- The setting for SimilarityRules must consist of a list of rules of the form , where the give elements to compare, and v gives their similarity.
- The can be either explicit characters or other elements, or patterns.
- A rule for gives the score for a deletion; a rule for gives the score for an insertion.
- SimilarityRules->Automatic is effectively equivalent to , giving a score of for any pair of identical elements, and a score of for any mismatch, deletion or insertion.
- The following named settings for SimilarityRules implement various similarity matrices typically used for particular bioinformatics purposes:
"BLAST" alignment of nucleotide sequences "BLOSUM62" local alignment of related amino acid sequences "BLOSUM80" local alignment of similar sequences "PAM30" global alignment of very similar amino acid sequences "PAM70" global alignment of related sequences "PAM250" global alignment of dissimilar sequences
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