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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. Template:App Location

Running the application using modules

To use usearch with the environment modules system at HPC the following commands are available:

Get module information for usearch:

$module spider usearch

Load the default application module:

$module load usearch

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_USEARCH_DIR - directory where usearch is located.

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: <bibtex> @article{Edgar12082010, author = {Edgar, Robert C.}, title = {Search and clustering orders of magnitude faster than BLAST}, year = {2010}, doi = {10.1093/bioinformatics/btq461}, abstract ={Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely-used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.Availability: Binaries are available at no charge for non-commercial use at}, URL = {}, eprint = {}, journal = {Bioinformatics} } </bibtex>