Perl-based SNAP

SNAP calculates pairwise synonymous and nonsynonymous distances according to the Nei and Gojobori method for an alignment in table format. It outputs a synonynous and a non-synonymous distance matrix, an exhaustive pairwise codon-by-codon comparison, and a summary table.

PLEASE NOTE: Perl-SNAP does not truncate sequence names that are longer than 10 characters. This can cause trouble if you input one of the distance matrices into a Phylip program (such as Neighbor): the long sequence names cause the program to read the distance matrix incorrectly.

Web-based SNAP program

README

SNAP ftp site for Unix users

SNAP ftp site for PC users

Note to Safari users: please use Firefox or Internet Explorer if you experience ftp problems using Safari.