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    95 repositories

    • hyphy-eye

      Public
      Playing w Observable Framework
      JavaScript
      •1•0•2•1•Updated Apr 4, 2025Apr 4, 2025

    • datamonkey-js

      Public
      Datamonkey - Run state-of-the-art statistical models through the comfort of your browser
      JavaScript
      •
      Other
      •9•10•1•2•Updated Apr 3, 2025Apr 3, 2025

    • MSS-results

      Public
      HyPhy
      •1•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • molerate

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

    • hyphy

      Public
      HyPhy: Hypothesis testing using Phylogenies
      sciencec-plus-plusbioinformaticsevolutionstatistical-methodsphylogeneticscomparative-genomics
      HyPhy
      •
      Other
      •70•230•24•0•Updated Mar 31, 2025Mar 31, 2025

    • hyphy-analyses

      Public
      HyPhy standalone analyses
      PostScript
      •
      MIT License
      •18•40•44•0•Updated Mar 31, 2025Mar 31, 2025

    • hivtrace-wasm

      Public
      a WebAssembly implementation of the HIV-TRACE pipeline.
      JavaScript
      •0•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • service-datamonkey

      Public
      REST service driving Datamonkey3
      Go
      •
      MIT License
      •0•0•1•0•Updated Mar 25, 2025Mar 25, 2025

    • api-datamonkey

      Public
      API Spec for Datamonkey3
      C#
      •
      MIT License
      •0•0•1•0•Updated Mar 25, 2025Mar 25, 2025

    • hivtrace

      Public
      JavaScript
      •
      MIT License
      •14•24•5•1•Updated Mar 21, 2025Mar 21, 2025

    • hivtrace-viz

      Public
      JavaScript
      •9•8•0•4•Updated Mar 20, 2025Mar 20, 2025

    • service-slurm

      Public
      A test Docker build for SLURM with the SLURM REST API configured.
      Dockerfile
      •
      MIT License
      •4•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • CPE

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

    • cawlign

      Public
      C++
      •
      MIT License
      •2•3•2•0•Updated Feb 18, 2025Feb 18, 2025

    • phylotree.js

      Public
      Interactive viewer of phylogenetic trees
      d3jsvizualisationphylogenetic-trees
      JavaScript
      •
      MIT License
      •78•172•55•6•Updated Jan 28, 2025Jan 28, 2025

    • hyphy-site

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

    • datamonkey-js-server

      Public
      HyPhy
      •7•3•0•1•Updated Jan 13, 2025Jan 13, 2025

    • datamonkey-docs

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

    • hivclustering

      Public
      Infer molecular transmission networks from pairwise distance files (part of HIV-TRACE)
      Python
      •5•3•10•1•Updated Jan 6, 2025Jan 6, 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•2•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
      •4•4•1•1•Updated Jun 17, 2024Jun 17, 2024

    • tn93

      Public
      TN93 fast distance calculator
      C++
      •
      MIT License
      •8•16•10•1•Updated Jun 10, 2024Jun 10, 2024

    • hyphy-python

      Public
      C++
      •
      Other
      •1•0•0•2•Updated May 31, 2024May 31, 2024

    • cve-site

      Public
      Website for CVE
      Svelte
      •1•0•0•0•Updated May 17, 2024May 17, 2024

    • ogv-dating

      Public
      Scripts and results for estimating the dates of integrated HIV viruses using RNA samples from the same host
      HyPhy
      •
      MIT License
      •3•5•2•0•Updated May 2, 2024May 2, 2024

    • autotune-data

      Public
      This repository contains datasets utilized in the AUTO-TUNE manuscript for inferring HIV transmission clusters based on genetic distances.
      0•0•0•0•Updated Apr 29, 2024Apr 29, 2024