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

Source: hmmer-3.4.tar.gz

Previous HMMER3 releases

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 implements only fully local/local alignment. HMMER2 lacked DNA-DNA comparison that was present in HMMER1, and DNA/DNA comparison returned with nhmmer in HMMER3.1. The final stable release of HMMER2 was 2.3.2 (Oct 2003).

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 me. I should be able to dig most things out of revision control, if nothing else. I believe the versions below were the most widely distributed ones.