Multiple alignment program for amino acid or nucleotide sequences

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

• Mac OS X
• Linux
• Windows
• Source
• Changelog

The latest version is 7.520 (2023/Mar)

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.

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

• Manual (v6.240)
• Tips (not yet included in the manual) for large alignment, ncRNA alignment, profile alignment, etc.

Related Resources

• MAFFT server at EBI
• MAFFT server at the MPI Bioinformatics Toolkit
• ClustalW / MAFFT / PRRN at GenomeNet
• ClustalW / TCoffee / MAFFT in MyHits, SIB
• MAFFT service in T-REX web server
• MAFFT service in WABI, DDBJ
• CIPRES Science Gateway: TeraGrid resources for Phyogenetic tree inference
• Jalview: an alignment editor written in Java
• Pfam: Protein families database of alignments and HMMs
• Strap: Editor for multiple sequence alignment written in JAVA
• BioRuby: Ruby tools for bioinformatics
• aLeaves collects amino acid sequences from diverse animal genomes

References

• Rozewicki, Li, Amada, Standley, Katoh 2019 (Nucleic Acids Research 47:W5-W10) New!
  MAFFT-DASH: integrated protein sequence and structural alignment
  (describes web interface for sequence and structural alignments)
• Nakamura, Yamada, Tomii, Katoh 2018 (Bioinformatics 34:2490–2492)
  Parallelization of MAFFT for large-scale multiple sequence alignments.
  (describes MPI parallelization of accurate progressive options)
• Katoh, Rozewicki, Yamada 2019 (Briefings in Bioinformatics 20:1160-1166)
  MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
  (explains online service)
• Yamada, Tomii, Katoh 2016 (Bioinformatics 32:3246-3251) additional information
  Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees.
  (explains some options for aligning a large number of short sequences)
• Katoh, Standley 2016 (Bioinformatics 32:1933-1942)
  A simple method to control over-alignment in the MAFFT multiple sequence alignment program.
  (describes some options to avoid over-alignment)
• 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 2013 (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 (Bioinformatics 28:3144-3146)
  Adding unaligned sequences into an existing alignment using MAFFT and LAST.
  (describes the --add and --addfragments options)
• Katoh, Toh 2010 (Bioinformatics 26:1899-1900)
  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)

Contact

kazutaka.katoh@aist.go.jp

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

• mafft-*-without-extensions-src.tgz: BSD
• mafft-*-win*.zip: GPL
• Other packages include the codes of the Vienna RNA package, MXSCARNA and ProbConsRNA, for RNA structural alignment.  See their license notices.

© 2013 Kazutaka Katoh