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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 347

  2. treetime treetime Public

    Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

    Jupyter Notebook 249 58

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

    Processing pipeline for pan-genome visulization and exploration

    Python 143 39

  4. pangraph pangraph Public

    A bioinformatic toolkit to align genome assemblies into pangenome graphs

    C 120 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 66 15

Repositories

Showing 10 of 100 repositories
  • treetime Public

    Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

    neherlab/treetime’s past year of commit activity
    Jupyter Notebook 249 MIT 58 37 5 Updated Jan 29, 2026
  • pangraph Public

    A bioinformatic toolkit to align genome assemblies into pangenome graphs

    neherlab/pangraph’s past year of commit activity
    C 120 MIT 6 8 2 Updated Jan 20, 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 Jan 19, 2026
  • nextclade_data_workflows Public
    neherlab/nextclade_data_workflows’s past year of commit activity
    Python 5 1 11 1 Updated Jan 12, 2026
  • treponema-nextclade Public
    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
  • PoL1-course-materials Public

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

    neherlab/PoL1-course-materials’s past year of commit activity
    Jupyter Notebook 4 0 0 0 Updated Dec 1, 2025
  • ffpopsim Public

    FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter i…

    neherlab/ffpopsim’s past year of commit activity
    C++ 14 GPL-3.0 11 3 6 Updated Oct 14, 2025
  • SARS-CoV-2_variant-reports Public

    Informal summaries of notable SARS-CoV-2 lineages

    neherlab/SARS-CoV-2_variant-reports’s past year of commit activity
    111 12 0 0 Updated Aug 22, 2025
  • mlr_predict_variant_composition Public Forked from marie3003/mlr_predict_variant_composition
    neherlab/mlr_predict_variant_composition’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Aug 2, 2025
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