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    16 repositories

    • covariants

      Public
      Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
      trackingmutationvariantsnextstraincovid-19covid19sars-cov-2sarscov2mutation-distribution
      Python
      •
      GNU Affero General Public License v3.0
      •110•320•73•18•Updated Oct 20, 2025Oct 20, 2025

    • ppx-plots

      Public
      Plots of Pathoplexus data
      HTML
      •1•2•0•1•Updated Oct 20, 2025Oct 20, 2025

    • nextclade_d68

      Public
      Snakemake pipeline for creating a Nextclade dataset for Enterovirus D68
      Python
      •1•0•1•0•Updated Oct 17, 2025Oct 17, 2025

    • dataset-template-inferred-root

      Public template
      Python
      •2•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • enterovirus_a71

      Public
      Snakemake pipeline for creating interactive real-time phylogenetic trees
      Python
      •0•0•0•0•Updated Sep 11, 2025Sep 11, 2025

    • HCoV_229E

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • HCoV_OC43

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • hodcroftlab

      Public
      Website for hodcroft lab
      SCSS
      •0•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • evd68-converter

      Public
      JavaScript
      •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • coxsackievirus_a16

      Public
      Python
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • EVclades

      Public
      EVclades is an Enterovirus-adapted version of Art Poon’s fluclades pipeline for automated clade assignment.
      Jupyter Notebook
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • coxsackievirus_a6

      Public
      Code for Coxsackievirus A6 build on nextstrain.org
      Python
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • template_nextstrain

      Public template
      Template for building your own Nextstrain workflow
      Python
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • compare-alignments

      Public
      Guide of comparing alignments made by different methods/parameters
      Python
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • poliovirus_recombination

      Public
      Phylogenetics and recombination analysis of Enterovirus C with a focus on vaccine-derived polioviruses
      Python
      •0•0•0•1•Updated Mar 11, 2025Mar 11, 2025

    • evd68_demo

      Public
      Demo files for EVD68 build
      0•0•0•0•Updated May 2, 2024May 2, 2024