Parallelization of MAFFT for large-scale multiple sequence alignments

Bioinformatics. 2018 Jul 15;34(14):2490-2492. doi: 10.1093/bioinformatics/bty121.


Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences.

Availability and implementation: This feature is available in MAFFT versions 7.355 or later at

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Protein Structure, Secondary
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods
  • Sequence Analysis, RNA / methods
  • Software*