neherlab

Computational biology at the Biozentrum, Basel

86 followers
Basel, Switzerland
https://neherlab.org

Overview
Repositories
Projects
Packages
People

Popular repositories Loading

covid19_scenarios covid19_scenarios Public

Models of COVID-19 outbreak trajectories and hospital demand

JavaScript 1.4k 345
treetime treetime Public

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Jupyter Notebook 254 61
pan-genome-analysis pan-genome-analysis Public

Processing pipeline for pan-genome visulization and exploration

Python 146 38
pangraph pangraph Public

A bioinformatic toolkit to align genome assemblies into pangenome graphs

C 128 6
SARS-CoV-2_variant-reports SARS-CoV-2_variant-reports Public

Informal summaries of notable SARS-CoV-2 lineages

111 12
pan-genome-visualization pan-genome-visualization Public

Forked from wdingx/pan-genome-visualization

Visualization of the pan-genome output by panX

JavaScript 68 16

Repositories

Type Language

Select language

All C C++ CSS HTML Java JavaScript Julia Jupyter Notebook MATLAB Python Rust Shell Smarty TeX TypeScript

Sort

pangraph Public
A bioinformatic toolkit to align genome assemblies into pangenome graphs

neherlab/pangraph's past year of commit activity

C 128 MIT 6 7 9 Updated Aug 19, 2026
treetime Public
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

neherlab/treetime's past year of commit activity

Jupyter Notebook 254 MIT 61 39 5 Updated Aug 18, 2026
nanopore_basecalling Public Forked from vdruelle/nanopore_basecalling
Pipeline to perform nanopore basecalling on Scicore

neherlab/nanopore_basecalling's past year of commit activity

Python 0 MIT 2 0 1 Updated Aug 14, 2026
treetime-nightly Public
early builds of treetime

neherlab/treetime-nightly's past year of commit activity

0 0 0 0 Updated Aug 12, 2026
nextclade_data_workflows Public

neherlab/nextclade_data_workflows's past year of commit activity

Python 6 1 12 1 Updated Aug 3, 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 Jul 1, 2026
SARS2-mut-fitness-v2 Public
Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.

neherlab/SARS2-mut-fitness-v2's past year of commit activity

Jupyter Notebook 0 MIT 3 0 0 Updated Jun 26, 2026
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 Jun 1, 2026
pango-tree Public

neherlab/pango-tree's past year of commit activity

Python 0 0 0 0 Updated May 22, 2026
data-to-physical-models-in-biology-materials Public
Materials for the course "From Data to Physicsal models in Biology" -- Part Neher

neherlab/data-to-physical-models-in-biology-materials's past year of commit activity

Jupyter Notebook 1 0 0 0 Updated May 5, 2026