Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.

TLDR

Existing methods such as those of Miyata and Yasunaga and Li et al. produce comparable results to the new approaches even though they do not weight different codon substitutions. The study presents two simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. These methods compute substitution counts directly from sequence data without assigning weights to codon changes.

Abstract

Two simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions are presented. Although they give no weights to different types of codon substitutions, these methods give essentially the same results as those obtained by Miyata and Yasunaga's and by Li et al.'s methods. Computer simulation indicates that estimates of synonymous substitutions obtained by the two methods are quite accurate unless the number of nucleotide substitutions per site is very large. It is shown that all available methods tend to give an underestimate of the number of nonsynonymous substitutions when the number is large.