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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.


 New in v11 

subtree command

Extracts the subtree under a given node in a tree file tabbed format. See tree_cvt command for converting a Newick tree to tabbed format. The node is specified as its integer node index in the tabbed file.

The -newickout option specifies an output file in Newick format.

The -tabbedout option specifies an output file in tabbed format.


usearch -subtree big.tree -node 123 -newickout sub.tree