HMMER3.1 beta test 1 released


The HMMER dev team is happy to announce an upgrade release of HMMER3, release 3.1. A beta test version of the code is publicly available as a tarball available for download, or from, where you’ll also find precompiled binary releases for Mac and Linux.

HMMER 3.1 includes nhmmer and nhmmscan, programs for DNA/DNA homology searches with profile HMMs. nhmmer has already been incorporated in RepeatMasker, in collaboration with Arian Smit and colleagues, and is the software underlying the Dfam database of profiles for mobile DNA elements.

HMMER 3.1 database searches are about twice as fast as HMMER 3.0 was, fulfilling old campaign promises.

HMMER 3.1 includes hmmpgmd, the parallel search daemon underlying HMMER Web Services at

This code is expected to be stable, but we’re releasing it as a beta test just to be careful. After some time in the wild, we’ll make a release candidate, and if you folks haven’t chewed any of that up too badly, we’ll make the final 3.1 release reasonably soon.

Congratulations to Travis Wheeler, 3.1’s build master — note the TJW on the notes below the fold, not an SRE — the first HMMER release managed by someone besides me (Sean).

Meanwhile… slowly, slowly, HMMER4 takes shape, as the gnomes of HMMER Labs toil sleeplessly on their latest monstrosities. The long awaited return of glocal alignment has been delayed into HMMER4, because the changes required turned out to be, um, quite extensive.

Detailed release notes for 3.1b1 are below the fold.
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