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    44 repositories

    • read2tree

      Public
      a tool for inferring species tree from sequencing reads
      Python
      •
      MIT License
      •18•146•18•0•Updated Feb 19, 2025Feb 19, 2025

    • foldtree2

      Public
      foldtree2
      Jupyter Notebook
      •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • FastOMA

      Public
      FastOMA is a scalable software package to infer orthology relationship.
      evolutioncomparative-genomicsorthologybioinformatics
      Python
      •
      Mozilla Public License 2.0
      •14•70•7•1•Updated Feb 16, 2025Feb 16, 2025

    • HogProf

      Public
      Phylogenetic profiling with orthology data
      Jupyter Notebook
      •
      MIT License
      •2•10•0•1•Updated Feb 11, 2025Feb 11, 2025

    • Rmath4-python

      Public
      The standalone Rmath library from R version 4 for Python
      C
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • OMArk

      Public
      Python
      •
      GNU Lesser General Public License v3.0
      •7•69•5•3•Updated Feb 4, 2025Feb 4, 2025

    • pyoma

      Public
      Python library to interact with OMA hdf5 files
      Python
      •
      Mozilla Public License 2.0
      •0•1•0•1•Updated Jan 27, 2025Jan 27, 2025

    • pylabeledrf

      Public
      A package to compute the Robinson Fould distance extended to labeled topologies.
      Jupyter Notebook
      •
      MIT License
      •0•5•0•1•Updated Jan 24, 2025Jan 24, 2025

    • pyopa

      Public
      A fast implementation of optimal pairwise alignments with python
      C
      •
      Mozilla Public License 2.0
      •2•7•2•6•Updated Jan 24, 2025Jan 24, 2025

    • omamer

      Public
      OMAmer - tree-driven and alignment-free protein assignment to sub-families
      Python
      •
      GNU Lesser General Public License v3.0
      •5•16•3•1•Updated Jan 24, 2025Jan 24, 2025

    • fold_tree

      Public
      snakemake pipeline for creating trees from sequence sets
      Jupyter Notebook
      •
      MIT License
      •9•73•4•0•Updated Jan 18, 2025Jan 18, 2025

    • nf-oma-browser-build

      Public
      Nextflow pipeline to convert OMA to OMA browser
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Jan 16, 2025Jan 16, 2025

    • edgehog

      Public
      Infering ancestral synteny with hierarchical orthologous groups
      Python
      •
      MIT License
      •0•12•0•1•Updated Dec 17, 2024Dec 17, 2024

    • omataxonomy

      Public
      taxonomy
      Python
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Dec 10, 2024Dec 10, 2024

    • OMAnnotator

      Public
      Consensus genome annotation using OMA
      Python
      •0•9•2•0•Updated Dec 4, 2024Dec 4, 2024

    • django-matomo-api-tracking

      Public
      Django Matomo app allowing server side traffic tracking
      Python
      •
      Other
      •1•1•1•1•Updated Nov 7, 2024Nov 7, 2024

    • gethogs

      Public
      A tool to infer Hierarchical Orthologous Groups (HOGs) from pairwise orthologs
      Python
      •
      MIT License
      •0•0•0•1•Updated Nov 7, 2024Nov 7, 2024

    • ldo_study

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • matreex

      Public
      HTML
      •2•16•0•0•Updated Oct 25, 2024Oct 25, 2024

    • treeCl

      Public
      Phylogenetic clustering package
      C++
      •
      MIT License
      •0•1•0•0•Updated Oct 7, 2024Oct 7, 2024

    • yeast_fusion_segmenter

      Public
      retrain yolov8 to segment and label yeast cells with interupted fusion phenotypes
      Jupyter Notebook
      •0•1•0•0•Updated Sep 27, 2024Sep 27, 2024

    • SIBBiodiversityBioinformatics2024

      Public
      HTML
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • phylo-io

      Public
      Phylo.IO JS tree viewer
      JavaScript
      •
      MIT License
      •10•28•5•1•Updated Aug 6, 2024Aug 6, 2024

    • OmaStandalone

      Public
      OMA standalone repository
      Python
      •
      Other
      •3•4•3•0•Updated Jul 30, 2024Jul 30, 2024

    • OmaDB

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•2•0•0•Updated Apr 18, 2024Apr 18, 2024

    • pyham

      Public
      Python
      •
      MIT License
      •5•10•9•1•Updated Mar 19, 2024Mar 19, 2024

    • pyomadb

      Public
      PyOMADB is a python client to the OMA browser, using the REST API.
      Python
      •
      GNU Lesser General Public License v3.0
      •1•2•1•0•Updated Jan 17, 2024Jan 17, 2024

    • pyomabrowser

      Public
      Django based webserver for omabrowser
      JavaScript
      •
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Nov 10, 2023Nov 10, 2023

    • SIBBiodiversityBioinformatics2023

      Public
      GNU General Public License v3.0
      •3•2•0•0•Updated Sep 7, 2023Sep 7, 2023

    • f1000_PhylogeneticTree

      Public
      A tutorial on using OMA Browser and OMA Standalone for phylogenetic species trees reconstruction. Scripts referred to in the tutorial paper can be found here.
      Python
      •
      MIT License
      •0•1•1•0•Updated Aug 27, 2023Aug 27, 2023