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usearch website  

USEARCH is a unique high-throughput sequence analysis tool. It is a distributed as single binary program that implements a suite of algorithms comparable to BLASTN, BLASTP, BLASTX, BLASTCLUST, CD-HIT, CD-HIT-EST, CD-HIT-2D, CD-HIT-EST-2D, CD-HIT-OTU, CD-HIT-454, ChimeraSlayer, Perseus, RAPsearch and more. It supports a rich set of sequence matching options, including E-values, identity, coverage (fraction of query or target sequence covered by the alignment) and maximum gap length, and a range of output file formats including FASTA, BLAST-like, user-defined tabbed text and a native format designed for clustering applications. Supported alignment styles include local (gapped and ungapped), like BLAST, and global, which is most often used in clustering applications. User-settable parameters allow tuning of substitution scores, gap penalties and Karlin-Altschul statistics.

Available Versions

  • 5.0.151 and 5.1.221 (EL5).
  • 5.2.32 (EL6).

Note: only 32-bit binaries are available limiting the memory use to less then 4GB. If a 64-bit binary is needed it will have to be purchased from the author.

Required Modules

modules documentation


  • usearch

Usage Policy

Our license only allows the usage of a 32-bit binary for teaching and non-profit (academic research) purposes. If your use falls outside of these categories please procure a license from the author.


If you publish research that uses usearch you have to cite it as follows:

Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST
Bioinformatics, 2010
Author : Edgar, Robert C.
Title : Search and clustering orders of magnitude faster than BLAST
Publication : Bioinformatics
Date : 2010