One of the programs in the molphy package calculates amino acid distance matrices.
There is a reference ot it on Joe Felsenstein's webpage:
I can send you a macintosh version of my program GCUA that will do this,
although it needs fasta-formatted protein-coding DNA sequences as input
(it converts to proteins and then calculates a distance matrix).
Thorsten Burmester wrote:
>> Does anybody know a program that measures the metric distances of
> proteins by their amino acid compositions? Preferably one that can read
> alignment files. I don't want to do this work by hand...
> Thorsten Burmester
>thorsten at erfurt.thur.de
Dr. James O. McInerney,
Dept. Biology, Dept. Zoology,
Natl. Univ. Ireland, The Natural History Museum,
Maynooth, and Cromwell road,
Co. Kildare, Ireland London SW7 5BD, UK.
Phone +353 1 708 3860 +44 171 938 9163
Fax +353 1 708 3845 +44 171 938 9158
email james.o.mcinerney at may.iej.mcinerney at nhm.ac.ukhttp://www.may.ie/academic/biology/jmbioinformatics.shtml