gubbinsGubbins (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.
For more information visit the gubbins website.
These versions of gubbins are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.