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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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11
 New in v11 

cluster_tree command

Generates clusters from a tree file by setting an distance threshold (d). A clusters is a maximal sub-tree where the distance from lowest common ancestor node to all leaves in the subtree is <= d.

The distance threshold is specified by the -id option. The value is a fractional identity, so e.g. -id 0.97 means identity 97% or equivalently distance 0.03.

Output is written to a tabbed text file specifed by the -clusterout option. Fields in the file are #1=cluster_number, #2=sequence label.

Example

usearch -cluster_tree seqs.tree -id 0.97 -clusterout clusters.txt