Added, base work for add_alpha_to_mapping_file
Updated test data, all tests are passing
Updated, the script_info dictionary
Added, docstrings and cleaned up some code
Modified, (test_)process_sff.py, util.py

util.py now has is_gzip function. process_sff.py now raises exception if
the user tries to process a gzipped sff with sfftools=True.
Removed support for raxml v703 from make_phylogeny.py. Added PyNAST 1.2 as the new dependency version for QIIME. These fixes remove the deprecation warnings related to muscle and raxml.
Merge pull request #443 from jrrideout/deprecation_warnings

Removing deprecation warnings
Modified pick_otus.py library code

explicitly checks if self.Params['db_filepath'] is None before calling
abspath
modified process_sff.py library code

Moved checking for gzipped file into a private subroutine,
_fail_on_gzipped_sff
Merge pull request #445 from adamrp/pick_otus2

Modified pick_otus.py library code
Merge pull request #442 from adamrp/process_sff

Process sff
Resolved issue435, column headers in mislabeling now mislabeled_probability_above_0.xx
refactored supervised learning app controller
Updated test_supervised_learning.py to reflect new mislabeling file format
Resolved issue 436. Added tutorial for removing mislabeled samples.
Now correctly handles mapping files with only one column
Added detrending functionality
Merge branch 'master' into redosl
Updated supervised learning app controller to follow intended style of app controllers more closely
Removed extraneous print statement