distmat calculates the evolutionary distances between every pair of sequences in a multiple alignment. The sequences must be aligned before running this program.
Here is a sample session with distmat:
% distmat pax.align Creates a distance matrix from multiple alignments Multiple substitution correction methods for proteins 0 : Uncorrected 1 : Jukes-Cantor 2 : Kimura Protein Method to use : 2 Output file [outfile.distmat]:
Mandatory qualifiers (bold if not always prompted):
Optional qualifiers (bold if not always prompted):