Scaling of parallel multiple sequence alignment on the supercomputer JUQUEEN

In this paper is proposed optimization, scaling, performance evaluation and profiling of parallel multiple sequence alignment based on ClustalW algorithm on the supercomputer BlueGene/Q, so-called JUQUEEN, for the case study of the influenza virus sequences. For this purpose a parallel I/O interface for simultaneous and independent access to single file collectively has been designed and verified on the basis of parallel program implementation on the supercomputer JUQUEEN.

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