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/SARS-CoV-2_variant-reports
Informal summaries of notable SARS-CoV-2 lineages
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
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/flu_clades
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/CompBio2023
simple viral consensus assembly
neherlab/flu-ingest
neherlab/PoL1-course-materials
Notebook and script of the PoL1 course at the university of Basel
neherlab/2024_msc_thesis_otter
neherlab/Aionostat_ressources
Ressources used to make the Aionostat
neherlab/CCHFV
neherlab/h5nx-Clades
neherlab/HIV-nextclade
neherlab/minimizer
Rust implementation of a minimizer index
neherlab/nanopore_basecalling
Pipeline to perform nanopore basecalling on Scicore
neherlab/nextclade_data
DO NOT USE. This is for testing new stuff on https://github.com/nextstrain/nextclade_data
neherlab/outlier-detection
neherlab/phylogeography
neherlab/Rpi_test_tools
Scripts to test the Rpi for the morbidostat
neherlab/rsv_intrahost_2024
Workflow for RSV analyses on Nextstrain.org
neherlab/RSV_nextclade_trial
neherlab/SARS2-mut-fitness-v2
Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.
neherlab/sc2-phylo-workflow
demonstraion workflow for SC2 phylogenetic analysis using nextclade
neherlab/simple-annotator
neherlab/TreeKnit.jl
TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).