Modified usearch61 denovo chimera check to just look for Y and N chimera flags, as some system-dependent randomness affects other numbers for uchime output file.
Modified identify_chimeric_seqs.py script to have single credits line with all authors, modified script example with usearch61 to not use split_by_sample option to avoid error when output file already exists.
Merge pull request #948 from jrrideout/issue-703

Fixed read-only permissions in tests.
Merge pull request #947 from jrrideout/clozupone-OTUcat

otu_cateogry_significance.py warnings now suppressed
fixes based on @jrrideout's comments
Merge pull request #945 from gregcaporaso/issue-850

completed otu picking "tutorial"
removing old output
added new output

Fixes #885.
Merge pull request #951 from gregcaporaso/issue-885

Issue 885
Merge branch 'compare_alpha_div_improvement' of git://github.com/wdwvt1/qiime into wdwvt1-compare_alpha_div_improvement
renamed for clarity
Updated -d description to be more informative.

Also added newlines to the ends of output files that are created.
Groups now split into two columns in output format.
Updated qiime_test_data output.
filled in remaining sections
added to tutorial index
moved metadata description to a new doc since it's used for filtering fasta and distance matrices too
linked to tutorial index
fixed formatting error
Updated script description.