[Biopython-dev] [Bug 1876] Bio.pairwise2 generates incorrect Needleman-Wunsch score_matrix

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1876


jchang at biopython.org changed:

           What    |Removed                     |Added
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             Status|NEW                         |ASSIGNED




------- Comment #5 from jchang at biopython.org  2005-10-07 15:58 -------
The two implementations use different algorithms, and the bookkeeping in the
score matrix is done differently.  For an illustration of the algorithm used in
Biopython, see:
http://www.maths.tcd.ie/~lily/pres2/sld006.htm

The score matrices are different and not comparable.  However, the final
alignment, score, and traceback should be the same.  Please let me know if they
are not.

I chose this algorithm because it was simpler for me to generate a correct
traceback.




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