JSUBST is a program to calculate environment-specific substitution tables from annotated protein sequence alignments. Alignments may be between at least one protein of known structure and any number of protein sequences.
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Environment-Specific Substitution Tables Improve Membrane Protein Alignment
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
Bioinformatics (2011) 27 (13): i15-i23.