cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Contact email address, kazutaka.katoh@aist.go.jp, is temporarily unavailable from 2018/Feb/7.  If you sent an email to this address but have received no response, then please re-send the email to katoh@ifrec.osaka-u.ac.jp.

About

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 7.409 (2018/Aug; Windows) or 7.407 (2018/Jul; Mac, Linux, source). 

BUG!! Versions 7.380–7.392 had a bug in the --add and --merge options.  Please update to version 7.394 or higher.

Input Format

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

The type of input sequences (amino acid or nucleotide) is automatically recognized.

Usage

% 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

References

Contact

kazutaka.katoh@aist.go.jp

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:

katoh@ifrec.osaka-u.ac.jp

License

© 2013 Kazutaka Katoh