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    12 repositories

    • TOGA2

      Public
      TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments
      C
      •
      MIT License
      •1•20•3•0•Updated Jan 5, 2026Jan 5, 2026

    • make_lastz_chains

      Public
      Portable solution to generate genome alignment chains using lastz
      bioinformaticsgenomicsbioinformatics-pipeline
      Python
      •
      MIT License
      •14•60•15•1•Updated Dec 20, 2025Dec 20, 2025

    • TOGA

      Public
      TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
      bioinformaticsgenomicsbioinformatics-pipelinegenome-annotation
      Python
      •
      MIT License
      •27•202•2•1•Updated Nov 23, 2025Nov 23, 2025

    • TFforge

      Public
      Identifying transcription factors involved in phenotypic differences between species
      Python
      •
      MIT License
      •3•1•3•0•Updated Oct 27, 2024Oct 27, 2024

    • REforge

      Public
      Regulatory Element Forward Genomics to associate transcription factor binding site divergence in regulatory elements with phenotypic differences between species
      Python
      •
      MIT License
      •3•8•6•0•Updated Oct 27, 2024Oct 27, 2024

    • GenomeAlignmentTools

      Public
      Tools for improving the sensitivity and specificity of genome alignments
      C
      •
      MIT License
      •16•58•14•0•Updated Jan 17, 2024Jan 17, 2024

    • IterativeErrorCorrection

      Public
      Iterative error correction of long reads
      Python
      •
      MIT License
      •3•13•4•1•Updated Dec 9, 2022Dec 9, 2022

    • CESAR2.0

      Public
      C
      •
      MIT License
      •11•29•8•0•Updated Dec 1, 2022Dec 1, 2022

    • GeneLossPipe

      Public
      Perl
      •
      MIT License
      •7•25•2•0•Updated Nov 29, 2022Nov 29, 2022

    • ForwardGenomics

      Public
      Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework
      Perl
      •
      MIT License
      •8•24•9•0•Updated Nov 29, 2022Nov 29, 2022

    • Parasol_LSF_Slurm

      Public
      A parasol-like wrapper around LSF or Slurm for efficiently handling batches of jobs on a compute cluster
      Perl
      •
      MIT License
      •2•2•4•0•Updated Jan 14, 2021Jan 14, 2021

    • CESAR

      Public
      Coding Exon Structure Aware Realigner
      Python
      •
      MIT License
      •1•5•0•1•Updated Mar 30, 2017Mar 30, 2017