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    101 repositories

    • tools-iuc

      Public
      Tool Shed repositories maintained and developed by the Intergalactic Utilities Commission
      HTML
      •
      MIT License
      •500•0•3•0•Updated Feb 4, 2026Feb 4, 2026

    • hivtrace-viz

      Public
      JavaScript
      •11•10•0•3•Updated Feb 3, 2026Feb 3, 2026

    • hyphy

      Public
      HyPhy: Hypothesis testing using Phylogenies
      sciencec-plus-plusbioinformaticsevolutionstatistical-methodsphylogeneticscomparative-genomics
      HyPhy
      •
      Other
      •70•250•10•0•Updated Feb 1, 2026Feb 1, 2026

    • phylotree.js

      Public
      Interactive viewer of phylogenetic trees
      phylogenetic-treesd3jsvizualisation
      JavaScript
      •
      MIT License
      •79•194•1•0•Updated Jan 31, 2026Jan 31, 2026

    • datamonkey-js-server

      Public
      JavaScript
      •7•3•1•3•Updated Jan 29, 2026Jan 29, 2026

    • datamonkey-js

      Public
      Datamonkey - Run state-of-the-art statistical models through the comfort of your browser
      JavaScript
      •
      Other
      •9•10•1•6•Updated Jan 23, 2026Jan 23, 2026

    • CAPHEINE

      Public
      Automated evolutionary annotation of existing datasets using Nextflow
      Nextflow
      •
      MIT License
      •0•1•5•0•Updated Jan 15, 2026Jan 15, 2026

    • cawlign

      Public
      C++
      •
      MIT License
      •4•3•4•0•Updated Jan 6, 2026Jan 6, 2026

    • hyphy-readmes

      Public
      HyPhy
      •0•1•0•0•Updated Jan 6, 2026Jan 6, 2026

    • hyphy-analyses

      Public
      HyPhy standalone analyses
      PostScript
      •
      MIT License
      •19•52•48•0•Updated Jan 5, 2026Jan 5, 2026

    • DRHIP

      Public
      Data Reduction for HyPhy with Inference Processing. A toolkit for analyzing and summarizing HyPhy evolutionary selection analysis results
      Python
      •
      MIT License
      •1•0•1•0•Updated Dec 12, 2025Dec 12, 2025

    • silverback-user-manual

      Public
      silverback-user-manual
      JavaScript
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • hivtrace

      Public
      JavaScript
      •
      MIT License
      •15•22•5•1•Updated Nov 19, 2025Nov 19, 2025

    • service-datamonkey

      Public
      REST service driving Datamonkey3
      Go
      •
      MIT License
      •0•0•3•0•Updated Nov 7, 2025Nov 7, 2025

    • api-datamonkey

      Public
      API Spec for Datamonkey3
      C#
      •
      MIT License
      •0•0•1•0•Updated Nov 5, 2025Nov 5, 2025

    • hivclustering

      Public
      Infer molecular transmission networks from pairwise distance files (part of HIV-TRACE)
      Python
      •5•5•9•1•Updated Oct 15, 2025Oct 15, 2025

    • MSS-results

      Public
      HyPhy
      •1•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • BioExt

      Public
      A few handy bioinformatics tools not already within BioPython
      Python
      •12•3•2•1•Updated Oct 8, 2025Oct 8, 2025

    • hyphy-python

      Public
      C++
      •
      Other
      •1•0•0•2•Updated Oct 8, 2025Oct 8, 2025

    • cpe-website

      Public
      TypeScript
      •
      MIT License
      •1•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • service-slurm

      Public
      A test Docker build for SLURM with the SLURM REST API configured.
      Shell
      •
      MIT License
      •4•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • homebrew-bio

      Public
      :beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers
      Ruby
      •
      Other
      •119•0•0•0•Updated Aug 27, 2025Aug 27, 2025

    • hyphy-eye

      Public
      Playing w Observable Framework
      JavaScript
      •1•0•2•0•Updated Aug 14, 2025Aug 14, 2025

    • tn93

      Public
      TN93 fast distance calculator
      C++
      •
      MIT License
      •7•19•10•1•Updated Jul 16, 2025Jul 16, 2025

    • web-datamonkey

      Public
      web mockup of custom dm3 stylesheet, header and hero -- https://d-callan.github.io/dm3-web-mock
      TypeScript
      •0•0•0•0•Updated May 15, 2025May 15, 2025

    • hivtrace-wasm

      Public
      a WebAssembly implementation of the HIV-TRACE pipeline.
      JavaScript
      •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

    • molerate

      Public
      MoleRate data
      Python
      •
      The Unlicense
      •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • CPE

      Public
      Temple CPE Hugo Site
      TeX
      •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • hyphy-site

      Public
      HyPhy Markdown Site
      CSS
      •
      MIT License
      •8•0•1•0•Updated Jan 22, 2025Jan 22, 2025

    • datamonkey-docs

      Public
      Documentation for Datamonkey/HyPhy
      hyphydatamonkey
      TypeScript
      •1•0•0•1•Updated Jan 8, 2025Jan 8, 2025