BN-BS is a software to estimate branch lengths in terms of synonymous and nonsynonymous substitutions per site, while the tree topology is given. The program uses the modified Nei-Gojobori method (Zhang et al. 1998) to estimate pairwise synonymous and nonsynonymous distances among present-sequences and then estimates branch lengths and their variances by using the ordinary least-squares method.
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Zhang J., H. F. Rosenberg, and M. Nei (1998)
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
Proc. Natl. Acad. Sci. USA 95:3708-3713.