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 two features that are still
missing in HMMER2 and HMMER3. First, it had the
hmmt
program for training HMMs from initially unaligned sequences (and
hence creating multiple alignments). Second, HMMER1 was used
extensively for DNA sequence analysis. We are just now fully
implementing DNA/DNA comparison for HMMER3. 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 includes glocal and global alignment modes that HMMER3 lacks,
because HMMER3 currently implements only fully local/local
alignment. The final stable release of HMMER2 was 2.3.2 (Oct 2003).
HMMER3 test releases
These links are to archived versions of the 2009-2010 alpha, beta, and release candidate test releases.
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.
