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@neherlab

Models of COVID-19 outbreak trajectories and hospital demand
JavaScript 1.4k 346
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Jupyter Notebook 252 60
Processing pipeline for pan-genome visulization and exploration
Python 145 39
A bioinformatic toolkit to align genome assemblies into pangenome graphs
C 127 6
Informal summaries of notable SARS-CoV-2 lineages
111 12

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Showing 10 of 103 repositories

pangraph Public
A bioinformatic toolkit to align genome assemblies into pangenome graphs
neherlab/pangraph’s past year of commit activity
C
127
MIT
6 6 4
Updated Jun 12, 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 Jun 11, 2026
treetime Public
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
neherlab/treetime’s past year of commit activity
Jupyter Notebook
252
MIT
60 39 4
Updated Jun 11, 2026
neherlab/SARS-CoV-2_variant-reports’s past year of commit activity
neherlab/nextclade_data_workflows’s past year of commit activity
Python
6 1 12 1
Updated May 27, 2026
neherlab/pango-tree’s past year of commit activity
Python 0 0
0 0
Updated May 22, 2026
neherlab/data-to-physical-models-in-biology-materials’s past year of commit activity
Jupyter Notebook
1
0
0 0
Updated May 5, 2026
neherlab/mut-fitness-general’s past year of commit activity
Python 0 MIT
2 0 0
Updated Apr 8, 2026
neherlab/mutation-rates-nt-freq’s past year of commit activity
Python 0 0
0 0
Updated Mar 11, 2026
neherlab/HIV-nextclade’s past year of commit activity
Python 0
2 0 0
Updated Mar 5, 2026

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