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Parallelization of the MAFFT multiple sequence alignment program.

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.

SUBMITTER: Katoh K

PROVIDER: S-EPMC2905546 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

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Parallelization of the MAFFT multiple sequence alignment program.

Katoh Kazutaka K Toh Hiroyuki H

Bioinformatics (Oxford, England) 20100428 15

<h4>Summary</h4>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 refin ...[more]

PMID: 20427515

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