Force Biopython's Bio.Align to use Smith-Waterman algorithm

Question

[sean.cascarina]

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.

[Joe]

To the best of my knowledge you will only be able to do this with the localxx/globalxx methods of Pairwise2.