MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

By Kazutaka Katoh, Kazuharu Misawa, K. Kuma, T. Miyata. 2002

15,812 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “MAFFT is an MSA program, ﬁrst released in 2002 (Katoh et al. 2002).”
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega (2011, background): “1 (http://www.clustal.org) DIALIGN 2.2.1 (http://dialign.gobics.de/) FSA 1.15.5 (http://sourceforge.net/projects/fsa/) Kalign 2.04 (http://msa.sbc.su.se/cgi-bin/msa.cgi) MAFFT 6.857 (http://mafft.cbrc.jp/alignment/software/source.html) MSAProbs 0.9.4 (http://sourceforge.net/projects/msaprobs/files/)”
A Convex Atomic-Norm Approach to Multiple Sequence Alignment and Motif Discovery (2016, neutral): “(Katoh et al., 2002), and MUSCLE (Edgar, 2004).”
Reproducibility of computational workflows is automated using continuous analysis (2017, methodology): “The sequences were aligned using MAFFT 23 and converted to PHYLIP interleaved format using EMBOSS Seqret 33 .”
Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e (2020, neutral): “For each of the four HCoV data sets, full-length sequences were aligned to a reference genome using the augur align command ( Hadfield et al., 2018 ) and MAFFT ( Katoh et al., 2002 ).”
From primordial clocks to circadian oscillators (2023, methodology): “A multiple sequence alignment of the selected 1,538 sequences was generated using MAFFT 39–41 (Supplementary Dataset 1).”
The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. (2010, methodology): “…for the alignment of multiple sequences, 2) MUSCLE (Edgar 2004) that implements several iterative refinement steps, and 3) the L-INS-i algorithm of the program package MAFFT (Katoh et al. 2002) that also implements iterative refinement and additionally uses a consistency score (Katoh et al. 2005).”
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. (2007, methodology): “Alignments generated by Rose were cleaned from gaps and new alignments were reconstructed using ClustalW version 1.83 (Thompson et al., 1994), Mafft version 5.531 ( Katoh et al., 2002, 2005 ), and Probcons version 1.1 (Do et al., 2005).”
The genus Cladosporium (2012, methodology): “The sequences were aligned using the online version of MAFFT (mafft. cbrc.jp/alignment/server/index.html; Katoh et al. 2002), followed by manual correction by eye using Sequence Alignment Editor v. 2.0a11 (Rambaut 2002).”
Field and Laboratory Methods for DNA Studies on Deep-sea Isopod Crustaceans (2014, methodology): “1994) and MAFFT (Katoh et al. 2002) were used and subsequently alignments were checked and corrected by hand where necessary.”
The accuracy of several multiple sequence alignment programs for proteins (2006, methodology): “The last phase is the iterative refinement which optimizes the Gotoh's weighted sum of pairs (WSP) [26] score, with a group-to-group alignment [27] and the tree-dependent restriction partition technique [24].”
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark (2005, background): “23,24 To objectively compare the quality of the numerous multiple sequence alignment methods available today, high-quality benchmarks are crucial.”