 274, 276, 278, 280, 281, 283, 288, 290, 297, 299], "alst": 169, "alt": [68, 70, 117, 181, 197, 198], "alt_id": 169, "alt_nam": 76, "alt_unit": 197, "altcolor": 104, "altcolour": 104, "alter": [18, 23, 217, 272], "altern": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 30, 31, 32, 45, 67, 76, 81, 83, 86, 90, 92, 99, 117, 120, 134, 135, 152, 158, 162, 168, 169, 172, 182, 236, 237, 238, 246, 251, 252, 271, 272, 282, 289, 290, 291], "alternative_location_id": 172, "although": [6, 7, 8, 11, 12, 15, 22, 23, 25, 42, 68, 70, 127, 218, 222, 237, 251, 260, 278], "altitud": 197, "altloc": [135, 158, 162, 169], "altloc_match": [133, 169], "altnam": 23, "altschul": [2, 3, 32, 68], "altschul1990": [0, 2, 13], "alubi": 206, "alui": 206, "alwai": [0, 3, 4, 6, 7, 8, 13, 14, 15, 20, 30, 32, 83, 157, 169, 182, 183, 217, 218, 222, 236, 237, 238, 241, 242, 247, 251, 254, 259, 260, 265, 278, 288, 297], "am": [0, 2, 3, 7], "amano": 25, "ambigu": [11, 13, 22, 30, 31, 76, 236, 251, 260, 261, 264, 270], "ambiguous_nucleotid": 76, "ambiguous_nucleotide_alphabet": 76, "ambiguous_nucleotide_valu": 76, "ambiguous_protein": 76, "ambiguous_protein_alphabet": 76, "ambiguous_protein_valu": 76, "ambiguouscodont": [27, 75, 76], "ambiguousforwardt": [27, 75, 76], "amen": 15, "amend": 260, "american": 8, "amid": [152, 169], "amino": [0, 2, 3, 11, 12, 14, 15, 23, 30, 32, 68, 71, 76, 79, 80, 137, 154, 169, 182, 214, 222, 236, 245, 248, 260, 261, 262, 263, 265, 272, 290, 297], "amino_acid": 0, "amino_acids_cont": 265, "amino_acids_perc": [261, 265], "aminoacid": [167, 265], "among": [4, 13, 15, 18, 20, 32, 80, 217, 275], "amount": [0, 6, 11, 13, 71, 92, 100, 169, 237, 264], "amplicon": 80, "amplif": 82, "amplifi": [27, 72, 79, 80, 82, 253], "an": [2, 3, 4, 5, 6, 8, 9, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 80, 81, 83, 84, 85, 86, 89, 90, 91, 92, 93, 94, 97, 99, 100, 102, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 125, 126, 127, 129, 130, 132, 134, 135, 136, 139, 140, 142, 143, 144, 149, 151, 152, 153, 154, 155, 156, 157, 158, 159, 161, 164, 169, 170, 172, 175, 177, 179, 180, 182, 183, 185, 188, 190, 193, 195, 196, 197, 198, 199, 202, 203, 204, 205, 209, 210, 214, 215, 216, 217, 218, 222, 236, 237, 238, 239, 240, 241, 245, 246, 248, 250, 251, 252, 253, 256, 258, 259, 260, 261, 264, 265, 267, 269, 270, 272, 273, 274, 275, 276, 277, 278, 279, 282, 283, 284, 291, 295, 296, 297, 298, 299, 302, 303, 304, 306], "anacaacao": 169, "anal": 264, "analog": [0, 3, 20, 21, 237], "analys": [23, 182], "analysi": [0, 2, 3, 6, 7, 9, 13, 15, 16, 17, 21, 25, 26, 27, 30, 32, 73, 109, 129, 169, 177, 182, 185, 193, 195, 206, 207, 208, 238, 265, 283, 307], "analyz": [0, 2, 4, 6, 26, 84, 169, 182, 307], "anc": [30, 32], "ancenstor": 209, "ancestor": [17, 132, 183], "ancestr": 32, "anchor": [30, 32, 80, 221], "anchor_len": [30, 279], "anchorspac": [30, 32], "ander": 2, "andrew": 2, "andrzej": 267, "angl": [100, 104, 133, 136, 144, 152, 154, 160, 169, 176], "angle2": 158, "angle_avg": [133, 169], "angle_dif": [133, 169], "angle_kei": 169, "angle_pop_sd": [133, 169], "angle_rad": 176, "angstrom": [15, 158, 169], "ani": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 45, 52, 53, 56, 60, 65, 66, 67, 68, 73, 80, 83, 86, 93, 94, 103, 104, 105, 108, 117, 119, 129, 132, 136, 139, 140, 144, 150, 152, 160, 168, 169, 172, 176, 177, 182, 183, 186, 197, 198, 217, 218, 222, 229, 236, 237, 238, 240, 241, 246, 248, 251, 252, 253, 256, 258, 260, 261, 262, 264, 265, 269, 272, 274, 277, 278, 281, 288, 297, 299, 305], "anisimova": 182, "anisotrop": [15, 135, 162], "anisou_arrai": [135, 162], "anl": 262, "ann": [0, 53, 197], "anneal": 80, "annot": [0, 2, 3, 6, 12, 17, 19, 20, 22, 23, 25, 26, 27, 30, 32, 37, 39, 46, 52, 53, 56, 62, 66, 68, 99, 104, 133, 149, 153, 181, 183, 188, 197, 198, 221, 222, 229, 237, 244, 245, 248, 250, 251, 252, 253, 255, 256, 260, 272, 277, 301, 302, 303, 307], "annotatedchromosomeseg": [8, 27, 98, 99], "annotation_upd": [25, 272], "announc": [9, 69], "annual": 2, "annurev": 2, "anomal": 270, "anoth": [3, 4, 5, 6, 7, 8, 11, 12, 14, 15, 16, 17, 20, 21, 22, 23, 30, 57, 62, 65, 66, 104, 130, 139, 152, 159, 163, 166, 169, 197, 204, 214, 216, 217, 222, 237, 238, 251, 253, 260, 270, 272, 278, 299], "answer": [5, 6, 19, 169, 279], "antao": [2, 7, 26], "anticip": 7, "anticonsensu": [11, 27, 283, 290], "antoni": 2, "anymor": [9, 251, 258], "anyon": [5, 24, 30, 237, 299], "anystr": 246, "anyth": [3, 7, 17, 22, 30, 31, 91, 99, 103, 134, 152, 253, 299], "anyuri": 197, "anywai": [0, 3], "anywher": [6, 269], "aoacacaacb": 169, "aoutfeat": [79, 80], "ap": [11, 272], "ap001509": 66, "apaf": 183, "apai": 207, "apalsnt": 0, "apalsntklriapgsfysvtlgt": 0, "apart": [22, 237, 256], "api": [7, 14, 15, 17, 18, 23, 68, 70, 83, 99, 119, 164, 177, 209, 217, 237, 252, 274, 276, 303, 307], "api_kei": [7, 83], "aplca": 197, "aplysia": 197, "apmap": 134, "appar": [0, 20, 56, 238, 251], "appear": [0, 3, 11, 12, 13, 15, 17, 36, 37, 38, 73, 80, 93, 108, 123, 126, 132, 183, 207, 238, 244, 251, 269, 273], "append": [0, 6, 8, 10, 12, 13, 22, 23, 25, 27, 30, 32, 60, 84, 129, 182, 209, 214, 236, 260, 270, 278], "append_item": [68, 71], "append_set": [128, 129], "appendix": [26, 182, 307], "appl": [5, 153], "appli": [0, 3, 4, 6, 11, 12, 13, 15, 16, 17, 20, 21, 23, 32, 56, 68, 69, 70, 73, 80, 133, 135, 139, 153, 163, 166, 169, 175, 183, 197, 217, 237, 238, 239, 251, 260, 264, 267, 270, 274, 278, 280, 281, 288], "applic": [0, 2, 4, 6, 7, 9, 13, 15, 18, 22, 24, 27, 30, 68, 71, 73, 79, 83, 158, 169, 177, 181, 197, 218, 236, 264, 268, 283], "applicationerror": [27, 67], "appliedbiosystem": 239, "applies_to": 197, "applymtx": [133, 169], "approach": [3, 4, 6, 7, 8, 9, 13, 20, 32, 84, 99, 100, 107, 169, 238, 251, 264, 269, 294], "approci": 3, "appropri": [0, 4, 6, 9, 12, 13, 15, 21, 23, 30, 83, 84, 104, 121, 169, 182, 222, 237, 238, 251, 253, 260, 269, 278, 287, 288, 293, 294], "approv": 7, "approxim": [6, 11, 13, 32, 141, 182, 251, 264, 270, 294], "approximationfor": 32, "apr": [7, 83, 149, 278], "aptahdslpspat": 12, "aq": 0, "aqcbl": 53, "aqrk": 250, "aqua": 183, "aqvk": 13, "aqvkghgkkvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaah": 13, "ar": [0, 1, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 73, 76, 80, 81, 82, 83, 84, 88, 91, 92, 93, 94, 97, 99, 100, 101, 102, 103, 104, 107, 108, 109, 110, 117, 118, 119, 121, 122, 123, 125, 126, 127, 129, 130, 132, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 146, 149, 151, 152, 154, 155, 157, 158, 160, 164, 166, 167, 168, 169, 172, 174, 177, 178, 182, 183, 197, 198, 199, 201, 204, 207, 209, 210, 214, 215, 217, 218, 221, 222, 226, 227, 229, 231, 234, 236, 237, 238, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 255, 256, 258, 260, 261, 262, 263, 264, 265, 269, 270, 272, 273, 274, 275, 277, 278, 280, 281, 283, 287, 288, 289, 290, 292, 294, 295, 297, 298, 299, 303], "arab1": 238, "arabidopsi": [3, 8, 20, 23, 238, 275, 278], "arabidopsis_thaliana": 8, "arabinos": 260, "arac": 260, "arang": 13, "arbit": 214, "arbitrari": [11, 12, 13, 16, 17, 104, 130, 177, 180, 183, 197, 198, 253], "arbitrarili": [11, 13, 158, 169], "archaebacterium": 0, "archaeohip": 56, "archaeopteryx": 17, "architectur": [15, 69, 197, 198], "archiv": [5, 6, 8, 9, 15, 68, 69, 94, 149, 251, 275], "area": [5, 15, 16, 99, 137, 145, 157, 299, 300], "aren": [9, 17, 21, 102, 149, 251], "arg": [13, 29, 30, 62, 69, 84, 104, 131, 169, 183, 197, 230, 233, 272, 291, 303, 304], "arginin": 263, "argmax_x": 270, "argo": 265, "argter": 261, "arguabl": [20, 22], "argument": [0, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 17, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 42, 45, 47, 49, 51, 52, 54, 55, 56, 60, 64, 67, 68, 69, 71, 73, 80, 83, 85, 86, 88, 89, 90, 91, 92, 94, 99, 100, 101, 102, 103, 104, 107, 108, 109, 110, 116, 119, 120, 126, 127, 135, 136, 137, 142, 143, 144, 146, 149, 151, 155, 156, 162, 169, 182, 183, 193, 195, 197, 201, 204, 205, 206, 207, 210, 211, 212, 213, 214, 217, 218, 221, 236, 237, 238, 241, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 258, 259, 260, 261, 263, 264, 265, 269, 270, 271, 272, 274, 278, 279, 280, 281, 282, 283, 288, 290, 297, 299, 302, 303], "aris": 15, "arithmet": [4, 17, 73, 199], "arkin": 182, "arndcqeghilkmfpstwyvbzx": 13, "arnt": 11, "aromat": [261, 265], "around": [1, 4, 9, 15, 19, 32, 53, 66, 100, 129, 141, 146, 155, 158, 176, 177, 238], "arrai": [4, 6, 7, 11, 15, 18, 29, 30, 54, 68, 73, 127, 135, 139, 140, 146, 156, 162, 169, 172, 175, 176, 177, 216, 270, 275, 283, 290, 299], "arrang": [12, 16], "arrow": [15, 104], "arrowhead_length": [8, 104], "arrowshaft_height": [8, 104], "art": 17, "artemi": [8, 99, 104], "artemis_color": [98, 104], "articl": [7, 15, 17, 83, 100, 123, 197, 234, 237], "articletitl": 7, "artifici": [11, 251], "arylamin": 7, "as_con": 53, "as_fasta": [27, 238, 241], "as_fasta_2lin": [27, 238, 241], "as_fastq": [27, 238, 251], "as_fastq_illumina": [27, 238, 251], "as_fastq_solexa": [27, 238, 251], "as_handl": [27, 91, 152, 158], "as_phyloxml": [17, 181, 183, 197], "as_qual": [27, 238, 251], "as_tab": [27, 238, 256], "as_typ": [30, 36], "asa": [137, 145, 157], "asap": 260, "ascend": [6, 209], "asci": 251, "ascii": [6, 17, 23, 25, 69, 214, 236, 238, 251, 260, 270, 278], "asequ": [12, 67, 79, 80], "asi": 67, "asid": [12, 66], "ask": [0, 6, 7, 8, 11, 19, 20, 23, 61, 207], "asldkfla": 13, "asn": [3, 7, 13, 15, 69, 70, 162], "asn_glycosyl": 25, "asp": [13, 15, 34, 280], "asparagal": 7, "asparagin": [13, 14], "aspart": [13, 14, 263], "aspect": 24, "aspgluserileasn": 222, "asplei": 206, "aspttgaatgatgaaaata": 222, "assembl": [133, 158, 169, 243, 268], "assemble_residu": [133, 169], "assemble_residues_s": [133, 169], "assembli": [0, 6, 13, 30, 136, 149, 152, 158, 169, 238, 243, 253, 268, 269], "assembly_num": 149, "assemblyv": 238, "assert": [0, 12, 13, 15, 23, 59, 169, 238, 278], "assertalmostequ": 24, "assertequ": 24, "assess": [13, 32, 74, 182], "assign": [3, 4, 7, 8, 12, 14, 15, 17, 20, 21, 22, 67, 69, 73, 100, 120, 121, 122, 125, 127, 143, 153, 157, 176, 182, 197, 251, 264, 265, 277, 282, 299], "assist": 186, "associ": [0, 6, 12, 13, 21, 27, 30, 32, 52, 54, 66, 68, 69, 73, 80, 129, 132, 139, 149, 177, 182, 197, 198, 209, 217, 237, 245, 255, 257, 270, 275, 277, 290, 295, 303], "assort": [23, 262, 276], "assum": [0, 3, 4, 6, 7, 11, 12, 15, 19, 23, 24, 30, 32, 60, 67, 71, 94, 125, 135, 151, 153, 157, 183, 209, 217, 231, 237, 238, 251, 252, 253, 261, 265, 270, 277, 287, 290, 303], "assumpt": [7, 12, 125, 127, 238, 246], "aster": [241, 260], "aster_no_wrap": 241, "asterisk": [0, 13, 22, 236, 250, 261], "astlesavlg": 0, "astqkaekev": 250, "astral": [7, 15, 27, 123, 209, 214], "astral_fil": 209, "astronom": 30, "asx": 261, "asym": 172, "ata": 22, "ataaatagattattccaaataatttatttatgtaagaacaggatgggaggggga": 21, "ataaatcttc": 7, "atacttacctgacaggggaggcaccatgatcacacaggtggtcctcccagggcgaggctc": 30, "atacttacctgacaggggaggcaccatgatcacacaggtggtcctcccagggcgaggctcttccattgcactgcgggagggttgacccctgcgatttccccaaatgtgggaaactcgactgtataatttgtggtagtgggggactgcgttcgcgctatcccccg": 30, "atacttacctggcaggggagataccatgatcacgaaggtggttttcccagggcgaggctt": 30, "atacttacctggcaggggagataccatgatcacgaaggtggttttcccagggcgaggcttatccattgcactccggatgtgctgacccctgcgatttccccaaatgtgggaaactcgactgcataatttgtggtagtgggggactgcgttcgcgctttcccctg": 30, "atagccccag": 7, "atagtctcat": 7, "ataset": 80, "atataattct": 7, "atc": [22, 30], "atccatctgg": 7, "atccattgcactccggatgtgctgacccctgcgatttccccaaatgtgggaaactcgact": 30, "atcccg": 22, "atcctatgct": 7, "atcg": [12, 30], "atcgacgtcg": 236, "atcgswu": 261, "atctactaat": 7, "atctcagaggatggatggacca": 0, "atctgataccttgttcagatttcaaaatagttgtagccttatcctggttttacagatgtgaaactttcaa": 238, "atcttatcaacaaaactcaaagttcctaactgagacacgcaacaggggataagacaaggcacacaggggataggnnnnnnnnnnn": 253, "atdlidqtwp": 12, "ateamdslktqaidlisqtwpvvttvvvaglviklfkkfvsra": 12, "ateamdslktqaidlisqtwpvvttvvvaglvirlfkkfsska": 12, "ateamnslktqatdlidqtwpvvtsvavaglairlfkkfsska": 12, "atemsgyawa": 12, "ateyigyawa": 12, "atg": [22, 260, 279], "atgactca": 11, "atgactcatc": 11, "atgc": [17, 182, 240, 264], "atgcgt": 279, "atgctgggctcgaacgagtcc": 30, "atgctgggctcgaacgagtccgtgtatgccctaagctgagcccgtcg": 30, "atggaagaag": 7, "atggcacggaagtga": 236, "atggccattgtaatgggccgctgaaagggtgcccgatag": 22, "atggcgtttaccttgaccaacaagaacgtggttttcgtggccggtctgggaggcattggt": 13, "atgggaaccgcg": 13, "atgggaaccgcgctgcttttgctactggccgcgctctgcgccgcaggtggggccctggag": 13, "atgggcaatatccttcggaaaggtcagcaaat": 222, "atgggccgc": 22, "atgnnnnnnnnnnatcccgnnnnnnnnnnttgca": 22, "atgtaaaaat": 7, "atgtcgtttactttgaccaacaagaacgtgattttcgttgccggtctgggaggcattggt": 13, "atgtctcgt": [30, 279], "athel": 2, "atla": [2, 53], "atm": [15, 133, 169], "atmnamendx": [15, 169], "atol": 168, "atom": [25, 27, 31, 119, 133, 134, 136, 138, 139, 141, 143, 144, 145, 146, 148, 149, 151, 152, 154, 155, 156, 157, 158, 159, 160, 162, 163, 166, 167, 168, 169, 170, 172, 173, 175, 176, 209, 214, 238, 248], "atom1": [15, 135], "atom2": [15, 135], "atom3": 15, "atom4": 15, "atom_chain": [133, 169], "atom_coord": 169, "atom_count": 172, "atom_index_on": 172, "atom_index_two": 172, "atom_list": [15, 146, 163, 175], "atom_nam": [135, 172], "atom_r": [133, 169], "atom_sernum": [133, 169], "atom_to_internal_coordin": [15, 133, 136, 144, 158, 160, 168, 169], "atomarrai": [133, 168, 169], "atomarrayca": 169, "atomarrayindex": [15, 169], "atomarrayph": 169, "atomarrayvalid": 169, "atomcoordsin": 169, "atomic_radii": 157, "atomiter": [27, 238, 248], "atomkei": [15, 27, 133, 152, 168, 169], "atomndx": 169, "atomscal": 158, "atr": [4, 73], "att": [13, 22], "attach": [17, 130, 132, 157, 183, 197, 270], "attccattct": 7, "attcgatacc": 7, "attctgatat": 7, "attempt": [3, 7, 13, 19, 20, 21, 22, 29, 30, 71, 125, 218, 222, 237, 260, 270, 278, 288], "attent": 278, "attgtctctcagtgtg": 0, "attgtctcttacggtg": 0, "attqkaekev": 250, "attr": [84, 89, 104, 252], "attract": 17, "attribut": [3, 4, 7, 8, 11, 12, 17, 20, 21, 23, 30, 31, 35, 36, 37, 38, 39, 42, 45, 46, 47, 51, 52, 62, 67, 68, 71, 73, 76, 83, 84, 87, 88, 93, 94, 97, 99, 101, 103, 104, 112, 113, 114, 117, 120, 126, 127, 136, 144, 152, 157, 160, 161, 168, 169, 177, 183, 193, 197, 199, 204, 207, 209, 210, 211, 212, 213, 214, 217, 218, 221, 222, 226, 229, 234, 237, 252, 260, 265, 269, 272, 275, 282, 287, 295, 297], "attributeerror": [0, 17], "attttcactt": 7, "attttttacg": 7, "attttttacgaacctgtggaaatttttggttatgacaataaatctagtttagta": 7, "atwtrtaass": 0, "atwtrtavss": 0, "au": [0, 4, 7, 18, 53, 123, 201, 204, 274], "au099534": 7, "aucguuuuac": 66, "auggccauug": 261, "auggccauuguaaugggccgcuga": 261, "auggccauuguaaugggccgcugaaagggugcccgauag": 22, "augucucgu": 30, "august": [2, 9], "auml": 3, "auspic": 17, "austrocylindropuntia": 7, "ausubel": 72, "auth": [7, 172], "auth_chain": 143, "auth_residu": 143, "authent": 7, "author": [7, 11, 15, 21, 25, 26, 53, 87, 93, 123, 133, 143, 174, 197, 237, 272, 274, 295, 303], "author_nam": 83, "auto": [30, 32, 67, 79, 80, 250, 283], "auto_format": [68, 70], "autocommit": [301, 303, 304], "autodoc": 306, "autom": [2, 3, 7], "automat": [2, 3, 4, 7, 9, 11, 12, 13, 17, 19, 22, 23, 24, 25, 30, 32, 67, 68, 69, 80, 83, 149, 152, 183, 197, 217, 237, 238, 251, 253, 260, 264, 269, 270, 306], "automz": 0, "autosql": [0, 36, 38], "autosql_data": 0, "autosqlt": [0, 27, 30, 36], "auwera": [2, 8], "auxiliari": 7, "avail": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 30, 34, 52, 62, 67, 68, 70, 71, 73, 76, 83, 84, 88, 99, 104, 126, 134, 149, 158, 166, 168, 172, 182, 199, 202, 209, 217, 218, 221, 222, 226, 227, 229, 234, 251, 263, 264, 270, 274, 280, 281, 287, 290, 299, 300], "averag": [4, 11, 15, 16, 32, 73, 108, 152, 156, 169, 182, 186, 203, 264, 265, 270], "average_height": [16, 299], "avg": 169, "avg_rslt": 169, "avhasldkflasvstvltskyr": 12, "avmgrwkggraag": 22, "avoid": [3, 4, 6, 7, 8, 9, 11, 15, 17, 21, 24, 27, 31, 60, 67, 80, 108, 119, 149, 169, 176, 182, 183, 209, 238, 246, 251, 270, 274, 278], "avp": 23, "avpgr": 68, "avtpvknq": 0, "avtpvknqgqcgscwsf": 0, "avtpvknqgqcgscwsfsttgnvegqhfisqnklvslseqnlvdcdhecmeyegeeacdegcngglqpnaynyiiknggiqtessypytaetgtqcnfnsanigakisnftmip": 0, "awai": [8, 68, 80], "awar": [7, 15, 32, 218, 221, 229, 237], "ax": [54, 104, 300], "axi": [4, 8, 12, 13, 15, 31, 100, 104, 117, 126, 169, 176], "axis_label": 104, "axis_seq": 31, "axislabel": 126, "ay851611": 7, "ay851612": [7, 83], "ayako": 2, "ayass": 7, "azimuth": 176, "azup_achc": 0, "azup_achci": 0, "b": [0, 2, 3, 4, 7, 8, 11, 13, 17, 22, 27, 30, 32, 36, 37, 45, 53, 62, 67, 73, 80, 83, 84, 98, 100, 104, 107, 108, 109, 118, 126, 135, 136, 137, 149, 152, 162, 169, 172, 177, 182, 183, 206, 209, 210, 211, 215, 220, 230, 233, 236, 238, 247, 248, 249, 250, 261, 263, 264, 265, 268, 269, 270, 278, 280, 295], "b01": [16, 299], "b02": 299, "b03": 299, "b04": 299, "b05": 299, "b06": 299, "b1": [0, 30, 268, 270], "b1174": 114, "b1175": 114, "b12": 299, "b2": [0, 30, 268, 270], "b3_649_fc8437_r1_1_1_183_714": 251, "b3_649_fc8437_r1_1_1_362_549": 251, "b3_649_fc8437_r1_1_1_397_389": 251, "b3_649_fc8437_r1_1_1_610_79": 251, "b3_649_fc8437_r1_1_1_850_123": 251, "b4059": 260, "b64": 15, "b65": 15, "b66": 15, "b67": 15, "b7": 0, "b9": 0, "b_": 11, "b_8148": 0, "b_color": 8, "b_ehoa": 244, "b_factor": 162, "b_hxb2r": 244, "b_i": 11, "b_rec": 8, "b_vs_c": 8, "ba": [7, 11, 295], "baa31520": [241, 260], "baa33523": 238, "baboon": 0, "bac": [21, 103, 270], "bacillu": 13, "back": [3, 6, 7, 11, 12, 15, 17, 19, 21, 22, 23, 25, 55, 76, 84, 159, 168, 169, 191, 197, 209, 214, 236, 251, 258, 260, 274, 278, 303, 305], "back_tabl": [75, 76], "back_transcrib": [22, 27, 236], "backbon": [15, 140, 158, 167, 169], "backbonefil": [0, 62], "backboneonli": 158, "backboneselect": 169, "backend": 209, "background": [8, 11, 13, 27, 104, 117, 283, 287, 290, 294], "backslash": 270, "backtranscrib": 264, "backward": [12, 21, 30, 104, 107, 109, 207, 237, 260, 265, 303], "backward_algorithm": [106, 107], "backward_var": 109, "bacteri": [6, 16, 22, 238], "bacteria": [2, 22, 93], "bacteriologi": 2, "bacteriophag": 8, "bad": [21, 23, 251, 260, 278], "bailei": 2, "bailey1994": [2, 11], "baj87517": 25, "balaena": 272, "balaenoptera": 272, "balanc": [11, 21], "ball": 157, "baltimor": 216, "bam": [0, 23, 268, 270, 278], "bam_fil": [268, 270], "bamhi": [8, 207], "ban": [7, 65], "ban04711": 25, "band": [270, 275], "bang": 100, "bank": [88, 149, 214, 238, 245], "baq": 270, "bar": [4, 8, 103, 104, 270], "barbatum": 23, "barchartdistribut": [27, 98, 103], "barcod": 270, "barlei": 25, "barrier": 5, "bartek": [2, 26], "bartram": 7, "base": [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 123, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 160, 161, 162, 163, 165, 166, 169, 170, 171, 172, 173, 175, 176, 177, 179, 180, 182, 183, 184, 185, 187, 188, 189, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 230, 231, 232, 233, 234, 235, 236, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 268, 269, 270, 271, 272, 273, 274, 275, 278, 280, 281, 282, 283, 284, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 299, 302, 303, 304, 305], "base64binari": 197, "base_count": 93, "base_feature_format": [92, 93], "base_format": [92, 93], "base_id": [283, 287], "basefreq": [79, 80], "baselin": 104, "baseml": [17, 181, 192], "basemlerror": [181, 192, 193], "basetre": [13, 27, 181, 197, 198], "bashrc": 149, "basi": [4, 11, 95, 149, 295], "basic": [0, 1, 2, 3, 6, 8, 9, 11, 12, 15, 17, 18, 19, 21, 22, 23, 24, 67, 94, 101, 107, 139, 177, 218, 236, 237], "basicchromosom": [8, 27, 98], "bass": 263, "bassi": 262, "batch": [7, 12, 25, 59, 182, 202, 203, 274, 276], "batch_siz": [7, 25, 276], "bateman": 0, "batzogl": 32, "baum": [109, 121], "baumwelchtrain": [27, 106, 109], "bay": [9, 122, 127], "bb": 0, "bbcol": [0, 62], "bbr025": 252, "bbtacgcbb": 11, "bbtpgrp3": 0, "bc": [169, 181, 183, 198, 270, 278], "bc015878": 7, "bc067218": 7, "bcf": 270, "bchuh": 270, "bcif": 15, "bcjt": 251, "bct": [21, 93], "bdata": 83, "bdbbccdd": 0, "bdhkmnrvxy": 261, "bdist_rpm": 5, "be037100": 1, "beauti": 19, "becam": [3, 15], "becaus": [3, 6, 7, 8, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 30, 65, 66, 88, 95, 108, 139, 182, 183, 198, 209, 217, 218, 221, 222, 238, 251, 265, 269, 278], "becom": [4, 5, 6, 7, 11, 17, 20, 22, 23, 84, 94, 217, 218, 237, 245, 251, 255, 270], "bed": [13, 27, 30, 36, 38, 270], "bed12": [0, 38], "bed3": 0, "bed6": 0, "bedexample2": 0, "bedmaf": 0, "bedn": [0, 35, 36], "bedtobigb": [0, 36, 37], "been": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 19, 20, 21, 24, 25, 30, 32, 67, 68, 83, 94, 104, 108, 120, 122, 127, 132, 149, 154, 182, 199, 212, 217, 248, 251, 253, 260, 264, 270, 277, 278, 282, 290], "befor": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 65, 73, 83, 84, 88, 92, 99, 117, 121, 125, 169, 183, 198, 222, 237, 241, 252, 261, 270, 278, 290, 297], "beforehand": [25, 252], "beforeposit": [21, 27, 237], "begin": [0, 3, 4, 6, 7, 11, 15, 17, 20, 22, 30, 36, 44, 45, 56, 61, 89, 136, 169, 217, 230, 236, 237, 250, 251, 265, 279, 297], "beginn": 5, "begun": 20, "behav": [4, 15, 17, 20, 68, 135, 236, 237, 260], "behavior": [0, 4, 11, 16, 17, 20, 23, 30, 183, 217, 218, 237], "behaviour": [30, 64, 76, 260, 264, 288, 294, 297], "being": [1, 3, 4, 7, 8, 12, 13, 15, 16, 18, 21, 23, 30, 31, 32, 61, 65, 73, 108, 162, 182, 237, 260, 270, 278], "believ": 275, "belong": [4, 11, 13, 15, 32, 73, 84, 88, 93, 132, 272, 282, 288, 299], "below": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 16, 17, 19, 21, 22, 23, 24, 71, 72, 80, 90, 119, 149, 158, 169, 198, 203, 217, 251, 253, 263, 274, 278, 279, 288, 290], "bend": [15, 137], "benefit": [0, 1, 5, 6, 13, 15, 19, 158, 169, 217, 238, 278], "benner22": [13, 199], "benner6": [13, 199], "benner74": [13, 199], "benzoat": 113, "bep": 25, "berg": 265, "berkelei": [211, 212, 283], "berlin": 2, "bernard": 2, "bernstein": 149, "bertil": 32, "besid": [11, 217], "best": [2, 4, 5, 6, 11, 12, 13, 14, 15, 19, 20, 23, 24, 30, 32, 69, 73, 79, 80, 175, 182, 199, 216, 229, 238, 270, 297], "best_hit_overhang": [68, 69], "best_hit_score_edg": [68, 69], "bestn": 0, "bestscor": 270, "beta": [0, 4, 12, 13, 14, 15, 27, 30, 112, 120, 137, 152, 169, 172, 199, 211, 238, 241, 272, 280], "better": [4, 6, 7, 8, 13, 14, 15, 17, 71, 182, 237, 260, 261, 297], "between": [0, 3, 6, 7, 11, 13, 14, 15, 16, 17, 20, 21, 22, 30, 32, 35, 36, 56, 68, 69, 73, 80, 83, 94, 99, 100, 101, 104, 108, 109, 117, 127, 130, 132, 135, 138, 140, 143, 156, 161, 163, 166, 169, 172, 175, 176, 177, 182, 183, 186, 197, 198, 204, 209, 214, 217, 222, 226, 237, 238, 251, 261, 264, 265, 270, 278, 282, 289, 297, 299, 300], "betweenposit": [21, 27, 237], "bewar": [11, 21, 278], "beyer": [13, 30], "beyond": [8, 11, 20, 21, 30, 217], "bf": [11, 295], "bf_search": [177, 178, 180], "bfac": 152, "bfactor": [135, 152, 169], "bfile": 11, "bg": 11, "bg569293": 7, "bg_prob": 294, "bgcolor": [115, 117], "bgz": [23, 217, 238, 278], "bgzf": [23, 27, 217, 238], "bgzfblock": [27, 278], "bgzfreader": [27, 278], "bgzfwriter": [27, 278], "bgzip": [23, 278], "bia": [6, 229, 270], "bias": [237, 272], "bib": 252, "bibiserv": 32, "bibliograph": 7, "bibliographi": [26, 307], "bidiagon": 4, "bielefeld": 32, "bif72": 238, "bifurc": [17, 132, 183], "big": [0, 5, 6, 7, 12, 149, 204, 237, 278], "big_fil": 6, "bigarrow": 8, "bigb": [27, 30, 37, 38], "bigendian": 23, "bigger": [32, 207, 222], "biggest": 20, "bigmaf": [27, 30], "bigpsl": [27, 30], "bil285": 8, "bill": [12, 56, 59, 217, 226], "bin": [0, 6, 85, 265], "binari": [0, 1, 3, 6, 7, 23, 25, 27, 32, 36, 37, 38, 45, 54, 67, 68, 83, 145, 153, 182, 186, 197, 198, 202, 203, 238, 242, 247, 251, 252, 253, 254, 259, 260, 270, 278], "binary_charact": [181, 197, 198], "binary_cif": [15, 27, 133], "binary_constraint": [181, 182], "binarycharact": [27, 181, 197], "binarycif": 165, "binarycifpars": [15, 27, 133, 165], "bind": [0, 2, 11, 25, 53, 177, 185, 256, 260, 264, 272, 288, 295], "bindin": 0, "binomi": [2, 4], "bio": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 303, 306, 307], "bio_assembly_index": 172, "bioassembli": 172, "bioassmbli": 172, "bioch": [59, 226], "biochem": [53, 177, 264], "biochemistri": 264, "biochimica": 83, "biocomput": 3, "biocorba": 237, "biodatabas": 303, "bioentri": 303, "bioinf": 250, "bioinformat": [0, 2, 4, 5, 7, 8, 9, 15, 19, 20, 22, 32, 69, 73, 83, 152, 169, 182, 262], "bioinformatician": 15, "biojava": [6, 7, 9, 251], "biol": [0, 74, 129, 140, 149, 157, 264], "biolog": [2, 10, 15, 20, 22, 27, 75, 109, 149, 197, 236, 237, 272, 299, 301, 303], "biologi": [0, 2, 5, 7, 9, 19, 21, 23, 27, 32, 83, 130, 182], "biologist": [0, 7, 12, 15, 19, 21], "biomed": [2, 238, 250, 253], "biomedcentr": 218, "bionj": [181, 182], "bioperl": [6, 7, 9, 20, 66, 237, 238, 251, 255, 261, 262, 303], "biophysica": 83, "biopolym": [2, 264], "biopython": [0, 1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 30, 31, 32, 56, 65, 67, 68, 69, 70, 80, 81, 83, 84, 92, 104, 112, 113, 114, 118, 119, 152, 156, 158, 167, 168, 169, 171, 172, 177, 178, 181, 182, 198, 209, 210, 217, 226, 234, 236, 237, 238, 240, 249, 251, 253, 256, 264, 270, 274, 280, 281, 297, 298, 301, 302, 303, 304, 305, 306], "biopythondeprecationwarn": 27, "biopythonexperimentalwarn": 27, "biopythonparserwarn": 27, "biopythonwarn": [27, 147, 197, 236], "biopythooon": [7, 83], "biorubi": [9, 251], "biosci": 153, "bioscienc": 2, "bioseq": 301, "bioseqdatabas": [301, 302, 305], "biosoftwar": 242, "biospam": 24, "biospamtestaddit": 24, "biospamtestdivis": 24, "biosql": [7, 9, 19, 237, 306, 307], "biostar": 279, "biosynthesi": [23, 25], "biosystem": [238, 239], "biotech": 254, "biovar": [6, 8, 21, 238], "bipartit": [94, 182], "bipartition_filenam": [181, 182], "bipoython": 158, "birch": [2, 7], "birnei": [2, 237], "bisect": 263, "bisection_method": 263, "bisulfit": 270, "bit": [0, 3, 5, 6, 8, 11, 12, 13, 17, 19, 20, 23, 31, 68, 69, 71, 75, 133, 169, 182, 183, 238, 247, 251, 253, 270, 278, 283], "bit_scor": 3, "bitmap": [8, 104], "bitmask": 169, "bitscor": [20, 218, 226, 229, 234], "bitscore_raw": [20, 218], "bitwis": [0, 52], "bj": 83, "bjellqvist": 263, "bl": [30, 32], "bl_ord_id": 218, "black": [6, 8, 104, 183], "blackbriar": 0, "blackmould": 265, "blackshield": 32, "blanco": 7, "blank": [0, 5, 71, 139, 162, 214, 241, 256, 260], "blanklin": 206, "blast": [2, 5, 8, 9, 13, 26, 27, 32, 55, 67, 217, 219, 220, 221, 226, 229, 270, 274, 307], "blast_cutoff": 71, "blast_formatt": 69, "blast_frag": 20, "blast_hit": 20, "blast_hsp": 20, "blast_id": 218, "blast_qresult": 20, "blast_record": 3, "blast_record_copi": 3, "blast_recordt": 3, "blast_slic": [3, 20], "blast_tab": [217, 218], "blast_xml": [217, 218], "blastal": [3, 69], "blastallcommandlin": 69, "blastdb": [68, 70], "blastdb_vers": [68, 69], "blastio": [20, 27, 217, 221], "blastjson": 3, "blastn": [3, 13, 20, 30, 68, 69, 70, 71, 199, 218], "blastoutput2": 3, "blastoutput_db": 218, "blastoutput_program": 218, "blastoutput_refer": 218, "blastoutput_vers": 218, "blastp": [3, 13, 30, 68, 69, 70, 71, 199, 218], "blastpars": [27, 68, 71], "blastpgp": [3, 69, 71], "blastpgpcommandlin": 69, "blasttabindex": [217, 218, 219], "blasttabpars": [217, 218, 219], "blasttabwrit": [217, 218, 219], "blastx": [3, 68, 69, 70, 71, 218], "blastxml": 71, "blastxmlindex": [217, 218, 220], "blastxmlpars": [217, 218, 220], "blastxmlwrit": [217, 218, 220], "blat": [0, 2, 3, 20, 30, 45, 217, 221], "blat4": 221, "blat_frag": 20, "blat_hit": 20, "blat_hsp": 20, "blat_hsp2": 20, "blat_qresult": 20, "blatio": [20, 27, 217], "blatpslindex": [27, 217, 221], "blatpslpars": [27, 217, 221], "blatpslwrit": [27, 217, 221], "blatspec": 221, "blattner": 2, "bleasbi": 2, "bloack": 0, "block": [0, 2, 3, 7, 12, 13, 20, 23, 24, 27, 36, 37, 39, 46, 61, 62, 66, 68, 72, 73, 97, 128, 129, 220, 221, 222, 223, 224, 225, 226, 229, 230, 238, 250, 252, 253, 278], "block_siz": [218, 220], "block_start_offset": 278, "blockcount": [0, 36], "blocked_in": 72, "blocks_5": 13, "blocks_per_lin": [238, 245], "blocksiz": [0, 36, 37, 79, 80, 129, 221], "blog": 61, "blosum": [13, 14, 32], "blosum45": [13, 68, 70, 182, 199], "blosum50": [13, 199], "blosum62": [3, 11, 13, 14, 30, 32, 68, 69, 182, 199, 290, 297], "blosum62mt": 32, "blosum80": [68, 70, 199], "blosum90": 199, "blown": 59, "blue": [8, 9, 15, 17, 99, 104, 169, 181, 183, 198], "blunt": 206, "bm": [0, 53, 145], "bmc": [2, 32, 69], "bmedi": 206, "bmp": [8, 104], "bmr": 32, "bob": [2, 124], "bodi": 8, "bogusparamet": 80, "boil": 23, "bolser": 2, "bommarito": 264, "bond": [136, 144, 152, 158, 160, 169, 172, 265, 272], "bond_count": 172, "bond_ord": 172, "bond_rot": [133, 152, 169], "bond_set": [133, 152, 169], "bondradiu": 158, "bone": 7, "bonu": [6, 278], "book": [6, 7, 17, 83, 218], "bool": [15, 54, 135, 136, 139, 144, 149, 152, 155, 158, 160, 162, 166, 168, 169, 176, 183, 197, 260], "boolean": [6, 17, 32, 67, 69, 80, 94, 104, 127, 129, 143, 148, 151, 152, 154, 162, 169, 182, 183, 197, 218, 221, 229, 236, 237, 253, 260, 270, 297, 303], "boot": [181, 182], "bootlabel": [30, 32], "bootseq": 12, "bootstrap": [12, 27, 30, 32, 80, 128, 129, 132, 181, 182, 183, 186, 197, 238], "bootstrap_branch_length": [181, 182], "bootstrap_consensu": [27, 181, 186], "bootstrap_se": [181, 182], "bootstrap_tre": [27, 181, 186], "border": [8, 104], "bore": 11, "botani": 7, "both": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 20, 21, 23, 25, 30, 32, 56, 59, 63, 65, 69, 71, 80, 104, 109, 135, 158, 169, 182, 183, 188, 197, 214, 217, 218, 221, 222, 229, 234, 237, 251, 260, 264, 270, 278, 290, 297, 299], "bother": 15, "botstein": 2, "bottom": [21, 99, 104], "bought": 6, "bound": [8, 13, 21, 104, 115, 117, 156, 197, 198, 274], "boundari": [11, 21, 35, 46, 51, 61, 237], "bourn": 166, "boutfeat": [79, 80], "bowden": 2, "box": [8, 104], "bp": [0, 6, 7, 8, 11, 21, 23, 30, 83, 207, 222, 270, 278, 283], "bp_length": 99, "bpatomarrai": 169, "bq": 270, "br": 278, "bracket": [4, 215], "bracteata": 23, "brad": [2, 26], "bradtiana": 23, "bradtianaa": 23, "branch": [32, 80, 132, 182, 183, 186, 197, 198], "branch_label": 17, "branch_length": [13, 17, 181, 183, 184, 187, 189, 197, 198, 199], "branch_length_onli": 190, "branch_length_unit": 197, "branch_stdev": 183, "branchcolor": [27, 181, 183, 197], "branchlength": 132, "branchlength2support": [128, 132], "branchlength_sd": 132, "branchlengths_onli": 132, "brandon": 2, "brassica": 238, "breadth": [17, 180, 183], "break": [0, 3, 6, 7, 8, 13, 15, 17, 18, 19, 23, 66, 94, 99, 149, 158, 169, 198, 207, 222, 242, 245, 251, 255, 260, 278], "breez": 20, "brenner": [30, 32], "breslauer": 264, "brian": 2, "brice": 149, "bridg": [15, 80, 137, 203, 265, 272], "brief": [7, 9, 15, 32, 79, 80, 123], "briefli": [3, 7, 19, 23, 32], "bright": [23, 100], "bring": [12, 23, 278], "broad": [2, 23], "broken": 8, "brought": 17, "brown": [2, 8, 32, 183], "browser": [3, 7, 10, 35, 61], "bruce": 2, "brudno": 32, "brush": 19, "brute": [6, 21], "bryan": 2, "br\u00fcssow": 2, "bs_tree": 132, "bsd": 9, "bsequenc": [12, 67, 79, 80], "bsh1236i": 206, "bshfi": 206, "bsni": 206, "bspani": 206, "bsthhi": 206, "bstree": 132, "bsubtili": 13, "bt": 275, "btg299": 2, "btgst": 0, "bth078": [2, 73], "bth349": 2, "btk021": 2, "btop": [55, 218], "btp163": 2, "btp352": 2, "btpe": 4, "btw": 15, "bu": 286, "bucket": 146, "bucket_s": 146, "buffer": [0, 129, 168], "bug": [17, 24, 42, 130, 210, 218, 222, 226, 277], "bug6yxxskwecffh0l08jzalghq": 238, "build": [3, 5, 6, 8, 23, 24, 25, 27, 32, 45, 53, 60, 67, 69, 80, 108, 109, 148, 162, 166, 169, 182, 186, 193, 195, 196, 198, 199, 209, 217, 237, 238, 246, 270, 279, 285, 303], "build_atomarrai": [133, 169], "build_edraarrai": [133, 169], "build_peptid": [15, 154], "build_tre": [181, 199], "builder": 108, "built": [0, 1, 3, 5, 6, 9, 11, 12, 15, 19, 20, 21, 22, 23, 24, 27, 32, 61, 67, 169, 183, 209, 221, 260, 274, 278, 283, 299], "builtin": [91, 278], "bulb": 264, "bulk": [16, 20], "bullbrees": 265, "bunch": [7, 23, 103, 123, 182], "bundl": [8, 36, 37, 149, 251], "burden": 67, "buri": 5, "burrow": 270, "bussel": 124, "buster": [11, 283, 286, 293], "butterworth": 7, "bwa": [0, 270], "bwaaligncommandlin": [268, 270], "bwabwaswcommandlin": [268, 270], "bwaindexcommandlin": [268, 270], "bwamemcommandlin": [268, 270], "bwasampecommandlin": [268, 270], "bwasamsecommandlin": [268, 270], "bwasw": 270, "bwasw_cmd": 270, "bwt": 270, "bwtsw": 270, "by_seri": 7, "bypass": 13, "byte": [0, 3, 6, 17, 22, 23, 30, 36, 90, 91, 104, 150, 164, 197, 219, 220, 221, 225, 226, 232, 236, 238, 241, 245, 246, 247, 249, 251, 256, 257, 260, 278, 303], "bytearrai": [0, 22, 236, 303], "byteord": 247, "bytesio": 238, "bytestream": 90, "bz2": 23, "bzip": 11, "bzip2": [1, 23], "c": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 17, 19, 22, 23, 29, 30, 31, 32, 46, 62, 66, 67, 69, 73, 76, 80, 84, 118, 129, 135, 137, 139, 140, 146, 149, 152, 154, 157, 159, 166, 168, 169, 172, 175, 177, 182, 183, 218, 222, 229, 236, 247, 251, 260, 261, 263, 264, 268, 269, 270, 278, 280, 288, 296, 297, 299], "c00017": 112, "c00023": 112, "c00099": 112, "c00294": 112, "c00298": 112, "c00348": 112, "c00349": 112, "c01": [16, 299], "c01386": 112, "c02": 299, "c03": [16, 299], "c05": 299, "c1": [0, 30], "c12": 299, "c2": [0, 30], "c2h2": 11, "c4": [166, 222], "c4fbb762c4a87ebd": 262, "c_": 11, "c_alpha": 153, "c_color": 8, "c_rec": 8, "c_seq": 264, "c_ug268a": 244, "ca": [0, 11, 25, 86, 90, 135, 136, 140, 141, 152, 154, 156, 162, 166, 169, 172, 273], "ca1": 15, "ca2": 15, "ca3": 15, "ca_a_0": 169, "ca_b_0": 169, "ca_bind": 272, "ca_coord": [15, 140, 169], "ca_depth": [15, 27, 133, 156], "caa": [0, 22], "caa63439": 21, "caa90861": 21, "caaa": [0, 13, 30], "caaaaaaaaaaaaaaaacacaaaaaaaaaaaaaaaaaaaa": 56, "caaaacacaaacag": 253, "caaacaacaacaaaaaaaacaaaaaaaaaaaaaaaaaaaa": 56, "caaacc": 12, "caagccctgc": 0, "caagccctgcgcgctcagccggagtgtcccgggccctgctttccttttc": 0, "caagtggtatcaacgcagag": 253, "caatgccgga": 7, "cab531": 21, "cabio": 2, "cac": 22, "caccuaacaauaaguaagucagcagugagau": 66, "cacga": 66, "cacgagaggagcggaggcgaggggtgaacgcggagcactccaatcgctcccaactagaggtccacccaggacccagagacctggatttgaggctgctgggcggcagatggagcgatcagaagaccaggagacgggagctggagtgcagtggctgttcacaagcgtgaaagcaaagattaaaaaatttgtttttatattaaaaaa": 0, "cacgtg": 11, "cacgtgatgtcctc": 11, "cacgtgccgcgcgc": 11, "cacgtgggaggtac": 11, "cach": [0, 6, 7, 36, 44, 45, 84, 149, 169, 265, 278, 297], "cactacea": 7, "cacti": 7, "cactu": 12, "cad": [13, 15], "cadist": [15, 169], "cag": 22, "cagaaaa": 222, "cagcccgggggatccactagttctagagcggccgccaccgcggtggagctc": 206, "caggctgcgcggtttctatttatgaagaacaaggtccgtatgatagttgattgtcatgca": 260, "cagttcgccacaa": 199, "cagttttcgttaagagaacttaacattttcttatgacgtaaatga": 23, "cai": 261, "caiatcasyp": 0, "cal_dn_d": [27, 279, 281], "calc_affine_penalti": [27, 297], "calc_allele_genotype_freq": [201, 202], "calc_angl": [15, 27, 133, 176], "calc_dihedr": [15, 27, 133, 176], "calc_diversities_fis_with_ident": [201, 202], "calc_diversities_fis_with_s": [201, 202], "calc_fs_exposur": 15, "calc_fst_al": [201, 202], "calc_fst_pair": [201, 202], "calc_hs_exposur": 15, "calc_ibd": [201, 203], "calc_ibd_diplo": [201, 202], "calc_ibd_haplo": [201, 202], "calc_rho_al": [201, 202], "calc_rho_pair": [201, 202], "calceolu": 7, "calcium": [15, 172, 272], "calcul": [0, 6, 9, 11, 17, 20, 22, 23, 27, 30, 31, 32, 34, 36, 44, 45, 52, 73, 80, 107, 108, 109, 120, 122, 127, 129, 132, 134, 135, 137, 141, 145, 156, 157, 166, 169, 175, 176, 182, 183, 186, 194, 199, 202, 203, 216, 221, 257, 261, 262, 263, 264, 265, 267, 270, 281, 282, 283, 287, 290, 294, 297, 299, 300], "calculate_consensu": [11, 12, 283, 290], "calculate_dn_d": [13, 27, 30, 34], "calculate_dn_ds_matrix": [13, 27, 30, 34], "calculate_pseudocount": [11, 283, 287], "calibr": [53, 270], "calif": 83, "california": [2, 6, 197], "californica": 197, "californicum": 23, "calippu": 56, "caljac1": 0, "caljac3": 0, "caljac3tocaljac4": 0, "caljac4": 0, "call": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 21, 22, 23, 24, 25, 30, 41, 45, 49, 54, 56, 58, 59, 60, 61, 64, 66, 67, 68, 71, 73, 80, 84, 85, 89, 99, 104, 108, 119, 121, 122, 135, 139, 143, 149, 151, 153, 156, 157, 158, 168, 169, 176, 182, 185, 197, 199, 202, 203, 205, 209, 217, 236, 237, 238, 241, 245, 246, 247, 248, 250, 251, 252, 253, 255, 260, 264, 265, 268, 270, 271, 274, 277, 278, 281, 283, 287, 288, 293, 297, 298, 299, 303, 305], "callabl": [183, 251], "callback": [3, 20, 120, 121, 122, 217, 238, 297], "calledprocesserror": 67, "caller": [68, 199, 270, 277], "calmd": 270, "calmd_cmd": 270, "calpha": 154, "cam": [15, 209, 210, 211, 212], "camacho": 69, "cambridg": 2, "came": [93, 278], "camp_phospho_sit": 25, "can": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 35, 45, 46, 51, 54, 56, 59, 60, 61, 66, 67, 68, 69, 71, 72, 73, 80, 81, 83, 84, 88, 89, 91, 92, 94, 99, 101, 102, 104, 107, 108, 109, 119, 121, 130, 134, 135, 137, 140, 146, 148, 149, 152, 154, 157, 158, 169, 172, 180, 182, 183, 185, 186, 197, 199, 202, 205, 207, 209, 210, 211, 212, 213, 214, 217, 218, 221, 222, 229, 236, 237, 238, 241, 242, 245, 246, 247, 249, 250, 251, 252, 253, 254, 256, 258, 260, 261, 263, 264, 265, 269, 270, 271, 272, 273, 274, 278, 281, 288, 289, 290, 291, 292, 297, 298, 299, 305, 306, 307], "cancerchromosom": 7, "candid": [6, 21, 270], "canfam2": 0, "canfam3": 22, "cannarozzi": 2, "cannot": [0, 3, 4, 7, 12, 15, 23, 27, 30, 45, 56, 68, 72, 152, 169, 188, 190, 198, 236, 238, 246, 251, 269, 278], "canon": [15, 86, 90, 99, 154, 272, 275], "cantor": 182, "canva": 105, "cap": [27, 89, 270], "capabl": [15, 95, 99], "capit": [9, 11, 20, 198, 202, 203], "capmapq": 270, "cappbuild": [15, 27, 133, 154], "capqcoef": 270, "capsid": 15, "capsmap": [27, 72], "caption": 99, "captur": [2, 11, 12, 15, 67, 169, 197], "car": 122, "carbohyd": 272, "carbohydr": 0, "carbon": [135, 169, 172], "carboxyl": [25, 79, 80], "care": [3, 4, 5, 6, 7, 12, 15, 17, 21, 23, 24, 109, 130, 237, 243, 274], "carlsward": 7, "carolin": 2, "carri": [65, 73], "cartesian": 169, "cartn_i": 15, "caryophyllal": 7, "casari": 265, "casava": [238, 251], "casbon": [7, 71], "cascad": [17, 197], "case": [0, 1, 3, 4, 7, 8, 9, 11, 12, 13, 17, 19, 20, 21, 23, 24, 30, 32, 33, 38, 51, 56, 67, 68, 69, 70, 73, 83, 94, 95, 104, 107, 117, 135, 154, 162, 169, 176, 182, 183, 197, 205, 214, 217, 218, 221, 222, 226, 234, 236, 237, 238, 241, 251, 253, 260, 261, 262, 270, 275, 283, 288, 290, 297, 298], "caselect": [15, 169], "casual": 17, "cat": [22, 181, 182, 270, 278], "cataatttga": 7, "catalyst": 177, "catalyt": [25, 53, 86], "catalyz": 118, "catch": [8, 23, 25, 32, 278], "catcnagatgacactacgactacgactcagactac": 256, "categor": [3, 100, 182], "categori": [5, 6, 7, 79, 80, 90, 100, 182, 248, 273], "catergori": [79, 80], "catgggcaaatattatacgcaaggcgacaaggtgctgatgccgctggcgattca": 260, "cath_huma": 0, "cath_human": [0, 56], "cation": 264, "catmix": 182, "catt": 30, "cattatgttc": 7, "cattctggaa": 7, "cattgttgagatcacataataattgatcgagttaatctggaggatctgtttact": [19, 23], "catttattgc": 7, "caught": [21, 27, 135, 151], "caus": [3, 4, 13, 15, 20, 21, 68, 72, 92, 169, 182, 251, 270], "caution": 237, "cautiou": 21, "caven": [2, 11, 283], "cavener1987": [2, 11], "caviti": 158, "cb": [15, 53, 141, 152, 169], "cb_at_origin": 15, "cbcbgggttbbcgggceecttsbeebshhhhsttccbsscssccbcbgggttbccsttceecttsbeebshhhhsttccb": 0, "cbcbgggttbbcgggceecttsbeebshhhhsttccbsscssccbcbgggttbccsttceecttsbeebshhhhsttccbsscssccbcbgggttbccgggceecttsbeebshhhhsttccbsscssccccbtttttbccsttceecttsceebshhhhsttccbsscc": 0, "cbeta": 158, "cc": [0, 11, 22, 25, 30, 53, 86, 90, 222, 295], "cc_author": 88, "cc_ft_desc": 88, "cc_ft_kei": 88, "cc_matrix_typ": 88, "cc_max_repeat": 88, "cc_scaling_db": 88, "cc_site": 88, "cc_skip_flag": 88, "cc_taxo_rang": 88, "cc_version": 88, "cca": 22, "ccaaac": 12, "ccaaccacaacccacaccccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccacaaccccacacccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccaccacccacaccccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccaccaccccacacccaaaaaaaaaaaaaaaaaaaa": 56, "ccaaccccccccccacacccaaaaaaaaaaaaaaaaaaaa": 56, "ccacca": 12, "ccaccccccacccccaca": 0, "ccacgaatat": 7, "ccacgctaagagaagtgccggag": 283, "ccatg": 11, "ccatggcccgggggggagctccagctgccatagctattcgaactatagcttaag": 207, "ccc": 22, "cccaaa": 12, "cccaac": 12, "cccaagtgttctgatagctaatgtgaaaaagaagcatgtgcccaccagtaagctttgtgg": 0, "cccaagtgttctgattgcctctgtgaaaaagaaacatgggcccgctaataagatttgcaa": 0, "cccacc": 12, "cccacccccccccacaccccaaaaaaaaaaaaaaaaaaaa": 56, "cccc": [0, 4, 13, 30], "ccccaa": 12, "ccccaaaaaaaaaaagggg": [0, 13, 30], "ccccagcattctggcagacacagtg": 0, "ccccatttg": [30, 68], "ccccca": 12, "ccccccc": [0, 13, 30], "cccccccaaaaaaaaaaagggggg": [0, 13, 30], "ccccccccccc": 0, "cccccccccccccccccccccccccc": 0, "ccccccccccccccccccccccccccccccccccccccc": 0, "ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccceeccchhhc": 0, "cccccccccccccccceecccceeccccccccccccccccccccccccccccccccccccccccceeccccccccccccc": 0, "cccccccccccccccceecccceeccccccccccccccccccccccccccccccccccccccccceecccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccceeccchhhcccccccccccc": 0, "cccccccgggggg": [0, 13, 30], "ccccgggg": [0, 13, 30], "cccggg": 8, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaag": 20, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttc": 3, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttccttt": [3, 20], "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttccttttagagg": 3, "ccctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttccttttagaggg": 20, "ccctctagagggaagcgctttctgtggtctgaaagaaaagaaagtgcttc": 3, "cccttcttgtcttcagcgtt": 21, "cccttcttgtcttcagcgttctcc": 21, "cccttcttgtcttcagcgtttctcc": [21, 238, 251], "cccttttgggtttnttnttggtaaannnttcccgggtgggggnggtnnngaaa": 238, "cccxc": [0, 30], "cccxccc": 30, "cccxccxc": [0, 30], "ccg": [6, 22], "ccgcc": 241, "ccgcccaaagt": 222, "ccgcg": 30, "ccgg": [30, 66], "ccgggccgtactttcctttt": 0, "ccggttttt": 0, "ccgtatagga": 7, "ccgtg": 11, "ccguaaa": 66, "ccp4": 15, "ccp4mg": 15, "cct": 22, "cctact": 12, "cctatacctttctttcatgagaa": 0, "cctatacctttcttttatgagaa": 0, "cctatttaat": 278, "cctctacagggaagcgctttctgttgtctgaaagaaaagaaagtgcttcc": 3, "cctgaatgtg": 22, "cctgtacc": 0, "ccz78521": 23, "cd": [0, 3, 7, 8, 21, 22, 23, 38, 68, 94, 169, 236, 237, 238, 245, 260, 275, 278], "cd1": 169, "cd2": 169, "cdao": [17, 27, 181, 185, 188], "cdao_to_obo": [27, 181, 188], "cdaoio": [27, 181], "cdata": [4, 73], "cdd": 7, "cdd_delta": 69, "cdf_chi2": [181, 192, 194], "cdg": 0, "cdii": 206, "cdkl": 13, "cdna": 25, "cdna2genom": [0, 42, 222], "cdot": 4, "cdt": [4, 73], "ce": [166, 169], "ce1": 169, "ce2": 169, "ce3": 169, "cealign": [27, 133], "cel": [28, 29], "celest": 2, "celfil": [24, 27, 28], "celi": 263, "cell": [0, 2, 4, 10, 16, 73, 90, 162, 172, 263], "celldata": [4, 73], "cellosauru": [27, 85], "cellular": 7, "center": [4, 8, 15, 30, 32, 73, 104, 135, 139, 146, 169, 175, 265], "center_of_mass": [133, 135, 139], "centr": [7, 8, 104, 115, 117, 141, 263], "central": [5, 7, 19, 22, 104, 123, 140, 169, 253, 265], "centroid": 73, "cephalotaxu": 17, "certain": [5, 8, 11, 12, 15, 17, 19, 21, 23, 67, 102, 139, 182, 203, 204, 238, 299], "cf": [86, 209, 211, 216], "cfoi": 206, "cfreq": [13, 34, 281], "cg": [0, 11, 15, 30, 169, 182, 297], "cg1": 169, "cg2": 169, "cga": [22, 30, 236], "cgactcagaggtt": 283, "cgactcgcgcttacaagg": 283, "cgat": 30, "cgatcg": 30, "cgatcgagtgaatccggaggaccggtgtactcagctcaccgggggcattgctcccgtggt": 23, "cgaut": 236, "cgc": [19, 22, 23], "cgcgc": 241, "cgcgtg": 11, "cgct": 30, "cgctaaaagctaggatatatccgggtagctag": 22, "cgg": [22, 30], "cggagccagcgagcatatgctgcatgaggacctttctatcttacattatggctgggaatc": 238, "cggagccagcgagcatatgctgcatgaggacctttctatcttacattatggctgggaatcttactctttc": 238, "cggccgggcctctcatcggt": 253, "cgggatccca": 249, "cggt": [0, 30], "cggttttt": 0, "cgi": [3, 19, 22, 85, 209, 253, 265], "cgl": 15, "cglaacasyp": 0, "cgt": [22, 30, 260, 279], "cgta": 264, "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgatgagaccgtgg": [19, 23], "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgatgagaccgtggaataaa": 23, "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgatgagaccgtggaataaacgatcgagtg": [19, 23], "cgtaacaaggtttccgtaggtgaacctgcggaaggatcattgttgagatcacat": 23, "cgtac": 270, "cgtc": 241, "cgtcgcaatt": 7, "cgtgtatgccctaagctgagcccgtcg": 30, "cgtt": 30, "cgttcca1agatgtgggcatgagcttac": 264, "cgttccaaagatgtgggcatgagcttac": 264, "cgu": [66, 260], "cguuccaaagaugugggcaugagcuuac": 264, "cguuucuacaa": 66, "cguuucuacaaggug": 66, "cgvsnfvst": 0, "ch": 263, "ch2": 169, "ch34": 2, "chaaa": 0, "chain": [2, 12, 13, 27, 30, 128, 130, 132, 133, 134, 135, 137, 138, 139, 140, 143, 144, 146, 148, 149, 152, 154, 155, 156, 157, 158, 159, 160, 162, 168, 169, 170, 172, 173, 176, 184, 187, 189, 214, 215, 248, 250, 272], "chain_a": 15, "chain_count": 172, "chain_id": [15, 134, 137, 138, 162, 172], "chain_indic": 172, "chain_list": 15, "chain_nam": 172, "chainexcept": [27, 128, 130], "chainid": [137, 138, 152, 168, 214, 215], "chainselector": [27, 133, 138], "chalcon": [21, 23, 25], "challeng": 19, "chanc": [3, 6, 12, 15, 68], "chang": [2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 17, 19, 21, 23, 26, 27, 30, 34, 68, 70, 80, 83, 84, 85, 103, 108, 109, 126, 145, 149, 152, 158, 162, 169, 176, 177, 182, 183, 191, 217, 236, 237, 241, 260, 261, 265, 270, 277, 280, 297, 303], "changed_this_week": 15, "changedir": 24, "channel": [8, 105], "chaperon": 104, "chapman": [2, 7, 9, 26], "chapman2000": [2, 9], "chapter": [0, 3, 5, 6, 7, 8, 11, 12, 13, 14, 16, 17, 19, 20, 21, 22, 23, 24, 56, 236, 238], "chapter4": 83, "char": [0, 15, 36, 97, 134, 146, 152, 159, 169, 176, 197, 236, 260, 297], "chara": 297, "charact": [0, 4, 6, 11, 12, 13, 14, 15, 16, 17, 22, 23, 30, 31, 32, 38, 50, 51, 56, 65, 66, 83, 84, 85, 89, 94, 129, 176, 182, 197, 198, 214, 236, 238, 241, 244, 248, 250, 251, 252, 253, 260, 261, 264, 269, 278, 281, 290, 297, 299], "character": 25, "characterdatahandlerescap": [83, 84], "characterdatahandlerraw": [83, 84], "characterist": [15, 17, 175, 183, 272], "charb": 297, "charbuff": [27, 128, 129], "charg": [12, 13, 15, 80, 135, 162, 172, 263, 265], "charge_at_ph": [261, 263, 265], "charit": 149, "charl": 2, "charlist": 129, "charpartit": 129, "chars_to_ignor": [12, 31], "charset": 129, "chart": [8, 103], "chchhhhcccctcccttchhhhhhhhhhhhhhhhhhhhctt": 12, "check": [0, 3, 4, 6, 7, 9, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 32, 68, 70, 76, 80, 83, 84, 104, 119, 125, 129, 130, 134, 136, 139, 140, 148, 152, 154, 155, 168, 169, 182, 183, 188, 193, 222, 236, 237, 251, 253, 260, 264, 270, 303], "check_output": 67, "checkpoint": [69, 181, 182], "checksum": [27, 238, 261], "chem": [0, 264], "chem_correct": [27, 261, 264], "chemcomp": 172, "chemic": [16, 112, 117, 119, 214, 264, 265, 272], "chen": 264, "cheng": 2, "chenna": 32, "chenopodium": 3, "chester": 264, "chhhhhhtt": 0, "chi": [2, 15, 152, 169, 194], "chi1": [15, 152, 169], "chi2": [152, 169, 181, 182, 192, 202], "chi3": [152, 169], "chi4": [152, 169], "chi5": [152, 169], "chicken": 30, "child": [12, 15, 17, 130, 131, 135, 139, 155, 159, 169, 179, 180, 183, 185, 197, 209], "child_dict": [133, 139], "child_edg": [178, 179, 180], "child_ent": 15, "child_id": 15, "child_list": [15, 133, 139], "children": [15, 17, 135, 139, 157, 178, 179, 180, 183, 197, 198, 209, 213, 252], "chimer": 270, "chimera": [15, 158], "chimp": [0, 22], "chimpanze": [0, 30], "chip": [11, 288], "chiral": [15, 169], "chitin": 0, "chix": 169, "chloroplast": [7, 23, 272, 278], "chn": [168, 169], "chn1": 15, "cho1": [11, 291], "cho2": [11, 291], "choic": [6, 9, 11, 12, 15, 17, 20, 22, 23, 100, 237, 290], "choli": 0, "choos": [3, 4, 6, 7, 8, 11, 13, 20, 23, 30, 80, 287], "chop": 138, "chosen": [4, 13, 76, 152, 260, 261, 269, 270], "chr": [8, 251], "chr1": [0, 13, 30, 36, 37, 38], "chr10": 0, "chr14": 22, "chr18": 0, "chr19": [0, 20], "chr2": [0, 13], "chr22": 0, "chr3": [0, 13, 22, 45], "chr4": [0, 13, 22], "chr6": [0, 22], "chr7": [0, 22], "chr8": [0, 22], "chr9": 0, "chr_diagram": 8, "chr_i": 8, "chr_ii": 8, "chr_iii": 8, "chr_iv": 8, "chr_percent": 99, "chr_v": 8, "christian": [2, 259], "christoph": 2, "chrom": [0, 13, 36], "chromatogram": 269, "chromend": [0, 36], "chromosom": [0, 3, 7, 13, 22, 23, 27, 30, 36, 37, 38, 46, 61, 98, 99, 102, 103, 197, 238, 245, 270, 275], "chromosome_nam": 99, "chromosomecount": [27, 98, 102], "chromosomeseg": [8, 27, 98, 99, 102], "chromsiz": 0, "chromstart": [0, 36], "chrun_ki270385v1": 13, "chrun_ki270392v1": 13, "chrun_ki270394v1": 13, "chrun_ki270423v1": 13, "chs3_brofi": [23, 85], "chung": 2, "chunk": [0, 23, 30, 94], "chunksiz": 290, "chy": 0, "chykaenaavqvldsvnitlnaedelknavglvrpvsvafqvi": 0, "chykaenaavqvldsvnitlnaedelknavglvrpvsvafqvidgfrqyksgvytsdhcgttpddvnhavlavgygvengv": 0, "chylomicron": 25, "ci": [11, 123, 283, 286], "cic": [15, 169], "cic2": [15, 169], "cid": 265, "cif": [15, 170, 173, 214, 238, 248], "cifatomiter": [27, 238, 248], "cifseqresiter": [27, 238, 248], "cifsyntax": 170, "cigar": [0, 42, 55, 217, 223], "cin": 123, "cine": 245, "circl": [8, 99, 117], "circle_cor": [8, 104], "circleci": 84, "circular": [8, 21, 93, 104, 237, 250, 261, 278], "circumv": [7, 152], "citat": [83, 87, 153, 272], "citation_1": 83, "cite": [7, 9, 264], "citi": 73, "ciz78533": [19, 23], "cj": 7, "ckf": 0, "ckfqpgkaigfvkdvanitiydeeamveavalynpvsfafevt": 0, "ckfqpgkaigfvkdvanitiydeeamveavalynpvsfafevtqdfmmyrtgiysstschktpdkvnhavlavgygekngi": 0, "cl": [0, 53, 54, 84, 122, 197, 209, 211, 237], "cl0020": 53, "cl0049": 0, "cla": [6, 27, 32, 209, 211], "cla_handl": 209, "clade": [13, 25, 27, 132, 181, 183, 184, 185, 186, 187, 189, 190, 197, 198, 199], "clade_rel": [181, 197, 198], "claderel": [27, 181, 197], "cladist": 129, "claim": 265, "clan": [0, 53], "clarifi": [15, 21, 22], "clash": 169, "class": [2, 4, 6, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 24, 25, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 158, 160, 161, 162, 163, 165, 166, 169, 170, 171, 172, 173, 175, 176, 177, 179, 180, 182, 183, 184, 185, 186, 187, 188, 189, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 219, 220, 221, 223, 224, 225, 226, 228, 230, 231, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 263, 265, 269, 270, 271, 272, 273, 275, 278, 280, 281, 282, 283, 284, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 299, 302, 303, 304, 305], "classic": [11, 15, 30, 69, 152, 169, 283, 291], "classic_b": [152, 169], "classif": [7, 9, 11, 53, 93, 113, 120, 127, 140, 209, 210, 211, 272, 282, 295], "classifi": [13, 27, 30, 84, 120, 122, 127, 140, 282], "classmethod": [30, 36, 183, 185, 188, 190, 197, 280, 281], "classnam": [10, 113], "classproperti": 84, "claus": 9, "clavata": 23, "claw": 250, "clean": [15, 56, 60, 92, 95, 238, 246, 251], "clean_valu": [92, 95], "cleandata": 17, "cleaner": [92, 95], "cleanup": 172, "clear": [6, 9, 12, 15, 25, 67, 119, 169, 198, 260, 274], "clear_ic": [133, 169], "clear_transform": [133, 169], "clearer": [8, 238], "clearest": 6, "clearli": [5, 12, 15, 24], "cleav": 72, "clever": 6, "clf1_schpo": 53, "click": 5, "client": [68, 183, 197], "climb": 182, "clin": 264, "cline": [32, 67, 69, 80], "clip": [0, 6, 52, 253, 270], "clip11262": 8, "clip_qual_left": 253, "clip_qual_right": 253, "clog": 24, "clone": [7, 21, 25, 93, 103, 206, 238, 275], "cloner": 259, "close": [1, 3, 7, 8, 9, 11, 13, 20, 22, 23, 24, 27, 30, 56, 61, 68, 83, 91, 129, 181, 182, 217, 238, 241, 250, 252, 253, 278, 298, 301, 303], "closer": [4, 20, 25, 92], "closest": [4, 176], "closur": 61, "cloud": 4, "clu": [32, 229], "clustal": [0, 12, 13, 23, 27, 30, 32, 56, 57, 238, 246], "clustal_consensu": 0, "clustal_data": 12, "clustalio": [27, 56], "clustaliter": [27, 56, 57], "clustalo": 32, "clustalomega_clin": 32, "clustalomegacommandlin": [30, 32], "clustalout": [30, 32], "clustalw": [5, 9, 13, 19, 30, 32, 40, 50, 56, 57, 238], "clustalw2": [12, 32], "clustalw_aln": 32, "clustalw_clin": 32, "clustalw_ex": 12, "clustalwcommandlin": [30, 32], "clustalwrit": [27, 56, 57], "clustalx": 12, "cluster": [2, 7, 9, 11, 13, 24, 25, 26, 27, 30, 32, 123, 182, 209, 217, 275, 283, 286, 288, 293, 307], "cluster1": [30, 32], "cluster2": [30, 32], "cluster_num": 229, "cluster_threshold": [181, 182], "cluster_threshold_fast": [181, 182], "clusterbust": [27, 283], "clustercentroid": [4, 27, 73], "clusterdist": [4, 27, 73], "clusterid": [4, 73], "clusteringout": [30, 32], "clusters": [30, 32], "clutter": 251, "clw": [30, 32], "clwout": [30, 32], "clwstrict": [30, 32], "clwstrictout": [30, 32], "cm": 8, "cmap": [15, 169], "cmask": [4, 73], "cmbi": [15, 137, 250], "cmd": [3, 12, 17, 32, 67, 69, 80, 182, 253, 270], "cmeyegeeac": 0, "cml": 17, "cmodulo": [206, 207], "cmp_scc": [27, 209], "cn": 123, "cnr": 15, "co": [11, 94, 269, 295], "coa": 113, "coatb_bpi2": 12, "coatb_bpi22": 12, "coatb_bpif": 12, "coatb_bpif1": 12, "coatb_bpik": 12, "coatb_bpm1": 12, "coatb_bpm13": 12, "coatb_bpzj": 12, "coatb_bpzj2": 12, "cochran": [2, 4], "cock": [2, 6, 7, 9, 26, 133, 251], "cock2009": [2, 9], "cock2010": [2, 6, 9], "cockerham": [202, 203], "codata": 32, "code": [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 34, 49, 55, 59, 64, 65, 67, 68, 69, 70, 71, 74, 76, 79, 80, 81, 82, 83, 84, 85, 87, 89, 90, 91, 92, 94, 100, 106, 111, 112, 113, 114, 115, 119, 120, 122, 123, 124, 131, 136, 137, 138, 139, 143, 149, 152, 154, 158, 162, 165, 166, 169, 172, 175, 181, 183, 196, 197, 198, 201, 204, 205, 209, 214, 215, 222, 236, 237, 238, 241, 248, 250, 251, 260, 261, 268, 272, 273, 274, 276, 278, 279, 280, 281, 282, 297, 298, 304, 305, 306], "codec": 236, "coded_bi": [3, 68], "codeml": [17, 181, 192], "codeml_nssites_al": 17, "codemlerror": [181, 192, 195], "codeset": 0, "coding2cod": [42, 222], "coding_and_optim": 69, "coding_dna": [22, 236], "coding_dna2": 236, "coding_dna3": 236, "coding_sequ": 6, "codon": [0, 2, 6, 21, 22, 30, 32, 34, 36, 76, 195, 222, 236, 237, 261, 279, 280, 281], "codon_align": 13, "codon_aln": [279, 280], "codon_seq1": 281, "codon_seq2": 281, "codon_start": [7, 21, 94, 237], "codon_t": [13, 30, 34, 76, 279, 280, 281], "codonadaptationindex": [27, 261], "codonalign": [27, 30], "codonfreq": 17, "codonposit": 0, "codonposset": 0, "codons_block": 129, "codons_onli": 129, "codonseq": [27, 279, 280], "codont": [22, 27, 30, 75, 236, 237, 261], "coef": 177, "coeffici": [11, 177, 265, 270], "cofactor": [86, 113], "coffe": [32, 48, 63], "coffset": 278, "cog1583": 94, "cohort": 197, "coil": [234, 272], "col": [0, 30, 31, 299], "col_def": 97, "cold": 3, "coli": [6, 13, 22, 83, 209, 260], "collab": 94, "collabor": [6, 94, 245], "collaps": [17, 128, 130, 132, 181, 183, 222], "collapse_al": [17, 181, 183], "collapse_genera": [128, 132], "collect": [0, 5, 6, 9, 11, 12, 13, 16, 25, 27, 30, 75, 102, 110, 117, 139, 149, 160, 177, 178, 209, 214, 215, 237, 270, 279, 287, 288, 299], "collis": [15, 23], "colloc": 153, "colon": [182, 230, 244, 250], "color": [0, 6, 8, 16, 25, 99, 100, 102, 104, 105, 117, 181, 183, 197, 198, 270], "color0": 283, "color1": 283, "color2": 283, "color3": 283, "color4": 283, "color_auto": 283, "color_nam": [181, 183], "color_schem": [102, 283], "color_to_reportlab": [27, 98, 105], "colorimetr": 16, "colornam": 183, "colorschem": 104, "colorspir": [27, 98], "colortransl": [98, 104], "colour": [8, 99, 100, 104], "columba": 174, "column": [0, 3, 4, 6, 7, 10, 12, 13, 16, 20, 30, 31, 32, 33, 35, 36, 38, 49, 51, 52, 53, 56, 61, 62, 64, 66, 68, 69, 73, 129, 149, 176, 182, 199, 207, 209, 218, 221, 229, 238, 256, 276, 279, 280, 283, 290, 296, 299, 303], "column_annot": [0, 27, 30, 53, 66], "columnmean": [4, 73], "com": [3, 4, 5, 7, 15, 23, 25, 32, 99, 140, 158, 169, 218, 227, 234, 239, 270, 283, 299], "combin": [0, 2, 4, 6, 7, 8, 10, 12, 15, 22, 23, 25, 27, 30, 32, 52, 56, 80, 95, 128, 129, 169, 182, 199, 237, 238, 241, 250, 251, 260, 264, 272, 278, 280], "combinatori": [129, 166], "combined_matrix": 129, "come": [0, 1, 3, 8, 11, 12, 15, 20, 21, 23, 30, 169, 221, 222, 278, 303], "comjnl": 2, "comma": [0, 7, 9, 10, 16, 32, 36, 69, 83, 182, 270, 274], "command": [0, 1, 3, 4, 6, 9, 11, 12, 14, 15, 17, 19, 23, 24, 27, 32, 56, 59, 67, 68, 69, 80, 129, 156, 169, 182, 193, 195, 196, 218, 234, 251, 260, 270, 285, 303, 304, 306], "commandlin": [27, 32, 67, 69, 80, 128, 129], "commenc": 22, "comment": [0, 6, 11, 20, 21, 24, 25, 30, 36, 53, 81, 86, 88, 90, 93, 104, 113, 123, 129, 132, 152, 169, 177, 