Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

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