MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences


MAFFT 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.

Input Format

Fasta format.  example1 (LSU rRNA), example2 (protein)

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

Related Resources





Copyright © 2013 Kazutaka Katoh