HMMER3: a new generation of sequence homology search software

Overview

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called “profile hidden Markov models” (profile HMMs).

Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

The current version is HMMER 3.0rc2 (9 March 2010), the second release candidate for the HMMER3 project.

Download

Source:	[Download: 3.9MB]	MD5: `4a3d8e217556e8ea791d5eaeafb3b072`
with Linux/Intel ia32 binaries:	[Download: 11.3MB]	MD5: `5e1f2be91122f4a15a7b9c2b6d895564`
with Linux/Intel x86_64 binaries:	[Download: 13.1MB]	MD5: `c6d42075d2bbd85227f051ad8306c185`
with MacOSX/Intel binaries:	[Download: 8.2MB]	MD5: `a2a91de34b263e8a6d8336439dcf8447`

Briefly, to compile from source:


   % tar zxf hmmer-3.0rc2.tar.gz  

   % cd hmmer-3.0rc2              

   % ./configure                  

   % make                         

   % make check

The 'make check' is optional; it runs a test suite.

All the binary tarballs include source code, plus a binaries/ directory containing precompiled binaries. Installing HMMER takes nothing other than moving these binaries wherever you want them.

We believe HMMER compiles and runs on any POSIX-compliant system with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX. For more installation and configuration options, see the Installation chapter of the User Guide (included in the package, and also linked below).

Documentation

The HMMER User's Guide: [PDF, 76 pages].

Release notes for the current release.

See the blog Cryptogenomicon for more information and discussion about HMMER3.

The theory behind profile HMMs: R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998.

Other publications from the Eddy group.

Support (lack thereof)

HMMER is not intended to be commercial software. In particular, it comes with no promise of support whatsoever. We are generally not able to respond individually to requests for help with the package, beyond the help already provided in HMMER's documentation. We do respond gratefully to useful suggestions for improved documentation, and to bug reports.

Reporting bugs

Email me, and please give me enough information (concisely) that I can reproduce the problem.

Archive of previous versions

3.0rc1	10 Feb 2010	[Source code tarball]	[Release notes]
3.0b3	13 Nov 2009	[Source code tarball]	[Release notes]
3.0b2	21 Jun 2009	[Source code tarball]	[Release notes]
3.0b1	17 Jun 2009	[Source code tarball]	[Release notes]
3.0a2	12 Mar 2009	[Source code tarball]	[Release notes]
3.0a1	12 Jan 2009	[Source code tarball]

HMMER:
Overview
Download
Documentation
Support
Reporting bugs
Archive

Blog:
Cryptogenomicon

The Pfam Consortium:
Janelia Farm
Cambridge
Stockholm
France
South Korea

HHMI Janelia Farm:
Eddy lab
Janelia Farm
HHMI