These help pages are primarily designed to give users a very brief introduction to HMMER, sufficient such that the user will have a better understanding of the website search methods and results. They do not describe the details of profile hidden Markov models (HMMs) in the use of sequence analysis.


Your questions are important to us. Please contact us through our contact form at We will respond as quickly as possible, but please bear in mind that we do not have a dedicated staff member to run the helpesk.

Software bug reports will typically be dealt with by Sean Eddy, but may get deferred to others within the HMMER project team. (See

To expedite our response to your questions, please provide us with as much information as possible so that we can recreate the problem. Useful things to include are:

  • Input data (or examples, but just sufficient to recreate the problem).
  • The URL of the page where you are having the problem.
  • The steps to follow to reproduce the problem.
  • Information about the browser that you are using and it version, and also the OS you are running.

Staying informed

The target databases are updated on a monthly basis. Additionally there will be bug fixes and new website features. To keep up to date with these, see one of the following:

  • Changelog - lists new features, bug fixes and improvements made to the site.
  • Twitter - follow hmm3r for micro-blogs about the HMMER software updates, target database updates and new Web features.
  • Cryptogenomicon blog - more detailed discussions of HMMER related topics, including the website.