Wed Dec  5 14:33:35 GMT 2001
JDB

This program takes a FASTA file, and produces a OC input file as
output. The FASTA file should be an alignment. The code finds the begining
and end of the sequence in each alignment, the number of residues for
in each sequence, and then does an all against all pairwise identity
calculation. This is the number of identical residues divided by the
number of residues in the longest sequence, shared gaps are ignored. A
percentage is returned.

BUGS
Very little error checking is done on the filling of the structures with
FASTA data.
It seems quite slow to do the pairwise comparisons.