Parallel CLUSTAL W for PC Clusters

This paper presents a parallel version of CLUSTAL W, called pCLUSTAL. In contrast to the commercial SGI parallel Clustal, which requires an expensive shared memory SGI multiprocessor, pCLUSTAL can be run on a range of distributed and shared memory parallel machines, from high-end parallel multiprocessors (e.g. Sunfire 6800, IBM SP2, etc.) to PC clusters, to simple networks of workstations. We have implemented pCLUSTAL using C and the MPI communication library, and tested it on a PC cluster. Our experimental evaluation shows that our pCLUSTAL code achieves similar or better speedup on a distributed memory PC clusters than the commercial SGI parallel Clustal on a shared memory SGI multiprocessor. Key Words: Multiple Sequence Alignment, CLUSTAL W, Parallel Computing, Computational Biochemistry.

• Type: Conference
• Year: 2003
• Where: ICCSA
• Authors: James Cheetham, Frank K. H. A. Dehne, Sylvain Pitre, Andrew Rau-Chaplin, Peter J. Taillon
• Keywords: Applied Computing, Commercial Sgi Parallel, ICCSA 2003, Memory Sgi Multiprocessor, Sgi Parallel Clustal