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    38 repositories

    • twt

      Public
      Generic framework for the coalescent simulation of pathogen trees within host trees in R
      R
      •
      GNU Affero General Public License v3.0
      •2•3•9•0•Updated Feb 26, 2026Feb 26, 2026

    • covizu

      Public
      Rapid analysis and visualization of coronavirus genome variation
      JavaScript
      •
      MIT License
      •20•48•11•7•Updated Feb 14, 2026Feb 14, 2026

    • sierra-local

      Public
      Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
      Python
      •
      GNU General Public License v3.0
      •8•13•8•1•Updated Feb 9, 2026Feb 9, 2026

    • surfaces

      Public
      Do surface-exposed virus proteins have higher dN/dS?
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • OpenRDP

      Public
      An open-source re-implementation of the RDP4 recombination detection program
      Python
      •
      GNU General Public License v3.0
      •2•4•14•0•Updated Aug 23, 2025Aug 23, 2025

    • Bioplus

      Public
      In-house scripts that extend the functionality of Biopython
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • bayroot

      Public
      Bayesian root-to-tip regression for dating reservoir sequences
      R
      •
      MIT License
      •3•7•0•0•Updated Feb 27, 2025Feb 27, 2025

    • tragula

      Public
      Mapping networks of shared research expertise by word embedding analysis
      Python
      •
      MIT License
      •0•0•3•0•Updated Feb 3, 2025Feb 3, 2025

    • gromstole

      Public
      Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
      Python
      •
      MIT License
      •4•3•7•0•Updated Jul 18, 2024Jul 18, 2024

    • constellations

      Public
      Python
      •
      Other
      •17•0•2•0•Updated May 1, 2024May 1, 2024

    • fluclades

      Public
      Genetic taxonomy of influenza A virus subtypes
      Python
      •
      MIT License
      •0•3•0•0•Updated Apr 22, 2024Apr 22, 2024

    • dynsbmR

      Public
      Fork of read-only mirror of the CRAN R package repository. dynsbm — Dynamic Stochastic Block Models. Homepage: http://lbbe.univ-lyon1.fr/dynsbm
      C++
      •
      GNU General Public License v3.0
      •4•0•1•0•Updated Mar 6, 2024Mar 6, 2024

    • clustuneR

      Public
      Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
      R
      •
      GNU General Public License v3.0
      •0•0•4•0•Updated Dec 31, 2023Dec 31, 2023

    • ovrf-viz

      Public
      Review article on overlapping reading frames in viruses
      Python
      •
      MIT License
      •0•3•5•0•Updated Oct 24, 2023Oct 24, 2023

    • tn

      Public
      Optimization of genetic clustering methods by predictive modeling
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 11, 2023Sep 11, 2023

    • clmp

      Public
      Genetic clustering with Markov-modulated Poisson processes
      C
      •
      GNU General Public License v3.0
      •4•1•7•0•Updated Sep 7, 2023Sep 7, 2023

    • HexSE

      Public
      Simulation of molecular evolution with overlapping reading frames
      Python
      •
      GNU General Public License v3.0
      •2•4•5•0•Updated Jun 13, 2023Jun 13, 2023

    • sup

      Public
      Sequencing Uncertainty Propagation
      R
      •0•0•3•0•Updated Mar 14, 2023Mar 14, 2023

    • vindels

      Public
      Developing an empirical model of sequence insertion and deletion in virus genomes
      R
      •0•1•1•0•Updated Jun 21, 2022Jun 21, 2022

    • test

      Public
      Python
      •1•0•0•0•Updated Apr 21, 2022Apr 21, 2022

    • Poplars

      Public
      Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database
      Shell
      •
      GNU Affero General Public License v3.0
      •0•0•12•0•Updated Nov 10, 2021Nov 10, 2021

    • cophylo

      Public
      Data and scripts associated with manuscript on Tree Metrics of Cophylogeny
      R
      •2•1•0•0•Updated Mar 9, 2021Mar 9, 2021

    • tuning-disorder-virus

      Public
      Ensemble classifier of intrinsic protein disorder for viruses
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 26, 2020Nov 26, 2020

    • plodex

      Public
      Interactive visualization of SARS-CoV-2 variants
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•3•0•Updated Oct 7, 2020Oct 7, 2020

    • sam2conseq

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •1•7•6•0•Updated Jun 2, 2020Jun 2, 2020

    • MiCall-Lite

      Public
      Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping
      Python
      •
      GNU Affero General Public License v3.0
      •11•5•5•0•Updated Mar 27, 2020Mar 27, 2020

    • indelrates

      Public
      Data and scripts used for HIV-1 group M indel rate estimation project
      Python
      •1•0•0•0•Updated Feb 5, 2020Feb 5, 2020

    • Kaphi

      Public
      Kernel-embedded ABC-SMC for phylodynamic inference
      R
      •
      GNU Affero General Public License v3.0
      •2•4•14•0•Updated Aug 19, 2019Aug 19, 2019

    • highlineR

      Public
      An implementation of LANL's Highlighter web app in R for batch processing and scaling
      R
      •
      GNU General Public License v3.0
      •2•1•11•0•Updated Aug 1, 2019Aug 1, 2019

    • comet-prot

      Public
      Book chapter for upcoming Springer book Computational Methods in Protein Evolution
      HyPhy
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2018Nov 8, 2018