Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates

Author:

Dunn Katherine A.,Kenney Toby,Gu Hong,Bielawski Joseph P.ORCID

Funder

Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada

Publisher

Springer Science and Business Media LLC

Subject

Ecology, Evolution, Behavior and Systematics

Reference71 articles.

1. Anisimova M, Liberles D. Detecting and understanding natural selection. In: Cannarozzi GM, Schneider A, editors. Codon evolution: mechanisms and models: Oxford University Press; 2012. p. 73–96.

2. Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Pond SLK. CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol. 2010;6(8):e1000885.

3. Dayhoff MO, Eck RV, Park CM. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure. Vol. 5. Washington, D.C: National Biomedical Research Foundation; 1972. p. 89–99.

4. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992;8(3):275–82.

5. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 2001;8(5):691–9.

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