Parallelization of the MAFFT multiple sequence alignment program

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


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 This version currently supports the Linux operating system only.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Sequence Alignment / methods*
  • Software*