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

Parallelization of the MAFFT multiple sequence alignment program.

Author information

1
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. kazutaka.katoh@aist.go.jp

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.

PMID:
20427515
PMCID:
PMC2905546
DOI:
10.1093/bioinformatics/btq224
[Indexed for MEDLINE]
Free PMC Article

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