|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]|
|3.0rc2||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]|
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).
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.