Improved variance estimators for one- and two-parameter models of nucleotide substitution

摘要

The current variance estimators for Jukes and Cantor’s one-parameter model and Kimura’s two-parameter model tend to seriously underestimate the true variances when the proportion of nucleotide differences between the two sequences under study is not small. In this paper, we developed improved variance estimators, using a higher order Taylor expansion and empirical methods. The new estimators outperform the conventional estimators and provide accurate estimates of the true variances.