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  1. covid19_scenarios covid19_scenarios Public

    Models of COVID-19 outbreak trajectories and hospital demand

    JavaScript 1.4k 344

  2. treetime treetime Public

    Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

    Jupyter Notebook 257 64

  3. pan-genome-analysis pan-genome-analysis Public

    Processing pipeline for pan-genome visulization and exploration

    Python 147 37

  4. pangraph pangraph Public

    A bioinformatic toolkit to align genome assemblies into pangenome graphs

    C 129 6

  5. SARS-CoV-2_variant-reports SARS-CoV-2_variant-reports Public

    Informal summaries of notable SARS-CoV-2 lineages

    112 12

  6. pan-genome-visualization pan-genome-visualization Public

    Forked from wdingx/pan-genome-visualization

    Visualization of the pan-genome output by panX

    JavaScript 70 16

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Showing 10 of 107 repositories
  • treetime-nightly Public

    early builds of treetime

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    neherlab/treetime-nightly's past year of commit activity
    0 0 0 0 Updated Nov 12, 2026
  • treetime Public

    Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

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    neherlab/treetime's past year of commit activity
    Jupyter Notebook 257 MIT 64 42 7 Updated Nov 12, 2026
  • pan-genome-analysis Public

    Processing pipeline for pan-genome visulization and exploration

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    neherlab/pan-genome-analysis's past year of commit activity
    Python 147 GPL-3.0 37 34 1 Updated Nov 11, 2026
  • treeknit Public

    Infers reassortment from the trees of the segments of a virus, such as the HA and NA trees of influenza

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    neherlab/treeknit's past year of commit activity
    Rust 1 MIT 0 0 0 Updated Nov 3, 2026
  • hivwholeweb Public Forked from iosonofabio/hivwholeweb

    Web application for deep sequencing on longitudinal HIV-1 samples from patients.

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    neherlab/hivwholeweb's past year of commit activity
    HTML 1 5 0 0 Updated Nov 2, 2026
  • pangraph Public

    A bioinformatic toolkit to align genome assemblies into pangenome graphs

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    neherlab/pangraph's past year of commit activity
    C 129 MIT 6 7 9 Updated Oct 28, 2026
  • nextclade_data_workflows Public

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    neherlab/nextclade_data_workflows's past year of commit activity
    Python 6 1 12 1 Updated Oct 27, 2026
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

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    neherlab/bioconda-recipes's past year of commit activity
    Shell 0 MIT 4,247 0 0 Updated Oct 21, 2026
  • PoL1-course-materials Public

    Notebook and script of the PoL1 course at the university of Basel

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    neherlab/PoL1-course-materials's past year of commit activity
    Jupyter Notebook 4 0 0 0 Updated Oct 14, 2026
  • mut-fitness-general Public Forked from neherlab/SARS2-mut-fitness-v2

    Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.

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    neherlab/mut-fitness-general's past year of commit activity
    Python 0 MIT 3 0 0 Updated Oct 12, 2026
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