Verticall: A fast and robust tool for recombination detection in large-scale bacterial genomic datasets (opens in new tab)

The inference and removal of horizontally acquired genomic regions is a crucial step in phylogenomics analyses for evolutionary studies. Existing tools perform well on clonal lineage-focused datasets on the scale of hundreds of genomes, but are limited in their ability to analyse larger or more diverse datasets. Here we present Verticall, a tool to identify recombinant regions in bacterial assemblies and generate recombination-free phylogenies, which scales to thousands of genomes from clonal...