Estimation of Synonymous and Nonsynonymous Branch Lengths from Pairwise Distances. BN-BS is designed for estimating 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. The program is written in C language and can be used on IBM PC compatible computers with the windows95 operating system.

To use the program, you need an input file containing the protein coding DNA sequences (see infile for an example). This file begins with two numbers: the number of sequences and the number of nucleotides per sequence (sequence length). The second line will be the name of the first sequence, and the third line will be the first sequence, and so on.

Only A, G, C, T, a, g, c, and t are allowed in sequences. Gaps should be removed and sequences should be aligned beforehand. The last line of the file is the tree topology of the sequences. The tree format is the same as that used in PHYLIP package (Felsenstein 1995). Note that the tree is unrooted, so trification rather than bification is required for the deepest branching node

The license of this software is Freeware, you can free download and free use this calculator software.