MAFFT pipeline

MAFFT specifications

Information


Unique identifier OMICS_00979
Name MAFFT
Alternative names EBI-MAFFT, M.A.F.F.T.
Interface Web user interface
Restrictions to use None
Input data Some protein or DNA sequences.
Input format FASTA
Computer skills Basic
Version 7.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/MAFFT

Subtool


  • E-INS-I

Documentation


Maintainer


  • person_outline Kazutaka Katoh <>

Information


Unique identifier OMICS_00979
Name MAFFT
Alternative names EBI-MAFFT, M.A.F.F.T.
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some protein or DNA sequences.
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
License BSD 3-clause “New” or “Revised” License, GNU General Public License version 3.0
Computer skills Advanced
Version 7.310
Stability Stable
Source code URL https://mafft.cbrc.jp/alignment/software/source.html
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/MAFFT

Subtool


  • E-INS-I

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Kazutaka Katoh <>

Publications for MAFFT

MAFFT citations

 (194)
2018
PMCID: 5750389

[…] batcov-hku2 (abq57208.1), and mhv-a59 (aaa46455.1)., the above-mentioned nucleotide or protein sequences were aligned with multiple alignment using fast fourier transform (mafft; https://mafft.cbrc.jp/alignment/software/) within the geneious 10 software package (biomatters, auckland, new zealand). for each coronavirus species, s protein sequence alignments enabled us to determine […]

2018
PMCID: 5771137

[…] genomes were categorized by class and sequencing status. the sequences of all copies of genes encoding 16s rrna were extracted from the complete genomes. alignment was performed using the mafft (v7.222) plug-in [49] in geneious (v10.2.3) [50] set to the following parameters: automatic detection for the algorithm; a scoring matrix of 200 pam/k = 2; a gap opening penalty of 1.53; […]

2018
PMCID: 5788922

[…] via family-companion (http://family-companion.toulouse.inra.fr). sequence clustering was performed using a p-value cut-off of 1 × 10−5, and a percent match cut-off of 80. sequences were aligned with mafft v7.27168. columns with more than 50% of gaps were removed. phylogenetic trees were computed with iq-tree (automatic mode)69 and drawn with itol (https://itol.embl.de/)., the beco method […]

2018
PMCID: 5804118

[…] 6.0.6 (biomatters) and introns were removed prior to alignment based on the amino acid sequence of previously published sequences. all sequences, including sequences from genbank, were aligned using mafft (katoh and standley 2013) on the server accessed at http://mafft.cbrc.jp/alignment/server/. maximum likelihood (ml) phylogenetic tree inference was performed using raxml (stamatakis 2006) […]

2018
PMCID: 5810265

[…] and mg596305–mg596307) (pufl) and mf563649–mf563683, mg010638–mg010645, and mg596308–mg596310 (pufm) as shown in supplementary table s1., multiple sequence alignments (msas) were produced with mafft v7.305b (katoh et al., 2002; katoh and standley, 2013) from all pufl and pufm sequences and were visually inspected for consistency. mafft was run with parameters ‘–globalpair –maxiterate […]

MAFFT institution(s)
Graduate School of Information Sciences, Tohoku University, Sendai, Japan; Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; Immunology Frontier Research Center, Osaka University, Suita, Japan
MAFFT funding source(s)
Supported by the Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) from Japan Agency for Medical Research and Development (AMED), and JSPS KAKENHI Grant Number 16K07464.

MAFFT review

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Sayoni Das

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Web
Very efficient, well-documented and easy to use MSA tool