ENH: method to shuffle tip names on a tree
ENH: 3-order magnitude performance bump
BUG: error in example
parse_qseq.
Add support for QSEQ parsing.
Add support for QSEQ parsing.
PEP8 changes.
PEP8 changes.
Decode data first before calling the split method.
Remove unused code.
Catch AttributeError on str.decode - Python 3.x support.
Add details on sequence ID format and record namedtuple attributes to the parse_qseq return docstring.  Change filter_ to filtered and define it as a boolean.
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