Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
View/ Open
Author
Page, Andrew J.
Connor, Thomas R.
Delaney, Aidan J.
Keane, Jacqueline A.
Bentley, Stephen D.
Parkhill, Julian
Harris, Simon R.
Published Version
https://doi.org/10.1093/nar/gku1196Metadata
Show full item recordCitation
Croucher, Nicholas J., Andrew J. Page, Thomas R. Connor, Aidan J. Delaney, Jacqueline A. Keane, Stephen D. Bentley, Julian Parkhill, and Simon R. Harris. 2015. “Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.” Nucleic Acids Research 43 (3): e15. doi:10.1093/nar/gku1196. http://dx.doi.org/10.1093/nar/gku1196.Abstract
The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330336/pdf/Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAACitable link to this page
http://nrs.harvard.edu/urn-3:HUL.InstRepos:14351121
Collections
- SPH Scholarly Articles [6362]
Contact administrator regarding this item (to report mistakes or request changes)