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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



Tree commands

  calc_distmx  Calculate sparse distance matrix
  cluster_tree  Construct clusters from tree using distance cutoff
  subtree  Extract subtree under given node
  tree2distmx  Calculate distance matrix implied by tree
  tree_cvt  Convert tree between tabbed and Newick formats
  tree_subset  Extract tree for subset of leaves