The latest version is 7.490, 2021/Oct/30.
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)
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.
- 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
- 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)
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