MAFFT statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MAFFT
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Tool usage distribution map

This map represents all the scientific publications referring to MAFFT per scientific context
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Associated diseases

This word cloud represents MAFFT usage per disease context
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Popular tool citations

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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

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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


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Versioning


No version available

Documentation


Maintainer


  • person_outline Kazutaka Katoh

Publications for MAFFT

MAFFT citations

 (4747)
call_split

The first isolate of Candida auris in China: clinical and biological aspects

2018
PMCID: 5959928
PMID: 29777096
DOI: 10.1038/s41426-018-0095-0
call_split See protocol

[…] The internal transcribed sequences (ITS) of C. auris BJCA001 and previously reported isolates were aligned using mafft v7.015b. The Maximum- Likelihood phylogenetic tree was generated using RAxML v7.3.2. The General Time Reversible (GTR) model and Gamma distribution with Invariant sites (G + I) were adopted. Sch […]

library_books

Identification and tissue distribution of chemosensory protein and odorant binding protein genes in Tropidothorax elegans Distant (Hemiptera: Lygaeidae)

2018
Sci Rep
PMCID: 5958050
PMID: 29773848
DOI: 10.1038/s41598-018-26137-6

[…] lm.nih.gov/). Multiple sequence alignment was conducted using DNAMAN 6.0. Amino acid sequence alignments of the matured OBPs and CSPs from T. elegans and other Hemipteran species were performed using MAFFT (http://mafft.cbrc.jp/alignment/server/clustering.html), and phylogenetic trees were constructed using PhyML in Seaview v.4 using the Jones-Taylor-Thomton (JTT) model with 1000-fold bootstrap re […]

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), N […]

call_split

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

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] old 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. Only 3 […]

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 esti […]

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

[…] iploid 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 with Ph […]


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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