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    98 repositories

    • CAPHEINE

      Public
      Automated evolutionary annotation of existing datasets using Nextflow
      Nextflow
      •
      MIT License
      •0•0•3•0•Updated Sep 5, 2025Sep 5, 2025

    • hyphy

      Public
      HyPhy: Hypothesis testing using Phylogenies
      sciencec-plus-plusbioinformaticsevolutionstatistical-methodsphylogeneticscomparative-genomics
      HyPhy
      •
      Other
      •69•239•11•1•Updated Sep 5, 2025Sep 5, 2025

    • MSS-results

      Public
      HyPhy
      •1•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • hivtrace-viz

      Public
      JavaScript
      •11•10•0•2•Updated Sep 2, 2025Sep 2, 2025

    • DRHIP

      Public
      Data Reduction for HyPhy with Inference Processing. A toolkit for analyzing and summarizing HyPhy evolutionary selection analysis results
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • service-datamonkey

      Public
      REST service driving Datamonkey3
      Go
      •
      MIT License
      •0•0•1•0•Updated Aug 29, 2025Aug 29, 2025

    • service-slurm

      Public
      A test Docker build for SLURM with the SLURM REST API configured.
      Shell
      •
      MIT License
      •5•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • homebrew-bio

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

    • cawlign

      Public
      C++
      •
      MIT License
      •2•3•4•0•Updated Aug 26, 2025Aug 26, 2025

    • hyphy-analyses

      Public
      HyPhy standalone analyses
      PostScript
      •
      MIT License
      •18•46•46•0•Updated Aug 22, 2025Aug 22, 2025

    • datamonkey-js

      Public
      Datamonkey - Run state-of-the-art statistical models through the comfort of your browser
      JavaScript
      •
      Other
      •9•10•6•2•Updated Aug 21, 2025Aug 21, 2025

    • phylotree.js

      Public
      Interactive viewer of phylogenetic trees
      d3jsvizualisationphylogenetic-trees
      JavaScript
      •
      MIT License
      •78•187•57•0•Updated Aug 15, 2025Aug 15, 2025

    • hyphy-eye

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

    • datamonkey-js-server

      Public
      JavaScript
      •7•3•1•3•Updated Aug 11, 2025Aug 11, 2025

    • hivclustering

      Public
      Infer molecular transmission networks from pairwise distance files (part of HIV-TRACE)
      Python
      •5•5•10•1•Updated Jul 29, 2025Jul 29, 2025

    • api-datamonkey

      Public
      API Spec for Datamonkey3
      C#
      •
      MIT License
      •0•0•1•0•Updated Jul 29, 2025Jul 29, 2025

    • tn93

      Public
      TN93 fast distance calculator
      C++
      •
      MIT License
      •7•18•10•1•Updated Jul 16, 2025Jul 16, 2025

    • hivtrace

      Public
      JavaScript
      •
      MIT License
      •15•25•5•1•Updated May 21, 2025May 21, 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

    • hyphy-vision

      Public
      Visualize HyPhy results in your browser
      JavaScript
      •12•4•1•4•Updated Nov 26, 2024Nov 26, 2024

    • BioExt

      Public
      A few handy bioinformatics tools not already within BioPython
      Python
      •12•3•1•1•Updated Aug 29, 2024Aug 29, 2024

    • selection-tutorial

      Public
      Creative Commons Zero v1.0 Universal
      •1•3•5•0•Updated Aug 3, 2024Aug 3, 2024

    • Endothermy

      Public
      HyPhy
      •2•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • LabSite

      Public
      Website for the ACME Lab
      JavaScript
      •
      MIT License
      •7•1•0•20•Updated Jul 10, 2024Jul 10, 2024

    • idepi

      Public
      IDentify EPItopes
      Python
      •
      GNU General Public License v3.0
      •3•4•1•1•Updated Jun 17, 2024Jun 17, 2024