AMPS (Alignment of Multiple Protein Sequences) is a suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. AMPS also implements flexible pattern matching and database scanning options. AMPS includes functions for running randomisations to estimate the significance of sequence similarities.
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Barton, G. J. (1990),
“Protein Multiple Sequence Alignment and Flexible Pattern Matching“,
Meth. Enzymol., 183, 403-428.