182, 184, 187, 189, 201, 204, 205, 217, 218, 219, 237, 241, 244, 258, 270, 272, 287, 288, 295], "comment_lin": [201, 204, 205], "commentari": 244, "comments_are_confid": 190, "commerci": [7, 11], "commiss": 25, "commit": [301, 303], "common": [1, 6, 7, 9, 11, 12, 13, 17, 19, 20, 21, 22, 23, 30, 31, 56, 68, 70, 107, 132, 152, 169, 183, 186, 197, 217, 238, 251, 290], "common_ancestor": [17, 128, 132, 181, 183], "common_nam": [181, 197, 198], "commonli": [0, 1, 4, 8, 17, 23, 30, 73, 83, 295], "commun": [2, 6, 7], "comp": 7, "comp_auto": 283, "comp_based_stat": [68, 69], "compact": [0, 20, 23, 42, 94, 222], "compactli": 209, "compani": 15, "compar": [2, 4, 6, 7, 8, 9, 13, 16, 17, 20, 21, 27, 34, 80, 98, 104, 132, 135, 139, 155, 168, 169, 182, 183, 185, 222, 236, 237, 260, 270, 278, 280, 290, 294, 297, 299], "comparativescatterplot": [27, 98, 101], "compare_coordin": [135, 139, 155], "compare_residu": [27, 133, 168], "comparison": [2, 3, 6, 7, 9, 11, 12, 13, 16, 22, 42, 71, 74, 80, 137, 168, 169, 196, 222, 236, 237, 251, 260, 263, 283], "compass": 27, "compat": [0, 3, 5, 10, 12, 16, 18, 21, 30, 37, 69, 104, 132, 151, 169, 183, 190, 197, 207, 237, 251, 260, 265, 270, 278, 297, 303], "compbia": 272, "competit": 9, "compil": [5, 6, 24, 169, 197, 288], "complain": [20, 152], "complement": [6, 8, 13, 19, 27, 30, 68, 79, 80, 94, 157, 236, 237, 260, 264, 269, 270, 278, 283, 290, 305], "complement_rna": [27, 236], "complementar": 80, "complementari": [11, 80, 264], "complet": [0, 3, 4, 6, 7, 8, 11, 14, 17, 19, 20, 21, 22, 23, 25, 45, 56, 61, 67, 68, 71, 73, 83, 104, 123, 169, 183, 198, 222, 236, 237, 238, 246, 247, 250, 258, 260, 270, 275, 278, 298, 303], "complete_protein": 279, "complex": [0, 6, 7, 15, 17, 21, 23, 24, 25, 32, 117, 158, 169, 237, 238, 264, 267, 274], "compli": [65, 283], "complianc": 197, "compliant": 11, "complic": [6, 7, 15, 21, 22, 23, 24, 31, 240], "compon": [2, 20, 24, 73, 99, 111, 115, 117, 169, 287], "compos": [18, 201, 204, 209, 263], "composit": [7, 32, 69, 99, 263, 267, 283], "composition": 272, "composition_based_statist": [68, 70], "compound": [10, 15, 21, 27, 111, 115, 116, 117, 119, 174, 237, 274], "compoundloc": [27, 237], "comprehens": [6, 20, 23, 24, 25, 182], "compress": [0, 1, 7, 12, 15, 25, 36, 37, 38, 149, 217, 238, 270, 278], "compresslevel": 278, "compris": [16, 17, 104, 169, 183, 278], "comput": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 15, 19, 20, 21, 23, 25, 27, 32, 69, 83, 108, 127, 132, 133, 149, 153, 157, 169, 176, 177, 182, 194, 199, 202, 216, 217, 221, 237, 263, 265, 267, 270, 278, 283, 287, 290], "computation": 8, "con": [11, 53, 123, 290], "concaten": [46, 53, 56, 60, 66, 71, 95, 214, 238, 260, 270, 278], "concentr": [80, 264], "concept": [15, 20, 21, 169, 269], "concern": 5, "concis": [12, 23, 25, 179, 180, 209, 210, 211, 215, 260], "conclus": [7, 251], "concord": [30, 297], "conda": 5, "condit": [0, 4, 14, 17, 20, 23, 24, 69, 73, 127, 182, 183, 186, 217, 229], "confer": 2, "confid": [0, 27, 181, 183, 184, 187, 189, 197, 198], "confidence_as_branch_length": 190, "config": [22, 84], "configur": [7, 24, 83, 99, 169, 193, 195, 196], "confirm": [0, 15, 21, 169, 275], "conflict": 272, "conform": [169, 185, 217, 265, 270], "confus": [1, 3, 9, 17, 20, 21], "confusingli": 251, "congruenc": 132, "congruenti": 4, "coniferal": 17, "conjunct": 152, "conn": [303, 304], "connect": [3, 7, 11, 17, 23, 37, 46, 56, 83, 103, 130, 132, 169, 176, 177, 179, 180, 183, 209, 278, 283, 288, 303, 304, 305], "connectiong": 132, "connector": 303, "cons": [238, 249, 268, 271], "consecut": [0, 4, 73, 100, 104, 141, 154, 221, 272, 277], "consed_sampl": 240, "consel": 182, "consens": [80, 132], "consensu": [0, 2, 17, 27, 30, 31, 53, 66, 80, 128, 132, 181, 240, 269, 270, 283, 290], "consensus_tre": 132, "consequ": 15, "conserv": [0, 2, 12, 69, 94, 104, 182, 260], "consid": [0, 2, 4, 5, 7, 9, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 30, 32, 53, 62, 66, 73, 120, 183, 221, 226, 236, 237, 238, 251, 256, 260, 264, 270, 276, 278, 281, 282, 298, 299], "consider": [0, 3, 4], "consist": [0, 3, 4, 6, 7, 11, 12, 13, 14, 15, 17, 20, 24, 30, 32, 38, 51, 52, 63, 66, 68, 73, 83, 99, 102, 135, 158, 169, 214, 215, 217, 221, 237, 238, 251, 255, 256, 260, 297], "consol": [24, 32, 207], "consolewidth": [206, 207], "consortium": 93, "consre": 132, "consrtm": 93, "constant": [32, 128, 129, 177, 182, 264], "constitu": [21, 155], "constitut": 22, "constrain": 182, "constraint": [181, 182], "constraintweight": [181, 182], "constre": 132, "construct": [0, 3, 6, 11, 12, 15, 17, 22, 23, 30, 32, 67, 68, 69, 119, 129, 143, 151, 154, 162, 183, 188, 190, 197, 198, 199, 209, 237, 238, 242, 270, 274, 280, 281, 287, 288], "constructor": [13, 21, 183, 186, 197, 199, 209, 265], "consult": [6, 27, 30, 182], "consum": [32, 92, 94, 162, 204], "consumpt": [14, 23], "cont": 24, "contact": [3, 7, 27], "contain": [0, 1, 3, 4, 6, 8, 11, 12, 13, 14, 16, 17, 19, 20, 21, 23, 24, 25, 30, 32, 33, 35, 36, 37, 39, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 58, 59, 60, 61, 62, 64, 66, 67, 68, 69, 73, 74, 76, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 92, 94, 99, 100, 101, 104, 105, 107, 108, 109, 113, 120, 121, 124, 128, 135, 139, 141, 144, 146, 149, 150, 155, 160, 169, 182, 183, 185, 186, 191, 197, 198, 199, 201, 202, 204, 205, 209, 217, 222, 226, 234, 236, 238, 242, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 259, 263, 264, 265, 269, 270, 271, 273, 274, 275, 277, 278, 280, 281, 282, 283, 286, 290, 293, 295, 296, 297, 298, 299, 303], "content": [0, 2, 3, 11, 13, 15, 18, 23, 29, 31, 36, 37, 38, 50, 84, 89, 90, 129, 149, 158, 202, 220, 221, 236, 264, 265, 273, 278, 288, 290], "contenthandl": [27, 85, 89, 238, 252], "context": [4, 22, 54, 84, 91, 99, 185, 236, 261], "contextu": 59, "contig": [6, 22, 27, 93, 94, 238, 240, 268, 269, 270, 271], "contig1": 240, "contig2": 240, "contig3": 269, "contig6394": 0, "contigu": [0, 16, 20, 169, 217, 270], "conting": 202, "continu": [0, 3, 6, 7, 8, 9, 13, 15, 24, 31, 188, 190, 198, 236, 237, 270], "contrari": 21, "contrast": [0, 3, 11, 20, 236], "contribut": [1, 4, 6, 11, 19, 24, 26, 109, 124, 133, 169, 275, 290, 307], "contributor": 5, "control": [8, 12, 13, 17, 19, 30, 32, 67, 69, 80, 99, 100, 152, 169, 182, 193, 195, 196, 200, 201, 203, 207, 238, 261, 265, 270, 272, 278, 298, 299], "conv": 119, "conveni": [0, 13, 15, 17, 20, 108, 169, 183, 237, 253], "convent": [4, 8, 11, 12, 15, 21, 22, 27, 61, 66, 73, 104, 197, 229, 236, 251, 278, 290, 297], "converg": [4, 71, 109, 122], "convers": [4, 6, 11, 20, 22, 23, 27, 32, 105, 221, 229, 251, 274], "convert": [0, 3, 4, 7, 9, 11, 13, 15, 17, 22, 27, 30, 32, 52, 56, 68, 69, 83, 90, 93, 119, 132, 152, 158, 168, 169, 183, 188, 191, 198, 209, 214, 217, 236, 237, 238, 248, 251, 253, 261, 262, 264, 270, 274, 280, 281, 299, 303], "convert_absolute_support": [128, 132], "cookbook": [17, 19, 23, 83, 169, 307], "cooki": 7, "cool": [3, 5, 7, 19, 23, 25, 26, 307], "cooper": 197, "coord": [15, 115, 117, 135, 140, 152, 156, 162, 168, 169, 175, 176, 216, 253], "coord_spac": [27, 133, 176], "coordin": [3, 4, 6, 8, 13, 16, 20, 21, 22, 25, 27, 30, 32, 35, 39, 46, 51, 52, 53, 55, 61, 68, 73, 99, 101, 117, 125, 126, 135, 136, 139, 140, 141, 143, 144, 149, 152, 155, 158, 160, 162, 166, 167, 168, 169, 172, 175, 176, 197, 198, 202, 214, 216, 221, 222, 226, 229, 231, 237, 238, 270], "coordinates1": 0, "coordinates2": 0, "coords1": 175, "coords2": 175, "coot": 15, "cope": [7, 12, 22, 42, 65, 71, 222, 237, 251, 261], "copi": [0, 3, 6, 8, 12, 17, 19, 21, 24, 30, 36, 54, 133, 135, 139, 149, 157, 169, 176, 236, 237, 260, 270, 281, 297, 299], "copy_initncac": [15, 133, 169], "copyright": [11, 123, 295], "cor6_6": [238, 245], "core": [3, 7, 11, 17, 20, 30, 32, 53, 80, 169, 268, 270, 280, 281, 283, 288], "cornel": 124, "corner": 8, "cornish": 2, "cornish1985": [2, 11], "corpor": 123, "corr": 264, "corr_dict": 279, "correct": [6, 7, 9, 16, 23, 32, 68, 83, 123, 182, 202, 214, 251, 260, 264, 304], "correctedqueri": [7, 83], "correctli": [4, 7, 15, 71], "correl": [11, 73, 182, 263, 290], "correspond": [0, 3, 4, 7, 10, 11, 13, 15, 16, 17, 21, 22, 25, 30, 37, 46, 61, 67, 68, 73, 83, 84, 86, 104, 108, 117, 139, 141, 154, 158, 161, 167, 176, 182, 183, 184, 187, 189, 197, 237, 248, 253, 270, 278, 279, 280, 287, 295, 303], "corrupt": [21, 68, 84], "corruptedxmlerror": [7, 27, 68, 83, 84], "coru": 269, "cosin": 169, "cost": [3, 11, 13, 14, 32, 68, 69, 80, 222, 270], "could": [0, 1, 3, 6, 7, 8, 9, 12, 15, 20, 21, 22, 23, 24, 25, 30, 31, 56, 63, 76, 88, 99, 103, 137, 197, 217, 236, 237, 248, 251, 253, 264, 274, 278], "couldn": 9, "count": [6, 11, 13, 14, 15, 17, 21, 22, 23, 27, 30, 31, 32, 34, 56, 60, 61, 68, 69, 71, 83, 93, 94, 102, 108, 109, 121, 132, 168, 169, 182, 183, 186, 197, 202, 203, 221, 236, 237, 238, 253, 260, 261, 264, 265, 270, 274, 280, 283, 287, 290, 295, 297, 303], "count_amino_acid": [261, 265], "count_termin": [17, 128, 132, 181, 183], "counterpart": [7, 20, 217], "coupl": [7, 11, 15, 17, 23, 169, 182], "cours": [3, 4, 5, 6, 7, 12, 15, 19, 20, 21, 23, 56, 238, 251, 253, 260, 278, 298, 299], "coval": [158, 169, 272], "covari": [4, 300], "cover": [3, 5, 7, 8, 12, 17, 19, 20, 21, 22, 23, 24, 59, 74, 217, 237, 274], "coverag": [5, 69], "cowan3": 265, "cowan7": 265, "cox": [2, 7, 269], "cprev": 182, "cpu": [0, 53, 69, 182, 278], "cpython": [217, 238], "cpzant": 244, "cpzgab": 244, "cq": 0, "cq797900": 245, "cqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggcdg": 0, "cr": [7, 278], "cr407631": 7, "cr_class": [133, 169], "crab_anapl": 250, "crab_bovin": 250, "crab_pir": 250, "crafqyhskeqqcvimaenrkssiiirmrdvvlfekkvylsecktgngknyrgtmsktkn": 25, "cram": 270, "crash": 182, "crc": 262, "crc32": [27, 261, 262, 272], "crc64": [23, 27, 261, 262], "cre_class": 169, "creat": [3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 17, 18, 19, 20, 22, 23, 24, 25, 27, 30, 31, 32, 33, 35, 36, 37, 38, 42, 45, 47, 49, 51, 52, 54, 60, 64, 67, 69, 72, 73, 80, 81, 83, 84, 88, 99, 102, 104, 105, 108, 121, 123, 129, 131, 135, 136, 137, 140, 143, 144, 146, 148, 149, 151, 152, 158, 160, 161, 162, 169, 172, 176, 182, 183, 185, 186, 188, 197, 198, 202, 204, 207, 209, 210, 217, 222, 236, 237, 238, 241, 245, 246, 250, 251, 252, 257, 260, 264, 270, 272, 278, 283, 288, 290, 295, 297, 298, 302, 303, 304, 305], "create_contingency_t": [201, 202], "created": 7, "creation": [15, 61, 169], "credenti": 288, "cress": 23, "crf": 123, "cri": 123, "cricetulu": 3, "crick": [22, 32], "crit": 264, "criteria": [11, 20, 288], "criterion": [15, 122], "critic": 238, "crn_drome": 53, "cron": 149, "cronjob": 15, "crook": 7, "crop": 6, "crop_matrix": [128, 129], "cross": [7, 12, 15, 21, 90, 93, 104, 119, 176, 248, 252, 260, 272, 302], "cross_refer": [25, 272], "cross_track_link": [8, 104], "crosslink": [8, 98, 104], "crosslnk": 272, "crossmatch": 269, "crosspeak": 125, "crp0": 289, "crystal": [83, 133, 175, 216], "crystallin": 250, "crystallogr": 175, "crystallograph": [15, 172, 238], "crystallographi": [25, 144], "csa": 53, "csa_con": 53, "csb": 169, "csblab": 140, "csd": [6, 248], "cse": 221, "csequenc": 67, "cshlp": 221, "csqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcggg": 0, "css": 183, "cst": [15, 169], "cstatu": [128, 129], "csv": [16, 298, 299], "csviter": [27, 298, 299], "ct": [0, 12, 27, 182, 240, 268, 269], "cta": [12, 22], "ctaaatgatatacgattccacta": 0, "ctaaatgatatacgattccactatgtaaggtctttgaatcatatcataaaagacaatgta": 0, "ctaaccagcagcacgaccacccttccaacgacccataacagc": 22, "ctacg": 264, "ctactacag": 12, "ctactacaggtg": 12, "ctagct": [12, 30], "ctagctacccggatatatcctagcttttagcg": 22, "ctagctag": [12, 30], "ctagtagtgt": 7, "ctatcgggcaccctttcagcggcccattacaatggccat": 22, "ctattcattc": 7, "ctc": [13, 22], "ctcaaggttgttgcaagggggtctatgtgaacaaa": 0, "ctcaattttg": 7, "ctcatttttc": 7, "ctcc": 21, "ctccgtaagaaggtgctgcc": 253, "ctccgtcgga": 249, "ctcctgctgctggctgcgctcggcgccgcaggtggagcactggag": 13, "ctcgacgtcg": 236, "ctg": [12, 13, 21, 22, 30, 62], "ctgaaaa": 222, "ctgaaaacctaagtaggagaatcaactaaggataat": 22, "ctgaaaacctaagtaggagagacagttaaagataat": 22, "ctgaaatcctgaatgtgagagtcaatcaaggatggt": 22, "ctgcacctagctacgagtgag": 283, "ctgcccagaat": 222, "ctgctgatxgcacgaggttatgg": 264, "ctgctgctgctggctgcgctctgcgccgcaggtggggcgctggag": 13, "ctggaacgtacttgctggtttcgctactatttcaaacaagttagaggccgttacctcgggcgaacgtataaaccattctg": 62, "ctggacaccagcaaggagctgctcaagcgcgatctgaagaacctggtgatcctcgaccgc": 13, "ctggagtctt": 7, "ctggcgtccggagctgggacgt": 0, "ctggcttcaa": 7, "ctgtc": [30, 31], "ctl_file": [193, 195, 196], "ctt": [22, 62], "cttgaagaaa": 7, "ctttggtgagaatttttgtttcagtgttaaaagtttg": 0, "cttttgctactggccgcgctctgcgccgcaggtggggccctggag": 13, "cube": 145, "cucuac": 66, "cucumi": [21, 23], "cue": 17, "cuga": 22, "cull": [69, 152, 169], "culling_limit": [68, 69], "cullpdb_pc20_res2": [15, 152, 169], "cultivar": 197, "cultur": 16, "cumbersom": [15, 18], "cumul": [17, 183, 194], "cur_chromosom": 8, "cur_diagram": 99, "cur_draw": [99, 103], "curat": [11, 25], "curl": 23, "current": [0, 3, 4, 5, 6, 7, 10, 11, 12, 13, 15, 16, 17, 18, 19, 24, 29, 32, 34, 37, 46, 66, 67, 68, 80, 85, 99, 100, 102, 103, 104, 107, 108, 109, 119, 122, 124, 125, 126, 139, 149, 153, 162, 164, 169, 182, 193, 195, 196, 197, 198, 199, 204, 211, 237, 250, 263, 270, 274, 276, 278, 281, 283, 302, 303, 304], "current_angl": 169, "current_releas": 23, "current_sect": 10, "cursor": [303, 304], "curtin": [18, 201, 204], "curv": [16, 299, 300], "curve_fit": 300, "custom": [0, 7, 8, 10, 11, 16, 17, 30, 36, 38, 67, 99, 149, 158, 169, 182, 217, 218, 241, 251, 261, 304], "custom_field": 218, "custom_map": 261, "cut": [3, 4, 8, 27, 69, 72, 73, 80, 158, 206, 207, 260], "cutoff": [15, 53, 68, 69, 70, 186], "cuts_in": 72, "cutsit": 72, "cutter": 206, "cv": 11, "cvcl_xxxx": 90, "cviaii": 206, "cvla": 13, "cw": [30, 32, 203], "cwd": 67, "cxc": [0, 30], "cy": [13, 15, 155, 238, 265], "cyan": [8, 183], "cyanel": 272, "cyano": 4, "cyano_result": 4, "cyano_result_k_a2": 4, "cyano_result_k_g2": 4, "cyano_result_k_g2_a2": 4, "cyanobacteri": 2, "cycl": 32, "cyg": [15, 169], "cylind": [15, 100, 158, 169], "cymon": [2, 269], "cypripedioidea": [7, 19], "cypripedium": [7, 19, 23], "cys1_dicd": 0, "cys1_dicdi": [0, 56], "cys2his2": [11, 283], "cysargtyrhi": 222, "cystein": [25, 265], "cystin": 265, "cytoband": [7, 275], "cytolog": 275, "cytosin": 270, "cytosol": 4, "cz": 169, "cz2": 169, "cz3": 169, "d": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 17, 22, 25, 27, 30, 32, 34, 59, 62, 68, 69, 80, 118, 131, 149, 169, 177, 182, 222, 237, 251, 261, 263, 264, 265, 268, 269, 270, 280, 281, 283, 297, 300], "d05": 299, "d0lrbacxx": 0, "d1": [169, 250], "d1anu1": [211, 212], "d1d": 169, "d1danl2": 210, "d1tpt_1": 209, "d2": 169, "d2a_map": 169, "d2d": 169, "d2h": [15, 133, 168, 169], "d3": [15, 169], "d5hbib_": 209, "d90040": 7, "d90042": 7, "d_": 4, "d_eli": 244, "d_mm251": 244, "da": [7, 13, 123, 154, 169], "da2": 169, "da3": 169, "da4509dc64a87ebd": 262, "dad": 274, "dai": 15, "daili": 15, "dali": 32, "dalk": [2, 7], "dan": 2, "danger": 17, "dangl": 264, "dark": 8, "darken": [27, 98, 105], "darker": 105, "darkgreen": 8, "darkseagreen": 104, "darl": 2, "darling2004": [0, 2], "dash": [0, 12, 15, 30, 33, 43, 68, 117], "dat": [11, 13, 23, 25, 86, 88, 272], "data": [2, 3, 7, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 46, 52, 53, 54, 56, 61, 63, 66, 67, 68, 69, 71, 73, 83, 84, 86, 87, 88, 89, 90, 92, 93, 94, 97, 100, 101, 103, 104, 109, 111, 115, 119, 120, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 137, 143, 145, 149, 150, 151, 152, 158, 164, 166, 168, 169, 172, 177, 178, 182, 183, 185, 198, 199, 201, 202, 204, 205, 209, 214, 236, 238, 245, 251, 252, 253, 257, 260, 261, 264, 269, 271, 272, 274, 275, 277, 278, 281, 282, 288, 289, 291, 295, 298, 299, 300, 303, 307], "data_class": [25, 272], "data_file_divis": [21, 23, 93], "data_gener": [201, 205], "data_quartil": [98, 104], "data_t": [27, 124, 126], "data_typ": [11, 287, 288], "data_upd": 88, "databa": 303, "databas": [0, 3, 9, 10, 12, 13, 15, 17, 18, 20, 21, 22, 26, 61, 66, 68, 69, 70, 71, 80, 83, 90, 93, 94, 111, 112, 113, 114, 115, 117, 119, 152, 164, 174, 177, 209, 217, 218, 226, 229, 238, 245, 248, 250, 252, 260, 268, 270, 272, 274, 275, 276, 277, 283, 287, 288, 295, 301, 302, 303, 304, 305, 307], "database_length": 71, "database_lett": 71, "database_nam": 71, "database_sequ": 71, "databaseload": [301, 305], "databaseremov": [301, 305], "databasereport": [27, 68, 71], "datafil": [11, 23, 79, 80, 169], "datahandl": [27, 83, 84], "datahandlermeta": [27, 83, 84], "datalabel": 126, "dataset": [6, 7, 10, 15, 126, 182, 264], "datatyp": [0, 56, 181, 182, 197], "date": [0, 3, 5, 7, 9, 11, 12, 19, 21, 23, 27, 67, 71, 83, 88, 90, 93, 123, 133, 152, 169, 172, 181, 197, 198, 272, 295], "datestamp": 214, "datestr": 152, "datetim": 197, "datetyp": 7, "datom": 169, "datoms_needs_upd": 169, "datum": 197, "daunt": 20, "davi": 7, "david": [2, 3, 68, 263], "dayhoff": [2, 182, 199], "dayhoff1978": [2, 13], "daylateanddollarshort": 15, "db": [3, 7, 11, 23, 68, 69, 71, 83, 113, 119, 152, 169, 174, 234, 238, 245, 270, 272, 274, 283, 287, 303, 305], "db1": 169, "db2": 169, "db3": 169, "db_gencod": [68, 69], "db_genetic_cod": [68, 70], "db_handl": 209, "db_hard_mask": [68, 69], "db_idx": 217, "db_name": [303, 305], "db_object_id": 277, "db_object_nam": 277, "db_ref": 237, "db_soft_mask": [68, 69], "db_sourc": 93, "db_xref": [7, 21, 94], "dbcl": 274, "dbd": 288, "dbentri": 119, "dbfrom": [7, 83], "dbg": 80, "dbid": [303, 305], "dbinfo": 7, "dbj": [238, 241, 260], "dblink": [21, 93, 112, 113, 114], "dblist": [7, 83], "dbname": [7, 83, 272, 303], "dbref": [248, 252], "dbref1": 248, "dbref2": 248, "dbseqrecord": [301, 302, 303], "dbserver": [301, 303, 305], "dbsize": [68, 69], "dbto": 7, "dbtype": [68, 69], "dbutil": [301, 303], "dbxref": [0, 3, 12, 20, 21, 23, 27, 68, 234, 248, 260, 301, 302], "dc": [69, 250], "dc525629": [0, 30], "dcmut": 182, "dcom": [7, 123], "dcoordspac": [133, 169], "dcsvalid": [133, 169], "dct": 207, "dcut": 72, "dd": [88, 152], "dd1": 169, "dd11": 169, "dd12": 169, "dd13": 169, "dd2": 169, "dd21": 169, "dd22": 169, "dd23": 169, "dd3": 169, "dd728": 0, "ddassaatsk": 250, "ddbj": [94, 237, 245, 274, 275], "ddd": 0, "ddddbffff7a": 0, "ddefault": [69, 270], "ddmpn": 13, "ddpeeksavnn": 14, "ddvnhavlav": 0, "de": [0, 2, 4, 6, 7, 9, 15, 25, 26, 27, 32, 53, 66, 73, 86, 130, 149, 169, 174, 209, 250, 273, 289, 295], "de1": 169, "de2": 169, "de21": 169, "de22": 169, "de3": 169, "de_tabl": 264, "deactiv": 182, "deal": [1, 6, 7, 9, 11, 12, 15, 19, 21, 22, 23, 24, 27, 28, 30, 59, 74, 84, 95, 107, 108, 110, 129, 133, 139, 162, 217, 222, 237, 238, 251, 261, 268, 275, 276, 279, 280, 281, 298], "dealign": [30, 32], "dealt": [7, 15, 20, 95], "debug": [3, 12, 17, 30, 32, 67, 71, 76, 79, 80, 92, 93, 94, 148, 177, 182, 183, 237, 260, 270, 275, 278, 297, 299], "debug_level": 92, "dec": 13, "decemb": 25, "decept": 7, "decid": [7, 17, 20, 22, 23, 32, 67, 69, 80, 84, 182, 270, 285], "decim": [11, 119, 197, 251, 270, 286], "decis": [104, 264], "declar": [0, 36, 84, 252], "decod": [0, 3, 7, 14, 25, 27, 108, 109, 171, 236, 238, 278], "decoded_data": 15, "decomposit": [2, 4, 15, 216], "decompress": [15, 23, 25, 270, 278], "decor": 15, "decreas": [0, 4, 30, 182, 222, 264], "dedic": [0, 16, 24], "deduc": 7, "deduct": [30, 270, 297], "deep": [2, 169, 176], "deepcopi": [3, 17, 169], "deeper": 20, "deepest": [17, 183], "def": [3, 6, 8, 13, 15, 20, 23, 24, 32, 68, 70, 122, 218, 238, 241, 251, 253, 297], "default": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 16, 17, 20, 21, 22, 23, 24, 27, 30, 31, 32, 35, 36, 37, 38, 42, 49, 51, 52, 54, 64, 65, 67, 68, 69, 70, 72, 73, 80, 83, 84, 89, 92, 99, 102, 104, 108, 109, 127, 129, 132, 135, 136, 137, 138, 140, 143, 144, 145, 148, 149, 151, 152, 154, 157, 158, 160, 164, 166, 168, 169, 182, 183, 186, 195, 197, 199, 207, 217, 218, 221, 222, 229, 236, 237, 238, 241, 250, 251, 260, 261, 263, 264, 265, 270, 274, 276, 277, 278, 282, 283, 286, 288, 290, 297, 298, 299, 303, 304], "default_encod": 198, "default_feature_color": 99, "default_pseudo": [106, 108], "default_stop_codon": 76, "default_str": 71, "defaultpars": [133, 171], "defici": [202, 203], "defin": [0, 2, 3, 4, 6, 7, 10, 11, 14, 15, 16, 21, 23, 24, 27, 30, 31, 32, 35, 36, 37, 38, 39, 45, 46, 51, 52, 55, 61, 73, 84, 89, 91, 99, 100, 104, 116, 117, 132, 134, 135, 136, 141, 145, 147, 152, 153, 166, 167, 169, 172, 176, 177, 182, 183, 197, 202, 203, 209, 236, 237, 238, 247, 251, 253, 260, 261, 263, 265, 269, 270, 272, 278, 290, 291, 296, 297, 300, 303], "defined_rang": [27, 236], "definit": [0, 3, 7, 11, 13, 21, 23, 53, 68, 69, 71, 88, 105, 114, 117, 135, 139, 140, 155, 167, 169, 177, 197, 210, 212, 215, 251, 273, 278], "deflin": 69, "deg": 202, "degc": 264, "degcngglqp": 0, "degener": [11, 253, 283, 290], "degenerate_consensu": [11, 27, 283, 290], "degrad": [104, 152, 197], "degre": [8, 15, 32, 100, 104, 169], "dehal": 182, "dehek": [12, 13], "dehkr": [12, 13], "dehoon2004": [2, 4, 9], "dehydrogenas": 113, "del": [0, 6, 67, 236, 260], "del_featur": [98, 104], "del_graph": [98, 104], "del_set": [98, 104], "del_track": [98, 104], "delai": [32, 83], "deleg": 21, "delet": [0, 13, 15, 17, 30, 33, 55, 61, 67, 69, 80, 104, 129, 130, 136, 169, 183, 197, 222, 236, 251, 260, 270], "deliber": [6, 8, 21, 22, 56], "delimit": [4, 51, 83, 104, 236, 238, 256, 270], "delin": 2, "delknavglv": 0, "delta": [4, 12, 30, 169, 199, 241, 264], "deltablast": 69, "delv": 19, "demand": [5, 23, 30, 236, 238], "demarc": 0, "dememor": [202, 203], "demo": [0, 30], "demonstr": [8, 10, 15, 23, 169, 251], "dendrogram": [4, 17, 73], "dendropi": 17, "denomin": 4, "denot": [6, 15, 20, 73, 104, 217, 229, 236], "densiti": [25, 218, 294], "density_percent_sol": 15, "dep": [24, 123], "depart": 7, "depend": [0, 3, 4, 5, 7, 8, 11, 12, 13, 15, 16, 17, 20, 22, 23, 24, 25, 27, 30, 32, 71, 73, 80, 83, 104, 157, 169, 217, 229, 236, 237, 238, 264, 274, 278, 287, 297, 299, 300], "deposit": [15, 152, 172], "deposition_d": [15, 172, 174], "deprec": [3, 9, 14, 21, 27, 30, 32, 67, 83, 85, 92, 120, 127, 209, 212, 237, 265, 275, 282, 283], "deprecationwarn": 27, "depth": [12, 13, 17, 23, 156, 180, 181, 183, 197, 270], "der": [2, 8], "deriv": [0, 5, 15, 16, 22, 24, 25, 32, 60, 83, 99, 102, 107, 125, 144, 148, 182, 183, 198, 207, 214, 237, 248, 288], "des_handl": 209, "desc": [88, 181, 197, 198, 234], "descend": [3, 17, 20, 132, 183, 197, 209], "describ": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 17, 22, 23, 25, 30, 32, 36, 39, 46, 51, 55, 56, 61, 68, 69, 72, 73, 74, 80, 81, 84, 87, 88, 100, 104, 107, 109, 117, 121, 123, 136, 144, 149, 158, 160, 169, 175, 182, 185, 197, 210, 211, 213, 234, 237, 238, 250, 251, 253, 260, 261, 270, 272, 274, 278, 291, 296, 298, 299], "descript": [0, 3, 4, 6, 7, 10, 11, 13, 15, 17, 19, 20, 21, 23, 25, 27, 30, 33, 43, 68, 69, 70, 71, 72, 73, 88, 89, 93, 94, 104, 109, 113, 117, 121, 123, 132, 169, 172, 179, 180, 181, 197, 198, 209, 210, 211, 217, 218, 222, 226, 229, 234, 238, 241, 247, 250, 251, 252, 253, 256, 260, 270, 272, 275, 277, 295, 297, 303, 305], "descriptionext": [27, 68, 71], "descriptionextitem": [27, 68, 71], "descriptor": 278, "desier": 2, "design": [0, 4, 6, 8, 9, 11, 12, 15, 19, 21, 24, 30, 73, 81, 95, 101, 102, 103, 108, 177, 222, 238, 251, 253, 261, 263, 264, 278, 281], "desir": [4, 12, 15, 16, 21, 23, 30, 61, 73, 104, 176, 182, 209, 217, 251, 270], "desktop": 25, "despit": [15, 20, 23, 193, 195], "destin": [9, 68, 83, 108, 164], "destroy_transit": [106, 108], "detach": 139, "detach_child": [133, 139], "detach_par": [133, 135, 139], "detail": [0, 3, 6, 7, 8, 11, 12, 13, 14, 15, 17, 19, 20, 21, 23, 24, 27, 30, 59, 67, 68, 69, 83, 92, 135, 169, 182, 201, 202, 217, 221, 222, 239, 247, 248, 251, 253, 260, 264, 269, 270, 274, 276, 303], "detect": [0, 2, 3, 4, 7, 11, 15, 23, 25, 29, 32, 66, 68, 83, 125, 158, 169, 217, 238, 250, 251, 264], "detectednuc": 125, "determin": [0, 4, 11, 12, 20, 23, 50, 56, 80, 84, 104, 146, 152, 169, 182, 207, 238, 261, 265, 270, 288], "determinist": [4, 73], "deuter": 168, "deuterium": 169, "dev": [0, 9, 27, 67, 152, 169], "dev0": [9, 26, 307], "develop": [3, 5, 6, 9, 15, 16, 17, 19, 21, 24, 25, 27, 32, 59, 157, 158, 169, 182, 275], "developerinfo": 3, "deviat": [4, 11, 15, 104, 135, 152, 162, 169, 175, 216, 270, 290, 300], "devic": 278, "devot": 5, "df": [17, 183, 194], "df_search": [177, 178, 180], "dfwd": 169, "dg": [2, 32, 169], "dg1": 169, "dg11": 169, "dg12": 169, "dg13": 169, "dg2": 169, "dg21": 169, "dg22": 169, "dg23": 169, "dg3": 169, "dgfrqyksgv": 0, "dgfrqyksgvytsdhcgttpddvnhavlavgygvengv": 0, "dgtsta": 12, "dgtstaateamnslktqatdlidqtwpvvtsvavaglairlfkkfsska": 12, "dgtstatsya": 12, "dgtstatsyateamnslktqatdlidqtwpvvtsvavaglairl": 12, "dgtstatsyateamnslktqatdlidqtwpvvtsvavaglairlfkkfss": 12, "dgtstatsyateamnslktqatdlidqtwpvvtsvavaglairlfkkfsska": 12, "dh": 169, "dh11": 169, "dh12": 169, "dh1ndx": 169, "dh2": 169, "dh21": 169, "dh22": 169, "dh2ndx": 169, "dhhkk": [12, 13], "di": [15, 25, 90, 152, 169], "diabet": 274, "diacylglycerol": 25, "diag": [30, 32], "diagbreak": [30, 32], "diaglength": [30, 32], "diagmargin": [30, 32], "diagnos": 67, "diagon": [6, 12, 30, 32, 69, 125, 199, 270], "diagram": [3, 4, 15, 98, 99, 104], "dialign": 32, "dialign2": 32, "dialign_clin": 32, "dialigncommandlin": [30, 32], "diamond": 15, "diaz": 7, "dic": [170, 248, 263], "dice": [15, 27, 133], "dict": [8, 13, 54, 76, 84, 86, 90, 123, 126, 127, 139, 142, 157, 164, 168, 169, 177, 183, 197, 209, 210, 214, 217, 236, 238, 260, 261, 265, 273, 279, 290, 295, 302], "dict_kei": [7, 21, 23], "dict_on": 6, "dict_two": 6, "dictionarai": 84, "dictionari": [0, 3, 6, 7, 8, 9, 11, 12, 13, 15, 17, 18, 20, 21, 22, 25, 30, 31, 39, 52, 53, 66, 67, 68, 76, 82, 83, 84, 86, 90, 100, 102, 104, 107, 108, 109, 117, 121, 123, 126, 127, 134, 137, 139, 141, 142, 157, 161, 169, 170, 172, 174, 185, 197, 201, 202, 203, 207, 210, 214, 217, 222, 236, 237, 238, 240, 244, 248, 251, 253, 257, 260, 261, 263, 264, 265, 272, 273, 277, 282, 287, 290, 295, 297, 299, 303], "dictionary_match": [27, 297], "dictionaryel": [27, 83, 84], "dictyostelium": 93, "did": [0, 4, 8, 11, 12, 65, 69, 94, 251], "didddddddddddddddddddddddddddddddddddddddddddddddiddidddddddddddddddddddddddiiidddddddddddddddddddddd": 0, "didn": [7, 12], "die": [79, 80], "differ": [0, 1, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 42, 56, 65, 66, 68, 69, 72, 73, 80, 83, 84, 94, 99, 100, 101, 102, 104, 121, 126, 133, 135, 143, 144, 146, 168, 169, 177, 182, 199, 204, 207, 214, 217, 222, 226, 229, 238, 243, 248, 251, 253, 260, 261, 263, 264, 265, 270, 272, 274, 278, 281, 287, 288, 297, 300], "differenc": 80, "differenti": [2, 18, 66, 72, 202], "differentialcutsit": [27, 72], "difficult": [3, 4, 6, 7, 8, 15, 23], "difficulti": [8, 20, 24], "diffseq": 80, "diffseqcommandlin": [27, 79, 80], "dig": 12, "digest": [6, 8, 206], "digit": [16, 118, 182, 201, 204, 205, 214, 270], "diglycerid": 25, "dih": 168, "dihdral": 169, "dihedr": [136, 144, 154, 160, 169, 176], "dihedra": [15, 152, 158, 167, 168, 169], "dihedra_sign": 169, "dihedraangl": [15, 169], "dihedraanglerad": 169, "dihedrakei": 169, "dihedral14": 169, "dihedral_sign": [15, 133, 169], "dihedralen": 169, "dihedrandx": [15, 169], "dihedron": [15, 27, 133, 152, 169], "dihydroxypterocarpan": 113, "diiron": 25, "dilemma": 2, "dim": [13, 54, 127, 175, 216], "dimens": [0, 4, 11, 56, 73, 120, 175, 216], "dimension": [4, 13, 25, 127, 169, 263, 272, 290], "dimer": [30, 32], "dineen": 32, "dinucleotid": 21, "dipcn": 0, "diploid": [202, 203, 205], "dir": [25, 149, 209, 210], "dir_path": 209, "dirac": 15, "direct": [4, 6, 7, 8, 15, 16, 17, 22, 32, 67, 71, 91, 92, 94, 100, 109, 117, 141, 156, 177, 178, 179, 180, 183, 229, 237, 264, 278], "directli": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 20, 21, 23, 24, 30, 32, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 69, 80, 83, 84, 92, 99, 105, 107, 108, 125, 169, 182, 183, 185, 191, 197, 218, 222, 236, 238, 247, 251, 253, 255, 256, 260, 270, 271, 283, 285, 294, 298, 305], "directori": [0, 5, 7, 9, 12, 13, 15, 17, 18, 24, 67, 69, 83, 84, 124, 140, 149, 153, 157, 164, 182, 193, 195, 196, 202, 203, 209, 251, 270], "direntri": 91, "dirqgpkepfrdyvdrfyktlraeqasqevknw": 154, "dirti": [23, 31, 132], "disabl": [32, 69, 80, 169, 218, 270, 303], "disadvantag": 3, "disallow": [7, 13, 108, 270], "discard": [0, 6, 32, 226, 264, 270], "discoideum": 93, "disconcord": 270, "disconnect": 130, "discontigu": 69, "discontinu": 7, "discount": 169, "discourag": [9, 24, 71, 92, 251, 278], "discov": [2, 11, 19, 21, 83], "discoveri": 11, "discrep": [11, 169, 214], "discret": [12, 127, 182], "discuss": [5, 6, 7, 8, 11, 12, 15, 19, 21, 22, 108, 169], "diseas": [90, 113, 264], "disembl": 15, "disequilibrium": [18, 202, 203], "disk": [7, 12, 23, 25, 30, 56, 83, 217, 238, 278, 298], "disord": [135, 136, 139, 155, 158, 169], "disorderd": 139, "disordered_add": [133, 135, 139, 155], "disordered_get": [133, 139], "disordered_get_id_list": [133, 139], "disordered_get_list": [133, 135, 139], "disordered_has_id": [15, 133, 139], "disordered_remov": [133, 135, 139, 155], "disordered_select": [15, 133, 135, 139], "disorderedatom": [15, 27, 133, 135, 139, 155], "disorderedentitywrapp": [15, 27, 133, 135, 139, 155], "disorderedresidu": [15, 27, 133, 136, 139, 155], "disp": 209, "displai": [0, 2, 4, 6, 12, 15, 17, 20, 32, 36, 80, 94, 99, 101, 102, 103, 104, 119, 128, 132, 169, 182, 183, 197, 222, 297, 303], "display_id": 303, "display_info": [101, 103], "displayrepresent": [27, 98], "disput": 19, "dissimilar": 182, "dist": [4, 5, 8, 9, 32, 73, 80, 83, 132, 156], "dist_pearson": [11, 283, 290], "dist_pearson_at": [283, 290], "distanc": [11, 17, 32, 73, 80, 100, 128, 132, 135, 154, 156, 169, 181, 182, 183, 197, 199, 202, 203, 237, 270, 282], "distance1": [30, 32], "distance2": [30, 32], "distance_calcul": 199, "distance_fn": 282, "distance_matrix": 199, "distance_plot": [15, 133, 169], "distance_to_internal_coordin": [15, 133, 169], "distancecalcul": [27, 181, 199], "distancematrix": [4, 13, 27, 73, 181, 199], "distancetreeconstructor": [13, 27, 181, 199], "distant": [17, 183], "distinct": [3, 4, 6, 15, 17, 20, 69, 182, 221, 270], "distinguish": [0, 6, 15, 23, 30, 68, 100, 222], "distmat": 32, "distmat_ful": [30, 32], "distmat_full_it": [30, 32], "distmat_in": [30, 32], "distmat_out": [30, 32], "distplot": 169, "distplot_to_dh_arrai": [15, 133, 169], "distribut": [0, 4, 6, 7, 9, 11, 12, 13, 17, 25, 27, 98, 100, 101, 108, 152, 167, 181, 182, 194, 197, 198, 270, 283, 290, 294], "distributionpag": [27, 98, 103], "disulfid": [265, 272], "disulphid": [79, 80], "div": 169, "diverg": [11, 32], "divers": 202, "divid": [4, 7, 11, 12, 13, 15, 16, 30, 73, 102, 104, 108, 241, 256, 264, 270, 278, 290], "divis": [7, 12, 24, 93, 104, 197, 261], "djacent": 80, "dkt": 169, "dkvnhavlav": 0, "dl": [13, 175, 250], "dlen": 176, "dlp": 6, "dlqllikavnlfpagtnsrwevianymnihsssgvkrtakdvigkakslqkldp": 68, "dlqllikavnlfpagtnsrwevianymnihsssgvkrtakdvigkakslqkldphqkddinkkafdkfkkehgvvpqadnatpserf": 68, "dlshg": 13, "dm": [199, 209, 211], "dmb_prot": 250, "dmitrovski": 2, "dmso": 264, "dmsofactor": 264, "dmvvveipklgkeaavkaikewgq": 23, "dn": [13, 34, 280, 281], "dn7_mets5": 0, "dn7a_sac": 0, "dn7a_sacs2": 0, "dn7a_sacs2tvkfkykgeekqvdiskikkvwrvgkmisftydegggktgrgavsekdapkellqmlek": 0, "dn7e_sula": 0, "dn7e_sulac": 0, "dn7e_sulackvrfkykgeekevdtskikkvwrvgkmvsftydd": 0, "dn_constructor": 13, "dn_ds_method": 280, "dn_tree": 13, "dna": [0, 2, 6, 7, 10, 11, 12, 13, 19, 21, 22, 23, 30, 31, 32, 56, 76, 80, 83, 93, 154, 168, 182, 196, 197, 199, 236, 237, 238, 245, 250, 251, 252, 253, 259, 260, 261, 264, 267, 272, 278, 281, 290], "dna_bind": 272, "dna_de1": 264, "dna_imm1": 264, "dna_model": [181, 199], "dna_nn1": 264, "dna_nn2": 264, "dna_nn3": 264, "dna_nn4": 264, "dna_protein": 32, "dna_rna": [0, 45], "dna_seq": 22, "dna_tmm1": 264, "dnac1": 264, "dnac2": 264, "dnaconc": [79, 80], "dnadist": 80, "dnafreq": [30, 32], "dnamatrix": [30, 32], "dnaml": 17, "dnapar": 80, "dnastrid": 32, "dnd": [12, 17, 32], "dntp": 264, "do": [0, 1, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 36, 37, 38, 39, 46, 49, 51, 52, 60, 64, 68, 80, 84, 92, 117, 120, 129, 158, 169, 182, 197, 206, 207, 216, 217, 221, 229, 236, 237, 238, 240, 245, 246, 248, 249, 251, 260, 264, 269, 270, 271, 278, 282, 288, 297, 302, 303, 305, 307], "do_featur": 94, "doc": [0, 1, 3, 8, 9, 10, 12, 19, 20, 24, 25, 32, 50, 65, 68, 70, 83, 87, 88, 94, 105, 117, 126, 164, 199, 245, 253, 272, 273, 277, 296], "docstr": [3, 5, 8, 9, 19, 24, 83, 297, 306], "docsum": 7, "docsumlist": 7, "doctest_suit": 24, "doctestsuit": 24, "doctyp": 7, "document": [0, 1, 3, 6, 7, 9, 10, 11, 12, 14, 15, 17, 18, 19, 20, 21, 23, 24, 27, 30, 32, 56, 65, 67, 68, 83, 85, 86, 88, 89, 94, 99, 135, 169, 182, 197, 201, 204, 217, 221, 222, 234, 236, 237, 238, 243, 248, 251, 252, 253, 272, 295, 296], "documentor": 19, "doe": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 20, 21, 22, 23, 24, 25, 30, 54, 59, 66, 68, 70, 76, 83, 85, 99, 119, 136, 144, 152, 158, 160, 168, 169, 182, 202, 204, 217, 222, 229, 236, 237, 238, 241, 250, 251, 260, 261, 269, 270, 274, 278, 283, 288, 297, 303], "does_not_exist": 85, "doesn": [3, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31, 99, 104, 108, 149, 176, 197, 269, 270], "dog": [0, 22], "doi": [2, 32, 69, 73, 100, 137, 175, 182, 197, 251, 252, 262, 267], "dom": [9, 27, 209, 229, 252], "domain": [0, 7, 15, 21, 25, 27, 69, 181, 197, 198, 209, 210, 211, 212, 214, 215, 217, 229, 231, 237, 260, 272, 288], "domain_architectur": [181, 197, 198], "domain_exp_num": 229, "domain_included_num": 229, "domain_inclusion_ethresh": [68, 69], "domain_index": 229, "domain_obs_num": 229, "domain_reported_num": 229, "domainarchitectur": [27, 181, 197], "domainsclusteredbyev": [27, 209], "domainsclusteredbyid": [27, 209], "domest": 122, "domtab": [217, 231], "don": [0, 3, 5, 7, 8, 9, 12, 17, 20, 21, 22, 23, 25, 32, 99, 108, 143, 152, 182, 191, 237, 251, 260, 264, 270, 297], "donat": 15, "done": [0, 1, 3, 4, 5, 6, 7, 8, 11, 15, 17, 19, 21, 22, 23, 24, 67, 95, 125, 127, 182, 204, 221, 236, 248, 253, 299, 302, 303], "donna": 2, "donor": [80, 90], "doolitl": 265, "doolittl": 265, "dopamin": 15, "dot": [4, 12, 13, 15, 20, 30, 32, 65, 73, 80, 104, 169, 176, 216, 237, 297], "dotdiff": [79, 80], "doti": 264, "doubl": [4, 8, 9, 12, 21, 22, 129, 158, 169, 172, 197, 236, 261, 264], "double_strand": 261, "dougla": [2, 32, 175], "douthart": 169, "douw": 2, "down": [11, 15, 17, 20, 22, 23, 24, 71, 139, 157, 250, 270, 296], "downgrad": 270, "download": [0, 1, 3, 6, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 84, 90, 105, 149, 164, 221, 238, 245, 274, 283], "download_all_assembli": [133, 149], "download_cif_for": [27, 133, 164], "download_entire_pdb": [15, 133, 149], "download_obsolete_entri": [133, 149], "download_pdb_fil": [133, 149], "downsid": 23, "downstream": [21, 83, 132, 183], "downward": 132, "dp": [7, 32, 123], "dp_method": 109, "dpi": 104, "dpparttre": [30, 32], "dq110336": 7, "dr": [0, 11, 12, 25, 53, 86, 90, 295], "dr_false_neg": 88, "dr_false_po": 88, "dr_posit": 88, "dr_potenti": 88, "dr_unknown": 88, "draft": 20, "drain": 169, "dramat": 270, "draw": [4, 6, 8, 17, 98, 99, 102, 103, 104, 105, 182], "draw_ascii": [12, 17], "draw_graphviz": 17, "draw_rel": 105, "draw_to_fil": [98, 101], "drawback": 3, "drawn": [4, 8, 17, 99, 104], "dread": 237, "drev": 169, "drill": 20, "drive5": 32, "driver": [303, 304, 305], "droadhc": 13, "droadhca": 13, "droadhcb": 13, "droadhcc": 13, "droadhcd": 13, "droadhcf": 13, "droadhcg": 13, "droadhch": 13, "droadhci": 13, "droadhcj": 13, "droadhck": 13, "drop": [0, 17, 21, 66, 183, 270, 305], "dropoff": [69, 270], "dropoff_1st_pass": 71, "drosophila": [2, 13, 283], "drug": [119, 274], "drwxrwxr": 149, "ds_constructor": 13, "ds_of_read4": 269, "ds_tree": 13, "dset": 169, "dsetvalid": 169, "dshdppphl": 0, "dsname": 7, "dssp": [0, 27, 133, 172], "dssp_dict": 137, "dssp_dict_from_pdb_fil": [27, 133, 137], "dssp_tupl": 137, "dssp_version": 137, "dstype": 7, "dstypenam": 7, "dsvnitlna": 0, "dt": [11, 90, 295], "dtaselect": 263, "dtd": [3, 68, 71, 83, 84, 117, 218], "dtring": 69, "dtype": [0, 4, 11, 13, 15, 30, 54, 73, 79, 80, 169], "dual": [9, 236], "ductap": 16, "due": [4, 6, 7, 9, 11, 13, 15, 16, 17, 24, 67, 85, 145, 151, 158, 222, 229, 270, 278, 303], "duf57": 94, "dufayard": 182, "duke": 269, "dumb_consensu": [12, 30, 31], "dummi": [30, 99, 237, 260, 278, 282], "dunbrack": [15, 152, 169], "dunker": 169, "dup": 241, "duplex": 264, "duplic": [3, 23, 155, 168, 181, 197, 198, 226, 238, 241, 270], "durat": 197, "durbin": [2, 13, 52, 107, 108, 109], "durbin1998": [2, 11, 13], "dure": [2, 4, 13, 15, 16, 17, 30, 32, 80, 107, 148, 158, 169, 182, 183, 199], "dust": [68, 69], "dustmask": 69, "dvanitiyd": 0, "dvllganggvlvfepndfsvkagetitfknnagyphnvvfdedavpsgvdvski": 0, "dy": 80, "dye": 16, "dylddefin": 0, "dylnapgetysvklta": 0, "dynam": [13, 30, 69, 107, 109, 193, 195, 196, 294, 297], "dynamicprogram": [27, 106], "dz": 169, "dz1": 169, "dz2": 169, "dz3": 169, "e": [0, 1, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 16, 17, 20, 21, 22, 23, 24, 30, 31, 32, 34, 45, 53, 54, 56, 67, 68, 69, 70, 71, 73, 76, 80, 81, 83, 88, 94, 99, 104, 108, 109, 118, 119, 126, 129, 132, 135, 137, 139, 145, 146, 149, 155, 158, 159, 162, 164, 166, 169, 172, 182, 183, 197, 199, 207, 209, 210, 211, 212, 214, 215, 217, 221, 226, 229, 236, 237, 238, 241, 248, 250, 251, 253, 260, 261, 263, 264, 265, 268, 269, 270, 272, 274, 278, 280, 283, 287, 288, 297, 299, 303], "e0": 168, "e06": 299, "e1": 168, "e12": 299, "e3mfgyr02_random_10_read": [6, 253], "e3mfgyr02f7z7g": 253, "e3mfgyr02fr9g7": 253, "e3mfgyr02ftg": 253, "e3mfgyr02gazm": 253, "e3mfgyr02gfkuc": 253, "e3mfgyr02gpgb1": 253, "e3mfgyr02hhz8o": 253, "e3mfgyr02ja6il": 253, "e3mfgyr02jhd4h": 253, "e3mfgyr02jwq7t": 253, "e9490": 182, "e_": 109, "e_class": 169, "e_freq_t": [12, 31], "e_value_thresh": 3, "eac": 73, "each": [0, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 34, 35, 36, 37, 38, 39, 42, 43, 46, 51, 52, 53, 56, 60, 62, 63, 65, 66, 67, 68, 69, 71, 72, 73, 80, 81, 83, 84, 86, 90, 94, 99, 100, 101, 102, 103, 104, 108, 109, 116, 117, 120, 121, 122, 127, 129, 130, 131, 139, 146, 155, 157, 158, 161, 168, 169, 175, 176, 177, 182, 183, 185, 186, 198, 201, 202, 203, 204, 209, 210, 211, 212, 213, 214, 216, 217, 218, 221, 222, 236, 238, 240, 241, 244, 245, 247, 248, 250, 251, 253, 256, 257, 258, 260, 261, 265, 269, 270, 271, 274, 276, 278, 280, 282, 283, 290, 297, 299, 303], "eaifegftfyktvsiririnrgeavyigtlwkelnvyrkldkeerefykflydcglg": 94, "eal": 14, "eamveavali": 0, "earli": [7, 15, 27, 69, 251, 253], "earlier": [3, 6, 12, 13, 14, 17, 20, 21, 22, 23, 32, 251], "earrai": 238, "eas": [15, 79, 80, 222, 264], "eas51_64": 0, "eas54_6_r1_2_1_413_324": [238, 251], "eas54_6_r1_2_1_443_348": [238, 251], "eas54_6_r1_2_1_540_792": [238, 251], "eas56_57": 0, "easi": [0, 5, 6, 7, 8, 9, 11, 12, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 56, 82, 93, 97, 99, 102, 137, 217, 237, 238, 251], "easier": [3, 5, 6, 7, 8, 9, 12, 16, 19, 20, 21, 23, 119, 169, 183, 203, 217, 274, 283], "easiest": [5, 8, 15, 207, 260, 303], "easili": [5, 6, 9, 11, 15, 17, 21, 22, 23, 251, 260], "easter": [7, 23], "eastern": 3, "easycontrol": [200, 201], "ebi": [0, 6, 32, 209, 222, 234, 245, 250, 274, 277], "eblosum62": [0, 11, 290], "ebml": 274, "ebug": 270, "ebyntm": 22, "ec": [10, 23, 25, 86, 112, 113, 117, 118, 123, 197], "ec_5": 10, "echo": 214, "echtel1": 0, "ecitmatch": [27, 83], "ecnumb": 25, "eco": 25, "ecoli": 13, "ecori": [8, 207], "ecosystem": 10, "ecuy": [2, 4], "ed": [2, 216], "edat": 123, "eddi": 2, "eddylab": 229, "edg": [8, 69, 169, 177, 178, 179, 180, 183, 265], "edgar": 32, "edgssaatsk": 250, "edit": [0, 2, 6, 8, 12, 21, 22, 94, 236, 237, 251, 260, 270], "editor": [8, 12, 17, 19, 23], "edkflhlnyvsdlliphpihleilvqilqcrikdvpslhllrllfheyhnlnslitsk": 7, "ednaful": [11, 290], "edra": 169, "edron": [27, 133, 169], "edron_r": [133, 169], "eds40773": 238, "edu": [0, 15, 18, 32, 35, 36, 37, 38, 39, 46, 50, 51, 59, 61, 65, 124, 156, 190, 199, 201, 204, 209, 211, 212, 214, 221, 226, 247, 263, 269], "eeee2": 0, "eeeeesssseeeeettteeeeeesssseeeee": 0, "eek": 13, "eeubsr": 270, "ef1": 4, "ef590892": 83, "ef590893": 83, "efetch": [8, 9, 23, 27, 83, 274], "eff": [3, 68], "effect": [3, 4, 11, 15, 68, 69, 71, 182, 183, 217, 236, 238, 270, 283], "effective_database_length": 71, "effective_hsp_length": 71, "effective_query_length": 71, "effective_search_spac": 71, "effective_search_space_us": 71, "effector": 113, "effici": [2, 4, 6, 15, 23, 25, 56, 153, 182, 198, 203, 238, 253, 257, 269, 278], "effort": [3, 6], "efg23vgg": 238, "efr": 123, "eft": 13, "eg": [15, 32, 135, 140, 175, 182, 216, 234], "eggert": [2, 13], "egmqcscgpd": 250, "egmqcscgvd": 250, "egqueri": [27, 83], "egqueryresult": [7, 83], "ei": 14, "eigenvalu": [4, 73], "eigenvector": 4, "eight": [4, 7, 11, 80, 264], "ein": 123, "einfo": [27, 83], "einfo3": 7, "einfo_020511": 7, "einforesult": 7, "einvert": 80, "einvertedcommandlin": [27, 79, 80], "eisen": [2, 4, 73], "eisen1998": [2, 4], "eisenberg": 265, "either": [0, 3, 4, 5, 7, 8, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 25, 31, 32, 56, 67, 69, 73, 76, 80, 83, 91, 99, 104, 123, 126, 129, 137, 182, 183, 193, 195, 197, 198, 199, 205, 209, 217, 218, 222, 226, 229, 236, 237, 238, 241, 250, 261, 263, 269, 272, 274, 278, 297, 298, 303], "ekdrfsvnld": 250, "eksmikkrymhlteeilkenpnicaymapsldarqdivvvevpklgkeaaqkaikewgqp": 23, "ekyfnftlipkkdiienkryyliisspdkrfievlhnkikdldiitiglaqfqlrktk": 94, "el": 267, "elabor": [11, 17, 20], "electron": [123, 272], "electrophoresi": 263, "eleg": 6, "elegantli": 3, "elem": [116, 198, 258], "element": [0, 2, 4, 6, 7, 9, 12, 13, 15, 17, 18, 22, 23, 25, 30, 31, 53, 54, 69, 73, 83, 84, 104, 105, 108, 115, 116, 117, 120, 126, 135, 139, 158, 162, 168, 169, 172, 183, 197, 198, 199, 201, 202, 218, 234, 252, 265, 282, 297], "elementdecl": [83, 84], "elementtre": 198, "eleven": [6, 7, 25], "elh": 13, "elif": [6, 297], "elink": [27, 83], "elkan": 2, "ellipsoid": 4, "elong": 4, "els": [0, 6, 8, 12, 13, 15, 19, 23, 30, 93, 99, 169, 275, 299], "elsewher": [0, 6, 22, 81, 210, 211, 212, 213], "elw": 182, "em": [4, 32, 73], "em0": [268, 270], "em1": [268, 270], "em2": [268, 270], "email": [3, 7, 23, 68, 70, 83], "emb": [13, 19, 21, 23, 24, 253], "embed": [244, 278], "embl": [15, 21, 22, 23, 25, 32, 92, 94, 234, 237, 238, 245, 260, 274, 275], "embl_ind": [92, 94], "embl_spac": [92, 94], "emblcdsfeatureiter": [27, 238, 245], "embliter": [27, 238, 245], "emblscann": [27, 92, 94], "emblwrit": [27, 238, 245], "emboss": [2, 5, 9, 11, 13, 14, 27, 30, 56, 58, 66, 67, 208, 238, 250, 251, 255, 290], "emboss_consensu": 0, "embossio": [27, 56], "embossiter": [27, 56, 58], "embryophyta": [7, 25], "emerg": 174, "emiss": [30, 32, 107, 108, 109, 110, 121], "emission_alphabet": 108, "emission_count": 109, "emission_lett": 108, "emission_prob": 108, "emission_pseudo": 108, "emission_st": 108, "emission_titl": 110, "emissions_count": 109, "emit": [108, 121], "emmseqdgylaesinkdieecnaiieqfidylr": 260, "empir": [2, 32, 80, 182, 264], "emploi": [0, 30, 168, 197], "empti": [0, 3, 4, 8, 11, 13, 15, 25, 30, 36, 37, 38, 46, 49, 64, 67, 72, 99, 104, 108, 109, 135, 159, 169, 172, 197, 205, 209, 211, 230, 236, 241, 261, 278, 295, 299], "empty_status_charact": [30, 46], "en": [7, 53, 66, 263, 274], "ena": 6, "enabl": [6, 11, 15, 17, 18, 32, 67, 69, 169, 217, 270, 303], "encapsul": [8, 15, 21, 107, 122], "encephalosi": 23, "encod": [0, 3, 6, 7, 13, 14, 22, 25, 68, 76, 83, 84, 90, 182, 198, 236, 238, 251, 253, 260, 261, 270, 278, 297], "encount": [4, 7, 11, 20, 83, 84, 222], "encourag": [5, 6, 22, 23, 24, 92, 251], "encyclopedia": [111, 115, 119], "end": [0, 3, 4, 5, 6, 8, 9, 11, 12, 13, 14, 15, 17, 20, 21, 22, 23, 24, 27, 30, 31, 32, 35, 36, 46, 51, 56, 61, 62, 63, 66, 68, 71, 80, 84, 89, 90, 94, 95, 99, 104, 125, 130, 136, 138, 154, 169, 182, 183, 197, 204, 214, 215, 217, 221, 222, 226, 229, 234, 236, 237, 238, 245, 252, 260, 261, 264, 265, 269, 270, 274, 275, 278, 297, 299, 303], "end1": 236, "end2": 236, "end_extend_gap_scor": 13, "end_gap_scor": 13, "end_i": 103, "end_open_gap_scor": 13, "end_po": 21, "end_x": 103, "end_x_posit": 99, "end_y_posit": 99, "enda": [98, 104], "endara": 7, "endb": [98, 104], "enddbrefel": [238, 252], "enddescriptionel": [238, 252], "endeavor": 3, "endel": [85, 89], "endelementhandl": [83, 84], "endentryel": [238, 252], "enderrorelementhandl": [83, 84], "endextend": [79, 80], "endgap": [30, 32], "endian": 0, "endintegerelementhandl": [83, 84], "endnamespacedeclhandl": [83, 84], "endopen": [79, 80], "endoribonucleas": 0, "endpoint": [10, 68, 70], "endpropertyel": [238, 252], "endrawelementhandl": [83, 84], "endresid": 215, "endsequenceel": [238, 252], "endseqxmlel": [238, 252], "endskipelementhandl": [83, 84], "endspeciesel": [238, 252], "endstringelementhandl": [83, 84], "endswith": [27, 236], "endweight": [79, 80], "energi": [19, 104], "enf": 13, "enforc": [7, 32, 117, 197, 217], "engelman": 265, "engin": [166, 253, 265], "english": [3, 7], "enhanc": 69, "enjoi": 19, "enough": [3, 5, 6, 8, 15, 19, 20, 21, 23, 127, 251, 270], "ensg00000197372": 11, "ensur": [3, 4, 7, 11, 22, 23, 24, 30, 68, 71, 91, 104, 108, 152, 217, 237, 238, 280], "ent": [11, 15, 169], "enter": [7, 65, 182], "enterobacteri": 2, "entir": [1, 7, 17, 20, 21, 23, 31, 60, 64, 66, 183, 185, 209, 214, 237, 253, 261, 265, 267], "entirerli": 269, "entireti": 65, "entiti": [15, 27, 84, 133, 134, 136, 144, 146, 148, 152, 155, 157, 158, 159, 160, 168, 170, 172, 173], "entity_1": 134, "entity_2": 134, "entity_attribut": 97, "entity_id": [15, 97], "entity_list": 159, "entity_property_list": 134, "entity_typ": [97, 172], "entrez": [3, 8, 9, 19, 22, 23, 24, 26, 27, 68, 69, 70, 76, 119, 123, 238, 274, 275, 303, 307], "entrez_links_new_window": [68, 70], "entrez_queri": [68, 69, 70], "entrezf": 7, "entrezgene_gen": 7, "entrezgene_track": 7, "entri": [0, 7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 25, 27, 30, 60, 66, 83, 84, 85, 86, 87, 88, 90, 92, 111, 112, 113, 114, 115, 116, 117, 119, 125, 126, 139, 140, 149, 152, 167, 168, 169, 176, 182, 201, 212, 222, 226, 234, 237, 238, 241, 246, 248, 251, 252, 258, 260, 272, 273, 274, 275, 303], "entropi": [3, 13, 68, 122, 264, 283], "entry1": [115, 117], "entry2": [115, 117], "entry_nam": [25, 85, 272], "entrynum": 126, "enum": 55, "enum_test": [202, 203], "enumer": [0, 6, 8, 12, 22, 55, 68, 158, 169, 202], "enumerate_atom": [27, 133, 152], "env": [67, 229], "env_end": 229, "env_endtyp": 229, "env_num": 229, "env_start": 229, "envelop": [69, 217, 229], "environ": [7, 12, 15, 67, 83, 149, 157, 169], "envis": 102, "envlist": 24, "envpython": 24, "envz": 260, "enzmy": 206, "enzym": [7, 9, 10, 27, 72, 85, 111, 112, 118, 206, 207, 272, 274], "eof": 278, "eorder": [4, 73], "ep": [8, 30, 32], "epislon": 12, "epo_prt_select": 245, "epoch": 4, "epost": [27, 83], "epost_020511": 7, "epostresult": 7, "eprimer3": [80, 81], "epsilon": [12, 13, 30, 181, 182, 199], "epsilon_prot": 265, "epub": 175, "epubd": 7, "eqal": 68, "eqnlvdcdh": 0, "eqqlvdcagg": 0, "eqqlvdcaqd": 0, "equal": [0, 4, 6, 7, 11, 12, 13, 14, 15, 17, 20, 22, 25, 30, 68, 73, 84, 104, 108, 135, 136, 139, 150, 155, 157, 168, 169, 177, 179, 180, 183, 237, 251, 260, 261, 264, 270, 282, 290, 294, 297, 299], "equal_weight": [27, 282], "equat": [6, 11, 15], "equcab1": 0, "equilibrium": [13, 182], "equin": 23, "equiv": 4, "equival": [0, 3, 4, 7, 15, 22, 24, 30, 69, 139, 169, 197, 237, 238, 241, 245, 248, 251, 261, 264, 270, 274, 278, 300, 302], "equiveal": 161, "equvial": 270, "eras": 214, "erbos": 80, "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggat": 0, "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqc": 0, "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqg": 0, "eric": [2, 26, 122, 133], "err": [67, 182], "err_output": 67, "errata": 32, "erratum": 123, "erron": [15, 21], "error": [3, 4, 6, 12, 14, 17, 21, 24, 25, 27, 29, 32, 67, 68, 73, 79, 80, 83, 84, 89, 107, 119, 125, 145, 149, 168, 169, 182, 193, 195, 196, 198, 209, 214, 238, 251, 258, 261, 270, 272, 294, 298], "errorel": [7, 27, 83, 84], "errorfil": [79, 80], "erw": 68, "escap": [83, 84], "escherichia": [13, 209], "esearch": [27, 83, 274], "esearch1": 83, "esfviymfiv": 250, "esfviymfvv": 250, "esk": 6, "esoter": 93, "especi": [3, 5, 7, 9, 10, 12, 19, 102, 177, 260, 270], "espel": [27, 83], "essenc": [3, 4, 183], "essenti": [1, 3, 5, 6, 10, 13, 14, 15, 17, 20, 21, 22, 32, 100, 236, 258, 260, 270, 274], "est": [0, 7, 30, 79, 80, 275], "est2genom": [42, 80, 222], "est2genomecommandlin": [27, 79, 80], "est48004": 68, "establish": [0, 11], "estim": [2, 6, 13, 18, 32, 80, 108, 109, 121, 127, 152, 182, 196, 202, 203, 251, 253, 264], "estimate_nm": [201, 202, 203], "estimate_param": [106, 109], "estradiol": 113, "esummari": [27, 83], "esyvvymfvv": 250, "et": [4, 6, 8, 9, 11, 13, 17, 32, 34, 65, 69, 73, 83, 107, 108, 109, 137, 140, 238, 252, 264, 265, 281, 288, 299, 300], "eta": 12, "etandem": 80, "etandemcommandlin": [27, 79, 80], "etc": [5, 6, 7, 8, 9, 11, 14, 21, 30, 99, 117, 133, 152, 159, 169, 182, 217, 221, 229, 237, 253, 260, 261, 264, 269, 272, 275, 278, 288, 303], "etglsemrl": 250, "ethan": 2, "etherington": 2, "etre": 198, "ets1": 288, "eu": 222, "eu490707": 7, "euarc": 0, "euclidean": [73, 282], "eudicotyledon": 7, "eugen": 2, "eukaryot": [6, 16, 21], "eukaryota": [7, 23, 25], "euphyllophyta": 7, "european": [0, 2, 278], "eutil": 7, "eva": 2, "eval": [30, 68], "evalu": [0, 3, 4, 11, 17, 20, 68, 69, 143, 151, 182, 183, 209, 218, 226, 229, 234, 237, 260, 264, 291, 292], "evalue_cond": 229, "even": [4, 5, 7, 9, 11, 12, 13, 17, 19, 20, 21, 22, 23, 27, 30, 31, 32, 56, 80, 104, 222, 237, 238, 251, 264, 278, 288], "evenli": [100, 108], "event": [4, 6, 11, 13, 17, 27, 94, 181, 183, 197, 198, 252], "eventu": [20, 67, 191], "ever": [3, 79, 127, 149, 228], "everi": [3, 6, 8, 15, 16, 17, 23, 24, 30, 61, 67, 71, 84, 127, 169, 215, 234, 245, 255, 260, 264, 270, 278, 282, 288, 299], "everybodi": 3, "everydai": [4, 22], "everyth": [3, 5, 6, 7, 11, 12, 19, 21, 23, 69, 94, 95, 99, 101, 148, 152, 252, 305], "evid": [15, 21, 197, 240, 272, 277], "evl": [30, 297], "evo": 182, "evol": 7, "evolut": [2, 13, 19, 50, 65, 182, 190, 199], "evolutionari": [2, 12, 13, 32, 182], "evolutionaryontologi": 185, "evrnak": 22, "evrnakacgt": 22, "evrstn": 0, "evssvstspv": 250, "ewan": [2, 237], "eweight": [4, 73], "ex": [12, 32, 67, 182, 221], "ex1": [0, 278], "ex1_head": [0, 278], "ex1_refresh": 278, "exact": [6, 7, 17, 20, 21, 45, 61, 99, 119, 152, 222, 237], "exact_loc": 21, "exact_mass": 119, "exactli": [0, 3, 4, 7, 8, 10, 11, 12, 15, 17, 20, 21, 23, 25, 30, 86, 87, 88, 90, 92, 93, 113, 135, 217, 238, 241, 251, 253, 283, 288, 298, 299], "exactposit": [21, 27, 68, 237], "examin": [15, 270, 282], "exampl": [0, 1, 3, 6, 9, 10, 11, 12, 14, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 35, 36, 37, 38, 41, 46, 51, 53, 56, 58, 59, 60, 61, 62, 66, 67, 68, 69, 73, 80, 83, 85, 91, 94, 101, 104, 108, 109, 112, 113, 114, 116, 117, 122, 125, 126, 133, 134, 135, 139, 140, 148, 152, 154, 157, 158, 169, 170, 173, 176, 182, 183, 197, 199, 201, 204, 207, 215, 217, 218, 221, 222, 229, 234, 236, 237, 238, 241, 244, 246, 249, 250, 251, 252, 253, 256, 260, 261, 263, 264, 270, 272, 274, 277, 279, 282, 283, 288, 291, 292, 297, 298, 299, 303, 305], "example_do": 238, "example_filenam": 272, "examplealign": 182, "exampletre": 182, "exc_traceback": [45, 68], "exc_typ": [45, 68], "exc_valu": [45, 68], "exce": [32, 221], "exceed": 15, "excel": [6, 7, 23], "except": [0, 4, 6, 12, 13, 15, 16, 17, 21, 22, 23, 25, 27, 29, 30, 32, 37, 46, 56, 67, 68, 69, 72, 76, 83, 84, 92, 94, 113, 129, 130, 131, 132, 136, 144, 147, 151, 152, 160, 168, 169, 188, 190, 193, 195, 196, 197, 198, 217, 222, 236, 237, 238, 241, 251, 253, 260, 261, 270, 272, 278, 283, 288, 295, 297, 298, 299, 305], "excerpt": 22, "excess": [0, 4, 7, 202, 241, 270], "exchang": 4, "excit": [5, 8], "exclam": 251, "exclud": [0, 8, 15, 17, 22, 24, 32, 80, 129, 130, 169, 182, 183, 234, 236, 270], "exclude_doctest_modul": 24, "exclude_filenam": [181, 182], "excludedregion": [79, 80], "exclus": [20, 222, 263], "excus": 22, "execut": [3, 4, 12, 24, 25, 32, 67, 68, 69, 89, 137, 156, 169, 183, 202, 221, 301, 303, 304], "execute_and_fetch_col0": [301, 303], "execute_and_fetchal": [301, 303], "execute_on": [301, 303], "executemani": [301, 303, 304], "exelixi": [17, 182], "exercis": 158, "exhaust": [23, 42, 182, 222, 270], "exist": [3, 4, 12, 13, 14, 15, 17, 18, 19, 20, 21, 23, 24, 25, 32, 56, 83, 85, 104, 117, 129, 139, 149, 152, 169, 176, 183, 193, 209, 217, 238, 251, 260, 264, 265, 270, 272, 303], "exit": [32, 67, 91, 182], "exn": [0, 30, 222], "exn_22_m_cdna2genome_vulgar": 0, "exn_22_m_coding2coding_fshift": 222, "exn_22_m_genome2genom": 222, "exn_22_m_ner_cigar": 30, "exon": [20, 21, 61, 237], "exoner": [20, 27, 30, 217, 223, 224, 225], "exonerate_cigar": [217, 222], "exonerate_text": [217, 222], "exonerate_vulgar": [217, 222], "exoneratecigarindex": [217, 222, 223], "exoneratecigarpars": [217, 222, 223], "exonerateio": [27, 217], "exoneratetextindex": [217, 222, 224], "exoneratetextpars": [217, 222, 224], "exoneratevulgarindex": [217, 222, 223, 225], "exoneratevulgarpars": [217, 222, 225], "exp": [100, 229, 270], "exp_ca": 15, "exp_cb": 15, "exp_f": 15, "expand": 169, "expasi": [9, 19, 23, 24, 26, 27, 265, 272, 307], "expasy_url": 85, "expatpars": 89, "expclust": [4, 73], "expect": [0, 2, 3, 4, 6, 7, 8, 9, 12, 13, 15, 20, 21, 23, 27, 31, 32, 35, 36, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 70, 71, 90, 94, 99, 102, 104, 152, 182, 197, 198, 202, 203, 221, 222, 229, 237, 238, 240, 241, 244, 245, 247, 249, 250, 251, 252, 253, 255, 256, 259, 278, 290, 298], "expect_high": [68, 70], "expect_low": [68, 70], "expected_frequ": [12, 13], "expens": 32, "experi": [4, 15, 16, 19, 20, 21, 23, 144, 152, 214, 264], "experiment": [4, 10, 16, 21, 25, 27, 172, 197, 214, 270, 272], "experimnetal_method": 172, "expert": [181, 182], "expid": [4, 73], "explain": [4, 5, 7, 12, 15, 20, 21, 24, 30, 83, 121, 203, 251, 278], "explainflag": [79, 80], "explan": [0, 68, 83, 108, 182, 209], "explanatori": 11, "explicit": [8, 9, 12, 17, 21, 24, 61, 158, 237, 238, 260, 261, 278], "explicitli": [0, 3, 7, 8, 9, 12, 20, 21, 22, 23, 32, 104, 158, 169, 177, 218, 237, 251, 260, 288], "explor": [11, 15, 17, 182], "exponenti": [11, 16], "export": [11, 149, 158, 169], "export_fasta": [128, 129], "export_phylip": [128, 129], "export_search_strategi": [68, 69], "expos": [15, 169, 236, 278], "exposur": [2, 141, 157], "exposurecn": [27, 133, 141], "express": [0, 2, 4, 5, 6, 7, 17, 20, 21, 23, 30, 56, 73, 96, 169, 183, 197, 215, 238, 251, 261, 275], "exptre": 4, "ext": 202, "extend": [3, 5, 6, 8, 9, 10, 12, 13, 14, 15, 20, 24, 27, 30, 32, 36, 68, 69, 71, 76, 80, 169, 177, 186, 209, 214, 217, 218, 236, 264, 270, 272, 297], "extend_gap_scor": [13, 30], "extend_penalti": 0, "extenda": 297, "extendb": 297, "extens": [2, 3, 6, 9, 13, 14, 15, 18, 22, 23, 24, 32, 35, 68, 69, 71, 80, 129, 137, 153, 166, 222, 237, 253, 270, 297], "extent": 272, "extern": [11, 12, 15, 24, 27, 83, 84, 183, 197, 198, 295], "externalentityrefhandl": [83, 84], "extinct": 265, "extra": [0, 11, 17, 21, 23, 36, 38, 56, 168, 226, 237, 238, 248, 251, 278], "extra_indic": 36, "extract": [0, 3, 6, 7, 8, 10, 12, 13, 17, 19, 20, 21, 22, 25, 27, 30, 31, 62, 68, 94, 126, 133, 138, 182, 191, 201, 205, 214, 217, 218, 226, 237, 238, 251, 253, 260, 270, 274, 296, 299, 300, 306], "extraindex": [0, 36, 38], "extrem": [6, 13, 19, 21, 23, 272], "exu": 80, "ey": 13, "eyltapgetfsvtltv": 0, "f": [0, 2, 3, 7, 8, 11, 12, 13, 14, 15, 16, 17, 22, 30, 32, 54, 68, 69, 76, 80, 107, 135, 139, 149, 169, 182, 203, 216, 237, 244, 251, 253, 260, 261, 263, 264, 265, 268, 270, 278, 289, 291, 292, 299], "f001": 238, "f002": 238, "f1": [237, 250], "f1x4": [13, 34, 281], "f2": 237, "f2cxe6": 25, "f3": 237, "f3x4": [13, 34, 281], "f61": [13, 34, 281], "f81": 182, "f84": 182, "f_": 18, "f_bz163a": 244, "f_handl": 6, "fa": [0, 6, 13, 30, 32, 38, 62, 80, 182, 209, 211, 238, 270], "faa": [12, 13, 14, 23, 56, 69, 80, 238], "faadda": 