Our quest is at an end.

Monty Python and the Holy Grail

Four years in development, and a year in testing: HMMER3 has reached its first public production release. Do we have time for a beer and a small celebration before we write the manuscripts and move straight on to 3.1 development? No? Thought not.

HMMER3 is available for download as a source code tarball. Over at, there are also links for downloading tarballs including precompiled binaries for Linux/Intel ia32, Linux/Intel x86_64, and Mac OS/X Intel platforms.

The release notes for 3.0 follow:

HMMER 3.0 release notes
SRE, Sun Mar 28 09:12:01 2010

This is the first release of HMMER 3.0.

H3 has been in testing since January 2009. It is now ready for production use. This means we'll actually accept the blame now if it doesn't work. It has been stable for many months. It is already widely deployed in its beta test versions for Pfam, Interpro, and other protein databases.

We are already working on 3.1. 3.1 is expected to bring in several new features that did not make it into 3.0, including DNA/DNA searches, and a wider set of alignment formats beyond Stockholm and aligned FASTA. But before that happens, we're going to take a sort of breather, and finish the manuscripts that describe how H3 works.

There are only small differences in 3.0 relative to the previous 3.0rc2 release:

  • The User's Guide now documents the UCSC SAM profile software's A2M format, which H3 can export but not read, at present. (A2M is not aligned FASTA.)
  • Issues detected by the cppcheck static analyzer have been fixed.