API: removed math, skbio.math.$ -> skbio.$
TST: corrected import path for test_subsample.py
TST: moved test_subsample.py as nose ignores any subpackage with an `_`
API: made ordination.utils private
MAINT: pep8
MAINT: pep8
Remove skbio.app subpackage in favor of burrito.
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
Merge pull request #561 from ebolyen/issue541

API: removed math, skbio.math.$ -> skbio.$
Merge branch 'master' into issue-523

Conflicts:
	CHANGELOG.md
expanded API-level tests
Merge pull request #565 from jairideout/issue-523

Remove skbio.app subpackage in favor of burrito.