Install USEARCH in less than a minute
Most bioinformatics tools are complex and hard to install with dependencies on third-party software. Installing USEARCH couldn't be simpler -- it's distributed as one standalone executable with no dependencies. Download the binary file, make sure the execute bit is set, and you're ready to run.
Speed is good
The unique high performance offered by USEARCH encourages you to explore your data, enabling new insights and suggesting new analyses that you might not have tried with slower tools.
The USEARCH documentation has hundreds of high-quality, hyperlinked pages which have been continually refined and improved over several years based on user feedback.
Many powerful algorithms in one small
Unlike alternative tools such as BLAST and CD-HIT, which include several binaries with different sets of capabilities and options, USEARCH combines many nucleotide and protein search and clustering algorithms into a single binary with a consistent command line interface. The Linux binary is only 2Mb, so load time is almost instantaneous.
No need for a database creation step or to
specify file types
USEARCH automatically detects whether you are using FASTA or an indexed database and whether a FASTA file contains nucleotide or amino acid sequences. For ad hoc searches, there is no need for a separate database creation step, USEARCH can search directly in a FASTA file.
Rich options for selecting and reporting
USEARCH offers a uniquely flexible and consistent set of output options with user-specified file formats and accept options for selecting hits. These options reduce the need for downstream processing with custom scripts. Most parameters and options are consistently supported across most clustering and search commands, reducing your learning curve.
Technical support for USEARCH is provided directly by the developer. I answer most emails same day. Providing excellent support is a high priority for me because the reputation of USEARCH and my support for the software is critical to its success. Most users discover USEARCH through recommendations from colleagues. I will strive to provide solutions to your problems and add new features if needed.