12, "faaddaakaafdsltaqatemsgyawalvvlvvgatvgiklfkkfvsra": 12, "faaddatsqa": 12, "faaddatsqakaafdsltaqatemsgyawalvvlvvgatvgikl": 12, "faaddatsqakaafdsltaqatemsgyawalvvlvvgatvgiklfkkfv": 12, "faaddatsqakaafdsltaqatemsgyawalvvlvvgatvgiklfkkfvsra": 12, "face": [25, 149], "facil": [11, 15], "facilit": [11, 15, 177, 260, 278], "fact": [3, 15, 19, 23, 25, 56, 193, 195, 236, 251], "facto": 6, "factor": [4, 11, 25, 32, 105, 135, 152, 162, 169, 172, 264, 288, 295], "faei": 206, "fafbyproteinrec": 277, "fai": 270, "faidx": 270, "faii": 206, "fail": [3, 4, 7, 9, 13, 16, 18, 24, 68, 80, 83, 84, 85, 92, 152, 168, 169, 193, 195, 196, 236, 251, 270, 303], "failobj": 76, "failur": [7, 24, 83, 92, 236, 237], "fairli": [1, 5, 7, 15, 21], "fake": 251, "fall": [6, 21, 237, 260], "fals": [0, 3, 4, 7, 8, 11, 15, 17, 20, 21, 22, 30, 31, 32, 36, 37, 38, 49, 51, 52, 64, 67, 68, 69, 70, 73, 80, 83, 88, 91, 94, 104, 105, 127, 129, 132, 135, 136, 139, 140, 143, 144, 148, 149, 151, 152, 153, 154, 155, 158, 160, 162, 166, 168, 169, 170, 176, 183, 184, 185, 187, 188, 189, 190, 193, 195, 196, 199, 202, 204, 218, 219, 220, 221, 226, 231, 236, 237, 238, 239, 253, 258, 260, 261, 264, 265, 270, 277, 279, 281, 283, 288, 294, 297, 299, 303, 305], "famili": [0, 2, 7, 8, 11, 12, 19, 25, 68, 197, 209, 211, 288], "familiar": [7, 11, 12, 20, 24, 30, 299], "famou": 13, "fan": 19, "fanci": [15, 31, 91, 169], "fancier": 31, "fanhfmvlcg": 250, "faq": [35, 46, 51, 61, 221, 247], "faqblat": 221, "faqformat": [35, 46, 51, 61, 247], "far": [4, 8, 19, 20, 21, 100, 251, 278], "farfavrygk": 0, "farfavrygksyesaaevrrrfrifsesleevrstn": 0, "fas1": [11, 291], "fas2": [11, 291], "fasciculatum": 23, "fashion": 23, "fasman": 265, "fast": [0, 2, 12, 14, 23, 30, 31, 32, 69, 146, 182, 253, 270, 278], "fast_bam": [268, 270], "fasta": [1, 3, 7, 8, 9, 11, 12, 13, 14, 15, 20, 22, 27, 30, 32, 55, 56, 59, 60, 62, 66, 67, 69, 80, 91, 129, 161, 182, 209, 217, 238, 241, 246, 250, 251, 252, 253, 256, 260, 270, 274, 278], "fasta36": 0, "fasta_align": 161, "fasta_aln": 32, "fasta_data": 23, "fasta_format_str": 22, "fasta_guid": 226, "fasta_list2": 226, "fasta_seq": 32, "fasta_sourc": 251, "fasta_str": 3, "fasta_www2": 226, "fastaio": [6, 23, 27, 56, 217, 238, 251], "fastaiter": [27, 238, 241, 246], "fastam10index": [27, 217, 226], "fastam10iter": [27, 56, 59], "fastam10pars": [27, 217, 226], "fastaout": [30, 32], "fastapair": [30, 32], "fastaparttre": [30, 32], "fastatwolineiter": [27, 238, 241], "fastatwolinepars": [27, 238, 241], "fastatwolinewrit": [27, 238, 241], "fastawrit": [27, 238, 241], "faster": [0, 3, 4, 6, 7, 8, 14, 23, 32, 36, 37, 84, 94, 166, 169, 182, 217, 238, 270, 297], "fastest": [11, 56, 92, 181, 182, 238, 270], "fastmmcifpars": [27, 133, 143], "fastq": [2, 9, 21, 238, 240, 249, 251, 253, 260, 270, 278], "fastq_dict": 238, "fastqgeneraliter": [6, 23, 27, 238, 251], "fastqilluminaiter": [27, 238, 251], "fastqilluminawrit": [27, 238, 251], "fastqphrediter": [27, 238, 251], "fastqphredwrit": [27, 238, 251], "fastqsolexaiter": [27, 238, 251], "fastqsolexawrit": [27, 238, 251], "fasttre": [17, 182], "fasttree_ex": 182, "fasttreecommandlin": [181, 182], "fasttreewin32": 182, "fatal": 151, "fati": 206, "fau": 123, "faucher": 265, "favor": [7, 275], "favorit": [7, 11, 12, 17, 19, 20, 23, 265], "fbgn0000210": 11, "fc": 182, "fconsens": 80, "fconsensecommandlin": [27, 79, 80], "fcygrllctv": 250, "fcygrlvctv": 250, "fdir": 140, "fdnadist": 80, "fdnadistcommandlin": [27, 79, 80], "fdnapar": 80, "fdnaparscommandlin": [27, 79, 80], "fe2": 25, "fe2s2": 25, "feat": 197, "featur": [0, 3, 6, 7, 9, 14, 15, 19, 20, 22, 23, 25, 27, 38, 68, 80, 92, 93, 94, 95, 98, 99, 104, 122, 127, 158, 177, 182, 217, 222, 238, 245, 251, 255, 260, 272, 282, 301, 302], "feature_clean": 92, "feature_end_mark": [92, 94], "feature_fn": 122, "feature_head": [238, 245], "feature_i": 8, "feature_id": 104, "feature_kei": 94, "feature_loc": 237, "feature_qualifier_ind": [92, 94], "feature_qualifier_spac": [92, 94], "feature_seq": 21, "feature_start_mark": [92, 94], "feature_t": 94, "feature_x": 8, "featurea": 104, "featureb": 104, "featureloc": [27, 237], "featurepars": [27, 92], "featureposit": 21, "featureset": [8, 98, 104], "featuret": [27, 272], "featurevalueclean": [27, 92, 95], "feb": [0, 7, 74, 83, 88, 261], "februari": [9, 20, 87], "fed": 12, "feed": [25, 85, 89, 92, 94, 191], "feedback": [5, 6, 27], "feedstock": 5, "feel": [5, 19, 108, 146], "fefec": 0, "felcat3": 0, "felsenstein": [0, 17, 65, 129], "feng": 199, "fennel": 2, "fesfgdl": 13, "fetch": [3, 7, 11, 15, 20, 23, 25, 83, 85, 149, 274, 288, 303], "fetch_dbid_by_dbnam": [301, 303], "fetch_motif": [11, 287, 288], "fetch_motif_by_id": [11, 287, 288], "fetch_motifs_by_nam": [11, 287, 288], "fetch_ncbi_taxonomi": [303, 305], "fetch_seqid_by_access": [301, 303], "fetch_seqid_by_display_id": [301, 303], "fetch_seqid_by_identifi": [301, 303], "fetch_seqid_by_vers": [301, 303], "fetch_seqids_by_access": [301, 303], "few": [0, 3, 8, 10, 12, 15, 17, 18, 20, 23, 25, 31, 68, 251, 264], "fewer": 270, "ff": [0, 30, 32], "ff8000": 183, "ffer": 3, "fffdfhghhhjjjijjjjijjjgedhhgghgbgiigiiab": 0, "fft": [30, 32], "fg": 182, "fgcolor": [115, 117], "fgkeftppvqaayqkvvagvanalahkyh": 13, "fh": [0, 11, 94, 245], "fhfkswmskhrkty": 0, "fhv": 6, "fi": [202, 203], "fibronectin": 211, "fid": 140, "fiddli": 6, "field": [0, 2, 4, 7, 15, 17, 18, 20, 23, 25, 27, 30, 36, 38, 51, 61, 66, 83, 119, 126, 133, 139, 162, 169, 218, 219, 248, 251, 252, 256, 258, 263, 270, 274, 275, 276, 277, 278, 295, 297], "field_nam": 277, "fieldlist": 7, "fieldn": 126, "fieldnam": [133, 169], "fieldval": 277, "fifteen": 16, "fifth": 278, "fifti": 6, "fig": [6, 8, 15, 17], "figur": [3, 6, 8, 19, 22, 102], "file": [1, 2, 3, 8, 9, 10, 16, 17, 18, 22, 24, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 76, 78, 80, 82, 83, 84, 86, 87, 88, 90, 92, 93, 94, 95, 96, 99, 101, 103, 104, 105, 112, 113, 114, 116, 117, 121, 123, 125, 126, 128, 129, 133, 135, 137, 140, 141, 142, 143, 145, 148, 149, 150, 151, 152, 153, 154, 158, 162, 164, 165, 167, 168, 169, 170, 171, 173, 174, 182, 183, 185, 188, 190, 191, 193, 195, 196, 198, 199, 201, 202, 203, 204, 205, 208, 209, 210, 211, 212, 213, 214, 217, 218, 219, 220, 221, 222, 226, 229, 232, 234, 236, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 283, 284, 286, 287, 293, 295, 296, 299, 303], "file_format": 149, "file_handl": 209, "file_nam": 270, "file_path": 171, "file_typ": 137, "fileformat": 238, "filehandl": [142, 143, 148, 151, 170], "filenam": [0, 1, 6, 7, 8, 9, 12, 13, 15, 17, 19, 20, 23, 30, 32, 56, 67, 68, 73, 80, 83, 84, 104, 105, 126, 129, 137, 138, 141, 142, 143, 149, 153, 158, 171, 182, 209, 210, 214, 217, 219, 220, 221, 223, 224, 225, 226, 231, 232, 238, 241, 250, 251, 270, 278, 298, 303], "fileno": [27, 278], "fileobj": 278, "filepars": [200, 201], "filepath": [170, 173], "fileprefix": 182, "filerecord": [200, 201, 204], "fill": [0, 5, 11, 15, 89, 99, 102, 104, 169, 248, 270, 287], "fill_chromosom": [98, 102], "fill_color": 99, "filt": 7, "filter": [7, 10, 15, 17, 20, 21, 56, 67, 68, 69, 70, 79, 80, 169, 183, 238, 270, 277], "filter_and_trim": 253, "filter_func": [3, 20], "filtered_qresult": 20, "filtering_db": [68, 69], "fin": [136, 158, 169, 272], "final": [0, 3, 4, 7, 12, 15, 17, 20, 21, 23, 32, 45, 66, 69, 99, 100, 104, 169, 182, 190, 193, 195, 196, 202, 214, 221, 246, 251, 253, 260, 269, 270, 278], "final_optim": 166, "finalize_structur": [171, 172], "find": [1, 3, 4, 5, 6, 8, 10, 12, 13, 15, 17, 18, 19, 21, 23, 24, 25, 27, 30, 32, 36, 68, 80, 81, 83, 84, 85, 94, 119, 121, 146, 154, 167, 169, 175, 183, 186, 214, 216, 226, 229, 236, 237, 270, 278, 283, 289, 290, 291, 292, 294, 297], "find_ani": [17, 181, 183], "find_clad": [17, 181, 183], "find_el": [17, 181, 183], "find_orfs_with_tran": 6, "find_start": [92, 94], "find_stat": [27, 121], "finder": 11, "fine": [6, 8, 9, 13, 20, 278], "finer": 169, "finger": [11, 272, 283], "fingerprint": 88, "finish": [8, 12, 17, 19, 22, 67, 130, 169, 183, 198, 252], "fir": 123, "firebrick": 8, "first": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 30, 31, 32, 35, 46, 51, 56, 61, 65, 67, 68, 69, 73, 80, 99, 104, 109, 117, 126, 129, 132, 137, 149, 154, 169, 172, 180, 182, 183, 197, 204, 221, 222, 236, 237, 238, 241, 247, 249, 251, 256, 260, 261, 265, 269, 270, 274, 276, 277, 278, 283, 288, 297, 298, 299, 303], "first_align": 12, "first_index": 283, "first_lin": 1, "first_model": 15, "first_pag": 83, "first_primer_seq": 82, "first_record": [23, 30], "first_row": 299, "first_tag": 84, "firstli": [3, 6, 8, 251], "firstlin": 126, "fisher": 202, "fit": [0, 2, 4, 5, 7, 8, 16, 21, 27, 30, 120, 127, 178, 202, 203, 216, 229, 237, 243, 251, 270, 280, 298, 299, 300], "fitch": [32, 199], "fite": 0, "fitzgerald": 2, "five": [0, 7, 8, 12, 16, 20, 21, 51, 118, 251], "fix": [0, 11, 15, 21, 24, 32, 146, 152, 163, 175, 176, 182, 270, 277, 278, 303], "fix_alpha": 17, "fixedbranch": [30, 32], "fixmat": 270, "fixmate_cmd": 270, "fkauff": [130, 269], "fkkkkf": 30, "fknyylnnk": 0, "fknyylnnkeaiftddlpvadylddefinsiptafdwrtrg": 0, "fkskinenykvtfta": 0, "fkswmskhrk": 0, "fkswmskhrkty": 0, "fl": [7, 13], "fl1": 237, "fl2": 237, "fl3": 237, "fla": 7, "flag": [0, 3, 15, 17, 20, 52, 104, 135, 136, 152, 154, 155, 158, 162, 169, 214, 217, 218, 221, 222, 226, 229, 270, 297, 303], "flag_disord": [133, 135, 155], "flank": [2, 59, 80, 141, 283], "flat": [7, 10, 11, 13, 23, 94, 238, 255, 275], "flavanoid": 25, "flavonoid": 23, "flavor": [4, 15, 20, 71, 218, 226, 229], "flefqdkfnk": 0, "flefqdkfnkki": 0, "flength": 140, "flexibl": [4, 6, 7, 9, 15, 19, 23, 169, 177, 207, 261, 265], "flickr": 19, "flicwvpyai": 250, "flight": 123, "flip": [6, 8, 104], "float": [3, 4, 6, 17, 24, 54, 68, 69, 71, 73, 80, 104, 135, 140, 141, 146, 152, 157, 158, 162, 166, 168, 169, 176, 182, 183, 197, 216, 251, 261, 263, 265, 267, 270, 286], "float0": [135, 162], "float1_color": [98, 104], "float32": 11, "float64": [4, 15, 73, 169], "float64p4": 169, "florian": 2, "florida": 7, "flow": [6, 253], "flow_index": 253, "flow_kei": 253, "flow_valu": 253, "flowgram": [6, 238, 253], "fluorophor": 261, "flush": [27, 30, 56, 68, 238, 278, 298], "flvcwvpya": 250, "flx": 6, "fly": [6, 13, 20, 25], "flyfactorsurvei": [11, 283], "fm": 140, "fmd": 264, "fmdfactor": 264, "fmdmethod": 264, "fme": 154, "fmn": 53, "fmodel": [30, 32], "fmt": [0, 3, 4, 13, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 68, 183, 246, 283], "fmt_": [27, 68, 71], "fn": [30, 32], "fn_list": 126, "fna": [6, 7, 8, 21], "fname": [153, 202, 203, 204, 218, 222, 283], "fneighbor": 80, "fneighborcommandlin": [27, 79, 80], "fnnf": 0, "fnny": 0, "fnr": [11, 294], "focu": [19, 21, 22, 25], "focus": [8, 12, 15, 16, 19, 263], "focuss": 8, "fold": [209, 211, 272], "folder": [6, 8, 20, 21, 24, 149, 166], "folk": 3, "follow": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 42, 43, 45, 52, 54, 56, 59, 62, 65, 66, 68, 73, 76, 80, 86, 88, 90, 92, 94, 99, 104, 123, 135, 137, 140, 148, 158, 169, 170, 173, 177, 182, 197, 204, 207, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 241, 246, 247, 248, 250, 251, 253, 256, 260, 261, 272, 274, 280, 283, 290, 295, 297, 298, 299], "font": [8, 104], "fontnam": 105, "fontsiz": 105, "foo": [17, 270], "foo1": 17, "foo2": 17, "foo3": 17, "footer": [42, 45, 56, 59, 60, 238, 240, 246, 269], "fop": [30, 32], "forc": [6, 12, 15, 20, 21, 30, 32, 148, 169, 240, 270], "force_gener": 297, "foreground": 117, "forg": 5, "forget": [7, 15, 251], "forgotten": 5, "forkhead": 11, "form": [0, 3, 4, 6, 7, 9, 11, 15, 16, 25, 30, 45, 69, 72, 84, 93, 107, 126, 137, 140, 169, 182, 197, 237, 272, 278, 290], "formal": 172, "formaldehyd": 264, "formamid": 264, "format": [1, 2, 4, 6, 7, 8, 9, 10, 13, 16, 17, 18, 20, 22, 24, 25, 27, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 71, 73, 78, 80, 82, 83, 85, 87, 88, 89, 92, 93, 94, 97, 99, 104, 105, 117, 118, 129, 132, 148, 149, 150, 151, 152, 158, 162, 165, 169, 181, 182, 183, 185, 188, 190, 197, 198, 199, 201, 204, 207, 209, 210, 211, 213, 214, 219, 220, 223, 224, 225, 227, 228, 230, 231, 232, 233, 235, 236, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 264, 268, 270, 271, 272, 274, 275, 276, 277, 278, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 297, 299, 303], "format1": 35, "format2": 51, "format23": 248, "format5": [46, 61], "format_align": [14, 27, 30, 33, 35, 39, 40, 43, 45, 46, 47, 49, 50, 51, 52, 53, 297], "format_alignemt": 297, "format_branch_length": 190, "format_confid": 190, "format_entrez_queri": [68, 70], "format_label": [27, 181, 185], "format_object": [68, 70], "format_output": [206, 207], "format_phylip": [181, 199], "format_spec": [30, 71, 183, 260, 283], "format_typ": [3, 68, 70], "formatt": 54, "formatvers": [0, 62], "former": [0, 11, 15, 257], "formfe": 236, "formula": [11, 12, 109, 112, 119, 221, 251, 264], "formuleaa": 167, "fortran": 9, "fortun": [3, 12], "forum": 5, "forward": [0, 6, 7, 8, 11, 12, 13, 15, 34, 76, 80, 104, 107, 109, 135, 139, 169, 237, 251, 252, 261, 280], "forward_algorithm": [106, 107], "forward_gc": 81, "forward_length": 81, "forward_seq": 81, "forward_start": 81, "forward_t": [22, 75, 76], "forward_tm": 81, "forward_var": 109, "forwardinput": [79, 80], "forwardref": [136, 144, 155, 160], "foster": 2, "found": [0, 3, 4, 5, 6, 7, 9, 12, 13, 15, 17, 18, 22, 23, 24, 25, 30, 53, 54, 56, 67, 68, 71, 72, 73, 80, 84, 102, 104, 140, 169, 172, 182, 183, 195, 198, 210, 211, 212, 213, 214, 217, 236, 237, 238, 251, 252, 253, 258, 270, 271, 274, 275, 283, 290, 295, 298, 299, 300], "foundat": [2, 5, 238, 250], "four": [0, 4, 8, 15, 17, 20, 23, 25, 149, 169, 176, 217, 251, 261, 264, 283], "fourcolumn": 11, "fourrow": 11, "fourth": [0, 11, 15, 20, 23, 169, 251, 278], "fout": 31, "fp": [7, 91, 123], "fphf": 13, "fpr": [11, 294], "fprotdist": 80, "fprotdistcommandlin": [27, 79, 80], "fprotpar": 80, "fprotparscommandlin": [27, 79, 80], "fq": 270, "fq_dict": 6, "fqatrl": 0, "fr": [13, 15, 17, 153, 182, 245], "frac": [4, 6, 11, 12, 16], "fracsampl": [79, 80], "fraction": [23, 80, 264, 265, 270, 290], "fractur": 260, "fragaria": 23, "fragil": 24, "fragment": [7, 8, 20, 22, 27, 32, 83, 88, 104, 133, 140, 169, 214, 215, 217, 221, 222, 229, 238, 243, 250, 268, 270, 278], "fragment1": 140, "fragment2": 140, "fragment_data": 140, "fragment_s": 104, "fragmentmapp": [27, 133], "frame": [0, 4, 13, 20, 22, 27, 30, 69, 71, 218, 222, 236, 237, 261, 281], "frame_shift_penalti": [68, 69], "frameshift": [13, 71, 222, 272, 281], "frameshift_minus_one_scor": 13, "frameshift_minus_scor": 13, "frameshift_minus_two_scor": 13, "frameshift_one_scor": 13, "frameshift_plus_one_scor": 13, "frameshift_plus_scor": 13, "frameshift_plus_two_scor": 13, "frameshift_scor": [13, 30], "frameshift_two_scor": 13, "framework": [3, 5, 26, 32, 177, 307], "francisco": 83, "franck": 7, "frank": [2, 130, 269], "frederick": 2, "free": [3, 5, 6, 7, 11, 15, 19, 24, 69, 87, 88, 93, 137, 172, 197, 244, 250, 270, 272], "freedom": 202, "freeli": [2, 5, 7, 9, 27, 83], "frefix": 270, "freier": 264, "freq": [11, 80], "freqsfrom": [79, 80], "frequenc": [11, 12, 13, 27, 30, 31, 32, 34, 80, 132, 181, 182, 202, 203, 265, 275, 281, 283, 286, 290, 293], "frequencypositionmatrix": [27, 283, 290], "frequent": [1, 11, 251, 265], "frg": 32, "fri": 0, "frick": 2, "friedberg": [2, 26], "friend": [7, 19], "friendli": 7, "frog": 250, "from": [2, 3, 4, 6, 8, 9, 10, 14, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 29, 30, 31, 32, 40, 41, 45, 47, 50, 52, 53, 54, 55, 56, 57, 58, 59, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 76, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 99, 100, 102, 104, 108, 109, 111, 112, 113, 114, 115, 116, 117, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 132, 135, 136, 137, 139, 140, 144, 146, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 160, 165, 166, 168, 169, 170, 171, 172, 173, 174, 176, 177, 180, 182, 183, 185, 186, 190, 193, 194, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 206, 207, 209, 210, 214, 215, 216, 217, 218, 219, 220, 221, 222, 224, 225, 226, 232, 236, 237, 238, 240, 242, 245, 247, 248, 249, 251, 252, 253, 254, 255, 256, 258, 260, 261, 263, 264, 265, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 283, 286, 287, 288, 289, 290, 291, 292, 293, 295, 296, 297, 298, 299, 303, 305, 306, 307], "from_byt": [30, 36], "from_clad": [181, 183, 197], "from_hex": [181, 183], "from_level": 104, "from_msa": [279, 280], "from_nam": [181, 183], "from_seq": [279, 281], "from_seqfeatur": [181, 197], "from_seqrecord": [181, 197], "from_stat": 108, "from_str": [0, 30, 36, 181, 185, 188, 190], "from_tre": [17, 181, 197], "fromstr": [27, 237], "front": [183, 236], "frozen": 23, "frozenset": [30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 68, 219, 220, 221, 223, 224, 225, 226, 230, 231, 232, 233, 236, 237, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259, 281, 291], "fruit": 13, "frustrat": 19, "frutig": 263, "fsa": 182, "fseqboot": 80, "fseqbootcommandlin": [27, 79, 80], "fsm": [30, 32], "fst": [202, 203], "ft": [94, 182, 245], "ftable_doc": 245, "ftid": 272, "ftitmytslh": 250, "ftp": [6, 7, 8, 15, 22, 23, 25, 76, 90, 93, 94, 153, 277], "ftreedist": 80, "ftreedistcommandlin": [27, 79, 80], "ftvtmytsmh": 250, "ftvtmytsmn": 250, "fuchsia": 183, "fucosyltransferas": 113, "fujii": 25, "fulfil": [0, 3], "full": [0, 3, 4, 6, 8, 9, 10, 12, 13, 14, 15, 17, 20, 22, 23, 24, 25, 32, 45, 59, 67, 80, 104, 108, 123, 131, 135, 139, 140, 152, 155, 168, 188, 197, 217, 221, 226, 229, 236, 237, 238, 256, 257, 260, 261, 269, 278, 281, 288], "full_id": [15, 139], "full_rf_tabl": 281, "full_sequ": [14, 297], "full_transl": [279, 281], "fullhelp": [30, 32], "fulli": [11, 21, 22, 23, 36, 73, 169, 260, 270, 278, 288, 305], "fullnam": [7, 135, 162], "fun": [8, 19], "function": [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 35, 36, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 73, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 99, 100, 104, 105, 108, 109, 110, 112, 113, 114, 116, 119, 120, 121, 122, 123, 127, 130, 138, 149, 169, 172, 176, 182, 183, 185, 186, 188, 190, 191, 194, 198, 201, 204, 205, 209, 217, 218, 237, 238, 240, 241, 244, 245, 247, 248, 249, 250, 251, 253, 255, 256, 259, 260, 261, 262, 263, 269, 270, 271, 272, 273, 274, 277, 278, 280, 282, 283, 290, 291, 292, 297, 298, 299, 300, 303, 305], "fund": 19, "further": [0, 3, 4, 5, 6, 7, 11, 15, 20, 61, 68, 69, 89, 91, 99, 104, 169, 182, 237, 252, 258, 260, 303], "furthermor": [8, 20, 237, 278], "fusion": 197, "futur": [0, 3, 7, 15, 16, 23, 27, 30, 32, 67, 68, 69, 70, 80, 83, 92, 177, 182, 209, 236, 237, 260, 270, 277, 285], "fuzzi": [6, 92, 237], "fuzznuc": 80, "fuzznuccommandlin": [27, 79, 80], "fuzzpro": 80, "fuzzprocommandlin": [27, 79, 80], "fwghkhffsshfssqmvsegfgvileipfssqlvssleekkipkyqnlrsihsifpfl": 7, "fwsqpyrihikqlsnysfsflgyfssvlenhlvvrnqmlensfiinlltkkfdtiapv": 7, "g": [0, 1, 2, 3, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, 24, 30, 31, 32, 53, 56, 62, 66, 67, 68, 69, 70, 73, 76, 80, 88, 94, 99, 104, 108, 109, 119, 123, 129, 132, 135, 137, 139, 145, 146, 149, 152, 153, 155, 158, 159, 162, 164, 169, 172, 179, 180, 182, 183, 197, 199, 202, 203, 209, 210, 211, 212, 214, 215, 216, 217, 221, 226, 229, 236, 237, 238, 241, 247, 248, 249, 250, 251, 253, 260, 261, 263, 264, 265, 268, 269, 270, 272, 274, 278, 280, 287, 288, 296, 297, 299], "g116295259": 7, "g116295260": 7, "g13550663": 7, "g13576946": 7, "g16198419": 7, "g16198420": 7, "g219411": 7, "g219412": 7, "g219415": 7, "g219416": 7, "g25137": 68, "g26680": 238, "g26684": 68, "g26685": 238, "g29385": 238, "g45501306": 7, "g45501307": 7, "g47115198": 7, "g47115199": 7, "g59899": 7, "ga": [0, 13, 14, 30, 53], "gaa": [0, 7, 22, 76], "gaaa": [0, 13, 30], "gaaaaggaaagtacggcccggccactccgggtgtgtgctaggagggctta": 0, "gaaattgtat": 278, "gaac": 14, "gaact": [13, 30], "gaactgg": 30, "gaacttaacattttcttatgacgtaaatgaagtttatatataaatttcctttttattgga": 23, "gaactttggc": 7, "gaagaggaaaagtagatccctggcgtccggagctgggacgt": 0, "gaaqtcsatlagnhlmrda": 0, "gaattactat": 240, "gaattc": [8, 260], "gabor": 2, "gabriel": 262, "gac": [14, 22], "gacagctag": 12, "gaccagagcctcgcatggggg": 283, "gaccctgatttgttgttgggccgcctcgggagcgtccatggcgggt": 23, "gacct": 30, "gacctg": 30, "gacgaaagtattaat": 222, "gacgccggggat": 283, "gacgscwtf": 0, "gacttaatagcc": 0, "gae": 23, "gaf": [276, 277], "gaf20field": 277, "gafbyproteiniter": [27, 276, 277], "gafiter": [27, 276, 277], "gag": [22, 76], "gagatcagagggccg": 283, "gagatctccgccc": 199, "gagatttactgactttcctagaatagtttctctactggaaacctgatgcttttataagccattgtgatta": 238, "gagatttccgcct": 199, "gagavivgsdpdlsverplyelvwtgatllpdsegaidghlrevgltfhllkdvpglisk": [21, 23], "gagcqsggcdg": 0, "gagggtgttgatcatgatgatggcg": 251, "gahageygaeal": 13, "gain": [14, 197], "gained_count": 197, "gainesvil": 7, "gamma": [0, 12, 30, 79, 80, 172, 181, 182, 199, 241, 280], "gammacoeffici": [79, 80], "gammai": 182, "gammalogtopaup": 182, "gander": 3, "gap": [3, 7, 9, 12, 14, 20, 27, 30, 31, 32, 33, 39, 42, 43, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 68, 69, 71, 79, 80, 129, 158, 166, 182, 197, 218, 221, 222, 236, 237, 240, 260, 261, 270, 281, 295, 297], "gap_a_fn": 297, "gap_b_fn": 297, "gap_char": [279, 281, 297], "gap_consensu": [30, 31], "gap_extend": [3, 268, 270], "gap_funct": 297, "gap_num": [20, 218], "gap_open": [3, 268, 270], "gap_penalti": [0, 71], "gap_scor": [12, 13, 30], "gap_trigg": [68, 69, 71], "gap_x_dropoff": 71, "gap_x_dropoff_fin": 71, "gapcost": [68, 70], "gapdist": [30, 32], "gapext": [30, 32], "gapextend": [12, 30, 32, 67, 68, 69, 79, 80], "gaplimit": [79, 80], "gaponli": [128, 129], "gapopen": [12, 30, 32, 67, 68, 69, 79, 80, 218], "gapopen_num": [218, 221], "gappenalti": [79, 80], "gaprat": [30, 32], "garcia": 2, "gari": 2, "gascuel": [65, 182], "gaston": 2, "gat": [13, 22, 30, 222], "gatacgcagtcatattttttacacaattctctaatcccgacaaggtcgtaggtc": 21, "gatatcaagg": 7, "gatc": [21, 76], "gatcctcaaa": 7, "gatcg": 22, "gatcgatgggcctatataggatcgaaaatcgc": 22, "gatctggacc": 7, "gatgacggtgt": 6, "gatgggaaacccatggccgagtgggaagaaaccagctgaggtcacatcaccagaggagggagagtgtggcccctgactcagtccatcagcttgtggagctg": 0, "gatgggcc": 22, "gatgtgcaatacctttgtagaggaa": 251, "gather": [22, 53], "gattattaga": 7, "gattgctttt": 7, "gatttctcgg": 7, "gattttgggg": 7, "gau": 66, "gauc": 76, "gaugagggu": 66, "gaugagggucucuac": 66, "gave": [7, 8, 12, 19, 71], "gavlimfpstcnqywdehkr": [15, 169], "gb": [0, 1, 3, 6, 7, 8, 12, 13, 21, 23, 30, 32, 68, 83, 92, 237, 238, 245, 260, 278], "gb_base_ind": [92, 93], "gb_feature_ind": [92, 93], "gb_feature_internal_ind": [92, 93], "gb_internal_ind": [92, 93], "gb_line_length": [92, 93], "gb_other_internal_ind": [92, 93], "gb_sequence_ind": [92, 93], "gb_vrl": 23, "gbgtw": 11, "gbk": [3, 7, 8, 19, 23], "gbrel": 93, "gbrows": 305, "gbseq_access": 7, "gbseq_creat": 7, "gbseq_definit": 7, "gbseq_divis": 7, "gbseq_featur": 7, "gbseq_length": 7, "gbseq_locu": 7, "gbseq_moltyp": 7, "gbseq_organ": 7, "gbseq_oth": 7, "gbseq_primari": 7, "gbseq_refer": 7, "gbseq_sequ": 7, "gbseq_sourc": 7, "gbseq_stranded": 7, "gbseq_taxonomi": 7, "gbseq_topologi": 7, "gbseq_upd": 7, "gbvrl": 23, "gbvrl1": 23, "gbvrl2": 23, "gbvrl3": 23, "gbvrl38": 23, "gbvrl4": 23, "gbwithpart": 7, "gc": [0, 8, 11, 12, 22, 23, 30, 53, 66, 76, 80, 261, 264, 290], "gc123": [27, 261], "gc_content": [283, 290], "gc_fraction": [0, 6, 22, 27, 30, 261], "gc_frame": 261, "gc_map": [30, 53], "gc_skew": [27, 261], "gc_valu": 6, "gca": [22, 76], "gcaaggcttctacacccgtactcgaatg": 264, "gcaattatcc": 7, "gcacaagcat": 7, "gcacaggctgcggaaattacgttagtcccgtcagtaaaattacagataggcgatcgtgat": 22, "gcacgtccctgagca": 283, "gcagctgaaaaca": 0, "gcataatttgtggtagtgggggactgcgttcgcgctttcccctg": 30, "gcatt": 11, "gcc": [5, 19, 22, 23], "gccacgtaatgggccgctgaaagggtgcccga": 22, "gccactagcagagcagggggc": 283, "gccatcgtaatgggccgctgaaagggtgcccga": 22, "gccattgtaatgggccgctgaaagggtgcccga": 22, "gcccagttcgttcagttgtg": 62, "gcccatatatgg": [11, 283], "gccggttgctgttcattagg": 283, "gcclamp": [79, 80], "gcg": [22, 27, 32, 48, 56, 63, 76, 261, 262], "gcg_checksum": 262, "gcgattttcgatcctatataggcccatcgatc": 22, "gcgctcagccggagtgtcccgggccctgc": 0, "gcgctcagccggagtgtcccgggccctgctttcctttt": 0, "gcgctggag": 13, "gcggcatgtgaaa": 11, "gcgta": 11, "gck": [238, 242], "gckio": [27, 238], "gckiter": [27, 238, 242], "gclmkkssivatiitilsgsanaassqlip": 6, "gcngglp": 0, "gcngglpsqafeyikyng": 0, "gcngglpsqafeyikynggidteesypykgvngv": 0, "gcq": 0, "gcqgglp": 0, "gcqgglpsqafeyilynk": 0, "gcqgglpsqafeyilynkgimgedtypyqgkdgi": 0, "gct": [22, 236], "gctaa": 236, "gctagcggagtgtatactggcttactatgttggcactgatgagggtgtcagtga": 260, "gctgtagtaag": 22, "gctgttatgggtcgttggaagggtggtcgtgctgctggttag": 22, "gcttatgtaa": [11, 283], "gcu": 236, "gcuaa": 236, "gcuguuaugggucguuggaaggguggucgugcugcugguuag": 22, "gd": 7, "gd_diagram": 8, "gd_feature_set": 8, "gd_labels_default": 8, "gd_track_for_featur": 8, "gdai": 197, "gdb": 7, "gdct": 104, "gdd": [8, 104], "gddiagram": 8, "gde": 32, "gdfeatureset": 8, "gds16": 7, "gds_featur": 8, "gdt_featur": 8, "gdutil": 8, "gdvv": 261, "ge": [7, 13], "geal": 14, "gee": 0, "geez": 3, "geffer": 2, "geialwslvv": 250, "gemkeqtewhrvvlfgklaevaseylrkgsqvyiegqlrtrkwtdq": 260, "gen": 18, "gen_kei": [133, 169], "gen_tupl": [133, 169], "genafpair": [30, 32], "genbank": [3, 6, 8, 9, 22, 24, 27, 32, 68, 80, 104, 237, 238, 245, 256, 260, 274, 275, 278], "genbank_ind": [92, 94], "genbank_spac": [92, 94], "genbankcdsfeatureiter": [27, 238, 245], "genbankiter": [27, 238, 245], "genbankscann": [27, 92, 94], "genbankwrit": [27, 238, 245], "gene": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 17, 19, 21, 22, 23, 27, 34, 73, 96, 99, 104, 111, 113, 115, 117, 119, 123, 182, 197, 202, 237, 238, 242, 260, 273, 274, 275, 277, 280], "gene2xml": 7, "gene_associ": 277, "gene_color": 8, "gene_descript": 10, "gene_id": [7, 10, 275], "gene_identifi": 10, "gene_nam": [25, 272], "gene_record": 260, "gene_symbol": 10, "geneclust": [4, 73], "geneid": [4, 7, 21, 73, 94, 260, 278], "genellina": 262, "genenam": [4, 7, 73], "geneontologi": 277, "genepop": [27, 200], "genepop_dir": [202, 203], "genepopcontrol": [200, 201, 202, 203], "gener": [0, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 42, 44, 45, 52, 55, 56, 59, 60, 61, 66, 67, 68, 71, 76, 80, 83, 91, 93, 96, 99, 100, 107, 108, 109, 110, 116, 123, 125, 126, 127, 132, 139, 158, 168, 169, 176, 178, 182, 183, 185, 186, 188, 190, 197, 198, 205, 217, 218, 222, 237, 238, 239, 241, 242, 245, 246, 247, 251, 252, 253, 254, 256, 258, 259, 260, 261, 264, 269, 270, 272, 273, 274, 283, 288, 290, 296, 297, 299], "genera": 19, "generic_by_id": 76, "generic_dbutil": [301, 304], "genericpositionmatrix": [27, 283, 290], "genesymbol": 0, "genet": [0, 2, 6, 13, 22, 26, 30, 50, 65, 69, 76, 80, 99, 190, 199, 200, 236, 237, 260, 261, 264, 307], "genetic_cod": [68, 70, 261], "geneticcod": 7, "genetre": 4, "genic": 202, "genom": [0, 2, 3, 7, 8, 10, 11, 13, 20, 21, 22, 30, 32, 35, 36, 37, 38, 39, 46, 51, 52, 61, 79, 80, 93, 104, 111, 115, 119, 197, 200, 221, 237, 238, 245, 247, 270, 275, 278], "genome2genom": [42, 222], "genome_align": 0, "genomediagram": [2, 7, 9, 26, 27, 98, 99, 123, 307], "genomeprj": 7, "genomeproject": 21, "genotyp": [202, 203, 270], "genpept": [7, 238], "gensat": 7, "genu": [93, 132, 197], "genuin": 20, "geo": 27, "geodet": 197, "geodetic_datum": 197, "geograph": [197, 198], "geometr": [4, 139], "geometri": [139, 169], "georg": 2, "gerald": 2, "germ": 0, "get": [3, 5, 6, 7, 8, 10, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 30, 31, 32, 34, 49, 54, 60, 64, 67, 68, 70, 75, 76, 82, 83, 85, 92, 93, 97, 104, 108, 109, 117, 119, 132, 139, 140, 149, 154, 156, 159, 164, 169, 171, 175, 179, 180, 182, 183, 197, 199, 202, 204, 205, 209, 214, 216, 236, 237, 238, 245, 246, 248, 251, 252, 253, 258, 260, 265, 274, 276, 278, 280, 281, 296, 297, 299, 300, 303], "get_acc": 23, "get_access": 23, "get_acgt": [283, 296], "get_alignment_length": [12, 27, 30, 56, 59], "get_all_assembli": [133, 149], "get_all_entri": [133, 149], "get_all_obsolet": [15, 133, 149], "get_allel": [201, 203], "get_allele_frequ": [201, 203], "get_alleles_all_pop": [201, 203], "get_aln_length": [279, 280], "get_altloc": [15, 133, 135], "get_amino_acids_perc": [261, 265], "get_angl": [15, 133, 169], "get_anis": [15, 133, 135], "get_area": [27, 298, 300], "get_arrai": [133, 176], "get_artemis_colorschem": [98, 104], "get_atom": [15, 133, 136, 144, 155, 160], "get_avg_fi": [201, 203], "get_avg_fst_pair": [201, 203], "get_avg_fst_pair_locu": [201, 203], "get_basic_info": [201, 203], "get_bfactor": [15, 133, 135], "get_blank_emiss": [106, 108], "get_blank_transit": [106, 108], "get_ca_list": [133, 154], "get_chain": [133, 144, 160], "get_charg": [133, 135], "get_codon": [279, 281], "get_codon_num": [279, 281], "get_color": [27, 98, 100], "get_color_dict": [27, 98, 100], "get_colorschem": [98, 104], "get_column": [30, 31, 298, 299], "get_coord": [15, 133, 135, 140], "get_data": [98, 104, 128, 130], "get_dbutil": [301, 304], "get_dist": [181, 199], "get_dn_ds_matrix": [279, 280], "get_dn_ds_tre": [279, 280], "get_drawn_level": [98, 104], "get_f_stat": [201, 203], "get_featur": [8, 98, 104], "get_fi": [201, 203], "get_from_decod": [133, 171], "get_full_id": [15, 133, 135, 139], "get_full_rf_t": [279, 281], "get_fullnam": [15, 133, 135], "get_genotype_count": [201, 203], "get_gi": 238, "get_graph": [98, 104], "get_guide_coord_from_structur": [133, 166], "get_head": [15, 133, 151], "get_heterozygosity_info": [201, 203], "get_id": [15, 98, 104, 128, 130, 133, 135, 139, 140], "get_indiv": [200, 201, 205], "get_individu": [201, 204], "get_init_rm": [27, 133, 175, 216], "get_iter": [133, 139, 161], "get_kgml": [115, 117], "get_length": [15, 133, 169], "get_level": [98, 104, 133, 135, 139], "get_list": [15, 133, 139], "get_map": [133, 161], "get_markov_model": [106, 108], "get_matrix_by_nam": 288, "get_model": [133, 160], "get_multilocus_f_stat": [201, 203], "get_nam": [15, 133, 135], "get_node_info": [181, 185], "get_nontermin": [17, 181, 183], "get_occup": [15, 133, 135], "get_par": [15, 133, 135, 139], "get_path": [17, 181, 183], "get_phi_psi_list": [133, 154], "get_predict": [27, 133, 164], "get_prev": [128, 130], "get_prodoc_entri": [25, 27, 85], "get_property_valu": [283, 296], "get_prosite_entri": [25, 27, 85], "get_prosite_raw": [25, 27, 85], "get_qresult_id": [222, 223, 224, 225], "get_radiu": [133, 135], "get_raw": [6, 23, 217, 218, 219, 220, 221, 222, 224, 225, 226, 229, 232, 238, 298, 299], "get_recent_chang": [133, 149], "get_residu": [15, 30, 31, 133, 136, 144, 160, 169], "get_resnam": [15, 133, 154, 155], "get_resname_list": [133, 140], "get_rm": [27, 133, 175, 216], "get_rotran": [27, 133, 175, 216], "get_row": [298, 299], "get_scor": [181, 199], "get_segid": [15, 133, 155], "get_segment_info": [98, 102], "get_seq": [133, 153], "get_seq_by_acc": [301, 303], "get_seq_by_id": [301, 303], "get_seq_by_v": [301, 303], "get_seqres_fil": [133, 149], "get_seqs_by_acc": [301, 303], "get_sequ": [15, 133, 154], "get_serial_numb": [133, 135], "get_set": [98, 104], "get_sigatm": [15, 133, 135], "get_sign": [298, 299], "get_siguij": [15, 133, 135], "get_spherical_coordin": [27, 133, 176], "get_splic": [56, 61], "get_sprot_raw": [23, 25, 27, 85], "get_start_end": [27, 128, 129], "get_status_list": [133, 149], "get_structur": [15, 133, 137, 140, 143, 148, 150, 151, 154, 156, 157, 162, 165, 169, 170, 171, 173], "get_structural_models_for": [27, 133, 164], "get_structure_from_url": [15, 133, 171], "get_subseq_as_str": [301, 303], "get_succ": [128, 130], "get_support": [27, 181, 186], "get_surfac": [15, 27, 133, 156], "get_tau_list": [133, 154], "get_taxa": [128, 132], "get_temp_imagefilenam": [27, 98, 105], "get_termin": [17, 128, 132, 181, 183], "get_text": [283, 296], "get_theta_list": [133, 154], "get_tim": [298, 299], "get_track": [98, 104], "get_trail": [15, 133, 151], "get_transform": [27, 133, 175, 216], "get_unique_par": [27, 133, 159], "get_unpacked_list": [15, 133, 136, 155], "get_vector": [15, 133, 135], "getascend": [27, 209], "getascendentfromsql": [27, 209], "getastraldomainsfromfil": [27, 209], "getastraldomainsfromsql": [27, 209], "getatom": [209, 214], "getattr": 16, "getchildren": [27, 209], "getdescend": [27, 209], "getdescendentsfromsql": [27, 209], "getdomain": [27, 209], "getdomainbysid": [27, 209], "getdomainfromsql": [27, 209], "getnodebysunid": [27, 209], "getpar": [27, 209], "getroot": [27, 209], "getseq": [27, 209], "getseqbysid": [27, 209], "getseqmap": [209, 214], "getter": 169, "getvalu": [0, 12, 23, 56, 238, 253], "gevalwslvv": 250, "gf": [0, 53, 66], "gf_map": [30, 53], "gfa": 243, "gfa1": [238, 243], "gfa1iter": [27, 238, 243], "gfa2": [238, 243], "gfa2iter": [27, 238, 243], "gfaio": [27, 238], "gff": 274, "gff3": 237, "gfiarefnrk": 250, "gfpvnfltlf": 250, "gg": [0, 30], "gga": [21, 22, 76], "ggaaacaaagtttttctcaacatag": 251, "ggactacgacaatagctcagg": 12, "ggactc": 0, "ggatcc": 8, "ggatctacttttcctcttc": 0, "ggatgactgttacaggcttagctttgtgtgaaanccagtcacctttctcctaggtaatgagtagtgctgt": 238, "ggaucuucggaucu": 261, "ggc": 22, "ggcaccctggaggccatccagtggaccaagcactgggactccggcatc": 13, "ggcaccctggaggccatccagtggtccaagcactgggactccggcatc": 13, "ggege8bb": 0, "ggg": [0, 3, 20, 22, 76], "gggaatgttaaccaaatga": 0, "gggaggagatcgccccaaacgtatggtgagtcgggcg": 62, "gggccgcuga": 261, "gggccgtac": 0, "gggcgaacgtataaaccattctg": 62, "gggg": [0, 13, 30], "ggggatgctaagccaatgagttgttgtctctcaatgtg": 0, "gggggg": [0, 13, 30], "ggggtatttt": 7, "gggt": 30, "gggta": 11, "gggtt": [11, 30], "ggh": 241, "gghvnpavtfgafvggnitllrgivyiiaqllgstvaclllkfvtndmavgvfslsagvg": 260, "ggt": [0, 22, 23, 30], "ggtaccctggaggccatccagtggtccaagcactgggactccggcatc": 13, "ggtaccgggccccccctcgaggtcgacggtatcgataagcttgatatcgaattc": 207, "ggtaccgggccccccctcgaggtcgacggtatcgataagcttgatatcgaattcctg": 206, "ggtcatccta": 7, "ggtctacatgttggttaacc": 253, "ggtgcagagccgagtcacggggttgccagcacagg": 0, "ggtggggg": 0, "ggtt": [13, 22], "ggttacacttaccgataatgtctctgatga": 237, "ggtttgagaaagagaaatgagataa": 251, "ggtttt": 0, "ggua": 66, "ggug": 66, "ggwktcsgtcttststrhrgrsgw": 0, "ggwktcsgtcttststrhrgrsgwsartttaaclrasrksmraacsrsag": 0, "ghnvetikgmipdg": 0, "gi": [0, 1, 3, 7, 12, 13, 19, 20, 21, 23, 30, 56, 68, 69, 70, 93, 94, 217, 218, 238, 241, 256, 260, 275, 303], "gi_al": 218, "gi_list": 7, "gi_mask": [68, 69], "gi_mask_nam": [68, 69], "gi_str": 7, "gibson": 32, "gidteesypi": 0, "gidteesypykgvngv": 0, "gif": [8, 104], "giideibcff": 0, "giklfkkfa": 12, "giklfkkft": 12, "giklfkkfv": 12, "gilist": [68, 69], "gimgedtypi": 0, "gimgedtypyqgkdgi": 0, "gina": 2, "giqtessypi": 0, "giqtessypytaetgtqcnfnsanigakisnftmip": 0, "gish": 2, "github": [5, 9, 27, 140, 227, 234, 243], "githubusercont": [4, 25], "give": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 19, 21, 22, 23, 24, 27, 30, 35, 46, 51, 56, 61, 67, 68, 70, 71, 83, 94, 99, 100, 104, 107, 112, 113, 114, 117, 122, 126, 132, 214, 217, 237, 238, 241, 250, 251, 260, 269, 271, 274, 278, 282, 297, 298, 299, 303], "given": [0, 4, 6, 7, 8, 11, 12, 14, 15, 17, 20, 22, 23, 30, 31, 32, 34, 56, 60, 64, 69, 71, 73, 76, 83, 91, 94, 102, 104, 108, 116, 119, 120, 121, 122, 126, 127, 129, 136, 139, 140, 146, 149, 150, 159, 162, 169, 171, 180, 182, 183, 185, 186, 187, 188, 190, 191, 197, 199, 201, 203, 209, 214, 217, 219, 221, 224, 225, 232, 236, 237, 238, 245, 251, 253, 257, 261, 262, 263, 264, 265, 270, 281, 282, 283, 288, 290, 294, 297, 299, 300, 303, 305], "gkg108": 2, "gkheerqdeh": 250, "gkp1137": [2, 251], "gl": 13, "glai": 206, "glenn": 2, "gln": 13, "glncsffsicnwkfidyinrlfqiiylckn": 6, "glob": [23, 217, 238], "global": [4, 12, 13, 14, 17, 30, 80, 83, 109, 183, 202, 203, 226, 262, 297], "global_dtd_dir": [83, 84], "global_xsd_dir": [83, 84], "globald": 14, "globaldx": 297, "globalm": 297, "globalmc": 297, "globalmx": 297, "globalpair": [30, 32], "globalxx": [14, 297], "glossari": [127, 282], "glpinfmtlf": 250, "glpinfmtli": 250, "gltpfngyta": 0, "gltpfngytaatwtrtavssvgmnipyhgasylvrnqelrswtaadkaaqmpwr": 0, "gltpfngytaatwtrtavssvgmnipyhgasylvrnqelrswtaadkaaqmpwrrnrqsc": 0, "gltpsngyta": 0, "gltpsngytaatwtrtaassvgmnipydgasylvrnqelrswtaadkaaqmpwrrnmqsc": 0, "gltpssgyta": 0, "gltpssgytaatwtrtavssvgmnipyhgasylvrnqelrswtaadkaaqmpwrrnrqsc": 0, "glu": [13, 15], "gluconeogenesi": 116, "glucos": 3, "glue": [8, 214], "glutam": 13, "glutamin": 13, "gly": [13, 15, 140, 169], "gly_cbeta": [15, 133, 169], "gly_onli": 15, "glycan": [119, 274], "glycin": [3, 15, 20, 169], "glycolysi": 116, "glyconnect": 272, "glycoprotein": 113, "glycosyl": 272, "glyselect": 15, "gmonth": 197, "gmonthdai": 197, "gn": 123, "gnfvspvknq": 0, "gnl": 218, "gnm_terminu": 275, "gnu": [23, 278], "gnvl": 13, "go": [0, 1, 3, 4, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 67, 99, 109, 197, 234, 238, 251, 273, 274, 277, 307], "goa": [27, 276], "goa_uniprot": 277, "goa_yeast": 277, "goal": [20, 217], "goe": [4, 24, 27, 84, 149], "gojobori": [2, 13, 34, 281], "gol": 0, "gold": [0, 2, 183], "goldenpath": [0, 36, 37, 38, 39, 221], "goldman": [2, 13, 32, 34, 182, 281], "goldman1994": [2, 13], "goldsack": 265, "golub": [2, 15, 216], "golub1971": [2, 4], "golub1989": [2, 15], "gompertz": [16, 27, 298, 299, 300], "goncalo": 2, "gone": 260, "gonnet": [2, 32], "gonnet1992": 199, "gonzalez": 7, "good": [3, 5, 6, 7, 8, 12, 15, 19, 20, 23, 24, 109, 251, 270], "good_bas": [268, 270], "good_qual": 6, "good_read": 6, "goodi": 7, "googl": [17, 19, 197], "gorder": [4, 73], "got": [0, 3, 5, 6, 7, 8, 12, 19, 20, 241, 278], "goto": [2, 111, 115, 119, 251], "gotoh": [13, 30], "gov": [3, 7, 8, 12, 19, 22, 23, 68, 70, 71, 76, 83, 93, 94, 96, 97, 218, 234, 245, 253, 262, 272], "gp": [0, 7, 23, 201], "gp_inform": 277, "gpa": [276, 277], "gpa_iter": [27, 276, 277], "gpad": 277, "gpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgyc": 0, "gpi": [3, 276, 277], "gpi_iter": [27, 276, 277], "gpipe": 68, "gpl": 5, "gpl28": 7, "gplaiaadav": 0, "gpssr": 0, "gpyppsvdwrkkgnfvspvknqgacgscwtf": 0, "gpyppsvdwrkkgnfvspvknqgacgscwtfsttgalesaiaiatgkmlslaeqqlvdcaqdfnni": 0, "gpytdftp": 68, "gqcgscwsf": 0, "gr": [0, 2, 12, 13, 14, 53, 66, 123], "gr_map": [30, 53], "grab": [7, 25], "gradat": 100, "gradient": 263, "gradual": 6, "graem": 2, "graham": 2, "grai": [6, 17, 183], "grain": 13, "grand": 265, "grandchild": 130, "grant": 123, "graph": [6, 8, 103, 104, 117, 177, 178, 180, 185], "graph_id": 104, "graphdata": [98, 104], "graphic": [4, 9, 12, 17, 26, 27, 111, 115, 117, 183, 197, 238, 243, 261, 307], "graphset": [8, 98, 104], "grasp": 21, "grate": 5, "gravi": [261, 265], "great": [5, 7, 23, 272], "greater": [3, 17, 19, 21, 31, 32, 135, 136, 139, 152, 169, 182, 241, 260, 275], "greatli": [5, 270], "greedi": 69, "green": [0, 4, 8, 17, 104, 181, 183, 198], "greener": 133, "greenhous": 19, "grei": [8, 104, 183], "grep": 6, "greytrack": [8, 104], "greytrack_font": 104, "greytrack_font_color": 104, "greytrack_font_colour": 104, "greytrack_font_rot": 104, "greytrack_fonts": 104, "greytrack_label": 104, "gri_agm677": 244, "grid": [4, 73], "griseu": 3, "grishin": [2, 74], "gritti": 21, "grossli": 20, "ground": 23, "group": [0, 4, 9, 11, 15, 30, 32, 84, 103, 117, 132, 139, 172, 199, 217, 221, 226, 251, 270, 272, 288], "group_nam": 172, "group_numb": 172, "group_typ": 172, "grouping_constraint": [181, 182], "groupsiz": [30, 32], "grow": [11, 20], "grown": [6, 16], "growth": [16, 300], "grusonia": 23, "gs_map": [30, 53], "gse16": 7, "gse16_famili": 7, "gse21512": 11, "gskgcatgtgaaa": [11, 291], "gsl": 254, "gst": 0, "gt": [0, 30, 68, 182, 222], "gta": [0, 22, 76], "gtaacagaaaataaaatttaaatagaaacttaaaggcc": 0, "gtaacagaaaataaaatttaaatagaagcttaaaggct": 0, "gtac": 22, "gtat": 31, "gtataatttgtggtagtgggggactgcgttcgcgctatcccccg": 30, "gtatc": [30, 31], "gtatcaacag": 7, "gtatcagaag": 7, "gtattatttaatggcatacactcaa": 251, "gtc": [0, 22], "gtcagc": 12, "gtcagctag": 12, "gtccatcgcaaagcgtggggc": 283, "gtcccagtattcggatttgtctgccaaaacaatgaaattgacacagtttacaac": 6, "gtg": [12, 22, 76, 236], "gtgaaaaagatgcaatctatcgtactcgcactttccctggttctggtcgctcccatggca": 22, "gtgcaagtat": 278, "gtgccctaagcatactaggcg": 283, "gtgccgttaccatcggtgacgaaagtattaat": 222, "gtggccattgtaatgggccgc": 236, "gtggccattgtaatgggccgctgaaagggtgcccgatag": 236, "gtgta": 11, "gtleaiqwskhwdsgi": 13, "gtleaiqwtkhwdsgi": 13, "gtr": [4, 73, 181, 182], "gtrcat": 182, "gtrcat_gamma": 182, "gtrcat_gammai": 182, "gtrfreq": [181, 182], "gtrgamma": 182, "gtrgammai": 182, "gtrmix": 182, "gtrmixi": 182, "gtrrate": [181, 182], "gtt": [0, 22, 30], "gttacccgg": 11, "gttctaccacaaaagaaaaagagactttggggtttggtagtttgtcataacactactccg": 260, "gttgcttctggcgtgggtggggggg": [238, 251], "gttgtaattc": 7, "gttgtctcttatggtg": 0, "gttt": 0, "gttttggagt": 7, "gttttt": 0, "gua": 76, "guanidinium": 53, "guarante": [4, 11, 83, 108, 109, 183, 218, 288], "gucgugaau": 66, "guess": [3, 6, 7, 12, 15, 20, 21, 23, 149, 222, 300], "guess_lag": [27, 298, 300], "guess_plateau": [27, 298, 300], "guest": 288, "gug": 76, "gui": [2, 4, 7, 9, 222, 265], "guiba": 140, "guid": [3, 8, 12, 32, 166, 218, 221, 226, 229], "guidelin": [3, 5, 23, 104, 119, 274], "guidetre": 32, "guidetree_in": [30, 32], "guidetree_out": [30, 32], "guindon": [65, 182], "gunzip": [15, 23], "guruprasad": 265, "gv": [15, 137], "gva": 6, "gvltvngprk": 250, "gweight": [4, 73], "gyear": 197, "gyearmonth": 197, "gyfifgptgc": 250, "gyfvfgptmc": 250, "gyfvfgqtgc": 250, "gygekngi": 0, "gygvengv": 0, "gymnosperm": 17, "gysakntifr": 0, "gytyr": 237, "gz": [1, 4, 6, 7, 15, 23, 25, 94, 277], "gzip": [1, 4, 7, 23, 25, 217, 238, 270, 278], "g\u00e9raldin": 2, "g\u00f6\u00dfling": 2, "h": [2, 3, 7, 12, 13, 14, 15, 16, 17, 22, 23, 25, 32, 68, 69, 71, 80, 113, 137, 145, 152, 153, 162, 169, 182, 251, 260, 261, 268, 270, 272, 275, 299], "h0": 0, "h01": [16, 299], "h02": 299, "h03": 299, "h05": 299, "h1": [0, 125, 126, 169], "h12": 299, "h1d_map": 169, "h1kei": 169, "h2": 169, "h2aa": 169, "h2kei": 169, "h3": 169, "h_": [11, 15], "h_glc": 15, "h_j": 11, "ha": [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 45, 56, 67, 68, 73, 83, 92, 99, 100, 104, 107, 108, 109, 117, 120, 122, 127, 130, 132, 134, 139, 143, 149, 158, 169, 172, 182, 183, 201, 202, 205, 209, 212, 217, 221, 222, 229, 236, 237, 248, 251, 253, 260, 261, 265, 270, 274, 277, 278, 282, 283, 290, 299], "ha2": 169, "ha3": 169, "hack": [15, 169], "had": [1, 3, 6, 7, 15, 20, 23, 31, 101, 217, 240], "haimov": 265, "half": [20, 53, 61, 84, 99, 141, 182, 217, 221, 265, 275], "hall": 7, "halt": 4, "hamelryck": [2, 7, 9, 15, 26, 133], "hamelryck2003a": [2, 9, 15], "hamelryck2003b": [2, 15], "hamelryck2005": [2, 15], "han": 197, "hand": [0, 3, 7, 8, 11, 12, 13, 15, 19, 20, 21, 22, 23, 25, 84, 264], "handbook": 2, "handi": [7, 15, 25, 134], "handicap": 12, "handl": [0, 3, 5, 6, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 23, 24, 25, 29, 30, 32, 54, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 71, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 99, 101, 103, 104, 112, 113, 114, 116, 118, 119, 121, 123, 126, 129, 132, 137, 143, 152, 158, 169, 172, 182, 183, 185, 188, 190, 191, 198, 199, 201, 205, 209, 210, 211, 212, 213, 214, 217, 219, 220, 221, 222, 223, 224, 225, 226, 228, 230, 231, 232, 233, 235, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 259, 260, 261, 269, 271, 272, 273, 274, 275, 277, 278, 283, 284, 286, 287, 289, 291, 292, 293, 295, 296, 298, 299, 305], "handle_motif": [283, 296], "handleish": 91, "handlemissingdocumentdefinit": [83, 84], "handler": [84, 252], "handsak": 2, "hang": 5, "hansson": 7, "haploid": [201, 202, 203, 204, 270], "happen": [6, 7, 8, 12, 15, 17, 20, 21, 22, 56, 99, 169, 214, 251, 253, 260, 278], "happi": [5, 19], "harald": 2, "hard": [0, 5, 7, 8, 12, 14, 20, 23, 52, 64, 69, 238, 240, 248, 249, 270, 278, 298], "hard_clip_left": [0, 52], "hard_clip_right": [0, 52], "hardi": [18, 202, 203], "hardli": 127, "hare": 197, "haruo": 2, "has_id": [15, 133, 136, 139], "has_missing_residu": 15, "has_support": [128, 132], "hasegawa": 182, "hash": [23, 69, 139, 169, 236, 237, 287], "hash_index": [68, 69], "hashcod": 177, "hasheddomainsbyev": [27, 209], "hasheddomainsbyid": [27, 209], "hasn": [5, 7], "hat": 53, "hatom": 169, "hatoms_needs_upd": 169, "hatomsr": 169, "haubrock": 2, "haunsberg": 2, "haussler": 2, "have": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 35, 36, 37, 38, 43, 46, 47, 51, 56, 61, 62, 66, 67, 68, 69, 71, 72, 73, 80, 83, 92, 94, 99, 102, 104, 107, 108, 109, 117, 123, 135, 136, 137, 143, 144, 146, 148, 149, 152, 154, 155, 157, 158, 160, 168, 169, 170, 172, 173, 175, 176, 182, 183, 191, 195, 197, 199, 202, 205, 207, 214, 217, 218, 221, 222, 229, 236, 237, 238, 246, 247, 251, 253, 260, 261, 264, 265, 270, 278, 285, 288, 290, 297, 299, 300], "haven": [1, 20], "hb": 169, "hb1": 169, "hb2": 169, "hb3": 169, "hba_human": [12, 13, 14], "hbb_human": [12, 13, 14], "hbond": 169, "hc": [11, 295], "hcoordspac": 169, "hcut": 152, "hd": 0, "hd1": 169, "hd11": 169, "hd12": 169, "hd13": 169, "hd2": 169, "hd21": 169, "hd22": 169, "hd23": 169, "hd3": 169, "hdpi": [11, 283], "hdr": 168, "he": 169, "he1": 169, "he2": 169, "he21": 169, "he22": 169, "he3": 169, "head": [7, 8, 15, 104, 174], "header": [0, 11, 13, 15, 27, 32, 33, 40, 42, 43, 45, 46, 47, 51, 52, 56, 59, 60, 61, 68, 71, 94, 126, 151, 152, 162, 168, 169, 172, 174, 204, 209, 217, 221, 223, 224, 225, 238, 244, 246, 247, 248, 253, 259, 270, 277, 278], "header_dict": 15, "header_sam_fil": 270, "header_width": [92, 94, 238, 245], "headlin": 126, "hear": 12, "heat": [8, 104], "heavi": 7, "heavili": [0, 21, 237], "hec": 153, "heck": [3, 9, 12, 23, 83], "hed": 168, "hedgehog": 238, "hedra": [15, 152, 158, 167, 168, 169], "hedraangl": [15, 169], "hedrakei": 169, "hedral12": [15, 169], "hedral23": [15, 169], "hedralen": 169, "hedrandx": 169, "hedron": [27, 133, 152, 158, 169], "hedron1": 169, "hedron2": 169, "hedrondispatch": 158, "hedronmatcherror": [27, 133, 169], "hedronomet": [15, 169], "hedronometr": 169, "hehl": 2, "hei": 3, "height": [8, 16, 104, 115, 117], "hein": 2, "held": [6, 12, 23, 117, 238, 251, 269, 289], "helic": [15, 260], "helix": [9, 11, 15, 32, 53, 137, 236, 260, 265, 272], "helixendin": [30, 32], "helixendout": [30, 32], "helixgap": [30, 32], "helloworld": 67, "help": [0, 3, 6, 7, 8, 9, 12, 17, 18, 19, 21, 23, 24, 25, 30, 32, 36, 37, 38, 39, 67, 68, 69, 70, 79, 80, 95, 99, 104, 108, 129, 181, 182, 209, 217, 221, 250, 262, 270, 281, 286, 297, 306], "help_input": [201, 204], "help_mkt": [34, 280], "helper": [8, 12, 23, 92, 100, 238, 251, 298, 303, 304], "helvetica": [104, 105], "hematopoiet": 2, "hemoglobin": [13, 14], "henc": [4, 15, 20, 73, 238], "henerargiyerfvvvh": 53, "heng": [2, 52], "henikoff": 2, "henikoff1992": [2, 13], "henrik": 9, "her": [143, 151], "here": [0, 1, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 23, 24, 26, 30, 66, 68, 73, 83, 99, 137, 143, 158, 169, 182, 197, 201, 204, 207, 217, 218, 221, 222, 234, 237, 238, 251, 260, 264, 275, 276, 277, 278, 288, 299, 307], "heringa": 32, "heron": [15, 169], "hertz": [11, 294], "het": [0, 15, 270], "hetatm": [15, 143, 145, 154, 168, 169, 248], "hetatom": 214, "hetero": [136, 139, 162], "heterogen": 182, "heterozyg": 270, "heterozygos": 203, "heterozygot": [202, 203, 270], "hetfield": 15, "hetflag": 15, "heuer": [2, 251], "heurist": [2, 182, 270], "hevein": 0, "hex": [17, 30, 68, 105, 117], "hexadecim": 183, "hexbinari": 197, "hexstr": 183, "hf": 7, "hfgkeft": 13, "hflipliii": 250, "hflvpfviif": 250, "hftiplivif": 250, "hg": [13, 135, 162, 169], "hg1": 169, "hg11": 169, "hg12": 169, "hg13": 169, "hg16": 0, "hg18": 0, "hg18_dna": 0, "hg18kgchr7": 0, "hg19": [0, 20], "hg19_dna": [0, 221], "hg19tohg38": 0, "hg2": 169, "hg21": 169, "hg22": 169, "hg23": 169, "hg3": 169, "hg38": [0, 13, 22], "hgapresidu": [30, 32], "hgdownload": 221, "hgfedcba": 251, "hgfisrefhr": 250, "hgkheerqd": 250, "hgkkv": 13, "hh": [2, 44, 169, 227], "hh11": 169, "hh12": 169, "hh2": 169, "hh21": 169, "hh22": 169, "hhai": 206, "hhblit": [0, 44], "hhhh": 12, "hhhhhh": [12, 53], "hhhhhhh": 12, "hhhhhhhh": 12, "hhhhhhhhhhhhh": 53, "hhhhhhhhhhhhhh": [12, 53], "hhhhhhhhhhhhhhhhhhhhh": 12, "hhhhhhhhhhhhhhhhhhhhhhh": 12, "hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh": 12, "hhhhhttthhhhhhhhhhhhhhhhhhhhhh": 260, "hhr": [0, 22, 27, 30], "hhsearch": [0, 44], "hhsuit": [217, 227, 228], "hhsuite2": 217, "hhsuite2_text": [217, 227], "hhsuite2textpars": [217, 227, 228], "hhsuiteio": [27, 217], "hi": [13, 25, 90, 130, 143, 151, 273], "hick": 264, "hicut": 69, "hidden": [0, 2, 9, 32, 44, 104, 106, 108, 229], "hiddenmarkovmodel": [27, 106, 108], "hide": [15, 104, 136], "hie": [27, 209], "hie_handl": 209, "hierarch": [13, 73], "hierarchi": [15, 17, 20, 90, 139, 209, 210, 211, 212, 213, 217, 273], "higgin": 32, "high": [2, 3, 6, 7, 10, 11, 15, 16, 17, 20, 23, 32, 68, 92, 101, 104, 123, 169, 217, 251, 303], "higher": [6, 12, 13, 14, 15, 21, 69, 99, 157, 237, 251, 264, 270, 275, 286, 290, 300], "highest": [11, 13, 15, 104, 135, 236, 275], "highli": [3, 32, 149, 297], "highlight": [3, 8, 15], "hihara": [2, 4], "hihara2001": [2, 4], "hill": [182, 202, 203], "hin1ii": 206, "hin6i": 206, "hindiii": 8, "hinp1i": 206, "hist": 6, "histidin": 260, "histor": [24, 71, 151, 297], "histori": [90, 123], "hit": [0, 7, 19, 25, 27, 68, 69, 70, 71, 74, 88, 182, 217, 218, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 234, 270, 290], "hit_access": 218, "hit_al": 20, "hit_coverag": [27, 74], "hit_def": [71, 218], "hit_end": [218, 221, 222, 226, 229, 234], "hit_endtyp": 229, "hit_filt": 20, "hit_fram": [218, 222], "hit_frame_al": 222, "hit_gap_num": 221, "hit_gapopen_num": 221, "hit_id": [20, 71, 218], "hit_inter_rang": [20, 222], "hit_inter_span": 20, "hit_kei": 20, "hit_len": 218, "hit_map": 20, "hit_placehold": 230, "hit_rang": 20, "hit_range_al": 20, "hit_span": 20, "hit_span_al": [20, 221], "hit_split_codon": 222, "hit_start": [20, 218, 221, 222, 226, 229, 234], "hit_start_al": 221, "hit_strand": [20, 221, 222, 226, 229], "hitlist_s": [68, 70], "hiu": 12, "hiv": 15, "hivb": 182, "hivw": 182, "hke": 56, "hkt": 169, "hky2": 32, "hky85": 182, "hla": [245, 250], "hla00489": 250, "hla00490": 250, "hla00491": 250, "hla00492": 250, "hla00493": 250, "hla01083": 250, "hllesdlfpa": 250, "hllvvccnsfqrilcflkdpfmhyvryqgkailaskgtlilmkkwkfhlvnfwqsyfh": 7, "hlmrda": 0, "hlqesellpa": 250, "hm": 202, "hmm": [0, 27, 32, 53, 229, 231, 234], "hmm_as_hit": [229, 231], "hmm_descript": 0, "hmm_input": [30, 32], "hmm_name": 0, "hmmbuild": [0, 53], "hmmer": [20, 217, 229, 230, 231, 232, 233], "hmmer2": [217, 230], "hmmer2_text": [217, 229], "hmmer2textindex": [217, 229, 230], "hmmer2textpars": [217, 229, 230], "hmmer3": [217, 231, 232, 234], "hmmer3_domtab": [217, 229], "hmmer3_tab": [217, 229], "hmmer3_text": [217, 229], "hmmer3domtabhmmhitindex": [217, 229, 231], "hmmer3domtabhmmhitpars": [217, 229, 231], "hmmer3domtabhmmhitwrit": [217, 229, 231], "hmmer3domtabhmmqueryindex": [217, 229, 231], "hmmer3domtabhmmquerypars": [217, 229, 231], "hmmer3domtabhmmquerywrit": [217, 229, 231], "hmmer3domtabpars": 231, "hmmer3tabindex": [217, 229, 231, 232], "hmmer3tabpars": [217, 229, 232], "hmmer3tabwrit": [217, 229, 232], "hmmer3textindex": [217, 229, 233], "hmmer3textpars": [217, 229, 233], "hmmerio": [27, 217], "hmmfrom": 229, "hmmpfam": [217, 229], "hmmscan": [217, 229], "hmmscan3": 229, "hmmscore": [0, 33], "hmmsearch": [0, 53, 217, 229], "hmmsearch3": 229, "hmmto": 229, "hn": 126, "hoc": 256, "hochstrass": 263, "hocomoco": [11, 283], "hoh": 152, "hokc": 260, "hold": [6, 7, 12, 15, 16, 19, 21, 23, 27, 30, 49, 56, 64, 66, 71, 74, 86, 87, 88, 90, 93, 97, 99, 102, 104, 105, 109, 112, 113, 114, 120, 121, 122, 123, 125, 127, 169, 201, 204, 205, 210, 211, 212, 213, 217, 238, 251, 260, 269, 271, 272, 278, 282, 289, 291, 292], "holder": [134, 158], "homag": 20, "home": [7, 84, 222], "homeo": 288, "homepag": 182, "homer": [2, 11, 283], "hominida": 272, "homo": [3, 20, 68, 90, 93], "homo_sapien": 7, "homodimer": 260, "homog_rot_mtx": [27, 133, 176], "homog_scale_mtx": [27, 133, 176], "homog_trans_mtx": [27, 133, 176], "homogen": [15, 169, 176], "homol": [7, 275], "homolog": 3, "homologen": 7, "homologi": [2, 275], "homologu": 274, "homopolym": [253, 268, 270], "homozygot": [202, 203], "hood": [17, 217], "hoon": [2, 4, 7, 9, 26, 73], "hope": [9, 21, 23, 108, 169], "hopefulli": [3, 5, 7, 8, 12, 19, 21, 30], "hopeless": 3, "hopkin": 216, "hordeum": 25, "hordijk": 182, "hori": 25, "horizont": [4, 6, 8, 73], "hornisch": 2, "hors": [0, 56], "host": [2, 5, 11, 209, 272, 288, 303, 305], "host_organ": [25, 272], "host_taxonomy_id": 272, "hostnam": [0, 288, 303], "hot": [15, 169], "houdt": 2, "hour": [4, 7, 16, 32, 182], "household": 4, "how": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 23, 25, 30, 31, 68, 73, 80, 83, 84, 100, 104, 132, 137, 182, 219, 231, 232, 237, 243, 248, 251, 253, 264, 274, 278], "howev": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 25, 30, 56, 66, 68, 73, 83, 94, 182, 217, 218, 221, 222, 236, 237, 238, 240, 243, 251, 253, 260, 261, 269, 274, 278, 283, 298, 299], "hoxd70": 199, "hp": [11, 295], "hpc": 182, "hpych4iv": 206, "hpyse526i": 206, "hr": [22, 222], "hs_exp": 141, "hsa": [10, 119], "hse": [15, 141], "hsealpha": 15, "hsebeta": 15, "hsexposur": [15, 27, 133], "hsexposureca": [27, 133, 141], "hsexposurecb": [27, 133, 141], "hsi08034": 7, "hsiung": 2, "hsp": [27, 68, 69, 71, 217, 218, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 234], "hsp70": 4, "hsp92ii": 206, "hsp_align": 218, "hsp_bit": 218, "hsp_densiti": 218, "hsp_evalu": 218, "hsp_filter": 20, "hsp_gap": 218, "hsp_hit": 218, "hsp_hseq": 218, "hsp_ident": 218, "hsp_map": 20, "hsp_midlin": 218, "hsp_pattern": 218, "hsp_posit": 218, "hsp_qseq": 218, "hsp_queri": 218, "hsp_score": 218, "hspai": 206, "hspfragment": [217, 218, 221, 222, 226, 229, 234], "hsps_gap": 71, "hsps_no_gap": 71, "hsps_prelim_gap": 71, "hsps_prelim_gapped_attemp": 71, "hsv": 100, "ht": [202, 288], "htc": 275, "html": [0, 3, 9, 10, 15, 17, 25, 30, 32, 35, 36, 37, 38, 39, 46, 50, 51, 53, 56, 61, 65, 66, 68, 69, 70, 83, 85, 89, 94, 119, 182, 183, 190, 199, 201, 204, 209, 210, 211, 212, 214, 221, 236, 238, 243, 245, 247, 248, 250, 272, 274, 286], "htmlout": [30, 32], "htselex": 288, "htslib": 52, "http": [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 18, 19, 21, 22, 23, 25, 27, 32, 34, 35, 36, 37, 38, 39, 46, 50, 51, 52, 53, 56, 59, 61, 65, 66, 68, 69, 70, 71, 73, 83, 85, 86, 87, 88, 89, 90, 94, 96, 97, 99, 100, 105, 111, 115, 116, 117, 119, 122, 137, 140, 145, 149, 150, 156, 158, 167, 169, 170, 181, 182, 185, 188, 190, 197, 199, 201, 204, 209, 210, 211, 212, 214, 218, 221, 226, 227, 229, 234, 237, 239, 243, 245, 247, 248, 250, 251, 252, 253, 258, 262, 263, 265, 267, 270, 272, 273, 274, 277, 278, 279, 280, 283, 286, 299, 301], "http_proxi": [7, 149], "httprespons": 68, "hu": 122, "huge": [1, 3, 13, 31, 32, 182], "hugh": 263, "hughei": 2, "hughey1996": [0, 2], "human": [0, 7, 10, 11, 13, 15, 20, 21, 22, 23, 25, 30, 45, 68, 93, 117, 119, 197, 221, 238, 260, 263, 264, 270, 272, 274, 299], "human_pathwai": 10, "hundr": [4, 19, 20], "hunt": 6, "hurt": 270, "hutchinson": 265, "hvdp": 13, "hwi": 0, "hxkei": 169, "hyb": 80, "hybrid": [7, 20, 264, 275], "hybridis": 80, "hybridprob": [79, 80], "hydro": [30, 32], "hydrocarbon": 7, "hydrofactor": [30, 32], "hydrogen": [15, 138, 158, 169, 272], "hydrolyz": 25, "hydropathi": 265, "hydrophil": [32, 265], "hydrophob": [32, 265], "hyilp": 80, "hyper": 0, "hyperlink": 83, "hypohippu": 56, "hypothet": [3, 12, 94, 104], "hz": 169, "hz1": 169, "hz2": 169, "hz3": 169, "i": [0, 2, 3, 4, 5, 6, 8, 10, 11, 12, 13, 14, 16, 18, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 42, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56, 59, 61, 62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 85, 86, 88, 89, 90, 91, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 118, 119, 120, 121, 122, 123, 125, 126, 127, 129, 130, 132, 134, 135, 136, 137, 138, 139, 140, 141, 143, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 162, 163, 164, 166, 168, 169, 170, 172, 173, 175, 176, 177, 178, 179, 180, 182, 183, 185, 186, 188, 190, 191, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 216, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 268, 269, 270, 271, 272, 274, 275, 277, 278, 280, 281, 282, 283, 286, 287, 288, 290, 291, 294, 295, 296, 