Parallel CLUSTAL W for PC Clusters
This paper presents a parallel version of CLUSTALW, 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.
KeyWordsMultiple Sequence Alignment CLUSTALW Parallel Computing Computational Biochemistry
Unable to display preview. Download preview PDF.
- H.G. Higgins, A.J. Bleasby, and R. Fuchs. CLUSTAL V: improved software for multiple sequence alignment. CABIOS, 8:189–191, 1992.Google Scholar
- H.G. Higgins and P.M. Sharp. Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS, 5:151–153, 1989.Google Scholar
- Performance optimization of clustal w: Parallel clustal w, ht clustal, and multiclustal. http://www.sgi.com/ industries/sciences/chembio/resources/papers/Clustal_DevNews/Clustal_DevNews.html.