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- Title
Robust inference of positive selection from recombining coding sequences.
- Authors
Scheffler, Konrad; Martin, Darren P; Seoighe, Cathal
- Abstract
Accurate detection of positive Darwinian selection can provide important insights to researchers investigating the evolution of pathogens. However, many pathogens (particularly viruses) undergo frequent recombination and the phylogenetic methods commonly applied to detect positive selection have been shown to give misleading results when applied to recombining sequences. We propose a method that makes maximum likelihood inference of positive selection robust to the presence of recombination. This is achieved by allowing tree topologies and branch lengths to change across detected recombination breakpoints. Further improvements are obtained by allowing synonymous substitution rates to vary across sites.
- Publication
Bioinformatics (Oxford, England), 2006, Vol 22, Issue 20, p2493
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btl427