297, 298, 299, 300, 302, 303, 305, 306, 307], "i51200": 250, "i_thresh": [68, 70], "ia": 68, "iahpggpaildqvelklglkqeklkatrkvlsnygnmssacvlfildemrkasakeglgt": 23, "iaiiie65i": 251, "ian": 2, "iatgkmlsla": 0, "ibarra": 7, "ic": [11, 31, 168, 169, 273, 294], "ic_": [12, 158], "ic_chain": [15, 27, 133, 158, 169], "ic_data": [15, 27, 133, 152, 169], "ic_data_sidechain": 169, "ic_dupl": [15, 27, 133, 168, 169], "ic_rebuild": [15, 27, 133, 169], "ic_residu": [15, 27, 133, 152, 158, 168, 169], "ic_vector": 31, "icm": 288, "icod": [15, 162, 169, 214], "id": [0, 1, 3, 4, 6, 8, 9, 11, 12, 13, 15, 16, 19, 20, 21, 22, 23, 25, 27, 30, 32, 34, 36, 37, 38, 39, 45, 47, 53, 59, 60, 61, 62, 65, 66, 68, 69, 71, 76, 83, 85, 86, 88, 90, 93, 94, 104, 112, 113, 114, 115, 116, 117, 118, 123, 130, 132, 133, 134, 135, 136, 137, 139, 140, 143, 144, 149, 151, 152, 155, 160, 162, 165, 168, 169, 171, 172, 181, 183, 184, 187, 189, 197, 198, 209, 211, 212, 214, 215, 217, 218, 221, 222, 223, 224, 225, 226, 229, 234, 237, 238, 240, 241, 244, 245, 246, 248, 249, 250, 251, 252, 253, 255, 256, 260, 270, 272, 273, 274, 275, 278, 279, 280, 287, 288, 295, 298, 299, 302, 303, 304, 305], "id1": 272, "id123456": 256, "id123457": 256, "id2": 272, "id3": [169, 272], "id32": 169, "id32_dh_index": 169, "id3_dh": 169, "id3_dh_index": 169, "id_al": 218, "id_dict": 238, "id_fil": 6, "id_handl": 6, "id_i": 8, "id_list": 7, "id_of_previous_nod": 132, "id_ref": 197, "id_ref_0": 197, "id_ref_1": 197, "id_sourc": 197, "id_width": [56, 65], "id_x": 8, "idcod": [152, 158, 168], "iddo": [2, 26], "idea": [1, 5, 7, 12, 15, 19, 21, 23, 108, 238, 278], "ideal": [0, 5, 7, 12, 19, 20, 23, 24, 27, 99, 270], "ident": [3, 4, 8, 11, 12, 13, 17, 19, 20, 21, 22, 23, 27, 30, 32, 68, 69, 71, 80, 132, 168, 176, 199, 202, 203, 209, 221, 236, 238, 251, 270, 290, 297], "ident_num": [20, 218, 221], "ident_pct": [218, 221, 226], "identif": [2, 20, 169, 250], "identifi": [0, 3, 4, 8, 11, 12, 15, 16, 19, 20, 21, 23, 25, 30, 47, 53, 56, 65, 68, 69, 70, 71, 73, 83, 85, 90, 93, 104, 112, 114, 117, 119, 123, 129, 135, 136, 137, 138, 139, 140, 144, 154, 155, 160, 162, 169, 182, 183, 197, 198, 209, 210, 211, 213, 217, 226, 236, 237, 238, 241, 251, 252, 256, 260, 262, 270, 272, 273, 274, 275, 280, 295, 299, 303], "identity_match": [27, 297], "idiom": 15, "idiosyncrat": [0, 42], "idlist": [7, 83], "idmmpmm": [11, 283], "idtglsemrl": 250, "idtyp": [7, 83], "idx": [20, 23], "idx_filenam": 217, "idx_nam": 238, "idxstat": 270, "ie": [15, 31, 92, 93, 99, 108, 136, 137, 140, 156, 176, 237], "ieee": 7, "ieislnqikdgwkiidvkdryydfrnksfsafsnwlrdlkeqslrkynnfcgknfyf": 94, "iep": [80, 263], "iep_clin": 80, "iepcommandlin": [27, 79, 80], "if6hivcnrsqdvniaoefazysc6i4": 262, "iff": 177, "ifound": 4, "ifwcnf2pi": 23, "ifxa": 292, "ifyepveifgydnksslvlvkrlitrmyqqnflissvndsnqkg": 7, "ig": [32, 56, 238, 244], "igio": [27, 238], "igiter": [27, 238, 244], "ignment": 0, "ignor": [4, 11, 12, 13, 15, 20, 21, 23, 24, 27, 31, 32, 59, 66, 67, 69, 88, 94, 141, 152, 167, 169, 182, 198, 218, 238, 240, 244, 251, 256, 261, 264, 270, 278, 283, 290, 298], "ignore_com": 132, "ignore_error": [7, 83, 84], "ignore_lower_cas": 283, "ignore_msa_mast": [68, 69], "ihgfedcba": 251, "ii": [0, 4, 8, 73, 122, 183, 251, 294], "iieqfidylr": 260, "iii": [8, 211, 251], "iiiiii1": 251, "iiiiiii": 251, "iiiiiiiiiiiiciigiiiii": 251, "iiiiiiiiiiiiiiicdiiiii": 251, "iiiiiiiiiiiiiiiiiiiiiiiiiiiiicii": 251, "iij": 13, "iis_converg": 122, "iiv": 0, "ij": [11, 12], "ik": 7, "ikawa": 25, "ikeuchi": 2, "ikhkylwsep": 0, "ikhkylwsepqncsat": 0, "il": [13, 15], "ill": 80, "illumina": [2, 6, 238, 251, 270], "illumina_13": [268, 270], "illumina_fak": 251, "illumnia": 238, "illustr": [0, 2, 6, 7, 8, 13, 20, 21, 23, 30, 134, 135, 139, 140, 251], "ilmfq": 270, "im": 32, "imag": [6, 7, 8, 15, 17, 19, 68, 99, 104, 105, 116, 117, 119, 169, 197], "imagin": [18, 20], "imgt": [167, 238, 245], "imgteduc": 167, "imgtiter": [27, 238, 245], "imgtwrit": [27, 238, 245], "imit": [3, 8], "imm_tabl": 264, "immedi": [3, 7, 20, 21, 169, 278], "immobil": 263, "immun": 21, "immut": [4, 13, 22, 23, 236], "imoto": [2, 7], "implement": [2, 4, 6, 7, 10, 11, 12, 13, 15, 17, 21, 30, 32, 34, 67, 73, 76, 83, 92, 100, 107, 108, 109, 123, 126, 139, 143, 146, 148, 151, 158, 169, 175, 177, 178, 179, 180, 183, 185, 199, 217, 229, 236, 237, 238, 246, 252, 257, 260, 261, 264, 265, 270, 278, 280, 288, 290, 291, 302, 303, 304], "impli": [20, 117], "implic": 53, "implicit": 20, "implicitli": 0, "import": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 32, 45, 53, 54, 56, 59, 62, 66, 67, 68, 69, 73, 76, 80, 83, 85, 90, 91, 92, 99, 104, 116, 122, 123, 126, 135, 137, 139, 140, 148, 154, 156, 157, 169, 170, 173, 176, 182, 183, 199, 206, 207, 216, 217, 218, 221, 222, 236, 237, 238, 240, 245, 247, 248, 249, 251, 253, 260, 261, 262, 263, 264, 265, 269, 270, 272, 274, 276, 277, 278, 279, 280, 281, 282, 283, 288, 289, 291, 292, 295, 297, 298, 299, 303, 305], "import_imagemap": 105, "import_search_strategi": [68, 69], "importantli": [5, 8], "importerror": 27, "impos": [15, 238], "imposs": [21, 95, 222], "impract": 7, "improv": [2, 3, 6, 8, 15, 17, 19, 23, 32, 122, 152, 182, 248, 270, 278, 300], "imshow": [6, 15, 169], "in1": [30, 32, 270], "in2": [30, 32, 270], "in_bam": [268, 270], "in_con": 53, "in_fil": [32, 56, 137, 217, 238], "in_fmt": 217, "in_format": [56, 217, 238, 274], "in_handl": [6, 23, 85, 238], "in_kwarg": 217, "in_msa": [68, 69], "in_plac": 20, "in_pssm": [68, 69], "in_rad": 169, "inappropri": [0, 30], "inbox": 5, "inc": [229, 242], "incent": 23, "incept": 9, "inch": 104, "includ": [0, 1, 3, 4, 5, 6, 7, 9, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 36, 38, 47, 52, 56, 59, 66, 67, 68, 69, 72, 76, 80, 83, 94, 99, 129, 130, 133, 135, 136, 139, 145, 149, 152, 154, 158, 162, 169, 176, 183, 197, 207, 214, 237, 238, 240, 243, 248, 251, 253, 260, 261, 264, 265, 269, 270, 272, 274, 276, 278, 280, 281, 283, 288, 291, 295, 297, 299, 307], "include_codon": 129, "include_miss": 129, "includecod": 158, "includedregion": [79, 80], "inclus": [3, 6, 61, 68, 69, 215, 217, 229, 251], "inclusion_ethresh": [68, 69], "incompat": [6, 69, 251, 278, 297, 303], "incompatibli": 108, "incomplet": [0, 2, 10, 15, 134, 135, 139, 140, 182, 278], "inconsist": [4, 13, 214], "incorpor": 32, "incorrect": [7, 27, 108, 270], "incorrectli": 15, "increas": [0, 4, 7, 30, 73, 183, 270, 297], "increasingli": 20, "incred": 19, "increment": [1, 35, 36, 37, 38, 39, 42, 46, 51, 52, 53, 66, 71, 143, 166, 169, 183, 198, 299], "ind1": [18, 201, 204, 205], "ind2": [18, 201, 204], "inde": [6, 12, 25], "indel": 270, "indent": [12, 198, 206, 207, 238, 245], "independ": [0, 17, 80, 127, 169, 229], "index": [2, 3, 7, 8, 9, 11, 12, 13, 15, 16, 17, 21, 22, 27, 30, 36, 37, 38, 45, 47, 54, 61, 68, 69, 72, 73, 83, 91, 94, 104, 125, 126, 131, 137, 149, 154, 169, 172, 176, 183, 197, 201, 209, 210, 214, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 229, 230, 231, 232, 233, 236, 238, 241, 253, 257, 260, 261, 265, 270, 278, 279, 280, 281, 289, 290, 291, 292, 297, 299, 303], "index1": [4, 73], "index2": [4, 73], "index_cmd": 270, "index_db": [6, 9, 20, 23, 27, 217, 238], "index_filenam": [217, 238], "index_nam": [68, 69], "index_to_on": [27, 133, 154], "index_to_thre": [27, 133, 154], "indexerror": 13, "indic": [3, 4, 6, 7, 10, 11, 12, 13, 15, 16, 17, 20, 21, 22, 24, 27, 30, 32, 68, 73, 92, 104, 105, 109, 119, 121, 127, 129, 135, 139, 143, 149, 151, 158, 169, 172, 182, 183, 197, 214, 215, 217, 222, 236, 237, 248, 264, 266, 270, 272, 275, 278, 280, 297, 299], "indirectli": [7, 278, 303], "indiv": 204, "individu": [0, 4, 8, 13, 15, 18, 20, 21, 24, 25, 30, 45, 83, 90, 157, 158, 167, 177, 182, 197, 201, 202, 204, 205, 217, 222, 238, 260, 286, 289, 291, 292, 293, 295, 296], "indraneel": 2, "ineffici": 20, "inequ": [0, 4, 17, 109, 135, 139, 169, 237], "inexact": 21, "inf": [11, 122, 202, 270], "infect": 6, "infer": [0, 17, 30, 137, 182, 270], "infer_coordin": [27, 30], "infil": [12, 30, 32, 79, 80, 174, 268, 270], "infin": [11, 251], "infinit": 7, "influenc": 108, "infmt": [30, 32], "infn": 126, "info": [3, 5, 7, 15, 31, 92, 93, 101, 102, 103, 112, 113, 114, 119, 168, 169, 183, 191, 202, 203, 237, 269, 275], "info_cont": 12, "info_upd": 88, "inform": [1, 2, 3, 4, 5, 6, 9, 10, 11, 13, 15, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 35, 36, 37, 38, 42, 45, 46, 50, 51, 52, 53, 59, 62, 65, 66, 68, 71, 72, 73, 74, 77, 80, 81, 82, 83, 84, 86, 87, 88, 90, 92, 93, 94, 97, 99, 101, 102, 103, 104, 113, 117, 120, 122, 123, 127, 129, 132, 135, 143, 153, 158, 169, 172, 182, 183, 185, 197, 201, 203, 204, 205, 209, 210, 211, 212, 213, 214, 218, 221, 222, 226, 227, 229, 234, 238, 241, 243, 247, 248, 250, 251, 252, 253, 256, 257, 260, 262, 269, 270, 271, 272, 273, 275, 277, 278, 282, 283, 286, 287, 288, 293, 295, 296, 299, 305], "information_cont": [12, 30, 31], "infraclass": 197, "infracohort": 197, "infradivis": 197, "infrakingdom": 197, "infralegion": 197, "infraphylum": 197, "infratrib": 197, "ingar": 263, "ingo": 2, "inh": 270, "inher": 4, "inherit": [0, 3, 11, 15, 17, 45, 68, 71, 183, 237, 280, 281, 286, 289, 291, 293, 295, 296], "inhibitor": 113, "ini": 24, "init": [4, 169, 264], "init1_scor": 226, "init_a": 264, "init_atom": [133, 162], "init_atom_coord": [133, 169], "init_chain": [133, 162], "init_edra": [133, 169], "init_g": 264, "init_met": 272, "init_model": [133, 162], "init_residu": [133, 162], "init_seg": [133, 162], "init_structur": [133, 162, 171, 172], "initatom": [152, 169], "initi": [0, 4, 13, 15, 17, 20, 21, 29, 30, 31, 32, 36, 60, 62, 67, 68, 69, 71, 72, 73, 74, 76, 80, 81, 82, 84, 86, 87, 88, 89, 90, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 138, 139, 140, 141, 144, 145, 149, 150, 152, 153, 154, 155, 156, 157, 158, 160, 161, 162, 163, 165, 168, 169, 172, 175, 176, 177, 179, 180, 182, 183, 184, 185, 187, 188, 189, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 215, 216, 219, 220, 221, 226, 228, 230, 231, 232, 233, 235, 237, 247, 249, 252, 253, 258, 259, 263, 264, 265, 269, 270, 271, 272, 273, 275, 278, 280, 281, 282, 283, 284, 287, 289, 290, 291, 292, 294, 295, 297, 299, 305], "initial_prob": 108, "initialid": [4, 73], "initialis": [29, 148, 149, 169, 170, 173], "initn_scor": 226, "initncac": 169, "inittau": [4, 73], "inlin": 158, "inner": [12, 13, 272], "inner1": [13, 199], "inner2": [13, 199], "inner3": 199, "inner4": 199, "innocua": 8, "ino1": [11, 291], "ino_up800": [11, 291], "inorgan": 25, "inosin": 112, "inpenalti": 270, "inplac": 236, "input": [0, 3, 4, 6, 7, 8, 10, 11, 12, 13, 15, 17, 19, 21, 22, 24, 25, 26, 27, 30, 31, 32, 37, 45, 50, 54, 59, 60, 65, 66, 67, 68, 69, 73, 80, 81, 82, 83, 91, 94, 104, 116, 119, 125, 126, 129, 153, 156, 157, 166, 169, 171, 175, 176, 181, 182, 193, 195, 196, 199, 229, 241, 246, 248, 249, 251, 258, 261, 268, 270, 274, 278, 297, 299, 307], "input1": [30, 32], "input_bam": [268, 270], "input_bam1": 270, "input_bam2": 270, "input_bam_fil": 270, "input_chain_indic": 172, "input_fil": [6, 68, 69, 268, 270], "input_head": 270, "input_sorted_bam": 270, "input_transform": 172, "input_tre": [181, 182], "input_typ": [68, 69], "inputfil": [50, 65], "inputord": [30, 32], "inputrecord": [27, 79, 82], "inrec": 277, "insdc": [94, 237, 245], "insdcio": [27, 238], "insdcscann": [27, 92, 94], "insect": [11, 288], "insensit": [0, 22, 30, 68, 261, 270], "insert": [0, 12, 15, 22, 27, 30, 32, 33, 55, 133, 136, 139, 143, 162, 169, 172, 214, 215, 221, 236, 270, 275, 295], "insert_gap": [128, 129], "insertion_cod": 172, "insertpenalti": 270, "insid": [20, 25, 32, 104, 149, 169, 270], "insist": [7, 9, 23], "insosin": 264, "inspect": [15, 17, 278, 299], "inspir": [8, 100, 201, 261], "instability_index": [261, 265], "instabl": 265, "instal": [3, 5, 6, 7, 8, 12, 15, 16, 17, 19, 24, 67, 99, 104, 288, 299], "instanc": [3, 4, 7, 9, 12, 13, 16, 17, 21, 23, 24, 27, 30, 31, 36, 54, 67, 91, 109, 129, 132, 135, 140, 160, 162, 182, 183, 185, 188, 190, 193, 195, 196, 197, 198, 209, 214, 234, 236, 237, 260, 265, 269, 272, 283, 287, 288, 291, 292, 295, 297, 299, 303], "instant": 6, "instantan": 6, "instanti": [99, 107, 143, 151, 169, 185, 187, 190, 198], "instead": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 38, 45, 51, 56, 63, 65, 67, 69, 71, 73, 80, 83, 84, 92, 102, 108, 120, 132, 139, 143, 151, 169, 182, 183, 185, 186, 197, 217, 218, 221, 229, 236, 238, 240, 241, 250, 251, 253, 255, 256, 265, 269, 270, 275, 278, 282, 283, 285, 290, 294, 298, 303], "institut": [7, 52, 251, 253], "instruct": [5, 7, 12, 104], "instrument": [6, 16, 251], "insulin": [25, 157], "insur": 125, "int": [0, 7, 8, 13, 17, 21, 36, 54, 64, 71, 83, 84, 88, 99, 104, 117, 125, 126, 130, 134, 136, 139, 140, 141, 144, 148, 149, 150, 152, 157, 158, 162, 164, 169, 176, 186, 197, 236, 237, 238, 251, 253, 260, 262, 270, 276, 302], "int255_color": [98, 104], "int32": [0, 13], "int_node_label": 17, "intact": 17, "integ": [0, 3, 4, 6, 8, 12, 15, 17, 20, 21, 23, 30, 32, 34, 54, 56, 68, 69, 71, 73, 80, 83, 84, 85, 89, 104, 117, 136, 152, 172, 182, 183, 197, 217, 236, 237, 238, 251, 260, 263, 267, 272, 274, 278, 282, 286, 298, 299, 302], "integerel": [27, 83, 84], "integr": [8, 9, 15, 19, 20, 68, 104, 217, 264, 274], "intellig": [2, 104], "intelligenet": [56, 238, 244], "intend": [3, 6, 11, 20, 30, 45, 59, 67, 84, 91, 92, 94, 99, 129, 177, 178, 182, 197, 217, 237, 246, 256], "intens": [29, 104], "intent": 9, "intention": 177, "inter": [15, 23], "interact": [3, 5, 15, 17, 19, 20, 27, 69, 79, 80, 82, 164, 165, 169, 177, 182, 276, 306], "interacton": 177, "interat": 277, "interatom": 169, "interchang": [177, 182, 199, 237, 251], "interconvert": [80, 169], "intereact": 15, "interest": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 32, 40, 83, 88, 93, 97, 99, 143, 169, 272, 278], "interestingli": 21, "interfac": [6, 7, 9, 10, 12, 15, 17, 20, 21, 23, 27, 30, 56, 59, 67, 80, 83, 85, 92, 99, 108, 123, 145, 156, 166, 177, 185, 193, 195, 196, 202, 203, 204, 217, 218, 234, 238, 251, 259, 302, 303], "interfer": 0, "interlac": [0, 23, 56, 65, 66, 238, 246], "interlaced2": 182, "interleav": [0, 32, 49, 50, 64, 65, 66, 129, 182, 270], "interleave_by_partit": 129, "intermedi": [80, 168, 182, 278], "intermediari": 104, "intern": [2, 7, 12, 13, 17, 19, 22, 23, 27, 30, 49, 56, 61, 63, 64, 68, 71, 80, 83, 92, 94, 103, 104, 116, 132, 136, 138, 144, 152, 160, 167, 168, 169, 183, 209, 236, 238, 241, 245, 247, 248, 251, 253, 260, 264, 271, 272, 274, 278, 299, 302, 303, 304], "internal_coord": [27, 133, 136, 152, 158, 160], "internal_extend_gap_scor": 13, "internal_feature_format": [92, 93], "internal_format": [92, 93], "internal_gap_scor": 13, "internal_gc": 81, "internal_length": 81, "internal_open_gap_scor": 13, "internal_seq": 81, "internal_start": 81, "internal_tm": 81, "internal_to_atom": 169, "internal_to_atom_coord": [158, 169], "internal_to_atom_coordin": [15, 133, 136, 144, 158, 160, 169], "internet": [4, 7, 11, 19, 23, 25, 68, 70, 149, 238, 283], "interpol": [8, 15, 22, 169, 299], "interpret": [2, 7, 8, 9, 11, 12, 13, 15, 17, 20, 27, 65, 95, 123, 183, 197, 236, 238, 241, 248, 251, 253, 260], "interpro": [0, 53, 234], "interproscan": [217, 235], "interproscan_xml": [217, 234], "interproscanio": [27, 217], "interproscanxmlpars": [217, 234, 235], "intersect": 6, "interv": [16, 20, 104, 107, 217, 263, 265, 270, 275], "interven": 20, "interwork": 5, "intestin": 7, "intramem": 272, "intramolecular": 10, "intre": [181, 182], "intree1": [181, 182], "intreefil": [79, 80], "intrins": 25, "intro": 209, "introduc": [6, 8, 9, 11, 12, 17, 19, 20, 21, 22, 23, 88, 226, 238, 250, 251, 258], "introduct": [12, 19, 20, 21, 23, 26, 27, 209, 307], "intron": [0, 3, 6, 7, 21, 53, 66, 69, 80, 222, 237], "intronpenalti": [79, 80], "intuit": [16, 21, 237], "invalid": [10, 25, 56, 65, 67, 80, 129, 169, 236, 237, 238, 251], "invar": 182, "invarcoeffici": [79, 80], "invarfrac": [79, 80], "invari": [15, 80, 177, 182], "invent": 4, "invergo": 2, "invers": [6, 8], "inverse_indic": [0, 27, 30], "invert": [8, 99, 104, 128, 129], "investig": [6, 15, 123], "invoc": 270, "invok": [3, 12, 20, 32, 67, 68, 69, 70, 80, 104, 182, 221, 238, 270, 283, 285, 298], "involv": [11, 19, 21, 24, 25, 169, 177, 182, 272], "io": [0, 1, 4, 12, 15, 17, 23, 32, 56, 64, 90, 133, 148, 169, 170, 173, 238, 241, 243, 245, 246, 249, 251, 253, 256], "ioerror": 209, "ion": [253, 264, 272], "iota": 12, "iowa": 2, "ip": [7, 123, 263], "ipf": 260, "iplv": 0, "ipmsnktgvv": 250, "ippeeq": 0, "ipr": 234, "ipr001472": 94, "ipr002743": 94, "ipr003107": 53, "ipr003212": 0, "iptafdwrtr": 0, "ipython": 17, "ir": [30, 32, 123], "irad": 123, "irapeanum": [19, 23], "iron": [25, 112], "irrespect": [13, 119], "irrevers": 117, "is20aa": 169, "is_aa": [15, 27, 133, 154], "is_align": 197, "is_backbon": [133, 169], "is_bifurc": [17, 128, 132, 181, 183], "is_compat": [128, 132], "is_diplo": 203, "is_disord": [15, 133, 135, 139, 155], "is_frag": 20, "is_ident": [128, 132], "is_includ": 229, "is_intern": [128, 132], "is_monophylet": [17, 128, 132, 181, 183], "is_nucl": [27, 133, 154], "is_parent_of": [17, 128, 130, 181, 183], "is_pqr": [15, 148, 151, 162], "is_pretermin": [17, 128, 132, 181, 183], "is_react": [115, 117], "is_termin": [17, 128, 132, 181, 183], "isaccept": 169, "isatti": [27, 278], "isbn": 169, "isdomaininev": [27, 209], "isdomaininid": [27, 209], "isfil": [7, 12], "isfin": 89, "isfortran": 54, "isinst": [3, 68, 237], "isiz": 270, "islic": [25, 276], "isligslskaqfctvlghpiskpiwtdfsdsdildrfcricrnlcryhsgsskkqvli": 7, "islow": [27, 236, 260], "isn": [3, 7, 8, 9, 12, 20, 21, 23, 56, 71, 183, 251, 278, 305], "iso": [104, 278], "isoelectr": [80, 263, 265], "isoelectric_point": [261, 263, 265], "isoelectricpoint": [27, 261, 265], "isoform": 272, "isol": [15, 23, 137, 202, 203, 272, 278], "isolectin": 0, "isoleucin": 15, "isomeras": [3, 10], "isotop": 265, "isotrop": [15, 135], "isotropt": 135, "isprofil": [30, 32], "isqnklvsl": 0, "issn": 123, "issu": [3, 5, 7, 11, 15, 22, 23, 27, 67, 68, 123, 143, 151, 158, 168, 169, 237, 251, 261, 278, 288], "isupp": [27, 236, 260], "ital": 7, "item": [0, 3, 4, 9, 15, 20, 22, 30, 36, 37, 54, 71, 73, 83, 109, 131, 136, 159, 181, 197, 199, 201, 210, 214, 217, 236, 238, 301, 302, 303], "itemindex": [27, 121], "itemrgb": [0, 36], "itemsperslot": [0, 36, 37], "iter": [0, 3, 4, 6, 7, 9, 10, 12, 16, 17, 20, 22, 25, 27, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 71, 73, 74, 81, 83, 87, 88, 92, 94, 100, 108, 109, 112, 113, 114, 116, 120, 121, 122, 123, 129, 131, 134, 135, 139, 154, 159, 161, 164, 169, 183, 185, 186, 188, 190, 197, 198, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 217, 219, 220, 221, 226, 228, 230, 232, 233, 235, 237, 238, 239, 240, 241, 242, 244, 246, 247, 248, 249, 250, 251, 253, 254, 256, 257, 258, 259, 260, 261, 269, 270, 271, 273, 274, 276, 277, 278, 286, 293, 296, 298, 299, 303], "iteration_queri": 218, "iterative_refin": [30, 32], "itertool": [25, 276], "ith": 177, "itoh": 25, "itreekpavt": 250, "its": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 32, 36, 44, 45, 49, 52, 53, 61, 64, 65, 68, 69, 80, 83, 99, 104, 117, 119, 132, 135, 139, 141, 149, 155, 156, 157, 169, 182, 183, 198, 209, 217, 218, 222, 229, 237, 238, 251, 252, 260, 263, 264, 269, 270, 278, 282, 287, 288, 289, 291, 292, 298, 299, 303], "its1": [19, 23], "its2": [19, 23], "itself": [0, 1, 3, 4, 7, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 24, 25, 30, 59, 68, 84, 93, 108, 117, 143, 151, 183, 185, 197, 201, 209, 214, 222, 236, 250, 251, 260, 263, 264], "itv": 0, "iub": 32, "iucr": 170, "iupac": [11, 22, 77, 80, 172, 214, 261, 265], "iupacdata": [27, 75], "iv": 8, "ivspvknq": 0, "ivspvknqahcgscwtf": 0, "ivspvknqahcgscwtfsttgaleaaytqatgknislseqqlvdcaggfnnf": 0, "iw": [30, 32], "ix": [4, 73], "ixi_234": 0, "ixi_235": 0, "iyfl005w": 11, "iystsehtgeqvmrtldeviasrspesqtr": 6, "j": [0, 2, 3, 4, 6, 7, 11, 12, 13, 17, 30, 32, 59, 68, 73, 74, 80, 125, 126, 129, 140, 149, 153, 157, 177, 182, 197, 251, 261, 263, 264, 269, 270], "ja": [2, 7, 13, 157], "jag": 8, "jaggi": 8, "jame": [2, 71], "jan": [0, 21, 149], "jannaschii": 94, "januari": [11, 88], "japan": [245, 274], "japanes": 250, "jaroslaw": 2, "jason": 166, "jaspar": [27, 283], "jaspar2014": 287, "jaspar2018": 288, "jaspar5": [11, 283, 287, 288], "jaspar_db_host": [11, 288], "jaspar_db_nam": [11, 288], "jaspar_db_pass": [11, 288], "jaspar_db_us": [11, 288], "jaspar_dflt_collect": 288, "jaspar_motif": 11, "java": [2, 4, 73], "jb": 2, "jc69": 182, "jd": 32, "jdb": [11, 288], "jeff": [2, 26], "jeffrei": 2, "jennif": 2, "jf": 182, "jfashya": 23, "jid": 123, "jill": 2, "jim": 247, "jinghui": [3, 68], "jitter": [98, 100], "jmb": 32, "jmbi": 2, "jn0120": 250, "joao": [133, 166], "job": [19, 82, 149, 182, 217], "jobnam": [4, 73], "joe": [0, 17, 65, 133], "johann": 2, "john": [2, 216, 262], "johnson": 199, "join": [4, 5, 6, 7, 10, 21, 22, 80, 94, 158, 169, 182, 199, 237, 260, 278], "joint": [6, 169], "jointli": 270, "jonathan": 2, "jone": [2, 7, 32, 182, 199, 265], "jorja": 2, "jour": 7, "journal": [2, 7, 8, 17, 21, 83, 93, 123, 137, 182, 197, 237], "journal_refer": [15, 174], "journal_titl": 83, "jp": [10, 32, 105, 111, 115, 116, 117, 119, 245, 274], "jpeg": 8, "jpg": 104, "jq660890": 7, "jq660906": 7, "jq660907": 7, "jq660908": 7, "jq660909": 7, "jr": [149, 152, 169], "json": [3, 16, 274, 298, 299], "json2": [3, 68], "jsoniter": [27, 298, 299], "jsonwrit": [27, 298, 299], "jt": [7, 123], "jth": 177, "jtreeview": 4, "jtt": [30, 32, 182], "juan": 2, "judg": [12, 15], "judici": 15, "jue": 2, "jueown6dphgz9nayowsgtod9tto": 23, "juke": 182, "jul": [7, 21, 93, 149, 175], "juli": [9, 87, 90, 210, 211, 213], "jumbl": [79, 80], "jump": [3, 5, 17, 19, 217, 238, 278], "jun": [7, 23, 175], "june": [7, 9, 25], "jupe": [2, 8], "jupe2012": [2, 8], "juret": 265, "jussieu": 153, "just": [0, 3, 5, 6, 7, 8, 9, 11, 12, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 49, 56, 64, 67, 71, 80, 83, 93, 94, 97, 99, 101, 104, 107, 108, 110, 129, 132, 152, 169, 182, 183, 191, 197, 203, 218, 236, 237, 238, 240, 241, 243, 251, 253, 255, 260, 264, 265, 278, 288, 297, 298, 303, 304, 305], "justic": 83, "justif": 25, "justweight": 80, "jusweight": [79, 80], "k": [0, 2, 3, 7, 9, 11, 12, 13, 14, 15, 17, 20, 22, 23, 25, 30, 32, 34, 53, 68, 71, 73, 80, 100, 109, 169, 182, 183, 260, 264, 265, 267, 268, 270, 281, 282], "k12": 22, "k80": 182, "k_i": 11, "ka": [2, 12], "ka_param": 71, "ka_params_gap": 71, "kaa": 6, "kaafdslqa": 12, "kaafdsltaq": 12, "kaafnslqa": 12, "kachitvichyanukul": [2, 4], "kachitvichyanukul1988": [2, 4], "kaenaavqvl": 0, "kag": [4, 73], "kamei": 2, "kamiya": 25, "kanamori": 25, "kanehisa": [2, 111, 115, 119], "kaplan": 2, "kappa": [3, 17, 30, 32, 68, 217], "kara": 2, "karlin": [3, 68], "karplu": 32, "katoh": 32, "katrin": 2, "katsuhara": 25, "kauff": [2, 130, 269], "kb": 7, "kbp": 104, "kcf": 119, "kcluster": [4, 27, 73], "kd": [4, 15, 146], "kdaggrvctnnyccskwgscgigpgycgag": 0, "kdkfsvnldv": 250, "kdtree": [15, 146], "keaaaaqq": 250, "keaaaqqq": 250, "keep": [0, 3, 4, 6, 7, 9, 10, 11, 12, 17, 19, 20, 21, 23, 24, 67, 69, 133, 183, 197, 222, 238, 249, 251, 260, 270], "keftppvqaayqkvvagvanalahkyh": 12, "kegg": [26, 27, 105, 197, 274, 307], "kegg_conv": [27, 111, 119], "kegg_find": [10, 27, 111, 119], "kegg_get": [10, 27, 111, 119], "kegg_info": [27, 111, 119], "kegg_link": [27, 111, 119], "kegg_list": [10, 27, 111, 119], "keggapi": [10, 119], "keggid": 117, "kei": [0, 3, 6, 7, 8, 11, 13, 15, 17, 18, 20, 21, 22, 24, 25, 27, 30, 37, 39, 46, 53, 54, 66, 68, 76, 82, 83, 84, 85, 86, 90, 93, 94, 95, 100, 104, 107, 108, 117, 121, 126, 127, 133, 134, 137, 141, 155, 169, 174, 181, 183, 197, 201, 202, 209, 210, 214, 217, 219, 221, 226, 230, 232, 233, 236, 237, 238, 240, 244, 245, 251, 257, 260, 263, 264, 270, 272, 273, 277, 278, 283, 287, 289, 290, 291, 292, 295, 297, 299, 301, 303], "keidrareiyerfvyvh": 53, "keidrareiyerfvyvhpdvknwikfarfe": 53, "keidrarsvyqrflhvhginvqnwikyakf": 53, "keidraruiyerfvavh": 53, "kel": 2, "keller": 53, "kendal": 73, "kennard": 149, "kent": [2, 221, 247], "kent2002": [0, 2], "kept": [3, 6, 7, 15, 21, 23, 32, 151, 198, 260, 269, 299], "ker20427": 3, "kevla": [30, 297], "key_func": 217, "key_funct": [20, 23, 217, 238], "key_nam": [95, 296], "keyatom": 126, "keyerror": [3, 6, 8, 45, 76, 102, 108, 305], "keys_to_process": [92, 95], "keywd": [83, 209], "keywlist": [25, 27, 272], "keyword": [0, 3, 7, 14, 15, 17, 20, 21, 23, 30, 53, 67, 72, 73, 83, 89, 93, 104, 119, 169, 183, 197, 217, 218, 221, 260, 272, 273, 297, 299], "kfdpklrfpwvtitpivlregkivilkgdkyykvfvkrleelkkynlikkkepileep": 94, "kfgakf": 281, "kfiyafskrkkrflwllynsyvyeceylfqflrkqssylrstssgvflerthlyvki": 7, "kfppwv": 281, "kgar": [22, 236], "kgg": [4, 73], "kgml": [27, 105, 111, 119], "kgml_parser": [111, 115], "kgml_pathwai": [111, 115, 116], "kgml_vi": [27, 98], "kgmlcanva": [27, 98, 105], "kgmlparser": [111, 115, 116], "kgtfatl": 13, "kgvngv": 0, "khfspeelkv": 250, "kidera": 265, "kieelnliai": 0, "kikfkykgqdlevdiskvkkvwkvgkmvsftydd": 0, "kikuta": 25, "kilivddqygirillnevfnkegyqtfqaanglqaldivtk": 56, "kill": [128, 130], "kim": 265, "kimmen": 2, "kimron1": 23, "kimura": [30, 32], "kin": 238, "kinahn": 0, "kinas": 113, "kind": [4, 5, 7, 8, 11, 12, 13, 19, 20, 21, 25, 30, 84, 92, 93, 101, 102, 103, 107, 110, 217, 264], "kindli": 53, "kingdom": 197, "kit": [238, 242], "kitareewan": 2, "kkvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaahlpaeftp": 12, "kl": [109, 130], "kloo": 2, "klr": 13, "klriapgsfysvtlgt": 0, "kmedoid": [4, 27, 73], "kml": 197, "kne": 0, "knetvmagyivstgplaiaadav": 0, "knew": 25, "knmpywivkn": 0, "knn": 27, "know": [0, 3, 5, 7, 9, 12, 16, 17, 19, 20, 21, 23, 24, 30, 67, 209, 229, 277, 278], "knowledg": [15, 19], "knowledgebas": [23, 25, 255, 272], "known": [0, 3, 4, 7, 11, 12, 15, 20, 21, 22, 29, 30, 67, 109, 152, 154, 209, 214, 236, 251, 290, 297], "knownstatetrain": [27, 106, 109], "ko": [116, 117], "ko00010": 116, "ko01100": 116, "koehl": 140, "koetzl": 149, "kohonen": [2, 4], "kohonen1997": [2, 4], "kolodni": 140, "konieczni": 72, "konopka": 267, "kpmanfrfg": 250, "kpmgnfrfgn": 250, "kpmsnfrfge": 250, "kqfrnclitt": 250, "kqfrncmitt": 250, "kreitman": [34, 280], "krishna": 2, "kristian": [15, 133, 174], "krogh": 2, "krogh1994": [0, 2], "krp": 292, "kr\u00f3l": 2, "ksgelrqtppasstlhlrlilqrsgvmmel": 6, "kskithlvfcttsgvdmpgcdyqltkllglrpsvkrfmmyqqgcfaggtvlrmakdlaen": 23, "ksnylrgt": 0, "ktn": 13, "ktupl": [30, 32], "kullback": 11, "kuma": 32, "kumar": 2, "kun": 250, "kunzmann": 9, "kurita": 25, "kvkfkykgeekevdiskikkvwrvgkmvsftydd": 0, "kvlgdmveih": 250, "kvrfkykgeekevdtskikkvwrvgkmvsftydd": 0, "kw": [25, 273], "kwarg": [30, 32, 54, 62, 67, 69, 80, 84, 91, 100, 104, 169, 182, 183, 185, 187, 188, 190, 191, 197, 217, 220, 223, 224, 225, 230, 231, 232, 233, 270, 283, 303], "kwd": [72, 283, 291], "kx265011": 7, "kx265012": 7, "kx265013": 7, "kx265014": 7, "kx265015": 7, "ky": 0, "kyh": [12, 14], "kyoto": [111, 115, 119], "kyr": [12, 13, 14], "kyripadvdp": 250, "kyte": 265, "kytedoolitl": 265, "kyushu": 32, "l": [2, 3, 4, 7, 13, 14, 22, 30, 32, 68, 80, 90, 100, 109, 113, 126, 135, 140, 141, 148, 152, 154, 169, 170, 173, 175, 176, 182, 222, 251, 260, 261, 263, 265, 268, 270], "l12": 169, "l13": 169, "l14": 169, "l23": 169, "l31939": [238, 245], "l7gjjfe6w": 238, "la": 123, "laahlpa": 13, "lab": 21, "label": [0, 4, 8, 15, 17, 22, 42, 99, 102, 104, 117, 126, 143, 177, 178, 179, 180, 183, 185, 188, 197, 222, 260], "label_angl": [8, 104], "label_color": [8, 104], "label_compound": 105, "label_font": 104, "label_map": 105, "label_ortholog": 105, "label_posit": [8, 104], "label_reaction_entri": 105, "label_s": [8, 99, 104], "label_sep_perc": 99, "label_strand": 104, "labess": 153, "lack": [15, 17, 183, 260], "lactic": 2, "lactococcu": 8, "ladder": [17, 132, 181, 183, 190], "ladero": 2, "ladi": [7, 19], "laepwkys": 250, "laepwkysvl": 250, "laepwqys": 250, "lag": [16, 300], "laieryiv": 250, "laieryivvc": 250, "laitsslssd": 250, "lambda": [3, 6, 16, 17, 20, 23, 30, 68, 71, 183, 217, 238], "lamprei": [30, 250], "land": 2, "lander": 2, "landscap": [8, 104], "languag": [4, 6, 7, 9, 15, 19, 123, 278], "larg": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 21, 23, 25, 30, 32, 83, 84, 104, 116, 149, 158, 182, 205, 217, 238, 274, 278, 280, 290], "largefilepars": [200, 201], "larger": [6, 7, 13, 20, 23, 32, 71, 169, 237, 265, 270, 278], "largerecord": 205, "largest": [11, 13, 69, 73, 149], "larkin": 32, "larri": 2, "last": [0, 3, 4, 5, 7, 8, 13, 14, 15, 17, 20, 21, 22, 23, 30, 32, 45, 56, 67, 68, 69, 76, 80, 83, 85, 88, 123, 126, 129, 154, 182, 183, 217, 221, 222, 236, 237, 238, 241, 251, 260, 264, 269, 270, 278, 283, 298, 303, 304], "last_align": 12, "last_id": [301, 303, 304], "last_record": [23, 30], "last_row": 299, "lastli": 10, "lastupd": 7, "lat": [181, 197, 198], "later": [0, 4, 6, 7, 8, 9, 13, 15, 17, 19, 20, 21, 23, 32, 48, 63, 65, 67, 69, 73, 169, 260, 278], "latest": [9, 11, 19, 27, 210, 211, 213, 288], "lathyru": 260, "latin": 23, "latin1": 278, "latitud": 197, "latter": [0, 7, 15, 84, 143, 151, 198, 257, 270, 278], "launch": 17, "laveryivvc": 250, "lavlataava": 0, "law": 169, "layout": [15, 22, 23, 51, 66, 68, 70, 94, 99], "lazi": [0, 30, 108, 182, 236, 238], "lc": 15, "lcase_mask": [68, 69, 70], "lcc": [27, 261], "lcc_mult": [27, 261, 267], "lcc_simp": [27, 261, 267], "lccgknpfgd": 250, "lccgknplgd": 250, "ld": 13, "le": [30, 32], "lead": [0, 3, 6, 12, 13, 15, 17, 32, 67, 94, 135, 182, 183, 236, 241, 260, 270, 297], "leaf": [17, 99, 182, 183, 209], "learn": [9, 19, 120, 282], "learner": 127, "least": [1, 2, 3, 4, 6, 7, 14, 15, 19, 22, 25, 32, 69, 72, 146, 169, 217, 238, 251, 275, 283, 288, 298], "leav": [12, 17, 20, 104, 182, 183, 237, 238, 241, 251, 253], "lecb": 12, "lectin": 0, "lecuyer1988": [2, 4], "leeuwenhoek": 2, "lefort": 182, "left": [0, 4, 6, 8, 11, 12, 13, 15, 21, 24, 30, 73, 94, 99, 104, 149, 152, 176, 237, 246, 251, 253, 260, 265, 299], "left_extend_gap_scor": 13, "left_gap_scor": 13, "left_multipli": [15, 133, 176], "left_open_gap_scor": 13, "leftcount": 0, "leftgreedi": 129, "leftstatu": 0, "leg": 169, "legaci": [3, 67, 149, 209, 218, 237, 276], "legal": 5, "legion": 197, "leibler": 11, "leighton": 2, "len": [0, 1, 3, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 45, 59, 62, 66, 68, 81, 116, 131, 169, 186, 217, 218, 221, 236, 237, 238, 240, 244, 247, 250, 251, 253, 256, 260, 270, 278, 283, 298], "len1": 158, "len12": [133, 169], "len23": [133, 169], "len3": 158, "len_adaptor": 6, "len_and_id": 6, "len_prim": 6, "len_record": 6, "len_tre": 186, "length": [0, 3, 4, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, 25, 27, 30, 31, 32, 35, 36, 37, 38, 39, 43, 46, 51, 52, 55, 56, 59, 61, 65, 68, 69, 70, 71, 72, 73, 74, 80, 81, 85, 99, 104, 126, 127, 131, 135, 136, 140, 144, 152, 160, 162, 169, 172, 182, 183, 186, 197, 201, 204, 205, 218, 219, 220, 221, 226, 229, 232, 236, 237, 238, 241, 244, 250, 251, 256, 257, 260, 261, 264, 265, 270, 272, 275, 278, 280, 281, 283, 288, 290, 295, 297, 300], "lenna": 133, "lenton": 262, "leopard": 250, "lep": [30, 32], "leq": 4, "less": [4, 6, 7, 8, 11, 13, 15, 20, 21, 30, 32, 83, 99, 135, 136, 139, 169, 182, 203, 207, 217, 237, 238, 251, 260, 278, 290, 297], "let": [0, 3, 5, 6, 7, 8, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 84, 183, 236, 238, 251, 253, 260, 278], "letter": [6, 11, 12, 13, 14, 15, 19, 21, 22, 25, 30, 31, 33, 53, 54, 59, 66, 71, 76, 80, 107, 108, 109, 149, 154, 169, 172, 209, 214, 215, 222, 236, 248, 250, 251, 260, 261, 263, 290, 295, 297, 299, 302], "letter1": 108, "letter2": 108, "letter_annot": [0, 6, 21, 27, 52, 53, 66, 240, 249, 251, 253, 260], "letters_per_block": [238, 245], "letters_per_lin": [238, 245], "lettter": 30, "leu": [13, 15], "leucin": 13, "level": [6, 7, 8, 10, 15, 17, 20, 21, 22, 24, 25, 27, 32, 36, 37, 67, 69, 84, 89, 99, 101, 104, 119, 123, 133, 135, 139, 145, 146, 152, 157, 158, 159, 168, 169, 172, 182, 183, 197, 198, 209, 217, 229, 238, 241, 251, 256, 270, 274, 278, 303], "level_tag": 89, "levin": 199, "levitt": 140, "lewicki": 2, "lexp": [30, 32], "lf": 278, "lflerleenhyntytskkhaeknwfvglkkngsckrgprthygqkailf": 265, "lfvlavftvf": 0, "lg": [30, 32, 182], "lgs_t": [30, 32], "lgv": 0, "lhah": 13, "lhivvvdddpgtcvyiesvfaelghtcksfvrpeaaeeyilthp": 56, "li": [2, 4, 13, 32, 34, 52, 53, 66, 261, 263, 281], "li1985": [2, 13], "li2009": [0, 2], "li_con": 53, "lib": [8, 24, 84, 99, 102, 275], "librari": [0, 1, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 19, 24, 25, 73, 80, 140, 177, 200, 208, 234, 270, 274, 275, 278, 298], "librdf": 185, "licens": [5, 9, 15, 137, 166], "lid": [7, 123, 275], "lie": [4, 222], "liebold": 0, "life": [12, 19, 21, 253, 265], "lifson": 264, "lift": [0, 30], "lifted_align": 30, "lifted_transcript": 0, "liftov": 0, "liftover_align": 0, "ligan": 112, "ligand": [25, 53, 112, 138], "ligand_bind": 66, "ligas": 113, "light": [2, 8], "lightblu": 8, "lightgreen": 104, "lightgrei": 8, "lightweight": [177, 252], "ligm": 245, "like": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 30, 31, 32, 35, 39, 45, 46, 51, 56, 61, 66, 67, 68, 69, 70, 76, 80, 83, 84, 91, 92, 93, 95, 99, 101, 103, 104, 110, 120, 123, 129, 134, 135, 139, 145, 146, 149, 158, 169, 177, 182, 197, 199, 201, 205, 209, 210, 211, 212, 213, 214, 217, 218, 221, 229, 236, 237, 238, 241, 244, 245, 247, 248, 250, 251, 253, 254, 255, 256, 258, 259, 260, 261, 269, 270, 271, 272, 278, 282, 283, 296, 297, 302, 303], "likelihood": [2, 13, 17, 109, 120, 182, 193, 194, 195, 270], "likelihoood": 121, "likewis": [8, 21, 23, 66], "liliopsida": [7, 25], "lime": 183, "limit": [0, 3, 6, 7, 11, 12, 15, 17, 18, 20, 23, 32, 50, 65, 68, 69, 70, 83, 119, 152, 158, 197, 217, 236, 251, 270, 274, 278], "lin": 9, "lin2566": 8, "lin2567": 8, "lin2568": 8, "lin2570": 8, "lin2571": 8, "lin2572": 8, "lin2573": 8, "lin2574": 8, "lin2575": 8, "lin2576": 8, "lin2577": 8, "lin2578": 8, "lin2579": 8, "lin2580": 8, "lin2581": 8, "linalg": 15, "line": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 21, 22, 23, 24, 25, 27, 30, 32, 33, 35, 37, 42, 43, 46, 51, 52, 53, 56, 59, 61, 65, 66, 67, 68, 69, 71, 80, 81, 83, 88, 90, 94, 99, 103, 104, 117, 123, 126, 129, 132, 143, 149, 152, 154, 156, 162, 168, 169, 174, 176, 182, 190, 201, 204, 205, 207, 210, 211, 212, 213, 214, 217, 218, 222, 223, 224, 225, 226, 230, 234, 238, 241, 244, 245, 248, 250, 251, 255, 256, 260, 269, 270, 271, 272, 273, 274, 275, 277, 278, 280, 285, 295, 297], "line_count": 162, "line_length": [68, 69], "line_width": 110, "lineageex": 7, "linear": [2, 4, 7, 8, 15, 16, 21, 23, 80, 83, 99, 104, 250, 270], "linearlyinterpolatedcolor": 8, "linedistribut": [27, 98, 103], "lines": [206, 207], "linewidth": 104, "link": [2, 4, 7, 9, 15, 19, 69, 83, 93, 104, 112, 114, 117, 119, 128, 130, 158, 167, 169, 177, 197, 218, 226, 227, 229, 234], "link_xi": 8, "linkag": [4, 15, 18, 32, 73, 202, 203, 238, 243], "linker": 69, "linknam": [7, 83], "linkout": 83, "linksetdb": [7, 83], "linn": 129, "linux": [5, 6, 23, 67], "lion": 6, "lip": 32, "lipas": 25, "lipid": 272, "lipl_bovin": 25, "lipl_cavpo": 25, "lipl_chick": 25, "lipl_felca": 25, "lipl_human": 25, "lipl_mous": 25, "lipl_musvi": 25, "lipl_papan": 25, "lipl_pig": 25, "lipl_rat": 25, "lipl_sheep": 25, "lipman": [2, 3, 32, 59, 68], "lipoprotein": 25, "list": [0, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 49, 51, 54, 56, 60, 61, 62, 64, 65, 67, 68, 69, 71, 72, 73, 76, 80, 81, 82, 83, 84, 87, 88, 89, 93, 94, 99, 100, 101, 102, 103, 104, 108, 109, 112, 113, 114, 117, 119, 120, 121, 122, 123, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 137, 139, 140, 146, 149, 152, 154, 155, 156, 159, 163, 167, 169, 172, 175, 177, 179, 180, 182, 183, 186, 197, 198, 201, 202, 203, 204, 205, 207, 209, 210, 214, 217, 218, 222, 226, 236, 237, 238, 246, 248, 251, 257, 259, 260, 261, 265, 267, 269, 270, 272, 273, 274, 276, 277, 280, 282, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 297, 298, 299, 302, 303], "list_ambiguous_codon": [27, 75, 76], "list_any_id": [301, 303], "list_biodatabase_nam": [301, 303], "list_bioentry_display_id": [301, 303], "list_bioentry_id": [301, 303], "list_of_seq": 22, "list_of_tre": 132, "list_possible_protein": [27, 75, 76], "listel": [27, 83, 84], "listeria": 8, "listfil": 149, "liter": 251, "literatur": [3, 7, 11, 12, 13, 15, 68, 197, 198], "littl": [0, 6, 8, 12, 19, 23, 107, 182, 217, 251, 253, 270, 278], "liu": 32, "live": [17, 72], "liver": 7, "ll": [0, 3, 5, 6, 7, 8, 11, 12, 13, 17, 19, 20, 21, 22, 23, 24, 25, 30, 67, 95, 99, 101, 191, 251, 260], "llc": 254, "llk": 6, "lllllaalcaaggal": 13, "llr": 11, "llshc": 13, "llvt": 13, "lmax": [30, 32], "lmb": [15, 209, 210, 211, 212], "lmcp": 153, "ln": [0, 90, 264], "lnl": 17, "lnsmgfgfvntkknsar": 94, "lo": [30, 32, 53, 66], "load": [0, 1, 3, 4, 6, 7, 8, 11, 12, 14, 15, 18, 19, 23, 27, 30, 35, 36, 37, 38, 39, 42, 46, 51, 52, 53, 54, 61, 62, 66, 84, 104, 118, 121, 152, 158, 168, 169, 171, 172, 193, 195, 196, 199, 205, 209, 214, 217, 236, 238, 248, 251, 257, 260, 275, 278, 297, 301, 303, 305], "load_database_sql": [301, 303], "load_seqrecord": [301, 305], "loader": [169, 301], "loadtestsfromnam": 24, "loan": [2, 15, 216], "lobri": 265, "loc": [209, 237], "loc110697660": 3, "loc2": 237, "local": [0, 2, 6, 7, 12, 13, 14, 19, 25, 30, 32, 42, 69, 84, 94, 109, 133, 137, 149, 157, 169, 182, 197, 218, 222, 226, 267, 270, 297], "local_dtd_dir": [83, 84], "local_xsd_dir": [83, 84], "locald": [14, 297], "localhost": 305, "localis": 2, "localm": 14, "localpair": [30, 32], "localpileup": [48, 63], "localtag": 198, "localxx": [14, 297], "locat": [6, 7, 8, 11, 12, 15, 24, 27, 32, 68, 69, 72, 93, 94, 99, 104, 123, 135, 162, 169, 172, 181, 193, 195, 196, 197, 198, 207, 209, 210, 214, 217, 234, 238, 245, 253, 260, 269, 272, 277], "locationparsererror": [27, 237], "loci": [18, 201, 202, 203, 204, 205], "loci_list": [18, 201, 204, 205], "lock": 264, "locu": [7, 8, 18, 21, 23, 83, 93, 94, 201, 202, 203, 204, 237, 245, 260, 278], "locus1": 203, "locus2": 203, "locus_nam": [202, 203], "locus_tag": [8, 21, 94, 99], "locuslink": [7, 275], "locut": 69, "lod": 270, "lofstedt": 7, "log": [4, 6, 9, 11, 12, 13, 30, 32, 67, 69, 93, 107, 109, 120, 122, 127, 158, 181, 182, 202, 203, 251, 264, 270, 288, 290, 294, 297], "log10": 251, "log2": [12, 13, 182], "log_2": [11, 294], "log_bas": [12, 31], "log_likelihood": [106, 109, 121], "log_odd": [11, 283, 290], "loga": [30, 32], "logarith": 251, "logarithm": [4, 11, 12, 13, 14, 31, 100, 127, 129, 251, 294, 297], "logdpalgorithm": [27, 106, 107], "logfil": [68, 69, 182], "logist": [16, 27, 120, 298, 299, 300], "logisticregress": 27, "logo": 9, "logo_end": 283, "logo_label": 283, "logo_start": 283, "logo_titl": 283, "long": [0, 3, 6, 7, 8, 13, 15, 20, 23, 25, 32, 66, 158, 169, 181, 182, 186, 197, 198, 238, 241, 250, 251, 256, 260, 270, 274, 298, 299], "long_vers": [30, 32], "longden": 2, "longer": [3, 4, 6, 7, 8, 12, 13, 14, 15, 17, 21, 23, 56, 65, 68, 70, 76, 83, 132, 149, 182, 183, 209, 238, 245, 246, 251, 258, 270], "longest": [4, 6, 30, 65], "longitud": 197, "longseq": [30, 32], "look": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 38, 53, 66, 80, 84, 93, 97, 101, 149, 169, 209, 251, 253, 260, 261, 278, 282, 297], "lookup": [8, 15, 69, 76, 107, 139, 146, 169, 209, 301, 303], "lookuperror": 17, "loop": [0, 3, 6, 7, 8, 11, 12, 21, 22, 23, 25, 30, 32, 45, 56, 112, 113, 114, 169, 238, 264, 274, 298], "loopgap": [30, 32], "loos": 288, "lop": [30, 32], "lopez": 32, "lose": [0, 13, 20, 30, 222], "loss": [166, 181, 197, 198], "lost": [0, 21, 30, 135, 169, 197, 260], "lost_count": 197, "lot": [1, 3, 5, 6, 7, 8, 9, 11, 12, 17, 19, 21, 22, 23, 24, 25, 31, 32, 99, 204, 238, 274], "lou78617": [238, 260], "love": [3, 12], "loveliesbleed": 260, "low": [6, 13, 15, 16, 25, 99, 104, 145, 238, 251, 264, 270, 274, 278], "lower": [0, 3, 4, 6, 9, 11, 12, 13, 14, 17, 21, 22, 23, 27, 30, 32, 33, 38, 51, 56, 68, 69, 70, 73, 79, 80, 104, 152, 169, 182, 183, 197, 217, 236, 237, 238, 253, 260, 264, 270, 275, 290, 298], "lowercas": [56, 236, 238, 260, 298], "lowerq": 104, "lowest": [11, 36, 37, 104, 236, 251], "lowscor": 25, "loxafr1": 0, "loytynoja": 32, "lpaeftpavhasldkflasvstvltskyr": 13, "lpc": 15, "lpetkdwr": 0, "lpgl": 5, "lpllcagawl": 0, "lplpv": 265, "lr": [7, 120, 123, 182], "lrr": 2, "ls_orchid": [3, 6, 19, 23], "ls_orchid_long": 23, "lsd": 13, "lshtvtdftdqmaqvglcqcvnvfldevtg": 6, "lsize": 140, "lspadktnv": 14, "lspadktnvkaa": [13, 14], "lspadktnvkaawgkvgahageygaealermflsfpttkti": [12, 14], "lspadktnvkaawgkvgahageygaealermflsfpttktyfphf": 13, "lsq": 216, "lsspadktnvkkaa": 14, "lst": 169, "lstring": 0, "lstrip": [27, 236], "lt": [7, 13, 83], "ltnavahv": 13, "lttqkaekev": 250, "lump": 218, "luo": 2, "lvffaedvgsnkgaiiglmvggvvia": 154, "lvvlvvgatv": 12, "lvvyp": 14, "lvvypwt": 13, "lwgkvnvdevg": 13, "lwl85": [13, 34, 280, 281], "ly": [13, 172], "lyrata": [3, 20], "lysatgagcgatgaaaata": 222, "lysin": [14, 80], "lysinemodifi": [79, 80], "lysozym": 157, "m": [0, 2, 3, 4, 7, 11, 12, 13, 14, 15, 16, 22, 25, 30, 32, 46, 55, 56, 59, 68, 73, 80, 111, 115, 119, 139, 140, 146, 149, 152, 153, 154, 157, 159, 168, 176, 182, 183, 197, 201, 217, 218, 226, 236, 237, 251, 253, 261, 265, 268, 270, 279, 283, 294, 297], "m0": 17, "m0_param": 17, "m1": 161, "m10": [27, 56, 59, 217], "m1734_0": 11, "m17827": 13, "m17828": 13, "m17830": 13, "m17831": 13, "m17832": 13, "m17833": 13, "m17834": 13, "m17835": 13, "m17836": 13, "m17837": 13, "m19547": 13, "m2": 161, "m2rotaxi": [27, 133, 176], "m81224": [238, 245], "m_code": 69, "m_cold": [1, 3, 69], "m_reb1": 11, "m_sub": 11, "ma": [3, 7, 20, 30, 32], "ma0001": [11, 288], "ma0002": 11, "ma0004": 11, "ma0047": 287, "ma0049": 288, "ma0052": 11, "ma0098": 288, "maagvkqlad": 260, "maagvkqladdrtllmagvshdlrtpltrirlat": 260, "maagvkqladdrtllmagvshdlrtpltrirlatemmseqdgylaesinkdie": 260, "mac": [5, 278], "macaca": [3, 20], "macaqu": [0, 22], "macclad": 0, "machin": [3, 9, 13, 16, 23, 56, 59, 182, 239, 298], "macintosh": 5, "mackenzi": 2, "macromolecul": 15, "macromolecular": [15, 133, 149, 160, 238], "madden": [3, 68], "maddison": [2, 129], "maddison1997": [0, 2], "made": [3, 4, 12, 13, 15, 18, 19, 21, 22, 31, 100, 183, 237, 251, 260, 283, 303], "maegeittftaltekfnlppgnykkpkllycsngghflrilpdgtvdgt": 265, "maeii": 206, "maf": [22, 27, 30, 37, 61, 278], "maf3": 0, "maf_fil": 61, "maf_project": 0, "mafblock": 0, "mafdot": 0, "mafft": 32, "mafft_clin": 32, "mafft_ex": 32, "mafftcommandlin": [30, 32], "mafindex": [27, 56, 61], "mafio": [27, 56], "mafiter": [27, 56, 61], "maftltnknvvfvaglggigldtskelvkrdlknlvildrienpaaiaelkainpkvtvt": 13, "maftobigmaf": 0, "mafwrit": [27, 56, 61], "magalha": 7, "magenta": 183, "magic": [3, 24, 278], "magnet": [125, 158, 169], "magnitud": [4, 73], "magnoliophyta": [7, 25], "magnoliopsida": 7, "mahabhashyam": 32, "maharvllla": 0, "maharvlllalavlataavavassssfadsnpirpvtdraastl": 56, "maharvlllalavlataavavassssfadsnpirpvtdraastlesavlgalgrtrhalr": 0, "mai": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 36, 37, 38, 45, 46, 52, 53, 56, 60, 65, 66, 67, 68, 70, 71, 73, 76, 81, 83, 84, 92, 93, 100, 104, 107, 116, 119, 137, 158, 169, 182, 183, 193, 195, 196, 197, 198, 209, 211, 214, 217, 218, 221, 222, 226, 229, 234, 237, 238, 240, 246, 248, 251, 260, 261, 264, 270, 272, 277, 278, 288, 297, 298, 303], "mail": [7, 8, 9, 17, 19, 27], "mailing_list": 19, "main": [1, 3, 5, 6, 7, 8, 9, 11, 12, 19, 20, 21, 24, 50, 65, 83, 88, 104, 129, 143, 209, 217, 238, 260, 298], "mainchain": [15, 169], "mainli": 217, "maintain": [9, 12, 83, 100, 217, 238], "mainten": 67, "maivmgr": [22, 260], "maivmgrwkga": 261, "maivmgrwkgar": [22, 236, 261], "maivmgrwkgaxxr": 261, "major": [3, 5, 7, 9, 21, 132, 186], "majority_consensu": [27, 181, 186], "majr": 7, "majumdar": 2, "majumdar2005": [2, 15], "make": [0, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 56, 67, 73, 80, 82, 93, 94, 97, 99, 102, 104, 108, 109, 117, 119, 129, 146, 149, 169, 182, 209, 217, 221, 222, 237, 238, 251, 253, 257, 260, 264, 265, 274, 278, 294, 298, 305], "make_back_t": [27, 75, 76], "make_dssp_dict": [27, 133, 137], "make_extend": [133, 169], "make_format": [206, 207], "make_protein_record": 6, "make_shuffle_record": 6, "make_t": [27, 261, 264], "make_tupl": 238, "make_virtual_offset": [27, 278], "makeblastdb": 69, "makematrix": [181, 182], "maket": 264, "malform": 270, "man": 121, "manag": [11, 91, 107, 129, 130, 131, 132, 169, 197], "mandatori": [7, 12, 21, 69, 182], "manderick": [2, 7, 9, 15], "mangalam": 7, "manhattan": 4, "mani": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 15, 16, 19, 20, 21, 22, 23, 24, 25, 32, 56, 60, 66, 69, 80, 83, 104, 133, 144, 182, 217, 219, 222, 231, 232, 236, 238, 243, 245, 265, 274, 288, 299, 303, 304], "manifest": 253, "manipul": [4, 7, 9, 15, 18, 19, 20, 23, 35, 46, 51, 61, 67, 71, 104, 126, 132, 169, 251], "manlfmvlfg": 250, "mann": 83, "manner": [15, 38, 110, 222, 237], "manor": 8, "manual": [7, 8, 11, 17, 19, 20, 23, 24, 31, 67, 68, 70, 182, 183, 209, 214, 245, 253, 264], "manufactur": 264, "manuscript": [8, 123], "map": [2, 3, 6, 10, 12, 13, 17, 20, 23, 27, 30, 52, 55, 69, 72, 73, 76, 83, 84, 99, 102, 104, 105, 108, 111, 115, 116, 117, 126, 134, 137, 140, 145, 161, 169, 172, 183, 197, 207, 209, 214, 221, 236, 251, 260, 263, 269, 270, 273, 275, 278, 279], "map_func": [3, 20], "mapal": [0, 13, 27, 30], "mapameeirqaqraegpaavlaigtstppnalyqadypdyyfritksehltelk": 23, "mapped_align": 13, "mapped_qresult": 20, "mapq": [52, 270], "maq": 6, "mar": [86, 88, 149], "march": 25, "marck": 259, "marena": 23, "margin": [104, 105, 182], "margouli": 2, "mark": [2, 6, 8, 27, 104, 169, 205, 229, 236, 237, 251, 270], "marker": [18, 72, 99, 201, 204, 205, 251, 275, 278], "marker_len": [201, 204, 205], "markov": [0, 2, 32, 44, 106, 107, 108, 109, 121, 229], "markov_model": [107, 109, 121], "markovmodel": [27, 106], "markovmodelbuild": [27, 106, 108], "marku": 2, "markup": 7, "markw": 236, "marmoset": 0, "marmur": 264, "maroon": 183, "marshak": 264, "marth": 2, "martin": 2, "masahiko": 2, "masatoshi": 2, "mase": [56, 238, 244], "mask": [0, 4, 27, 29, 30, 32, 38, 51, 53, 69, 73, 169, 247, 257, 283], "mask_data": [68, 69], "mask_desc": [68, 69], "mask_id": [68, 69], "maskel": 32, "masrgvnkvilvgnlgqdpevrympnggavanitlatseswrdkat": 260, "masrgvnkvilvgnlgqdpevrympnggavanitlatseswrdkatgemkeqt": 260, "mass": [112, 119, 135, 139, 261, 265], "mast": [27, 283, 291], "master": [4, 17, 25, 69], "mat": [30, 32], "mat_thr": [30, 32], "matbla": 13, "match": [0, 3, 6, 7, 8, 9, 12, 14, 15, 17, 20, 21, 22, 24, 25, 27, 30, 32, 33, 38, 42, 51, 55, 68, 69, 71, 79, 80, 83, 99, 104, 119, 132, 138, 168, 169, 175, 181, 183, 188, 214, 217, 218, 221, 226, 234, 237, 238, 247, 248, 251, 253, 260, 270, 274, 275, 277, 278, 288, 289, 290, 297], "match_column": 0, "match_dict": 297, "match_fn": 297, "match_num": 221, "match_rep_num": 221, "match_scor": [13, 30], "mate": 270, "mate_fil": [268, 270], "materi": 93, "math": [12, 15, 24, 169, 297], "mathdoc": 15, "mathemat": [7, 13], "mathew": 264, "mathml": 7, "mathrm": 12, "mati": 2, "matinits": [30, 32], "matk": 7, "matplotlib": [6, 15, 17, 169, 183], "matr": 7, "matres": [30, 32], "matric": [2, 9, 14, 15, 30, 34, 54, 80, 121, 129, 158, 169, 176, 199, 286, 287, 288, 290, 297, 299], "matrix": [0, 2, 3, 6, 14, 15, 27, 30, 31, 32, 49, 54, 56, 64, 68, 69, 70, 71, 73, 80, 88, 121, 129, 131, 135, 139, 158, 166, 169, 175, 176, 177, 181, 182, 199, 216, 270, 283, 286, 287, 288, 293, 295, 296, 297, 299], "matrix_id": [11, 287, 288], "matrix_nam": [68, 70], "matrixtyp": [79, 80], "matsumoto": 25, "matter": [3, 21, 23, 24, 25, 199], "matur": 272, "maturas": 7, "matys2003": [2, 11], "mau": 2, "mauv": [2, 27, 30, 56, 62], "mauve1": [0, 62], "mauveio": [27, 56], "mauveiter": [27, 56, 62], "mauvewrit": [27, 56, 62], "max": [2, 4, 6, 7, 8, 11, 15, 16, 17, 32, 69, 80, 145, 197, 237, 240, 251, 270, 283, 290, 299], "max_": 263, "max_cach": 278, "max_confid": 190, "max_file_sz": [68, 69], "max_gap": 166, "max_guidetree_iter": [30, 32], "max_hmm_iter": [30, 32], "max_hsp": [68, 69], "max_hsps_per_subject": [68, 69], "max_iis_iter": 122, "max_intron_length": [68, 69], "max_len": 8, "max_link": [30, 32], "max_newton_iter": 122, "max_num_thread": 149, "max_scor": [11, 279], "max_support": 132, "max_target_seq": [68, 69], "max_tri": 83, "maxbranch": [30, 32], "maxcount": 246, "maxdiagbreak": [30, 32], "maxdiff": 270, "maxdifftm": [79, 80], "maxdiv": [30, 32], "maxentropi": 27, "maxgc": [79, 80], "maxhour": [30, 32], "maxim": [2, 4, 207, 237, 270, 290], "maxima": 109, "maximum": [0, 4, 7, 8, 11, 13, 16, 17, 30, 32, 69, 73, 80, 83, 88, 104, 109, 121, 122, 149, 166, 181, 182, 193, 195, 197, 198, 236, 237, 246, 251, 263, 270, 278, 280, 299, 300], "maxit": [30, 32], "maxiter": [30, 32], "maxmem": 270, "maxmisprim": [79, 80], "maxnumseq": [30, 32], "maxocc": 270, "maxpallen": [79, 80], "maxpeptidebond": [15, 133, 158, 169], "maxpolyx": [79, 80], "maxr": 126, "maxrepeat": [79, 80], "maxseqlen": [30, 32], "maxsiz": [79, 80, 206, 207], "maxsplit": 236, "maxtm": [79, 80], "maxtre": [30, 32, 79, 80], "mayb": [5, 6, 7, 15, 274], "mb": 214, "mbed": 32, "mbox": 4, "mbp": 104, "mbstat": [3, 68], "mc": 207, "mcdonald": [34, 280], "mcgettigan": 32, "mclachlan": 199, "mcm": 0, "mcra": [17, 183], "mcwilliam": 32, "md": [0, 30, 52, 270], "mdiaihhpwi": 250, "mdirqgpkepfrdyvdrfyktlraeqasqevknwmtetllvqnanpdcktilkalgpgatleemmtacqg": 154, "mditihnpli": 250, "mdl": 168, "mdm78": 199, "me": [1, 3, 7, 9, 122, 182], "mean": [0, 3, 6, 7, 8, 11, 12, 14, 15, 16, 17, 19, 20, 21, 22, 23, 30, 64, 65, 69, 73, 76, 98, 104, 149, 152, 175, 182, 186, 197, 198, 199, 202, 203, 216, 217, 222, 236, 237, 238, 241, 250, 251, 260, 261, 263, 264, 265, 278, 283, 290, 297, 300], "meaning": [13, 14, 17, 132, 183, 303], "meaningless": 22, "meant": [20, 21, 31, 93, 97, 99, 103, 107, 207, 218, 237], "meantim": 277, "measur": [2, 4, 11, 12, 16, 32, 80, 152, 157, 169, 172], "mechan": [7, 19, 22, 67, 95, 158, 169], "med": [95, 124], "media": [0, 16], "median": 73, "medianq": 104, "medic": 7, "medium": [18, 23, 283], "medlin": [9, 11, 27, 93, 201, 237, 287, 288], "medline_id": [21, 93, 237], "medlinecit": [7, 83], "medoid": 73, "medydpwnlrfqskyksrda": 95, "meet": [183, 288], "mef2a": 11, "mega": [3, 68, 70], "megablast": [13, 30, 68, 69, 70, 199], "mehkevvlllllflksgqgeplddyvntqgaslfsvtkkqlgagsieecaakceedeeft": 25, "meier": 2, "meisner": 122, "melanogast": 13, "melt": [80, 264], "melting_temp": 264, "meltingtemp": [27, 261], "mem": 270, "member": [0, 4, 25, 68, 71, 72, 73, 81, 84, 89, 100, 122, 201, 205], "membership": [3, 6, 17, 20, 169, 183, 237], "membran": [3, 25, 260, 272], "meme": [27, 283, 289, 292], "meme10": 11, "memo": 169, "memoir": 167, "memori": [0, 1, 3, 4, 6, 7, 12, 14, 15, 21, 30, 56, 67, 68, 168, 169, 182, 198, 204, 205, 209, 214, 217, 238, 251, 253, 257, 269, 270, 278, 297], "memoryerror": 7, "memsav": [30, 32], "menlo": 2, "mention": [1, 3, 6, 7, 15, 19, 20, 21, 22, 23], "menunam": 7, "mercuri": [135, 162], "mere": 20, "merg": [4, 8, 32, 132, 270], "merge_bootstrap": 132, "merge_cmd": 270, "merge_with_support": [128, 132], "mergeai": 2, "merychippu": 56, "mesembryanthemum": 1, "mesh": [7, 123, 274], "meshmix": 158, "mesirov": 2, "mesohippu": 56, "mess": [20, 25, 204], "messag": [3, 12, 25, 27, 32, 67, 68, 80, 83, 84, 89, 168, 193, 195, 196, 270, 288], "messeng": 22, "messenger_rna": 22, "messi": 21, "met": [13, 15, 280], "meta": [11, 12, 46, 53, 66, 253, 269, 270], "meta_nod": 188, "metabol": [16, 104, 116], "metaclass": 84, "metadata": [0, 45, 46, 47, 61, 252, 287, 299], "metal": [25, 272], "metalailevalmetglyargtrplysglyala": 261, "metalailevalmetglyargtrplysglyalaarg": 261, "metalailevalmetglyargtrplysglyalaargt": 261, "metalailevalmetglyargtrplysglyalaxaaxaaargt": 261, "metalliduran": 2, "metaphor": 12, "meter": 197, "meth": 169, "methanococcu": 94, "methionin": [22, 154, 236, 272], "method": [0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 15, 16, 19, 20, 22, 23, 24, 25, 30, 31, 32, 34, 36, 45, 53, 54, 60, 61, 66, 67, 71, 73, 79, 80, 83, 91, 94, 99, 100, 104, 108, 109, 122, 126, 132, 135, 136, 139, 143, 148, 149, 151, 154, 169, 170, 172, 173, 176, 181, 182, 183, 186, 194, 197, 198, 199, 204, 207, 209, 236, 237, 238, 241, 246, 249, 251, 252, 253, 257, 260, 263, 264, 265, 270, 278, 280, 281, 282, 283, 288, 291, 294, 297, 299, 303, 305], "methyl": 112, "metric": [4, 197], "mexipedium": 19, "meyer": 149, "mf": 0, "mfa": 32, "mg": [15, 264], "mg2": 264, "mgc": 275, "mgf": 25, "mgggmisklfclaliflsssglaekntytakdilqnlelntfgnslshgiygkqttfkqteftniksntkkhialinkdnswmislkilgikrdeytvcfedfslirpptyvaihpllikkvksgnfivvkeikksipgctvyyh": 21, "mgltool": 156, "mgnpkvkahgkkvlgafsd": 13, "mgstm1": 0, "mgta": 13, "mgtalllllaalcaaggal": 13, "mh": 123, "mhda": 123, "mhp": 8, "mhz": 15, "mi": [0, 6], "mian": [0, 2], "michael": [2, 4, 73], "michel": [15, 156], "michiel": [2, 26], "microarrai": [2, 238, 298, 299, 300], "microbesonlin": [17, 182], "microphylum": 197, "microrna": [3, 20], "microsequ": 0, "microtu": [6, 8, 21, 238], "mid": 123, "middl": [3, 6, 8, 23, 68, 104], "midlin": [3, 68], "midpoint": [17, 183], "might": [3, 5, 6, 7, 8, 11, 12, 17, 18, 20, 21, 22, 23, 24, 32, 95, 110, 132, 143, 151, 183, 197, 202, 204, 238, 251, 253, 260, 269], "migrant": 202, "migrat": 18, "miller": [2, 3, 32, 68, 133, 137, 169], "millimolar": [80, 264], "million": [6, 23, 197], "milot": 2, "mimic": [6, 218, 221, 226, 264], "mimick": [3, 294], "mimicri": 7, "min": [6, 7, 11, 16, 182, 237, 251, 283, 290, 299], "min_": 263, "min_dist": [27, 133, 156, 202, 203], "min_ic": [11, 288], "min_len": 6, "min_length": 288, "min_link": [30, 32], "min_pro_len": 6, "min_protein_length": 6, "min_raw_gapped_scor": [68, 69], "min_scor": 11, "min_sit": 288, "minbaseq": 270, "minbestcolscor": [30, 32], "mincount": 246, "mind": [4, 7, 12, 19, 73, 103, 114], "mine": 114, "mingc": [79, 80], "minidb": 303, "minim": [0, 4, 8, 11, 15, 24, 27, 35, 46, 51, 61, 163, 166, 175, 177, 191, 198, 216, 237, 238, 270, 283, 290], "minimal_test": 292, "minimis": 209, "minimum": [6, 11, 13, 16, 21, 32, 69, 80, 104, 156, 181, 182, 197, 198, 237, 251, 263, 270, 299], "minlod": 270, "minmapq": 270, "minor": 270, "minoru": 2, "minpallen": [79, 80], "minr": 126, "minrepeat": [79, 80], "minscor": [79, 80], "minseedlen": 270, "minsiz": [79, 80], "minsmoothscor": [30, 32], "mintm": [79, 80], "minu": [15, 20, 63, 69, 119, 221, 222, 237, 251, 270], "minum": 299, "minut": [3, 4, 6, 15, 16, 23, 25], "minw": 11, "mir": [3, 20], "mir519a": 3, "mir520": 20, "mir520b": [3, 20], "mir520c": [3, 20], "mir_1": 217, "mir_2": 217, "mir_3": 217, "mirdita": 2, "mirna": [20, 217, 268, 270], "mirror": [15, 89, 149, 158, 169, 176, 303], "misalign": 270, "misawa": 32, "misc": [22, 76, 94], "miscellan": [21, 104, 261], "mishyblibraryfil": [79, 80], "mislead": [240, 303], "mismatch": [3, 6, 14, 20, 27, 30, 38, 42, 51, 68, 69, 71, 79, 80, 168, 218, 221, 264, 270, 297], "mismatch_num": [20, 218, 221], "mismatch_scor": [13, 30], "mismatchperc": [79, 80], "mismsc": 270, "mispriminglibrari": 80, "mispriminglibraryfil": [79, 80], "miss": [0, 5, 11, 12, 15, 18, 27, 56, 63, 73, 129, 151, 152, 158, 169, 197, 237, 238, 248, 251, 253, 270, 278], "missing_residu": 15, "missingatomerror": [27, 133, 169], "missingexternaldependencyerror": 27, "missingok": 169, "missingpythondependencyerror": 27, "mission": 123, "mistak": [3, 12, 15, 22], "mitchison": 2, "mito_t": 22, "mitochondri": [7, 22], "mitochondria": 8, "mitochondrion": 272, "mitogeneticcod": 7, "mix": [6, 22, 32, 83, 84, 182, 197, 237, 253, 261], "mixi": 182, "mixtur": [2, 6, 129], "miyano": [2, 7], "miyata": 32, "miyazawa": 265, "mj": 7, "mkdssp": 137, "mkkmqsivlalslvlvapmaaqaaeitlvpsvklqigdrdnrgyywdgghwrdh": 22, "mkqhkamivaivicitavvaalvtrkdlcevhirtgqtevavf": 260, "mkqhkamivalivicitavva": 237, "mkqhkamivalivicitavvaalvtrkdlcevhirtgqtevavf": [236, 260], "mkt": [34, 280], "mktest": [13, 27, 30, 34, 279, 280], "mkvil": 0, "mkvillfvlavftvfvss": [0, 56], "ml": [13, 34, 80, 182, 280, 281], "ml_estim": [106, 109], "mlacc": [181, 182], "mle": 121, "mlfrac": [79, 80], "mlgsnesrvcpklsp": 30, "mllen": [181, 182], "mlnni": [181, 182], "mlyi": 206, "mm": [53, 66, 121, 152, 158, 264], "mm10": [0, 22], "mm10tomm39": 0, "mm39": 0, "mm4": 0, "mm9": 0, "mmcif": [133, 137, 142, 143, 149, 150, 164, 169, 170, 172, 