[Biopython] Pairwise sequence aligner

[Michiel de Hoon]

Dear all,
For my work I needed a fast pairwise sequence aligner with more fine-grained control over gap penalties.I have implemented a C extension to do this, which is available in this branch on github:
https://github.com/mdehoon/biopython/tree/pairwise_aligner
There is some rudimentary documentation in Doc/Tutorial/chapter_align.tex (under section 6.5).Examples can be found in Tests/test_pairwise_aligner.py.

I think this aligner can be a replacement for pairwise2 aligner.In particular, it is more flexible and more Pythonic, using a PairwiseAligner object to store the alignment scoring scheme instead of interpreting the function name (as in pairwise2).
Comments are welcome.Note that this aligner returns PairwiseAlignment objects; it may be better to integrate this with the existing MultipleSeqAlignment class in Bio/Align.


Best,-Michiel


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