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]

Steps of how to use MAFFT with other programs to view a MSA
MAFFT
Developer(s)Kazutaka Katoh
Stable release
7.427 / 29 March 2019 (2019-03-29)
Repository
Written inC
Operating systemUNIX, Linux, Mac, MS-Windows
TypeBioinformatics tool
LicenceBSD [1]
Websitewebsite

See also

References
  1. 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/
  2. 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. PMC 135756. PMID 12136088.
  3. https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html%5B%5D
  4. 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.
  5. 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.
  6. 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. PMC 2387179. PMID 18439255.
  7. 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. PMC 3516148. PMID 23023983.


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