Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Nucleic Acids Research, ISSN: 1362-4962, Vol: 43, Issue: 3, Page: e15-null
2015
- 1,751Citations
- 916Captures
- 28Mentions
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
Citation Benchmarking is provided by Scopus and SciVal and is different from the metrics context provided by PlumX Metrics.
Metrics Details
- Citations1,751
- Citation Indexes1,747
- CrossRef1,747
- 1,553
- 1,195
- Policy Citations3
- Policy Citation3
- Patent Family Citations1
- Patent Families1
- Captures916
- Readers916
- 916
- Mentions28
- News Mentions28
- News28
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Article Description
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/sangerpathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.
Bibliographic Details
Oxford University Press (OUP)
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