Large scale multiple sequence alignment with simultaneous phylogeny inference
Journal of Parallel and Distributed Computing
High-speed Multiple Sequence Alignment on a reconfigurable platform
International Journal of Bioinformatics Research and Applications
C-based design methodology for FPGA implementation of clustalW MSA
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
A heterogeneous parallel system running open mpi on a broadband network of embedded set-top devices
Proceedings of the 7th ACM international conference on Computing frontiers
Parallel multiple sequence alignment with local phylogeny search by simulated annealing
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
GPU-ClustalW: using graphics hardware to accelerate multiple sequence alignment
HiPC'06 Proceedings of the 13th international conference on High Performance Computing
Embedded Processor Virtualization for Broadband Grid Computing
GRID '11 Proceedings of the 2011 IEEE/ACM 12th International Conference on Grid Computing
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Summary: Multiple sequence alignment is the NP-hard problem of aligning three or more DNA or amino acid sequences in an optimal way so as to match as many characters as possible from the set of sequences. The popular sequence alignment program ClustalW uses the classical method of approximating a sequence alignment, by first computing a distance matrix and then constructing a guide tree to show the evolutionary relationship of the sequences. We show that parallelizing the ClustalW algorithm can result in significant speedup. We used a cluster of workstations using C and message passing interface for our implementation. Experimental results show that speedup of over 5.5 on six processors is obtainable for most inputs. Availability: The software is available upon request from the second author.