Update to use latest skbio DistanceMatrix API

**Do not merge until https://github.com/biocore/scikit-bio/pull/245 is merged!**
Merge pull request #1487 from ElBrogrammer/skbio-dm-rename

Update to use latest skbio DistanceMatrix API
Merge branch 'master' of github.com:qiime/qiime into remove-cogent-DNA