Pinned Repositories
CoV_Seasonality
Model coronavirus seasonality and explore consequences for nCoV dynamics
covid19_scenarios
Models of COVID-19 outbreak trajectories and hospital demand
covid19_scenarios_data
Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project
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.
pan-genome-analysis
Processing pipeline for pan-genome visulization and exploration
pan-genome-visualization
Visualization of the pan-genome output by panX
pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
SARS-CoV-2_variant-reports
Informal summaries of notable SARS-CoV-2 lineages
treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
treetime_examples
A collection of documented examples using TreeTime
neherlab's Repositories
neherlab/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
neherlab/pan-genome-analysis
Processing pipeline for pan-genome visulization and exploration
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
neherlab/SARS-CoV-2_variant-reports
Informal summaries of notable SARS-CoV-2 lineages
neherlab/pan-genome-visualization
Visualization of the pan-genome output by panX
neherlab/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.
neherlab/nextclade_data_workflows
neherlab/BA286
BA.2.86 project with Sigal lab
neherlab/ncov-simple
neherlab/spike-only
Spike-only SARS-CoV-2 Nextstrain build
neherlab/data-to-physical-models-in-biology-materials
Materials for the course "From Data to Physicsal models in Biology" -- Part Neher
neherlab/PoL1-course-materials
Notebook and script of the PoL1 course at the university of Basel
neherlab/rsv_intrahost_2024
Workflow for RSV analyses on Nextstrain.org
neherlab/2024_msc_thesis_otter
neherlab/Aionostat_ressources
Ressources used to make the Aionostat
neherlab/CCHFV
neherlab/coolify-test
neherlab/h5nx-Clades
neherlab/HIV-nextclade
neherlab/nanopore_basecalling
Pipeline to perform nanopore basecalling on Scicore
neherlab/outlier-detection
neherlab/phylogeography
neherlab/recombinant_phages_study
neherlab/recombinant_population_analysis
neherlab/RSV-mut-fitness
Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.
neherlab/rsv_epidemiology_2025
A collection of code and data used for "Molecular Epidemiology of Respiratory Syncytial Virus in Switzerland from 2020 to 2024" publication.
neherlab/SARS2-mut-fitness-v2
Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.
neherlab/simple-annotator
neherlab/test-vercel
neherlab/TreeKnit.jl
TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).