[Biopython-dev] add dynamic programming alignment modules

[Jeffrey Chang]

On the flight home from ISMB, I coded up some modules to do pairwise 
alignments.  I went ahead and put them into the Bio.Align package 
because they seem most appropriate there -- I hope nobody objects!

There are two main modules: pairwise.py and fastpairwise.py.  The 
first one implements a slower, more general alignment algorithm.  The 
second is faster, but requires an affine gap penalty.  Right now, 
they're both implemented in python.  However, I broke the code up in 
such a way so that it won't be hard to swap out a piece of it with 
fast C code.  I didn't have time to do this on the flight, but might 
get to it at a later date.

Enjoy!

Jeff