Molecular Biology and Evolution, Vol 13, 650-659, Copyright © 1996 by Society for Molecular Biology and Evolution
Z Yang and S Kumar
We propose two approximate methods (one based on parsimony and one on
pairwise sequence comparison) for estimating the pattern of nucleotide
substitution and a parsimony-based method for estimating the gamma
parameter for variable substitution rates among sites. The matrix of
substitution rates that represents the substitution pattern can be
recovered through its relationship with the observable matrix of site
pattern frequences in pairwise sequence comparisons. In the parsimony
approach, the ancestral sequences reconstructed by the parsimony algorithm
were used, and the two sequences compared are those at the ends of a branch
in the phylogenetic tree. The method for estimating the gamma parameter was
based on a reinterpretation of the numbers of changes at sites inferred by
parsimony. Three data sets were analyzed to examine the utility of the
approximate methods compared with the more reliable likelihood methods. The
new methods for estimating the substitution pattern were found to produce
estimates quite similar to those obtained from the likelihood analyses. The
new method for estimating the gamma parameter was effective in reducing the
bias in conventional parsimony estimates, although it also overestimated
the parameter. The approximate methods are computationally very fast and
appear useful for analyzing large data sets, for which use of the
likelihood method requires excessive computation.
ORIGINAL ARTICLE
Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA. ziheng@mws4.biol.berkeley.edu
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