The AMPS package (Barton, 1990). This performs multiple sequence alignments and databank scanning.
AMAS (Livingstone and Barton, 1993, CABIOS, 9, 745-756). Analysis of Multiply Aligned Sequences. This package uses a sophisticated set-based method to identify patterns of residue conservation in multiple sequence alignments.
All programs are available by anonymous ftp from www.compbio.dundee.ac.uk. Please see the README file for details licencing and registration.