MAFFT specifications

Information


Unique identifier OMICS_00979
Name MAFFT
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
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 <>

MAFFT articles

MAFFT citations

 (206)
2018
PMCID: 5924465

[…] 10 porifera, 4 placozoa and 14 bilateria, plus 6 outgroups., translated sequences of cob, cox1–3, nad1, nad3 and nad5 (the most conserved ctenophore genes) were aligned at the amino acid level using mafft (version 7) [39] under the l-ins-i refinement strategy. the web server guidance 2 [40] was used to remove positions with a low confidence score (i.e., below 0.93), as well as positions present […]

2018
PMCID: 5910596

[…] of these genes were confirmed by molecular phylogenetic analysis (additional file 1: fig. s1, additional file 2: fig. s2). all sequences are shown in additional file 3: table s1 and aligned using mafft ver. 7 (https://mafft.cbrc.jp/alignment/server/) with the default parameters [37]. amino acid sites for tree construction were selected by trimal using a gap threshold value of 0.8 [38]. […]

2018
PMCID: 5923481

[…] motifs were not conserved (supplementary file 1). after filtering out proteins with differently evolving domains, there were 380 sequences (a 41% reduction). , for all sequence alignments, we used mafft v7 [30] optimized for accurate local alignment (options “l-insi-i --leavegappyregion --ep 0.123”). alignments were trimmed using trimal v1.2 [31] with gap threshold of 0.2. alignments […]

2018
PMCID: 5897033

[…] complex. a phylogenetic tree was initially built focused on the aaa atpase domain of 600 protein sequences belonging to fidgetin, spastin, katanin, sap1 and vps4 families. they were aligned using mafft einsi algorithm [70] and tree was built with phyml [69] using the lg model for aminoacid substitution and 4 categories in the discrete gamma model. this prior analysis helped to delineate […]

2018
PMCID: 5868767

[…] the three scores was regarded as the comparison score. the three scores are given in table 2, but only the comparison scores are presented in s1 table., using the algorithm l-ins-i as implemented in mafft [104], a multiple alignment for each family was created. to prevent non-conserved regions from showing in the hydropathy plots, we required that at least 30% of the proteins in a family must […]

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