Module: SeedSequence

The SeedSequence module generates initial infection sequence(s) and infection time(s) for a given seed node. See the source code to see what is defined by the abstract class.

List of Implementations

SeedSequence_CommunityVirusMigrationCoalescentGTRGamma

A migration coalescent tree is simulated where leaves are seed individuals labeled by their community, coalescence can only occur between individuals of the same community, and migration occurs across the communities at a user-specified rate
- The result is a single phylogenetic history for the seed sequences, but such that there is preference for coalescence between seeds in the same community (but coalescence across communities is not disallowed)
Then, a single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit and is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- msms
- Seq-Gen
- Must use a ContactNetworkGenerator module that creates communities
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- msms_path: The path to your msms executable (or simply "msms" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- community_seed_populations: The desired (constant) population size for each community's coalescent process (a list of positive integers)
  - See the msms manual for more information
- community_seed_migration_rates: The desired migration rates across communities, represented as a 2-dimensional dictionary where keys are integers representing the communities (0-based), e.g.:
```
{
    0: {
           1: 0.3, # migration rate from 0 to 1
           2: 0.5, # migration rate from 0 to 2
           ...
       },
    1: {
           0: 0.1, # migration rate from 1 to 0
           2: 0.6, # migration rate from 1 to 2
           ...
       },
       ...
}
```
  - See the msms manual for more information
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

SeedSequence_CommunityVirusPureCoalescentGTRGamma

The seeds in each community are coalesced via pure neutral Kingman Coalescence, and then the roots of the communities' trees are coalesced again
- The result is a single phylogenetic history for the seed sequences, but with the restriction that all seeds in a given community are in the same clade
Then, a single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit and is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
- Must use a ContactNetworkGenerator module that creates communities
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- community_root_population : The desired (constant) population size of the coalescent process of the roots of the communities' seed trees
- community_seed_populations: The desired (constant) population size for each community's coalescent process (a list of floats)
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

SeedSequence_HMMBuildEmit

A profile HMM is created from a user-specified multiple sequence alignment using hmmbuild, and seed sequences are randomly generated from this profile HMM using the hmmemit tool in the HMMER toolkit
Requirements:
- HMMER
Config Parameters:
- hmmbuild_path: The path to your hmmbuild executable (or simply "hmmbuild" if it is in your PATH variable)
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- hmmbuild_msafile: File containing multiple sequence alignment from which to create a profile HMM
- hmmbuild_options: The command-line options with which to run hmmbuild_options (just the options, not hmmfile_out nor msafile)
- hmmemit_options: The command-line options with which to run hmmemit (just the options, not hmmfile: you will specify hmmfile in the hmmemit_hmmfile config parameter)
  - Do not use the -o argument, as we use standard output to parse the hmmemit output

SeedSequence_HMMEmit

Seed sequences are randomly generated from a profile HMM using the hmmemit tool in the HMMER toolkit
Requirements:
- HMMER
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- hmmemit_hmmfile: File containing profile HMM(s) from which to generate seed sequences
  - If a file is specified containing multiple profile HMMs, a sequence will be generated from each and randomly selected with a uniform distribution
- hmmemit_options: The command-line options with which to run hmmemit (just the options, not hmmfile: you will specify hmmfile in the hmmemit_hmmfile config parameter)
  - Do not use the -o argument, as we use standard output to parse the hmmemit output

SeedSequence_NoSeqs

No sequences are generated
Requirements:
- Must use SequenceEvolution_NoSeqs module
- Must use Sequencing_NoSeqs module
Config Parameters:
- None

SeedSequence_PANGEA

Wrapper for PANGEA.HIV.sim
This is not supported in the Docker/Singularity images from FAVITES 1.1.11 onward
Requirements:
- R
- PANGEA.HIV.sim
- Must use ContactNetwork_PANGEA module
- Must use ContactNetworkGenerator_PANGEA module
- Must use EndCriteria_Instant module
- Must use NodeEvolution_PANGEA module
- Must use NodeSample_PANGEA module
- Must use NumBranchSample_All module
- Must use NumTimeSample_PANGEA module
- Must use PostValidation_Dummy module
- Must use SeedSelection_PANGEA module
- Must use SeedSequence_PANGEA module
- Must use SequenceEvolution_PANGEA module
- Must use SourceSample_PANGEA module
- Must use TimeSample_PANGEA module
- Must use TransmissionNodeSample_PANGEA module
- Must use TransmissionTimeSample_PANGEA module
- Must use TreeUnit_Same module
Config Parameters
- Rscript_path: The path to your Rscript executable (or simply "Rscript" if it is in your PATH variable)
- All pangea_ parameters, which correspond to PANGEA.HIV.sim parameters (see entry in FAVITES_ModuleList.json for complete list, and see PANGEA.HIV.sim help for details)
  - Use "" for default

SeedSequence_Random

Seed sequences are randomly generated from the DNA alphabet with equal probability for each nucleotide
Requirements:
- None
Config Parameters:
- seed_sequence_length: The desired length of the seed sequences

SeedSequence_RandomCodon

Seed sequences are randomly generated from the 61 non-STOP codons with equal probability for each codon
Requirements:
- None
Config Parameters:
- seed_sequence_codon_length : The desired number of codons in the seed sequences (i.e., seeds will have 3 times this length)

