erge branch 'master' of https://github.com/biocore/qiime into remote

updating to more recent version of qiime
Merge branch 'master' of https://github.com/biocore/qiime into add-swarm

merge latest changes from upstream master
added swarm
code review modifications + change of using 'uclust_otu_prefix_id' to 'denovo_otu_prefix_id' & all de novo tools
MAINT: updated imports from skbio app controller to import from burrito, fixes #1644
REL: added note to change log
Merge pull request #1645 from gregcaporaso/issue-1644

updated to use burrito instead of skbio.app
Merge pull request #1643 from ekopylova/add-swarm

Add swarm to pick_otus.py
issue 1646 resolved
Merge pull request #1647 from ekopylova/issue-1646

issue 1646 resolved Thanks @ekopylova
resolves issue #1649

adds documentation to what file format is acceptable for the script when using t
he --sample_id_fp option.

cleans up the lines of code that do the filtration when that option is passed.
Fixing qiime/rarefaction.py
Fixing qiime/split.py
Merge pull request #1652 from josenavas/biom21

Biom21
API/ENH: QIIME now depends on BIOM 2.1

QIIME should now depend on BIOM 2.1 and not in BIOM 2.0.1-dev, a note
has been added to the ChangeLog.md file.

Fixes #1590
Merge pull request #1654 from ElDeveloper/biom-2.1

API/ENH: QIIME now depends on BIOM 2.1
Merge pull request #1650 from wdwvt1/issue_1649

resolves issue #1649
Documentation update

Fixed link in the alpha_diversity.py script to point to correct page.
[skip ci]
Merge pull request #1659 from wdwvt1/docu_update

Documentation update
Fix merge conflicts