Some bugs crept through testing and into the 3.0b1 release of HMMER3. They’re fixed, and the link in the “3.0b1” release post below was quietly updated to the 3.0b2 tarball available for download on our FTP site.

I fixed a bug with the new code that deals with fragment-rich alignments (sometimes hmmbuild was failing, complaining about a failed “trace validation”). I also added the –tblout and –domtblout options to hmmscan, which should’ve been there in the first place.

Graduation day: HMMER3 beta test (3.0b1) release


The alpha test is complete, and the beta test phase begins today. HMMER3 beta test code is publicly available as a tarball available for download on our FTP site. Besides source code, the tarball also includes a binaries/ subdirectory with precompiled binaries for Intel/Linux systems, both 64-bit (in binaries/intel-linux-x86_64) and 32-bit (in binaries/intel-linux-ia32), and you can just copy these into some directory in your $PATH if you like. These should work on a wide variety of platforms but if you have any trouble, you can always compile your own version from the source code.

My attention is now going to turn toward writing up some papers on all this, and writing the HMMER3 documentation, because (of course) nobody’s going to find any bugs in the beta test, right?

The release notes for 3.0b1: Continue reading →