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amino acid identity and similarity matrices

jrbrown at ac.dal.ca jrbrown at ac.dal.ca
Wed May 12 07:12:26 EST 1993

I am interested in a DOS or MAC based program which
will output a matrix of %identical or % similar amino
acid positions of multiple aligned sequences.  I am
well aware of programs such as PROTDIST, MULTALIN,
CLUSTAL, FASTA, etc. which generate a scoring matrix.
However, for the purpose of generating a simple comparative
matrix (for a Table in a paper NOT for phylogenetic analysis),
I have yet to find a program which will simply score the number
of identical aa positions or similar aa positions (ie. Ileu, Leu
 and Val are similar but not identical).  

I would greatly appreciate any information on such a program.
Thank you.

Jim Brown
Dept. of Biochemistry
Dalhousie University
Halifax, N.S.

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