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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

allpairs_global command

See also
  Standard output file options
  Alignment parameters
  Alignment heuristics

Aligns all pairs of sequences in a FASTA file using global alignment.

You must either specify the -acceptall option, which aligns all pairs (except those for which no HSP is found), or accept options.

Example

usearch -allpairs_global pairs.fasta -alnout results.aln