title: rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny.
abstract: Retroviral and other reverse transcriptase (RT)-containing sequences may be subject to unique evolutionary pressures, and models of molecular sequence evolution developed using other kinds of sequences may not be optimal. Here we develop and present a new substitution matrix for maximum likelihood (ML) phylogenetic analysis which has been optimized on a dataset of 33 amino acid sequences from the retroviral Pol proteins. When compared to other matrices, this model (rtREV) yields higher log-likelihood values on a range of datasets including lentiviruses, spumaviruses, betaretroviruses, gammaretroviruses, and other elements containing reverse transcriptase. We provide evidence that rtREV is a more realistic evolutionary model for analyses of the pol gene, although it is inapplicable to analyses involving the gag gene.
authors.affiliation: Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA. mdimmic@umich.edu
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Dimmic
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Rest
authors.forename: David P
authors.initials: DP
authors.lastname: Mindell
authors.forename: Richard A
authors.initials: RA
authors.lastname: Goldstein
mesh_terms: D019943:Amino Acid Substitution; D019143:Evolution, Molecular; D005821:Genetic Techniques; D016013:Likelihood Functions; D010802:Phylogeny; D012194:RNA-Directed DNA Polymerase / Q000235:genetics*; D012190:Retroviridae / Q000145:classification / Q000201:enzymology* / Q000235:genetics*
chemical_list: D012194:RNA-Directed DNA Polymerase