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  • Title: rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny.
    Author: Dimmic MW, Rest JS, Mindell DP, Goldstein RA.
    Journal: J Mol Evol; 2002 Jul; 55(1):65-73. PubMed ID: 12165843.
    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.
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