To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.
SNAP calculates pairwise synonymous and nonsynonymous distances according to the Nei and Gojobori method for an alignment in table format. It outputs a synonymous and a nonsynonymous 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.