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.
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.
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 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
started working on new method of distance matrix class get_adjacent_distances

this will be useful for plotting change in distance between adjacent timepoints, for example in a timeseries or following a spatial gradient. this isn't working right now, but need to run for a bit, so want to commit what i currently have. need to figure out indexing into distance matrices.
first working version of get_adjacent_distances

decided not to implement this with qiime.util.DistanceMatrix as we're not really using that in many places, and it seems kind of clunky.
added strict mode and additional documentation
Merge pull request #664 from gregcaporaso/issue-663

updated links that were to svn version of documentation.
addressing comments from @jrrideout. thanks!
moved get_adjacent_distances to qiime.group
few minor clean-ups

also, previous commit changes the interface to match other distance extraction functions.
modified interface

now additionally returns the pair of sample ids corresponding to each distance. after working with this code to generate some plots that i'm interested in, i'm finding that i need this information as well.
improved code associated with the last commit to make it less clunky