Multiple sequence alignment

Richard A. Goldstein richard at
Tue Mar 3 00:00:26 EST 1992

We are interested in performing rapid multiple protein sequence alignments.
We are aware of two software packages that include such alignment programs:
clustal and gcg's pileup.  We would be interested in finding out:

  1.  Are there other programs that we should consider using? (We have
been using Silicon Graphics computers and a Cray-2.) 

  2.  What are reasonable values for the various default parameters?

  3.  Are there any subtleties that we should keep in mind?

Along similar lines, are there any programs available for doing
non-optimal alignments between two protein sequences?

Please respond via e-mail to:  richard at

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