Modifying exclude_seqs_by_blast.py in order to store the output in a folder.
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 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.
improved convert_fastaqual_fastq library code

made conversion from fasta + qual -> fastq more readable and
less confusing
further streamlined both directions of conversion
Replaced tests for certain errors

Rather than modify the test code, decided to leave in some "quality
assurance" tests
Removed some line continuations, added file naming function
Added buffering system for multiple file output
Added a tests: utility function, multiple output files

also did a little cleanup (could probably use more)
updated links that were to svn version of documentation.

the commands changed, so the svn version of the documentation wouldn't work.