Molecular Biology and Evolution, Vol 14, 1106-1113, Copyright © 1997 by Society for Molecular Biology and Evolution
X Gu and J Zhang
When the rate variation among sites is described by a gamma distribution,
an important problem is how to estimate the shape parameter alpha, which is
an index of the degree of among-site rate variation. The parsimony-based
methods for estimating alpha are simple but biased, i.e., alpha tends to be
overestimated. On the other hand, the likelihood-based methods are
asymptotically unbiased but take a huge amount of computational time. In
this paper, we have developed a new method to solve this problem: we first
estimate the expected number of substitutions at each site, which is
corrected for multiple hits, and then estimate the parameter alpha. Our
method is computationally as fast as the parsimony method, and the
estimation accuracy is much higher than that of parsimony and similar to
that of the likelihood method.
ORIGINAL ARTICLE
A simple method for estimating the parameter of substitution rate variation among sites
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802. xungu@imeg.bio.psu.edu
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