MAINT: updated list indexing format
MAINT: updated for clarity
Convert gradient results namedtuples to classes
Change OrdinationResults from namedtuple to regular class
MAINT: updated so more informative error message is printed if characters are in sequences that are not in the substitution matrix
Add changelog mention

Fixes #359.
Merge branch 'master' into issue-359

Conflicts:
	CHANGELOG.md
ENH: updated to better match SSW interface, thanks @ebolyen
MAINT: fixes doc bugs, and other comments from @ElBrogrammer
Merge pull request #469 from gregcaporaso/issue-457

addition of python functions for pairwise local and global alignment
Merge pull request #475 from ElBrogrammer/issue-464

Remove skbio.util.sort in favor of natsort package
Merge branch 'master' into issue-463
Merge pull request #480 from ElBrogrammer/issue-359

Change namedtuple subclasses to regular classes
ENH: added support for BIOM tables in a separate function
DOC: added to sphinx docs
ENH: added tests working with actual BIOM table objects, confirmed they pass
ENH: dropped dependence on biom-format in tests in favor of new helper object
MAINT: cleaned up docs, removed some examples that I'm not going to have working in time (see #481)
MAINT: various clean-ups in prep for review
MAINT: more clean-up in prep for review