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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.



allpairs_local command

See also
  Standard output file options
  Alignment parameters
  Alignment heuristics

Makes pair-wise all-vs.-all alignments of all pairs in a FASTA file. Alignments are local. No index is used. More than one alignment may be reported for a given pair.

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


usearch -allpairs_local seqs.fasta -alnout results.aln