Software:MAFFT
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| Developer(s) | Kazutaka Katoh |
|---|---|
| Stable release | 7.475
/ 23 November 2020 |
| Written in | C |
| Operating system | UNIX, Linux, Mac, MS-Windows |
| Type | Bioinformatics tool |
| Licence | BSD[1] |
| Website | mafft |
In bioinformatics, MAFFT (for multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version of MAFFT used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the Fast Fourier Transform.[2] Subsequent versions of MAFFT have added other algorithms and modes of operation,[3] including options for faster alignment of large numbers of sequences,[4] higher accuracy alignments,[5] alignment of non-coding RNA sequences,[6] and the addition of new sequences to existing alignments.[7]
See also
- Sequence alignment software
- Clustal
References
- ↑ The base MAFFT software is distributed under the BSD license, while versions for Microsoft Windows are licensed under the GNU General Public License. Some distributions of MAFFT contain software licensed under other licenses https://mafft.cbrc.jp/alignment/software/
- ↑ Katoh, Kazutaka; Misawa, Kazuharu; Kuma, Kei-ichi; Miyata, Takashi (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform". Nucleic Acids Research 30 (14): 3059–66. doi:10.1093/nar/gkf436. PMID 12136088.
- ↑ "MAFFT ver.7 - a multiple sequence alignment program". https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html.
- ↑ Katoh, K; Toh, H (2006). "PartTree: An algorithm to build an approximate tree from a large number of unaligned sequences". Bioinformatics 23 (3): 372–4. doi:10.1093/bioinformatics/btl592. PMID 17118958.
- ↑ Katoh, K; Kuma, K; Miyata, T; Toh, H (2005). "Improvement in the accuracy of multiple sequence alignment program MAFFT". Genome Informatics. International Conference on Genome Informatics 16 (1): 22–33. PMID 16362903.
- ↑ Katoh, Kazutaka; Toh, Hiroyuki (2008). "Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework". BMC Bioinformatics 9: 212. doi:10.1186/1471-2105-9-212. PMID 18439255.
- ↑ Katoh, Kazutaka; Frith, Martin C (2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics 28 (23): 3144–6. doi:10.1093/bioinformatics/bts578. PMID 23023983.
External links
- MAFFT Online Server
- MAFFT server at EBI
- ClustalW / MAFFT / PRRN at GenomeNet
- ClustalW / TCoffee / MAFFT in MyHits, SIB
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