>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.
I think it would be of interest to many people to review the available
software for multiple sequence alignments, the system they run on and their
strenghts and weaknesses. May there is a current review in the literature
someone knows of.
I know of three programs- seqapp for the Mac, MACAW primarily for the PC
but being adapted for the map, and PIMA-unix based. Since I haven't really
extensively used these programs, I reserve comments.
Robert D. Burk, M.D. email: burk at aecom.yu.edu
Albert Einstein College of Medicine FAX: (718) 918-0857
1300 Morris Park Ave.
Bronx, New York 10461