biocore/scikit-bio — pull request #540 by gregcaporaso (2014-07-13 19:42:21+00:00)
Title: added penalize_terminal_gaps parameter to control how terminal gaps are scored in global alignment

** NOT READY FOR MERGE **

@ebolyen, this fixes the issue we were working on yesterday. see my [updated example notebook here](http://nbviewer.ipython.org/github/gregcaporaso/sketchbook/blob/master/2014.07.12-alignment-experiments/alignment-filtering.ipynb).

Still need to add tests to this - will you review after that as you're most familiar with the issue?