ENH: added ability to not penalize terminal gaps in pairwise alignment
ENH: improve documentation of new functionality
ENH: fixed error where parameters were not being passed through
ENH: fixed typo in documentation
DOC: Fix typo in genetic code docstring

Fixes #536.
ENH: clarified comments
Merge pull request #539 from jairideout/issue-536

DOC: Fix typo in genetic code docstring
MAINT: added tests based on new functionality, currently failing
ENH: fixed bug where leading gaps were being penalized, even when penalize_terminal_gaps == False
ENH: updated output to match NEEDLE server output
MAINT: pep8 fixes
ENH: added test based on suggestion from @ebolyen
Merge branch 'master' of github.com:biocore/bipy into issue-537
REL: added note on changes based on suggestion from @ElDeveloper
Merge pull request #540 from gregcaporaso/issue-537

added penalize_terminal_gaps parameter to control how terminal gaps are scored in global alignment
Merge branch 'master' of git://github.com/biocore/scikit-bio into issue-225