Stars
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Visualise networks and trees in Python, with style.
A bioinformatic toolkit to align genome assemblies into pangenome graphs
Python package to manipulate pangenome graphs generated by PanGraph
Analysing the genomic context of mobile genes
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
Datasets for https://github.com/nextstrain/nextclade
Der vorliegende Datansatz enthält umfassende Informationen zu SARS-CoV-2-Infektionen in Deutschland, die gemäß dem Infektionsschutzgesetze (IfSG) von den Gesundheitsämtern an das Robert Koch-Instit…
2019 Wuhan Coronavirus data (COVID-19 / 2019-nCoV)
This is the development home of the workflow management system Snakemake. For general information, see
A Generalized Suffix Tree for any Python iterable using Ukkonen's algorithm, with Lowest Common Ancestor retrieval.
INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance
Analysis of fitness landscape of HIV-1 from longitudinal data
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Visualization of the pan-genome output by panX
Fast pairwise sequence alignment using SeqAn, in Python.
Accelerated BLAST compatible local sequence aligner.
Web application for deep sequencing on longitudinal HIV-1 samples from patients.
Pipeline components for real-time phylodynamic analysis
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.…