How did you produce your alignment? Did you use BLAST? http://www.ncbi.nlm.nih.gov/blast" Sequence alignment tools calculate the %identity, %similiarity, %gaps of the alignments they produce. One can then use a parser http://sapiens.wustl.edu/~ikorf/BPlite.html to get at the information you want.

In reply to Re: Similarity of strings by Anonymous Monk
in thread Similarity of strings by professa

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