Open AccessA simple method for estimating the parameter of substitution rate variation among sites
Author(s) -
Xun Gu,
J Zhang
Publication year - 1997
Publication title -
molecular biology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.637
H-Index - 218
eISSN - 1537-1719
pISSN - 0737-4038
DOI - 10.1093/oxfordjournals.molbev.a025720
Subject(s) - simple (philosophy) , substitution (logic) , variation (astronomy) , statistics , mathematics , biology , maximum likelihood , estimation theory , algorithm , computer science , astrophysics , philosophy , physics , epistemology , programming language
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.