Refactor print_tree code
Comment treestyle code
Merge commit 'ffbc4' into mutation

The purpose here was to get the helpful refactor which was done on a
branch I had not wanted to merge wholly.

Conflicts:
	tree_viz.py
Minor version bump to v0.1.1dev
Represent branch lengths as mutation counts

treeviz optionally multiplies the distances drawn from the PHYLIP
tree by the sequence length found in the associated *.phy file.
Reorganize runner functions to prepare for new entry points
Start adding code to reroot trees before rendering
Add basic functionality to identify pure subtrees

For now, it only prints each subtree, but it's a start.
Add option to output trees from analysis
Implemented lineage identification by distance

Now treeviz also identifies subtrees based on how many mutations they
share from the germline node.
Add CL argument to refrain from displaying tree

This option will be useful as long as the subtree analyses are still
tied in to the display program.
Improve error handling for germline rooting
Fix MANIFEST file

It had not been including README.
Ignore dist/ and compiled file MANIFEST
Add function to prune 0-length branches

Also add test for said function.
Fix packaging

Now the test module is properly included as a package in a __init__.py,
and tree_viz is in it's own directory in an __init__.py.
Re-indent some comments
Partially refactor functions into GermTree class
Finish major refactor into subclass of ete tree

I moved almost all of the informal methods extant for ete2.Tree
instances into a subclass, that way I can more smoothly break up the
functionality of this module into more manageable units.
Remove edges of zero length