Using the HMMER website

There are two flavours of HMMER documentation available: the first concerns the command line use of the tool; the second describes the use of HMMER through this website, which can be accessed using either the web interface or the application program interface (API).

The comprehensive command line documentation provides background on profile HMMs and the details of the different algorithms, as well as providing a description of all available options. This website provides access to the same algorithms, and makes available the more widely used command line options.

The results from the command line and website versions of HMMER are all identical for a given query, database and options. However, the website provides additional views of the results to permit a deeper analysis, using just a few mouse clicks.

Documentation for the website

The documentation is on ReadTheDocs at or download as a PDF file

Documentation for the HMMER software

Please see or download as a PDF file


Your questions are important to us. Use our contact form for any questions regarding the use of the HMMER servers. If you are referring to a specific result set, please include the job-id in the email.

For questions about the command line version HMMER, please email Sean Eddy ( ). See here, in the "reporting bugs section" .