HMMER 3.0rc2: HMMER3's release candidate 2

In a world where "a few days" means a month; in a world where "HMMER3 is ready" means another release candidate: ta-da! A release candidate!

HMMER3 release candidate two 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 3.0rc2 follow:

HMMER 3.0rc2 release notes: HMMER 3.0 release candidate 2
SRE, Sat Mar 6 11:37:47 2010

We are counting down to the first release of HMMER 3.0, after a year of alpha and beta testing. This is release candidate two (3.0rc2).

H3 is ready for production use. Indeed, 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 still not entirely happy with a number of issues, including the state of the documentation and the range of different formats (especially alignment formats) we read. And it would be nice if we'd finished the manuscripts describing how H3 works. But all this work will just have to continue.

Differences in 3.0rc2 relative to the previous 3.0rc1 release:

Two reported bugs have been fixed:

  • #h78 phmmer --acc segfaults when no accession is available
  • #h77 hmmalign corrupts column before an all-deleted column

Other improvements:

  • The test suite has expanded.
  • An error in man page documentation for hmmbuild --symfrac is fixed.
  • Portability to various UNIXen is improved, notably IBM AIX systems.
  • ./configure now handles --disable-{sse,vmx,dummy} properly.