Adding more information to open reference log
Added 2 histogram formatting code to qiime/format.py and unit test, in preparation for use with new quality_filter_fasta.py code
Addressing Greg's comments
Merge branch 'master' of git://github.com/qiime/qiime into upstream_log
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
updated changelog
fixed error in documentation; partially addresses #531
ported run_script_usage_tests from qcli
added text on the source of this code
Merge pull request #1245 from gregcaporaso/issue-531-doc

fixed error in documentation; partially addresses #531
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
Merge pull request #1242 from gregcaporaso/issue-1019

updated default rdp_max_memory
Merge pull request #1250 from gregcaporaso/issue-950

updated so script usage test output from all_tests.py is more informative
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.