rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny

• Published in: Journal of molecular evolution Vol. 55; no. 1; pp. 65 - 73
• Main Authors: Dimmic, Matthew W, Rest, Joshua S, Mindell, David P, Goldstein, Richard A
• Format: Journal Article
• Language: English
• Published: Germany Springer Nature B.V 01.07.2002
• Subjects: Amino Acid Substitution; Amino acids; Enzymes; Evolution, Molecular; Evolutionary biology; Genetic Techniques; Genomics; Likelihood Functions; Molecular biology; Phylogeny; Retroviridae - classification; Retroviridae - enzymology; Retroviridae - genetics; RNA-Directed DNA Polymerase - genetics; Virology
• ISSN: 0022-2844; 1432-1432
• DOI: 10.1007/s00239-001-2304-y

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.