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
Merge pull request #1412 from heatyen/info

Documentation fix
remove dependency on cogent.PROTEIN
Merge branch 'master' of github.com:qiime/qiime into remove-protein
Merge pull request #1420 from gregcaporaso/remove-protein

Remove protein