Benchmarking multi-rate codon models

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dc.contributor.authorDelport, Wayneen_ZA
dc.contributor.authorScheffler, Konraden_ZA
dc.contributor.authorGravenor, Mike B.en_ZA
dc.contributor.authorMuse, Spencer V.en_ZA
dc.contributor.authorPond, Sergei Kosakovskyen_ZA
dc.date.accessioned2011-05-15T16:00:15Z
dc.date.available2011-05-15T16:00:15Z
dc.date.issued2010-07-21
dc.descriptionCITATION: Delport, W. et al. 2010. Benchmarking multi-rate codon models. PLoS ONE, 5(7): e11587, doi:10.1371/journal.pone.0011587.
dc.descriptionThe original publication is available at http://journals.plos.org/plosone
dc.description.abstractThe single rate codon model of non-synonymous substitution is ubiquitous in phylogenetic modeling. Indeed, the use of a non-synonymous to synonymous substitution rate ratio parameter has facilitated the interpretation of selection pressure on genomes. Although the single rate model has achieved wide acceptance, we argue that the assumption of a single rate of non-synonymous substitution is biologically unreasonable, given observed differences in substitution rates evident from empirical amino acid models. Some have attempted to incorporate amino acid substitution biases into models of codon evolution and have shown improved model performance versus the single rate model. Here, we show that the single rate model of non-synonymous substitution is easily outperformed by a model with multiple non-synonymous rate classes, yet in which amino acid substitution pairs are assigned randomly to these classes. We argue that, since the single rate model is so easy to improve upon, new codon models should not be validated entirely on the basis of improved model fit over this model. Rather, we should strive to both improve on the single rate model and to approximate the general time-reversible model of codon substitution, with as few parameters as possible, so as to reduce model over-fitting. We hint at how this can be achieved with a Genetic Algorithm approach in which rate classes are assigned on the basis of sequence information content. © 2010 Delport et al.
dc.description.urihttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011587
dc.description.versionPublisher's version
dc.format.extent5 pages
dc.identifier.citationDelport, W. et al. 2010. Benchmarking multi-rate codon models. PLoS ONE, 5(7): e11587, doi:10.1371/journal.pone.0011587.
dc.identifier.issn1932-6203 (online)
dc.identifier.otherdoi:10.1371/journal.pone.0011587
dc.identifier.urihttp://hdl.handle.net/10019.1/11605
dc.language.isoen
dc.publisherPublic Library of Science
dc.rights.holderAuthors retain copyright
dc.subjectCodon modelsen_ZA
dc.titleBenchmarking multi-rate codon modelsen_ZA
dc.typeArticle
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