Gubbins
Genealogies Unbiased By recomBinations In Nucleotide Sequences
The Gubbins algorithm identifies likely regions of recombination based on elevated densities of base substitutions.
About
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) identifies recombination regions in the bacterial genome using an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.