stockholm writer initial addition
initial stockholm format writer files
stockholm parser initial commit
getting in line with new parse.sequences setup
test files added
taking care of PEP8/code cleanup
defaultdict usage, cleanup for readability
DOC: Add coding guidelines ported from pycogent

A lot of work has to go in still but at least it is being indexed in the
front page of the documentation.
DOC: Change camelcase to undersocres and add dm

dm is a valid abbreviation for distance matrix.
DOC:Add note about using PEP8 for name conventions
DOC: Add note about imports of matplotlib, etc
DOC: Add note about documentation
DOC: Minor updates to the module docs/imports
DOC: Fix link and add class level doc example

The numpy link had the incorrect casing hence nothing was going to be
linked to it.
Very hacked bioenv/BEST port from qiime.stats

But tests are passing!
Add test data to data directory
Match SampleID column name to what's used in QIIME

Doesn't really matter, but might as well be consistent.
Complete rewrite of bioenv algorithm

Much shorter and cleaner. The previous implementation had a bug where the environment variables weren't being scaled before calculating Euclidean distances. The results now match R's vegan::bioenv function.

Returns a pandas data frame for easy formatting of results that are very similar to what you get in R.

Still have a bunch of TODOs to fill out, more unit tests to add, performance testing, etc.
Ensure implicit column order is maintained
Add check for duplicate column names