SeedSequence_RandomWeighted

Seed sequences are randomly generated from the DNA alphabet with user-specified nucleotide frequencies
Users specify Pr(A), Pr(C), and Pr(G), and Pr(T) = 1 - Pr(A) - Pr(C) - Pr(G)
Requirements:
- None
Config Parameters:
- seed_sequence_length: The desired length of the seed sequences
- seed_prob_A: Probability of A
- seed_prob_C: Probability of C
- seed_prob_G: Probability of G

SeedSequence_User

Seed sequences specified by the user
Requirements:
- None
Config Parameters:
- num_seeds: The desired number of seed nodes
- seed_seqs: A list containing the seed sequences (seed_seqs must contain exactly num_seeds sequences)

SeedSequence_Virus

Seed sequences are randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit
Requirements:
- HMMER
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options

SeedSequence_VirusBirthDeathGTRCodon

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, a Birth-Death tree with one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Codon model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_birth_rate: The desired birth rate of the simulated Birth-Death tree
- seed_death_rate: The desired death rate of the simulated Birth-Death tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_codon_site1_rate: The desired rate of heterogeneity for site 1 of a codon
- seqgen_codon_site2_rate: The desired rate of heterogeneity for site 2 of a codon
- seqgen_codon_site3_rate: The desired rate of heterogeneity for site 3 of a codon

SeedSequence_VirusBirthDeathGTRGamma

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, a Birth-Death tree with one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_birth_rate: The desired birth rate of the simulated Birth-Death tree
- seed_death_rate: The desired death rate of the simulated Birth-Death tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

SeedSequence_VirusMeanCoalescentGTRCodon

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, the a Kingman Coalescent tree with expected coalescent times and one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Codon model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_population: The desired (constant) population size of the simulated coalescent tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_codon_site1_rate: The desired rate of heterogeneity for site 1 of a codon
- seqgen_codon_site2_rate: The desired rate of heterogeneity for site 2 of a codon
- seqgen_codon_site3_rate: The desired rate of heterogeneity for site 3 of a codon

SeedSequence_VirusMeanCoalescentGTRGamma

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, a Kingman Coalescent tree with expected coalescent times and one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_population: The desired (constant) population size of the simulated coalescent tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

SeedSequence_VirusNonHomYuleHeightGTRGamma

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, a non-homogeneous Yule tree with one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- HMMER
- Seq-Gen
- TreeSAP
- TreeSwift
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_height: The desired height of the simulated non-homogeneous Yule tree
- seed_speciation_rate_func: The desired speciation rate function of the simulated non-homogeneous Yule tree
  - E.g. "x**2 + 5"
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

SeedSequence_VirusPureCoalescentGTRCodon

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, the a pure neutral Kingman Coalescent tree with one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Codon model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_population: The desired (constant) population size of the simulated coalescent tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_codon_site1_rate: The desired rate of heterogeneity for site 1 of a codon
- seqgen_codon_site2_rate: The desired rate of heterogeneity for site 2 of a codon
- seqgen_codon_site3_rate: The desired rate of heterogeneity for site 3 of a codon

SeedSequence_VirusPureCoalescentGTRGamma

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, a pure neutral Kingman Coalescent tree with one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- DendroPy
- HMMER
- Seq-Gen
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_population: The desired (constant) population size of the simulated coalescent tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

SeedSequence_VirusYuleHeightGTRGamma

A single root sequence is randomly generated from a profile HMM prebuilt for a user-specified virus using the hmmemit tool in the HMMER toolkit, a Yule tree with one leaf per seed node is simulated, and the root sequence that was generated is evolved down the tree under a GTR Gamma model to generate a seed sequence for each seed node
Requirements:
- HMMER
- Seq-Gen
- TreeSAP
- TreeSwift
Config Parameters:
- hmmemit_path: The path to your hmmemit executable (or simply "hmmemit" if it is in your PATH variable)
- seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
- viral_sequence_type: The desired type of viral sequence to generate
  - See the URL variable at the beginning of the SeedSequence_Virus source code for valid options
- seed_height: The desired height of the simulated Yule tree
- seqgen_a_to_c: The desired transition rate from A to C (and C to A)
- seqgen_a_to_g: The desired transition rate from A to G (and G to A)
- seqgen_a_to_t: The desired transition rate from A to T (and T to A)
- seqgen_c_to_g: The desired transition rate from C to G (and G to C)
- seqgen_c_to_t: The desired transition rate from C to T (and T to C)
- seqgen_g_to_t: The desired transition rate from G to T (and T to G)
- seqgen_freq_a: The desired frequency of A
- seqgen_freq_c: The desired frequency of C
- seqgen_freq_g: The desired frequency of G
- seqgen_freq_t: The desired frequency of T
- seqgen_gamma_shape: The desired shape parameter of the Gamma distribution for site rate heterogeneity
- seqgen_num_gamma_rate_categories: The desired number of rate categories of the Gamma distribution for site rate heterogeneity (or "" for the default value, which is 0)

Niema Moshiri & Siavash Mirarab 2016

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