238, 248], "mmcif2dict": [15, 27, 133], "mmcif_dict": 15, "mmcif_pars": 164, "mmcif_pdbx_v40": 248, "mmcif_pdbx_v50": 248, "mmcifio": [15, 27, 133], "mmcifpars": [15, 27, 133, 162, 164, 170, 173, 238], "mmcipars": 143, "mmlib": 15, "mmm": [88, 270], "mmtf": [27, 133, 149], "mmtfio": [15, 133, 171], "mmtfparser": [15, 133, 171], "mmtk": 15, "mmtv": 68, "mmyqqgcfaggtvlrlakdlaennrgarvlvvcseitavtfrgpsethldsmvgqalfgd": [21, 23], "mn": 23, "mnemon": 123, "mngtegdnfi": 250, "mngtegpnfi": 250, "mnllltlltnttlalllvfi": 272, "mnmnm": 0, "mnp": 270, "mo_prob": 294, "mod": [11, 149, 218], "mod_r": 272, "mode": [1, 6, 7, 9, 13, 23, 25, 27, 30, 32, 36, 37, 45, 68, 79, 80, 83, 91, 129, 143, 182, 199, 241, 244, 245, 246, 247, 248, 249, 251, 252, 253, 256, 259, 264, 270, 271, 303], "model": [0, 2, 3, 7, 11, 12, 16, 17, 21, 25, 27, 30, 32, 33, 42, 44, 53, 68, 71, 80, 84, 99, 106, 107, 108, 109, 110, 121, 123, 125, 128, 133, 135, 136, 137, 138, 139, 140, 141, 145, 146, 148, 153, 156, 157, 158, 160, 161, 162, 168, 169, 170, 172, 173, 177, 181, 182, 185, 195, 199, 217, 222, 229, 234, 237, 248, 270, 299, 300], "model_id": [15, 138, 162, 172], "model_mask": 66, "model_nr": 15, "moder": [23, 270], "modif": [15, 23, 182, 218, 272], "modifi": [0, 3, 4, 11, 12, 13, 17, 20, 21, 24, 80, 93, 149, 154, 158, 166, 169, 182, 183, 191, 209, 214, 217, 218, 236, 241, 251, 278, 283, 294], "modify_record": [241, 251], "modr": 248, "modul": [0, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 307], "module_nam": [303, 304], "moieti": 272, "mol": [74, 119, 140, 149, 157, 264], "mol_seq": [181, 197, 198], "mol_typ": 7, "mol_weight": [10, 119], "molar": [264, 265], "molar_extinction_coeffici": [261, 265], "molbev": 2, "molecul": [15, 20, 21, 22, 56, 69, 104, 157, 166, 197, 214, 238, 250, 252, 260, 261, 272], "molecular": [0, 2, 7, 9, 10, 12, 19, 23, 27, 32, 83, 112, 119, 156, 169, 197, 198, 261, 265, 272], "molecular_weight": [27, 261, 265], "molecule_typ": [0, 21, 25, 56, 238, 252, 253, 260, 272], "molseq": [27, 181, 197], "moment": [149, 270, 277], "mondom5": 22, "mono": 259, "monoisotop": [261, 265], "monom": 0, "mononucleotid": 80, "monooxygenas": 113, "monophylet": [17, 132, 182, 183], "monoval": 264, "monphyli": 132, "month": 152, "montpelli": [17, 182], "moor": 7, "mopb_rhoca": 68, "more": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 35, 36, 37, 38, 45, 46, 49, 50, 51, 52, 53, 56, 59, 61, 64, 65, 66, 67, 68, 70, 71, 72, 73, 76, 80, 83, 84, 90, 91, 93, 99, 107, 108, 113, 117, 123, 129, 149, 155, 157, 169, 177, 182, 197, 198, 204, 207, 212, 214, 215, 217, 218, 221, 222, 226, 227, 229, 234, 237, 238, 239, 240, 251, 252, 253, 255, 260, 262, 269, 270, 271, 273, 274, 275, 278, 283, 288, 295, 297, 298, 299], "more_target": 183, "more_termin": 183, "moreov": 20, "morgenstern": 32, "mornon": 153, "most": [0, 1, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 45, 50, 56, 59, 65, 66, 67, 68, 69, 80, 83, 85, 99, 101, 108, 139, 149, 152, 177, 182, 183, 197, 201, 209, 217, 221, 222, 236, 237, 238, 241, 248, 251, 260, 264, 265, 278, 283, 298, 303], "mostli": [15, 32], "mot": [30, 32], "motif": [2, 9, 12, 26, 27, 32, 53, 114, 272, 307], "motif1": 11, "motif2": 11, "motif_1": 11, "motif_nam": [11, 291], "motifexplor": 296, "motifsm": 11, "motiv": [7, 19, 23], "mott": 238, "mous": [0, 11, 22, 30, 182], "move": [5, 6, 15, 20, 92, 100, 104, 132, 163, 169, 175, 176, 182, 237, 278], "move_track": [98, 104], "mp": [1, 182], "mp14h09": 1, "mpi": 182, "mpileup": 270, "mpwrrnmqsc": 0, "mpwrrnrqsc": 0, "mr": 80, "mrbay": 129, "mrc": [15, 209, 210, 211, 212], "mrca": [17, 183], "mre": 80, "mrlllelkalnsidkkqlsnyliqgfiynilknteyswlhnwkk": 94, "mrlllelkalnsidkkqlsnyliqgfiynilknteyswlhnwkknekyfnft": 94, "mrna": [3, 7, 21, 22, 68, 238, 275], "mrna1": 0, "mrna2": 0, "msa": [12, 30, 32, 69, 186, 199], "msa_master_idx": [68, 69], "msaprob": 32, "msaprobscommandlin": [30, 32], "msb": 32, "mse": [15, 154], "msei": 206, "msf": [27, 30, 32, 56, 63], "msf_aln": 32, "msfio": [27, 56], "msfiter": [27, 56, 63], "msfout": [30, 32], "msftltnknvifvaglggigldtskellkrdlknlvildrienpaaiaelkainpkvtvt": 13, "msm": [15, 156], "msms_exec": 156, "msms_home": 15, "msr": [30, 279], "mt": [32, 264], "mtart": 182, "mtfglvytvyataidpkkgslgtiapiaigfivgani": 241, "mtmam": 182, "mtrev": 182, "mttranslat": [30, 32], "mtx": [169, 176], "mu": [25, 217], "mu_": 16, "much": [0, 3, 4, 5, 6, 7, 11, 13, 15, 17, 19, 21, 22, 23, 25, 30, 83, 84, 92, 93, 94, 166, 175, 204, 209, 217, 218, 238, 264, 270], "mulatta": [3, 20], "multi": [23, 30, 32, 81, 94, 131, 180, 182, 183, 270, 278, 280], "multi_coord_spac": [27, 133, 176], "multi_rot_i": [27, 133, 176], "multi_rot_z": [27, 133, 176], "multidimension": 2, "multifurc": 182, "multigraph": [177, 178], "multilevel": 83, "multilocu": [202, 203], "multilocusfi": 202, "multilocusfst": 202, "multipass": [3, 68], "multipl": [1, 2, 3, 4, 6, 7, 11, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 43, 44, 45, 46, 53, 56, 59, 61, 62, 65, 66, 69, 71, 74, 81, 83, 84, 86, 88, 90, 92, 94, 99, 103, 104, 116, 130, 132, 149, 154, 169, 172, 181, 182, 186, 197, 199, 206, 217, 234, 236, 237, 241, 244, 246, 250, 251, 253, 260, 261, 267, 270, 271, 272, 275, 278, 281, 283, 288, 298, 307], "multiple_align": 71, "multiple_value_kei": [283, 295], "multiplealign": [27, 68, 71], "multipleseqalign": [0, 3, 9, 12, 20, 27, 30, 56, 59, 60, 61, 64, 65, 66, 71, 186, 197, 199, 217, 279, 280], "multipli": [6, 11, 12, 13, 15, 32, 107, 135, 139, 169, 175, 176, 216, 287], "multist": 131, "multivari": 4, "multiz": 0, "multiz28wayfram": 0, "munteanu": 7, "muscl": [7, 32, 48, 63, 197], "muscle3": 32, "muscle_clin": 32, "muscle_ex": 32, "musclecommandlin": [30, 32], "musculu": 217, "must": [0, 3, 5, 8, 10, 11, 12, 13, 14, 17, 20, 21, 23, 24, 30, 32, 35, 36, 37, 38, 47, 53, 54, 56, 61, 66, 67, 68, 69, 83, 92, 104, 107, 108, 117, 122, 127, 152, 169, 175, 182, 183, 186, 199, 207, 209, 214, 217, 229, 236, 237, 238, 247, 248, 250, 251, 260, 264, 270, 278, 288, 290, 297, 299, 303], "mutabl": [22, 236], "mutable_seq": 22, "mutableseq": [0, 9, 27, 30, 236, 237, 260, 261], "mutagen": 272, "mutagenesi": [264, 272], "mutant": 15, "mutat": [13, 22, 155], "mv": [12, 13, 14], "mvhl": [13, 14], "mvhltpeeksavtalwgkv": [12, 13, 14], "mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk": 12, "mvlspadktnvkaawgkvgahageygaealermflsfpttktyfphfdlshgsaqvkghg": 12, "mvtveefrraqcaegpatvmaigtatpsncvdqstypdyyfritnsehkvelkekfkrmc": 23, "mvvvivgati": 12, "mw": 265, "mwat": 0, "mwatlpllcagawllgv": [0, 56], "my": [3, 8, 9, 15, 17, 19, 23, 25, 32, 84, 108, 169, 207], "my_ace_fil": 269, "my_align": 12, "my_blast": [3, 20], "my_blat": 20, "my_cod": 131, "my_el": 83, "my_exampl": [12, 23], "my_gap_score_funct": 13, "my_info": 1, "my_info_handl": 1, "my_iter": 56, "my_loc": 21, "my_map": 207, "my_partially_defined_sequ": 236, "my_pssm": 12, "my_qblast_output": 3, "my_qblast_output_select": 3, "my_record": [23, 260], "my_seq": [19, 22, 236], "my_seq_featur": 8, "my_snp": 21, "my_str": 22, "my_undefined_sequ": 236, "mya": 197, "myapikei": 7, "myatom1": 15, "myatom2": 15, "mybed12fil": 0, "mybed3fil": 0, "mybed6fil": 0, "mychain": [15, 169], "mychain2": [15, 169], "mycic": 15, "mydatafil": 4, "myer": [2, 32], "myfastaread": 246, "myfil": [0, 7, 60, 246], "myfilenam": 0, "mylocalscript": 7, "mymotif": 11, "myprodocrecord": [25, 85], "myprositefil": 25, "myprositerecord": [25, 85], "myprotein": [15, 169], "myprotein2": [15, 169], "myprotein3": [15, 169], "myrandom": [15, 169], "myrecord": [241, 250], "myresult": 80, "myseq": 264, "mysequ": 80, "mysingleprositerecord": 25, "mysql": [209, 303, 304], "mysql_dbutil": [301, 304], "mysqlconnectoradaptor": [301, 303], "mysqldb": [209, 288, 303, 305], "mystery_seq": [3, 20], "mystr": 264, "myswissprotfil": 25, "mytabl": 264, "mytransfacfil": 11, "mytre": 73, "myunigenefil": 7, "myzipfil": 3, "m\u00fcnch": 2, "n": [0, 1, 3, 4, 6, 7, 10, 11, 12, 13, 14, 15, 17, 22, 23, 25, 30, 32, 38, 46, 51, 74, 80, 94, 119, 126, 129, 132, 135, 136, 149, 152, 153, 154, 166, 169, 175, 181, 182, 183, 185, 201, 207, 216, 221, 229, 237, 238, 245, 247, 251, 257, 260, 261, 263, 264, 265, 268, 270, 278, 290, 297], "n0": 183, "n1": [183, 250], "n15": [125, 126], "n3": 250, "n5kn7umj013": 3, "n5kn7umj013_1": 3, "n_": 12, "n_g": 270, "n_match": [25, 89], "n_num": 221, "n_point": 157, "n_rand_start": [181, 182], "n_seq": [25, 89], "n_x": 4, "n_y": 4, "na": [11, 80, 264, 295], "na_eq": 264, "naccess": [27, 133], "naccess_atom": [27, 133, 145], "naccess_binari": 145, "naccggatgta": 238, "nacgt": 91, "nacgtacgta": 251, "nad": 272, "nadh": [16, 113], "nag": 0, "nagaagagccgcnggcactt": 247, "nagaagagccgcnggcacttgantatcgtcgccaccagncgncttgntgg": 247, "naggctcggtta": 238, "naiv": [6, 7, 9, 76, 122, 127, 251], "naivebay": 27, "name": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45, 47, 49, 50, 51, 52, 53, 54, 56, 59, 61, 65, 67, 68, 69, 71, 73, 76, 80, 82, 83, 84, 86, 87, 88, 89, 90, 92, 93, 94, 99, 100, 101, 102, 103, 104, 112, 113, 114, 115, 117, 119, 121, 123, 125, 126, 129, 132, 135, 137, 139, 140, 141, 142, 143, 149, 151, 152, 154, 155, 158, 162, 167, 169, 172, 175, 181, 182, 183, 184, 185, 187, 189, 197, 198, 199, 201, 202, 204, 205, 207, 211, 217, 218, 221, 229, 234, 236, 237, 238, 241, 247, 249, 250, 251, 252, 253, 256, 257, 259, 260, 263, 269, 270, 272, 275, 278, 280, 287, 288, 289, 291, 292, 295, 296, 297, 299, 303, 304], "name1": 129, "name2": 129, "name_map": 12, "name_qualifi": [99, 104], "namedtupl": [0, 30, 169], "namelength": [30, 32], "namelist": 3, "namespac": [27, 84, 188, 197, 198, 252, 303], "namesrt": 270, "namewidth": [206, 207], "nan": [16, 299], "nannipu": 56, "nanomolar": 80, "naohisa": 2, "nar": [2, 69, 251], "naringenin": 23, "narrow": 129, "nasti": 251, "nat1": 7, "nat2": 7, "nation": [2, 32, 238, 250], "nativ": [11, 12, 20, 140, 218, 238, 253, 254, 270], "natl": [83, 264], "natom": 175, "natur": [20, 22, 100, 260, 294], "navi": 183, "navig": 17, "naynyiikng": 0, "nb": [2, 127, 183, 197], "nbk1762": 218, "nbk25499": 83, "nbk25501": [7, 83], "nbrf": [32, 238, 250], "nc": [0, 11, 53, 169, 207], "nc_000932": [92, 237, 238, 278], "nc_001136": 0, "nc_001145": 0, "nc_002703": 8, "nc_003070": 8, "nc_003071": 8, "nc_003074": 8, "nc_003075": 8, "nc_003076": 8, "nc_003132": 21, "nc_003212": 8, "nc_0058": 21, "nc_005816": [6, 7, 8, 21, 69, 238, 256], "nca": 169, "ncac": 169, "ncackei": 169, "ncaco": 169, "ncategori": [79, 80], "ncbi": [0, 6, 8, 9, 13, 19, 20, 21, 22, 23, 26, 32, 38, 68, 69, 70, 71, 76, 83, 84, 93, 94, 96, 97, 119, 123, 197, 218, 234, 236, 237, 238, 245, 251, 252, 253, 272, 274, 275, 303, 307], "ncbi_blast_url": [68, 70], "ncbi_blastoutput": [68, 71, 218], "ncbi_gi": [68, 70], "ncbi_taxonomi": 197, "ncbiblastformattercommandlin": [27, 68, 69], "ncbiblastncommandlin": [27, 68, 69], "ncbiblastpcommandlin": [27, 68, 69], "ncbiblastxcommandlin": [27, 68, 69], "ncbicodont": [27, 75, 76], "ncbicodontabledna": [27, 75, 76], "ncbicodontablerna": [27, 75, 76], "ncbideltablastcommandlin": [27, 68, 69], "ncbimakeblastdbcommandlin": [27, 68, 69], "ncbipsiblastcommandlin": [27, 68, 69], "ncbirpsblastcommandlin": [27, 68, 69], "ncbirpstblastncommandlin": [27, 68, 69], "ncbisearch": 7, "ncbitaxid": 252, "ncbitblastncommandlin": [27, 68, 69], "ncbitblastxcommandlin": [27, 68, 69], "ncbiwww": [3, 9, 27, 68], "ncbixml": [3, 27, 68], "nchar": [0, 56, 129], "ncid_01_206841095_130": 7, "ncifcrf": 12, "nclass": [181, 182], "ncluster": [4, 73], "ncog1583": 94, "ncol": 29, "ncolumn": 73, "ncontig": 269, "ncount": [0, 30, 38, 51], "ncrna": 32, "nctnctn": 12, "nd": 277, "nd1": 169, "nd2": 169, "ndarrai": [54, 135, 162, 169, 176], "ndg": 0, "ndx": [15, 169], "ne": [3, 169, 202], "ne1": 169, "ne2": 169, "nearest": [9, 15, 169, 182, 199, 223, 224, 225, 251, 253, 264, 282], "nearli": [15, 23], "neat": [6, 12, 22], "necessari": [3, 4, 8, 15, 20, 24, 61, 120, 132, 177, 217, 237, 264, 282], "necessarili": [4, 15, 17, 25, 109, 129, 183, 237], "need": [0, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 55, 61, 67, 73, 84, 90, 95, 99, 109, 137, 140, 152, 158, 168, 169, 172, 176, 178, 182, 191, 207, 209, 218, 221, 229, 236, 237, 238, 251, 260, 264, 269, 277, 278, 280, 298], "needl": [0, 13, 14, 41, 56, 58, 80], "needleal": 80, "needleallcommandlin": [27, 79, 80], "needlecommandlin": [27, 79, 80], "needleman": [12, 13, 30, 32], "needs_upd": 169, "neff": 0, "neg": [4, 11, 13, 30, 32, 69, 71, 73, 88, 99, 197, 237, 251, 270, 294, 297, 299], "negative_gilist": [68, 69], "negative_seqidlist": [68, 69], "negativeinteg": 197, "negcolor": 104, "nei": [2, 13, 34, 281], "nei1986": [2, 13], "neighbor": [4, 9, 15, 80, 141, 146, 182, 199, 264, 265, 282], "neighborbood": 73, "neighborhood": 282, "neighborsearch": [15, 27, 133], "neither": [84, 182, 197, 251], "nematod": 288, "neohippari": 56, "neph": [11, 283], "neq001": 94, "ner": [42, 222], "nescent": 17, "nest": [6, 8, 17, 20, 132, 182, 185, 217], "nestedmica": 296, "net": [4, 7, 15, 25, 32, 177, 270, 274, 278], "network": [4, 7, 23, 27, 83, 177, 209], "neubig": 7, "neural": 4, "neutral": [23, 34, 280], "never": [4, 207], "new": [0, 2, 4, 5, 6, 7, 8, 9, 11, 13, 15, 17, 18, 20, 21, 23, 25, 26, 30, 32, 36, 45, 54, 60, 67, 68, 69, 70, 71, 76, 84, 94, 104, 105, 109, 112, 113, 114, 120, 126, 127, 129, 132, 149, 153, 162, 169, 176, 177, 179, 180, 182, 183, 188, 190, 191, 197, 199, 205, 207, 236, 237, 238, 244, 246, 251, 252, 260, 261, 264, 265, 270, 278, 282, 283, 288, 295, 297, 299, 303, 307], "new_angl": 169, "new_clad": [181, 185, 190], "new_databas": [301, 303, 305], "new_graph": [98, 104], "new_id": [6, 23], "new_label": [181, 188], "new_seq": [22, 71], "new_set": [8, 98, 104], "new_succ": 130, "new_track": [8, 98, 104], "new_tre": 132, "newatomcoord": 169, "newbler": 6, "newentri": 126, "newer": [6, 7, 25, 251], "newest": 149, "newick": [12, 17, 27, 32, 132, 181, 182, 190, 191, 197, 199], "newick_doc": 190, "newickerror": [27, 181, 190], "newickfil": 182, "newickio": [27, 181, 191], "newlength": 169, "newli": [4, 15, 32], "newlin": [60, 65, 69, 94, 236, 238, 246], "newslett": 2, "newtabl": 264, "newton": 122, "newton_converg": 122, "newtre": [17, 30, 32], "newtree1": [30, 32], "newtree2": [30, 32], "nex": [0, 17], "nexml": [17, 27, 181, 188], "nexmlerror": [27, 181, 188], "nexmlio": [27, 181], "nexp": 73, "next": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, 25, 30, 37, 45, 46, 52, 53, 56, 57, 58, 60, 62, 63, 65, 66, 68, 92, 129, 131, 169, 183, 204, 218, 222, 230, 238, 246, 251, 252, 258, 267, 278, 298, 299, 300], "next_nonwhitespac": [128, 129], "next_until": [128, 129], "next_word": [128, 129], "nexu": [2, 12, 17, 27, 30, 32, 56, 64, 182, 183, 184, 185, 187, 188, 189, 190, 191, 197, 238], "nexus_instance1": 129, "nexus_instance2": 129, "nexuserror": [27, 128, 129, 131], "nexusio": [27, 56, 181], "nexusiter": [27, 56, 64], "nexuswrit": [27, 56, 64], "nfh": 245, "nfk": 13, "nfound": [4, 73], "nftmip": 0, "ng86": [13, 34, 280, 281], "ngc": 6, "ngene": 73, "ngktgrgavsekdapkellnmigk": 0, "ngktgrgavsekdapkellsmluk": 0, "ngktgrgavsekdapkelmdmlar": 0, "ngnhtfkmal": 0, "ngnhtfkmalnqfsdmsfa": 0, "ngnhtfkmalnqfsdmsfaeikhkylwsepqncsat": 0, "nh": 137, "nh1": 169, "nh2": 169, "nh2mec": 112, "nh_1_energi": 137, "nh_1_relidx": 137, "nh_2_energi": 137, "nh_2_relidx": 137, "nh_o_1_energi": 137, "nh_o_1_relidx": 137, "nh_o_2_energi": 137, "nh_o_2_relidx": 137, "nhaimgvaft": 250, "nhammgvaft": 250, "nhkadtkfgv": 0, "nib": [238, 247], "nibbl": [238, 247], "nibfrag": 247, "nibio": [27, 238], "nibiter": [27, 238, 247], "nibwrit": [27, 238, 247], "nice": [3, 5, 6, 7, 12, 15, 21, 23, 25, 30, 31, 36, 99, 103, 110, 169, 207, 260, 261, 280, 297], "nicer": [12, 14], "nich": 19, "nick": 2, "nicol": 2, "nicotiana": 23, "nid": [7, 93, 275], "nident": 218, "niekslkeaftplgisdwnstfwiahpggpaildqveaklglkeekmratrevlseygnm": [21, 23], "nielsen": [2, 13, 34, 196, 281], "nig": 245, "nih": [3, 7, 8, 19, 22, 23, 68, 70, 71, 76, 83, 93, 94, 96, 97, 218, 234, 245, 253, 272], "nil": 2, "nine": 0, "ninth": 12, "niter": [4, 73], "nitti": 21, "nj": [32, 80, 181, 182, 199, 280], "njtree": 199, "njumbl": [79, 80], "nkfadlssd": 0, "nkgarvlvvcseitavtfrgpndthldslvgqalfgdgaaaviigsdpipeverplfelv": 23, "nl": [15, 137, 250], "nlaiii": 206, "nlength": 6, "nlib": 0, "nlm": [3, 7, 8, 19, 22, 68, 70, 71, 83, 93, 94, 96, 97, 123, 218, 234, 245, 253, 272], "nlmcatalog": 7, "nm": [0, 123, 203, 264], "nm_000015": 7, "nm_001180731": 0, "nmeth0810": 100, "nmin": 73, "nmkqhkamivalivicitavvaalvtrkdlcevhirtgqtevavf": 260, "nmotif": 11, "nmr": [0, 15, 25, 27, 144], "nmrview": [125, 126], "nn": [169, 264], "nn_tabl": 264, "nna": 32, "nni": [181, 182, 199], "nnitreesearch": [27, 181, 199], "nnn": [30, 236], "nnnn": 270, "nnnnnnacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt": 260, "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn": 30, "no2nd": [181, 182], "no_altloc": [133, 158, 169], "no_greedi": [68, 69], "no_of_seq": 0, "noaa": 197, "noali": 229, "noanchor": [30, 32], "nobrief": [79, 80], "nocat": [181, 182], "nocor": [30, 32], "node": [4, 17, 27, 32, 73, 99, 117, 128, 132, 177, 178, 179, 180, 182, 183, 184, 185, 187, 189, 190, 197, 198, 209, 211, 213, 252, 296], "node1": 132, "node2": 132, "node_dict": 188, "node_id": [130, 132, 181, 197, 198], "node_typ": 209, "nodecodedict": 209, "nodedata": [27, 128, 130, 132, 184, 187, 189], "nodeexcept": [27, 128, 130], "nodelist": 296, "nodetyp": [210, 211], "noe": 125, "noed": 126, "noetool": [27, 124], "nofft": [30, 32], "nohgap": [30, 32], "nois": 53, "noisi": 17, "nolan": [2, 7], "nomatrix": [181, 182], "nome": [181, 182], "nomenclatur": [2, 25, 169], "noml": [181, 182], "non": [0, 3, 4, 7, 11, 12, 13, 14, 15, 17, 21, 22, 25, 30, 32, 45, 60, 67, 69, 73, 84, 85, 117, 126, 129, 143, 149, 154, 158, 169, 172, 183, 197, 198, 218, 221, 222, 230, 236, 237, 238, 246, 251, 253, 260, 261, 264, 272, 275, 297], "non_con": 272, "non_std": 272, "non_ter": 272, "nonconsecut": 221, "noncontigu": 221, "none": [0, 3, 4, 6, 8, 10, 11, 12, 13, 15, 17, 18, 20, 21, 22, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 72, 73, 76, 84, 85, 92, 94, 99, 102, 103, 104, 108, 119, 120, 121, 122, 127, 129, 130, 132, 135, 136, 137, 139, 143, 144, 145, 149, 151, 152, 156, 157, 158, 160, 162, 164, 165, 168, 169, 172, 176, 177, 179, 180, 183, 184, 185, 186, 187, 189, 190, 193, 195, 196, 197, 199, 201, 202, 203, 204, 205, 209, 210, 211, 212, 213, 214, 215, 217, 236, 237, 238, 240, 241, 246, 248, 249, 250, 251, 252, 253, 258, 260, 261, 263, 264, 269, 270, 272, 274, 275, 276, 278, 279, 280, 281, 282, 283, 287, 288, 290, 291, 292, 294, 295, 299, 303, 304], "noneel": [27, 83, 84], "nonetyp": 160, "nonexist": 7, "nonnegativeinteg": 197, "nonpositiveinteg": 197, "nonsci": 17, "nonsens": 253, "nonsynonym": [2, 196], "nontermin": [17, 183], "nontrivi": 15, "nonumb": 4, "nonzero": [17, 183], "nopgap": [30, 32], "nopost": [30, 32], "nopr": [181, 182], "noqa": 11, "nor": [7, 12, 15, 20, 84, 129, 182, 278], "noreturn": 260, "norm": [15, 133, 176, 251], "normal": [4, 5, 7, 11, 12, 13, 15, 21, 22, 23, 30, 32, 65, 67, 93, 121, 129, 133, 135, 143, 144, 151, 169, 176, 182, 236, 237, 238, 251, 261, 270, 281, 283, 288, 290, 302, 303, 305], "normalize_lett": [27, 209, 214], "normalizedstr": 197, "normsq": [133, 176], "noroot": [79, 80], "northern": 250, "noscor": [30, 32], "nose": 24, "nosecstr1": [30, 32], "nosecstr2": [30, 32], "nostatu": 11, "nosupport": [181, 182], "notabl": 17, "notat": [3, 14, 20, 21, 30, 236, 260, 299], "note": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 21, 22, 23, 24, 27, 30, 32, 45, 49, 56, 59, 60, 62, 64, 66, 67, 68, 69, 70, 71, 73, 76, 81, 83, 90, 94, 95, 99, 108, 117, 121, 123, 125, 129, 135, 137, 143, 149, 153, 158, 159, 168, 169, 177, 182, 202, 210, 211, 212, 213, 214, 217, 218, 221, 222, 226, 229, 236, 237, 238, 240, 242, 245, 246, 247, 248, 249, 251, 253, 254, 257, 259, 260, 261, 262, 263, 264, 265, 269, 270, 272, 274, 278, 287, 288, 290, 294, 297, 298, 299, 302], "notermini": [79, 80], "notextw": 229, "noth": [17, 31, 54, 65, 99, 241, 250, 275, 278], "notic": [4, 5, 6, 8, 11, 12, 19, 20, 21, 22, 23, 67, 166, 218, 222, 237, 238, 251, 253, 260, 278, 295], "notimplementederror": 21, "notion": [11, 108], "notop": [181, 182], "notre": [30, 32], "notredam": 32, "notrim": 6, "notxmlerror": [7, 27, 68, 83, 84], "nov": [23, 149], "novel": [25, 32], "novemb": [87, 122], "novoalign": 270, "novoalign_clin": 270, "novoaligncommandlin": [268, 270], "novocraft": 270, "now": [0, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 67, 71, 83, 92, 108, 149, 169, 209, 236, 237, 238, 250, 251, 253, 260, 278, 297], "nowadai": [3, 11], "noweight": [30, 32], "noxml": [30, 32], "np": [0, 12, 13, 15, 30, 32, 68, 169], "np_001075655": 7, "np_001107837": 238, "np_035004": 7, "np_051101": 238, "np_391444": [20, 218], "np_395230": 21, "np_418483": 260, "np_963295": 94, "np_995567": 256, "np_995568": 256, "np_995569": 256, "np_995570": 256, "np_995571": [21, 256], "np_995572": [238, 256], "np_995573": 256, "np_995574": 256, "np_995575": 256, "np_995576": 256, "np_bind": 272, "npass": [4, 73], "npe": 6, "npg": 267, "npirpvtdra": 0, "npix": 29, "npvsfafevt": 0, "nqfsdmsfae": 0, "nqiqgvicspdsgefmvtfetvmeikilhk": 6, "nr": [3, 68, 69, 70], "nr_030186": [3, 20], "nr_030188": [3, 20], "nr_030190": [3, 20], "nr_030191": [3, 20], "nr_030193": [3, 20], "nr_030194": [3, 20], "nr_030195": [3, 20], "nr_030198": [3, 20], "nr_030217": [3, 20], "nr_030218": [3, 20], "nr_030221": [3, 20], "nr_030222": [3, 20], "nr_032573": [3, 20], "nr_032574": [3, 20], "nr_032575": [3, 20], "nr_032587": [3, 20], "nr_032716": [3, 20], "nr_035837": [3, 20], "nr_035838": [3, 20], "nr_035845": [3, 20], "nr_035850": [3, 20], "nr_035851": [3, 20], "nr_035852": [3, 20], "nr_035856": [3, 20], "nr_035857": [3, 20], "nr_035860": [3, 20], "nr_035865": [3, 20], "nr_035866": [3, 20], "nr_035869": [3, 20], "nr_035870": [3, 20], "nr_035871": [3, 20], "nr_046654": 0, "nr_111921": [0, 45], "nr_children": 15, "nr_false_neg": 88, "nr_false_po": 88, "nr_partial": 88, "nr_posit": 88, "nr_sp_releas": 88, "nr_sp_seq": 88, "nr_total": 88, "nr_unknown": 88, "nread": 269, "nrep": 132, "nrfsdmswee": 0, "nrow": [29, 73], "ns3": 23, "ns_site": 17, "nsanigaki": 0, "nsequence_1": 0, "nsequence_2": 0, "nsldhgiliv": 0, "nssite": 17, "nt": [0, 3, 30, 32, 69, 181, 182, 261, 264], "nt_search": [27, 261], "nta": [30, 32], "ntax": [0, 56, 132], "ntitl": 7, "ntree": 132, "ntseq": 119, "nu": [238, 260], "nu3m_balph": 272, "nuc": [6, 11, 30, 32, 260, 290], "nuc1": 13, "nuc2": 13, "nuc3": 13, "nuc_list": 6, "nuc_rec": 6, "nuc_record": 6, "nuccor": [7, 19, 83, 274], "nucest": [7, 274], "nucgss": [7, 274], "nucl": 69, "nucl_penalti": [68, 70], "nucl_reward": [68, 70], "nucl_seq": 279, "nuclear": [30, 94], "nucleic": [2, 3, 12, 15, 32, 68, 111, 115, 119, 154, 166, 251, 261, 283], "nucleotid": [0, 2, 3, 11, 12, 19, 20, 21, 23, 30, 32, 34, 61, 68, 69, 70, 71, 76, 80, 83, 93, 94, 154, 182, 193, 195, 222, 226, 236, 237, 238, 245, 247, 251, 260, 261, 262, 264, 270, 272, 274, 275, 279, 283, 287, 290], "nucleotide_alphabet": [75, 76], "nucleotide_m8cc": 0, "nucleotide_record": 13, "nucleu": [125, 126], "null": [67, 270], "num": [3, 68, 169, 218], "num_align": [68, 69, 71], "num_bootstrap_search": [181, 182], "num_categori": [181, 182], "num_descript": [68, 69], "num_good_extend": 71, "num_group": 172, "num_hit": 71, "num_iter": [68, 69], "num_letters_in_databas": 71, "num_occurr": 11, "num_repl": [181, 182], "num_seqs_better_": 71, "num_sequ": 71, "num_sequences_in_databas": 71, "num_thread": [32, 68, 69], "number": [0, 2, 3, 6, 7, 8, 9, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 37, 42, 44, 45, 47, 49, 51, 54, 56, 60, 61, 68, 69, 70, 71, 73, 80, 83, 84, 86, 87, 88, 90, 93, 99, 100, 102, 104, 108, 109, 112, 113, 115, 117, 118, 119, 120, 121, 122, 123, 126, 130, 132, 134, 135, 139, 140, 141, 143, 149, 151, 157, 158, 169, 172, 175, 176, 177, 182, 183, 185, 186, 188, 190, 197, 202, 203, 207, 209, 214, 215, 216, 217, 221, 222, 229, 236, 237, 238, 246, 247, 248, 251, 252, 253, 257, 260, 265, 269, 270, 272, 274, 275, 276, 278, 280, 281, 282, 287, 288, 290, 291, 294, 295, 297, 298, 299, 303], "numberofcategori": 182, "numer": [4, 13, 15, 17, 88, 104, 107, 149, 152, 168, 169, 177, 197, 247, 251, 265, 272], "numit": [30, 32], "nummismatch": [79, 80], "numpi": [0, 4, 5, 12, 13, 15, 24, 30, 54, 68, 73, 135, 139, 140, 146, 156, 162, 168, 169, 176, 216, 238, 290, 299], "numreturn": [79, 80], "numthread": [30, 32], "nur1f": 270, "nv": 126, "nvde": 14, "nvdevggealgrllvvypwtqrf": 12, "nvdevggealgrllvvypwtqrff": 14, "nvdevggealgrllvvypwtqrffesfgdlstpdavmgn": 13, "nwk": 17, "nx3": [140, 175, 216], "nxdim": [175, 216], "nxgrid": [4, 73], "nydpwnlrfqskyksrda": 95, "nygrid": [4, 73], "nylrgt": 0, "nz": 169, "o": [2, 5, 7, 11, 12, 15, 23, 25, 30, 32, 53, 66, 85, 91, 97, 99, 137, 148, 149, 152, 157, 169, 170, 173, 182, 185, 188, 190, 191, 221, 251, 253, 261, 268, 270, 283, 295], "o16376": 53, "o16376_caeel": 53, "o23729": [23, 25, 85], "o23730": 25, "o23731": 25, "o46647": 25, "o_1_energi": 137, "o_1_relidx": 137, "o_2_energi": 137, "o_2_relidx": 137, "o_ant70": 244, "o_mvp5180": 244, "o_nh_1_energi": 137, "o_nh_1_relidx": 137, "o_nh_2_energi": 137, "o_nh_2_relidx": 137, "oa": 169, "oab": 123, "oanyself": [79, 80], "ob": 169, "obei": 7, "obf": 6, "obj": [54, 191, 198], "obj_typ": 188, "object": [3, 4, 6, 7, 8, 9, 14, 16, 18, 19, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 42, 45, 46, 47, 49, 51, 52, 54, 56, 59, 60, 61, 64, 66, 67, 68, 71, 72, 73, 74, 76, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 120, 121, 122, 123, 126, 127, 128, 129, 130, 131, 132, 134, 135, 136, 137, 138, 139, 140, 141, 143, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 161, 162, 163, 165, 166, 168, 169, 170, 171, 172, 173, 175, 176, 177, 179, 180, 183, 184, 185, 186, 187, 188, 189, 190, 197, 198, 199, 201, 202, 203, 204, 205, 207, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 224, 225, 226, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 269, 270, 271, 272, 273, 275, 278, 279, 280, 281, 282, 283, 284, 286, 288, 289, 291, 292, 293, 294, 295, 296, 297, 298, 299, 302, 303, 304, 305, 307], "objfun": 11, "objscor": [30, 32], "objwct": 68, "obo": [185, 188], "obolibrari": 185, "obscur": 7, "observ": [4, 11, 12, 13, 16, 22, 52, 109, 120, 121, 122, 127, 169, 202, 203, 214, 229, 251, 282], "observed_frequ": [12, 13], "obsess": 19, "obslt": 149, "obsolet": [12, 15, 32, 67, 69, 71, 80, 92, 94, 149, 182, 186, 207, 237, 241, 251, 270, 285], "obsolete_pdb": 149, "obtain": [0, 12, 13, 14, 22, 25, 30, 68, 92, 119, 140, 182, 203, 209, 221, 222, 270, 299], "obviou": [6, 7, 15, 288], "obvious": [7, 13, 15, 30, 169], "oc": [11, 53, 66, 169, 295], "occ": 169, "occacb": 169, "occasion": [7, 20, 21, 23], "occup": [15, 135, 155, 162, 169, 172], "occupi": 104, "occur": [0, 4, 7, 11, 12, 13, 15, 17, 21, 23, 30, 73, 83, 84, 145, 222, 236, 237, 272], "occurr": [4, 12, 13, 90, 182, 236, 260, 263, 270, 273, 291, 294], "ocd": 0, "ocdhpr": 0, "ochromend": 0, "ochroms": 0, "ochromstart": 0, "oci": 123, "ockholm": 32, "oct": [0, 149, 182], "octagon": 8, "octo": 8, "octob": 7, "octopu": 183, "octvu": 183, "od1": 169, "od2": 169, "odd": [11, 12, 13, 288, 290, 294], "oddsratio": 13, "odnaconc": [79, 80], "odoratu": 260, "oe1": [157, 169], "oe2": 169, "oendself": [79, 80], "oexcludedregion": [79, 80], "off": [0, 3, 8, 21, 23, 32, 68, 69, 70, 80, 117, 119, 125, 158, 182, 251, 270], "off_diagonal_rang": [68, 69], "offend": 272, "offer": [0, 3, 6, 9, 15, 21, 49, 64, 83, 98, 240, 241, 255, 274], "offici": [7, 9, 23, 68, 70, 119, 197, 212, 251], "offlin": 24, "offset": [6, 11, 20, 23, 32, 61, 100, 121, 141, 219, 220, 221, 224, 225, 226, 230, 232, 233, 237, 238, 251, 274, 278, 290], "often": [0, 1, 3, 4, 6, 7, 9, 11, 12, 15, 17, 19, 20, 21, 22, 23, 24, 132, 145, 182, 251, 264], "og": [15, 80, 169], "og1": 169, "ogcmax": [79, 80], "ogcmin": [79, 80], "ogcopt": [79, 80], "ogcperc": [79, 80], "oh": 169, "oi": 90, "oid": 123, "ointment": 6, "ok": [6, 7, 9, 23, 24], "ok_applies_to": [181, 197], "ok_datatyp": [181, 197], "ok_rank": [181, 197], "ok_typ": [181, 197], "old": [0, 6, 9, 12, 19, 21, 23, 26, 32, 68, 69, 70, 94, 182, 191, 236, 237, 251, 258, 260, 264, 278, 307], "old_refseq": 8, "oldatomcoord": 169, "older": [0, 1, 3, 5, 7, 8, 9, 11, 12, 21, 22, 25, 56, 65, 69, 71, 210, 212, 236, 238, 251, 295, 298], "oldtabl": 264, "oligo": [80, 264], "oligoinput": [79, 80], "oligonucleotid": 264, "oliv": 183, "olsen": 263, "omaxs": [79, 80], "omega": [15, 17, 32, 152, 169], "omg": [152, 169], "omia": 7, "omim": 7, "omins": [79, 80], "omishybmax": [79, 80], "omit": [20, 21, 54, 129, 217, 236, 238, 251, 260], "omit_nexu": 129, "omnibu": [7, 96], "onc": [0, 1, 3, 4, 5, 6, 7, 11, 12, 16, 19, 21, 22, 23, 30, 32, 56, 60, 61, 67, 73, 84, 90, 121, 158, 169, 205, 217, 238, 248, 251, 269, 273, 288, 298], "one": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 35, 39, 42, 43, 45, 46, 51, 52, 56, 61, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 80, 81, 83, 86, 87, 88, 90, 92, 93, 101, 104, 112, 113, 114, 116, 117, 119, 123, 130, 137, 139, 146, 149, 154, 157, 161, 163, 166, 169, 172, 177, 182, 183, 186, 197, 201, 204, 205, 207, 210, 211, 212, 213, 214, 215, 217, 221, 222, 228, 237, 238, 242, 245, 247, 249, 250, 251, 252, 254, 256, 259, 261, 264, 267, 269, 270, 271, 272, 273, 274, 275, 277, 278, 282, 283, 287, 288, 290, 295, 297, 298, 299, 300, 303], "one_alignment_onli": [14, 297], "one_letter_cod": 214, "one_to_index": [27, 133, 154], "one_to_one_orthologi": 197, "oneofposit": [21, 27, 237], "ones": [0, 7, 8, 10, 20, 132, 297], "ongo": 9, "onim": 274, "onli": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 33, 34, 36, 40, 45, 49, 52, 56, 59, 60, 64, 65, 68, 69, 70, 71, 73, 76, 80, 81, 83, 91, 92, 104, 116, 117, 119, 125, 129, 137, 138, 140, 143, 144, 149, 152, 158, 168, 169, 177, 182, 183, 197, 198, 199, 202, 205, 217, 222, 226, 228, 236, 237, 238, 241, 242, 245, 247, 249, 251, 252, 253, 254, 256, 257, 259, 260, 261, 265, 269, 270, 272, 274, 275, 277, 278, 281, 283, 287, 288, 290, 297, 298, 299], "onlin": [0, 3, 5, 7, 8, 9, 12, 13, 19, 21, 23, 24, 25, 83, 119, 209, 250], "online_doctest_modul": 24, "onto": [16, 166, 176, 182, 214, 216, 251], "ontologi": [17, 185, 273], "onward": [6, 9, 11, 18, 23, 80, 251], "oop": [11, 289, 291], "oow": 238, "op": [30, 32], "open": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 23, 24, 25, 27, 29, 30, 32, 56, 57, 60, 61, 62, 65, 66, 68, 69, 71, 80, 83, 84, 85, 90, 91, 92, 112, 113, 114, 116, 123, 129, 142, 143, 151, 158, 166, 198, 199, 204, 205, 217, 218, 221, 238, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 256, 259, 260, 269, 270, 271, 272, 277, 278, 283, 289, 291, 292, 297, 298, 303], "open_databas": [301, 303, 305], "open_dtd_fil": [83, 84], "open_gap_scor": [13, 30], "open_xsd_fil": [83, 84], "opena": 297, "openascad": 158, "openb": 297, "openscad": [15, 158, 169], "oper": [5, 6, 7, 9, 13, 15, 17, 22, 30, 32, 55, 56, 67, 80, 169, 176, 182, 183, 186, 237, 238, 251, 264, 278, 290], "operand": [260, 299], "ophri": 7, "opi3": [11, 291], "opisthorchi": 3, "opm": [16, 298], "opolyxmax": [79, 80], "opossum": 22, "oppos": 3, "opposit": [0, 4, 15, 169, 237], "opt": [8, 32, 226], "opt_scor": 226, "optim": [2, 4, 6, 13, 14, 23, 27, 32, 69, 73, 146, 166, 181, 182, 261, 265, 267], "optimis": [32, 56, 182, 238], "optimum": 80, "option": [0, 3, 4, 6, 7, 9, 12, 13, 15, 17, 20, 21, 22, 23, 24, 30, 31, 32, 33, 43, 45, 48, 54, 56, 59, 60, 63, 65, 67, 68, 69, 72, 73, 76, 79, 80, 83, 90, 92, 93, 97, 99, 104, 108, 109, 118, 119, 120, 121, 127, 129, 135, 136, 139, 143, 149, 151, 152, 158, 164, 166, 169, 182, 186, 188, 190, 193, 195, 196, 197, 214, 215, 217, 225, 236, 237, 238, 241, 244, 246, 247, 250, 251, 252, 253, 258, 260, 261, 265, 269, 270, 273, 274, 275, 276, 282, 297, 303], "opttm": [79, 80], "opuntia": [0, 3, 7, 12, 23, 30, 32, 80, 83], "opuntioidea": 7, "orang": [8, 183], "orchid": [6, 7, 19, 23, 25], "orchid_dict": 23, "orchid_rpl16": 7, "orchidacea": [7, 19], "orcutt": 2, "ord": [13, 251], "order": [0, 3, 4, 5, 6, 8, 11, 12, 15, 17, 19, 20, 23, 24, 27, 30, 31, 32, 36, 37, 38, 60, 61, 73, 76, 80, 84, 102, 103, 108, 119, 137, 159, 167, 169, 172, 177, 180, 183, 197, 198, 202, 207, 209, 218, 222, 237, 238, 260, 270, 278, 299], "ordered_aa_ic_list": [15, 169], "orderedlistel": [27, 83, 84], "orderedlocusnam": 272, "ordinari": [15, 23, 217, 238, 278], "orf": [4, 6, 73], "orf10": 8, "orf12": 8, "orf13": 8, "orf14": 8, "orf15": 8, "orf16": 8, "orf17": 8, "orf20": 8, "orf22": 8, "orf23": 8, "orf27": 8, "orf28": 8, "orf29": 8, "orf38": 8, "orf39": 8, "orf4": 8, "orf40": 8, "orf41": 8, "orf42": 8, "orf43": 8, "orf44": 8, "orf46": 8, "orf47": 8, "orf48": 8, "orf49": 8, "orf50": 8, "orf51": 8, "orf52": 8, "orf53": 8, "orf54": 8, "orf55": 8, "orf6": 8, "orf60": 8, "orf7": 8, "orf8": 8, "orf9": 8, "orf_list": 6, "orfnam": 272, "org": [2, 5, 6, 7, 8, 9, 12, 15, 17, 19, 21, 23, 25, 27, 32, 52, 53, 56, 66, 69, 73, 83, 85, 86, 87, 88, 89, 90, 94, 100, 117, 119, 137, 149, 150, 158, 167, 170, 181, 182, 185, 188, 197, 221, 229, 237, 245, 248, 251, 252, 258, 262, 263, 265, 267, 272, 273, 275, 277, 279, 286, 288, 301], "organ": [2, 6, 8, 10, 11, 19, 21, 23, 25, 27, 53, 66, 73, 93, 98, 99, 103, 113, 114, 116, 119, 197, 260, 272, 275], "organel": [7, 25, 272], "organis": 94, "organism_classif": [25, 66, 272], "organism_id": [25, 276], "orgn": [7, 83], "ori": 123, "orient": [8, 9, 22, 80, 104, 169, 295], "origin": [0, 3, 4, 6, 7, 8, 9, 11, 12, 15, 17, 19, 20, 21, 23, 30, 36, 44, 45, 56, 59, 63, 69, 76, 90, 93, 94, 95, 97, 102, 123, 125, 126, 133, 136, 158, 166, 168, 169, 174, 175, 176, 182, 183, 214, 217, 236, 237, 238, 251, 252, 253, 258, 260, 265, 270, 271, 272, 275, 277, 299], "original_blast_record": 3, "original_read": 6, "original_rec": 6, "originnuc": 125, "originresnum": 125, "orlean": 15, "ormandi": 122, "ortholog": [115, 116, 117], "orthologi": [114, 197, 274], "osaltconc": [79, 80], "osequ": 0, "oserror": [193, 195, 196], "osformat": [79, 80], "osiz": [79, 80], "osizeopt": [79, 80], "ossibl": 80, "ostrand": 0, "ot": 123, "other": [0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 21, 23, 24, 25, 26, 27, 30, 31, 32, 40, 52, 56, 57, 65, 66, 67, 69, 72, 73, 83, 84, 88, 91, 93, 99, 100, 102, 104, 105, 108, 117, 119, 123, 133, 135, 136, 139, 140, 146, 149, 155, 161, 166, 169, 175, 176, 181, 182, 183, 195, 197, 198, 199, 211, 214, 216, 217, 218, 222, 226, 229, 236, 237, 238, 241, 250, 256, 260, 261, 264, 265, 278, 280, 287, 288, 290, 295, 297, 299, 307], "other1": [18, 201, 204], "other_advanc": [68, 70], "other_internal_format": [92, 93], "other_tre": 17, "otherwis": [0, 8, 11, 15, 16, 17, 23, 30, 31, 32, 54, 67, 68, 83, 95, 99, 104, 108, 132, 135, 148, 149, 162, 169, 170, 173, 182, 183, 193, 195, 196, 236, 237, 251, 260, 264, 270, 275, 277, 288, 290, 297, 299], "otm": [79, 80], "otmmax": [79, 80], "otmmin": [79, 80], "otmopt": [79, 80], "oto": 123, "otogar1": 0, "otu": [80, 132], "ought": 20, "our": [1, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 17, 19, 20, 21, 23, 24, 27, 56, 67, 236, 238, 251], "ourselv": 20, "out": [0, 3, 5, 6, 7, 8, 9, 11, 12, 13, 16, 17, 19, 20, 21, 23, 24, 25, 30, 31, 32, 68, 69, 73, 80, 82, 92, 99, 102, 103, 110, 116, 131, 138, 148, 152, 170, 173, 181, 182, 195, 218, 221, 251, 253, 260, 265, 270, 278, 283, 292, 297, 303], "out_arr": 54, "out_ascii_pssm": [68, 69], "out_bam": 270, "out_block": [27, 96, 97], "out_dict": 137, "out_fil": [17, 32, 56, 193, 195, 196, 217, 238, 270], "out_fmt": 217, "out_format": [56, 217, 238, 274], "out_handl": [3, 6, 11, 12, 23, 25, 85, 214, 238, 251, 253], "out_kwarg": 217, "out_prefix": [268, 270], "out_pssm": [68, 69], "out_rad": 169, "out_stream": 3, "outdat": 7, "outer": 154, "outfil": [12, 30, 32, 67, 79, 80], "outfmt": [0, 3, 30, 32, 55, 68, 69], "outfn": 126, "outgo": 108, "outgrno": [79, 80], "outgroup": [17, 80, 132, 181, 182, 183], "outgroup_branch_length": 183, "outgroup_target": 183, "outlier": [4, 6, 29], "outlin": [17, 20, 32], "outlist": 126, "outord": [30, 32], "outperform": 15, "outprotrec": 277, "output": [1, 4, 6, 7, 8, 9, 11, 12, 15, 17, 18, 19, 21, 22, 24, 26, 27, 30, 31, 32, 33, 35, 36, 37, 38, 40, 41, 42, 44, 45, 47, 48, 49, 51, 52, 55, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 74, 80, 81, 82, 83, 89, 93, 98, 99, 100, 101, 103, 104, 121, 125, 137, 145, 148, 152, 153, 158, 167, 169, 170, 173, 182, 183, 193, 195, 196, 199, 207, 214, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 237, 240, 241, 243, 245, 246, 247, 249, 250, 251, 252, 253, 259, 260, 261, 268, 269, 270, 271, 274, 277, 278, 280, 283, 284, 291, 292, 303, 307], "output_bam": 270, "output_fil": [6, 99, 101, 103, 268, 270], "output_format": [99, 101, 103], "output_handl": 6, "output_sai_fil": 270, "output_sam_fil": 270, "outputeith": 32, "outputfilenam": 182, "outputformat": 234, "outputord": [30, 32], "outputrecord": [27, 79, 82], "outputtre": [30, 32], "outrec": 277, "outseq": [79, 80], "outsid": [7, 32, 104, 119, 303], "outtreefil": [79, 80], "ov": [11, 229, 295], "over": [0, 1, 4, 6, 7, 8, 9, 11, 12, 17, 19, 20, 21, 22, 25, 30, 36, 44, 45, 56, 60, 61, 65, 66, 67, 68, 70, 73, 74, 81, 83, 84, 85, 87, 88, 92, 104, 116, 123, 129, 131, 134, 139, 149, 161, 164, 185, 188, 190, 197, 198, 205, 207, 209, 210, 211, 212, 213, 214, 217, 219, 220, 221, 226, 228, 230, 232, 233, 237, 238, 240, 241, 244, 246, 247, 248, 250, 251, 253, 254, 256, 257, 258, 260, 261, 264, 267, 269, 271, 274, 276, 277, 278, 288, 298, 299, 303], "overal": [4, 11, 15, 99, 158, 202, 237], "overfit": 11, "overflowerror": 13, "overhang": [69, 158], "overhead": [23, 169, 217], "overlai": 8, "overlap": [8, 15, 22, 32, 36, 61, 79, 80, 152, 158, 167, 169, 182, 236, 260], "overlap_num": 229, "overload": [15, 119, 148, 274], "overrid": [12, 15, 17, 32, 64, 68, 69, 70, 99, 104, 158, 169, 197, 237, 261, 264], "overridden": [30, 45, 104, 207, 237, 246], "overview": [3, 7, 11, 13, 16, 17, 20, 23, 123, 169, 275], "overwork": 19, "overwrit": [23, 32, 56, 149, 238, 270], "overwritten": [12, 23, 149, 183, 197, 238], "ow": [30, 32], "owczarzi": 264, "owl": 185, "own": [0, 3, 6, 7, 11, 12, 13, 14, 17, 19, 20, 22, 23, 24, 61, 117, 123, 143, 151, 169, 218, 222, 229, 251, 253, 260, 264, 278, 291, 297], "owner": 123, "ox": 90, "oxfordjourn": 2, "oxid": 265, "oxopropano": 112, "oxt": 169, "oxygen": 15, "p": [0, 2, 4, 7, 12, 13, 15, 22, 23, 30, 32, 34, 53, 69, 80, 104, 107, 108, 123, 126, 127, 137, 140, 153, 157, 166, 169, 172, 176, 182, 194, 202, 237, 251, 261, 265, 268, 270, 279, 280, 281], "p0": 11, "p00321": 272, "p00520": 164, "p03618": 12, "p03619": 12, "p03620": 12, "p06858": 25, "p07175": 68, "p1": [177, 250], "p11151": 25, "p11152": 25, "p11153": 25, "p11602": 25, "p12497": 248, "p13125": 0, "p13689": 23, "p14921": 288, "p15416": 12, "p17304": 197, "p17886": 53, "p19801": 23, "p2": [0, 177, 237], "p24973": 272, "p33487": 23, "p49060": 25, "p49923": 25, "p53762": 11, "p55031": 25, "p57": 107, "p58": 107, "p61991": 0, "p62": 108, "p64": 109, "p68308": 272, "p69541": 12, "p87312": 53, "p_": [11, 12], "p_condit": 127, "p_e": 6, "p_emiss": 121, "p_initi": 121, "p_prior": 127, "p_transit": 121, "pa": [13, 32, 53, 263], "pablo": [2, 262], "pack": [0, 197], "packag": [0, 2, 3, 5, 7, 11, 16, 18, 25, 84, 100, 129, 137, 150, 156, 193, 195, 196, 303, 306, 307], "pad": [0, 13, 30, 65, 126], "padktnv": [13, 14], "paffakss": 250, "paffakssai": 250, "page": [3, 6, 7, 8, 9, 12, 17, 19, 21, 23, 25, 83, 85, 90, 99, 103, 104, 218, 222, 229, 234], "page_s": 8, "pages": [8, 104], "pagin": 123, "pai": 278, "pair": [0, 3, 6, 8, 12, 13, 14, 15, 18, 20, 23, 30, 32, 41, 54, 56, 58, 68, 79, 80, 81, 95, 99, 146, 161, 169, 176, 177, 179, 180, 182, 197, 199, 201, 202, 203, 204, 230, 251, 253, 270, 295, 297, 299, 303], "pairedfastaqualiter": [6, 27, 238, 251], "pairgap": [30, 32], "pairwis": [4, 6, 12, 15, 26, 30, 32, 34, 35, 36, 38, 39, 41, 42, 44, 51, 52, 55, 56, 58, 59, 68, 69, 73, 169, 196, 222, 270, 297, 307], "pairwise2": [26, 27, 307], "pairwise_align": 0, "pairwise_alignment1": 0, "pairwise_alignment2": 0, "pairwise_codon_align": 13, "pairwisealign": [0, 12, 13, 14, 27, 30, 68], "pale": 8, "palindrom": 80, "palindromecommandlin": [27, 79, 80], "palss": 2, "pam": [13, 14, 32], "pam200": 32, "pam250": 199, "pam30": [68, 70, 199], "pam70": [68, 70, 199], "paml": [9, 27, 181], "pan": [3, 20], "pandit": 265, "panel": 275, "panisc": [3, 20], "panther": 234, "pantro1": 0, "pantro2": 0, "pantro4": 22, "pantro5": [0, 30], "pantro5topantro6": [0, 30], "pantro6": [0, 30], "paper": [4, 7, 12, 19, 21, 59, 72, 264], "paphiopedilum": [19, 23], "paquet": 263, "par": [145, 181, 182], "para_agrtu": 68, "paragraph": 5, "parahippu": 56, "parallel": [8, 25, 169, 182], "parallelassembleresidu": [133, 169], "paralleliz": 9, "paralogi": 197, "param": [3, 16, 32, 68, 136, 169, 176], "param_dict": 265, "param_entrez_queri": 218, "param_evalue_threshold": [20, 218], "param_filt": 218, "param_gap_extend": 218, "param_gap_open": 218, "param_includ": 218, "param_matrix": 218, "param_pattern": 218, "param_score_match": 218, "param_score_mismatch": 218, "paramet": [3, 4, 7, 11, 12, 13, 14, 15, 17, 25, 27, 31, 32, 54, 67, 68, 69, 70, 71, 80, 83, 89, 100, 104, 105, 108, 109, 120, 121, 125, 126, 134, 135, 136, 137, 139, 140, 141, 144, 148, 149, 150, 152, 154, 155, 157, 158, 160, 163, 164, 165, 166, 168, 169, 170, 171, 172, 173, 175, 176, 182, 183, 185, 186, 187, 188, 189, 190, 197, 198, 199, 202, 207, 209, 218, 236, 237, 261, 263, 264, 265, 270, 276, 283, 290, 297, 299, 300], "parameter": 15, "parameters_entrez": 218, "parameters_expect": 218, "parameters_filt": 218, "parameters_gap": 218, "parameters_includ": 218, "parameters_matrix": 218, "parameters_pattern": 218, "parameters_sc": 218, "parametr": [4, 182], "paramfil": [30, 32], "paraphras": 7, "parent": [6, 15, 17, 21, 104, 117, 130, 133, 135, 139, 159, 169, 178, 179, 180, 183, 185, 190, 197, 209, 213, 237, 260], "parent_branch": 197, "parent_edg": [178, 179, 180], "parent_ent": 15, "parent_id": 132, "parent_seq": 237, "parent_sequ": 237, "parenthes": 182, "parenthesi": 20, "parenttaxid": 7, "park": 2, "parker": 265, "parlanc": 3, "pars": [0, 1, 8, 9, 11, 13, 17, 18, 20, 21, 24, 27, 29, 30, 32, 38, 45, 50, 53, 54, 55, 56, 57, 58, 59, 62, 63, 65, 66, 68, 69, 71, 74, 76, 79, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 111, 112, 113, 114, 115, 116, 118, 121, 123, 129, 137, 142, 143, 149, 150, 151, 152, 153, 162, 165, 174, 181, 185, 188, 190, 191, 193, 195, 196, 198, 201, 204, 205, 209, 210, 211, 212, 213, 214, 217, 218, 221, 222, 223, 224, 225, 226, 227, 229, 230, 234, 236, 237, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 268, 269, 271, 272, 273, 275, 278, 279, 283, 284, 286, 289, 291, 292, 293, 295, 296, 298, 299, 303], "pars_tre": 199, "parsabl": 209, "parse_alignment_block": [222, 223, 224, 225], "parse_btop": [30, 55], "parse_cds_featur": [92, 94], "parse_children": [181, 185], "parse_cigar": [30, 55], "parse_deflin": [68, 69], "parse_domain": [27, 209], "parse_featur": [92, 94], "parse_foot": [92, 94], "parse_format": 185, "parse_graph": [181, 185], "parse_handle_to_graph": [181, 185], "parse_head": [92, 94], "parse_hit": [229, 230], "parse_hsp": [229, 230], "parse_hsp_align": [229, 230], "parse_key_valu": [229, 230], "parse_pdb_head": [15, 27, 133, 248], "parse_preambl": [229, 230], "parse_printed_align": [0, 27, 30], "parse_qresult": [229, 230], "parse_record": [92, 94], "parse_seqid": [68, 69], "parse_xsd": [83, 84], "parseabl": 226, "parser": [0, 1, 2, 3, 6, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 25, 27, 29, 30, 41, 42, 45, 50, 52, 55, 56, 58, 59, 60, 63, 66, 68, 71, 83, 85, 88, 89, 90, 92, 96, 123, 128, 133, 140, 143, 148, 150, 151, 156, 164, 165, 169, 170, 173, 181, 185, 188, 190, 191, 198, 205, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 241, 242, 243, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 269, 271, 275, 276, 277, 283, 295, 298, 299], "parsererror": [27, 28, 29], "parserfailureerror": [27, 92], "parsimoni": [80, 129, 181, 182, 199], "parsimony_se": [181, 182], "parsimonyscor": [27, 181, 199], "parsimonytreeconstructor": [27, 181, 199], "parsiomni": 80, "part": [0, 4, 6, 8, 9, 11, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 37, 44, 46, 56, 59, 66, 73, 99, 117, 169, 183, 193, 195, 196, 197, 217, 221, 222, 236, 237, 238, 250, 252, 264, 269, 275, 278, 297, 299], "part_align": [53, 66], "parti": [8, 17, 253], "partial": [0, 3, 6, 7, 11, 21, 36, 66, 104, 119, 123, 201, 236, 238, 260, 263], "particip": 117, "particular": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 17, 19, 20, 21, 23, 30, 31, 83, 104, 108, 109, 183, 214, 236, 238, 260, 278, 299], "particularli": [3, 7, 20, 83, 237], "partit": [32, 129, 182], "partition_branch_length": [181, 182], "partition_filenam": [181, 182], "partli": [15, 21], "partner": 172, "partsiz": [30, 32], "parttre": [30, 32], "pas_con": 53, "pasquali": 263, "pass": [1, 3, 4, 6, 7, 10, 11, 12, 13, 15, 17, 18, 20, 21, 25, 30, 31, 32, 67, 68, 70, 73, 83, 89, 91, 92, 94, 100, 104, 105, 109, 117, 122, 158, 169, 172, 182, 193, 195, 196, 217, 218, 221, 236, 237, 240, 248, 264, 278, 283, 287, 288, 293], "passwd": [303, 305], "password": [11, 68, 70, 288, 303], "past": [24, 158, 236], "patch": 5, "path": [0, 3, 4, 7, 8, 12, 15, 17, 24, 30, 32, 37, 45, 67, 68, 83, 91, 100, 108, 109, 110, 112, 116, 117, 119, 149, 152, 153, 158, 164, 165, 166, 171, 182, 183, 193, 195, 209, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 258, 259, 269, 270, 271, 272, 303], "pathlib": 91, "pathlik": [150, 164, 238, 241, 245, 246, 249, 251, 256], "pathogen": [2, 104], "patholog": 116, "pathwai": [10, 27, 105, 111, 112, 113, 115, 116, 117, 118, 119, 234, 274], "pathway_fil": 10, "patient": 123, "patrick": [2, 9], "patser": [11, 294], "pattern": [1, 2, 3, 7, 25, 51, 68, 69, 79, 80, 88, 117, 283], "pattern_end": 218, "pattern_start": 218, "paul": 2, "paulu": 7, "paup": [32, 129, 132, 190], "pazar": [11, 288], "pazar_id": [11, 287, 288], "pbad30": 260, "pbad30_rc": 260, "pbd": 215, "pbluescript": [206, 207], "pbm": 288, "pbs_mc": [206, 207], "pbz78439": 19, "pc": [15, 73], "pc6": 90, "pca": [4, 27, 73], "pcassai": 7, "pcb_vectors_pymol": [133, 141], "pcc": 11, "pccompound": 7, "pclass": 169, "pcm": 11, "pcr": [80, 253, 264, 270], "pcsubstanc": 7, "pct": [7, 275], "pcut": 152, "pd": 0, "pdat": 7, "pdb": [0, 2, 7, 9, 12, 24, 25, 26, 27, 53, 83, 88, 123, 209, 214, 215, 238, 248, 260, 274, 307], "pdb1fat": 15, "pdb70": 0, "pdb7rsa": 169, "pdb_code": 149, "pdb_date": [27, 133, 152], "pdb_datestamp": 214, "pdb_file": [15, 145], "pdb_handl": 214, "pdb_id": [171, 248], "pdb_object": 148, "pdb_ref": [133, 149], "pdb_residue_str": [15, 133, 169], "pdb_seqr": 149, "pdb_struct": 88, "pdbatomiter": [27, 238, 248], "pdbconstructionexcept": [15, 27, 133, 147, 155], "pdbconstructionwarn": [27, 133, 147], "pdbdata": [27, 75], "pdbdescr": 83, "pdbexcept": [27, 133, 152, 168], "pdbid": [0, 152, 158, 168, 169, 214, 215], "pdbio": [15, 27, 133, 169, 238], "pdbioexcept": [27, 133, 147], "pdbj": 274, "pdbl": 15, "pdblist": [15, 27, 133], "pdbml": [149, 150], "pdbml_parser": 15, "pdbmlparser": [15, 27, 133], "pdbparser": [15, 27, 133, 137, 140, 143, 148, 154, 156, 157, 162, 169], "pdbseqresiter": [27, 238, 248], "pdbstructur": [164, 168], "pdbx": [15, 149], "pdbx_poly_seq_schem": 248, "pdf": [6, 8, 9, 15, 56, 83, 99, 101, 103, 104, 226, 229, 236, 238, 239, 263, 278], "pdir": [15, 149], "pdoc": [25, 88], "pdoc00001": [25, 85], "pdoc00004": 25, "pdoc00005": 25, "pdoc00110": 25, "pdvknwikfarfe": 53, "pdz78471": 23, "pe": 251, "peak": [7, 19, 125], "peaklist": [27, 124, 125, 126], "pear": [7, 12, 23], "pearson": [0, 2, 11, 12, 32, 55, 56, 59, 73, 182, 217, 226, 241, 290], "pearson1988": [0, 2], "peculiar": 4, "peek": [128, 129, 278], "peek_nonwhitespac": [128, 129], "peek_word": [128, 129], "peeksav": [13, 14], "peeksavtalwgkv": 14, "pemslei": 15, "pen": 32, "penal": [13, 14, 270, 297], "penalis": 32, "penalize_end_gap": 297, "penalize_extend_when_open": 297, "penalti": [9, 13, 14, 32, 68, 69, 71, 80, 182, 199, 238, 270, 297], "peopl": [5, 11, 19, 21, 23, 207], "peptid": [22, 32, 154, 169, 263, 272], "peptidoglycan": 0, "per": [0, 6, 7, 15, 18, 21, 30, 53, 56, 60, 64, 66, 69, 83, 85, 104, 119, 121, 149, 158, 167, 169, 182, 197, 201, 202, 204, 205, 217, 229, 238, 241, 251, 259, 260, 264, 270, 273, 274, 275, 278, 302], "perc_id": [68, 70], "perc_ident": [68, 69], "percent": [32, 69, 80, 209, 221, 264, 275], "percentag": [6, 8, 13, 31, 80, 99, 209, 261, 265], "percentcg": 283, "percentid": [30, 32], "perfect": [6, 21, 23, 30], "perfectli": 20, "perform": [7, 9, 11, 12, 15, 20, 22, 30, 32, 34, 56, 65, 69, 73, 80, 149, 182, 203, 238, 251, 270, 278, 290, 300], "perhap": [5, 6, 7, 12, 21, 22, 183, 191, 240, 241, 251], "period": [0, 4, 12, 33, 63, 65], "perl": [23, 288], "permiss": [15, 151], "permit": [100, 117, 169, 237], "permut": 4, "perna": 2, "peroxisom": 272, "perpendicular": [8, 176], "persist": [217, 305], "person": [6, 7, 15, 19, 21, 83, 123], "perspect": 56, "pertain": 20, "pesti": [6, 8, 21, 238], "pesticin": [21, 238], "petabyt": 278, "peter": [2, 26, 133, 263], "peterson": 133, "pevtnwlrwarfee": 53, "peyret": 264, "pf": 234, "pf02184": 53, "pf02294": 0, "pf05371": 12, "pf05371_seed": 12, "pfam": [0, 12, 21, 53, 56, 66], "pfam2": 0, "pfam_gc_map": [56, 66], "pfam_gr_map": [56, 66], "pfam_gs_map": [56, 66], "pfamseq": [0, 53], "pfm": [27, 283, 287, 288, 296], "pfm_format": 293, "pg": [0, 7, 108, 123], "pgdb": 304, "pgdb_dbutil": [301, 304], "pgm": 253, "pgt875": 0, "pgtygfycephagagmvgkvt": 0, "pgtygfycephagagmvgkvtv": 0, "pgtysfyctphrgagmvgtit": 0, "pgtysfyctphrgagmvgtitv": 0, "pgvygvkctphygmgmvgvv": 0, "pgvygvkctphygmgmvgvvev": 0, "ph": [263, 265], "phage": [2, 8, 104], "phage_coat_gp8": 12, "pharmaceut": 15, "phase": [158, 182, 270], "phd": [27, 238, 249, 268], "phd1": 249, "phdio": [27, 238], "phditer": [27, 238, 249], "phdwriter": [27, 238, 249], "phe": [13, 15, 169, 265], "pheatomselect": [15, 169], "phen_micro": [27, 298], "phenotyp": [26, 27, 307], "phenylalanin": [13, 15, 169], "pheromon": 7, "pheselect": 169, "phi": [3, 15, 68, 70, 137, 152, 154, 169], "phi_pattern": [68, 69, 70], "phl": 0, "phlyip": 56, "phmmer": [217, 229], "phmmer3": 229, "phobiou": 234, "phosphat": [3, 112, 261, 272], "phosphomutas": 10, "phosphoryl": 260, "phosphorylas": 209, "phosphotransferas": 10, "photo": 19, "phragmipedium": 19, "phrap": [238, 249, 268, 269, 271], "phred": [6, 238, 240, 249, 251, 253, 268, 270, 271], "phred_qual": [6, 21, 52, 240, 249, 251, 253, 260], "phred_quality_from_solexa": [27, 238, 251], "phrep": 251, "phst": 123, "phx": 183, "phy": [0, 12, 17, 30, 32, 56, 60, 182, 199], "phy_phyml_tre": 17, "phya": 260, "phyi": [30, 32], "phyiout": [30, 32], "phyl": 17, "phylip": [12, 17, 23, 27, 30, 32, 56, 60, 65, 80, 129, 132, 182, 190, 199, 238], "phylip3": 32, "phylipio": [27, 56], "phylipiter": [27, 56, 60, 65], "phylipout": [30, 32], "phylipwrit": [27, 56, 65], "phylo": [0, 2, 9, 12, 13, 24, 26, 27, 132, 307], "phylo_cookbook": 17, "phyloel": [27, 181, 197], "phylogenet": [0, 2, 7, 9, 12, 26, 56, 129, 130, 132, 181, 182, 183, 197, 198, 307], "phylogeni": [0, 17, 27, 32, 132, 181, 182, 183, 197, 198], "phylogent": 80, "phylogeograph": 197, "phylogram": 17, "phyloxml": [27, 181, 183, 198], "phyloxml_exampl": [17, 183], "phyloxmlerror": [27, 181, 198], "phyloxmlio": [27, 181, 183], "phyloxmlwarn": [27, 181, 197], "phylum": 197, "phyml": [17, 65, 182], "phymlcommandlin": [181, 182], "physalu": 272, "physic": [15, 158, 265], "physiol": 7, "physout": [30, 32], "phyto": 2, "phytochrom": 260, "phytopathologi": 2, "phz78458": 23, "pi": [15, 53, 135, 137, 139, 176, 261, 263, 265, 272], "pic": [144, 152, 167, 168, 169], "pic_accuraci": [133, 152, 168, 169], "pic_flag": [15, 133, 152, 169], "picard": 270, "picflag": [15, 152], "picflagsdefault": [133, 152, 169], "picflagsdict": [133, 169], "picio": [15, 27, 133, 169], "pick": [3, 6, 7, 8, 12, 15, 23, 32, 80, 102, 222], "pick_angl": [15, 133, 169], "pick_length": [15, 133, 169], "pickl": [30, 36, 54, 237, 297], "pict": 8, "pictur": [19, 99], "pid": [7, 93, 275], "pident": 218, "piec": [3, 6, 7, 8, 11, 260, 278], "pierr": 2, "pigment": 25, "pil": 8, "pilar": 2, "pileup": [48, 56, 63, 270], "pillow": 24, "pim": [21, 30, 32], "pin": 24, "pink": 183, "pip": 9, "pipe": [12, 17, 23, 270, 297], "pipelin": [6, 7, 238, 251], "pir": [25, 32, 238, 250], "pir_aln": 32, "pir_fram": 250, "pir_seq": 32, "pirio": [27, 238], "piriter": [27, 238, 250], "pirwrit": [27, 238, 250], "pisc": [152, 169], "pixel": 104, "pj": [7, 53], "pk": [3, 53, 263], "pk_ss": 53, "pkc_phospho_sit": 25, "pkvkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahh": 13, "pl": [15, 123, 182, 265, 270], "place": [3, 4, 5, 7, 11, 15, 17, 19, 22, 23, 30, 99, 104, 109, 119, 123, 152, 158, 168, 169, 177, 183, 214, 236, 237, 248, 251, 269, 275, 286], "placehold": [22, 277], "placement": [0, 8, 13, 30, 32], "plai": [7, 146, 221], "plain": [0, 1, 3, 6, 7, 8, 9, 13, 17, 19, 22, 23, 25, 30, 36, 68, 69, 70, 71, 83, 84, 89, 90, 94, 132, 185, 188, 190, 191, 197, 217, 222, 224, 228, 229, 233, 237, 238, 256, 258, 260, 261, 274, 276, 278, 297], "plain_newick": [132, 190], "plaintext": 104, "plan": [7, 18], "plane": [15, 169, 176], "plant": [2, 7, 19, 25, 93, 275], "plas_anav": 0, "plas_anava": 0, "plas_chlr": 0, "plas_horv": 0, "plas_horvu": 0, "plas_proh": 0, "plas_proho": 0, "plasma": [3, 25], "plasmid": [2, 6, 8, 21, 260], "plasmid_circular": 8, "plasmid_circular_nic": 8, "plasmid_linear": 8, "plasmid_linear_nic": 8, "plastid": 7, "plate": [16, 298, 299], "plate2": 299, "plate3": 299, "plateau": [16, 300], "plateid": 299, "platerecord": [16, 27, 298, 299], "platform": [7, 12, 16, 253, 270], "pleas": [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 18, 24, 25, 27, 29, 31, 32, 42, 50, 53, 65, 66, 68, 70, 73, 92, 120, 149, 152, 169, 182, 218, 222, 226, 241, 247, 251, 252, 253, 256, 264, 269, 274, 278, 282, 283, 297], "pleasant": 20, "pleckstrin": 217, "plenti": 9, "plfgwsryip": 250, "pliohippu": 56, "pln": [7, 23, 83, 93, 278], "plnyillnla": 250, "plnyillnlg": 250, "plnyillnlv": 250, "plo": 182, "plor": 15, "plot": [4, 8, 17, 23, 101, 169, 261, 265], "plq": 6, "plt": [15, 169], "plu": [0, 3, 7, 8, 9, 17, 20, 23, 32, 69, 169, 183, 221, 237, 251, 260, 261, 300], "plug": [31, 99], "plural": [0, 3, 11, 290], "plv": 56, "plvgwsryip": 250, "pm": [3, 16, 298, 299, 300], "pm01": [16, 298, 299], "pm09": [16, 298], "pm_fit": [27, 298], "pmc": [7, 83, 123, 234], "pmc310725p3": 7, "pmc3998142": 234, "pmc_id": 7, "pmc_pubm": 7, "pmcid": 7, "pmdml": 149, "pmic": 262, "pmid": [7, 34, 72, 83, 123, 153, 166, 175, 182, 280, 281, 299, 300], "pmismatch": [79, 80], "pmv": 15, "pn": 0, "pna": [2, 59], "pname": 153, "pnext": 52, "png": [6, 8, 11, 99, 104, 116, 283], "pnsldhgilivgysakntifrknmpywivknswgadwgeqg": 0, "pnsldhgilivgysakntifrknmpywivknswgadwgeqgyiylrrgkntcgvsnfvstsii": 0, "po": [11, 18, 31, 88, 129, 139, 201, 204, 223, 224, 225], "poacea": 25, "poal": 25, "pob": 80, "point": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 16, 17, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 36, 37, 65, 68, 73, 80, 84, 100, 101, 104, 129, 155, 157, 169, 175, 176, 177, 181, 182, 197, 198, 207, 216, 237, 251, 260, 263, 265, 278, 281, 282, 297, 299, 300], "pointer": [1, 3, 5, 13, 86, 158], "pointless": 23, "poke": 17, "pol_hv1n5": 248, "polar": [12, 13], "polar_angl": 176, "poll": 3, "pollin": 7, "pollut": 278, "polya": 275, "polygon": [27, 181, 197, 198], "polylin": 117, "polym": [143, 172], "polymorph": 72, "polynomi": 175, "polypeptid": [27, 133, 140, 263, 272], "polypeptide_domain": 0, "polypeptide_list": 15, "polypeptide_repeat": 53, "polypeptidebuild": 15, "polytomi": 132, "pomg": [152, 169], "ponabe2": 0, "pone": [137, 182], "ponnuswami": 265, "pooidea": 25, "poor": [6, 13, 19, 183, 251, 270], "poorli": [30, 270], "pop": [6, 17, 27, 201, 202, 204, 236], "pop_list": 201, "pop_nam": [18, 201, 202], "pop_po": [202, 203], "popen": 12, "popgen": [26, 27, 307], "popset": 7, "popul": [21, 26, 66, 169, 200, 201, 202, 203, 204, 205, 260, 303, 307], "popular": [4, 5, 7, 9, 11, 12, 18, 19, 20, 23], "port": 17, "portabl": 2, "portal": 