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

J Mol Evol. 2002 Jul;55(1):65-73. 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Substitution
  • Evolution, Molecular
  • Genetic Techniques
  • Likelihood Functions
  • Phylogeny*
  • RNA-Directed DNA Polymerase / genetics*
  • Retroviridae / classification
  • Retroviridae / enzymology*
  • Retroviridae / genetics*


  • RNA-Directed DNA Polymerase