Reconstruction of transmission trees using genomic data

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Bayesian inference of ancestral dates on bacterial phylogenetic trees

Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop

A pipeline for performing genome-wide association tests for bacterial genomes.

❗ This is a read-only mirror of the CRAN R package repository. PopGenome — An Efficient Swiss Army Knife for Population Genomic Analyses

Finds SNP sites from a multi-FASTA alignment file

Tools test whether admixture occurred and more

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Pan-genome wide association studies

Aggregate results from bioinformatics analyses across many samples into a single report.

⚡ ♒ Rapid prokaryotic genome annotation

Rapid large-scale prokaryote pan genome analysis

IPython and Jupyter tutorial for SBW 2016

Hirbin repository