8, "portion": [12, 61, 138], "portrait": 104, "pos_num": [20, 218], "pos_pct": [218, 226], "pos_specific_score_matrix": [12, 30, 31], "poscolor": 104, "posit": [0, 3, 4, 6, 8, 13, 14, 15, 17, 18, 22, 27, 30, 31, 32, 35, 36, 39, 44, 45, 46, 51, 52, 61, 66, 68, 69, 71, 73, 88, 99, 100, 104, 107, 114, 117, 125, 129, 135, 136, 139, 141, 146, 152, 158, 162, 169, 177, 182, 201, 203, 204, 217, 218, 222, 234, 236, 237, 240, 253, 257, 261, 263, 264, 265, 269, 270, 272, 278, 283, 286, 290, 293, 294, 295, 297, 303], "position_pad": [238, 245], "positionspecificscoringmatrix": [11, 27, 283, 290], "positionweightmatrix": [27, 283, 290], "positiveinteg": 197, "possess": 217, "possibl": [3, 5, 6, 7, 8, 11, 12, 15, 19, 20, 21, 23, 24, 27, 30, 34, 56, 66, 68, 72, 76, 84, 108, 122, 127, 175, 197, 217, 218, 221, 237, 238, 251, 256, 260, 261, 269, 275, 278, 281, 282, 290, 295, 303, 305], "possibli": [20, 30, 36, 68, 69, 88, 169, 197, 198, 237], "post": [6, 7, 19, 71, 83, 221, 253], "posted_d": 71, "posterior": [32, 53], "posterior_prob": 66, "postgresql": 304, "postord": [17, 183], "postscript": [8, 99], "posttransation": 272, "posttransl": 272, "potapov": 2, "potato": 2, "potenti": [3, 5, 6, 11, 12, 15, 20, 21, 23, 27, 88, 99, 177, 237, 251, 270, 278], "pothier": 153, "pou": 288, "power": [6, 7, 15, 23], "pp": [15, 53, 66, 149, 154, 169, 229], "pp_con": 53, "ppawagdrsh": 0, "ppb": [15, 154], "ppbuilder": [15, 27, 133, 154], "ppcp": 21, "ppcp1": [6, 8, 21], "ppo": 218, "ppsflrapsw": 250, "pqqpqggnqfsggaqsrpqqsapaapsneppmdfdddipf": 260, "pqr": [135, 148, 151, 162], "pqr_charg": [135, 162], "pqr_parser": 15, "pr": [7, 25, 86, 88], "practic": [4, 12, 15, 17, 21, 23, 127, 251, 264], "prang": [79, 80], "prank": 32, "prank_clin": 32, "prankcommandlin": [30, 32], "prb": 270, "prbnseq": 270, "pre": [5, 6, 30, 32, 169, 253, 260], "preambl": [94, 230], "precalcul": [4, 54], "preced": [0, 17, 169, 183, 288], "precis": [11, 13, 80, 157, 182, 216, 286, 290, 294], "pred": 122, "predecessor": [130, 132, 218], "predefin": [0, 17, 20, 38, 294], "predict": [0, 3, 15, 20, 25, 53, 110, 125, 164, 263, 275], "predicted_st": 110, "predicted_titl": 110, "predictno": [27, 124, 125], "predictor": [11, 283], "preexist": 104, "prefer": [3, 4, 6, 7, 8, 11, 12, 13, 15, 22, 30, 67, 73, 84, 169, 238, 251, 261, 270, 295], "prefix": [6, 17, 24, 32, 84, 97, 117, 129, 181, 183, 185, 188, 236, 268, 270], "prefwidth": [206, 207], "preker": 53, "prelim": 71, "preliminari": [69, 272], "preorder": [17, 183], "prepar": [12, 49, 64, 149, 163, 169, 175], "prepeptid": 272, "preprocess": 177, "preq1": 53, "prescrib": 104, "presenc": [20, 275, 299], "present": [1, 3, 4, 5, 6, 7, 8, 16, 20, 21, 23, 24, 25, 30, 52, 54, 69, 73, 94, 102, 104, 117, 129, 136, 139, 144, 149, 164, 172, 182, 197, 218, 221, 222, 226, 229, 236, 237, 251, 264, 270, 275, 299], "present_count": 197, "preserv": [0, 8, 15, 17, 20, 21, 23, 30, 84, 159, 183, 217, 222, 238, 253, 260], "preserve_atom_numb": [148, 170], "preset": 15, "press": [2, 169, 216], "presum": [13, 303], "pretend": [6, 253], "pretrain": 32, "pretti": [5, 6, 7, 12, 15, 22, 23, 237, 261], "prettifi": 117, "prettili": 297, "pretty_print_predict": [27, 106, 110], "pretty_str": [15, 133, 169], "prev": 130, "prevent": [0, 7, 11, 12, 24, 30, 32, 107, 236, 240, 251, 303], "previou": [6, 8, 12, 15, 20, 21, 22, 23, 24, 37, 46, 53, 68, 108, 158, 169, 240, 267], "previous": [4, 8, 15, 20, 21, 65, 83, 127, 251], "pri": 93, "price": 182, "prickli": [7, 12, 23], "primari": [21, 52, 83, 88, 152, 169, 303], "primarili": [0, 24, 30, 158], "primary_id": [302, 303], "primat": 93, "prime": 21, "primer": [12, 21, 27, 72, 79, 80, 81, 82, 251, 253, 264], "primer3": [27, 79, 80], "primer3commandlin": [27, 79, 80], "primer3plu": 264, "primer_nam": 82, "primer_read": 6, "primersearch": [27, 79, 80], "primersearchamplifi": 82, "primersearchcommandlin": [27, 79, 80], "primersearchoutputrecord": 82, "primit": [158, 183], "prin": 123, "princip": [2, 73], "principl": 23, "print": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 56, 59, 60, 62, 66, 67, 68, 69, 71, 76, 80, 83, 85, 90, 92, 104, 110, 112, 113, 114, 116, 122, 123, 129, 134, 135, 137, 154, 156, 157, 158, 168, 169, 176, 182, 183, 195, 199, 206, 207, 216, 217, 236, 237, 238, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 253, 256, 260, 261, 263, 264, 265, 269, 270, 272, 274, 277, 278, 279, 280, 281, 283, 288, 289, 291, 292, 295, 297, 298, 299], "print_a": [206, 207], "print_info_cont": [27, 30, 31], "print_matrix": [27, 297], "print_opt": [192, 195], "print_site_lnl": [181, 182], "print_that": [206, 207], "print_trac": [181, 182], "printabl": 158, "printer": 158, "printformat": [27, 206], "printlist": 207, "printnod": [30, 32], "printout": [14, 297], "prior": [6, 7, 9, 12, 21, 23, 99, 108, 109, 127, 237, 265, 270, 297], "pritchard": [2, 7, 8, 9], "pritchard2006": [2, 8, 9], "privat": [67, 71, 76, 89, 91, 94, 129, 169, 197, 202, 237, 252], "pro": [6, 13, 15, 30, 69, 169, 241, 260], "pro1": [13, 279], "pro2": [13, 279], "pro3": 13, "pro_align": 279, "prob": [0, 202], "probab": 0, "probabilist": [2, 32, 270], "probabl": [3, 4, 6, 8, 9, 11, 12, 13, 15, 21, 23, 32, 53, 62, 66, 107, 108, 109, 120, 122, 127, 169, 202, 203, 238, 251, 253, 260, 270, 282, 283, 290, 305], "probal": 251, "probcon": [0, 32], "probcons_clin": 32, "probconscommandlin": [30, 32], "probe": [7, 20, 80, 157, 238, 264], "probe_radiu": 157, "probe_s": 145, "problem": [1, 3, 5, 6, 7, 8, 9, 11, 12, 20, 21, 22, 23, 27, 92, 99, 107, 108, 136, 143, 144, 151, 158, 160, 169, 182, 198, 221, 226, 251, 278], "problemat": [21, 278], "proc": [83, 264], "proce": [7, 15, 182, 270], "procedur": [4, 15, 20, 32, 129], "proceed": [0, 2, 13, 32], "process": [0, 2, 4, 5, 6, 7, 9, 13, 15, 22, 53, 56, 67, 84, 89, 95, 99, 136, 145, 158, 169, 182, 190, 238, 258, 272], "process_asa_data": [27, 133, 145], "process_clad": [181, 185, 190], "process_rsa_data": [27, 133, 145], "processor": 32, "prodoc": [25, 27, 85], "produc": [3, 4, 8, 12, 15, 16, 17, 20, 22, 48, 59, 63, 69, 80, 94, 99, 103, 158, 183, 186, 222, 229, 238, 251, 253, 272], "product": [7, 8, 12, 13, 15, 16, 21, 27, 73, 80, 81, 94, 99, 113, 115, 117, 158, 176, 177, 264, 277], "product_id": 117, "prof": [17, 123], "profil": [2, 4, 11, 25, 30, 32, 74, 90, 229, 231, 265, 287, 288], "profile1": [30, 32], "profile2": [30, 32], "program": [0, 1, 2, 3, 4, 6, 7, 9, 11, 12, 13, 15, 17, 19, 20, 22, 23, 30, 32, 36, 37, 44, 55, 59, 65, 67, 68, 69, 70, 73, 74, 79, 80, 81, 82, 83, 107, 109, 137, 145, 153, 156, 158, 169, 182, 183, 199, 202, 203, 217, 218, 221, 222, 226, 229, 234, 238, 252, 254, 259, 262, 268, 269, 270, 283, 291, 292, 294, 296, 297], "programm": [7, 19, 20], "programmat": [7, 25, 89], "progress": [4, 32, 79, 80, 182], "progressivemauv": [0, 47, 56, 62], "prohibit": 4, "project": [5, 6, 7, 9, 15, 17, 21, 24, 27, 93, 94, 158, 169, 174, 176, 250], "projects_home_pag": 32, "prokaryot": [6, 8], "prolin": [15, 152], "proma": 2, "promot": [6, 23, 27, 260, 272], "prompt": [3, 12, 19, 80, 260, 297], "proof": [15, 169], "prop": [7, 134, 197], "prop_invar": [181, 182], "propag": [0, 12, 21, 30], "propagate_chang": [133, 169], "propep": 272, "propeptid": 272, "proper": [107, 251, 270], "properli": [4, 5, 129, 149, 182, 183, 237, 270], "properti": [0, 3, 8, 11, 12, 13, 17, 20, 21, 22, 27, 30, 32, 54, 67, 68, 69, 80, 84, 100, 104, 117, 134, 137, 139, 145, 169, 181, 182, 183, 193, 195, 196, 197, 198, 221, 222, 236, 237, 252, 256, 260, 265, 270, 283, 287, 290, 296, 302], "property_1": 134, "property_2": 134, "property_dict": 134, "property_kei": 134, "property_list": 134, "prophag": 8, "proport": [8, 104, 182], "proportoin": 80, "propos": [19, 265, 300], "proprietari": [3, 16], "prorul": 88, "prosit": [9, 27, 85, 86, 87, 89], "prosite_ref": 87, "prot": [0, 2, 9, 19, 23, 26, 32, 69, 86, 88, 89, 137, 197, 238, 255, 307], "prot_guidelin": 25, "prot_sequ": 265, "protcat_gammaimatrixnam": 182, "protcat_gammamatrixnam": 182, "protcatmatrixnam": 182, "protcatwag": 182, "protdist": 80, "proteas": 8, "protect": 25, "protein": [0, 2, 3, 4, 6, 7, 8, 11, 12, 13, 19, 20, 21, 22, 23, 25, 30, 32, 53, 56, 68, 69, 71, 74, 80, 83, 86, 88, 93, 94, 112, 117, 140, 149, 152, 153, 157, 158, 164, 166, 169, 175, 182, 196, 197, 198, 199, 209, 211, 214, 216, 221, 222, 226, 229, 234, 236, 237, 238, 250, 252, 260, 261, 263, 265, 272, 274, 275, 277, 279, 283, 290], "protein2": 25, "protein2dna": [42, 222], "protein2genom": [42, 222], "protein_align": 13, "protein_alphabet": [75, 76], "protein_exist": 272, "protein_id": [7, 21, 94], "protein_letters_3to1_extend": 214, "protein_model": [181, 182, 199], "protein_rec": 260, "protein_record": [13, 260], "protein_scal": [261, 265], "protein_seq": 22, "protein_sequ": 263, "proteinalpabet": 22, "proteinanalysi": [27, 261, 263, 265], "proteinclust": 7, "proteindomain": [27, 181, 197], "proteint": 93, "protgammaimatrixnam": 182, "protgammamatrixnam": 182, "protgi": [7, 275], "protid": [7, 275], "protmix": 182, "protmiximatrixnam": 182, "protmixmatrixnam": 182, "protml": 17, "proton": [152, 169], "prototyp": 177, "protpar": 80, "protparam": [27, 261, 263, 266], "protparamdata": [27, 261, 265], "protscal": 265, "protsim": [7, 275], "protsimlin": [27, 275], "proux": [2, 8], "proux2002": [2, 8], "proux_et_al_2002_figure_6": 8, "prove": [6, 8], "provid": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 20, 21, 23, 24, 25, 27, 30, 36, 37, 38, 42, 45, 53, 56, 60, 61, 65, 66, 67, 68, 70, 73, 80, 83, 91, 93, 94, 95, 99, 100, 104, 109, 119, 126, 130, 132, 137, 143, 148, 149, 150, 151, 152, 157, 158, 169, 182, 186, 197, 199, 204, 205, 209, 214, 215, 217, 218, 221, 222, 226, 229, 236, 237, 238, 246, 251, 253, 261, 268, 272, 274, 275, 278, 287, 288, 294, 297, 298, 299, 300, 303], "provis": [129, 130, 131, 132, 202], "proxi": [16, 149, 237, 260, 274], "proxyhost": 7, "prt": [22, 76, 272], "prune": [17, 128, 132, 181, 182, 183], "ps00001": [25, 85], "ps00004": 25, "ps00005": 25, "ps00387": 88, "ps50948": 25, "psd": 25, "psea": [27, 133], "psea2hec": [27, 133, 153], "pseq": 153, "pseudo": [11, 12, 69, 80, 108, 121, 141, 181, 182, 217], "pseudo_count": [12, 31], "pseudo_emiss": 121, "pseudo_initi": 121, "pseudo_transit": 121, "pseudocount": [11, 13, 27, 68, 69, 108, 182, 283, 287, 290], "pseudogen": 104, "psi": [15, 68, 69, 70, 71, 137, 152, 154, 169], "psiblast": [3, 27, 68, 69, 71], "psipr": 0, "psizeopt": [79, 80], "psl": [13, 20, 27, 30, 38, 45, 217, 221], "psl_34_001": [0, 217], "psl_34_004": 221, "pslayout": [0, 45, 221], "psltobigpsl": 0, "psltochain": 0, "pslx": [217, 221], "pslx_34_004": 221, "psp_test": [11, 283], "pssm": [12, 27, 30, 31, 69, 283, 288, 290, 294, 296], "pssm_reb1": 11, "pst": [30, 32, 123], "psycopg2": 304, "psycopg2_dbutil": [301, 304], "pt": [123, 175], "pthread": 182, "ptm": 272, "ptmlist": 272, "ptmmax": [79, 80], "ptmmin": [79, 80], "ptmopt": [79, 80], "ptr": 6, "pttk": 14, "ptz78488": 23, "pu": 11, "pub": [7, 15, 23, 153, 277], "pubdat": 7, "public": [3, 7, 8, 9, 16, 68, 83, 123, 129, 218, 221, 234, 251, 264, 265], "publicid": 84, "publicli": [8, 253], "publish": [7, 8, 9, 21, 123, 237, 264], "pubm": [9, 11, 19, 83, 123, 182, 237, 274, 288, 295], "pubmed1": 83, "pubmed_id": [7, 21, 93, 237], "pubmed_pmc_ref": 7, "pubmed_pubm": [7, 83], "pubmed_pubmed_alsoview": 7, "pubmed_pubmed_citedin": 7, "pubmed_pubmed_combin": 7, "pubmed_pubmed_f": 7, "pubmed_pubmed_ref": 7, "pubmed_pubmed_review": 7, "pubmed_pubmed_reviews_f": 7, "pubmed_result1": [7, 123], "pubmed_result2": [7, 123], "pubmedarticl": 7, "pubmedcentr": 83, "pull": [0, 5, 6, 12, 25, 131, 260, 274], "punctuat": 129, "pure": 182, "purin": 32, "purl": 185, "purpl": [8, 183], "purpos": [0, 7, 12, 13, 15, 17, 20, 24, 25, 30, 61, 84, 99, 108, 146, 197, 261, 281, 297, 305], "push_back": [229, 230], "put": [6, 7, 9, 12, 15, 23, 24, 31, 68, 70, 84, 104, 149, 163, 169, 175, 216, 277], "pv": [11, 13, 295], "pvalu": [11, 13, 291], "pvcgaael": 0, "pvcgaaelsvnsl": 56, "pvcgaaelsvnslek": 0, "pwdist": [30, 32], "pwdnamatrix": [30, 32], "pwgapext": [30, 32], "pwgapopen": [30, 32], "pwgenom": [30, 32], "pwgenomicdist": [30, 32], "pwm": [11, 27, 283, 288, 290], "pwmatrix": [30, 32], "px": [209, 211, 261], "py": [0, 5, 8, 9, 15, 24, 76, 116, 141, 152, 167, 169, 255, 261], "py38": 24, "py39": 24, "pycog": 17, "pycon": 24, "pyenv": 84, "pygresql": 304, "pyl": 261, "pylab": [6, 17], "pymmlib": 15, "pymol": [15, 141, 166], "pypi": [24, 217, 238], "pyplot": [15, 169], "pyrimidin": 32, "python": [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 32, 35, 39, 46, 51, 52, 61, 67, 68, 69, 80, 83, 84, 86, 89, 90, 123, 131, 158, 166, 172, 174, 175, 182, 183, 185, 197, 200, 218, 221, 236, 237, 238, 253, 260, 261, 270, 273, 274, 278, 284, 295, 297, 299, 303, 306, 307], "python3": [24, 84], "pywivkn": 0, "pywivknswgpqwgmng": 0, "pywivknswgpqwgmngyfliergknmcglaacasypiplv": 0, "pywlikn": 0, "pywliknswgadwgdng": 0, "pywliknswgadwgdngyfkmemgknmcaiatcasypvvaa": 0, "q": [0, 12, 13, 22, 30, 176, 182, 221, 237, 251, 261, 268, 270], "q06000": 25, "q08386": 68, "q29524": 25, "q8jzq5": 23, "q9t0q8": 12, "q9t0q8_bpi": 12, "q9t0q8_bpike": 12, "q9t0q9": 12, "q9t0q9_bpf": 12, "q9t0q9_bpfd": 12, "q9trc7": 23, "q_": [6, 12], "q_end1": [0, 30], "q_end2": [0, 30], "q_endn": [0, 30], "q_handl": 6, "q_i": 270, "q_l": 270, "q_start1": [0, 30], "q_start2": [0, 30], "q_startn": [0, 30], "qa": [13, 27, 268, 269], "qaarflfmknkvrmivdchakhvkvlqdeklpfdltlcgstlraphschlqymanmdsia": 260, "qacc": 218, "qaccver": 218, "qafeyikyng": 0, "qafeyilynk": 0, "qasgpertip": 250, "qatgknisl": 0, "qblast": [3, 9, 27, 68, 70], "qcov_hsp_perc": [68, 69], "qcp": [27, 133, 175], "qcprot": [27, 133], "qcpsuperimpos": [27, 133, 175], "qdfmmyrtgi": 0, "qdfmmyrtgiysstschktpdkvnhavlavgygekngi": 0, "qend": 218, "qend_mark": [218, 220], "qframe": 218, "qgi": 218, "qgkdgy": 0, "qgsgyafphasilsgiamshfyflvlhavk": 6, "qhkamiliv": 237, "qing": 2, "qinter": [202, 203], "qintra": [202, 203], "qkl": 68, "qlen": 218, "qllmspgqststtfpadapageytfycephrgagmvgkitv": 0, "qname": 252, "qncsat": 0, "qpgkaigfvk": 0, "qq": 176, "qquad": 22, "qr": 4, "qresult": [20, 217, 218, 219, 220, 221, 222, 231, 232, 235], "qresult2": 20, "qresult_end": [229, 230, 233], "qresult_start": [229, 230, 233], "qresults2": 20, "qrf": [13, 14], "qseq": 218, "qseqid": [69, 218], "qstart": [0, 218, 221], "qstart_id": 220, "qstart_mark": [218, 220], "qt": 182, "qtcsatlagn": 0, "qual": [23, 238, 240, 249, 251, 253, 260], "qual_digit": [268, 270], "qual_sourc": 251, "qualifi": [3, 7, 8, 21, 27, 68, 80, 92, 93, 94, 99, 104, 164, 237, 245, 260, 272, 275], "qualifier_ind": [238, 245], "qualifier_indent_str": [238, 245], "qualifier_indent_tmp": [238, 245], "qualiti": [0, 2, 13, 17, 21, 23, 32, 52, 182, 238, 240, 249, 251, 253, 260, 268, 269, 270, 302], "qualityio": [6, 23, 27, 238], "qualphrediter": [27, 238, 251], "qualphredwrit": [27, 238, 251], "qualtityio": 251, "quantiti": 6, "quartil": [98, 104], "quaternion": 175, "queri": [0, 3, 5, 12, 13, 20, 25, 27, 30, 38, 44, 45, 51, 52, 59, 61, 68, 69, 70, 71, 74, 83, 89, 119, 146, 169, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 229, 230, 231, 232, 233, 234, 260, 270, 274, 276, 299], "query_1": [68, 218], "query_128889": 3, "query_2": [68, 218], "query_3": 68, "query_4": 68, "query_5": 68, "query_69183": 3, "query_78041": 68, "query_al": 20, "query_believe_deflin": [68, 70], "query_coverag": [27, 74], "query_descript": 20, "query_end": [71, 218, 221, 222, 226, 229, 234], "query_end_extend_gap_scor": 13, "query_end_gap_scor": [13, 30], "query_end_open_gap_scor": 13, "query_endtyp": 229, "query_extend_gap_scor": 13, "query_fil": [68, 70], "query_fram": [218, 222], "query_frame_al": 222, "query_from": [3, 68, 70], "query_gap": [30, 55], "query_gap_num": 221, "query_gap_scor": 13, "query_gapopen_num": 221, "query_gencod": [68, 69], "query_id": [3, 20, 71], "query_inter_rang": 222, "query_internal_extend_gap_scor": 13, "query_internal_gap_scor": 13, "query_internal_open_gap_scor": 13, "query_is_protein": 221, "query_kei": 7, "query_left_extend_gap_scor": 13, "query_left_gap_scor": 13, "query_left_open_gap_scor": 13, "query_len": 3, "query_length": 71, "query_lett": 71, "query_loc": [68, 69], "query_mask": 3, "query_nam": 0, "query_open_gap_scor": 13, "query_rang": 20, "query_right_extend_gap_scor": 13, "query_right_gap_scor": 13, "query_right_open_gap_scor": 13, "query_span": 20, "query_span_al": 221, "query_split_codon": 222, "query_start": [20, 71, 218, 221, 222, 226, 229, 234], "query_start_al": 221, "query_strand": [221, 222, 226, 229], "query_to": [68, 70], "querya": 0, "queryb": 0, "queryc": 0, "querykei": 7, "queryresult": [217, 218, 219, 221, 222, 224, 225, 226, 229, 231, 232, 234], "querytransl": [7, 83], "question": [1, 5, 19, 20, 84, 182, 279], "queue": 169, "quick": [3, 7, 15, 20, 21, 23, 26, 31, 83, 132, 149, 152, 168, 169, 177, 217, 260, 307], "quickaln": 32, "quicker": [23, 209], "quickli": [0, 7, 13, 15, 17, 19, 21, 30, 152], "quicktre": [30, 32], "quiet": [30, 32, 143, 151, 157, 181, 182], "quikchang": 264, "quinoa": 3, "quirk": [7, 23], "quit": [0, 1, 3, 6, 8, 11, 12, 15, 19, 20, 21, 23, 222, 251], "quot": [32, 67, 94, 129, 181, 182], "quotestrip": [27, 128, 129], "quri": [27, 181, 185, 188], "r": [0, 1, 2, 4, 6, 7, 11, 12, 13, 15, 22, 23, 30, 32, 36, 37, 53, 59, 60, 67, 68, 74, 80, 91, 100, 116, 139, 140, 146, 149, 152, 157, 159, 168, 169, 172, 176, 177, 182, 183, 237, 238, 246, 253, 261, 268, 270, 277, 278, 279, 283, 299], "r1": 169, "r126": 0, "r1_cbeta_coord": 169, "r1_cbeta_index": 169, "r1chi2": 169, "r1chi2_index": 169, "r1chi2_kei": 169, "r1chi2_obj": 169, "r1chi2_valu": 169, "r2": 15, "r2_cbeta_coord": 15, "r2_cbeta_index": 15, "r2cacb": 15, "r2chi1": 15, "r2chi1_index": 15, "r2chi1_kei": 15, "r2chi1_object": 15, "r2ic": 15, "r2tau": 15, "r_": 4, "r_dna_nn1": 264, "r_free": 172, "r_method": [268, 270], "r_seed": [181, 182], "r_work": 172, "ra": [0, 11, 12, 53, 295], "rabgltr": 0, "rabgstb": 0, "rad": 176, "radial": 8, "radian": [169, 176], "radiat": 275, "radii": [157, 158, 169], "radii_dict": 157, "radiu": [4, 15, 104, 135, 141, 146, 154, 157, 162], "raf": [27, 209], "rai": [25, 144], "rainbow_color": 102, "rais": [3, 4, 7, 8, 11, 12, 13, 14, 17, 21, 22, 23, 25, 27, 30, 31, 56, 67, 68, 83, 84, 85, 89, 102, 108, 113, 136, 144, 152, 155, 160, 168, 169, 183, 188, 190, 198, 209, 217, 236, 237, 238, 241, 251, 253, 260, 261, 271, 283, 290, 298, 299, 300], "rak": [133, 169], "rak_cach": 169, "raltglsapgirsqtscdrlrelryvpvsl": 6, "ram": [23, 217, 238, 251, 278], "ran": [3, 24, 81, 92], "ranch": 80, "rand": 4, "rand_start": [181, 182], "random": [2, 7, 13, 15, 17, 23, 30, 56, 73, 80, 100, 108, 128, 132, 169, 181, 182, 183, 210, 214, 238, 251, 253, 256, 270, 278], "random_s00": 20, "random_starting_tre": [181, 182], "randomis": 80, "randomli": [4, 6, 108], "randommis": 80, "rang": [0, 2, 3, 6, 7, 11, 12, 13, 15, 18, 20, 21, 30, 32, 61, 69, 80, 88, 98, 99, 100, 102, 103, 104, 119, 169, 182, 236, 237, 251, 264, 265, 270, 274], "rank": [3, 7, 20, 73, 140, 181, 182, 197, 198], "rao": 199, "rapa": 238, "rapid": [175, 182, 210, 214], "rapid_bootstrap_se": [181, 182], "rapidli": [4, 11], "rare": [6, 17, 23], "rarer": 19, "rasmu": 2, "rasrksmraacsrsag": 0, "rasrksmraacsrsagsrpnrfaptlmsscitsttg": 0, "rasrksmraacsrsagsrpnrfaptlmsscitsttgppawagdrsh": 0, "rat": [0, 22, 182], "rate": [2, 11, 13, 32, 34, 79, 80, 83, 100, 182, 196, 270, 294], "rate_proport": 294, "rateancestor": 17, "rather": [6, 7, 12, 13, 15, 17, 21, 23, 24, 27, 32, 34, 62, 65, 66, 83, 84, 92, 197, 217, 237, 238, 251, 255, 269, 270, 278, 280, 303, 305], "ratio": [4, 11, 13, 32, 34, 80, 182, 194, 261, 281, 290], "ravier": 263, "raw": [4, 6, 7, 12, 15, 25, 59, 69, 84, 85, 92, 102, 128, 131, 218, 219, 220, 221, 224, 225, 226, 232, 238, 251, 253, 278], "rawdata": 54, "rawdist": [181, 182], "raxml": [17, 65, 182], "raxml_bipartitionfrequ": 182, "raxml_clin": 182, "raxml_reducedlist": 182, "raxmlcommandlin": [181, 182], "raxmlhpc": 182, "razip": 270, "rb": [3, 7, 23, 29, 68, 83, 247, 253, 278], "rbase": [15, 169], "rbg": 100, "rc": [21, 169, 250, 260], "rc_": 23, "rc_align": [0, 30], "rc_plasmid": 260, "rc_record": 260, "rcst": [15, 169], "rd": [15, 27, 156, 268, 269], "rd_of_read4": 269, "rdf": [185, 274], "rdrsdqhiqlqlsaesvgevyikstetgqylamdtsgllygsqtpseec": 265, "re": [3, 5, 6, 7, 8, 10, 12, 15, 17, 19, 20, 21, 23, 25, 27, 32, 68, 99, 111, 115, 119, 132, 134, 140, 143, 168, 169, 197, 204, 205, 209, 214, 221, 238, 251, 261, 270], "re_class": 169, "re_cod": [181, 197], "re_doi": [181, 197], "re_ref": [181, 197], "re_symbol": [181, 197], "re_valu": [181, 197], "reach": [0, 11, 12, 31, 100, 108, 129, 180, 183, 252, 270, 290], "reachabl": 108, "reactant": [117, 177], "reactant_id": [115, 117], "reaction": [27, 111, 113, 115, 116, 117, 118, 177, 274], "reaction_entri": [115, 117], "read": [1, 3, 4, 5, 7, 8, 9, 10, 14, 16, 17, 18, 19, 21, 22, 24, 25, 27, 28, 29, 30, 32, 41, 45, 50, 52, 54, 55, 56, 58, 59, 61, 65, 66, 68, 71, 73, 74, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 104, 111, 113, 115, 116, 123, 128, 129, 132, 149, 152, 169, 181, 182, 183, 192, 193, 195, 196, 198, 199, 200, 201, 204, 205, 217, 218, 221, 222, 230, 236, 237, 238, 240, 244, 247, 248, 249, 250, 251, 252, 253, 256, 257, 260, 268, 269, 270, 271, 272, 275, 277, 278, 281, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 298, 299], "read4": 269, "read_1": 270, "read_2": 270, "read_cal": [268, 270], "read_colorschem": [98, 104], "read_ctl_fil": [192, 193, 195, 196], "read_fil": [268, 270], "read_file1": [268, 270], "read_file2": [268, 270], "read_group": 270, "read_next": [229, 230], "read_pic": [15, 27, 133, 152, 168, 169], "read_pic_seq": [15, 27, 133, 152, 169], "reada": 0, "readabl": [0, 7, 11, 12, 13, 21, 22, 23, 25, 30, 45, 56, 59, 68, 80, 86, 90, 117, 197, 260, 280, 297, 299], "readb": 0, "readc": 0, "reader": [198, 278], "readfil": [268, 270], "readgroup": 270, "readi": [3, 5, 6, 12, 19, 117, 299], "readili": 20, "readjust": 129, "readlin": [1, 3, 27, 83, 278], "readm": [9, 149, 277], "readrochexmlmanifest": [27, 238, 253], "real": [0, 6, 12, 15, 17, 19, 21, 31, 69, 73, 100, 110, 141, 217, 222, 229, 251, 278], "real_stat": 110, "real_titl": 110, "realbranch": [30, 32], "realign": 270, "realis": 278, "realist": [2, 8, 10, 15], "realiti": 104, "realiz": [14, 15, 20], "realli": [1, 3, 5, 6, 7, 8, 11, 12, 15, 20, 21, 22, 23, 99, 149, 182, 236, 288, 305], "realproxi": 149, "reanchor": 221, "reappear": [0, 4], "rearrang": [2, 79, 80, 181, 182], "reason": [3, 6, 7, 9, 15, 21, 23, 27, 119, 178, 238, 251, 274], "reassign": 4, "reb1": 11, "rebas": 208, "rebuild": [168, 169], "rebuilt": 169, "rec": [6, 18, 21, 23, 238, 251, 260, 277], "rec1": 23, "rec2": 23, "rec3": 23, "rec_i": 8, "rec_loci": 18, "rec_on": 6, "rec_pop": 18, "rec_two": 6, "rec_x": 8, "recal": [3, 8, 20, 23], "recalcul": [0, 11, 21, 265], "recapitul": 11, "receiv": [3, 7, 27, 56, 89, 252], "recent": [0, 3, 4, 6, 7, 12, 13, 14, 17, 19, 21, 22, 23, 30, 32, 45, 56, 67, 68, 80, 85, 137, 149, 183, 217, 236, 237, 238, 241, 251, 260, 264, 278, 283, 298], "recent_orchid_pap": 7, "receptor": 15, "recnam": [23, 25], "recogn": [20, 23, 25, 226], "recognit": 8, "recommend": [2, 3, 4, 7, 9, 11, 12, 15, 23, 24, 30, 32, 56, 60, 67, 69, 80, 83, 86, 99, 152, 182, 197, 201, 217, 218, 251, 260, 264, 270, 278, 285], "recompil": 145, "reconsid": 7, "reconstruct": [0, 4, 15, 201, 204], "record": [0, 1, 4, 6, 8, 9, 11, 12, 13, 15, 16, 18, 19, 21, 22, 27, 28, 29, 30, 37, 46, 50, 52, 53, 56, 59, 60, 61, 62, 65, 66, 68, 69, 71, 73, 74, 79, 81, 82, 83, 85, 86, 87, 88, 89, 90, 92, 94, 96, 111, 112, 113, 114, 123, 145, 148, 152, 169, 177, 197, 200, 201, 204, 205, 209, 210, 211, 212, 213, 214, 215, 217, 220, 226, 237, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 259, 260, 268, 269, 270, 271, 272, 273, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 288, 289, 291, 292, 293, 295, 296, 299, 302, 303, 305], "record1": 21, "record2": [21, 251], "record2titl": [241, 250, 251], "record_complete_ancestri": 185, "record_dict": 238, "record_ha": [27, 276, 277], "record_index": 6, "record_iter": [6, 23, 251, 303], "record_start": [92, 94], "recordpars": [27, 92], "recov": [169, 297], "recreat": [4, 30, 68, 73, 305], "rectangl": [4, 117], "rectangular": [4, 73], "recurs": [17, 80, 107, 139, 152, 183, 185, 197, 198, 263], "red": [0, 4, 8, 17, 104, 122, 181, 183, 198], "reddi": 265, "redefin": [45, 60, 246], "redirect": [12, 69], "redistribut": 3, "redland": 185, "redmin": 5, "reduc": [4, 7, 8, 21, 23, 32, 169, 182, 265, 270, 278], "reducedbi": 182, "reduct": [16, 36, 182], "reductas": 113, "redund": [3, 158, 169, 251, 270], "reestim": 32, "ref": [0, 3, 7, 20, 21, 25, 27, 152, 197, 218, 237, 238, 256, 268, 270, 272], "ref_db": [21, 27, 237], "ref_list": 270, "ref_locu": 7, "ref_rec": 56, "refer": [0, 3, 4, 6, 7, 8, 9, 12, 13, 15, 17, 23, 24, 25, 27, 30, 32, 36, 39, 52, 53, 59, 61, 68, 71, 84, 85, 87, 88, 90, 92, 93, 109, 111, 115, 117, 119, 123, 132, 133, 135, 140, 152, 157, 169, 175, 177, 181, 182, 190, 197, 198, 201, 209, 216, 218, 222, 248, 252, 260, 263, 267, 268, 270, 272, 275, 283, 295, 302], "referenc": [7, 15, 21, 169, 197, 214], "reference_annot": 66, "reference_coord": [175, 216], "reference_fasta": 270, "reference_genom": 270, "reference_kei": [283, 295], "refin": [7, 30, 32, 182, 276], "refinew": [30, 32], "refinewindow": [30, 32], "reflect": [7, 8, 15, 21, 169, 217, 238], "reflist": 270, "refmat": [15, 27, 133, 176], "refresh": [181, 182], "refseq": 93, "refseq_rna": [3, 20], "reg": [229, 270], "regard": [4, 5, 6, 12, 14, 20, 24, 30, 84, 140, 177, 264], "regardless": [11, 25, 217, 226, 236, 237, 256], "regener": [0, 15, 169], "regex": [17, 169], "region": [0, 3, 6, 8, 12, 15, 20, 21, 30, 31, 32, 35, 36, 38, 39, 46, 51, 59, 61, 68, 80, 88, 102, 103, 104, 158, 197, 217, 222, 226, 236, 237, 248, 251, 253, 257, 268, 270, 272, 275, 297], "region1": 270, "region_num": 229, "regist": [0, 236], "register_ncbi_t": [27, 75, 76], "registri": 123, "regraft": 182, "regress": [5, 24, 120], "regul": [2, 3, 104, 260], "regular": [0, 3, 4, 6, 11, 17, 20, 79, 80, 99, 104, 143, 169, 182, 183, 217], "regularli": [1, 19], "regulatori": [8, 296], "rehead": 270, "reheader_cmd": 270, "reinhardt": 0, "reinsch": 2, "reinstal": 7, "reinvent": 178, "reject": 148, "rel": [0, 2, 4, 7, 12, 13, 15, 23, 24, 30, 31, 36, 104, 132, 137, 152, 169, 182, 193, 195, 237, 261, 265, 278, 283], "rel_scor": 11, "relat": [1, 3, 4, 5, 8, 10, 11, 12, 13, 20, 21, 22, 23, 28, 69, 73, 83, 93, 99, 111, 115, 117, 119, 146, 154, 169, 176, 197, 209, 251, 260, 270, 288, 301, 303, 305], "relationship": [0, 99, 117, 197, 198, 214], "relative_entropi": [11, 27, 283], "relax": [12, 17, 56, 65, 129, 182, 186, 241], "relaxedphylipiter": [27, 56, 65], "relaxedphylipwrit": [27, 56, 65], "reldat": 7, "releas": [0, 3, 5, 8, 9, 11, 12, 14, 17, 19, 22, 23, 25, 27, 67, 69, 86, 87, 88, 90, 92, 105, 117, 137, 149, 172, 209, 210, 211, 212, 213, 214, 234, 252, 272, 297, 303], "release_d": [15, 172, 174], "relev": [0, 7, 9, 10, 11, 15, 18, 21, 22, 24, 83, 117, 132, 158, 169, 214, 238, 260, 273, 298], "reli": [0, 15, 17], "reliabl": [0, 15, 104, 251, 275], "relink": [17, 130, 183], "reload": [23, 217, 238], "remain": [3, 4, 17, 20, 23, 30, 32, 68, 107, 132, 169, 183, 217, 236, 238, 250, 265, 298], "remaind": 104, "remark": [15, 25, 93], "rememb": [3, 6, 7, 9, 12, 15, 18, 20, 22, 23, 30, 66, 237], "remmert": 32, "remot": [1, 2, 3, 7, 68, 69, 83, 218, 274], "remov": [3, 6, 9, 12, 13, 15, 18, 21, 22, 23, 24, 27, 30, 32, 65, 67, 69, 80, 85, 91, 94, 99, 104, 117, 129, 130, 135, 138, 139, 148, 155, 158, 169, 170, 173, 177, 179, 180, 182, 190, 201, 204, 209, 217, 221, 230, 236, 239, 241, 244, 248, 250, 251, 253, 261, 264, 270, 285, 301, 303, 305], "remove_compon": [115, 117], "remove_edg": [178, 179, 180], "remove_entri": [115, 117], "remove_graph": [115, 117], "remove_loci_by_nam": [201, 204], "remove_loci_by_posit": [201, 204], "remove_locus_by_nam": [18, 200, 201, 204], "remove_locus_by_posit": [18, 200, 201, 204], "remove_nod": [178, 179, 180], "remove_popul": [18, 200, 201, 204], "remove_react": [27, 115, 117, 177], "remove_rel": [115, 117], "remove_succ": [128, 130], "removeprefix": [27, 236], "removesuffix": [27, 236], "renam": [3, 15, 20, 137], "render": [8, 15, 158, 183], "renderpm": [99, 104], "renumb": 104, "renumber_track": [98, 104], "reorder": [4, 13, 30, 32], "rep": [0, 27, 32, 79, 80, 177, 221, 229], "rep_record": 31, "repair": 10, "repair_gen": 10, "repair_pathwai": 10, "repeat": [0, 3, 4, 7, 8, 12, 20, 23, 24, 30, 38, 51, 53, 56, 68, 69, 80, 84, 152, 209, 221, 237, 246, 251, 268, 270, 272], "repeat_9606": 68, "repeat_unit": 53, "repeated_tag": 84, "repeatedli": [7, 11, 209], "repetit": [9, 19, 53, 73, 88, 203, 251, 272], "replac": [0, 3, 4, 5, 7, 10, 11, 13, 15, 22, 23, 27, 30, 31, 32, 60, 63, 65, 69, 80, 83, 93, 126, 129, 135, 157, 218, 236, 238, 251, 258, 260, 264, 270, 278, 304], "replace_entri": [27, 124, 126], "replacement_dictionari": [30, 31], "repli": 7, "replic": [80, 182, 186], "repmatch": [0, 30, 38, 51, 221], "report": [0, 3, 11, 12, 14, 22, 30, 32, 38, 42, 51, 71, 80, 123, 126, 130, 168, 169, 182, 218, 222, 226, 264, 268, 270, 272, 297], "report_": [27, 133, 168], "report_fil": 0, "reportdict": 168, "reportlab": [8, 24, 98, 99, 100, 102, 103, 104, 105], "repositori": [7, 24, 25, 27, 227], "repr": [0, 19, 23, 54, 68, 169, 183, 260], "repres": [0, 3, 6, 7, 8, 11, 12, 13, 15, 17, 19, 20, 21, 22, 25, 30, 31, 33, 43, 45, 61, 67, 68, 73, 76, 81, 82, 83, 84, 89, 99, 100, 102, 104, 108, 117, 122, 127, 129, 130, 131, 132, 135, 139, 140, 144, 148, 155, 156, 158, 160, 169, 176, 177, 183, 197, 199, 209, 210, 211, 212, 213, 214, 215, 217, 222, 236, 237, 238, 240, 247, 253, 256, 260, 264, 272, 275, 278, 283, 287, 288, 294, 299, 303], "represent": [0, 17, 20, 21, 30, 36, 54, 61, 67, 68, 76, 84, 86, 90, 92, 93, 95, 99, 102, 104, 105, 108, 112, 113, 114, 117, 121, 150, 154, 177, 179, 180, 183, 197, 201, 204, 207, 209, 222, 237, 247, 260, 283, 286, 287, 288, 293, 295, 296, 297, 299], "reproduc": [23, 169, 182], "republish": 123, "reqflag": 270, "request": [0, 3, 4, 6, 7, 8, 10, 11, 15, 25, 32, 68, 69, 83, 90, 104, 149, 177, 217, 236, 257, 260, 274, 278], "requir": [0, 3, 4, 6, 7, 8, 11, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 31, 32, 36, 56, 65, 67, 69, 72, 80, 83, 99, 104, 109, 119, 122, 158, 167, 169, 177, 182, 183, 185, 193, 195, 197, 217, 236, 237, 238, 241, 246, 252, 253, 260, 261, 270, 274, 278, 280, 283, 288, 290, 297], "require_multipl": 31, "reroot": [17, 183, 197], "rerun": 23, "res10": 15, "res152": [140, 156], "res157": 140, "res_": 168, "res_id": [134, 137], "res_list": 15, "resampl": [12, 80, 182], "resav": 4, "rescal": [107, 182], "rescu": [3, 20, 270], "resdict": 126, "research": [2, 7, 9, 15, 19, 32, 238, 250, 251, 253, 261, 283], "resembl": [11, 16], "reserv": [0, 7, 36, 207], "reset": [0, 3, 11, 13, 68, 71, 108, 197], "resetatom": 169, "resetloc": 169, "reshap": [13, 169], "resid": [137, 214], "residu": [12, 13, 14, 20, 21, 27, 31, 32, 68, 70, 71, 80, 93, 108, 125, 126, 133, 134, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 146, 148, 151, 152, 153, 154, 156, 157, 158, 159, 160, 161, 162, 167, 168, 169, 170, 172, 173, 209, 210, 212, 214, 221, 229, 248, 265, 272, 297], "residue1": 15, "residue2": 15, "residue_count_nam": [12, 31], "residue_d": 126, "residue_depth": [15, 27, 133, 156], "residue_dict": [124, 126], "residue_frequ": [12, 13], "residue_id": [15, 134], "residue_list": 15, "residue_typ": 93, "residuedepth": [15, 27, 133], "residuenumb": [30, 32], "resiz": 32, "resnam": [15, 140, 155, 162, 169], "resnamendx": [15, 169], "resolut": [15, 104, 157, 172, 174], "resolv": [25, 129, 185], "reson": 158, "resort": 3, "resourc": [3, 7, 9, 10, 85, 170, 197, 198, 238, 250], "respect": [0, 4, 11, 12, 13, 15, 17, 20, 21, 22, 30, 32, 45, 68, 83, 92, 122, 166, 182, 183, 209, 217, 238, 264, 265, 270, 290], "respiratori": 272, "respo": 169, "respons": [7, 104, 280, 303], "resseq": 162, "rest": [8, 10, 17, 20, 23, 27, 63, 94, 111, 128, 129, 274, 278], "restart": [69, 182], "restor": [15, 169, 217, 297], "restr_expr": [7, 275], "restrict": [6, 7, 8, 11, 15, 21, 27, 30, 65, 69, 108, 117, 119, 132, 169, 197, 217, 251, 260, 278], "restriction_batch": 207, "restriction_dictionari": [27, 206], "restrictionbatch": 207, "restructur": 21, "result": [0, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 34, 51, 59, 61, 68, 69, 71, 73, 80, 83, 84, 88, 89, 108, 119, 122, 127, 132, 157, 168, 169, 177, 182, 183, 186, 193, 195, 196, 202, 206, 207, 209, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 230, 232, 233, 238, 239, 247, 253, 267, 270, 274, 276, 277, 280, 289, 290, 291, 292, 297], "result_handl": 3, "result_iter": 25, "result_stream": 3, "resultdict": [15, 169], "results2": 7, "results_fil": [68, 70, 193, 195, 196], "retain": [3, 4, 6, 83, 169, 183, 270], "retmax": [7, 83], "retmod": [7, 9, 23, 83], "retrac": 4, "retract": 123, "retre": [30, 32], "retri": 83, "retriev": [3, 6, 11, 16, 20, 23, 45, 71, 83, 102, 104, 119, 149, 217, 270, 276, 288, 292, 301, 302, 303, 305], "retrieve_assembly_fil": [133, 149], "retrieve_pdb_fil": [15, 133, 149], "retstart": 7, "retsult": 81, "rettyp": [7, 23, 83], "return": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 59, 60, 61, 64, 65, 66, 67, 68, 70, 71, 73, 74, 76, 80, 83, 84, 85, 86, 89, 90, 91, 92, 93, 94, 95, 96, 97, 99, 100, 102, 104, 105, 107, 108, 109, 112, 113, 114, 116, 117, 119, 120, 121, 122, 125, 126, 127, 129, 130, 131, 132, 134, 135, 136, 137, 139, 140, 141, 142, 143, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 159, 160, 161, 162, 164, 165, 166, 168, 169, 170, 171, 173, 174, 175, 176, 177, 179, 180, 182, 183, 185, 188, 190, 193, 195, 196, 197, 198, 199, 201, 202, 203, 204, 207, 209, 210, 214, 217, 219, 220, 221, 223, 224, 225, 226, 230, 231, 232, 236, 237, 238, 239, 240, 241, 242, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 267, 269, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 286, 287, 288, 289, 290, 291, 292, 293, 295, 296, 297, 298, 299, 300, 303, 304], "return_r": 294, "return_raw_com": 258, "returncod": [12, 67], "returnlin": 125, "reus": [3, 6, 23, 71, 253], "reusabl": 19, "reused_seq": 71, "reuter": 2, "rev": [176, 264], "rev_align": 30, "rev_comp": 23, "revcomp": 11, "reveal": [2, 11, 12, 13], "revers": [3, 6, 8, 15, 17, 20, 27, 30, 68, 69, 79, 80, 104, 117, 169, 176, 177, 182, 183, 217, 236, 237, 253, 260, 270, 283, 290], "reverse_compl": [0, 6, 8, 11, 13, 19, 21, 22, 23, 27, 30, 236, 260, 283, 290], "reverse_complement_rna": [27, 236], "reverse_gc": 81, "reverse_length": 81, "reverse_seq": 81, "reverse_start": 81, "reverse_tm": 81, "reverseinput": [79, 80], "review": [2, 7, 24, 25, 276], "revis": [6, 123], "revolut": 100, "revolv": 100, "reward": [68, 69], "rewind": [27, 30, 45], "rewound": [36, 44, 45], "rewrit": 218, "rewriteformat": [79, 80], "rewritten": [4, 69, 73], "rf": [53, 66, 123], "rf_tabl": 281, "rfc": 7, "rfeifksnlg": 0, "rfind": [22, 27, 236], "rformat": [79, 80], "rfrifsesl": 0, "rg": [0, 270], "rgb": [0, 17, 100, 104, 105, 117, 183], "rgb2003": 124, "rgfile": 270, "rgifmsdtmvvngsggvpaflfsgstlssi": 6, "rgipp": 56, "rgippeeq": 0, "rh": [202, 203], "rhemac10": 0, "rhemac3": 22, "rhemac8": 0, "rhemac8torhemac10": 0, "rho": [30, 32], "rhodopsin": 250, "rhpanel": 275, "ribbon": 158, "ribosom": [13, 15, 23, 272], "ric": [15, 169], "ric0": 169, "rice": [2, 251], "rice2000": [0, 2], "rich": [12, 169, 260], "richard": [2, 16, 27, 52, 298, 299, 300], "richardson1981": 169, "richli": [21, 56], "rid": [3, 12, 68, 69, 218], "ride": [104, 207], "ridicul": 7, "right": [0, 3, 4, 5, 6, 8, 11, 12, 13, 15, 19, 21, 22, 30, 68, 71, 73, 99, 104, 135, 138, 139, 175, 216, 237, 238, 260, 269], "right_extend_gap_scor": 13, "right_gap_scor": 13, "right_multipli": [133, 176], "right_open_gap_scor": 13, "rightarrow": 22, "rightcount": 0, "rightstatu": 0, "rikyilrlscartlarkhkstvrtfmrrlgsglleeffmee": 7, "rin": 123, "rindex": [22, 27, 236], "ring": 158, "rise": 11, "risk": [3, 15, 119, 169, 274], "risler": 199, "rkglpyrlgi": 0, "rkglpyrlginrfsdmswe": 0, "rkglpyrlginrfsdmsweefqatrl": 0, "rl": [0, 11, 53, 250, 295], "rl1_ecoli": 272, "rll": 13, "rlqtfasnwr": 0, "rlt": 0, "rm": [0, 15, 53, 216], "rmdup": 270, "rmdup_cmd": 270, "rmflsf": [13, 14], "rmsd": [15, 140, 163, 166, 175, 216], "rn": [0, 11, 53, 123, 238, 278, 295], "rn3": 0, "rn5": 22, "rn6": 0, "rn6torn7": 0, "rn7": 0, "rna": [0, 13, 22, 23, 30, 32, 53, 56, 76, 93, 104, 154, 197, 236, 237, 238, 250, 252, 260, 261, 264], "rna1": [13, 260], "rna2": [13, 260], "rna3": 13, "rna_de1": 264, "rna_el": 53, "rna_ligand_adocbl": 53, "rna_ligand_aqcbl": 53, "rna_ligand_fmn": 53, "rna_ligand_guanidinium": 53, "rna_ligand_preq1": 53, "rna_ligand_sam": 53, "rna_ligand_thf_1": 53, "rna_ligand_thf_2": 53, "rna_ligand_tpp": 53, "rna_motif_k_turn": 53, "rna_nn1": 264, "rna_nn2": 264, "rna_nn3": 264, "rna_structural_el": 53, "rnaseq": 0, "rnext": [52, 169], "roa1_human": 303, "rob": [2, 133], "robert": 32, "robertson": [202, 203], "robin": 2, "robust": 4, "roch": [6, 21, 238, 251, 253], "rodger": 149, "rodrigu": [133, 166], "rof": 123, "role": 114, "roll": [157, 303], "rollback": [301, 303], "room": 99, "root": [13, 17, 32, 79, 80, 84, 132, 175, 180, 181, 183, 184, 185, 187, 188, 189, 190, 197, 198, 199, 209, 216, 252, 287, 303], "root1": [30, 32], "root2": [30, 32], "root_at_midpoint": [17, 181, 183], "root_with_outgroup": [17, 128, 132, 181, 183], "rooted": 17, "rose": 265, "roseman": 265, "rosemari": 69, "rosetta": 105, "rost": 137, "rot": [15, 135, 139, 216], "rotat": [8, 15, 104, 135, 139, 152, 158, 163, 166, 169, 175, 176, 216], "rotaxi": [15, 27, 133, 176], "rotaxis2m": [27, 133, 176], "rotein": 80, "rotert": 2, "rother": [15, 133, 174], "rotmat": [15, 27, 133, 135, 139, 176], "rotran": 15, "rough": 264, "roughli": [11, 15, 16, 157], "round": [3, 7, 15, 27, 32, 68, 71, 119, 157, 168, 182, 251, 253, 260], "roundoff": 24, "roundrectangl": 117, "rout": 117, "routin": [4, 15, 73, 158, 169, 287, 293], "row": [0, 3, 4, 7, 12, 13, 16, 20, 22, 30, 56, 62, 66, 68, 73, 83, 126, 176, 199, 221, 229, 238, 277, 279, 280, 283, 299, 303], "rpf": 123, "rpi": 123, "rpl16": [7, 23], "rpm": 5, "rprev": 169, "rpsblast": [3, 68, 69, 70], "rpsblastcommandlin": 69, "rpsdb": [68, 69], "rpsppg": 0, "rpsppgprrptgrpccsaaprrpqat": 0, "rpsppgprrptgrpccsaaprrpqatggwktcsgtc": 0, "rpsppgprrptgrpccsaaprrpqatggwktcsgtcttststrhrgrsgw": 0, "rpssm": 11, "rpstblastn": 69, "rpvsvafqvi": 0, "rpwm": 11, "rrgcsaqnpk": 0, "rrkehvskkrrpqkrprrrrffhrlrppd": 6, "rrna": [2, 19, 23], "rrpffpfhsp": 250, "rrplfswlap": 250, "rrrctaqnpk": 0, "rsa": 145, "rsa_data": 145, "rslt": 169, "rspfdypqyi": 250, "rsplit": [27, 236], "rspyeypqyi": 250, "rst": 9, "rst301": 11, "rstrip": [6, 10, 27, 230, 236, 278], "rsync": 23, "rt": [0, 1, 4, 11, 23, 25, 27, 53, 240, 268, 269, 278, 295], "rtllmagvshdlrtpltrirlatemmseqd": 260, "rtoe": 68, "rtol": 168, "rtrev": 182, "rtype": 149, "ru": 88, "ruan": 2, "rule": [0, 4, 7, 10, 11, 88, 122, 127, 132, 186, 251, 264, 280, 283], "run": [0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 23, 25, 27, 32, 55, 67, 68, 69, 73, 80, 81, 83, 133, 137, 145, 153, 169, 175, 182, 192, 193, 195, 196, 216, 217, 218, 237, 238, 247, 251, 270, 274, 289, 291, 292], "run_id": [181, 182], "run_naccess": [27, 133, 145], "run_psea": [27, 133, 153], "run_test": 24, "rundat": 0, "runner": 24, "runtim": [17, 136, 144, 160, 169], "runtimeerror": [7, 83], "runx1": 11, "ruplei": 157, "rusa": 8, "ruzzo": [2, 4], "rw": 149, "rx": [11, 90, 295], "rxpected_frequ": 13, "rxxxxx": 118, "s0022": 2, "s0108767305015266": 175, "s0168": 2, "s0q9zdocveec": 23, "s1": [0, 13, 177, 207], "s10482": 2, "s12859": 2, "s1jjn5": 238, "s2": [13, 25, 177], "s27231": 250, "sa": [53, 66, 270], "sa_con": 53, "saaqtllpdsegaidghlrevgltfhllkdvpgliskniekslveafqplgisdwnslfw": 23, "sab_sab1c": 244, "sabzaa4v2ele9": 238, "sacc": 218, "sacc_ver": 218, "sadreyev": 74, "safe": [3, 15, 17, 169, 183, 238, 278], "safenam": [27, 128, 129], "safer": [7, 83], "sai": [6, 8, 12, 15, 21, 22, 24, 25, 31, 65, 217, 251, 270], "sai_fil": [268, 270], "sai_file1": [268, 270], "sai_file2": [268, 270], "saira": 2, "sakai": 25, "sake": [6, 11], "salc": 264, "saldanha": [2, 4], "saldanha2004": [2, 4], "sallgi": 218, "sallseqid": 218, "salmon": [17, 183], "salt": [80, 264], "salt_correct": [27, 261, 264], "saltconc": [79, 80], "saltcorr": 264, "sam": [27, 30, 33, 53, 55, 270, 278], "sam1": [0, 278], "sam_fil": [268, 270], "sam_or_bam_fil": 270, "sambam": 278, "same": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 30, 31, 32, 43, 45, 54, 56, 65, 66, 68, 69, 71, 73, 84, 90, 94, 99, 102, 104, 119, 120, 126, 127, 129, 132, 135, 155, 169, 182, 183, 197, 199, 202, 209, 214, 216, 217, 221, 222, 226, 234, 237, 238, 241, 244, 248, 251, 260, 261, 264, 265, 267, 270, 277, 278, 280, 282, 283, 287, 288, 290, 297, 299], "samipf": [241, 260], "samp": 270, "sampe_cmd": 270, "sampl": [0, 4, 13, 73, 80, 90, 100, 104, 112, 113, 114, 169, 202, 251, 270, 280, 299], "sams": 270, "samse_cmd": 270, "samtool": [2, 23, 270, 278], "samtools_cat_cmd": 270, "samtools_faidx_cmd": 270, "samtools_idxstats_cmd": 270, "samtools_index_cmd": 270, "samtools_mpileup_cmd": 270, "samtools_phase_cmd": 270, "samtools_sort_cmd": 270, "samtools_targetcut_cmd": 270, "samtools_view_cmd": 270, "samtoolscalmdcommandlin": [268, 270], "samtoolscatcommandlin": [268, 270], "samtoolsfaidxcommandlin": [268, 270], "samtoolsfixmatecommandlin": [268, 270], "samtoolsidxstatscommandlin": [268, 270], "samtoolsindexcommandlin": [268, 270], "samtoolsmergecommandlin": [268, 270], "samtoolsmpileupcommandlin": [268, 270], "samtoolsphasecommandlin": [268, 270], "samtoolsreheadercommandlin": [268, 270], "samtoolsrmdupcommandlin": [268, 270], "samtoolssortcommandlin": [268, 270], "samtoolstargetcutcommandlin": [268, 270], "samtoolsversion0xsortcommandlin": [268, 270], "samtoolsversion1xsortcommandlin": [268, 270], "samtoolsviewcommandlin": [268, 270], "san": 83, "sanchez": 263, "sander": 137, "sanger": [2, 6, 7, 8, 12, 52, 104, 238, 251, 253], "sanger_fak": 251, "saniti": 15, "sanitis": 65, "sanitize_nam": [27, 56, 65], "sanjeev": 2, "sankoff": 199, "sanner": [15, 156], "santalucia": 264, "sapien": [3, 20, 68, 90, 93], "saqai": 206, "saqi": 7, "sas_con": 53, "sasa": [27, 133, 145], "sasano": 25, "satisfi": [4, 11, 169, 237], "sativu": [21, 23], "sato": 25, "satoru": 2, "sav": 13, "save": [6, 7, 10, 11, 12, 13, 15, 17, 19, 20, 23, 25, 27, 32, 69, 71, 73, 80, 84, 99, 121, 133, 148, 149, 169, 170, 171, 173, 182, 183, 222, 238, 249, 251, 260, 270, 283, 298], "save_ascii_pssm": 69, "save_dtd_fil": [83, 84], "save_each_pssm": [68, 69], "save_pssm": 69, "save_pssm_after_last_round": [68, 69], "save_xsd_fil": [83, 84], "savefig": 6, "savefil": 149, "saw": [6, 17, 20], "saxel": 2, "sb": 123, "sbc": [53, 66], "sbjct": [3, 71], "sbjct_end": 71, "sbjct_start": 71, "sc": [3, 15, 68, 169], "sc_match": [3, 71], "sc_mismatch": [3, 71], "sca": 169, "scad": [15, 169], "scadio": [15, 27, 133, 169], "scaffold": [0, 36], "scaffold_114895": 0, "scaffold_288249": 0, "scaffold_334": 0, "scaffold_75566": 0, "scalabl": 32, "scalar": 176, "scale": [2, 4, 7, 8, 10, 15, 32, 99, 102, 104, 107, 109, 122, 127, 158, 169, 176, 182, 202, 203, 222, 251, 263, 265, 270], "scale_color": 104, "scale_colour": 104, "scale_font": 104, "scale_fontangl": 104, "scale_fonts": 104, "scale_format": 104, "scale_largetick": 104, "scale_largetick_interv": 104, "scale_largetick_label": 104, "scale_num": [8, 99], "scale_segment_valu": [98, 102], "scale_smalltick": 104, "scale_smalltick_interv": 104, "scale_smalltick_label": 104, "scale_tick": 104, "scale_valu": 102, "scale_width": 283, "scalebranch": [30, 32], "scaleddpalgorithm": [27, 106, 107, 109], "scan": [6, 11, 23, 27, 85, 89, 214, 238, 253, 270, 296], "scanner": [27, 92], "scanprosit": [25, 27, 85], "scanprosite_doc": 89, "scatter": [4, 6, 101], "scatterplot": 4, "scc": [209, 210, 211], "sccs1": 209, "sccs2": 209, "scer_cad1": 0, "scer_s288c": 0, "scertf": [11, 283], "sch": 3, "scheer": 2, "schema": [3, 6, 9, 11, 84, 185, 303], "schemahandl": [83, 84], "scheme": [0, 6, 8, 13, 15, 30, 32, 102, 104, 137, 229, 237, 251, 278], "scheme_color": [98, 104], "schi": 206, "schiestl": 7, "schildkraut": 264, "schmeiser": [2, 4], "schmidt": [32, 65], "schmitt": [238, 252], "schneider": [2, 13, 199], "schneider1986": [2, 11], "schneider2005": [2, 13], "schutz": 121, "schwartz": 2, "sch\u00e4ffer": [3, 68], "sci": [53, 83, 264], "scienc": [2, 32, 253], "scientif": [9, 23, 197, 252], "scientific_nam": [181, 183, 197, 198], "scientificnam": 7, "scikit": [120, 282], "scinam": 3, "scipi": [16, 299, 300], "sco": [17, 182], "scop": [0, 7, 9, 15, 19, 27, 123], "scope": [11, 16, 217], "scopseq": 209, "score": [0, 2, 3, 8, 14, 20, 21, 23, 25, 27, 30, 31, 32, 35, 36, 37, 39, 42, 46, 51, 53, 68, 69, 71, 80, 83, 121, 182, 199, 217, 218, 221, 222, 226, 229, 234, 238, 240, 249, 251, 253, 260, 265, 270, 275, 283, 290, 294, 297, 302], "score_dict": 297, "score_onli": [14, 297], "scorecon": 53, "scorecons_70": 53, "scorecons_80": 53, "scorecons_90": 53, "scoredistribut": [27, 283, 294], "scorefil": [30, 32], "scorer": [27, 181, 199], "scoreread1": 270, "scoreread2": 270, "scoring_matrix": 13, "scount": [7, 275], "scratch": [0, 12, 17, 20], "screen": [12, 19, 30, 280], "scripp": [15, 156, 263], "script": [0, 3, 5, 6, 7, 8, 9, 17, 19, 23, 24, 25, 68, 76, 85, 141, 158, 209, 253], "scriptcentr": 5, "scrub": 303, "sd": 169, "sd_rslt": 169, "sdfgatfmtl": 250, "sdvpersipi": 250, "se": [0, 53, 66, 202], "sea": [6, 30, 153, 197], "seamless": 217, "sean": 2, "search": [0, 2, 3, 6, 8, 9, 12, 15, 19, 22, 26, 27, 30, 36, 37, 53, 56, 61, 68, 69, 70, 71, 80, 83, 89, 119, 133, 146, 180, 181, 182, 183, 186, 199, 207, 209, 217, 218, 221, 226, 229, 234, 260, 261, 270, 274, 276, 283, 289, 290, 307], "search_al": [133, 146], "search_author": 7, "search_count": [27, 274], "search_dict": 217, "search_idx": 217, "search_it": [27, 274], "search_result": 7, "search_target": 3, "search_taxon": [128, 132], "searchabl": 7, "searched_hmm": 0, "searcher": 199, "searchindex": [219, 220, 221, 226, 232], "searchio": [3, 27, 91], "searchsp": [68, 69], "searchsp_eff": [68, 70], "sebastian": 262, "sec_struc": 265, "second": [0, 2, 3, 4, 6, 7, 9, 11, 12, 13, 14, 15, 17, 18, 20, 22, 23, 24, 25, 30, 31, 32, 73, 80, 83, 117, 119, 169, 172, 181, 182, 197, 205, 207, 222, 241, 250, 251, 256, 260, 261, 265, 269, 270, 274, 278, 297, 299], "second_lin": 1, "second_primer_seq": 82, "second_record": 23, "second_seq": 12, "secondari": [0, 2, 11, 12, 21, 30, 32, 53, 66, 90, 104, 123, 137, 140, 152, 153, 169, 172, 260, 265, 270, 272, 295], "secondary_structur": [66, 260], "secondary_structure_fract": [261, 265], "secondary_structure_typ": 172, "secondli": [3, 6, 8, 10, 12, 21, 251], "secstrout": [30, 32], "sect3": 248, "section": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 30, 62, 71, 94, 109, 158, 169, 236, 237, 238, 245, 255], "section_dict": 6, "secundu": 56, "see": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 35, 36, 37, 38, 39, 46, 49, 50, 51, 52, 53, 56, 59, 61, 64, 65, 66, 67, 68, 69, 73, 83, 84, 85, 86, 87, 88, 89, 90, 92, 94, 97, 99, 104, 108, 109, 119, 129, 135, 137, 145, 150, 152, 153, 156, 158, 164, 165, 168, 169, 170, 181, 182, 184, 185, 187, 188, 189, 190, 199, 201, 202, 204, 209, 210, 212, 214, 217, 221, 222, 226, 229, 236, 237, 238, 240, 245, 247, 248, 249, 251, 252, 253, 255, 258, 260, 261, 262, 264, 265, 269, 270, 272, 273, 274, 275, 276, 278, 283, 295, 297, 301], "seed": [0, 4, 12, 30, 32, 53, 79, 80, 181, 182, 270], "seek": [0, 27, 204, 253, 278], "seek_posit": [201, 204], "seekabl": [27, 278], "seem": [3, 5, 7, 15, 20, 22, 30, 83, 299], "seen": [20, 21, 22, 23, 56, 71], "sefgpifmtv": 250, "seg": [68, 69], "segid": [15, 155, 162], "segmask": 69, "segment": [0, 3, 13, 15, 22, 30, 32, 39, 61, 68, 93, 99, 102, 103, 155, 158, 169, 236, 238, 243, 269], "segment_nam": 102, "seguid": [27, 238, 261, 262], "seguid_dict": [23, 238], "seiya": 2, "sel": 261, "select": [0, 8, 12, 13, 17, 23, 27, 30, 31, 32, 54, 59, 100, 106, 133, 135, 138, 139, 148, 149, 158, 169, 170, 173, 182, 183, 253, 288, 294, 299, 303], "selected_align": 0, "selector": [15, 169], "selenipedium": [7, 19], "selenomethionin": [15, 154], "selex": [11, 32, 288], "self": [0, 2, 8, 11, 15, 17, 23, 24, 30, 31, 36, 45, 54, 67, 68, 73, 80, 104, 125, 126, 132, 169, 176, 177, 183, 185, 197, 214, 236, 260, 261, 264, 265, 275, 283, 288, 290, 297, 299], "selfcomp": 264, "semant": [15, 137], "semi": [4, 104, 129, 244, 250], "send": [67, 83, 218], "sens": [3, 8, 12, 13, 15, 21, 32, 65, 99, 150, 169, 260, 278], "sensibl": [6, 7, 8, 21], "sensibli": [104, 251], "sensit": [32, 270], "sent": [7, 67], "sep": [7, 11, 15, 149, 152, 169, 236], "separ": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 20, 23, 32, 36, 65, 69, 80, 104, 108, 158, 169, 182, 183, 207, 210, 211, 212, 217, 218, 221, 226, 230, 237, 238, 250, 251, 256, 274, 297], "septemb": 7, "seq": [0, 3, 6, 7, 8, 9, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 27, 30, 31, 36, 37, 38, 53, 59, 60, 66, 68, 80, 88, 89, 91, 92, 94, 108, 109, 154, 169, 197, 206, 207, 209, 237, 238, 240, 241, 246, 247, 249, 251, 253, 256, 260, 261, 262, 263, 264, 265, 267, 279, 280, 281, 283, 288, 291, 297, 301, 302, 303, 304], "seq0": 12, "seq1": [0, 9, 12, 13, 14, 22, 27, 30, 261, 279], "seq11111": 23, "seq2": [0, 9, 12, 13, 14, 22, 30, 279], "seq222": 23, "seq3": [12, 27, 30, 261], "seq3333": 23, "seq4": [12, 23, 30], "seq5": 12, "seq555": 23, "seq6": [12, 23], "seq_con": [0, 12, 53], "seq_count": [12, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66], "seq_fil": 32, "seq_len": [6, 20, 218, 221, 226, 229], "seq_lett": 108, "seq_on": 6, "seq_rec": 303, "seq_record": [19, 23], "seq_stat": 108, "seq_two": 6, "seq_typ": [30, 32, 261], "seqa": [0, 14, 27, 30, 68, 297], "seqadv": 248, "seqal": [79, 80], "seqb": [0, 14, 27, 30, 68, 297], "seqboot": [12, 56, 80, 182], "seqc": [0, 30, 68], "seqfeatur": [3, 7, 27, 68, 92, 94, 99, 104, 197, 260, 272], "seqid": [3, 7, 68, 69, 303], "seqidlist": [68, 69], "seqinfo": [25, 272], "seqio": [0, 1, 3, 6, 7, 8, 9, 12, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 27, 40, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 80, 91, 92, 94, 217, 236, 237, 260, 271, 274, 276, 278, 279, 303], "seqmap": [27, 209, 214], "seqmapindex": [27, 209, 214], "seqmatchal": 80, "seqmatchallcommandlin": [27, 79, 80], "seqno": [30, 32], "seqno_rang": [30, 32], "seqnum": 214, "seqr": [214, 238, 248], "seqrec": 152, "seqrecord": [0, 3, 6, 7, 8, 9, 12, 13, 15, 19, 20, 22, 25, 27, 30, 36, 37, 38, 49, 61, 64, 66, 68, 92, 94, 152, 169, 197, 217, 222, 236, 238, 239, 240, 241, 242, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 261, 271, 279, 280, 281, 302, 303, 305], "seqret": [80, 250], "seqretcommandlin": [27, 79, 80], "seqtyp": [0, 7, 17, 30, 32, 79, 80, 275], "sequenc": [1, 2, 3, 8, 9, 10, 14, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 76, 79, 80, 81, 83, 86, 89, 93, 94, 104, 107, 108, 109, 110, 121, 129, 136, 138, 139, 149, 152, 154, 161, 162, 169, 172, 181, 182, 186, 193, 196, 197, 198, 199, 206, 207, 209, 213, 214, 215, 218, 221, 222, 226, 229, 234, 236, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 259, 260, 261, 262, 263, 264, 265, 267, 272, 274, 275, 276, 278, 279, 280, 281, 283, 287, 289, 290, 291, 295, 297, 298, 301, 303, 307], "sequence1": 13, "sequence1entri": [0, 62], "sequence1fil": [0, 62], "sequence1format": [0, 62], "sequence2": 13, "sequence2entri": [0, 62], "sequence2fil": [0, 62], "sequence2format": [0, 62], "sequence3entri": [0, 62], "sequence3fil": [0, 62], "sequence3format": [0, 62], "sequence_0": [0, 11, 291], "sequence_1": [0, 11, 291], "sequence_15": 11, "sequence_2": [0, 11, 291], "sequence_3": [11, 291], "sequence_4": [11, 291], "sequence_5": [11, 291], "sequence_6": [11, 291], "sequence_ac": [25, 89], "sequence_db": 89, "sequence_format": [92, 93], "sequence_head": [92, 94], "sequence_id": [11, 89, 291], "sequence_ind": [238, 245], "sequence_index": 172, "sequence_length": [25, 272], "sequence_nam": [11, 291], "sequence_numb": [12, 31], "sequence_rel": [181, 197, 198], "sequence_upd": [25, 272], "sequence_vers": [21, 23], "sequencea": [14, 297], "sequenceb": [14, 297], "sequencedataabstractbaseclass": [27, 236], "sequencefilenam": 182, "sequenceid": 69, "sequenceiter": [27, 238, 239, 241, 242, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 259], "sequencelin": [27, 275], "sequencerel": [27, 181, 197], "sequences1": 0, "sequences2": 0, "sequencewrit": [27, 238, 241, 246, 247, 249, 250, 251, 252, 253, 256, 259], "sequenti": [0, 23, 32, 50, 56, 65, 169, 181, 182, 238, 241, 246, 250, 278], "sequentialalignmentwrit": [27, 56, 57, 60, 61, 62, 65, 66], "sequentialphylipiter": [27, 56, 65], "sequentialphylipwrit": [27, 56, 65], "sequtil": [0, 6, 8, 22, 23, 27, 30, 238], "seqxml": [238, 252], "seqxmlio": [27, 238], "seqxmliter": [27, 238, 252], "seqxmlwrit": [27, 238, 252], "ser": [13, 15, 155], "seri": [0, 7, 13, 16, 35, 36, 39, 46, 51, 52, 55, 61, 93, 186], "serial": [135, 136, 158, 169, 172, 183, 185, 191, 198, 259, 299], "serial_num": [144, 162], "serial_numb": [135, 152, 162, 172], "serialclon": 238, "serin": 14, "serpina3": 7, "serv": [214, 278], "server": [0, 3, 7, 15, 68, 70, 149, 152, 169, 283, 288, 303, 305], "servic": [3, 9, 18, 68, 70, 119, 221, 274, 283], "session": [7, 217, 306], "session_cooki": 7, "set": [0, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 23, 24, 25, 27, 29, 30, 31, 32, 54, 56, 67, 68, 69, 70, 71, 72, 73, 80, 81, 83, 84, 92, 94, 99, 101, 102, 103, 104, 107, 108, 117, 119, 120, 122, 127, 128, 129, 130, 132, 133, 135, 139, 145, 149, 151, 152, 153, 155, 158, 162, 163, 166, 168, 169, 170, 172, 175, 177, 179, 180, 182, 183, 186, 195, 197, 199, 204, 209, 216, 217, 218, 221, 222, 229, 236, 237, 238, 247, 252, 261, 264, 265, 270, 272, 274, 277, 281, 282, 286, 288, 297, 298, 303, 304], "set_accuracy_95": [27, 133, 169], "set_all_featur": [98, 104], "set_all_track": [98, 104], "set_altloc": [133, 135], "set_angl": [15, 133, 169], "set_anis": [133, 135, 162], "set_atom": [15, 133, 163, 175], "set_atom_info": [171, 172], "set_bfactor": [133, 135], "set_bio_assembly_tran": [171, 172], "set_chain_info": [171, 172], "set_charg": [133, 135], "set_color": [98, 104], "set_colour": [98, 104], "set_coord": [15, 133, 135], "set_data": [98, 104, 128, 130], "set_dict": [15, 133, 170], "set_emission_pseudocount": [106, 108], "set_emission_scor": [106, 108], "set_entity_info": [171, 172], "set_equal_prob": [106, 108], "set_featur": [98, 104], "set_flex": [133, 158, 169], "set_group_bond": [171, 172], "set_group_info": [171, 172], "set_handl": [92, 94], "set_hbond": [133, 158, 169], "set_head": [133, 162], "set_header_info": [171, 172], "set_hit_access": [68, 71], "set_hit_def": [68, 71], "set_hit_id": [68, 71], "set_hit_len": [68, 71], "set_homog_trans_mtx": [27, 133, 176], "set_id": [104, 128, 130], "set_initial_prob": [106, 108], "set_inter_group_bond": [171, 172], "set_length": [15, 133, 169], "set_line_count": [133, 162], "set_model_info": [171, 172], "set_occup": [133, 135], "set_opt": 17, "set_par": [133, 135, 139], "set_paramet": [27, 67], "set_prev": [128, 130], "set_printopt": [0, 30, 216], "set_radiu": [133, 135], "set_random_emission_prob": [106, 108], "set_random_initial_prob": [106, 108], "set_random_prob": [106, 108], "set_random_transition_prob": [106, 108], "set_refer": [133, 166], "set_scal": [98, 102], "set_serial_numb": [133, 135], "set_sigatm": [133, 135, 162], "set_siguij": [133, 135, 162], "set_structur": [15, 133, 148, 169, 170, 173], "set_subtre": [128, 132], "set_succ": [128, 130], "set_symmetri": [133, 162], "set_transition_pseudocount": [106, 108], "set_transition_scor": [106, 108], "set_x_homog_rot_mtx": [27, 133, 176], "set_xtal_info": [171, 172], "set_y_homog_rot_mtx": [27, 133, 176], "set_z_homog_rot_mtx": [27, 133, 176], "setattr": 30, "setcas": [11, 290], "setter": 169, "settl": 20, "setup": [3, 5, 24], "seven": [3, 6, 12], "seventh": [0, 154], "sever": [0, 3, 4, 6, 7, 8, 11, 12, 15, 16, 20, 21, 22, 23, 25, 42, 53, 76, 98, 136, 217, 222, 237, 238, 251, 264, 265, 274, 278, 287], "sex": [7, 