ENH: porting python alignment functions from IAB

see #457. this commit provides first working version of ported smith-waterman
w/ affine gap alignment. a lot of work to do from here to get it ready for
scikit-bio.
added some notes and copyright info
ENH: added global alignment with NW
MAINT: added example from *Biological Sequence Analysis*
MAINT: ported blosum50 to pairwise.py
MAINT: added comment about future handling of subs. matrices
MAINT: starting to add tests of high-level functions
added more tests
started adding nucleotide alignment tests, but currently failing
ENH: added function to create nt substitution matrices
added test of local nuc alignment
changed type of score for consistency
found another failure with my local aligner... made some notes, more work soon...
ENH: updated procedure for choosing among equal scores

this provides better alignment with EMBOSS results
ENH: updated/expanded tests
ENH: expanded tests
ENH: generalized score/traceback generation for use with either NW or SW alignment
MAINT: generalized language in comments
MAINT: generalized variable names
MAINT: updated doc