MAFFT protocols

View MAFFT computational protocol

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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

Download


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 in pipelines

 (839)
2018
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] estimated with roary (v3.6.8) []; core genes were defined as those present in all 186 isolates with a 90% id cut-off. recombination was inspected using fastgear []. finally, core genes aligned with mafft [] were used to reconstruct the phylogenetic relationships by maximum likelihood using raxml [], with gtrcat model and automre for bootstraping. for each uruguayan group (i.e. ury1, ury2, […]

2018
PMCID: 5764404
PMID: 29324895
DOI: 10.1371/journal.ppat.1006780

[…] (i) 2009 h1n1 (n = 10,016); (ii) 2014 h3n2 (n = 5,584); and (iii) 2015 influenza b virus (n = 3,882). each sequence data set was aligned using the multiple-sequence alignment method available in the mafft program, using the fft-ns-1 strategy []. phylogenetic inference utilized the maximum likelihood (ml) method available in raxml (v8.2.10) [], applying the general time reversible (gtr) […]

2018
PMCID: 5766536
PMID: 29330451
DOI: 10.1038/s41598-017-16399-x

[…] divergence. together with four rt sequences from ty3/gypsy ltr retrotransposons, these combined sequences (hereafter referred to as “diverse library”) were aligned with the guidance2 program using mafft to generate bootstrap supported msa and to remove columns (–colcutoff) with confidence score below 0.95 (16/244 columns removed in the rt sequence from camv). the resulting msa was then used […]

2018
PMCID: 5767279
PMID: 29375602
DOI: 10.3389/fpls.2017.02227

[…] conserved protein domain sequences with 10–15 additional amino acids on the n-terminal and c-terminal ends were used for alignment. the alignment was done with the l-ins-i strategy implemented in mafft (version 7.310; katoh, ). the blosum62 scoring matrix and a gap opening penalty of 1.5 were selected to assess the phylogenetic relationship among the protein sequences. after the alignment, […]

2018
PMCID: 5767322
PMID: 29375610
DOI: 10.3389/fpls.2017.02241

[…] nt. a subsequent filtering phase was performed using deblur (amir et al., ) to obtain putative error-free sequences from the original data. a phylogenetic tree was therefore built by making use of mafft (katoh and standley, ) and fasttree 2 (price et al., ) allowing computation of subsequent diversity metrics., alpha-diversity (within-sample species richness) and beta-diversity (between-sample […]


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MAFFT in publications

 (3863)
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] newly sequenced c. psittaci strains from the epizootic cases, and to other previously described australian and global c. psittaci strains, the core 271 kbp genome was extracted from the whole-genome mafft alignment of 18 publicly available genomes of c. psittaci from a variety of hosts (6bc (nc_017287), m56 (cp0037950, ws_rt (nc_018622), gr9(gd) (nc_018620), mat116 (cp002744), 99dc5 (ke356190), […]

PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] the result of cross contamination. the resulting assemblies were screened for matches to the uce probes, and nontargets and paralogs were removed in phyluce. the resulting regions were aligned using mafft (), and quality-trimmed using a parallelized wrapper around gblocks (). we created three data sets from our “all taxa” data set. first, to examine the effects of number of loci in phylogeny […]

PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536

[…] e value of 1 × 10−05 were verified to be isip1 by a blastp best hit against version 3 of the p. tricornutum genome (). the resulting set of sequences was aligned using the first 20× iterations of mafft v8 and then the inbuilt alignment builder in geneious v.4.76 under the default criteria. where multiple sequences were retrieved for individual species, a species consensus was generated. […]

PMCID: 5954223
PMID: 29764943
DOI: 10.1128/mBio.00185-18

[…] the previously published japanese eel and marbled eel virus genomes. coding sequences of representative helicase genes were downloaded from genbank. helicase protein sequences were aligned using mafft with the e-ins-i alignment strategy and previously described parameters (, ). bayesian inference trees were constructed using mrbayes, with every 50 generations of the markov chain, monte carlo […]

PMCID: 5954217
PMID: 29764951
DOI: 10.1128/mBio.00770-18

[…] lt2 [genbank accession no. ae006468]) or generated in this study., the concatenated sequences of the seven housekeeping genes hisd, pure, suca, thra, aroc, dnan, and hemd were aligned using mafft v7.305b () with the l-ins-i algorithm. the maximum likelihood tree was reconstructed based on the alignment with iq-tree v1.6.1 (), using modelfinder () to identify the most appropriate model. […]


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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