The MPI-HMMER project has moved to a newer, more permanent location. Please visit http://www.mpihmmer.org for the latest news and access to the development source code.

The MPI-HMMER team is pleased to announce the impending release of MPI-HMMER. MPI-HMMER is a multiple-level optimization of the original HMMER 2.3.2 code by Sean Eddy of the HHMI Janelia Farms facility. This optimization provides multiple layers of acceleration, from micro-vectorization of the p7Viterbi algorithm through parallelization using MPI. The hmmsearch and hmmpfam were refactored from PVM code into MPI code, and various hand optimization and code improvements were made. The resulting code demonstrates good speedup and high parallelism on low latency connected systems with low OS jitter. This new implementation is approximately 4x faster than the PVM version of HMMER, approximately 12x faster than the baseline single CPU tests.

Please see the "Downloads" section for source. RPMs are available for some platforms as well, follow the link to Scalable Informatics to download them.

Portions of source code and other files distributed with MPI-HMMER are copyright by Wayne State University, Scalable Informatics LLC, and the University at Buffalo the State University of New York.

This program is free software; you can distribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. Accordingly, this program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

You may contact the primary author (John Paul Walters) via email at jwalters@wayne.edu.

See the file 'COPYRIGHT' for the details of the GNU General Public License

Some portions of MPI-HMMER are derivitive works of Sean Eddy's HMMER sequence analysis suite.