90], "sexual": 7, "sf": [126, 209, 211], "sff": [238, 251, 253], "sff_extract": 253, "sffinfo": [6, 251], "sffio": [6, 27, 238], "sffiter": [27, 238, 253], "sffwriter": [27, 238, 253], "sfi21": 2, "sfm": 123, "sformat": [79, 80], "sframe": 218, "sg": 169, "sgastskt": 250, "sgc0": [22, 76], "sgc1": 22, "sgi": 218, "sgqdryttevvvnvggtmqmlggrqgggapaggnigggqpqggwgq": 260, "sgsakslrmg": 0, "sgtartklllllaalcaaggal": 13, "sgtsrtkrllllaalgaaggal": 13, "sh": 182, "shade": 8, "shaft": [8, 104], "shall": 182, "shallow": 3, "shallowest": [17, 183], "shape": [8, 12, 27, 29, 30, 53, 54, 68, 100, 117, 175, 182], "share": [0, 6, 7, 12, 15, 30, 32, 94, 132, 169, 221], "sharma": 2, "sharp": 261, "she": 0, "sheer": 6, "sheet": 265, "sheeyl": 0, "sheeylerfeifksnlgkieelnliainhkadtkfgvnkfadlssd": 0, "sheeylerfeifksnlgkieelnliainhkadtkfgvnkfadlssdefknyylnnkeaiftddlpvadylddefinsiptafdwrtrg": 0, "shell": [3, 12, 17], "shibasaka": 25, "shield": 274, "shift": [13, 21, 30, 69, 71, 222, 237, 260, 264], "shimanouchi": 149, "shimodaira": 182, "shindyalov": 166, "short": [0, 6, 8, 9, 11, 12, 14, 15, 20, 21, 22, 23, 30, 68, 69, 70, 83, 104, 132, 169, 197, 237, 249, 251, 256, 260, 265, 269, 270, 272, 295, 303], "short_list": 6, "short_queri": [68, 70], "shortcut": [15, 20, 21, 217, 237, 260], "shorten": [12, 17], "shorter": [6, 14, 17, 19, 21, 22, 23, 30, 32, 238, 270], "shortest": 4, "shorthand": [15, 21, 169, 237, 260], "shortnam": [30, 32], "should": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 36, 38, 42, 43, 45, 51, 56, 59, 60, 61, 64, 66, 67, 69, 71, 72, 73, 83, 84, 92, 94, 95, 99, 101, 102, 103, 104, 107, 108, 109, 116, 120, 121, 126, 127, 148, 162, 169, 170, 173, 177, 182, 183, 197, 199, 202, 203, 204, 207, 217, 218, 221, 222, 230, 236, 237, 238, 246, 247, 248, 251, 253, 256, 258, 259, 260, 261, 264, 270, 277, 278, 280, 281, 282, 297, 298, 299, 303], "shouldn": [3, 5, 12, 16, 24, 67, 198, 305], "show": [0, 1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 67, 68, 69, 70, 72, 73, 80, 89, 99, 103, 104, 169, 182, 183, 197, 249, 251, 253, 260, 261, 278, 297], "show_compound": 105, "show_domain_hit": [68, 69], "show_end": 283, "show_errorbar": 283, "show_fineprint": 283, "show_gen": 105, "show_gi": [68, 69], "show_map": 105, "show_ortholog": 105, "show_overview": [68, 70], "show_reaction_entri": 105, "show_xaxi": 283, "show_yaxi": 283, "showalign": 0, "showalignemnt": 222, "showcigar": 0, "shown": [0, 3, 4, 6, 7, 8, 12, 13, 14, 15, 16, 17, 20, 22, 23, 24, 30, 33, 59, 66, 68, 71, 104, 143, 151, 154, 236, 237, 238, 250, 251, 253, 260, 280, 283, 297, 298, 299], "showtre": [30, 32], "showvulgar": 0, "showxml": [30, 32], "shrake": 157, "shrakeruplei": [27, 133, 157], "shtml": [226, 270], "shuffl": [4, 6, 73, 79, 80], "shuffled_rec": 6, "si": [104, 123, 161], "sibson": 2, "sibson1973": [2, 4], "sid": [209, 210, 211, 212], "side": [2, 6, 8, 12, 13, 15, 22, 23, 30, 84, 158, 183, 265], "sidechain": [15, 152, 167, 169], "siegffatlg": 250, "siever": 32, "sigatm": 15, "sigatm_arrai": [135, 162], "sigbio": 2, "sigil": 104, "sigma_i": 4, "sigma_x": 4, "sigmoid": [16, 299, 300], "sign": [5, 6, 7, 15, 52, 63, 83, 119, 169, 241, 251], "signal": [4, 16, 94, 272, 275, 299], "signatur": 234, "signature_ac": [25, 89], "signifi": 21, "signific": [7, 20, 74, 166], "significantli": [4, 14, 270], "siguij": 15, "siguij_arrai": [135, 162], "silenc": [17, 27], "silent": [18, 23, 24, 67, 152, 238, 298], "silico": 61, "silurian": 197, "silver": 183, "simeq": 11, "similar": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 19, 20, 21, 24, 32, 56, 67, 69, 71, 79, 80, 93, 97, 103, 119, 121, 158, 166, 182, 197, 209, 217, 221, 222, 226, 229, 260, 261, 265, 270, 274, 275, 290, 299], "similarli": [0, 3, 4, 7, 11, 12, 14, 15, 20, 21, 23, 25, 30, 67, 185, 217, 236, 237, 251, 256, 270], "simpl": [0, 2, 3, 4, 7, 9, 10, 11, 12, 13, 15, 17, 20, 21, 22, 23, 24, 30, 41, 51, 56, 58, 66, 67, 68, 76, 82, 104, 119, 136, 139, 154, 182, 191, 198, 203, 217, 222, 236, 237, 238, 251, 256, 260, 264, 265, 274, 278, 283, 299], "simple_chrom": 8, "simple_seq": 21, "simple_seq_r": 21, "simple_short": 62, "simplefastapars": [6, 23, 27, 238, 241], "simplefilt": 27, "simpleloc": [8, 27, 68, 237, 260, 272], "simpler": [66, 251, 274], "simplest": [11, 17], "simpli": [3, 7, 8, 11, 12, 13, 15, 17, 20, 21, 60, 68, 83, 149, 154, 183, 217, 238, 249, 260, 265, 290], "simplic": [6, 7, 15, 270], "simplifi": [11, 17, 45, 60, 69, 158, 246], "simplist": 6, "simul": [22, 182], "simulan": 13, "sinc": [1, 3, 5, 6, 7, 8, 9, 11, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 67, 84, 88, 95, 166, 182, 217, 221, 234, 236, 237, 238, 249, 251, 259, 260, 269, 270, 278, 297, 303, 305], "sincri": 153, "sinderen": 2, "singl": [0, 2, 3, 4, 6, 7, 8, 9, 11, 13, 15, 17, 18, 20, 21, 22, 23, 25, 27, 30, 31, 33, 35, 36, 39, 40, 44, 45, 46, 47, 49, 50, 51, 52, 53, 56, 57, 60, 61, 62, 65, 66, 68, 71, 73, 76, 80, 81, 82, 83, 92, 99, 102, 103, 104, 116, 119, 123, 126, 129, 130, 137, 144, 149, 158, 159, 169, 172, 176, 182, 183, 198, 201, 202, 209, 214, 215, 217, 221, 222, 226, 234, 236, 237, 240, 241, 242, 244, 245, 246, 247, 249, 250, 251, 253, 254, 255, 256, 259, 260, 261, 270, 271, 274, 275, 277, 278, 280, 283, 288, 290, 299, 303], "single_cov2": 0, "single_letter_cod": 172, "singleton": 270, "singular": [2, 3, 4, 15, 176, 216], "sink": [27, 177], "sink_interact": [27, 177], "sint": 104, "siphovirida": 2, "sister": [6, 21, 251], "site": [2, 3, 6, 7, 8, 9, 10, 14, 15, 19, 21, 23, 25, 34, 53, 68, 71, 80, 84, 88, 129, 182, 195, 206, 207, 221, 256, 260, 270, 272, 273, 274, 280, 283, 288, 295], "situ": 6, "situat": [3, 4, 5, 7, 12, 15, 23, 183], "six": [0, 3, 4, 6, 12, 15, 25, 169, 182, 261], "six_frame_transl": [27, 261], "sixmerpair": [30, 32], "sixth": [126, 154], "size": [0, 6, 7, 8, 13, 15, 22, 23, 25, 30, 32, 35, 36, 39, 46, 51, 61, 68, 69, 70, 71, 80, 81, 93, 99, 102, 104, 121, 135, 139, 146, 166, 169, 182, 198, 202, 203, 207, 221, 236, 248, 261, 265, 267, 270, 278], "sj": 161, "sj\u00f6lander": 2, "sk": 206, "ska": 12, "skew": 261, "skip": [0, 4, 7, 8, 13, 17, 21, 24, 27, 32, 83, 84, 94, 129, 143, 168, 204, 258, 270], "skip_char": 31, "skip_head": [201, 204], "skip_lett": 199, "skip_n": 129, "skip_parsing_error": 258, "skip_popul": [201, 204], "skip_whitespac": [128, 129], "skipcharacterdatahandl": [83, 84], "skipflag": 270, "skipin": [30, 32], "skiplist": 129, "skptcreggr": 0, "skptcreggrsgsakslrmgrrgcsaqnpkdshdppphl": 0, "skptcreggrsgsakslrmgrrgcsaqnpkrlt": 0, "skptcreggrsgsakslrmgrrrctaqnpkrlt": 0, "slash": [10, 260], "slater": 2, "slater2005": [0, 2], "sleep": 83, "sleep_between_tri": 83, "sleev": 23, "slen": 218, "slice": [3, 6, 8, 16, 20, 25, 30, 35, 45, 46, 51, 53, 61, 66, 104, 183, 197, 214, 217, 236, 251, 253, 260, 281, 299], "sliced_hit": 20, "slicer": 158, "slide": [6, 32, 267], "slightli": [0, 7, 11, 13, 20, 23, 32, 251], "slink": [2, 4], "slipper": [7, 19], "slonim": 2, "slope": [4, 16, 299], "slow": [3, 6, 12, 23, 30, 32, 157, 158, 181, 182, 278, 297], "slowdefault": 32, "slower": [6, 23, 32, 169, 182, 204, 253, 270], "slowest": [182, 270], "slownni": [181, 182], "slvmavvvndsdedgdsrdavlpqkkkrlwglvvchnttprfv": 260, "slxa": 251, "slxa_0001_1_0001_01": [251, 260], "slxa_0001_1_0001_01_rc": 260, "slxfq": 270, "sm": [0, 53, 270], "smai": 8, "small": [3, 4, 6, 7, 8, 12, 19, 23, 30, 104, 140, 158, 168, 169, 199, 238, 260, 278], "smaller": [4, 8, 13, 73, 99, 108, 217, 237, 270], "smallest": [4, 11, 73], "smart": 53, "smcra": [15, 143, 151], "smin": [30, 32], "smith": [0, 12, 13, 14, 30, 32, 69], "smooth": [17, 32], "smoother": 6, "smoothscoreceil": [30, 32], "smoothwindow": [30, 32], "smprint": [128, 129], "sn": [0, 169], "snake": 9, "snapgen": [238, 254], "snapgeneio": [27, 238], "snapgeneiter": [27, 238, 254], "snapshot": 9, "sndiyfnfqrfnetnlilqrdasvsssgqlrltnln": 15, "snedecor": [2, 4], "snedecor1989": [2, 4], "snfgpvfmtv": 250, "snippet": [8, 18, 19, 20, 22, 23, 24], "snoop": 19, "snp": [7, 21, 237, 260, 270, 274], "snucleotid": [79, 80], "so": [0, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 53, 54, 56, 62, 66, 68, 79, 80, 83, 84, 90, 93, 99, 101, 104, 107, 108, 109, 117, 123, 155, 158, 169, 182, 183, 197, 209, 217, 218, 229, 237, 238, 242, 251, 254, 260, 277, 278, 288, 289, 291, 294, 297], "soap": 274, "soapi": 274, "soappi": 274, "soc": 129, "social": 83, "sodium": 264, "soe": 221, "soedinglab": 227, "soft": [0, 7, 32, 69, 247], "soft_mask": [68, 69], "softwar": [0, 2, 7, 9, 11, 12, 15, 16, 17, 18, 32, 33, 69, 123, 129, 132, 153, 158, 169, 177, 182, 229, 238, 242, 251, 294], "software_commun": 239, "sole": [61, 177, 270], "solexa": [2, 6, 238, 251, 260], "solexa_exampl": 251, "solexa_fak": [251, 260], "solexa_qu": [251, 260], "solexa_quality_from_phr": [27, 238, 251], "solid": 15, "solut": [2, 6, 15, 21, 23, 73, 84], "solv": [6, 15], "solvent": [2, 15, 145, 156, 157], "som": [4, 73], "somclust": [4, 27, 73], "some": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 56, 66, 67, 68, 69, 70, 80, 84, 92, 99, 102, 103, 104, 107, 109, 110, 117, 121, 122, 127, 132, 134, 136, 144, 147, 149, 151, 152, 169, 177, 182, 186, 202, 207, 217, 218, 222, 226, 236, 237, 238, 251, 253, 260, 261, 278, 297, 299], "some_db": 270, "some_residu": 15, "some_seq": 270, "somehow": [12, 93], "someth": [3, 5, 6, 7, 8, 9, 11, 12, 15, 19, 20, 21, 22, 23, 24, 60, 93, 139, 149, 205, 269, 271, 288, 303], "sometim": [3, 6, 8, 15, 20, 21, 22, 23, 56, 65, 66, 182, 218, 226, 251, 264], "somewhat": [11, 119, 274], "somewher": [21, 237], "son": 130, "sonnhamm": [53, 66], "soon": [3, 15], "sorri": 19, "sort": [4, 12, 15, 17, 20, 23, 27, 30, 66, 73, 76, 104, 126, 133, 135, 155, 169, 183, 217, 237, 238, 268, 269, 270], "sort_kei": [3, 20], "sorted_orchid": 6, "sorted_qresult": 20, "sound": 20, "sourc": [0, 1, 2, 3, 4, 5, 7, 8, 9, 12, 16, 17, 19, 20, 21, 23, 24, 27, 30, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 61, 68, 83, 84, 93, 101, 108, 119, 123, 150, 165, 166, 177, 179, 180, 183, 197, 217, 221, 229, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 269, 271, 272, 277, 287, 306], "source_db": 119, "source_db_or_dbentri": 119, "source_interact": [27, 177], "source_vers": 252, "sourceforg": [4, 15, 32, 270, 274, 278], "sp": [30, 32, 68, 209, 211], "spa": 250, "space": [3, 4, 8, 11, 15, 23, 25, 32, 51, 65, 67, 68, 69, 71, 79, 80, 94, 95, 99, 100, 104, 123, 126, 129, 135, 158, 162, 169, 172, 176, 182, 207, 218, 236, 250, 251, 256, 270, 278, 282, 297], "space_equals_underscor": 132, "space_group": 172, "spacegroup": 162, "spacer": [22, 99], "spacerseg": [27, 98, 99], "span": [0, 3, 8, 20, 30, 158, 169, 237, 299], "spare": 25, "spatial": 202, "speak": [5, 11, 71], "spearman": 73, "spec": [170, 243, 270], "speci": [0, 7, 11, 13, 17, 23, 27, 34, 61, 90, 92, 93, 177, 183, 197, 209, 211, 252, 275, 280, 287, 288, 295], "special": [0, 4, 11, 13, 15, 17, 19, 23, 24, 30, 32, 38, 56, 65, 95, 99, 149, 177, 237, 241, 251, 260, 278], "specialis": [237, 278], "speciat": [17, 132, 181, 183, 197, 198], "speciation_or_dupl": 197, "speciesord": 0, "specif": [0, 3, 5, 7, 8, 9, 13, 17, 19, 20, 21, 23, 24, 25, 30, 31, 32, 37, 46, 53, 56, 66, 67, 68, 69, 76, 83, 92, 93, 99, 102, 105, 117, 139, 147, 152, 158, 165, 169, 172, 177, 182, 183, 197, 198, 217, 222, 229, 237, 238, 239, 248, 257, 260, 265, 270, 272, 274, 278, 283, 288, 290, 291, 298, 299], "specifi": [0, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 21, 22, 24, 27, 29, 30, 31, 32, 34, 36, 38, 51, 54, 56, 59, 65, 67, 68, 69, 70, 73, 80, 84, 92, 93, 95, 99, 102, 103, 104, 105, 108, 109, 117, 119, 127, 131, 135, 139, 149, 151, 158, 162, 164, 169, 176, 182, 183, 193, 195, 196, 197, 207, 212, 217, 218, 221, 229, 236, 238, 252, 259, 260, 261, 270, 274, 281, 282, 283, 288, 297, 298, 299, 303], "specificti": 288, "specimen_vouch": 7, "spectroscopi": 25, "speed": [6, 11, 14, 23, 32, 146, 182, 267, 270, 278], "spell": [8, 83, 104], "spellman": 2, "spent": [1, 270], "spermatophyta": [7, 25], "sphegod": 7, "sphere": [141, 157, 158, 169], "spheric": 176, "sphinx": 306, "spid": 0, "spider": 7, "spifrmpswl": 250, "spin": 123, "spiral": 100, "spit": 92, "spite": 0, "splice": [21, 22, 61, 79, 80, 237, 272], "spliceosom": 30, "splicepenalti": [79, 80], "split": [3, 6, 8, 9, 10, 15, 17, 18, 20, 23, 27, 65, 83, 128, 132, 181, 182, 183, 201, 217, 222, 236, 237, 238, 251, 260, 270, 278, 287], "split_akl": [133, 169], "split_in_loci": [18, 200, 201], "split_in_pop": [18, 200, 201], "split_jaspar_id": [283, 287], "split_virtual_offset": [27, 278], "spn": [30, 32], "sport": 122, "spot": [7, 278], "spr": [181, 182], "spread": 221, "springer": 2, "sprlength": [181, 182], "sprot": 85, "sprotein": [79, 80], "sprotxx": 272, "spscore": [30, 32], "spslspflmr": 250, "sq": [0, 53, 66, 94, 270], "sqflefqdkfnkki": 0, "sql": [11, 209, 303, 304], "sql_file": 303, "sqlite": [20, 217, 238, 304], "sqlite3": [6, 9, 23, 61, 304], "sqlite_dbutil": [301, 304], "sqlite_fil": 61, "sqrt": [4, 11, 182, 270], "squar": [2, 4, 13, 80, 175, 176, 194, 216, 287], "sr": 157, "sra": [6, 12], "sracaggtgkyg": 11, "srand": 4, "src": 221, "srebnik": 265, "srf": [11, 283], "sri": 2, "srifdqifg": 250, "srlfdqffge": 250, "srpnrfaptlmsscitsttgppawagdrsh": 0, "srr001": 6, "srr001666": 6, "srr001666_": 6, "srr001666_1": 6, "srr001666_2": 6, "srr014849": 6, "srr020": 6, "srr020192": 6, "srs004476": 6, "srspair": [0, 41], "srt": 270, "srv": 32, "ss": [0, 12, 53, 66, 93, 137, 270], "ss_con": [0, 12, 53, 66], "ss_dssp": 0, "ss_pred": 0, "ss_seq": 153, "ss_to_index": [27, 133, 137], "ssac": [21, 23], "sscssccbcbgggttbccgggceecttsbeebshhhhsttccbsscssccccbtttttbccsttceecttsceebshhhh": 0, "ssdna": 260, "ssearch": 226, "sseq": 218, "sseqid": [69, 218], "ssfinfo": 253, "sspd5i": 206, "sssseeeeeeettt": 0, "sssssshhhhhttthhhhhhhhhhhhhhhhhhhhhhthhhhhhhhhhhhhhhhhhhhhtt": 260, "sstart": 218, "st": [2, 7, 18, 32, 68, 90, 238, 275], "sta": 32, "stabil": [183, 265], "stabl": [3, 27, 30, 32, 104, 265, 272], "stack": [8, 104], "stack_width": 283, "stackexchang": [15, 169], "stackoverflow": 169, "stacks_per_lin": 283, "stage": [32, 69, 275], "stai": [3, 5, 7, 15, 17, 183], "stal": 32, "stamataki": 182, "stand": [4, 8, 11, 14, 99, 175, 216, 247, 278], "standad": 83, "standalon": [0, 5, 8, 9, 84, 221], "standard": [0, 1, 3, 4, 6, 7, 9, 11, 12, 13, 15, 17, 18, 22, 23, 24, 27, 30, 32, 65, 66, 67, 76, 80, 92, 104, 129, 131, 135, 143, 151, 152, 154, 162, 169, 182, 183, 197, 203, 204, 205, 214, 217, 222, 236, 237, 238, 251, 253, 260, 261, 264, 265, 270, 272, 278, 290, 300, 303], "standard_dna_t": [76, 261], "standard_t": 22, "standarddata": [27, 128], "standardis": 169, "stanford": [4, 32, 209, 214], "stannard": 300, "star": [30, 32], "start": [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36, 39, 43, 46, 51, 52, 53, 56, 61, 62, 65, 66, 69, 71, 72, 73, 80, 84, 89, 90, 93, 94, 99, 100, 104, 108, 129, 130, 136, 138, 139, 152, 154, 158, 169, 182, 183, 197, 199, 204, 215, 216, 217, 219, 221, 222, 226, 229, 232, 234, 236, 237, 238, 241, 242, 244, 245, 246, 247, 250, 251, 252, 253, 254, 256, 257, 259, 260, 270, 273, 274, 278, 279, 283, 295, 297, 299, 303, 307], "start1": 236, "start2": 236, "start_codon": [22, 75, 76], "start_i": 103, "start_offset": [220, 237], "start_po": 21, "start_read": [201, 204], "start_x": 103, "start_x_posit": 99, "start_y_posit": 99, "starta": [98, 104], "startb": [98, 104], "startdbrefel": [238, 252], "startdescriptionel": [238, 252], "startdocu": [238, 252], "startel": [85, 89], "startelementhandl": [83, 84], "startentryel": [238, 252], "startentryfieldel": [238, 252], "startentryfieldelementversion01": [238, 252], "starting_tre": [181, 182, 199], "startnamespacedeclhandl": [83, 84], "startpropertyel": [238, 252], "startrawelementhandl": [83, 84], "startresid": 215, "startsequenceel": [238, 252], "startseqxmlel": [238, 252], "startskipelementhandl": [83, 84], "startspeciesel": [238, 252], "startswith": [6, 27, 104, 236, 253], "stat": [0, 3, 7, 17, 20, 30, 32, 68, 123, 126, 194, 202, 203, 270], "stat_db_len": 218, "stat_db_num": 218, "stat_eff_spac": 218, "stat_entropi": 218, "stat_hsp_len": 218, "stat_kappa": 218, "stat_lambda": 218, "state": [0, 2, 3, 4, 11, 13, 15, 16, 20, 27, 30, 54, 55, 107, 108, 109, 110, 121, 122, 158, 176, 197, 218, 245, 251], "state_alphabet": 108, "state_lat": 108, "state_lett": 108, "state_path": 109, "statement": [6, 8, 23, 278, 303, 304], "static": [30, 36, 54, 84, 149, 169, 171, 197, 237, 297], "statist": [2, 3, 6, 11, 18, 20, 32, 68, 69, 74, 80, 119, 129, 166, 169, 182, 194, 202, 203, 217, 221, 251, 295], "statistics_db": 218, "statistics_eff": 218, "statistics_entropi": 218, "statistics_hsp": 218, "statistics_kappa": 218, "statistics_lambda": 218, "statu": [0, 7, 30, 32, 67, 123, 149, 168], "status_charact": [30, 46], "std": [11, 131, 152, 169, 218, 283, 290], "std_output": 67, "stddev": 169, "stderr": [12, 17, 32, 67, 182, 270], "stdev": [29, 98, 104], "stdfq": 270, "stdin": [0, 3, 4, 12, 67], "stdo": [30, 32], "stdout": [0, 12, 17, 24, 32, 67, 79, 80, 199, 217, 270], "steeyhh": 0, "steeyhhrlqtfasnwrkinahn": 0, "steinegg": 2, "steinegger2019": [0, 2], "step": [3, 4, 6, 7, 8, 10, 11, 12, 13, 15, 20, 21, 22, 23, 30, 32, 104, 107, 169, 177, 202, 299], "stephan": 2, "stephen": [2, 3, 68], "stepmatrix": [27, 128, 129], "stepwis": 182, "steve": 32, "steven": 2, "sth": [12, 53, 66], "stick": [22, 24, 237], "still": [1, 6, 7, 8, 9, 12, 17, 19, 20, 21, 23, 25, 68, 70, 107, 129, 166, 183, 218, 251, 276], "stl": [15, 158], "stm_stm": 244, "stmt": 185, "stoch": 177, "stochiometr": 177, "stochiometri": [27, 177], "stockholm": [12, 21, 27, 30, 56, 66, 238], "stockholm_format": [53, 66], "stockholm_multiple_alignment_format": 66, "stockholmio": [27, 56], "stockholmiter": [27, 56, 66], "stockholmwrit": [27, 56, 66], "stoichiometri": 177, "stone": 105, "stop": [0, 4, 6, 7, 9, 13, 22, 25, 36, 69, 76, 89, 109, 236, 270], "stop_codon": [22, 75, 76], "stop_symbol": [22, 236, 237, 260, 281], "stopiter": [0, 3, 23, 30, 68], "stopping_criteria": 109, "storag": [139, 185, 305], "store": [0, 1, 3, 4, 7, 12, 13, 14, 15, 20, 21, 23, 24, 25, 29, 30, 32, 35, 36, 37, 38, 39, 42, 45, 46, 51, 52, 53, 54, 56, 59, 61, 67, 68, 69, 71, 73, 76, 83, 84, 89, 93, 104, 123, 129, 130, 132, 135, 136, 149, 155, 164, 169, 171, 185, 197, 198, 217, 222, 234, 238, 239, 240, 247, 251, 257, 269, 272, 273, 275, 278, 280, 286, 287, 288, 293, 295, 296, 299, 301, 302, 305], "stormo": [2, 11, 294], "str": [0, 8, 9, 11, 12, 13, 21, 22, 31, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 62, 64, 67, 68, 71, 76, 84, 90, 91, 94, 125, 126, 131, 135, 139, 149, 150, 152, 158, 162, 164, 165, 168, 169, 176, 183, 185, 188, 190, 197, 199, 215, 236, 238, 241, 245, 246, 249, 251, 256, 260, 261, 262, 270, 276, 283, 299, 302], "straddl": 8, "strai": 17, "straight": [4, 6, 7, 12, 23, 31, 251], "straightforward": [3, 4, 7, 23, 93, 97, 107, 169, 183], "strain": 13, "strand": [0, 3, 6, 8, 11, 15, 20, 21, 22, 27, 30, 32, 36, 46, 61, 62, 68, 69, 71, 80, 99, 104, 137, 221, 222, 226, 229, 236, 237, 260, 261, 264, 269, 270, 272, 290, 291, 295], "strandendin": [30, 32], "strandendout": [30, 32], "strandgap": [30, 32], "strandless": 8, "strang": [17, 183, 278], "stranger": 12, "strategi": [6, 7, 32, 69, 83], "stream": [0, 3, 7, 27, 33, 35, 36, 37, 38, 40, 42, 45, 46, 47, 49, 51, 52, 68, 83, 90, 185, 188, 190, 198, 199, 220, 241, 244, 246, 247, 248, 249, 251, 252, 253, 257, 259, 277], "stream_or_path": 252, "streammodeerror": 27, "strength": 182, "strenm": 45, "streptophyta": [7, 23, 25], "streptophytina": 7, "stretch": [22, 253], "stretcher": [41, 80], "stretchercommandlin": [27, 79, 80], "strict": [11, 12, 15, 132, 135, 139, 155, 186, 241, 261, 264, 283, 295], "strict_consensu": [27, 181, 186], "strict_pars": 15, "stricter": [9, 238], "strictli": [3, 11, 12, 17, 65, 71, 132, 135, 139, 143, 155, 183, 283], "strictly_equ": [133, 135, 139, 155], "stride": [22, 260], "strider": [238, 259, 261], "string": [0, 3, 4, 6, 7, 9, 11, 13, 15, 17, 19, 20, 21, 25, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 43, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 61, 66, 67, 68, 69, 71, 73, 76, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 93, 94, 95, 97, 99, 104, 112, 113, 114, 116, 117, 119, 121, 126, 129, 131, 135, 136, 137, 140, 141, 143, 148, 149, 151, 153, 154, 155, 162, 168, 169, 170, 172, 173, 177, 179, 180, 182, 183, 185, 190, 191, 193, 195, 196, 197, 207, 209, 210, 211, 212, 213, 214, 215, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 229, 232, 234, 236, 237, 238, 241, 244, 248, 251, 253, 256, 260, 261, 262, 263, 264, 265, 267, 270, 272, 274, 275, 276, 278, 280, 283, 286, 287, 288, 290, 293, 295, 296, 297, 298, 299, 303], "stringel": [27, 83, 84], "stringio": [0, 1, 12, 17, 23, 32, 56, 168, 188, 199, 238, 253], "strip": [6, 10, 15, 27, 83, 135, 162, 236, 270], "strive": 93, "strong": [238, 240], "strongli": [24, 182, 201, 251, 260], "struct": [112, 113, 157], "struct_ref_seq": 248, "structur": [0, 2, 4, 7, 9, 11, 12, 21, 23, 25, 27, 30, 31, 32, 53, 66, 78, 83, 84, 99, 108, 112, 113, 116, 123, 132, 133, 135, 136, 137, 138, 139, 140, 143, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 161, 162, 163, 164, 165, 166, 168, 169, 170, 171, 172, 173, 175, 183, 185, 202, 209, 215, 216, 238, 248, 260, 265, 270, 272, 278], "structure_build": [143, 151], "structure_id": [15, 143, 162, 172], "structure_method": [15, 174], "structure_rebuild_test": [15, 27, 133, 168, 169], "structure_refer": [15, 174], "structurealign": [15, 27, 133], "structurebuild": [27, 133, 143, 151], "structured_comment_delim": [92, 94, 238, 245], "structured_comment_end": [92, 94, 238, 245], "structured_comment_start": [92, 94, 238, 245], "structuredecod": [133, 171, 172], "structureio": [27, 133, 148, 170, 173], "struggl": 9, "sts_d11570": 68, "sts_d11734": 238, "stsline": [27, 275], "stslspfylr": 250, "sttccbsscc": 0, "studi": 19, "stuff": [5, 7, 15, 26, 99, 237, 307], "stumbl": [42, 218, 222], "style": [0, 3, 5, 6, 8, 9, 15, 17, 20, 22, 23, 24, 27, 32, 38, 68, 79, 80, 104, 119, 149, 183, 197, 238, 240, 251, 253, 278, 281, 283, 298, 303], "su": [3, 20, 53, 66], "suarez": 2, "sub": [6, 7, 17, 19, 21, 22, 24, 27, 30, 32, 66, 80, 94, 99, 183, 184, 187, 189, 197, 236, 237, 238, 253, 260, 270, 299, 303], "sub_align": 30, "sub_featur": [21, 237, 272], "sub_plat": 299, "sub_rec": 251, "sub_record": [21, 66, 251, 260], "subalign": [30, 68, 182], "subclad": [17, 132, 183], "subclass": [3, 9, 13, 15, 17, 21, 27, 30, 45, 54, 60, 67, 68, 99, 130, 139, 148, 170, 173, 197, 199, 236, 246, 272, 284, 287, 291], "subcohort": 197, "subcompon": 99, "subcomponent_s": [98, 99], "subdirectori": [0, 4, 8, 12, 13, 15, 24], "subdivis": 197, "subel": [84, 117], "subfamili": [11, 19, 197, 295], "subfeatur": [104, 237], "subfigur": 6, "subform": 197, "subgenu": 197, "subject": [0, 7, 68, 69, 71, 123, 237], "subject_loc": [68, 69], "subkingdom": 197, "sublegion": 197, "submiss": [7, 93, 182], "submit": [3, 5, 7, 19, 218, 237], "submodul": [13, 20, 177, 200], "subnam": 25, "subnod": [4, 73, 130, 198], "suboptim": 270, "subord": 197, "subphylum": 197, "subplat": 299, "subplot": 6, "subprocess": [3, 9, 12, 17, 32, 67, 69, 80, 137, 156, 182, 270, 285], "subprogram": 217, "subregion": [80, 136, 169], "subscrib": 27, "subscript": [7, 12], "subsect": [0, 3, 11, 236], "subseq": 261, "subsequ": [0, 2, 4, 7, 13, 21, 27, 30, 83, 158, 182, 236, 260, 265, 270, 297], "subset": [6, 15, 23, 24, 54, 123, 148, 214, 299], "subsp": 23, "subspeci": 197, "substanc": 123, "substitut": [2, 9, 11, 22, 27, 30, 31, 32, 54, 80, 182, 195, 196, 199, 251, 288, 290, 304], "substitution_matric": [13, 14, 27, 30, 290, 297], "substitution_matrix": [11, 12, 13, 30, 290], "substr": [236, 303], "substrat": [113, 115, 117, 177], "substrate_id": 117, "subtili": 13, "subtl": 21, "subtleti": 19, "subtract": [4, 15, 139, 237, 278, 299], "subtract_control": [16, 298, 299], "subtre": [132, 182], "subtrib": 197, "subtyp": 117, "subulata": 7, "subunit": [4, 15, 169], "subvarieti": 197, "success": 12, "successfulli": [15, 19, 299], "successor": [3, 130, 132, 149], "suddenli": 19, "sueff": [30, 32], "suffici": [3, 15, 167, 169], "suffix": [17, 21, 183, 236, 260, 270], "suggest": [1, 4, 8, 12, 13, 17, 21, 23, 83, 158], "sugimoto": 264, "suit": [2, 3, 7, 8, 12, 14, 15, 17, 20, 24, 44, 56, 69, 112, 113, 114, 126, 218, 226, 227, 229, 238, 269], "suitabl": [4, 5, 6, 13, 15, 23, 46, 61, 80, 83, 100, 125, 158, 183, 238, 251, 274, 278], "suite3": 2, "sulfid": 25, "sulfido": 25, "sulfolobu": 0, "sulfur": 25, "sum": [0, 4, 11, 12, 13, 17, 21, 23, 30, 31, 32, 69, 73, 107, 108, 109, 128, 129, 132, 157, 183, 237, 265, 299], "sum_": [4, 11, 12, 270], "sum_branchlength": [128, 132], "sum_prob": 0, "sum_stat": [68, 69], "sum_statist": [68, 69], "summar": [3, 12, 31, 82, 129], "summari": [0, 3, 11, 16, 23, 30, 31, 68, 83, 84, 117, 123, 182, 183, 260, 280, 299, 303], "summaris": 207, "summary_align": 12, "summary_info": 31, "summaryinfo": [12, 27, 30, 31], "summat": 4, "summer": 17, "sunid": [209, 210, 211, 213], "sup": [15, 216], "supardii": 23, "super": [54, 236], "super_orthologi": 197, "superclass": 197, "supercohort": 197, "superdivis": 197, "superfamili": [11, 15, 197, 209, 211, 295], "supergroup": [11, 288], "superimpos": [8, 27, 133, 166, 169, 175, 216], "superlegion": 197, "superord": 197, "superphylum": 197, "superposit": 216, "superscript": 7, "superset": 278, "superspeci": 197, "supertrib": 197, "supervis": [127, 282], "supplement": 2, "suppli": [0, 3, 4, 7, 8, 12, 14, 15, 18, 19, 20, 21, 23, 30, 32, 108, 109, 152, 158, 169, 217, 218, 237, 260, 261, 278, 297], "support": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 70, 80, 84, 104, 132, 140, 149, 154, 158, 169, 171, 177, 178, 182, 183, 186, 191, 192, 193, 195, 196, 197, 199, 227, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 269, 270, 274, 276, 278, 283, 289, 290, 291, 292, 299, 302], "support_as_branchlength": 132, "suppos": [0, 1, 6, 7, 11, 12, 13, 14, 15, 19, 21, 22, 23, 108, 252, 278], "suppress": [15, 32, 51, 143, 151], "sure": [4, 5, 7, 15, 22, 23, 24, 56, 73, 117, 149, 182, 237, 238, 298], "surfac": [12, 15, 20, 53, 104, 137, 156, 157], "surface_access": 66, "surpris": [12, 20, 237], "surprisingli": 21, "surround": [32, 282], "suspect": 15, "sustain": 16, "sutisak": 2, "suv": 122, "suzuki": 2, "sv": [30, 32], "svd": [4, 216], "svdsuperimpos": [15, 27], "svg": [8, 99, 104], "sw": [126, 270], "sw_score": 226, "swap": [0, 30], "sweet": [8, 265], "sweetpea": [238, 260], "swgadwgdng": 0, "swgadwgeqg": 0, "swgpqwgmng": 0, "swift": [15, 137], "swiss": [0, 9, 19, 23, 26, 86, 88, 89, 197, 238, 255, 258, 276, 307], "swissio": [27, 238, 276], "swissiter": [27, 238, 255], "swissport": 23, "swissprot": [6, 9, 25, 27, 53, 85, 88, 238, 255, 258, 276], "swissprotid": 0, "swissprotparsererror": [27, 272], "switch": [4, 8, 12, 22, 30, 32, 68, 69, 73, 80, 99, 137, 169, 182, 202, 236, 260, 270], "swofford": [2, 129], "swshvsslvsasluiklfkkfsska": 12, "swtaadkaaq": 0, "sx": 90, "sy": [12, 17, 24, 25, 90, 199, 273], "syesaaevrr": 0, "syk_syk": 244, "sylvrnqelr": 0, "symbol": [0, 7, 10, 11, 13, 19, 21, 22, 123, 129, 137, 149, 181, 197, 198, 236, 260, 275, 297], "symbols0": 283, "symbols1": 283, "symbols2": 283, "symbols3": 283, "symbols4": 283, "symmetr": [0, 13, 30, 182, 297], "symmetri": 162, "synonym": [2, 90, 181, 196, 197, 198, 272, 273, 277], "syntax": [7, 9, 15, 16, 30, 170, 182, 185, 198, 237, 276, 299], "synthas": [21, 23, 25], "sysadmin": 149, "sysbio": 2, "sysnam": 113, "syst": [7, 129], "system": [0, 2, 3, 4, 5, 6, 7, 10, 12, 15, 19, 24, 27, 32, 33, 61, 67, 99, 169, 177, 182, 221, 241, 250, 251, 253, 278, 299], "systemat": [2, 19, 113, 129, 182], "systemid": 84, "syteni": 99, "szege": 122, "s\u00f6ding": [2, 32], "t": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 45, 46, 48, 56, 61, 63, 65, 66, 67, 69, 71, 76, 80, 99, 100, 102, 104, 108, 119, 122, 129, 131, 137, 143, 149, 152, 176, 182, 183, 191, 197, 198, 221, 222, 236, 237, 246, 247, 251, 260, 261, 264, 265, 268, 269, 270, 275, 278, 288, 292, 296, 297, 302, 305], "t0": [0, 13, 30], "t01001": 119, "t1": [0, 13, 30, 183, 264], "t100": 0, "t11": [0, 13, 30], "t134": 0, "t137": 0, "t1575": 0, "t2": [0, 13, 30, 183], "t265_11027": 3, "t3": 183, "t30": [0, 13, 30], "t35": 0, "t35m": 0, "t4": [0, 13, 30], "t40": [0, 13, 30], "t73": 0, "t8": [0, 13, 30], "t99": 0, "t_coffe": 32, "t_coffee_home_pag": 32, "t_end1": [0, 30], "t_end2": [0, 30], "t_endn": [0, 30], "t_start1": [0, 30], "t_start2": [0, 30], "t_startn": [0, 30], "ta": [13, 30, 32, 123, 236], "taa": [22, 76, 281], "taaaatatat": 7, "taaaga": 0, "taaattag": 0, "taagccctcctagcacacacccggagtggcc": 0, "taagcgtgcacgcgcaacacgtgcatta": 11, "taagga": 0, "taatgattct": 7, "tab": [4, 11, 12, 20, 23, 51, 104, 210, 211, 212, 217, 219, 226, 232, 236, 238, 256, 270], "tab_2226_tblastn_001": [20, 217], "tab_2226_tblastn_002": 217, "tab_2226_tblastn_003": 20, "tab_2226_tblastn_004": 218, "tab_2226_tblastn_005": 20, "tab_2226_tblastn_007": 20, "tab_2226_tblastn_008": 218, "tab_2226_tblastn_009": 218, "tabacum": 23, "tabb": 263, "tabio": [27, 238], "tabiter": [27, 238, 256], "tabix": 23, "tabl": [0, 3, 4, 6, 7, 11, 13, 15, 20, 21, 31, 32, 34, 36, 69, 76, 79, 80, 93, 94, 107, 126, 167, 202, 209, 217, 226, 229, 230, 231, 232, 236, 237, 238, 260, 261, 264, 280, 286, 293, 295, 296, 303, 304], "table_row": 97, "tabular": [3, 6, 20, 27, 30, 68, 69, 217, 218, 219, 226], "tabwrit": [27, 238, 256], "tac": [22, 76], "tacaa": 11, "tacaataattg": 0, "tacac": 11, "tacactgcattacaacccaagcatta": 11, "tacagatgtgaaactttcaagagatttactgactttcctagaatagtttctctactggaa": 238, "taccc": 11, "taccg": 30, "taccggtaacattacccggcgactttcccacgggctatc": 22, "tacg": 264, "tacgagaataatttctcatcatccagctttaacacaaaattcgca": 23, "tacgagaataatttctcatcatccagctttaacacaaaattcgcacagttttcgttaaga": 23, "tacgc": 11, "tacgcacttt": 7, "tacgt": 30, "tackl": [6, 8], "tacnc": 11, "tacqg": 154, "tactgtattg": 7, "tacttcaaag": 7, "tacttgttgatattggatcgaacaaactggagaaccaacatgctcacgtcacttttagtcccttacatattcctc": 3, "tacttgttggtgttggatcgaaccaattggaagacgaatatgctcacatcacttctcattccttacatcttcttc": 3, "tad": 20, "taetgtqcnf": 0, "tag": [0, 7, 8, 15, 22, 24, 30, 52, 68, 71, 76, 80, 83, 84, 197, 240, 252, 260, 269, 270], "tagaaaatca": 7, "tagcatacttgcnatcctttanccatgcttatcatangtaccatttgaggaattgntttg": 238, "tagctaagac": 22, "tagctcagg": 12, "taggcatacgtg": 30, "taggggtgcagagccgagtcacggggttgccagcac": 0, "tags2id": 94, "taii": 206, "tail": 275, "taipal": 288, "takashi": 2, "take": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 56, 83, 99, 104, 105, 120, 121, 122, 169, 182, 204, 217, 237, 238, 251, 260, 265, 270, 274, 278, 282, 288, 297, 298], "taken": [0, 4, 8, 10, 20, 30, 32, 80, 109, 182, 214, 240, 251, 256, 263, 270], "tale": 288, "talevich": [2, 9, 17, 26, 133], "talevich2012": [2, 9, 17], "talk": [7, 12, 21, 22, 23, 274], "tamayo": [2, 4], "tamayo1999": [2, 4], "tamo": 11, "tan": [183, 236], "tanaka": 25, "tanford": 265, "taq": 0, "tar": [76, 149], "target": [0, 3, 7, 12, 13, 15, 17, 20, 27, 30, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 46, 47, 49, 50, 51, 52, 53, 68, 69, 71, 79, 80, 81, 119, 129, 158, 169, 183, 186, 218, 222, 226, 229, 234, 241, 245, 246, 247, 251, 252, 253, 256, 259, 264, 270], "target1": [0, 183], "target2": [0, 183], "target_db": 119, "target_end_extend_gap_scor": 13, "target_end_gap_scor": [13, 30], "target_end_open_gap_scor": 13, "target_extend_gap_scor": 13, "target_gap": [30, 55], "target_gap_scor": 13, "target_internal_extend_gap_scor": 13, "target_internal_gap_scor": 13, "target_internal_open_gap_scor": 13, "target_left_extend_gap_scor": 13, "target_left_gap_scor": 13, "target_left_open_gap_scor": 13, "target_level": 159, "target_open_gap_scor": 13, "target_right_extend_gap_scor": 13, "target_right_gap_scor": 13, "target_right_open_gap_scor": 13, "target_seqnam": 61, "target_tre": 186, "targetcut": 270, "task": [6, 9, 12, 19, 23, 68, 69, 79, 80, 99, 108, 177, 182], "tast": [3, 20], "tasumi": 149, "tat": [22, 30, 76], "tat_mase_nuc": 244, "tataataattgtatatgtcacagaaaaaaatgaattttcaat": 0, "tatacataaa": 30, "tatacataaaagaag": 0, "tatacataaaagaagggggatgcggataaatggaaaggcgaaag": [12, 30], "tatacataaaagaagggggatgcggataaatggaaaggcgaaagaaagaa": 0, "tatacataaaagaagggggatgcggataaatggaaaggcgaaagaaagaaaaaaatgaat": 0, "tatacataaagtgtaccaga": 30, "tatacatt": 0, "tatacattaa": 30, "tatacattaaagaagggggatgcggataaatggaaaggcgaaag": [12, 30], "tatacattaaagaagggggatgcggataaatggaaaggcgaaagaaagaa": 0, "tatacattaaagaagggggatgcggataaatggaaaggcgaaagaaagaaaaaaatgaat": 0, "tatacattaaaggagggggatgcggataaatggaaaggcgaaag": [12, 30], "tatacattaaaggagggggatgcggataaatggaaaggcgaaagaaagaa": 0, "tatacattaaaggagggggatgcggataaatggaaaggcgaaagaaagaaaaaaatgaat": 0, "tatacattaagtataccaga": 30, "tatacattaagtgtaccaga": 30, "tatcacagcg": 7, "tatgaatggcgaggcaatcgctggcacctacacggaccgccgccaccgccgcgccaccat": 22, "tatgacaata": 7, "tatgcgaaga": 7, "tatgtagaaa": 7, "tatgtatatg": 7, "tatgtcatagaaaaaaatgaattttcaat": 0, "tatgtcattc": 278, "tatgtgtcag": 7, "tattctgatg": 7, "tattggatca": 7, "tau": [15, 73, 152, 154, 169], "tau_": 4, "tax": 17, "tax_group": [11, 287, 288], "taxa": [129, 132, 182, 183], "taxacea": 17, "taxid": [3, 7, 68, 69], "taxid_map": [68, 69], "taxlabel": 132, "taxon": [7, 11, 17, 21, 32, 80, 129, 132, 182, 183, 197, 277, 295], "taxon_id": 277, "taxon_list": 132, "taxonom": [11, 69, 88, 93, 197, 288, 295, 303], "taxonomi": [2, 7, 11, 21, 22, 23, 27, 69, 93, 181, 183, 197, 198, 252, 272, 274, 288, 303], "taxonomy_id": [25, 272], "taxonomyid": 69, "taylor": 182, "tba": 0, "tblast": 3, "tblastn": [68, 69, 70, 71, 218], "tblastx": [3, 68, 69, 70, 71, 218], "tc": [0, 53], "tca": 22, "tcaaatcctt": 7, "tcaacatctt": 7, "tcaaggatgt": 7, "tcaagtgtac": 7, "tcacggtggcctgttgaggcaggggctcacgctgacctctctcggcgtgggaggggccgg": 0, "tcacggtggcctgttgaggcaggggctcacgctgacctctctcggcgtgggaggggccggtgtgaggcaagggctcacgctgacctctctcggcgtgggag": 0, "tcacggtggcctgttgaggcagggggtcacgctgacctctgtccgcgtgggaggggccgg": 0, "tcag": [22, 253], "tcagaaagaagtaaggtaaa": 253, "tcagaaagacaagtggtatc": 253, "tcagaagcagtggtatcaac": 253, "tcagaatcat": 253, "tcagaatcatccacttttta": 253, "tcagactttcttctttaccg": 253, "tcagcggccgggcctctcat": 253, "tcagctccgtaagaaggtgc": 253, "tcagggactgcgagaaccaagcta": 13, "tcagggactgcgagaaccaagctactgctgctgctggctgcgctctgcgccgcaggtggg": 13, "tcagggactgcgagaaccaagctactgctgctgctggctgcgctctgcgccgcaggtggggcgctggag": 13, "tcagggacttcgagaaccaagcgc": 13, "tcagggacttcgagaaccaagcgcctcctgctgctggctgcgctcggcgccgcaggtggagcactggag": 13, "tcagggacttcgagaaccaagcgctcctgctgctggctgcgctcggcgccgcaggtggagcactggag": 13, "tcagggtctacatgttggtt": 253, "tcagggtctacatgttggttaacccgtactgatt": 253, "tcagtggtaatggggggaaa": 253, "tcagttttttttggaaagga": 253, "tcatattactntaagttctatagcatacttgcnatcctttanccatgcttatcatangtaccatttgagg": 238, "tcatgtgacca": 19, "tcattggttatggcagtggtcgtcaatgacagcgatgaagatggagatagccgtgacgca": 260, "tcc": [22, 76], "tccttctttg": 7, "tcctttcatg": 7, "tcg": [22, 30, 236, 280], "tcgacgtcg": 236, "tcgt": 260, "tcgtgtgcta": 7, "tchr1": 0, "tcoffe": 32, "tcoffee_clin": 32, "tcoffeecommandlin": [30, 32], "tct": [22, 76], "tctacgattgag": 283, "tctattccag": 7, "tctcctc": 12, "tctcgacgtcg": 236, "tctcttttct": 7, "tctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcg": 0, "tcttgagcga": 7, "tcttgatcga": 7, "tctttgtcgt": 7, "teach": 122, "teal": [8, 183], "team": [5, 234], "teamdslktq": 12, "teamnslktq": 12, "teardown": 24, "teas56_57": 0, "teassvsssq": 250, "teatsvstsq": 250, "techfak": 32, "technic": [22, 23, 25, 27], "techniqu": [4, 8, 107], "technologi": [10, 16, 158, 270], "tediou": 19, "tell": [4, 7, 11, 12, 22, 23, 27, 80, 217, 251, 253, 278], "telomer": [8, 99], "telomere_length": 8, "telomereseg": [8, 27, 98, 99, 102], "temp": [6, 251], "temp_filt": 253, "temp_path": 145, "temp_wat": 67, "temperatur": [80, 135, 172, 264], "temperature_factor": 172, "templat": [0, 15, 22, 24, 52, 69, 99, 191, 236, 264, 275], "template_dna": 22, "template_length": [68, 69, 70], "template_typ": [68, 69, 70], "temporari": [12, 17, 24, 105, 190, 251, 270], "ten": [4, 6, 12, 16, 23, 30, 217, 250, 251, 260], "tend": [4, 24, 73, 265], "ter": 261, "terl": 8, "term": [0, 4, 6, 8, 11, 13, 17, 18, 19, 20, 25, 30, 32, 35, 39, 46, 51, 52, 61, 83, 113, 119, 123, 169, 209, 213, 229, 252, 264, 274, 278], "termgap": [30, 32], "termin": [3, 4, 15, 17, 32, 90, 129, 132, 153, 169, 182, 183, 236, 245, 250, 255, 261, 264, 272], "terminal_gap_to_miss": [128, 129], "terminalgap": [30, 32], "termini": [32, 80], "terminologi": [17, 21, 22, 121], "terminu": [80, 275], "ters": 21, "test": [0, 3, 4, 6, 7, 8, 11, 14, 16, 17, 18, 20, 25, 26, 27, 34, 42, 71, 74, 79, 80, 86, 87, 88, 90, 91, 112, 113, 114, 126, 135, 139, 156, 168, 169, 182, 183, 194, 202, 203, 217, 218, 221, 222, 226, 229, 234, 236, 237, 238, 241, 249, 251, 260, 265, 275, 280, 281, 305, 307], "test1": 104, "test_": 24, "test_ac": 24, "test_addition1": 24, "test_addition2": 24, "test_align_bigb": 0, "test_alignio": 24, "test_biospam": 24, "test_biospammymodul": 24, "test_biosql": [24, 305], "test_biosql_seqio": 24, "test_cap": 24, "test_clustalw": 24, "test_division1": 24, "test_division2": 24, "test_even_bigendian": 247, "test_genic_diff_al": [201, 202], "test_genic_diff_pair": [201, 202], "test_genotypic_diff_al": [201, 202], "test_genotypic_diff_pair": [201, 202], "test_global_hz_defici": [201, 202], "test_global_hz_excess": [201, 202], "test_hw_glob": [201, 203], "test_hw_pop": [201, 203], "test_ld": [201, 202], "test_ld_all_pair": [201, 203], "test_pop_hz_defici": [201, 202], "test_pop_hz_excess": [201, 202], "test_pop_hz_prob": [201, 202], "test_seq": 11, "test_seqio": 24, "test_tutori": 24, "test_typ": 203, "test_xxx": 24, "testaddit": 24, "testcas": 24, "testdivis": 24, "testenv": 24, "testload": 24, "testrunn": 24, "testsuit": 24, "tetllvqnanpdcktilkalgpgatle": 154, "tetrachloroethen": 197, "tetrahedr": [15, 169], "tetrahedron": 169, "tetrazolium": 16, "teuvo": 2, "text": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 17, 19, 22, 23, 25, 27, 42, 45, 60, 67, 68, 69, 70, 71, 76, 83, 84, 85, 87, 89, 93, 94, 97, 99, 143, 185, 188, 190, 197, 199, 209, 217, 224, 228, 230, 233, 237, 238, 241, 244, 245, 246, 248, 249, 250, 251, 256, 258, 260, 271, 272, 274, 275, 276, 291, 292], "textco": 242, "textio": [150, 152], "textiowrapp": [4, 90], "textrm": [4, 6, 11, 13], "textstream": 90, "texttestrunn": 24, "texttt": 22, "textual": [21, 32, 201, 204], "textw": 229, "tf": [11, 288], "tf0000003": 11, "tf0000070": 288, "tf_class": [11, 287, 288], "tf_famili": [11, 287, 288], "tf_name": 288, "tfastx": 226, "tfb": 288, "tfbss": 11, "tfiiic": 4, "tg": [0, 11, 30, 222], "tga": [22, 76, 236], "tgaactagaatctcagaggatg": 0, "tgacctagaatctcagaggatg": 0, "tgactaagaa": 7, "tgatctccccatcctgccctg": 0, "tgatgccctcaccccctccgtgca": 0, "tgc": [22, 76], "tgca": 264, "tgcaaggcttctacacccgtactcgaatgc": 264, "tgcaatgcaaxrzxrz": 236, "tgccgttaccat": 222, "tgctagagaa": 7, "tgeglewgvlfgfgpgltvetvvlhsvat": 23, "tgg": [22, 76], "tggacgcgggg": 283, "tggcaatctt": 7, "tgggaggttttatgtgga": 251, "tgggaggttttatgtggaaagcagcaatgtacaaga": 251, "tgggtttaa": 281, "tggtaatggggggaaattta": 253, "tgkqnscqmsaiwqlrqntatktrqnrari": 6, "tgt": [22, 76], "tgtaacgaacggtgcaatagtgatccacacccaacgcctgaaatcagatccagg": 21, "tgtaacgaacggtgcaatagtgatccacacccaacgcctgaaatcagatccagggggtaatctgctctcc": 21, "tgtgaatttt": 7, "tgtgaggcaagggctcacactgacctctctcagcgtgggag": 0, "tgtgaggcaagggctcacgctgacctctctcggcgtgggag": 0, "tgttctgaaggaaggtgtgcgtgcgtgtgtgtgtgt": 251, "th": [11, 12, 104, 297], "th0": 0, "th1": 0, "thaimgvaft": 250, "thale": 23, "thaliana": [3, 8, 23, 238, 278], "than": [0, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 17, 19, 20, 21, 23, 24, 25, 27, 30, 31, 32, 34, 35, 46, 49, 51, 56, 61, 62, 64, 65, 66, 68, 69, 71, 83, 88, 92, 113, 135, 136, 139, 152, 166, 169, 182, 197, 198, 203, 207, 209, 217, 222, 237, 238, 240, 241, 251, 255, 260, 265, 269, 270, 271, 275, 280, 283, 288, 290, 297, 298, 303], "thank": [5, 15, 71], "thei": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 32, 35, 36, 37, 38, 39, 41, 51, 52, 58, 67, 68, 70, 71, 88, 94, 107, 108, 121, 143, 151, 152, 155, 164, 169, 178, 182, 183, 214, 217, 221, 222, 226, 237, 251, 260, 264, 270, 278, 297, 303], "thein": 264, "them": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 32, 45, 56, 66, 67, 68, 84, 92, 103, 104, 108, 136, 139, 149, 169, 182, 183, 185, 191, 217, 218, 221, 222, 229, 237, 238, 249, 251, 260, 270, 278, 280, 282, 303, 305], "themselv": [0, 4, 12, 15, 17, 20, 21, 66, 222, 251], "theobald": 175, "theoret": [4, 25, 177, 263], "theori": [6, 12, 217], "thereaft": 182, "therebi": 3, "therefor": [0, 3, 4, 6, 7, 11, 12, 15, 16, 21, 23, 30, 32, 35, 46, 51, 61, 68, 69, 73, 83, 99, 209, 234, 238, 240, 251, 278, 288], "thereof": 291, "thermodynam": 264, "thermophil": 0, "theta": [12, 154, 176], "thf": 53, "thi": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 80, 81, 82, 83, 84, 85, 86, 88, 89, 90, 92, 93, 94, 95, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 112, 113, 114, 116, 117, 119, 120, 124, 125, 126, 127, 128, 129, 132, 134, 135, 136, 137, 138, 139, 140, 143, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 162, 165, 167, 169, 172, 175, 177, 179, 180, 182, 183, 185, 186, 188, 190, 191, 197, 198, 199, 202, 203, 204, 205, 207, 209, 210, 212, 213, 214, 215, 216, 217, 218, 221, 222, 226, 227, 229, 234, 236, 237, 238, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 263, 264, 265, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 279, 280, 281, 282, 283, 285, 288, 290, 291, 292, 295, 296, 297, 298, 299, 300, 302, 303, 305, 306, 307], "thick": [0, 8, 36, 104], "thickend": [0, 36], "thickstart": [0, 36], "thiel": 2, "thin": 8, "thing": [1, 3, 5, 7, 9, 11, 12, 15, 17, 19, 20, 21, 23, 25, 26, 27, 30, 31, 45, 60, 80, 92, 95, 99, 158, 169, 216, 237, 246, 251, 260, 297, 307], "thingivers": [15, 158, 169], "think": [1, 5, 11, 13, 15, 17, 19, 20, 21, 30, 102, 237, 264], "thiomac": 11, "third": [0, 3, 4, 6, 7, 8, 12, 13, 15, 17, 21, 22, 30, 169, 222, 251, 261], "thirdli": 251, "thirteenth": 21, "thoma": [2, 3, 9, 26, 68, 133, 296], "thompson": 32, "thornton": 265, "thorough": [79, 80, 182], "thorton": 182, "those": [3, 4, 6, 8, 9, 10, 12, 16, 17, 22, 23, 24, 27, 76, 83, 84, 94, 102, 105, 157, 182, 191, 207, 251, 253, 260, 261, 283, 288, 297], "though": [3, 9, 11, 12, 13, 17, 20, 21, 23, 30, 183, 197, 237, 270, 303], "thought": [237, 264], "thousand": [3, 20, 182, 204, 217, 251], "thr": [13, 15, 30, 32], "thread": [30, 32, 69, 149, 181, 182, 270], "three": [0, 3, 4, 6, 7, 8, 11, 12, 13, 15, 16, 17, 20, 22, 23, 25, 30, 62, 73, 83, 94, 104, 119, 141, 149, 154, 169, 205, 209, 222, 236, 248, 251, 261, 264, 265, 272, 274, 278, 281, 299], "three_to_index": [27, 133, 154], "threepluson": 283, "thresh": [79, 80], "threshold": [0, 3, 6, 9, 12, 27, 30, 31, 32, 68, 69, 70, 71, 79, 80, 109, 132, 182, 229, 268, 270, 283, 290], "threshold_balanc": [11, 283, 294], "threshold_fnr": [11, 283, 294], "threshold_fpr": [11, 283, 294], "threshold_pats": [11, 283, 294], "through": [0, 3, 5, 6, 7, 10, 11, 16, 17, 19, 20, 21, 23, 25, 30, 31, 62, 71, 84, 92, 100, 104, 107, 135, 152, 169, 183, 191, 197, 203, 215, 218, 226, 227, 229, 234, 236, 238, 278], "throughout": [1, 11, 15, 21, 270], "throughput": [7, 10, 16, 23, 32], "throw": [76, 236], "thrust": 12, "thu": [4, 5, 8, 13, 14, 15, 18, 19, 20, 21, 22, 64, 68, 70, 71, 76, 99, 127, 132, 169, 182, 237, 251, 253, 264, 269, 270, 278, 282], "thumb": [4, 264], "thylakoid": 272, "thymidin": 209, "ti": [7, 20, 123], "tiago": [2, 26], "tick": [8, 104], "tid": 270, "tidi": [24, 85, 91, 148, 170, 173, 251], "tien": 137, "tiff": 104, "tiffin": [11, 283], "tightest": 0, "tightli": [19, 217], "tild": [63, 251], "tim": 2, "time": [0, 1, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 25, 32, 56, 68, 69, 73, 80, 83, 84, 92, 99, 109, 169, 182, 186, 197, 209, 222, 238, 251, 253, 258, 265, 267, 270, 274, 288, 294, 299], "timothi": 2, "tini": 23, "tip": [5, 6, 17, 19, 69], "tissu": [7, 275], "titl": [3, 6, 7, 11, 21, 23, 25, 53, 68, 69, 71, 83, 93, 99, 101, 103, 117, 123, 129, 152, 168, 172, 207, 237, 241, 250, 251, 272, 275, 295], "title_s": 99, "titlemainlist": 7, "titsslsldg": 250, "tj": 32, "tkk": 68, "tl": [94, 182], "tlen": 52, "tln": 0, "tlr": 182, "tm": [30, 32, 53, 66, 264], "tm_con": 53, "tm_gc": [27, 261, 264], "tm_nn": [27, 261, 264], "tm_wallac": [27, 261, 264], "tmf": 0, "tmm_tabl": 264, "tmp": [145, 270], "tmp_directori": 145, "tn93": 182, "tn_x": 8, "tn_y": 8, "tname": [301, 304], "tnm": 0, "tny": 12, "to_align": [181, 197], "to_dict": [23, 27, 217, 238, 251, 283, 287], "to_gener": [68, 71], "to_hex": [181, 183], "to_level": 104, "to_networkx": 17, "to_phylogeni": [181, 197], "to_phyloxml_contain": [181, 197], "to_process": 95, "to_rgb": [181, 183], "to_seqfeatur": [181, 197], "to_seqrecord": [181, 197], "to_stat": 108, "to_stop": [6, 22, 236, 237, 260], "to_str": [98, 104, 128, 132, 181, 185, 188, 190], "toclarecord": [27, 209], "todai": 19, "todd": 2, "todesrecord": [27, 209], "todo": 7, "togeth": [0, 6, 7, 8, 9, 11, 12, 13, 14, 21, 22, 23, 30, 61, 62, 66, 71, 83, 130, 169, 214, 217, 218, 238, 243, 251, 260, 278, 297], "togow": [24, 27, 119], "toh": 32, "tohierecord": [27, 209], "token": [197, 272], "told": 12, "tom": 12, "tomultipleseqalign": [279, 280], "ton": [13, 31], "tonsist": 13, "too": [3, 6, 7, 8, 12, 15, 17, 20, 21, 22, 23, 24, 30, 56, 108, 237, 238, 251, 278], "took": [6, 23, 56, 108, 238, 253, 298], "tool": [0, 2, 3, 5, 6, 7, 9, 11, 14, 15, 17, 19, 23, 26, 27, 30, 32, 40, 41, 42, 48, 50, 55, 56, 57, 58, 59, 63, 65, 66, 67, 68, 69, 70, 74, 80, 83, 126, 156, 182, 217, 218, 221, 222, 226, 250, 251, 253, 264, 278, 283, 285, 289, 290, 307], "toolkit": [2, 7, 123, 218], "top": [0, 2, 3, 4, 11, 12, 15, 20, 21, 23, 24, 84, 99, 101, 104, 139, 158, 163, 175, 181, 182, 198, 216, 241, 251, 256, 278, 302], "topdiag": [30, 32], "topic": [5, 6, 7, 22], "topm": [181, 182], "topo_dom": 272, "topolog": [7, 182, 272], "topologi": [4, 17, 21, 182, 183, 197], "toresnum": 125, "torrent": 253, "torsion": 154, "toseq": [279, 281], "tossgap": [30, 32], "total": [0, 4, 7, 11, 12, 13, 17, 23, 25, 30, 71, 108, 109, 183, 197, 202, 203, 221, 261, 264, 270, 275, 287, 290], "total_branch_length": [17, 181, 183], "total_len": 23, "total_num_atom": 172, "total_num_bond": 172, "total_num_chain": 172, "total_num_group": 172, "total_num_model": 172, "toth": [2, 7, 8], "toth2006": [2, 8], "touch": [7, 8, 32], "toward": [8, 12, 237, 261, 270], "toxic": 260, "tp": [0, 13, 53], "tpc": 2, "tpda": 13, "tpp": 53, "tpr": 53, "tqueri": [0, 13, 30], "tr": 278, "tra": 76, "trace": [7, 17, 55, 128, 130, 169, 181, 183, 238, 251, 253, 275], "traceback": [0, 3, 4, 7, 13, 21, 22, 23, 30, 45, 56, 67, 68, 69, 80, 85, 217, 236, 237, 238, 241, 251, 260, 264, 278, 283, 298], "tracheophyta": [7, 25], "track": [0, 4, 6, 7, 10, 20, 22, 23, 98, 104, 158, 162, 169, 251, 270], "track_geneid": 7, "track_i": 8, "track_level": 104, "track_siz": 104, "track_statu": 7, "track_x": 8, "tracker": [5, 226], "tracklin": 104, "trackscale_fonts": 104, "trade": [23, 169, 270], "tradeoff": 264, "tradit": [101, 278], "traffic": 15, "trail": [0, 6, 12, 15, 94, 135, 207, 230, 236, 260, 297], "trailer": [15, 151], "train": [11, 27, 30, 32, 106, 107, 109, 120, 121, 122, 127, 282], "train_bw": [27, 121], "train_vis": [27, 121], "trainer": [27, 106], "training_data": 121, "training_seq": 109, "training_seq_prob": 109, "training_set": [122, 127], "trainingsequ": [27, 106, 107, 109], "tran": [6, 13, 21, 112, 135, 139, 199, 216], "tranalign": 80, "tranaligncommandlin": [27, 79, 80], "trans_": 6, "trans_len": 6, "trans_tabl": 6, "transact": [7, 303], "transcrib": [22, 27, 236], "transcript": [0, 2, 7, 9, 11, 13, 21, 30, 35, 36, 51, 68, 275], "transcriptom": 7, "transfac": [2, 27, 283], "transfer": [6, 17, 21, 104, 113, 197, 270], "transferas": [10, 23], "transform": [4, 6, 15, 23, 32, 102, 107, 128, 129, 133, 135, 139, 158, 166, 169, 172, 175, 176, 177, 216, 222, 238, 251, 278], "transgen": 261, "transient": [7, 83, 269], "transit": [13, 32, 34, 80, 108, 109, 182, 272, 281], "transition_count": 109, "transition_prob": 108, "transition_pseudo": 108, "transitions_from": [106, 108], "transitions_to": [106, 108], "transl_tabl": [7, 21, 94, 237], "translat": [2, 3, 4, 7, 9, 12, 13, 15, 21, 23, 27, 30, 32, 34, 42, 68, 69, 76, 83, 94, 95, 98, 104, 135, 136, 139, 153, 159, 162, 163, 166, 175, 176, 216, 222, 236, 237, 245, 260, 261, 279, 280, 281, 283], "translationerror": [27, 75, 76, 236], "translationset": 7, "transliter": 123, "transloc": 113, "translocas": 272, "transmem": 272, "transmembran": [32, 53, 66, 272], "transpar": 8, "transport": 272, "transpos": [0, 4, 13, 15, 30, 54, 73, 169], "transvers": [13, 32, 34, 79, 80, 182, 281], "transweight": [30, 32], "tranvers": 80, "travers": [183, 185], "trbg361": 260, "tre": 199, "treat": [4, 5, 7, 11, 12, 15, 17, 23, 30, 31, 32, 65, 67, 69, 80, 83, 182, 197, 222, 236, 251, 260, 261, 270], "tree": [2, 4, 12, 13, 15, 27, 30, 32, 36, 37, 56, 73, 80, 128, 130, 146, 149, 176, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 193, 195, 197, 198, 199, 209, 252, 264, 280], "tree1": [17, 30, 32], "tree2": [30, 32, 132], "tree_constructor": 186, "tree_method": 280, "tree_puzzl": 65, "tree_uri": 185, "treeclust": [4, 27, 73], "treeconstruct": [13, 24, 27, 181], "treeconstructor": [27, 181, 186, 199], "treedist": 80, "treeelement": [17, 27, 181, 183, 197], "treeerror": [27, 128, 132], "treekpaiag": 250, "treemixin": [17, 27, 181, 183], "treeout": [30, 32], "treeprint": [79, 80], "treesearch": [27, 181, 199], "treetext": [185, 188, 190], "treetyp": [79, 80], "treeview": [2, 73], "trembl": [25, 89, 255], "trend": [2, 53], "tri": [1, 3, 5, 6, 12, 15, 16, 21, 23, 83, 182, 237, 264], "triacylglycerol": 25, "triangl": [4, 8, 15, 80], "triangular": 73, "tribe": 197, "trick": [6, 12, 19, 22, 23, 253], "tricki": [6, 14, 251], "trifurc": [17, 183], "trigger": [13, 27, 69, 222, 226, 251, 252, 270], "trim": [21, 238, 239, 251, 253, 268, 270, 277], "trim_adaptor": 6, "trim_prim": 6, "trimmed_primer_read": 6, "trimmed_read": 6, "trip": 19, "tripabl": 23, "tripl": [17, 119, 185, 202, 203], "triplet": 222, "triticea": 25, "triticum": 0, "trivial": [6, 7, 12, 13, 22, 23, 158], "trmviimvif": 250, "trmvvimvvf": 250, "trmvvlmvig": 250, "trna": [2, 8, 237, 250], "trna_chrom": 8, "troglodyt": [3, 20], "troubl": 24, "trout": [79, 80], "trp": [13, 265], "trr": 76, "tru1i": 206, "tru9i": 206, "true": [0, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 17, 20, 21, 22, 24, 25, 29, 30, 31, 32, 36, 37, 38, 49, 51, 52, 64, 67, 68, 69, 70, 73, 76, 80, 83, 88, 91, 94, 104, 105, 117, 125, 127, 129, 132, 135, 139, 140, 143, 148, 149, 151, 152, 153, 154, 158, 166, 168, 169, 176, 177, 179, 180, 183, 188, 190, 193, 195, 196, 197, 198, 199, 202, 203, 204, 209, 217, 218, 220, 221, 230, 231, 236, 237, 238, 251, 253, 258, 260, 261, 264, 265, 276, 277, 278, 281, 283, 287, 290, 295, 297, 299, 303, 304], "truncat": [12, 20, 30, 32, 65, 68, 129, 251, 260, 268, 270, 278, 280, 299], "trust": [52, 53, 251, 253], "trustabl": 201, "truth": 183, "try": [3, 5, 6, 7, 8, 9, 11, 12, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 45, 60, 84, 108, 149, 169, 217, 218, 236, 238, 246, 251, 253, 260, 270, 305], "trypsin": 112, "tryptophan": 288, "ts_tv_ratio": [181, 182], "tsa": 94, "tsm": 270, "tsn": 0, "tso": 0, "tspasirppagpssr": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqat": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqatggwk": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqatggwktcsgtc": 0, "tspasirppagpssrpamvssrrtrpsppgprrptgrpccsaaprrpqatggwktcsgtcttststrhrgrsgwsartttaaclrasrksmraacsrsagsrpnrfaptlmsscitsttgppawagdrsh": 0, "tspasirppagpssrrpsppgprrptgrpccsaaprrpqatggwktcsgtctt": 0, "tsq": 12, "tstart": [0, 221], "tsv": 256, "tsy": 12, "tt": [0, 21, 30, 123, 264], "tta": [13, 21, 22], "ttaa": [30, 68], "ttaaact": 0, "ttaaccccatttg": [30, 68], "ttaagaaactggaaatgagggttgaatgacaaactt": 22, "ttactcgaat": 7, "ttactctttcatctgataccttgttcagatttcaaaatagttgtagccttatcctggttt": 238, "ttaggttcgg": 7, "ttagtaaacc": 7, "ttarget": [0, 13, 30], "ttatgctttaattcaaaac": 0, "ttatttacga": 7, "ttatttctct": 7, "ttc": [22, 76], "ttcaaggcttctacacccgtactcgaatgc": 264, "ttcatataaa": 7, "ttcatttata": 7, "ttcc": 0, "ttccattgcactgcgggagggttgacccctgcgatttccccaaatgtgggaaactcgact": 30, "ttcggtaccctccatgacccacg": 62, "ttcggtaccctccatgacccacgaaatgagggcccagggtatgctt": 62, "ttctcaaatg": 7, "ttctcaagga": 7, "ttctggcgtg": 251, "tte": 68, "ttg": [13, 22], "ttgaaaa": 22, "ttgaaaaactgattattagagtcaattaaggatagt": 22, "ttgaaaacctgaatgtgagagtcactcaaggatagt": 22, "ttgaaaacctgaatgtgagagtcagtcaaggatagt": 22, "ttgacwcytgcycwg": 291, "ttgaleaayt": 0, "ttgaleaaytqatgknislseqqlvdcaggfnnf": 0, "ttgalesaia": 0, "ttgalesaiaiatgkmlslaeqqlvdcaqdfnni": 0, "ttgatcggtgacaaattttttacaaagaactgtaggacttgctacttctccctc": 23, "ttgca": 22, "ttggcaggccaaggccgatggatca": [238, 251], "ttggtctcaa": 7, "ttgnvegqhf": 0, "ttgnvegqhfisqnklvslseqnlvdcdhecmeyegeeacdegcngglqpnaynyiikng": 0, "ttgta": 11, "ttgtatcgta": 7, "ttgtcgaaag": 7, "ttgtggtgggaat": 0, "ttk": 13, "ttl": 274, "ttratio": [79, 80], "ttststrhrgrsgw": 0, "ttststrhrgrsgwsartttaaclrasrksmraacsrsagsrpnrfaptlmsscitsttg": 0, "ttt": [0, 12, 13, 21, 22, 30, 68, 76, 236], "tttaaa": 30, "tttaaaaaa": 30, "tttaaaaaaaaa": 30, "tttaaaaaaaaaaattt": 30, "tttaaacacctttttggatg": 62, "tttaaacatccctcggcccgtcgcccttttataatagcagtacg": 62, "tttaaacatccctcggcccgtcgcccttttataatagcagtacgtgagaggagcgccctaagctttgggaaattcaagc": 62, "tttc": 30, "tttcctatagctataggaccaatccacttaccatacgcccggcgtcgcccagtccggttcggtaccctccatgacccacg": 62, "tttccttttc": 0, "tttcttcggt": 7, "tttcttcgta": 7, "tttcttgcccccatagactgagaccttccctaaata": 251, "tttggtagta": 7, "tttggttact": 7, "tttggttagaa": 0, "tttt": 0, "ttttaa": 281, "ttttcagagg": 7, "ttttgccgga": 7, "ttttgtttgaatcctaaac": 0, "ttttgttttaatcctaaac": 0, "tttttagaag": 7, "tttttttctt": 7, "ttttttttggaaaggaaaac": 253, "ttwsxo45s3zcliby4x": 238, "tty": 278, "tuc2009": 8, "tuc2009_01": 8, "tuc2009_03": 8, "tuc2009_05": 8, "tuc2009_06": 8, "tuc2009_07": 8, "tuc2009_08": 8, "tuc2009_09": 8, "tuc2009_10": 8, "tuc2009_11": 8, "tuc2009_12": 8, "tuc2009_13": 8, "tuc2009_14": 8, "tuc2009_15": 8, "tuc2009_17": 8, "tuc2009_18": 8, "tuc2009_19": 8, "tuc2009_20": 8, "tuc2009_22": 8, "tuc2009_23": 8, "tuc2009_24": 8, "tuc2009_26": 8, "tuc2009_46": 8, "tuc2009_48": 8, "tuc2009_49": 8, "tuc2009_52": 8, "tumor": 7, "tune": [8, 15, 270], "tupbel1": 0, "tupl": [0, 4, 6, 8, 13, 14, 15, 16, 20, 21, 23, 30, 36, 54, 71, 73, 87, 88, 94, 99, 101, 102, 104, 105, 108, 109, 112, 113, 114, 117, 121, 134, 135, 137, 139, 149, 169, 176, 177, 183, 202, 205, 209, 210, 215, 217, 222, 231, 232, 236, 238, 241, 251, 260, 261, 264, 265, 272, 278, 297, 299, 303], "tuq": 0, "turn": [0, 1, 6, 7, 8, 9, 11, 12, 15, 17, 20, 23, 30, 32, 53, 56, 67, 68, 69, 70, 76, 80, 100, 137, 142, 182, 217, 238, 241, 251, 260, 265, 270, 272, 295, 298], "turner": 264, "turtl": [119, 185, 274], "tutori": [3, 5, 6, 9, 19, 22, 32, 56, 69, 80, 83, 92, 169, 182, 236, 238, 270, 307], "tv": 80, "tvkfkykgeekqvdiskikkvwrvgkmisftydegggktgrgavsekdapkellqmlek": 0, "tvmagyivst": 0, "tvn": 0, "tweak": [9, 83], "twelfth": 21, "twelv": 13, "twenti": 16, "twice": [30, 32, 90, 205], "two": [0, 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, 30, 32, 34, 56, 61, 67, 68, 73, 76, 80, 81, 92, 94, 99, 101, 102, 108, 109, 117, 130, 132, 135, 139, 140, 146, 155, 161, 163, 166, 169, 175, 176, 177, 182, 183, 197, 198, 209, 216, 217, 222, 226, 237, 238, 241, 244, 247, 250, 251, 252, 256, 257, 260, 261, 263, 265, 269, 270, 278, 280, 281, 282, 295, 297, 299, 300], "two_motif": 11, "twobit": [0, 23, 238, 257], "twobitio": [27, 236, 238], "twobititer": [27, 238, 257], "txid158330": 7, "txmap": 275, "txt": [0, 4, 6, 7, 10, 11, 12, 17, 20, 25, 56, 67, 80, 85, 90, 93, 104, 123, 149, 182, 217, 218, 244, 270, 272, 273, 289], "txt_1": [210, 211], "ty": [0, 11, 13, 14, 295], "type": [0, 3, 7, 8, 11, 12, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 38, 45, 53, 54, 56, 68, 69, 73, 76, 80, 83, 84, 88, 93, 101, 104, 107, 116, 117, 122, 123, 125, 127, 131, 134, 135, 136, 137, 139, 140, 149, 150, 151, 154, 155, 164, 165, 172, 176, 177, 181, 182, 183, 197, 198, 209, 211, 214, 217, 225, 229, 234, 236, 237, 238, 246, 250, 252, 260, 261, 262, 263, 264, 