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. 2010 Aug 1;26(15):1899-900.
doi: 10.1093/bioinformatics/btq224. Epub 2010 Apr 28.

Parallelization of the MAFFT multiple sequence alignment program

Kazutaka Katoh  1 , Hiroyuki Toh
Affiliations

Parallelization of the MAFFT multiple sequence alignment program

Kazutaka Katoh et al. Bioinformatics. .

Abstract

Summary: Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library. Two natural parallelization strategies (best-first and simple hill-climbing) were implemented for the iterative refinement stage. Based on comparisons of the objective scores and benchmark scores between the two approaches, we selected a simple hill-climbing approach as the default.

Availability: The parallelized version of MAFFT is available at http://mafft.cbrc.jp/alignment/software/. This version currently supports the Linux operating system only.

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Figures

Fig. 1.
Fig. 1.
Efficiency of parallelization for an iterative refinement option (L-INS-i) with two parallelization strategies (best-first and simple hill-climbing) and a progressive option (L-INS-1). Lines correspond to the ideal situation where (Elapsed time with n threads) = (Elapsed time with single thread) / n. The command-line arguments are: Best-first, mafft-linsi --bestfirst --thread n input Simple hill-climbing, mafft-linsi --thread n input Progressive, mafft-linsi --maxiterate 0 --thread n input
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