Parallelization of the MAFFT multiple sequence alignment program

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ID: 301379
2010
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Abstract
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.
Reference Key
openalex_W2141747524 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Kazutaka Katoh, Hiroyuki Toh
Journal BMC Bioinformatics
Year 2010
DOI
10.1093/bioinformatics/btq224
URL
https://academic.oup.com/bioinformatics/article-pdf/26/15/1899/48853336/bioinformatics_26_15_1899.pdf
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