Farrar's striped SIMD Smith/Waterman

Michael Farrar's striped SIMD Smith/Waterman source code [swsse2; Bioinformatics, 2007], is now available under an open source license for the first time. You can download it [here].

In 2007, Michael Farrar introduced a beautiful method for speeding up sequence alignment algorithms. Farrar's "striped" algorithm rearranges dynamic programming matrix indices …




HMMER 3.2.1

HMMER 3.2.1 is now available, fixing some small issues, mostly portability issues having to do with compilation on PowerPC machines and ancient x86 machines.

Thanks to the GCC Compile Farm folks for access to ppc64be and i686 machines that I'm using for testing now!




HMMER 3.2 release

The glorious master plan was to finish HMMER4 while hoping that HMMER3 stayed stable. Alas, HMMER4 development has been even slower than expected, and bugs and bitrot have accumulated on HMMER3. Here's a new HMMER 3.2 release to tide us all over. I'm managing HMMER releases again, with Travis …




Thread count in HMMER3

It's come to my attention (one helpful email, plus some snarky subtweets) that the --cpu flag of HMMER3 search programs may have a bad interaction with some cluster management software.

The --cpu n argument is documented as the "number of parallel CPU workers to use for multithreads". Typically, you want …




hmmer.org is updating

hmmer.org is moving off of Janelia tonight, into the great cloud. You may see some flakiness as DNS nameservers update.




HMMER 3.1 beta test 2 released

The HMMER dev team is happy to announce a bugfix release of HMMER3.1, release 3.1 beta 2, aka 3.1b2. Following Google's ineffable lead in having perpetual beta test periods, 3.1 has been in beta test now for two years. When we said before that 3.1 …




Join Rob's HMMER team

Rob Finn's HMMER web services team is expanding. We're looking for people to apply to two new positions to help Rob and Jody push forward on some important ideas for our services. We're pushing in the direction of using more phylogenetic information (species trees) as we compute database homology searches …




More domains and motifs

In the latest version of the HMMER website we have focused on enhancing the recognition and display of domains and motifs found in query sequences. To achieve this we added two new features to the site, additional HMM databases and simple motif detection.

Additional protein family HMM databases

We have …




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