Gubbins

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) can be used to identify recombination.

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) can be used to identify recombination 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.

Further information

Learn and support

For more information and advice on using this software please see the user manual and our GitHub page.

License and Citation

Gubbins is available under GPL2.

If you make use of this software in your research, please cite as:

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J and Harris SR

Nucleic acids research 2015;43;3;e15
PUBMED: 25414349; PMC: 4330336; DOI: 10.1093/nar/gku1196