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

T Ota; M Nei

doi:10.1093/oxfordjournals.molbev.a040140

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

Mol Biol Evol. 1994 Jul;11(4):613-9. doi: 10.1093/oxfordjournals.molbev.a040140.

Authors

T Ota¹, M Nei

Affiliation

¹ Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802.

PMID: 8078400
DOI: 10.1093/oxfordjournals.molbev.a040140

Abstract

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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Computer Simulation*
Models, Genetic*
Mutation*
Selection, Genetic

Grants and funding

GM-20293/GM/NIGMS NIH HHS/United States