Port pycogent backports application controllers to brokit

I've removed the application controllers hosted on pycogent backports and I fixed the imports to use the brokit one. I've also modified the `setup.py` file in order to install brokit.

The app controllers removed were:
- usearch
- uclust
- seqprep
- fastq_join
- blat
- rdp
- bwa
- mothur