MODIFIED, map_reads_to_reference supports choice of genetic_code

Modified the script with a --genetic_code option and modified the library
code to be aware of the option. Also changed the test code to include
the new option.
Merge branch 'map_reads_to_reference' of github.com:adamrp/qiime into map_reads_to_reference
modified NCBI web reference

URL is now more descriptive
Add functions to download UCLUST and FastTree

These two functions will try to download FastTree (and build it using
gcc) and UCLUST. The resulting executables will be copied to the scripts
directory. This is a similar pattern to what was being done with the
denoiser.

Fixes #1246
Merge branch 'map_reads_to_reference' of github.com:adamrp/qiime into map_reads_to_reference
Merge branch 'master' of https://github.com/qiime/qiime into map_reads_to_reference
Remove dependency on cogent for setup.py

This script is now PIP-installable, at least for the base install.
Add MANIFEST.in & minor modifications to setup.py
Add MANIFEST to .gitignore
Add denoiser files to the exclude
Remove qiime_test_data from setup build

Fixes #1246
Change -lm flag for FastTree
Merge branch 'master' of git://github.com/qiime/qiime into issue_1246
Change name from QIIME->qiime
Fixing default value for params

Was set to {}, which can cause problems.
Changing imports to pull from pycogent_backports
Add app controllers to pycogent_backports

Controllers for BLAT and BWA, plus tests
Update app_available

The standard output and standard error streams are no longer seen on
screen, instead these are now redirected to /dev/null.

Add docstring to the function.
Add changes on versions and functionality

The following was changed:
    - Update versions of matplotlib to be greater than 1.1.0 but less
      than 1.3.1.
    - Update version of BIOM to be 1.3.1 only.
    - Redirect the output of app_available to /dev/null
    - Make the building_stack not executed if egg_info is passed as an
      argument to the script.
Update link to NCBI URL, update changelog