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
simplified ul_confidence_bounds

* precomputed values are now a table instead of elifs
* two possible returns
* cyclomatic complexity down from a score of 60 to 8
added credit
simplified entropy check
rework of filter_alignment.apply_lane_mask_and_gap_filter

* no more temporary files
* cyclomatic complexity down from 34 to 9
* much smaller method
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.
Update code for mpl 1.3.1 upgrade

Test in tests/test_stats.py was checking the x ticks of an empty plot, which apparently are different between mpl 1.1.0 and 1.3.1.

In this case, the fix is to remove the test since it is version-specific and isn't all that useful.

I manually ran through the tutorials for make_distance_boxplots.py, make_distance_comparison_plots.py, and compare_distance_matrices.py and the generated figures look good.

Any other scripts you'd like me to manually test? Switching mpl versions is always a little scary...