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    56 repositories

    • nf-oma-browser-build

      Public
      Nextflow pipeline to convert OMA to OMA browser
      Nextflow
      •
      MIT License
      •0•2•0•0•Updated Mar 25, 2026Mar 25, 2026

    • fastoma-bench

      Public
      Automatic benchmarking of Fastoma over time
      Python
      •0•2•0•0•Updated Mar 25, 2026Mar 25, 2026

    • foldtree2

      Public
      foldtree2
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •4•9•6•0•Updated Mar 24, 2026Mar 24, 2026

    • ESM3di

      Public
      using ESM2 to translate amino acids to 3di sequences to create foldseek
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • FastOMA

      Public
      FastOMA is a scalable software package to infer orthology relationship.
      bioinformaticsevolutioncomparative-genomics
      bioinformaticsevolutioncomparative-genomicsorthology
      Python
      •
      Mozilla Public License 2.0
      •17•93•8•5•Updated Mar 17, 2026Mar 17, 2026

    • yeast_fusion_segmenter

      Public
      retrain yolov8 to segment and label yeast cells with interupted fusion phenotypes
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 12, 2026Mar 12, 2026

    • SIBBiodiversityBioinformatics2025

      Public
      HTML
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • fold_tree

      Public
      Infers a phylogenetic tree from protein structures
      Jupyter Notebook
      •
      MIT License
      •17•101•9•0•Updated Mar 3, 2026Mar 3, 2026

    • pyoma

      Public
      Python library to interact with OMA hdf5 files
      Python
      •
      Mozilla Public License 2.0
      •0•1•0•3•Updated Feb 27, 2026Feb 27, 2026

    • django-matomo-api-tracking

      Public
      Django Matomo app allowing server side traffic tracking
      Python
      •
      Other
      •1•1•0•2•Updated Feb 24, 2026Feb 24, 2026

    • matreex

      Public
      HTML
      •2•17•0•0•Updated Feb 16, 2026Feb 16, 2026

    • ampliphy

      Public
      Improve phylogenetic inference by amplifying multiple sequence alignment with homologous sequences
      Nextflow
      •
      MIT License
      •1•4•0•0•Updated Feb 13, 2026Feb 13, 2026

    • phylo-io

      Public
      Phylo.IO JS tree viewer
      JavaScript
      •
      MIT License
      •11•35•5•1•Updated Jan 21, 2026Jan 21, 2026

    • OMAnnotator

      Public
      Consensus genome annotation using OMA
      Python
      •2•31•4•0•Updated Jan 14, 2026Jan 14, 2026

    • ampliphy-analysis

      Public
      Scripts used to generate the data and figures of AmpliPhy project
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 1, 2026Jan 1, 2026

    • orthoxml-tools

      Public
      Tools for working with OrthoXML files.
      Python
      •
      GNU General Public License v3.0
      •1•4•15•0•Updated Dec 30, 2025Dec 30, 2025

    • read2tree

      Public
      a tool for inferring species tree from sequencing reads
      Python
      •
      MIT License
      •19•160•22•0•Updated Dec 9, 2025Dec 9, 2025

    • OMArk

      Public
      Python
      •
      GNU Lesser General Public License v3.0
      •7•91•10•0•Updated Dec 3, 2025Dec 3, 2025

    • omamer

      Public
      OMAmer - tree-driven and alignment-free protein assignment to sub-families
      Python
      •
      GNU Lesser General Public License v3.0
      •5•22•4•1•Updated Nov 21, 2025Nov 21, 2025

    • OmaStandalone

      Public
      OMA standalone repository
      Python
      •
      Other
      •3•7•3•1•Updated Nov 21, 2025Nov 21, 2025

    • pyham

      Public
      Python
      •
      MIT License
      •7•11•9•4•Updated Nov 21, 2025Nov 21, 2025

    • omataxonomy

      Public
      taxonomy
      Python
      •
      GNU General Public License v3.0
      •0•0•0•2•Updated Nov 20, 2025Nov 20, 2025

    • Foldtree_ProstT5

      Public
      Foldtree using ProstT5 to run comparisons. Not benchmarked. Use at your own risk
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 14, 2025Nov 14, 2025

    • GenomeViewer

      Public
      Vue
      •0•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • pyopa

      Public
      A fast implementation of optimal pairwise alignments with python
      C
      •
      Mozilla Public License 2.0
      •2•7•1•5•Updated Oct 27, 2025Oct 27, 2025

    • pyomabrowser

      Public
      Django based webserver for omabrowser
      JavaScript
      •
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Oct 21, 2025Oct 21, 2025

    • edgehog

      Public
      Infering ancestral synteny with hierarchical orthologous groups
      Python
      •
      MIT License
      •3•38•2•5•Updated Oct 17, 2025Oct 17, 2025

    • corecut

      Public
      command line tool to extract consensus regions from sets of homologous structures
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • HogProf

      Public
      Phylogenetic profiling with orthology data
      Jupyter Notebook
      •
      MIT License
      •2•13•0•1•Updated Oct 10, 2025Oct 10, 2025

    • ancestral_genomes

      Public
      Get estimated ancestral genome sizes using OMA and other orthology databases
      Jupyter Notebook
      •0•1•0•0•Updated Jul 31, 2025Jul 31, 2025