Parallelization of the MAFFT multiple sequence alignment program

By Kazutaka Katoh, Hiroyuki Toh. 2010

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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.

Subfields: Genetics, Molecular Biology, Spectroscopy

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, background): “These improvements and techniques were mostly reported in individual papers (Katoh et al. 2009; Katoh and Toh 2010; Katoh and Frith 2012; Katoh and Standley 2013).”