Added 2 histogram formatting code to qiime/format.py and unit test, in preparation for use with new quality_filter_fasta.py code
Resolves issue #1065

Changes the 'simpson_e' calculation to be increase as evenness increases. Reference thread:
https://groups.google.com/forum/#!searchin/qiime-forum/simpsons%2420e/qiime-forum/F7GvTT2Elgw/rU8fnNfLoNMJ
Added another example

Added another test calculation from another ecology lab. Given that the literature definition of this function is unclear, I wanted to have another resource which validates our interpretation.
Changed permissions to 644.
Removed commented line
Adjusting formatting in split_libraries_fastq

Line lengths adjusted, indentation adjusted, use of "is" and "is not" when
doing comparisons with None. Changed a try-except to use dict.get function.

Fixes #1251
Remove "versions" from the QIIME overview tutorial

The document was pointing to an FTP site that read "QIIME-1.5.0" and in
turn was confusing users. I've changed this such that there's now a
folder named qiime-files in thebeast.colorado.edu where I've copied the
current contents of qiime/examples/qiime_tutorial/ and updated the
documentation of tutorial.rst.

Fixes #1137
Rename folder to be qiime_overview_tutorial.zip
Fixes issue with emtpy tables if data points are missing. Fixes #1197
Test catches raised error when data points are missing. Fixes #1197.
Fixing formatting on several lines
Modifications and test additions to resolve issue #1160
Fix #1157

Resolve the problem where OTU maps would contain duplicated observation
identifiers and in turn would cause the biom formatter to fail.

The problem was originated because the command being executed was:

    cat otu_map_1.txt otu_map_2.txt otu_map_3.txt >> full_map.txt

I've change this such that the '>>' operator is replaced with '>' hence
overwritting the file named full_map.txt in case it existed i. e. when
passing the --force flag from the script interface.
Fixed script usage test
Fixed contrib
Modified test and function.

There is an untested function in this code that makes boxplots. The build failed because that function called the modified function from the previous commit.
updated to latest version of pycogent's uclust.py
updated to latest version of pycogent's uclust.py
Fixing more line formatting
Stylistic fix