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MAFFT parallel

MAFFT parallel

A parallelized version of MAFFT multiple sequence alignment (MSA) tool. The parallelization is based on the POSIX Threads library with two approaches: best-first and simple hill-climbing in the alignment refinement stage.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: FASTA; Clustal
  • Software interface: Command-line user interface
  • Language: C
  • Operating system: Linux; Microsoft Windows; Mac OS X
  • License: FASTA
  • Cost:
  • Version name: 7.428 / 7.427
  • Maturity: Stable
  • Credit: KAKENHI for Young Scientists (B) 21700326 from Monbukagakusho, Japan (to K.K.).
  • Contact: katoh _at_
  • Collection: -


Katoh K, Toh H "Parallelization of the MAFFT multiple sequence alignment program." Bioinformatics. 2010 Aug 1;26(15):1899-900.
PMID: 20427515

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