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 7.428 (Windows), 7.427 (others), 2019/May.

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

• 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 in press) 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 2017 (Briefings in Bioinformatics, in press)
  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