Updated documentation, includes input / output file descriptions
Addressed @gregcaporaso comments for clarity
Address @gregcaporaso comments
Changed command line flags refs in documentation
Merge pull request #1372 from lkursell/improve_openref_doc

Update documentation for pick_open_reference_otus.py - #1296
fixes #1400
this test file isn't used anymore
removed redundant usage example
added error check
wrapped line
added note on change
Merge pull request #1401 from gregcaporaso/issue-1400

fixes issue 1400
change qiime.org/emperor to http://biocore.github.io/emperor in doc / website .rst files
change from http://biocore.github.io/emperor to http://emperor.colorado.edu
Merge pull request #1411 from justin212k/emperor_doc

change qiime.org/emperor to http://biocore.github.io/emperor
Update stats code to use latest dm API

sample_ids -> ids
num_samples -> shape[0]
Documentation fix
Documentation fix
Merge pull request #1414 from jrrideout/bipy-dm-updates

Update qiime.stats code to use latest DistanceMatrix API
documentation fix