Updated documentation, includes input / output file descriptions
Fix FastTree version check when non-interactive

Fixes the FastTree version check when running in non-interactive mode. Based on @spikebike's suggested regex.

Fixes #1371.
fix issue with "version" having different case

grep command has to be case-insensitive
Remove qiime.util.DistanceMatrix and unit tests
Remove DistanceMatrix usage from test_format.py

Also cleaned up related test code so that it uses mock stats results dictionaries. This makes the test code much simpler and decouples it from qiime.stats.
Merge branch 'master' into issue-829
added new parameters for more control over row labels
Merge branch 'master' of github.com:qiime/qiime into issue-751
updated changelog
modified handling of level to make more consistent with other scripts
replaced try/except with if/else
addressing comments from @wasade
Merge pull request #1381 from jrrideout/issue-1371

Fix FastTree version check when non-interactive
Merge pull request #1387 from gregcaporaso/issue-751

partially addresses #751
Update stats.py, test_stats.py

Now uses SymmetricDistanceMatrix.
update compare_categories.py lib code
update compare_distance_matrices.py lib code
relax print_qiime_config.py python version check

Is now okay with any python versions >= 2.7.0 and < 3.0.0. Also supports python
version strings like the kind found in Miniconda's python, e.g.:

Python 2.7.6 :: Continuum Analytics, Inc.

Fixes #1391.
Clean up

I find myself making these changes every time I use this script to make a new
QIIME-style py file.
Change error type to option_parser.error