Repositories list

• treetime

  Public
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

  phylogenetics

  phylogenetics

  Jupyter Notebook

  •

  MIT License

  •6060 forks•251251 stars•3939 issues•44 pull requests•Updated Apr 24, 2026Apr 24, 2026

• nextclade_data_workflows

  Public
  snakemakephylogeneticsnextstrain+ 2

  snakemakephylogeneticsnextstrainvirus-evolutionnextclade

  Python

  •11 fork•55 stars•1111 issues•11 pull request•Updated Apr 24, 2026Apr 24, 2026

• data-to-physical-models-in-biology-materials

  Public
  Materials for the course "From Data to Physicsal models in Biology" -- Part Neher

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• mut-fitness-general

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

  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• pangraph

  Public
  A bioinformatic toolkit to align genome assemblies into pangenome graphs

  bioinformaticsgenomejulia+ 4

  bioinformaticsgenomejuliabacteriagenome-assemblypangenomepangraph

  C

  •

  MIT License

  •66 forks•124124 stars•88 issues•22 pull requests•Updated Mar 27, 2026Mar 27, 2026

• SC2Epistasis

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

  Julia

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• mutation-rates-nt-freq

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• HIV-nextclade

  Public
  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• CCHFV

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 2, 2026Feb 2, 2026

• treponema-nextclade

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2026Jan 4, 2026

• tidy-tree

  Public
  build trees guided by a hierarchical lineage system

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 14, 2025Dec 14, 2025

• PoL1-course-materials

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

  Jupyter Notebook

  •00 forks•44 stars•00 issues•00 pull requests•Updated Dec 1, 2025Dec 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 an…

  C++

  •

  GNU General Public License v3.0

  •1111 forks•1414 stars•33 issues•66 pull requests•Updated Oct 14, 2025Oct 14, 2025

• SARS-CoV-2_variant-reports

  Public
  Informal summaries of notable SARS-CoV-2 lineages

  covid-19sars-cov-2virus-evolution+ 1

  covid-19sars-cov-2virus-evolutionsars-cov-2-variants

  1212 forks•111111 stars•00 issues•00 pull requests•Updated Aug 22, 2025Aug 22, 2025

• mlr_predict_variant_composition

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 2, 2025Aug 2, 2025

• rsv_epidemiology_2025

  Public
  A collection of code and data used for "Molecular Epidemiology of Respiratory Syncytial Virus in Switzerland from 2020 to 2024" publication.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2025Jul 2, 2025

• pan-genome-visualization

  Public
  Visualization of the pan-genome output by panX

  JavaScript

  •

  Other

  •2323 forks•6868 stars•77 issues•22 pull requests•Updated Jun 16, 2025Jun 16, 2025

• BA286

  Public
  BA.2.86 project with Sigal lab

  bioinformaticssnakemakecomputational-biology+ 7

  bioinformaticssnakemakecomputational-biologyphylogeneticsnextstraintreetimesars-cov-2virus-evolutiongenomic-epidemiologysars-cov-2-variants

  Python

  •

  MIT License

  •11 fork•33 stars•00 issues•11 pull request•Updated Jun 12, 2025Jun 12, 2025

• phylogeography

  Public
  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 19, 2025May 19, 2025

• test-vercel

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 18, 2025May 18, 2025

• ncov-simple

  Public
  Python

  •11 fork•22 stars•99 issues•11 pull request•Updated Apr 16, 2025Apr 16, 2025

• rsv-intrahost-nextstrain-2024

  Public
  A workflow for intrahost RSV analysis adapted from a Nextstrain pipeline

  Python

  •66 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2025Mar 6, 2025

• coolify-test

  Public
  Smarty

  •00 forks•00 stars•00 issues•11 pull request•Updated Feb 10, 2025Feb 10, 2025

• recombinant_population_analysis

  Public
  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 22, 2025Jan 22, 2025

• SARS2-mut-fitness-v2

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

  Jupyter Notebook

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 9, 2025Jan 9, 2025

• outlier-detection

  Public
  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 5, 2025Jan 5, 2025

• TreeKnit.jl

  Public
  TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).

  Julia

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jan 3, 2025Jan 3, 2025

• 2024_msc_thesis_otter

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 17, 2024Dec 17, 2024

• recombinant_phages_study

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 27, 2024Nov 27, 2024

• nanopore_basecalling

  Public
  Pipeline to perform nanopore basecalling on Scicore

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 27, 2024Sep 27, 2024