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    57 repositories

    • sufr

      Public
      Parallel Construction of Suffix Arrays in Rust
      bioinformaticsalgorithmlcpsuffix-array
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•9•0•0•Updated Nov 12, 2024Nov 12, 2024

    • DIPLOMAT

      Public
      Deep learning-based Identity Preserving Labeled-Object Multi-Animal Tracking (Beta)
      machine-learningdeep-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•3•0•Updated Nov 7, 2024Nov 7, 2024

    • BATH

      Public
      Better Alignments with Translated HMMER
      bioinformaticshidden-markov-modelsframeshifts
      C
      •
      Other
      •3•15•0•1•Updated Oct 30, 2024Oct 30, 2024

    • nail

      Public
      Nail is an Alignment Inference tooL
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•36•0•0•Updated Oct 30, 2024Oct 30, 2024

    • strobemers

      Public
      Strobemers in Rust
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 26, 2024Oct 26, 2024

    • nail-benchmarks

      Public
      A collection of reproducible benchmarks for nail
      Python
      •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • ULTRA

      Public
      ULTRA Locates Tandemly Repetitive Areas
      bioinformaticstandem-repeats
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•23•1•0•Updated Sep 13, 2024Sep 13, 2024

    • aurora

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Sep 11, 2024Sep 11, 2024

    • NINJA

      Public
      Nearly Infinite Neighbor Joining Application
      C
      •
      MIT License
      •7•5•19•0•Updated Sep 10, 2024Sep 10, 2024

    • AvxWindowFmIndex

      Public
      A fast, AVX2 and ARM Neon accelerated FM index library
      cbioinformaticsdata-structuresfm-index
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •3•30•0•0•Updated Aug 13, 2024Aug 13, 2024

    • sculu-rs

      Public
      Rust implementation of SCULU (Subfamily Clustering Using Label Uncertainty)
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • seqr

      Public
      FASTX sequence tool
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • face

      Public
      Processing FAISS hits with Python/Rust
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 12, 2024Jul 12, 2024

    • tallyman

      Public
      Tallyman helps you count sequence occurrences
      Jupyter Notebook
      •1•0•14•6•Updated Jun 28, 2024Jun 28, 2024

    • easel

      Public
      Sequence analysis library used by Eddy/Rivas lab code
      C
      •
      Other
      •26•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • atlas_md_download

      Public
      Download MD from https://www.dsimb.inserm.fr/ATLAS/index.html
      Python
      •0•0•0•0•Updated May 14, 2024May 14, 2024

    • trans-hmmer

      Public archive
      Fork of HMMER, containing translated search variants: hmmsearcht and hmmscant
      C
      •
      Other
      •70•1•0•0•Updated May 9, 2024May 9, 2024

    • wikijs

      Public
      Wiki.js | A modern and powerful wiki app built on Node.js | Wheeler Lab fork
      Vue
      •
      GNU Affero General Public License v3.0
      •2.7k•0•0•0•Updated May 7, 2024May 7, 2024

    • NEAR

      Public
      Makefile
      •0•2•0•0•Updated Apr 19, 2024Apr 19, 2024

    • Diviner

      Public
      Using Mirage2 MSAs to uncover exons hiding in plain sight
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 8, 2024Apr 8, 2024

    • VIBES

      Public
      Viral Integrations in Bacterial genomES
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•7•0•Updated Apr 1, 2024Apr 1, 2024

    • BATH-paper

      Public
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • VIBES-paper

      Public
      Nextflow
      •0•0•0•0•Updated Mar 17, 2024Mar 17, 2024

    • FastaVector

      Public
      A C library for reading/writing entire fasta files. Fasta files are loaded into internal buffers that store all headers and sequences such that each sequence and header can be found via a simple lookup function.
      bioinformatics
      C
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Mar 16, 2024Mar 16, 2024

    • hmmer

      Public
      HMMER: biological sequence analysis using profile HMMs
      C
      •
      Other
      •70•0•0•0•Updated Mar 11, 2024Mar 11, 2024

    • polyA

      Public
      Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)
      bioinformaticssequence-alignmentcompeting-annotationsconfidence-calculations
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•5•4•Updated Mar 8, 2024Mar 8, 2024

    • Mirage

      Public
      Mirage generates multiple sequence alignments of proteoforms by mapping sequences back to their coding regions on the genome and then compressing those mappings into alignments.
      biologyproteoformsbioinformatics
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •4•9•0•0•Updated Jan 5, 2024Jan 5, 2024

    • WASITAMATchISAW

      Public
      Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences
      benchmarkalignmentpalindromeproteomicspalindromessequence-alignmentfalse-positivereversaldecoydecoys
      Jupyter Notebook
      •0•0•0•0•Updated Jan 5, 2024Jan 5, 2024

    • P7HmmReader

      Public
      A simple C file reader for P7 profile HMM files generated by HMMER3 and other tools
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Dec 5, 2023Dec 5, 2023

    • HAVAC

      Public
      Hardware Accellerated Viterbi Additional Coprocessor (HAVAC) is an FPGA-accellerated implementation of the Single-segment Ungapped Viterbi algorithm for use in nucleotide sequence homology search
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Nov 14, 2023Nov 14, 2023