The current version is HMMER 3.1b2 (05 March 2015).

Source: [hmmer-3.1b2.tar.gz] 5.8 MB
with Linux/Intel ia32 binaries: [hmmer-3.1b2-linux-intel-ia32.tar.gz] 18.1 MB
with Linux/Intel x86_64 binaries: [hmmer-3.1b2-linux-intel-x86_64.tar.gz] 20.2 MB
with MacOSX/Intel binaries: [hmmer-3.1b2-macosx-intel.tar.gz] 13.5 MB

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

If you are looking for older versions of the software, try the archive section below.

Windows/Cygwin binaries

These binaries are compiled to run in Cygwin (a Linux emulator that can be installed in Windows; In our hands, they run cleanly in a default Cygwin install.

If you are uncomfortable running HMMER3.1 within Cygwin, you may download older HMMER3.0 binaries (graciously produced and provided by Sergey Smirnov at the NCBI) that run in Windows without a Cygwin dependency.

hmmer-3.1b2-cygwin32.tar.gz: 32-bit [hmmer-3.1b2-cygwin32.tar.gz] 15MB
hmmer-3.1b2-cygwin64.tar.gz: 64-bit [hmmer-3.1b2-cygwin64.tar.gz] 16MB

Archive of stable representatives of the HMMER1, HMMER2, and HMMER3 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).

Windows binaries

These binaries have been graciously produced and provided by Sergey Smirnov at the NCBI. Please see the readme.txt included within the zip file for installation hints and contact details. (v3.0): [] 3.2MB

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.