neherlab

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

SARS-CoV-2_variant-reports

Informal summaries of notable SARS-CoV-2 lineages

pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

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

nextclade_data_workflows

flu_clades

HIVEVO_reversion

Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion

SVVC

simple viral variant caller

BA286

BA.2.86 project with Sigal lab

ncov-simple

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

flu-ingest

TreeKnit-web

h5NCtest

HIV-nextclade

minimizer

Rust implementation of a minimizer index

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

nextclade_testing_gffs

outlier-detection

pangraph-paper

latex source files for the pangraph paper

Rpi_test_tools

Scripts to test the Rpi for the morbidostat

RSV_nextclade_trial

sc2-phylo-workflow

demonstraion workflow for SC2 phylogenetic analysis using nextclade

simple-annotator