gubbins binary package in Ubuntu Xenial amd64

 Gubbins supports rapid phylogenetic analysis of large samples of
 recombinant bacterial whole genome sequences.
 .
 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.

Source package