The current version is HMMER 3.4 (15 August 2023).

Source: [hmmer-3.4.tar.gz]

For information on compiling from source please see our documentation page.

Previous HMMER3 releases

3.3.2 26 Nov 2020 [hmmer-3.3.2.tar.gz]
3.3.1 25 Jul 2020 [hmmer-3.3.1.tar.gz]
3.3 18 Nov 2019 [hmmer-3.3.tar.gz]
3.2.1 13 June 2018 [hmmer-3.2.1.tar.gz]
3.2 7 June 2018 [hmmer-3.2.tar.gz]
3.1b2 5 March 2015 [hmmer-3.1b2.tar.gz]
3.1b1 22 Apr 2013 [hmmer-3.1b1.tar.gz]
3.0 March 2010 [hmmer-3.0.tar.gz]
3.0rc2 8 Mar 2010 [hmmer-3.0rc2.tar.gz]
3.0rc1 10 Feb 2010 [hmmer-3.0rc1.tar.gz]
3.0b3 13 Nov 2009 [hmmer-3.0b3.tar.gz]
3.0b2 21 Jun 2009 [hmmer-3.0b2.tar.gz]
3.0b1 17 Jun 2009 [hmmer-3.0b1.tar.gz]
3.0a2 12 Mar 2009 [hmmer-3.0a2.tar.gz]
3.0a1 12 Jan 2009 [hmmer-3.0a1.tar.gz]

Archive of stable representatives of the HMMER1 and HMMER2 lineages

The 1992-1998 HMMER1 lineage was closer to the original Krogh/Haussler conception of profile HMMs. It includes a feature that is missing in HMMER2 and HMMER3: the hmmt program for training HMMs from initially unaligned sequences (and hence creating multiple alignments). The final stable release of HMMER1 was 1.8.5 (Feb 2006). The 1998-2003 HMMER2 lineage introduced the "Plan 7" profile HMM architecture (which HMMER3 still largely shares), and was the long-time foundation for Pfam and other protein domain databases. It still included glocal and global alignment modes that HMMER3 lacks, because HMMER3 currently implements only fully local/local alignment; HMMER2 lacks DNA-DNA comparison that was present in HMMER1, and has returned in HMMER3.1. The final stable release of HMMER2 was 2.3.2 (Oct 2003).

2.3.2 Oct 2003 [hmmer-2.3.2.tar.gz]
1.8.5 Feb 2006 [hmmer-1.8.5.tar.gz]

Other archived versions of HMMER2 and HMMER1

If, for some reason, you want to obtain a source code copy of a version that you know existed, but which doesn't appear in the links below, contact us. We should be able to dig most things out of revision control, if nothing else. We believe the versions below were the most widely distributed ones.

2.4i Dec 2006 [hmmer-2.4i.tar.gz]
2.3.1 Jun 2003 [hmmer-2.3.1.tar.gz]
2.3 Apr 2003 [hmmer-2.3.tar.gz]
2.2g May 2001 [hmmer-2.2g.tar.gz]
2.1.1 Dec 1998 [hmmer-2.1.1.tar.Z]
1.8.4 Jul 1997 [hmmer-1.8.4.tar.Z]