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Molecular Biology and Evolution, Vol 11, 613-619, Copyright © 1994 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site

T Ota and M Nei
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802.

Nei and Gojobori (1986) developed a simple method to estimate the numbers of synonymous (ds) and nonsynonymous (dN) substitutions per site. In the present paper, we have developed a method for computing variances and covariances of ds's and dN's and of the proportions of synonymous (ps) and nonsynonymous (pN) differences. We also have developed a method for computing the variances of mean dS, dN, pS, pN, without constructing a phylogenetic tree of the genes. We have conducted computer simulations based on simple evolutionary models and have shown that the new method gives good estimates of variances and covariances.
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