USEARCH documentation 

USEARCH features and performance

OTU clustering
The otupipe script is provided for high-throughput, high-accuracy OTU clustering based on USEARCH. 

Edgar,R.C. (2010), Search and clustering orders of magnitude faster than BLAST, Bioinformatics.
doi: 10.1093/bioinformatics/btq461

Edgar,RC, Haas,BJ, Clemente,JC, Quince,C, Knight,R (2011) UCHIME improves sensitivity and speed of chimera detection, Bioinformatics doi: 10.1093/bioinformatics/btr381.

How to install and use my command-line programs.

Version 5.1 USEARCH manual (PDF).
Version 5.0 USEARCH manual (PDF).
Version 5.0 UCHIME manual (PDF).

Older documentation

OTU clustering
See otupipe home page.

New features and bug reports
Change logs.
Comments on comparing CD-HIT and the UCLUST algorithm in USEARCH.