is a multiple sequence alignment program for
unix-like operating systems.
It offers a range of multiple alignment methods,
L-INS-i (accurate; for alignment of <∼200 sequences),
FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc
Download and Installation
The latest version is 7.149 (2014/Apr).
The gap scoring scheme has been changed in version 7.1xx.
The new version tends to insert more gaps into gap-rich regions.
To disable this change, add the --legacygappenalty option.
Fasta format. example1 (LSU rRNA)
The type of input sequences (amino acid or nucleotide)
is automatically recognized.
% mafft [arguments] input > output
An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites:
% mafft-linsi input > output
A fast option (FFT-NS-2) for a larger sequence alignment:
% mafft input > output
If not sure which option to use,
% mafft --auto input > output
Katoh, Standley 2013
(Molecular Biology and Evolution 30:772-780)
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
(outlines version 7)
Kuraku, Zmasek, Nishimura, Katoh
(Nucleic Acids Research 41:W22-W28)
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
(describes an interactive sequence collection/selection service by aLeaves, MAFFT and Archaeopteryx)
Katoh, Frith 2012
Adding unaligned sequences into an existing alignment using MAFFT and LAST.
(describes the --add and --addfragments options)
Katoh, Toh 2010
Parallelization of the MAFFT multiple sequence alignment program.
(describes the multithread version)
Katoh, Asimenos, Toh 2009
(Methods in Molecular Biology 537:39-64)
Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics for DNA Sequence Analysis edited by D. Posada
(outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences)
Katoh, Toh 2008
(BMC Bioinformatics 9:212)
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
(describes RNA structural alignment methods)
Katoh, Toh 2008
(Briefings in Bioinformatics 9:286-298)
Recent developments in the MAFFT multiple sequence alignment program.
(outlines version 6;
Fast Breaking Paper in Thomson Reuters' ScienceWatch)
Katoh, Toh 2007
(Bioinformatics 23:372-374) Errata
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
(describes the PartTree algorithm)
Katoh, Kuma, Toh, Miyata 2005
(Nucleic Acids Res. 33:511-518)
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
(describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)
Katoh, Misawa, Kuma, Miyata 2002
(Nucleic Acids Res. 30:3059-3066)
MAFFT: a novel method for rapid multiple sequence alignment based on
fast Fourier transform.
(describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)
Copyright © 2013 Kazutaka Katoh