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.
Merge branch 'master' of git://github.com/biocore/scikit-bio into guidelines

Conflicts:
	doc/source/index.rst
Merge branch 'master' of git://github.com/biocore/scikit-bio into guidelines
DOC: Update How should I format my code? section
DOC: Reorganize to make PEP8 more evident

It should be immediately clear that we follow PEP8 conventions for
variable, function, module, namings, etc.
DOC/BUG: Fix RST directives to render code
DOC: Update section about testing