RIMD, Osaka Univ. Osaka Univ.
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 <∼30,000 sequences), etc.

Download and Installation

The latest version is 7.525 (2024/Mar)

BUG!! Versions 7.463 – 7.486 had a serious bug in the FFT-NS-i option; unnecessarily much memory was requested and the calculation sometimes failed.  This bug also affected the --auto option.  Please use 7.487 or higher.  (2021/Jul/25)

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




BUG!! Temporarily unavailable since 2018/Feb/7.  If you sent an email to the above address but have received no response, then re-send the email to:



© 2013 Kazutaka Katoh