aminoacid alignment

[Warren Lathe]

Along the lines re: Dr. Farmers request for a good alignment program,  I was
wondering if anyone knew of a good program for aligning amino acid sequences.
I would prefer something that I could ftp or obtain easily, but any good 
program will do.    I am specifically looking for a program that does not use
chemical properties of amino acids but rather a mutation matrix to align, such
as the mutation matrix in Gonnet et al, Science 256: 1443-1445.

            

             Thanks in advance,

                    Trey 

--
Warren C. Lathe III (Trey)
Biology Dept. University of Rochester
email:  trey at thelab.biology.rochester.edu
        madda at troi.cc.rochester.edu