updates to remove cogent dependency
removed cogent dependency
removed one of the cogent dependencies
updated for skbio interface change
fixed some errors due to bad imports
Minor doc fixes for issue #1533
Merge pull request #1539 from gregcaporaso/issues-1502-1538

work on removing cogent dependency and handling an skbio interface change
Merge pull request #1540 from wdwvt1/group_sig_docs

Minor doc fixes for issue #1533