Modified add_qiime_labels.py script to use a standard metadata mapping file instead of custom mapping file to be more intuitive to use with the rest of QIIME.  Updated unit tests.
Added changes to add_qiime_labels script/library to Changelog
Changed relatedness.py library to run significantly faster and use less memory by vectorizing operations where possible and reducing redundant calculations.
Modified the documentation on the scripts and the header documentation to be clearer and more accurately reflect what was being calculated.
Merge branch 'add_qiime_labels' of github.com:walterst/qiime

Conflicts:
	ChangeLog.md
Modified relatedness_library.py and its tests to reflect the new functions and to add a little more documentation.
Updated the documentation again to reflect the tests of NRI and NTI against phylocom4.2.
Modified the script relatedness.py to update the documentation and the tests to be clearer and handle more cases of error.
Merge pull request #577 from walterst/add_qiime_labels

Modified add_qiime_labels.py script to use a standard metadata mapping f...
commit
Merge branch 'master' of github.com:qiime/qiime into denoise_tutorial_update
replace :file: tags with double backticks. Replace note with more visible warning.
Removed unnecessary imports.
Updated to reference biom-format 1.1.2.
Made message clearer.
Merge pull request #655 from jrrideout/biom-1.1.2

Updated to reference biom-format 1.1.2.
updated links that were to svn version of documentation.

the commands changed, so the svn version of the documentation wouldn't work.
Merge pull request #654 from jensreeder/denoise_tutorial_update

update denoising_454 tutorial
Merge pull request #664 from gregcaporaso/issue-663

updated links that were to svn version of documentation.
Modified two lines to address comments of @wasade.