I changed the behavior of beta_diversity.py -r xxx using unifrac-like measures to now only warn the user when there's no information on a sample (no counts in an otu table, or none that match the phylogenetic tree. Those comparisons are meaningless, but when two samples are absent any information, they now return a distance of 1 with -r, but 0 without the -r flag (i.e., computing the whole matrix). This is tricky to change, and I think since we clearly list those distances as meaningless, it's a non-ideal but ok approach.
Merge pull request #682 from justin212k/676

fixing issue #676.  beta_diversity.py -r now only warns when run on samples with no data