Parallelization of the MAFFT multiple sequence alignment program.
CONCLUSIONS
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.


BACKGROUND
The parallelized version of MAFFT is available at http://mafft.cbrc.jp/alignment/software/. This version currently supports the Linux operating system only.
Katoh
Kazutaka
K
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. kazutaka.katoh@aist.go.jp
Toh
Hiroyuki
H
D016415:Sequence Alignment / Q000379:methods*; D012984:Software