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Parallelization of the MAFFT multiple sequence alignment program

2010; Oxford University Press; Volume: 26; Issue: 15 Linguagem: Inglês

10.1093/bioinformatics/btq224

1367-4811

Kazutaka Katoh, Hiroyuki Toh,

Bacteriophages and microbial interactions

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. Contact: kazutaka.katoh@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online.