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 [0]: 2
Output file [outfile.distmat]:

Mandatory qualifiers (bold if not always prompted):

[-msf] (seqset)

File containing a sequence alignment.

-nucmethod (menu)

Multiple substitution correction methods for nucleotides.

-protmethod (menu)

Multiple substitution correction methods for proteins.

[-outf] (outfile)

A name for the distance matrix.

Optional qualifiers (bold if not always prompted):

-ambiguous (boolean)

Use the ambiguous codes in the calculation of the Jukes-Cantor method, or if the sequences are proteins.

-gapweight (float)

Weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods.

-position (integer)

Choose base positions to analyse in each codon e.g., 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases.

-calculatea (boolean)

Forces the calculation of the a-parameter in the Jin-Nei Gamma distance calculation. Otherwise, the default is 1.0 (see -parametera option).

-parametera (float)

User-defined parameter to use in the Jin-Nei Gamma distance calculation. The suggested value (and default) is 1.0.