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Protocols

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


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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


debian.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Kazutaka Katoh

Publications for MAFFT

MAFFT citations

 (4174)
library_books

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

2018
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), […]

library_books

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
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. […]

library_books

Multiple origins of green blood in New Guinea lizards

2018
Sci Adv
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 […]

library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] genomes and in one copy in haploid genomes using the stand-alone blast+ 2.7.1 [] and processing of the results with a custom script. sequences from each resulting cds cluster were aligned with mafft 7.215 with the “--auto” option and default parameters [], the alignment was optimized with gblocks 0.91 using options “-b3=10 -b4=3 -b5=n” [] and used for the reconstruction of phylogeny […]

library_books

High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

2018
PMCID: 5952520
PMID: 29764472
DOI: 10.1186/s13071-018-2880-y

[…] sequences identified during the species analysis were extracted from all samples using the “get.lineage” command in mothur. these sequences were visualized in geneious, and aligned using mafft, with the fft-ns-1 algorithm. once aligned, the file was split according to the dominate sequence variant observed visually. the variant file was then re-aligned, and a consensus sequence […]

library_books

Microscopic and Molecular Evidence of the First Elasmobranch Adomavirus, the Cause of Skin Disease in a Giant Guitarfish, Rhynchobatus djiddensis

2018
MBio
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 […]


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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