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- Title
rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny.
- Authors
Dimmic, Matthew W; Rest, Joshua S; Mindell, David P; Goldstein, Richard A
- 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.
- Publication
Journal of molecular evolution, 2002, Vol 55, Issue 1, p65
- ISSN
0022-2844
- Publication type
Journal Article
- DOI
10.1007/s00239-001-2304-y