MAINT: added failing tests where input type has been changed for input in private functions
MAINT: updated type for inputs to private functions
ENH: updated to support comptuing scores and traceback from Alignment objects
ENH: updated traceback to work from Alingment objects
MAINT: updated so all public functions can now provide str, BiologicalSequence, or Alignment objecs as input
MAINT: added basic test of private methods ability to align alignments
MAINT: split substitution score computation to new function for easier testing
MAINT: added tests, fixed typo
MAINT: added another test
expanded API-level tests
MAINT: expanded tests
MAINT: added code and tests to explicitly disallow locally aligning alignments. we don't have use cases for this right now, and it's not clear how it would work exactly
MAINT: added new function to reduce code duplication
DOC: updated documentation
MAINT: cleaned up function and documentation
MAINT: PEP8 fixes
MAINT: pep8 fixes
MAINT: py3 fix
Merge branch 'master' of github.com:biocore/bipy into issue-550
MAINT: grammatical fix