Ulla: a program for calculating environment-specific amino acid substitution tables

Summary: Amino acid residues are under various kinds of local environmental restraints, which influence substitution patterns. Ulla, a program for calculating environment-specific substitution tables, reads protein sequence alignments and local environment annotations. The program produces a substitution table for every possible combination of environment features. Sparse data is handled using an entropy-based smoothing procedure to estimate robust substitution probabilities. Availability: The Ruby source code is available under a Creative Commons Attribution-Noncommercial License along with additional documentation from http://www-cryst.bioc.cam.ac.uk/ulla. Contact: semin@cryst.bioc.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.