A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny |
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Authors: | Huai-Chun Wang Karen Li Edward Susko Andrew J Roger |
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Institution: | (1) Department of Biochemistry and Molecular Biology, Dalhousie University, B3H 1X5 Halifax, N.S., Canada;(2) Department of Mathematics and Statistics, Dalhousie University, B3H 3J5 Halifax, N.S., Canada;(3) Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Dalhousie University, Canada |
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Abstract: | Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT) or Whelan and Goldman (WAG) models,
are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the
average amino acid frequencies of the data set under examination (e.g JTT + F). Variation in the evolutionary process between
sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ) distribution. However, sites in proteins
also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution
matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical
amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. |
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Keywords: | |
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