neherlab's repositories
pan-genome-analysis
Processing pipeline for pan-genome visulization and exploration
SARS-CoV-2_variant-reports
Informal summaries of notable SARS-CoV-2 lineages
pan-genome-visualization
Visualization of the pan-genome output by panX
ffpopsim
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 is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.
python_morbidostat
Control software for a morbidostat reactor based on arduino and python
HIVEVO_reversion
Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion
SC2_variant_rates
analyze substitution rate and mutation behavior within variants.
spike-only
Spike-only SARS-CoV-2 Nextstrain build
CompBio2023
simple viral consensus assembly
nextclade-dataset-template
Template to create a simple Nextclade dataset from scratch
nextclade_data
DO NOT USE. This is for testing new stuff on https://github.com/nextstrain/nextclade_data
pangraph-paper
latex source files for the pangraph paper
Rpi_test_tools
Scripts to test the Rpi for the morbidostat
sc2-phylo-workflow
demonstraion workflow for SC2 phylogenetic analysis using nextclade