Removing pycogent_backports.usearch.py
Removing pycogent_backports/uclust.py
Removing pycogent_backports/seqprep.py and pycogent_backports/fastq_join.py
removing pycogent_backports/(blat,rdp_classifier).py
removing pycogent_backports/(bwa,mothur).py
Update setup.py to install brokit
Deleting tests for the application controllers of blat and bwa
Fixing imports to brokit
Merge branch 'master' of git://github.com/qiime/qiime into brokit
Merge pull request #1438 from josenavas/brokit

Port pycogent backports application controllers to brokit