265, 272, 275, 276, 278, 288, 294, 295, 297], "typecod": [120, 127, 282], "typeerror": [0, 22, 236], "typic": [0, 3, 4, 7, 8, 11, 12, 13, 15, 16, 17, 21, 22, 23, 24, 25, 27, 30, 32, 34, 35, 36, 39, 45, 51, 52, 56, 67, 69, 80, 83, 112, 113, 114, 117, 123, 126, 137, 148, 149, 156, 170, 173, 182, 195, 209, 214, 236, 238, 245, 248, 250, 251, 260, 264, 270, 271, 277, 278, 298], "typvnt": 68, "tyr": [13, 154, 265], "u": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 15, 17, 19, 21, 22, 23, 25, 32, 73, 76, 80, 83, 122, 182, 236, 237, 260, 261, 268, 269, 270, 278, 300], "u1": [0, 30], "u78617": [238, 260], "uab": [34, 280], "uac": 76, "uaccgguaacauuacccggcgacu": 261, "uaccuagcuacgaaaagaaugcaguuaaugu": 66, "uag": 76, "uau": 76, "ubiquinon": [113, 272], "ubiquit": 23, "ucaacacucu": 66, "ucaauaugg": 66, "ucc": 76, "ucg": 236, "ucl": 17, "ucsc": [13, 35, 36, 37, 38, 39, 46, 51, 61, 221, 238, 247, 257], "ucsc_mm9_chr10": 0, "ucsc_test": 0, "ucsf": 15, "ucu": 76, "udf1": 122, "udf2": 122, "udf3": 122, "ufunc": 54, "uga": 76, "ugc": 76, "ugcaaggcuucuacacccguacucgaaugc": 264, "ugcaaugcaaxrzxrz": 236, "ugg": 66, "ugu": [66, 76], "ui": [7, 83], "uid": [7, 83], "uin": 123, "uint": [0, 36], "uiuc": 15, "uk": [0, 2, 6, 8, 15, 17, 32, 104, 145, 209, 210, 211, 212, 222, 234, 245, 250, 277], "ultim": [3, 19], "ultra_paralogi": 197, "umcn": [15, 137], "umist": 145, "uml": [3, 15], "un": [230, 297], "unaffect": 15, "unalign": [12, 32], "unambigu": [15, 76, 236, 261, 264, 267], "unambiguous_dna_by_id": 22, "unambiguous_dna_by_nam": 22, "unannot": 8, "unassign": 197, "unavoid": 251, "uncaught": [15, 139], "uncent": 73, "uncer": 131, "uncertain": [131, 237], "uncertainposit": [27, 237], "uncertainti": 272, "unchang": [23, 260], "uncharacter": [94, 277], "unclear": [11, 21], "uncom": 218, "uncompl": 269, "uncompress": [23, 25, 270, 278], "uncondition": 69, "unconvert": [268, 270], "undecaprenyl": 112, "undef_cod": 261, "undefin": [0, 11, 22, 36, 37, 38, 236, 251, 290], "undefined_seq": 22, "undefinedsequenceerror": [22, 27, 236], "under": [0, 2, 4, 5, 6, 7, 8, 9, 11, 12, 13, 16, 17, 19, 20, 21, 23, 24, 37, 39, 46, 67, 68, 93, 104, 109, 123, 182, 183, 217, 236, 240, 244, 247, 249, 251, 253, 300], "underflow": 107, "undergon": 14, "underli": [4, 7, 11, 13, 15, 20, 25, 67, 73, 198, 222, 238, 249, 251, 295], "underlin": 4, "underscor": [9, 214], "understand": [8, 10, 12, 19, 21, 169], "understood": 66, "undervalu": 24, "undisord": 136, "unequ": [11, 297], "unexpect": [13, 23], "unexplain": 4, "unfold": 159, "unfold_ent": [15, 27, 133, 159], "unfortun": [3, 7, 14, 23, 251], "ungap": [0, 11, 42, 68, 69, 222, 279, 281], "ungap_seq": 281, "ungapped_align": [0, 68, 70], "uni": [32, 130], "unic": 287, "unicod": [0, 13, 68, 83, 278], "unicorn_gen": 3, "unifi": [2, 11, 20], "uniform": [4, 5, 11, 23, 79, 80, 100, 182, 197, 270, 290], "unigen": [9, 27], "unigenerecord": 7, "union": [21, 150, 164, 169, 236, 237, 260], "uniparc": 274, "uniprot": [21, 23, 27, 85, 164, 197, 237, 238, 250, 252, 255, 258, 272, 273, 274], "uniprot_sprot": [23, 25], "uniprotio": [27, 238, 255], "uniprotiter": [27, 238, 258], "uniprotkb": [89, 197, 255], "uniqid": [4, 73], "uniqu": [0, 4, 6, 7, 10, 11, 12, 15, 20, 23, 69, 73, 76, 104, 108, 123, 135, 139, 159, 172, 177, 179, 180, 182, 197, 209, 210, 211, 213, 217, 234, 238, 260, 262, 270, 272, 275, 288], "unique_speci": 13, "uniqueifi": [27, 133, 159], "uniref100": 274, "uniref50": 274, "uniref90": 274, "unist": [7, 275], "unit": [6, 8, 11, 13, 16, 21, 24, 27, 53, 99, 104, 158, 172, 182, 197, 249], "unit_branch_length": [17, 183], "unit_cel": 172, "unit_nam": 283, "unittest_suit": 24, "univers": [0, 2, 3, 4, 7, 216, 253, 278], "unix": [5, 32, 67, 149, 238, 278], "unk": [15, 21, 169, 260], "unknown": [0, 3, 4, 13, 17, 20, 21, 23, 30, 68, 71, 94, 104, 109, 135, 197, 205, 214, 236, 237, 247, 250, 260, 261, 272, 279], "unknown_seq": 22, "unknownposit": [21, 27, 237], "unless": [7, 15, 21, 23, 30, 45, 60, 99, 149, 152, 153, 183, 197, 238, 246, 260, 270, 278, 288, 299], "unlik": [4, 11, 15, 20, 83, 119, 169, 182, 207, 236, 238, 260, 265, 274, 278, 288], "unlink": [128, 130], "unlov": 19, "unmap": 0, "unmodifi": [3, 21], "unnam": 215, "unnecessari": [20, 270], "unnorm": 122, "unp": 248, "unpack": [15, 136, 155], "unpair": 270, "unpars": [42, 218, 222], "unpickl": [54, 237], "unpublish": 3, "unreach": 108, "unrealist": 15, "unrecognis": 248, "unroot": [17, 128, 132], "unsign": 278, "unsignedbyt": 197, "unsignedint": 197, "unsignedlong": 197, "unsignedshort": 197, "unsort": [3, 20], "unspecifi": 15, "unstabl": 265, "unstructur": 21, "unsuit": 217, "unsur": 272, "unsurprisingli": 15, "until": [0, 3, 4, 7, 9, 23, 25, 31, 68, 84, 94, 129, 169, 198, 237, 260, 269, 270], "untitl": 0, "untransform": [175, 216], "untrim": 6, "unus": [151, 253], "unweight": [182, 199], "unwrap": 104, "unzip": [6, 278], "uof": 123, "uoffset": 278, "up": [0, 1, 3, 4, 5, 6, 7, 9, 11, 12, 14, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 59, 66, 67, 73, 83, 84, 85, 91, 93, 94, 95, 99, 104, 108, 119, 125, 132, 133, 138, 148, 169, 170, 173, 182, 183, 209, 214, 237, 238, 241, 242, 245, 251, 255, 260, 278, 299], "updat": [0, 3, 7, 8, 9, 11, 12, 24, 30, 32, 54, 76, 83, 88, 123, 136, 144, 149, 160, 169, 176, 182, 264, 295, 299], "update_dcoordspac": [133, 169], "update_emiss": [106, 109], "update_fn": [120, 121, 122], "update_ncbi_codon_t": 76, "update_pdb": [15, 133, 149], "update_transit": [106, 109], "updated": 7, "upgma": [13, 32, 80, 181, 199, 280], "upgmatre": 199, "upgmb": 32, "upgrad": 9, "upon": [15, 42, 61, 129, 218, 222, 265], "upper": [0, 11, 20, 21, 22, 27, 30, 32, 33, 38, 51, 80, 104, 162, 197, 236, 237, 241, 251, 253, 260, 274, 290], "uppercas": [16, 135, 169, 214, 236, 260, 262, 264], "upperq": 104, "uq": 0, "ura": 76, "uri": [27, 84, 181, 185, 188, 197, 198], "url": [3, 4, 7, 10, 25, 68, 70, 83, 84, 90, 105, 111, 115, 117, 119, 149, 171, 197, 198, 274], "url_bas": [3, 68, 70], "urlapi": [68, 70], "urlerror": 83, "urllib": [4, 7, 25, 83, 90], "urlopen": [4, 25, 90], "us": [0, 2, 3, 4, 5, 6, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 76, 78, 79, 80, 81, 83, 84, 89, 90, 91, 92, 93, 94, 95, 98, 99, 100, 101, 102, 103, 104, 107, 108, 109, 110, 112, 113, 114, 116, 117, 118, 119, 121, 122, 125, 126, 127, 129, 130, 131, 132, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 146, 148, 149, 151, 152, 153, 154, 155, 156, 157, 158, 162, 164, 166, 168, 169, 172, 175, 176, 177, 178, 182, 183, 186, 189, 191, 193, 195, 196, 197, 198, 199, 202, 204, 207, 208, 209, 210, 214, 216, 217, 218, 221, 222, 226, 229, 231, 236, 237, 238, 239, 240, 241, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 269, 270, 271, 272, 274, 275, 276, 277, 278, 280, 281, 282, 283, 287, 288, 290, 291, 294, 295, 296, 297, 298, 299, 302, 303, 304, 305, 306, 307], "usa": [2, 7, 80, 264], "usabl": [17, 217], "usag": [0, 1, 7, 10, 12, 17, 21, 23, 24, 25, 27, 29, 30, 45, 60, 67, 69, 83, 107, 119, 123, 133, 152, 169, 182, 199, 217, 238, 240, 246, 269, 271, 272, 274, 298], "use_fuzzi": 92, "use_index": [68, 69], "use_model_flag": 148, "use_raw_hit_id": [218, 220], "use_raw_query_id": [218, 220], "use_sw_tback": [68, 69], "usehistori": 7, "usekimura": [30, 32], "uselog": [30, 32], "user": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 24, 30, 31, 32, 45, 56, 67, 83, 104, 143, 148, 151, 157, 169, 182, 193, 195, 196, 199, 217, 218, 221, 226, 229, 236, 246, 274, 280, 281, 288, 299, 303, 305], "user_funct": 122, "userguid": [8, 229], "userlist": [15, 68], "userman": 272, "userman_doc": 245, "usernam": [68, 70, 303], "userseq1": 25, "userset": 264, "usetre": [30, 32], "usetree1": [30, 32], "usetree2": [30, 32], "usual": [0, 3, 4, 6, 8, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 30, 68, 158, 169, 183, 197, 236, 237, 238, 251, 253, 260, 269, 270], "utf": [7, 90, 236, 278], "util": [7, 10, 15, 18, 22, 27, 83, 84, 92, 106, 222, 238, 247, 265, 268, 274, 294, 304], "utiliz": 9, "utsugi": 25, "uuaaucgagcucaacacucuucguauauccuc": 66, "uuc": 76, "uucuacaaggug": 66, "uuu": 76, "uv": 25, "uveyeaqsv5edqonfoemmvea": 238, "uw": 11, "v": [0, 2, 4, 8, 11, 13, 15, 16, 22, 27, 30, 32, 73, 76, 80, 100, 152, 169, 182, 261, 265, 268, 270, 300], "v0": [105, 117], "v1": [0, 176, 265], "v2": [176, 229], "v3": [32, 176, 229], "v4": [0, 176], "v5": 0, "v6": 32, "v7": [0, 32], "v8": 0, "v_final": [98, 100], "v_init": [98, 100], "vaa": 56, "vafyifthqg": 250, "vagvan": 13, "vaivmgr": 236, "vaivmgrwkgar": 236, "val": [13, 169, 197, 202], "val1": 277, "val2": 277, "valentin": 32, "valid": [4, 6, 7, 10, 13, 15, 20, 22, 27, 32, 67, 68, 70, 71, 83, 84, 117, 119, 136, 169, 176, 182, 186, 191, 198, 207, 236, 237, 251, 252, 264, 270], "validationerror": [7, 27, 83, 84], "valin": [22, 236], "valiv": 237, "valu": [0, 2, 3, 6, 7, 8, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 23, 27, 30, 31, 32, 34, 35, 36, 37, 38, 42, 51, 53, 54, 55, 65, 67, 68, 69, 70, 71, 73, 76, 80, 82, 83, 84, 92, 93, 94, 95, 99, 100, 102, 103, 104, 105, 107, 108, 117, 119, 121, 122, 126, 127, 129, 132, 137, 141, 145, 152, 157, 158, 169, 176, 177, 181, 182, 183, 184, 186, 194, 197, 198, 199, 210, 216, 218, 221, 222, 226, 229, 230, 236, 237, 238, 241, 251, 253, 260, 261, 263, 264, 265, 267, 270, 272, 275, 277, 278, 280, 283, 286, 288, 290, 292, 295, 296, 297, 299, 300, 301, 303], "valuea": 251, "valueerror": [4, 11, 13, 17, 22, 23, 25, 27, 29, 30, 31, 56, 67, 68, 80, 84, 85, 92, 183, 217, 236, 237, 238, 241, 251, 253, 260, 261, 264, 271, 272, 278, 283, 290, 298], "valueexcept": 25, "values_are_confid": [188, 190], "values_are_support": 132, "valueset": 264, "van": [2, 8, 15, 216], "vanderauwera2009": [2, 8], "var_seq": 272, "vari": [7, 11, 16, 21, 152, 168, 238], "variabl": [3, 4, 7, 11, 12, 14, 15, 21, 23, 67, 68, 70, 73, 83, 101, 107, 109, 126, 149, 169, 175, 229, 278, 304], "varianc": 4, "variant": [2, 4, 5, 6, 12, 20, 23, 68, 104, 169, 217, 218, 238, 245, 251, 260, 264, 270, 272, 278], "variat": [2, 4, 8, 80, 168, 268, 270], "varieti": [5, 17, 197], "variou": [3, 9, 12, 15, 20, 75, 80, 158, 199, 217, 268, 278, 283, 290, 293], "vassssfad": 0, "vcnhfmvlcg": 250, "vd": 0, "vdpv": 13, "ve": [3, 5, 6, 7, 8, 12, 15, 16, 17, 19, 20, 21, 23, 24], "vecscreen": 69, "vector": [4, 8, 9, 15, 27, 34, 73, 122, 127, 133, 135, 139, 141, 169, 175, 281], "vector1": 15, "vector2": 15, "vector3": 15, "vector4": 15, "vector_to_axi": [27, 133, 176], "vectoris": 169, "vectorxscalar": 176, "vectorxvector": 176, "vendor": 298, "ver_agm3": 244, "verb": 4, "verbos": [0, 15, 17, 24, 30, 32, 42, 79, 80, 104, 136, 144, 149, 152, 153, 160, 168, 169, 193, 195, 196, 270], "veri": [0, 5, 6, 7, 8, 9, 12, 13, 15, 19, 20, 21, 22, 23, 25, 30, 32, 56, 94, 149, 158, 169, 177, 182, 209, 238, 240, 251, 253, 260, 264, 278], "verifi": [0, 4, 13, 138, 152, 169], "verlag": 2, "versa": 27, "version": [0, 1, 6, 7, 8, 9, 11, 12, 14, 15, 17, 20, 21, 23, 24, 25, 27, 29, 30, 32, 42, 45, 51, 54, 56, 65, 68, 69, 70, 71, 76, 80, 83, 84, 88, 90, 93, 132, 133, 137, 158, 169, 181, 182, 208, 209, 210, 214, 217, 218, 221, 222, 226, 227, 228, 229, 234, 236, 238, 240, 243, 251, 252, 253, 267, 269, 270, 277, 278, 283, 287, 288, 295, 298, 303], "version1": 170, "version_6": 32, "version_str": 137, "versu": 183, "vertebr": [2, 11, 22, 283, 288], "vertex": 156, "vertic": [4, 8, 23, 73, 99, 156, 197, 236], "vertre": 166, "vesca": 23, "vestergaard": 9, "vev": 0, "vg": 14, "vgmnipydga": 0, "vgmnipyhga": 0, "vh": 13, "vhmlnkgkdgamvfepaslkvapgdtvtfiptdk": 0, "vhmlnkgkdgamvfepaslkvapgdtvtfiptdkghnvetikgmipdgaeafk": 0, "vi": [7, 123, 182], "via": [3, 5, 7, 9, 12, 13, 14, 15, 17, 19, 21, 23, 24, 27, 30, 32, 35, 36, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 69, 71, 80, 99, 117, 119, 169, 182, 197, 218, 226, 229, 234, 236, 237, 238, 240, 241, 244, 245, 247, 248, 249, 250, 251, 252, 253, 255, 256, 270, 278, 285, 297, 303, 305], "vice": 27, "victor": 2, "vie": 32, "view": [2, 6, 7, 15, 21, 54, 69, 73, 100, 169, 177, 193, 195, 196, 265, 270, 278, 306], "viewer": 17, "viewpoint": 4, "vihinen": 265, "viklfkkfv": 12, "violat": 182, "viral": 23, "virginia": [59, 226], "viridiplanta": [7, 23, 25], "virlfkkfss": 12, "virtual": [15, 207, 278], "virtual_offset": 278, "viru": [6, 23, 272], "virus": [6, 23], "visibl": [0, 121, 182], "visit": [4, 239], "visual": [2, 4, 6, 7, 15, 17, 22, 30, 72, 117, 123, 141, 183], "visualis": 105, "viterbi": [30, 32, 106, 108], "viverrini": 3, "vk": 13, "vkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg": 12, "vkhfspeelk": 250, "vkkilyikalflctviklrrfifsvnnmkf": 6, "vkkmqsivlalslvlvapmaaqaaeitlvpsvklqigdrdnrgyywdgghwrdh": 22, "vklgadsgalefvpktltiksgetvnfvnnagfphnivfdedaipsg": 0, "vklgadsgalefvpktltiksgetvnfvnnagfphnivfdedaipsgvnadai": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpak": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlak": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlakslshk": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlakslshkqllmspgqststtfpadapageytfycephrgagmvgkit": 0, "vklgsdkgllvfepakltikpgdtveflnnkvpphnvvfdaalnpaksadlakslshkqllmspgqststtfpadapageytfycephrgagmvgkitv": 0, "vkr": 6, "vkvlgdviev": 250, "vldl": 25, "vllganggvlvfepndfsvkagetitfknnagyphnvvfdedavpsg": 0, "vltvsaprkq": 250, "vmd": 15, "vn": 0, "vnslek": 0, "vntifkei": 260, "vocabulari": 272, "vol": 126, "vol1": 6, "volum": [2, 3, 15, 83, 123, 156, 169], "volunt": [5, 9], "von": 264, "vorata": 2, "voucher": 7, "vpag": 0, "vpfsnktgla": 250, "vpmsnktgvv": 250, "vpnwikaarfeec": 53, "vqikmgtdkyaplyepkalsisagdtvefvmnkvgphnvifdk": 0, "vqikmgtdkyaplyepkalsisagdtvefvmnkvgphnvifdkvpagesap": 0, "vrl": 23, "vskisq": 0, "vskisqeeyltapgetfsvtltv": 0, "vspa": 250, "vss": 0, "vstv": 13, "vt": 182, "vtiqhkklrt": 250, "vtltdnvsd": 237, "vtml240": 32, "vtnalvfeivmtfglvytvyataidpkkgslgtiapiaigfivgani": 260, "vtv": 0, "vtvqhkklrt": 250, "vulgar": [0, 42, 217, 225], "vulgari": 183, "vv": [11, 295], "vvaa": 0, "vvtsvavagl": 12, "vvttvvvagl": 12, "v\u00f6hringer": 2, "w": [0, 2, 3, 4, 6, 7, 10, 11, 12, 13, 15, 22, 23, 25, 32, 40, 45, 53, 56, 57, 59, 80, 85, 91, 126, 145, 162, 169, 182, 183, 226, 236, 238, 241, 245, 246, 250, 251, 256, 261, 264, 265, 268, 270, 278, 281, 298, 299], "w3": 185, "w33": 32, "w36": 32, "w7079": 90, "w_i": 4, "w_ij": 261, "w_prot": 0, "wa": [0, 3, 4, 6, 7, 8, 9, 11, 13, 14, 15, 17, 19, 20, 21, 22, 23, 25, 27, 42, 48, 63, 65, 67, 68, 69, 71, 73, 80, 84, 88, 100, 102, 103, 108, 134, 137, 183, 185, 188, 190, 217, 218, 221, 222, 226, 229, 234, 237, 238, 240, 250, 251, 253, 260, 261, 268, 269, 278, 283, 296, 299, 303], "wacnc": 11, "wacvc": 11, "wag": [32, 181, 182], "wai": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 30, 34, 56, 65, 73, 92, 93, 99, 102, 135, 163, 169, 175, 177, 182, 183, 191, 207, 222, 229, 236, 237, 238, 260, 269, 281, 303], "wait": [7, 12, 67], "walk": 4, "wallac": [7, 32, 264], "walter": 2, "wang": [152, 169], "want": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 23, 24, 30, 32, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 92, 99, 102, 108, 149, 151, 154, 169, 182, 183, 205, 207, 218, 221, 237, 238, 241, 251, 253, 260, 278, 281, 283, 297, 298, 303], "warn": [6, 7, 8, 12, 15, 23, 25, 27, 32, 56, 79, 80, 83, 89, 108, 143, 151, 169, 197, 237, 238, 251, 260, 261, 270, 288, 300], "warren": 2, "washington": [3, 50, 65, 190, 199], "wasn": [19, 71], "wast": [3, 6, 67], "watch": [12, 23], "water": [0, 14, 41, 58, 67, 80, 138, 139, 143, 152, 157, 162, 169, 172], "water_cmd": 67, "watercommandlin": [27, 67, 79, 80], "waterloo": 0, "waterman": [0, 2, 12, 13, 14, 30, 32, 69], "waterman1987": [2, 13], "watkin": 264, "watson": [22, 32], "wayn": 2, "wb": [3, 6, 23, 36, 45], "wbiom": [201, 204], "wc": 202, "wcor413": 3, "wdvktvtgvlhhpfhltfslcpegatqsgr": 6, "we": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 35, 45, 46, 51, 59, 61, 64, 66, 67, 68, 69, 80, 84, 90, 91, 92, 93, 94, 95, 99, 100, 101, 102, 105, 107, 108, 109, 117, 166, 169, 182, 183, 191, 199, 217, 222, 236, 237, 238, 240, 241, 243, 247, 249, 251, 253, 255, 260, 265, 270, 278, 285, 287, 288, 290, 298, 302], "web": [0, 3, 7, 9, 10, 12, 15, 18, 19, 25, 68, 83, 90, 182, 218, 221, 229, 234, 272, 274], "webb": [2, 3, 68], "weblogo": [11, 27, 283], "webpag": 7, "websevic": 274, "websit": [0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 19, 21, 59, 85, 164, 197, 226, 272, 274, 283], "wed": 0, "week": 15, "weekdai": 3, "weekend": [3, 7], "weekli": [15, 149], "weight": [0, 9, 17, 30, 31, 32, 73, 79, 80, 112, 119, 120, 122, 128, 129, 132, 182, 184, 187, 189, 199, 261, 265, 272, 282, 283, 290, 296], "weight1": [30, 32], "weight2": [30, 32], "weight_filenam": [181, 182], "weight_fn": 282, "weighted_stepmatrix": [128, 129], "weighti": [30, 32], "weinberg": [18, 202, 203], "weir": [202, 203], "weird": 22, "welch": [109, 121], "welcom": [11, 20, 32, 177], "well": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 19, 20, 21, 22, 23, 25, 27, 30, 45, 53, 55, 60, 73, 116, 127, 169, 182, 183, 207, 209, 217, 218, 237, 246, 251, 253, 257, 278, 283, 295, 298, 299], "well1": 299, "well2": 299, "wellcom": [52, 251, 253], "wellid": 299, "wellrecord": [16, 27, 298, 299], "wen": 2, "wenglab": 286, "went": 67, "were": [0, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 17, 20, 22, 23, 30, 42, 63, 71, 94, 169, 219, 222, 231, 232, 237, 251, 260, 278], "western": 278, "wet": 21, "wetmur": 264, "wg": 94, "wgklqviglsmwmvlfsqrfddwlneqeda": 6, "wgkv": 13, "wgkvgahag": 14, "wgs84": 197, "whale": 272, "what": [2, 3, 4, 5, 6, 7, 8, 11, 12, 15, 20, 21, 22, 23, 24, 25, 26, 41, 58, 67, 80, 83, 99, 108, 109, 130, 146, 148, 169, 183, 199, 207, 217, 229, 236, 237, 238, 251, 260, 275, 278, 307], "whatev": [3, 8, 169], "wheel": [5, 8, 178], "wheeler": [129, 270], "whelan": 182, "when": [0, 1, 3, 4, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 34, 45, 55, 56, 59, 60, 61, 65, 66, 67, 68, 69, 70, 71, 73, 80, 81, 83, 84, 91, 93, 97, 99, 102, 104, 108, 109, 117, 132, 149, 152, 166, 169, 182, 183, 186, 188, 190, 198, 209, 214, 217, 218, 221, 222, 229, 236, 237, 238, 246, 251, 252, 253, 256, 260, 261, 263, 269, 270, 281, 282, 290, 295, 297, 298, 302, 303], "whenev": [13, 197, 221], "where": [0, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 36, 56, 59, 65, 67, 72, 82, 83, 84, 92, 93, 94, 99, 100, 103, 104, 108, 118, 121, 125, 126, 127, 129, 139, 140, 149, 154, 156, 169, 176, 177, 182, 183, 201, 202, 203, 212, 217, 221, 222, 236, 237, 238, 248, 251, 256, 260, 263, 269, 270, 272, 278, 288, 295, 297, 300, 303, 307], "wherea": [0, 4, 7, 15, 63, 83, 237], "whether": [0, 3, 4, 11, 15, 16, 17, 20, 30, 68, 70, 71, 73, 84, 92, 95, 99, 104, 127, 135, 139, 155, 168, 169, 183, 221, 222, 229, 261, 270, 279, 297, 303], "which": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 35, 37, 39, 42, 43, 45, 46, 49, 51, 52, 53, 56, 59, 63, 64, 66, 67, 68, 69, 70, 71, 73, 76, 80, 83, 84, 91, 92, 93, 94, 96, 99, 100, 101, 102, 104, 107, 108, 109, 110, 119, 120, 125, 126, 129, 132, 134, 135, 143, 148, 149, 152, 157, 166, 169, 170, 173, 175, 177, 182, 186, 197, 199, 206, 207, 209, 210, 216, 217, 229, 231, 236, 237, 238, 240, 244, 246, 248, 250, 251, 252, 253, 255, 257, 260, 261, 263, 264, 265, 268, 269, 270, 271, 272, 273, 274, 277, 278, 283, 288, 290, 294, 295, 297, 298, 299, 303], "whichcod": [79, 80], "while": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 30, 32, 45, 56, 73, 83, 90, 94, 122, 149, 153, 158, 169, 217, 218, 229, 238, 251, 257, 260, 264, 265, 272, 278, 298], "white": [2, 6, 7, 8, 23, 95, 183], "whitehead": 253, "whitelist": 67, "whitespac": [65, 94, 129, 169, 182, 230, 236, 241, 251, 264], "whitten": 7, "who": [5, 7, 11, 12, 21, 22, 30, 299], "whole": [0, 3, 6, 7, 8, 13, 15, 17, 21, 22, 23, 30, 46, 56, 61, 183, 197, 204, 205, 209, 217, 222, 238, 260, 269, 270, 297], "whose": [6, 16, 25, 30, 119, 236, 253, 260, 274, 288], "why": [6, 7, 8, 9, 12, 19, 20, 23, 30, 229, 251, 260], "wiaf": 7, "wid": 299, "wide": [2, 4, 5, 6, 9, 12, 18, 61, 251, 274, 278], "wider": 80, "width": [11, 17, 65, 79, 80, 115, 117, 129, 181, 183, 197, 198, 207, 229, 270, 278], "wiki": [5, 6, 9, 12, 17, 19, 21, 23, 53, 56, 66, 181, 227, 234, 236, 263, 301], "wikipedia": [11, 53, 66, 263], "wilczy\u0144ski": [2, 26], "wild": 15, "wildcard": [0, 11, 13, 30, 38, 51], "wildli": 20, "wilk": 137, "wilkinson": 2, "william": [0, 2, 7, 55, 149], "willing": 5, "wilm": 32, "wilson": 265, "wimalacaap": 250, "wimalacavp": 250, "wimalscaap": 250, "win32": 12, "window": [5, 6, 12, 30, 32, 61, 67, 69, 71, 182, 238, 261, 265, 267, 278], "window_masker_db": [68, 69], "window_masker_taxid": [68, 69], "window_s": [68, 69, 71, 166], "windowmask": 69, "windows": 265, "wing": 11, "wingend": 2, "wingless": 68, "wise": [0, 4, 13, 30, 182], "wish": [11, 21, 27, 45, 60, 61, 158, 182, 246, 248, 260], "with_assembli": 149, "with_prim": 6, "with_primer_trim": 6, "within": [2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 15, 19, 20, 21, 23, 24, 31, 56, 73, 80, 99, 107, 108, 146, 156, 169, 172, 182, 183, 197, 209, 217, 236, 237, 252, 253, 256, 260, 269, 270, 274, 278, 281, 288, 303, 306], "within_block_offset": 278, "withinposit": [21, 27, 237], "without": [0, 3, 4, 6, 7, 11, 12, 13, 15, 17, 21, 22, 23, 30, 56, 67, 71, 73, 80, 83, 99, 105, 113, 129, 130, 135, 166, 167, 169, 177, 182, 183, 199, 207, 214, 217, 218, 219, 221, 229, 238, 241, 251, 253, 260, 261, 270, 272, 278, 281], "wittmann": 0, "wjc39": 238, "wk": 53, "wnt": [68, 217], "wnt2": 68, "wnt3a": 68, "wnt4": 68, "wnt5a": 68, "wnt6": 68, "wolf": 145, "won": [0, 5, 6, 7, 8, 9, 12, 18, 20, 21, 23, 61, 65, 66, 149, 251, 292], "wonder": [3, 8, 19], "wong": 100, "word": [6, 7, 9, 11, 15, 20, 21, 23, 32, 68, 69, 70, 80, 129, 132, 237, 241], "word_siz": [68, 69, 70], "wordfind": 69, "wordsiz": [79, 80], "work": [0, 3, 5, 7, 8, 9, 11, 12, 14, 15, 16, 17, 20, 21, 23, 24, 30, 32, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 70, 71, 76, 87, 92, 93, 103, 107, 109, 110, 111, 112, 113, 114, 115, 119, 123, 124, 127, 137, 149, 158, 164, 169, 172, 181, 182, 193, 195, 196, 201, 205, 215, 217, 236, 237, 238, 240, 248, 249, 251, 260, 267, 270, 272, 274, 278, 298, 299], "workabl": 5, "workaround": 67, "workflow": [12, 17, 20, 222], "workhors": 23, "working_dir": [17, 181, 182, 193, 195, 196], "workselector": 169, "world": [3, 12, 19, 169], "worldwid": [9, 15], "worri": [6, 7, 17, 20, 21, 22, 23], "wors": [238, 251], "worth": 20, "would": [0, 1, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 35, 46, 51, 56, 61, 62, 63, 66, 67, 68, 69, 80, 94, 125, 149, 152, 182, 217, 236, 237, 238, 250, 251, 253, 260, 264, 270, 274, 278, 283, 298, 303], "wouldn": [6, 12, 20, 302], "wprintgc": 22, "wqfyiggv": 0, "wqfyiggvf": 0, "wqvmrl87qwcm9llo4": 238, "wr": [27, 240, 268, 269], "wrap": [9, 15, 17, 22, 23, 30, 32, 53, 66, 104, 129, 237, 238, 241, 250, 251, 303], "wrap_cursor": 303, "wrapper": [1, 3, 9, 10, 17, 30, 32, 67, 69, 80, 104, 139, 153, 155, 177, 182, 185, 188, 190, 191, 238, 270, 274, 277, 285, 303], "wright": 2, "writabl": 217, "write": [1, 4, 5, 6, 7, 8, 9, 10, 13, 17, 19, 21, 22, 25, 27, 30, 32, 33, 36, 37, 38, 40, 42, 45, 46, 47, 49, 51, 52, 56, 57, 60, 61, 62, 63, 64, 65, 66, 68, 80, 82, 85, 91, 98, 99, 101, 103, 104, 126, 129, 132, 138, 141, 148, 152, 153, 158, 164, 168, 169, 170, 173, 181, 182, 183, 185, 188, 190, 191, 198, 199, 209, 217, 218, 219, 220, 221, 229, 231, 232, 237, 238, 241, 244, 245, 246, 247, 249, 250, 251, 252, 253, 256, 259, 260, 270, 274, 277, 278, 283, 286, 287, 293, 295, 298, 299], "write_align": [30, 33, 36, 45, 49, 56, 57, 60, 61, 62, 64, 65, 66], "write_c": [268, 270], "write_cla": [27, 209], "write_cla_sql": [27, 209], "write_ctl_fil": [192, 193, 195, 196], "write_d": [27, 209], "write_des_sql": [27, 209], "write_end": 148, "write_fil": [30, 36, 37, 38, 45, 47, 49, 56, 60, 64, 217, 218, 219, 220, 221, 229, 231, 232, 238, 241, 246, 247, 250, 253, 259], "write_foot": [30, 42, 45, 56, 60, 238, 241, 246, 250, 252], "write_head": [30, 40, 42, 45, 46, 47, 51, 52, 56, 60, 61, 124, 126, 238, 241, 246, 247, 250, 252, 253], "write_hi": [27, 209], "write_hie_sql": [27, 209], "write_multiple_align": [30, 45], "write_nexus_data": [128, 129], "write_nexus_data_partit": [128, 129], "write_p": [15, 27, 133, 152, 168, 169], "write_pdb": [15, 27, 133, 168, 169], "write_record": [238, 241, 245, 246, 247, 249, 250, 251, 252, 253, 256], "write_scad": [15, 27, 133, 158, 169], "write_single_align": [30, 45], "write_to_str": [98, 104], "write_xxx_sql": 209, "writeabl": 199, "writeanc": [30, 32], "writebyproteinrec": [27, 276, 277], "writer": [0, 10, 27, 30, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 47, 49, 50, 51, 52, 53, 57, 60, 62, 64, 65, 66, 148, 181, 185, 188, 190, 191, 198, 217, 218, 219, 220, 221, 229, 231, 232, 241, 245, 246, 247, 250, 251, 253, 259, 299], "writerec": [27, 276, 277], "writetosql": [27, 209], "written": [0, 1, 3, 4, 8, 9, 12, 14, 15, 16, 17, 19, 20, 23, 30, 32, 47, 56, 65, 68, 69, 73, 80, 84, 99, 104, 129, 148, 149, 158, 166, 169, 170, 173, 182, 185, 188, 190, 193, 195, 196, 214, 217, 218, 219, 221, 222, 229, 231, 232, 238, 269, 270, 277, 286, 298], "wrong": [6, 9, 15, 21, 67, 149, 251], "wrongli": [251, 265], "wrote": [5, 12, 23, 24, 25], "wsize": 267, "wt": 14, "wu": [2, 3, 32], "wunsch": [12, 13, 30, 32], "ww": [90, 273], "wwpdb": [15, 78, 149, 150, 248], "www": [0, 5, 6, 7, 9, 10, 12, 15, 17, 19, 22, 25, 32, 52, 68, 70, 71, 83, 85, 86, 87, 88, 94, 96, 97, 99, 104, 105, 111, 115, 116, 117, 119, 122, 149, 158, 167, 170, 174, 182, 185, 188, 209, 218, 221, 222, 234, 237, 245, 248, 250, 252, 253, 258, 265, 270, 272, 273, 279, 299, 301], "www2": 15, "www6": 239, "wysok": 2, "x": [0, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 25, 30, 31, 32, 36, 56, 68, 69, 71, 73, 80, 99, 104, 115, 117, 118, 120, 127, 129, 133, 135, 136, 144, 149, 160, 169, 172, 176, 182, 185, 209, 214, 216, 221, 229, 236, 238, 243, 248, 260, 261, 264, 265, 270, 277, 279, 282, 286, 290, 297, 300], "x0": 0, "x03": 3, "x04": 3, "x1": 0, "x1e": 264, "x2": 176, "x3": 176, "x3x3": 176, "x55053": [238, 245], "x57361": 13, "x57362": 13, "x57363": 13, "x57364": 13, "x57365": 13, "x57366": 13, "x57367": 13, "x57368": 13, "x57369": 13, "x57370": 13, "x57371": 13, "x57372": 13, "x57373": 13, "x57374": 13, "x57375": 13, "x57376": 13, "x62281": [238, 245], "x77802": 303, "x92856": 21, "x_coord_list": 15, "x_i": 4, "x_posit": 99, "x_vs_y": 8, "xa": 270, "xaa": 261, "xaxis_label": 283, "xbbtool": 261, "xc": 122, "xcar": 122, "xctxctx": 12, "xcxxxxccxxxxxcxxxxxxcxxxcxxxxcxxxxxcxxx": 0, "xdna": [238, 259], "xdnaio": [27, 238], "xdnaiter": [27, 238, 259], "xdnawrit": [27, 238, 259], "xdrop_gap": [68, 69], "xdrop_gap_fin": [68, 69], "xdrop_ungap": [68, 69], "xe": 122, "xenologi": 197, "xfam": 12, "xfr": [30, 32], "xg": 0, "xgc_skew": [27, 261], "xhhhhhhhhhhhhhhhchhhhhhhhchhhhhhhhhhhhhhhhhhhhhhhc": 12, "xia": 264, "xke": 68, "xl": 104, "xlabel": 6, "xle": 261, "xlim": 6, "xm": [0, 27, 283], "xm_002875188": [3, 20], "xm_003527287": [3, 20], "xm_003539954": [3, 20], "xm_003723358": [3, 20], "xm_003827011": [3, 20], "xm_021875076": 3, "xm_776818": [3, 20], "xmax": 117, "xmfa": [47, 62], "xmin": 117, "xml": [3, 9, 11, 17, 20, 25, 32, 68, 69, 70, 71, 83, 84, 89, 105, 116, 117, 149, 150, 183, 197, 198, 217, 220, 235, 237, 238, 252, 253, 255, 258, 274, 276, 283, 289, 291, 296], "xml2": [3, 68], "xml_21500_blastn_001": 68, "xml_2212l_blastx_001": 68, "xml_2218_blastp_002": 68, "xml_2222_blastx_001": 3, "xml_2226_blastp_004": 217, "xml_2900_blastx_001_v2": 3, "xmldeclhandl": [83, 84], "xmsscanner": [27, 283, 296], "xo": 0, "xp_001487907": 7, "xp_009175831": 3, "xp_519631": 7, "xpk": [125, 126], "xpkentri": [27, 124, 126], "xpkheadlin": 126, "xpktool": [27, 124, 125], "xprtool": 125, "xr": 104, "xref": 234, "xrh_class": 169, "xsd": [84, 197, 234], "xt": 0, "xv": 122, "xx": [0, 11, 12, 14, 94, 209, 250, 295, 297], "xxmotif": 11, "xxx": [12, 24, 71, 85, 94, 107, 278], "xxxcxxxxccxxxxxcxxxxxxcxxx": 0, "xxxcxxxxccxxxxxcxxxxxxcxxxcxxxxcxxxxxcx": 0, "xxxx": [169, 273], "xxxxx": 169, "xyz": [15, 152, 168, 169, 176], "xz": [15, 169, 176], "y": [4, 6, 7, 8, 11, 12, 13, 14, 15, 22, 36, 68, 73, 76, 80, 99, 104, 115, 117, 120, 122, 129, 135, 136, 144, 145, 154, 160, 169, 172, 176, 182, 183, 216, 261, 265, 282, 297, 300, 303, 304], "y0": [16, 300], "y_": [16, 99], "y_i": 4, "y_list": 15, "y_on_x1": 216, "y_on_x2": 216, "ya19a_yeast": 277, "yaax": 22, "yakuba": 13, "yal001c": 4, "yal002w": 4, "yal003w": 4, "yal004c": 4, "yal005c": 4, "yal010c": 4, "yal019w": 277, "yal068c": 23, "yamamoto": 25, "yang": [2, 13, 34, 196, 281], "yang2000": [2, 13], "yaxis_label": 283, "yaxis_scal": 283, "yaxis_tic_interv": 283, "yb": 104, "ycar": 122, "ycf1": 7, "ycf2": 238, "ycm": [15, 169], "ydpwnlrfqskyksrda": 95, "ye": [0, 7, 69, 80, 122], "year": [6, 7, 8, 83, 197], "yeast": [4, 11, 277], "yee": 2, "yellow": [9, 122, 183], "yersinia": [6, 8, 21, 238], "yet": [4, 8, 11, 14, 17, 19, 23, 24, 30, 36, 44, 45, 80, 88, 107, 130, 132, 191, 230, 253, 274, 290], "yetfasco": [11, 283], "yeung": [2, 4], "yeung2001": [2, 4], "yfegffatlg": 250, "yfkmemgknm": 0, "yfkmemgknmcaiatcasypvvaa": 0, "yfliergknm": 0, "yfliergknmcglaacasypiplv": 0, "yiegffatlg": 250, "yield": [4, 6, 7, 11, 20, 30, 61, 64, 96, 185, 217, 219, 220, 221, 222, 226, 230, 232, 233, 241, 247, 250, 251, 253, 270, 271, 272, 273], "yiylrrgknt": 0, "yiylrrgkntcgvsnfvstsii": 0, "ykri": 206, "ylabel": 6, "ylim": 6, "ylr": 260, "ymax": 117, "ymetric": 80, "ymin": 117, "yn00": [13, 17, 34, 181, 192, 280, 281], "yn00error": [181, 192, 196], "ynpviyilmn": 250, "ynpviyimln": 250, "ynpviyivln": 250, "yongchao": 32, "yorf": 4, "york": 2, "you": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 38, 39, 40, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 73, 80, 81, 83, 90, 92, 93, 94, 95, 97, 99, 101, 102, 108, 109, 110, 119, 121, 123, 137, 140, 143, 146, 149, 151, 154, 157, 158, 159, 169, 176, 182, 183, 186, 197, 205, 207, 209, 214, 217, 218, 221, 222, 226, 229, 236, 237, 238, 240, 241, 244, 245, 246, 247, 249, 250, 251, 253, 255, 256, 260, 261, 264, 265, 269, 270, 274, 278, 281, 283, 288, 289, 290, 291, 292, 297, 298, 299, 302, 303, 305, 306, 307], "your": [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 13, 14, 17, 19, 20, 21, 22, 24, 30, 32, 56, 67, 69, 71, 80, 83, 125, 137, 149, 152, 158, 167, 169, 178, 182, 217, 218, 221, 222, 238, 251, 260, 264, 265, 270, 276, 278, 285, 288, 297, 298], "your_name_her": 129, "your_pssm": [12, 31], "yourdatabas": 11, "yourhostnam": 11, "yourpassword": 11, "yourself": [3, 5, 12, 23, 251, 260, 278, 302, 303], "yourusernam": 11, "yp_025292": 260, "yp_ppcp05": 21, "ypdyyfritnrehkaelkekfqrmcdksmikkrymylteeilkenpsmceymapsldarq": 23, "yppsvdwrkk": 0, "yqkv": 13, "yr": 14, "yrf": 6, "yripadvdpl": 250, "ysstschktp": 0, "yt": 104, "ytsdhcgttp": 0, "yukako": 2, "yv": 122, "yy": 152, "yyh": 6, "yyi": 12, "yytlkpevnn": 250, "yytlnpnfnn": 250, "yyyi": [88, 152], "yyyyyyyyywyyyywwyyywywyww": 251, "yyyyyyyyyywyyyywywwuwwwqq": 251, "yyyyyyyyyyyyywyywyysyyysi": 251, "yyyyyyyyyyyyyyyyyywwwwywi": 251, "yyyyyyyyyyyyyyyyyywywyysu": 251, "z": [0, 13, 15, 53, 135, 136, 144, 160, 169, 172, 176, 182, 197, 214, 268, 270], "z0": [169, 197], "z5100": 10, "z54145": 21, "z78439": [19, 23], "z78442": 23, "z78453": 23, "z78455": 23, "z78458": 23, "z78464": 23, "z78471": 23, "z78475": 23, "z78484": 23, "z78488": 23, "z78521": 23, "z78527": 23, "z78529": 23, "z78530": 23, "z78531": 23, "z78532": 23, "z78533": [19, 23], "z_score": 226, "z_slice": 145, "za": [169, 197], "zero": [3, 4, 7, 11, 12, 13, 14, 15, 20, 21, 22, 23, 30, 31, 35, 39, 45, 46, 51, 52, 61, 67, 68, 69, 73, 169, 199, 217, 221, 236, 237, 240, 241, 248, 250, 251, 253, 260, 261, 264, 270, 290, 297, 300], "zeta": 12, "zf": 11, "zfp": 11, "zhang": [3, 68], "zheng": [3, 68], "zhu": 2, "ziheng": 2, "ziliani": 262, "zimmerman": 265, "zinc": [11, 272, 283], "zip": [3, 8, 23, 122, 260, 278], "zipfil": 3, "zipper": 11, "zlib": [0, 36, 37, 38, 270, 278], "zmasek": 197, "zn_fing": 272, "zoom": 261, "zoop": [11, 283], "zrxzrxaacgtaacgt": 236, "zrxzrxaacguaacgu": 236, "zwieter": [299, 300], "zyxwvutsrqponmlkjhgfecb": 251, "zyxwvutsrqponmlkjihgfedcba": 251, "zzz": 12, "zzzzzzzzzzzxzvzzmvzrxrrrr": 251, "\u00e5": 15}, "titles": ["Sequence alignments", "Appendix: Useful stuff about Python", "Bibliography", "BLAST (new)", "Cluster analysis", "Where to go from here \u2013 contributing to Biopython", "Cookbook \u2013 Cool things to do with it", "Accessing NCBI\u2019s Entrez databases", "Graphics including GenomeDiagram", "Introduction", "KEGG", "Sequence motif analysis using Bio.motifs", "Multiple Sequence Alignment objects", "Pairwise sequence alignment", "Pairwise alignments using pairwise2", "Going 3D: The PDB module", "Bio.phenotype: analyze phenotypic data", "Phylogenetics with Bio.Phylo", "Bio.PopGen: Population genetics", "Quick Start \u2013 What can you do with Biopython?", "BLAST and other sequence search tools", "Sequence annotation objects", "Sequence objects", "Sequence Input/Output", "The Biopython testing framework", "Swiss-Prot and ExPASy", "Biopython Tutorial & Cookbook", "Bio package", "Bio.Affy package", "Bio.Affy.CelFile module", "Bio.Align package", "Bio.Align.AlignInfo module", "Bio.Align.Applications package", "Bio.Align.a2m module", "Bio.Align.analysis module", "Bio.Align.bed module", "Bio.Align.bigbed module", "Bio.Align.bigmaf module", "Bio.Align.bigpsl module", "Bio.Align.chain module", "Bio.Align.clustal module", "Bio.Align.emboss module", "Bio.Align.exonerate module", "Bio.Align.fasta module", "Bio.Align.hhr module", "Bio.Align.interfaces module", "Bio.Align.maf module", "Bio.Align.mauve module", "Bio.Align.msf module", "Bio.Align.nexus module", "Bio.Align.phylip module", "Bio.Align.psl module", "Bio.Align.sam module", "Bio.Align.stockholm module", "Bio.Align.substitution_matrices package", "Bio.Align.tabular module", "Bio.AlignIO package", "Bio.AlignIO.ClustalIO module", "Bio.AlignIO.EmbossIO module", "Bio.AlignIO.FastaIO module", "Bio.AlignIO.Interfaces module", "Bio.AlignIO.MafIO module", "Bio.AlignIO.MauveIO module", "Bio.AlignIO.MsfIO module", "Bio.AlignIO.NexusIO module", "Bio.AlignIO.PhylipIO module", "Bio.AlignIO.StockholmIO module", "Bio.Application package", "Bio.Blast package", "Bio.Blast.Applications module", "Bio.Blast.NCBIWWW module", "Bio.Blast.NCBIXML module", "Bio.CAPS package", "Bio.Cluster package", "Bio.Compass package", "Bio.Data package", "Bio.Data.CodonTable module", "Bio.Data.IUPACData module", "Bio.Data.PDBData module", "Bio.Emboss package", "Bio.Emboss.Applications module", "Bio.Emboss.Primer3 module", "Bio.Emboss.PrimerSearch module", "Bio.Entrez package", "Bio.Entrez.Parser module", "Bio.ExPASy package", "Bio.ExPASy.Enzyme module", "Bio.ExPASy.Prodoc module", "Bio.ExPASy.Prosite module", "Bio.ExPASy.ScanProsite module", "Bio.ExPASy.cellosaurus module", "Bio.File module", "Bio.GenBank package", "Bio.GenBank.Record module", "Bio.GenBank.Scanner module", "Bio.GenBank.utils module", "Bio.Geo package", "Bio.Geo.Record module", "Bio.Graphics package", "Bio.Graphics.BasicChromosome module", "Bio.Graphics.ColorSpiral module", "Bio.Graphics.Comparative module", "Bio.Graphics.DisplayRepresentation module", "Bio.Graphics.Distribution module", "Bio.Graphics.GenomeDiagram package", "Bio.Graphics.KGML_vis module", "Bio.HMM package", "Bio.HMM.DynamicProgramming module", "Bio.HMM.MarkovModel module", "Bio.HMM.Trainer module", "Bio.HMM.Utilities module", "Bio.KEGG package", "Bio.KEGG.Compound package", "Bio.KEGG.Enzyme package", "Bio.KEGG.Gene package", "Bio.KEGG.KGML package", "Bio.KEGG.KGML.KGML_parser module", "Bio.KEGG.KGML.KGML_pathway module", "Bio.KEGG.Map package", "Bio.KEGG.REST module", "Bio.LogisticRegression module", "Bio.MarkovModel module", "Bio.MaxEntropy module", "Bio.Medline package", "Bio.NMR package", "Bio.NMR.NOEtools module", "Bio.NMR.xpktools module", "Bio.NaiveBayes module", "Bio.Nexus package", "Bio.Nexus.Nexus module", "Bio.Nexus.Nodes module", "Bio.Nexus.StandardData module", "Bio.Nexus.Trees module", "Bio.PDB package", "Bio.PDB.AbstractPropertyMap module", "Bio.PDB.Atom module", "Bio.PDB.Chain module", "Bio.PDB.DSSP module", "Bio.PDB.Dice module", "Bio.PDB.Entity module", "Bio.PDB.FragmentMapper module", "Bio.PDB.HSExposure module", "Bio.PDB.MMCIF2Dict module", "Bio.PDB.MMCIFParser module", "Bio.PDB.Model module", "Bio.PDB.NACCESS module", "Bio.PDB.NeighborSearch module", "Bio.PDB.PDBExceptions module", "Bio.PDB.PDBIO module", "Bio.PDB.PDBList module", "Bio.PDB.PDBMLParser module", "Bio.PDB.PDBParser module", "Bio.PDB.PICIO module", "Bio.PDB.PSEA module", "Bio.PDB.Polypeptide module", "Bio.PDB.Residue module", "Bio.PDB.ResidueDepth module", "Bio.PDB.SASA module", "Bio.PDB.SCADIO module", "Bio.PDB.Selection module", "Bio.PDB.Structure module", "Bio.PDB.StructureAlignment module", "Bio.PDB.StructureBuilder module", "Bio.PDB.Superimposer module", "Bio.PDB.alphafold_db module", "Bio.PDB.binary_cif module", "Bio.PDB.cealign module", "Bio.PDB.ic_data module", "Bio.PDB.ic_rebuild module", "Bio.PDB.internal_coords module", "Bio.PDB.mmcifio module", "Bio.PDB.mmtf package", "Bio.PDB.mmtf.DefaultParser module", "Bio.PDB.mmtf.mmtfio module", "Bio.PDB.parse_pdb_header module", "Bio.PDB.qcprot module", "Bio.PDB.vectors module", "Bio.Pathway package", "Bio.Pathway.Rep package", "Bio.Pathway.Rep.Graph module", "Bio.Pathway.Rep.MultiGraph module", "Bio.Phylo package", "Bio.Phylo.Applications package", "Bio.Phylo.BaseTree module", "Bio.Phylo.CDAO module", "Bio.Phylo.CDAOIO module", "Bio.Phylo.Consensus module", "Bio.Phylo.NeXML module", "Bio.Phylo.NeXMLIO module", "Bio.Phylo.Newick module", "Bio.Phylo.NewickIO module", "Bio.Phylo.NexusIO module", "Bio.Phylo.PAML package", "Bio.Phylo.PAML.baseml module", "Bio.Phylo.PAML.chi2 module", "Bio.Phylo.PAML.codeml module", "Bio.Phylo.PAML.yn00 module", "Bio.Phylo.PhyloXML module", "Bio.Phylo.PhyloXMLIO module", "Bio.Phylo.TreeConstruction module", "Bio.PopGen package", "Bio.PopGen.GenePop package", "Bio.PopGen.GenePop.Controller module", "Bio.PopGen.GenePop.EasyController module", "Bio.PopGen.GenePop.FileParser module", "Bio.PopGen.GenePop.LargeFileParser module", "Bio.Restriction package", "Bio.Restriction.PrintFormat module", "Bio.Restriction.Restriction_Dictionary module", "Bio.SCOP package", "Bio.SCOP.Cla module", "Bio.SCOP.Des module", "Bio.SCOP.Dom module", "Bio.SCOP.Hie module", "Bio.SCOP.Raf module", "Bio.SCOP.Residues module", "Bio.SVDSuperimposer package", "Bio.SearchIO package", "Bio.SearchIO.BlastIO package", "Bio.SearchIO.BlastIO.blast_tab module", "Bio.SearchIO.BlastIO.blast_xml module", "Bio.SearchIO.BlatIO module", "Bio.SearchIO.ExonerateIO package", "Bio.SearchIO.ExonerateIO.exonerate_cigar module", "Bio.SearchIO.ExonerateIO.exonerate_text module", "Bio.SearchIO.ExonerateIO.exonerate_vulgar module", "Bio.SearchIO.FastaIO module", "Bio.SearchIO.HHsuiteIO package", "Bio.SearchIO.HHsuiteIO.hhsuite2_text module", "Bio.SearchIO.HmmerIO package", "Bio.SearchIO.HmmerIO.hmmer2_text module", "Bio.SearchIO.HmmerIO.hmmer3_domtab module", "Bio.SearchIO.HmmerIO.hmmer3_tab module", "Bio.SearchIO.HmmerIO.hmmer3_text module", "Bio.SearchIO.InterproscanIO package", "Bio.SearchIO.InterproscanIO.interproscan_xml module", "Bio.Seq module", "Bio.SeqFeature module", "Bio.SeqIO package", "Bio.SeqIO.AbiIO module", "Bio.SeqIO.AceIO module", "Bio.SeqIO.FastaIO module", "Bio.SeqIO.GckIO module", "Bio.SeqIO.GfaIO module", "Bio.SeqIO.IgIO module", "Bio.SeqIO.InsdcIO module", "Bio.SeqIO.Interfaces module", "Bio.SeqIO.NibIO module", "Bio.SeqIO.PdbIO module", "Bio.SeqIO.PhdIO module", "Bio.SeqIO.PirIO module", "Bio.SeqIO.QualityIO module", "Bio.SeqIO.SeqXmlIO module", "Bio.SeqIO.SffIO module", "Bio.SeqIO.SnapGeneIO module", "Bio.SeqIO.SwissIO module", "Bio.SeqIO.TabIO module", "Bio.SeqIO.TwoBitIO module", "Bio.SeqIO.UniprotIO module", "Bio.SeqIO.XdnaIO module", "Bio.SeqRecord module", "Bio.SeqUtils package", "Bio.SeqUtils.CheckSum module", "Bio.SeqUtils.IsoelectricPoint module", "Bio.SeqUtils.MeltingTemp module", "Bio.SeqUtils.ProtParam module", "Bio.SeqUtils.ProtParamData module", "Bio.SeqUtils.lcc module", "Bio.Sequencing package", "Bio.Sequencing.Ace module", "Bio.Sequencing.Applications package", "Bio.Sequencing.Phd module", "Bio.SwissProt package", "Bio.SwissProt.KeyWList module", "Bio.TogoWS package", "Bio.UniGene package", "Bio.UniProt package", "Bio.UniProt.GOA module", "Bio.bgzf module", "Bio.codonalign package", "Bio.codonalign.codonalignment module", "Bio.codonalign.codonseq module", "Bio.kNN module", "Bio.motifs package", "Bio.motifs.alignace module", "Bio.motifs.applications package", "Bio.motifs.clusterbuster module", "Bio.motifs.jaspar package", "Bio.motifs.jaspar.db module", "Bio.motifs.mast module", "Bio.motifs.matrix module", "Bio.motifs.meme module", "Bio.motifs.minimal module", "Bio.motifs.pfm module", "Bio.motifs.thresholds module", "Bio.motifs.transfac module", "Bio.motifs.xms module", "Bio.pairwise2 module", "Bio.phenotype package", "Bio.phenotype.phen_micro module", "Bio.phenotype.pm_fitting module", "BioSQL package", "BioSQL.BioSeq module", "BioSQL.BioSeqDatabase module", "BioSQL.DBUtils module", "BioSQL.Loader module", "API documentation", "Biopython Documentation"], "titleterms": {"": [4, 7, 15, 17], "10": 15, "3d": 15, "50": 15, "A": [8, 15, 19, 20], "In": 23, "The": [0, 3, 4, 7, 11, 13, 15, 20, 21, 24], "a2m": [0, 33], "abiio": 239, "about": [0, 1, 7, 19, 20, 237, 278], "absolut": 4, "abstract": 7, "abstractpropertymap": 134, "ac": 269, "access": [7, 11, 15, 16, 25], "aceio": 240, "acid": 13, "act": 22, "ad": [0, 21, 22], "adaptor": 6, "advanc": 238, "affi": [28, 29], "affin": 13, "aim": 278, "algorithm": 4, "align": [0, 12, 13, 14, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 238], "alignac": 284, "aligninfo": 31, "alignio": [56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66], "all": 15, "alphabet": 13, "alphafold_db": 164, "also": 197, "altloc": 15, "ambigu": 12, "amino": 13, "an": [0, 7, 11, 13, 15], "analysi": [4, 11, 34], "analyz": [13, 15, 16], "angl": [4, 15], "annot": [8, 21], "api": [10, 306], "appendix": 1, "applic": [17, 32, 67, 69, 80, 182, 270, 285], "approach": 15, "ar": 7, "argument": 3, "arrai": [0, 12, 13], "arrow": 8, "ask": 9, "associ": [7, 11, 15], "atom": [15, 135], "atomarrai": 15, "attribut": [0, 13, 15], "automat": 15, "b": 15, "bank": 15, "base": 237, "baseml": 193, "basetre": 183, "basic": 13, "basicchromosom": 99, "bed": [0, 35], "between": [4, 8, 12, 23], "bgzf": 278, "bibliographi": 2, "bigb": [0, 36], "bigmaf": [0, 37], "bigpsl": [0, 38], "binary_cif": 165, "binarycif": 15, "bio": [11, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300], "biolog": 19, "biopython": [5, 9, 19, 24, 26, 307], "bioseq": 302, "bioseqdatabas": 303, "biosql": [6, 301, 302, 303, 304, 305], "blank": 15, "blast": [0, 3, 20, 68, 69, 70, 71, 218], "blast_tab": 219, "blast_xml": 220, "blastio": [218, 219, 220], "blatio": 221, "block": 4, "bond": 15, "bottom": 8, "branch": 17, "broken": 15, "browser": 0, "bug": 5, "build": 15, "ca": 15, "calcul": [4, 12, 13, 15], "can": [9, 19], "cap": 72, "caption": 8, "case": [6, 15, 22], "categori": 25, "cd": 6, "cdao": 184, "cdaoio": 185, "cealign": 166, "celfil": 29, "cellosauru": 90, "centroid": 4, "chain": [0, 15, 39, 136], "chang": 22, "charact": 7, "checksum": [23, 262], "chi2": 194, "chromosom": 8, "cigar": 222, "citat": 7, "citi": 4, "cla": 210, "clade": 17, "class": [0, 3, 237], "clustal": 40, "clustalio": 57, "clustalw": [0, 12], "cluster": [4, 73], "clusterbust": 286, "code": [5, 8, 15], "codeml": 195, "codon": 13, "codonalign": [13, 279, 280, 281], "codonseq": 281, "codont": 76, "coeffici": 4, "color": 17, "colorspir": 100, "column": 11, "common": [0, 15], "commonli": 11, "compar": [0, 11, 22, 101], "comparison": 21, "compass": 74, "compat": 11, "complement": [0, 11, 21, 22, 23], "complet": 15, "compon": 4, "compound": 112, "compoundloc": 21, "compress": 23, "concaten": 22, "connect": 19, "consensu": [11, 12, 186], "contact": 15, "contain": [7, 15], "content": [12, 22, 26, 27, 28, 30, 32, 54, 56, 67, 68, 72, 73, 74, 75, 79, 83, 85, 92, 96, 98, 104, 106, 111, 112, 113, 114, 115, 118, 123, 124, 128, 133, 171, 177, 178, 181, 182, 192, 200, 201, 206, 209, 216, 217, 218, 222, 227, 229, 234, 238, 261, 268, 270, 272, 274, 275, 276, 279, 283, 285, 287, 298, 301, 306, 307], "contribut": 5, "control": [15, 16, 202], "convent": [20, 217], "convers": [56, 217, 238], "convert": [6, 8, 12, 20, 23], "cookbook": [5, 6, 26], "cool": 6, "coordin": [0, 15, 217], "copi": 15, "correct": 15, "correl": 4, "corrupt": 7, "cosin": 4, "count": [0, 7, 12], "creat": [0, 1, 11, 21], "cross": 8, "crystal": 15, "data": [0, 4, 6, 15, 16, 23, 75, 76, 77, 78], "databas": [6, 7, 11, 19, 23, 25], "date": 15, "db": 288, "dbutil": 304, "de": [11, 211], "deal": [3, 20], "default": 15, "defaultpars": 172, "defin": [13, 22], "demo": 17, "depth": 15, "describ": 21, "determin": 15, "diagram": 8, "dice": 138, "dictionari": 23, "dihedr": 15, "directli": 22, "discuss": 23, "disord": 15, "displayrepresent": 102, "distanc": [4, 15], "distribut": [5, 103], "do": [6, 19], "doctest": 24, "document": [5, 25, 306, 307], "dom": 212, "domtab": 229, "don": 19, "dot": 6, "down": 8, "download": [7, 15], "dssp": [15, 137], "dtd": 7, "duplic": 15, "dynamicprogram": 107, "e": 15, "each": [11, 15], "easycontrol": 203, "efetch": 7, "egqueri": 7, "einfo": 7, "elink": 7, "emboss": [0, 12, 41, 79, 80, 81, 82], "embossio": 58, "end": 7, "entir": 15, "entiti": 139, "entrez": [7, 83, 84], "entri": 6, "entropi": 11, "enzym": [25, 86, 113], "epost": 7, "error": [7, 15], "escap": 7, "esearch": 7, "espel": 7, "esummari": 7, "etc": 15, "euclidean": 4, "exact": 11, "exampl": [4, 5, 7, 8, 13, 15, 19, 90, 137, 206, 265, 278], "exoner": [0, 42, 222], "exonerate_cigar": 223, "exonerate_text": 224, "exonerate_vulgar": 225, "exonerateio": [222, 223, 224, 225], "expasi": [25, 85, 86, 87, 88, 89, 90], "export": 17, "exposur": 15, "extend": 0, "extens": 0, "extern": 17, "extract": [15, 16, 23], "factor": 15, "faq": 9, "fast": 15, "fasta": [0, 6, 19, 21, 23, 43, 226], "fastaio": [59, 226, 241], "fastq": [6, 23], "fatal": 15, "featur": [5, 8, 17, 21, 237], "field": 11, "file": [0, 4, 6, 7, 11, 12, 13, 15, 19, 20, 21, 23, 25, 56, 91, 238, 298], "filepars": 204, "filter": [3, 6], "find": [0, 7, 9, 11, 22], "format": [0, 3, 11, 12, 15, 19, 21, 23, 56, 217, 218, 221, 222, 226, 229, 234, 238, 298], "found": 11, "four": 11, "fragmentmapp": 140, "frame": [6, 217], "framework": 24, "frequenc": 0, "frequent": 9, "from": [0, 1, 5, 7, 11, 12, 13, 15, 21, 23], "full": 7, "function": [4, 17], "further": 8, "futur": 17, "fuzzi": 21, "g": 15, "gap": [0, 13], "gc": 6, "gcg": 0, "gckio": 242, "genbank": [7, 19, 21, 23, 92, 93, 94, 95], "gene": 114, "genepop": [18, 201, 202, 203, 204, 205], "gener": [4, 11, 13, 15, 19], "genet": 18, "genom": 6, "genomediagram": [8, 104], "geo": [7, 96, 97], "get": [0, 12, 23], "gfaio": 243, "glc": 15, "global": 7, "glucos": 15, "go": [5, 15], "goa": 277, "graph": 179, "graphic": [8, 15, 98, 99, 100, 101, 102, 103, 104, 105], "guidelin": 7, "ha": 11, "half": 15, "handl": [1, 4, 7], "heck": 1, "help": 5, "here": 5, "hetero": 15, "hh": 0, "hhr": 44, "hhsuite2_text": 228, "hhsuiteio": [227, 228], "hie": 213, "hierarch": 4, "histogram": 6, "histori": 7, "hit": [3, 20], "hmm": [106, 107, 108, 109, 110], "hmmer2": 229, "hmmer2_text": 230, "hmmer3": 229, "hmmer3_domtab": 231, "hmmer3_tab": 232, "hmmer3_text": 233, "hmmerio": [229, 230, 231, 232, 233], "hold": 237, "how": 15, "hsexposur": 141, "hsp": [3, 20], "hspfragment": 20, "html": 7, "huge": 7, "i": [1, 7, 9, 15, 17, 19], "ic_data": 167, "ic_rebuild": 168, "id": 7, "ident": 0, "identifi": [6, 7], "igio": 244, "includ": 8, "index": [0, 6, 20, 23], "indic": 0, "inform": [0, 7, 12, 17, 237], "input": [23, 56, 217, 238, 298], "insdcio": 245, "instal": 9, "instanc": 11, "integ": 13, "integr": 17, "interfac": [45, 60, 246], "intern": 15, "internal_coord": [15, 169], "internet": 3, "interpol": 16, "interproscan": 234, "interproscan_xml": 235, "interproscanio": [234, 235], "introduct": [3, 8, 9, 278], "isoelectricpoint": 263, "item": 7, "iter": [13, 15, 23], "iupacdata": 77, "jaspar": [11, 287, 288], "k": 4, "keep": 15, "kegg": [10, 111, 112, 113, 114, 115, 116, 117, 118, 119], "kei": 23, "kendal": 4, "keywlist": 273, "keyword": 25, "kgml": [115, 116, 117], "kgml_parser": 116, "kgml_pathwai": 117, "kgml_vi": 105, "knn": 282, "kreitman": 13, "larg": 20, "largefilepars": 205, "layout": 0, "lcc": 267, "length": [6, 15], "letter": 0, "level": 23, "like": 22, "lineag": 7, "link": [8, 11], "list": [5, 7, 23, 25], "load": 13, "loader": 305, "local": [3, 15], "locat": [21, 237], "logisticregress": 120, "logo": 11, "loop": 15, "love": 19, "low": 23, "m10": 226, "maf": [0, 46], "mafio": 61, "mail": 5, "maintain": 5, "make": 6, "manipul": [12, 16], "map": [0, 4, 15, 118], "markovmodel": [108, 121], "mast": [11, 289], "match": [11, 13], "matric": [11, 12, 13], "matrix": [4, 11, 12, 13, 290], "mauv": [0, 47], "mauveio": 62, "maxentropi": 122, "mcdonald": 13, "mean": 4, "measur": 15, "median": 4, "medlin": [7, 123], "medoid": 4, "meltingtemp": 264, "meme": [11, 291], "memori": 23, "messag": 7, "meta": 13, "method": [17, 21], "microarrai": 16, "minim": 292, "mismatch": [0, 13], "miss": [4, 7], "mmcif": 15, "mmcif2dict": 142, "mmcifio": 170, "mmcifpars": 143, "mmtf": [15, 171, 172, 173], "mmtfio": 173, "mode": 278, "model": [15, 20, 144], "modif": 17, "modifi": [15, 23], "modul": [11, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305], "moieti": 15, "molecular": 15, "motif": [11, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296], "msf": [0, 48], "msfio": 63, "multi": 0, "multigraph": 180, "multipl": [0, 8, 12, 13, 238], "muscl": 12, "mutableseq": 22, "mutat": 15, "naccess": 145, "naivebay": 127, "namespac": 278, "navig": 15, "ncbi": [3, 7], "ncbiwww": 70, "ncbixml": 71, "needl": 12, "neighborhood": 15, "neighborsearch": 146, "net": 23, "new": [3, 12], "newcom": 5, "newick": 189, "newickio": 190, "nexml": 187, "nexmlio": 188, "next": 19, "nexu": [0, 49, 128, 129, 130, 131, 132], "nexusio": [64, 191], "nibio": 247, "nice": 8, "nmr": [124, 125, 126], "node": 130, "noetool": 125, "nonsynonym": 13, "note": [20, 65], "novo": 11, "nucleotid": [6, 7, 13, 22], "number": [4, 13], "o": 17, "object": [0, 11, 12, 13, 15, 17, 20, 21, 22, 23], "obtain": [3, 7, 11, 15], "off": 6, "old": [3, 8], "onto": 15, "open": 6, "oper": 0, "option": 8, "order": 217, "organ": [4, 7], "other": [3, 15, 20], "otherwis": 7, "out": 15, "output": [0, 3, 20, 23, 56, 217, 238, 298], "over": [3, 13, 15, 23], "overview": 19, "packag": [9, 27, 28, 30, 32, 54, 56, 67, 68, 72, 73, 74, 75, 79, 83, 85, 92, 96, 98, 104, 106, 111, 112, 113, 114, 115, 118, 123, 124, 128, 133, 171, 177, 178, 181, 182, 192, 200, 201, 206, 209, 216, 217, 218, 222, 227, 229, 234, 238, 261, 268, 270, 272, 274, 275, 276, 279, 283, 285, 287, 298, 301], "pairwis": [0, 13, 14], "pairwise2": [14, 297], "paml": [17, 192, 193, 194, 195, 196], "paramet": 16, "pars": [3, 6, 7, 10, 12, 15, 16, 19, 23, 25], "parse_pdb_head": 174, "parser": [7, 23, 84], "partial": 22, "partit": 4, "pathwai": [177, 178, 179, 180], "pattern": 0, "pdb": [15, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176], "pdbdata": 78, "pdbexcept": 147, "pdbio": [148, 248], "pdblist": 149, "pdbml": 15, "pdbmlparser": 150, "pdbparser": 151, "pearson": 4, "per": 13, "perform": [4, 13], "perl": 11, "pfm": [11, 293], "phd": 271, "phdio": 249, "phen_micro": 299, "phenotyp": [16, 298, 299, 300], "phylip": [0, 50], "phylipio": 65, "phylo": [17, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199], "phylogenet": 17, "phyloxml": [17, 197], "phyloxmlio": 198, "pic": 15, "picio": 152, "pirio": 250, "plan": 17, "platform": 5, "pleas": 19, "plot": [6, 15], "plu": 6, "pm_fit": 300, "point": 15, "polypeptid": [15, 154], "popgen": [18, 200, 201, 202, 203, 204, 205], "popul": 18, "posit": [11, 12, 21], "pqr": 15, "pre": 13, "predefin": 13, "prematur": 7, "present": 15, "primari": 7, "primer": 6, "primer3": 81, "primersearch": 82, "princip": 4, "print": [0, 15], "printformat": 207, "problem": 15, "prodoc": 87, "produc": 6, "properti": 4, "prosit": [25, 88], "prot": 25, "protein": 15, "protparam": 265, "protparamdata": 266, "provid": 19, "proxi": 7, "psea": 153, "psi": 3, "psl": [0, 51], "pssm": 11, "pubm": 7, "python": [1, 217], "qcprot": 175, "qual": 6, "qualiti": 6, "qualityio": 251, "queri": [7, 10], "queryresult": 20, "question": [9, 15], "quick": [12, 19], "raf": 214, "random": [4, 6], "rank": 4, "raw": [16, 23], "read": [0, 6, 11, 12, 13, 15, 20, 23], "rebuild": 15, "record": [3, 7, 10, 23, 25, 93, 97, 238, 298], "refer": [11, 21, 166, 237], "rel": 11, "relat": [6, 7, 15], "rep": [178, 179, 180], "report": 5, "repres": 4, "represent": [4, 15], "request": 5, "residu": [15, 155, 215], "residuedepth": 156, "resseq": 15, "rest": 119, "restrict": [206, 207, 208], "restriction_dictionari": 208, "result": [3, 4], "retriev": [7, 25], "revers": [0, 11, 13, 21, 22, 23], "round": 23, "row": 11, "rp": 3, "run": [3, 17, 24], "sam": [0, 52], "sasa": 157, "save": [3, 4], "scadio": 158, "scan": 25, "scanner": 94, "scanprosit": 89, "scop": [209, 210, 211, 212, 213, 214, 215], "score": [6, 11, 12, 13], "scratch": 21, "search": [7, 11, 17, 20, 25], "searchio": [20, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235], "secondari": 15, "see": 197, "seguid": 23, "select": [11, 15, 159], "self": 4, "seq": [22, 236], "seqfeatur": [8, 21, 237], "seqio": [238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259], "seqrecord": [21, 23, 260], "sequenc": [0, 6, 7, 11, 12, 13, 15, 19, 20, 21, 22, 23, 217, 237, 268, 269, 270, 271], "sequtil": [261, 262, 263, 264, 265, 266, 267], "seqxmlio": 252, "server": 25, "set": 8, "sff": 6, "sffio": 253, "shape": 0, "sigil": 8, "simpl": [6, 8, 19], "simpleloc": 21, "singl": [12, 238, 298], "site": [11, 13], "slice": [0, 11, 12, 21, 22], "snapgeneio": 254, "solut": 4, "some": 15, "sort": [0, 3, 6], "space": 0, "spearman": 4, "special": 7, "specif": [11, 12, 15], "specifi": [23, 237], "spell": 7, "sphere": 15, "standalon": 3, "standard": 20, "standarddata": 131, "start": 19, "stockholm": [0, 53], "stockholmio": 66, "stop": 19, "store": [6, 11], "strand": [13, 217], "string": [1, 12, 22, 23], "structur": [15, 160], "structurealign": 161, "structurebuild": 162, "stuff": 1, "style": [12, 217], "submodul": [27, 28, 30, 56, 68, 75, 79, 83, 85, 92, 96, 98, 106, 111, 115, 124, 128, 133, 171, 178, 181, 192, 201, 206, 209, 217, 218, 222, 227, 229, 234, 238, 261, 268, 272, 276, 279, 283, 287, 298, 301], "subpackag": [27, 30, 98, 111, 133, 177, 181, 200, 217, 268, 283], "subsequ": 22, "substitut": [0, 12, 13], "substitution_matric": 54, "subtract": 16, "suggest": 7, "suit": 0, "summari": [7, 12], "superimpos": [15, 163], "support": [15, 217, 218, 221, 222, 226, 229, 234], "svdsuperimpos": 216, "swiss": 25, "swissio": 255, "swissprot": [23, 272, 273], "synonym": 13, "t": 19, "tab": [218, 229], "tabio": 256, "tabl": [22, 26, 307], "tabular": [0, 55], "talk": 19, "tau": 4, "technic": 278, "term": 7, "test": [5, 13, 15, 21, 24], "text": [222, 229, 278], "tfb": 11, "thi": 278, "thing": 6, "threshold": [11, 294], "through": 15, "todo": 169, "togow": 274, "tool": [12, 20], "top": 8, "torsion": 15, "tox": 24, "track": 8, "trainer": 109, "transcript": 22, "transfac": [11, 295], "translat": [6, 22], "travers": 17, "tree": [17, 132], "treeconstruct": 199, "treeview": 4, "trim": 6, "trip": 23, "turn": 22, "tutori": [24, 26], "two": 15, "twobitio": 257, "type": 4, "ucsc": 0, "uncent": 4, "unigen": [7, 275], "uniprot": [25, 276, 277], "uniprotio": 258, "unit": 5, "unittest": 24, "unknown": 22, "up": [8, 15], "upload": 7, "upper": 6, "us": [1, 7, 11, 13, 14, 15, 17, 23, 24], "usag": [13, 19, 137], "util": [95, 110], "valu": [4, 15, 217], "vector": 176, "version": 3, "view": 17, "vulgar": 222, "warn": 278, "water": [12, 15], "webenv": 7, "weight": [4, 11], "well": [15, 16], "what": [1, 9, 17, 19], "where": 5, "who": 15, "within": 17, "without": 8, "work": [6, 19, 22], "write": [0, 3, 11, 12, 15, 16, 20, 23, 24], "xdnaio": 259, "xm": 296, "xmfa": 0, "xml": [7, 15, 218, 234], "xpktool": 126, "yn00": 196, "you": 19, "your": [12, 23]}})
\ No newline at end of file