Version 3 of the FASTA packages contains many programs for searching DNA and
protein databases and one program (prss3) for evaluating statistical
significance from randomly shuffled sequences.  Several additional analysis
programs, including programs that produce local alignments, are available as
part of version 2 of the FASTA package, which is available as the port
biology/fasta.

FASTA is described in:  W. R. Pearson and D. J. Lipman (1988), "Improved
Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R.  Pearson
(1996) "Effective protein sequence comparison" Meth. Enzymol.  266:227-258;
Pearson et. al.  (1997) Genomics 46:24-36;  Pearson, (1999) Meth. in
Molecular Biology 132:185-219.

The FASTA3 suite is distributed freely subject to the condition that it may
not be sold or incorporated into a commercial product.