Force Biopython's Bio.Align to use Smith-Waterman algorithm
Based on the Biopython documentation, the algorithm used for alignment (i.e. Needleman-Wunsch, Smith-Waterman, Gotoh, or Waterman-Smith-Beyer) in Bio.Align is automatically chosen based on gap penalties. Is there a way to force a particular algorithm? I would like to use the Smith-Waterman algorithm with a BLOSUM matrix.
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sean.cascarina •
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sean.cascarina •
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To the best of my knowledge you will only be able to do this with the
localxx/globalxxmethods of Pairwise2.