Adding more information to open reference log
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
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
Fixing formatting on several lines
Making API logs callable
Fixes #1258
Merge pull request #1259 from jrrideout/issue-1258

Fixes #1258
updated to latest version of pycogent's uclust.py
updated to latest version of pycogent's uclust.py
Fixing more line formatting
Merge pull request #1113 from josenavas/upstream_log

Adding more information to open reference log
Merge branch 'master' into issue_1065
updated to latest version from pycogent
Merge pull request #1260 from gregcaporaso/uclust-update

updated to latest version of pycogent's uclust.py