Denis Schmidt (University of Frankfurt) has reported a critical bug against hmmalign in 3.0rc1.

Any time there is an alignment column consisting of all deletions, the code is supposed to remove the alignment column altogether; instead, it overwrites the previous alignment column with an all-delete column, which most likely …

After a year of alpha and beta testing, HMMER3 is ready. Release candidate 1 is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your \$PATH if you …

The final HMMER3 beta test release is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your \$PATH if you like. If the precompiled versions don't work for …

The truth will set you free. But not until it is finished with you.

David Foster Wallace, Infinite Jest

With the release of Pfam 24, HMMER3 beta test code has been pressed into service just a bit earlier than we're comfortable with. Though the 3.0b2 code seems to be …

Writing and drawing are slow, deliberate activities, so I tried to keep distractions to an absolute minimum, and I did everything myself. I liked this control, as it fostered a sense of craftsmanship. There was great personal satisfaction in attending to detail and quality, and I remain very proud of …

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 …

it is not necessary to accept everything as true, one must only accept it as necessary.

Franz Kafka, The Trial

As the unearthly whine of the Janelia compute cluster subsides after testing the beta1 release, power and lights are flickering back to life in Virginia, and I have a quiet …

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 …

There are two ways of spreading light: to be the candle or the mirror that reflects it.

Edith Wharton, Vesalius in Zante

On April 14, the US Patent and Trademark Office awarded us a trademark on HMMER. This is a good moment to explain how we plan to deal with …

Thanks to our panopticon-like ability to scan the Internets for people benchmarking the HMMER3 alpha release even though we told you not to, it's come to the attention of our Watchers that people are doing benchmarks using existing HMMER2 files (Pfam, SMART), taking advantage of HMMER3's ability to read or …