期刊
JOURNAL OF MOLECULAR EVOLUTION
卷 55, 期 1, 页码 65-73出版社
SPRINGER
DOI: 10.1007/s00239-001-2304-y
关键词
general reversible transition Markov model; HIV; lentivirus; maximum likelihood; method; retroid; pol gene
资金
- NHGRI NIH HHS [T32-HG00040] Funding Source: Medline
- NIGMS NIH HHS [GM08270] Funding Source: Medline
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, gamma-retroviruses, 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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