HMMER
User Guide
HMMER User's Guide (PDF)
Further Reading
Papers
- Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195 (2011).
- Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4:e1000069 (2008).
- Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 23:205-11 (2009).
Book
R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998.
Blog
See the blog Cryptogenomicon for more information and discussion about HMMER (among other things).
Support
Because I lead an academic research group, HMMER comes with no promise of support. I'm generally not able to respond individually to requests for help with the package, beyond the help already provided in HMMER's documentation. I do appreciate suggestions for better documentation, improvements, and bug reports.
Reporting bugs
You can open an issue or ask a question at the HMMER GitHub repository, or you can email me directly (sean@eddylab.org). Please provide enough information that I can recreate the problem. Useful things to include are:
- Input data (or examples, a small test case sufficient to recreate the problem).
- Information about the operating system you are using
- Which version of HMMER you're using, and whether you compiled from source or used a prepackaged distribution.
Without these pieces of information I have to make guesses and send emails back and forth with you to determine the cause of the issue, and then I get all frustrated and snippy because I'm usually pretty busy, and then you think I'm a jerk, and then I feel guilty and bad and have to go away and go for a run. Nobody wants all that drama.