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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

tree2distmx command

Calculates a a distance matrix from a tree in Newick format, which must have branch lengths specified. The distance between two leaf nodes in the tree is calculated as the sum over branch lengths of the shortest path between leaves.

The distance matrix is written to the filename given by the -distmxout option. See distance matrix for format options.

Example

usearch -tree2distmx tree,phy -distmxout mx.txt -format tabbed_pairs -distmxo fractid