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 geoff.biop.ox.ac.uk. Please see the README file for details licencing and registration. You can read manuals for the programs and some related papers at http://geoff.biop.ox.ac.uk/.