CS-BLAST/ CSI-BLAST

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Angermüller, C., Biegert, A., & Söding, J. (2012). Discriminative modelling of context-specific amino acid substitution probabilities. Bioinformatics, 28(24), 3240-3247.
Biegert, A., & Söding, J. (2009). Sequence context-specific profiles for homology searching. Proceedings of the National Academy of Sciences,106(10), 3770-3775.