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  1. TOGA 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 o…

    Python 169 23

  2. GenomeAlignmentTools GenomeAlignmentTools Public

    Tools for improving the sensitivity and specificity of genome alignments

    C 57 15

  3. make_lastz_chains make_lastz_chains Public

    Portable solution to generate genome alignment chains using lastz

    Python 54 8

  4. CESAR2.0 CESAR2.0 Public

    C 28 10

  5. GeneLossPipe GeneLossPipe Public

    Perl 24 7

  6. ForwardGenomics ForwardGenomics Public

    Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework

    Perl 22 8

Repositories

Showing 10 of 11 repositories
  • TFforge Public

    Identifying transcription factors involved in phenotypic differences between species

    Python 1 MIT 3 3 0 Updated Oct 27, 2024
  • REforge Public

    Regulatory Element Forward Genomics to associate transcription factor binding site divergence in regulatory elements with phenotypic differences between species

    Python 8 MIT 3 6 0 Updated Oct 27, 2024
  • make_lastz_chains Public

    Portable solution to generate genome alignment chains using lastz

    Python 54 MIT 8 30 0 Updated Oct 11, 2024
  • 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.

    Python 169 MIT 23 29 1 Updated Jun 20, 2024
  • GenomeAlignmentTools Public

    Tools for improving the sensitivity and specificity of genome alignments

    C 57 MIT 15 14 0 Updated Jan 17, 2024
  • IterativeErrorCorrection Public

    Iterative error correction of long reads

    Python 11 MIT 3 4 1 Updated Dec 9, 2022
  • CESAR2.0 Public
    C 28 MIT 10 8 0 Updated Dec 1, 2022
  • GeneLossPipe Public
    Perl 24 MIT 7 2 0 Updated Nov 29, 2022
  • ForwardGenomics Public

    Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework

    Perl 22 MIT 8 7 0 Updated Nov 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 2 MIT 2 4 0 Updated Jan 14, 2021
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