gives a number representing the Smith-Waterman similarity between strings or vectors u and v.
- SmithWatermanSimilarity[u, v] finds an optimal local alignment between the elements of u and v, and returns the number of one-element matches.
- For strings, setting the option IgnoreCase->True makes SmithWatermanSimilarity treat lowercase and uppercase letters as equivalent.
- With the default setting SimilarityRules->Automatic, each match between two characters contributes to the total similarity score, while each mismatch, insertion, or deletion contributes .
- The option GapPenalty specifies an additional cost to be subtracted from the similarity score for any run of insertions or deletions.
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