gubbins - 3.4-2 main

Gubbins supports rapid phylogenetic analysis of large samples of
recombinant bacterial whole genome sequences.
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Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
Sequences) is 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. Simulations demonstrate the algorithm generates highly accurate
reconstructions under realistic models of short-term bacterial
evolution, and can be run in only a few hours on alignments of hundreds
of bacterial genome sequences.