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@neherlab

neherlab

Computational biology at the Biozentrum, Basel

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  1. covid19_scenarios covid19_scenarios Public

    Models of COVID-19 outbreak trajectories and hospital demand

    JavaScript 1.4k 346

  2. treetime treetime Public

    Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

    Jupyter Notebook 251 58

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

    Processing pipeline for pan-genome visulization and exploration

    Python 144 39

  4. pangraph pangraph Public

    A bioinformatic toolkit to align genome assemblies into pangenome graphs

    C 122 6

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

    Informal summaries of notable SARS-CoV-2 lineages

    111 12

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

    Forked from wdingx/pan-genome-visualization

    Visualization of the pan-genome output by panX

    JavaScript 67 16

Repositories

Showing 10 of 102 repositories
  • treetime Public

    Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

    neherlab/treetime’s past year of commit activity
    Jupyter Notebook 251 MIT 58 38 4 Updated Mar 25, 2026
  • neherlab/nextclade_data_workflows’s past year of commit activity
    Python 5 1 11 1 Updated Mar 25, 2026
  • pangraph Public

    A bioinformatic toolkit to align genome assemblies into pangenome graphs

    neherlab/pangraph’s past year of commit activity
    C 122 MIT 6 8 2 Updated Mar 17, 2026
  • SC2Epistasis Public

    Package for quantifying epistasis in the SARS-CoV-2 mutational fitness landscape

    neherlab/SC2Epistasis’s past year of commit activity
    Julia 0 MIT 0 0 0 Updated Mar 16, 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.

    neherlab/mut-fitness-general’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Mar 13, 2026
  • neherlab/mutation-rates-nt-freq’s past year of commit activity
    Python 0 0 0 0 Updated Mar 11, 2026
  • HIV-nextclade Public
    neherlab/HIV-nextclade’s past year of commit activity
    Python 0 2 0 0 Updated Mar 5, 2026
  • CCHFV Public
    neherlab/CCHFV’s past year of commit activity
    Python 0 0 0 0 Updated Feb 2, 2026
  • neherlab/treponema-nextclade’s past year of commit activity
    0 0 0 0 Updated Jan 4, 2026
  • tidy-tree Public

    build trees guided by a hierarchical lineage system

    neherlab/tidy-tree’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Dec 14, 2025

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