Multiple alignment of DNA sequences with MAFFT.

By Kazutaka Katoh, G. Asimenos, Hiroyuki Toh. 2009

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Subfields: Molecular Biology, Plant Science

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “These improvements and techniques were mostly reported in individual papers (Katoh et al. 2009; Katoh and Toh 2010; Katoh and Frith 2012; Katoh and Standley 2013).”
A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies (2009, methodology): “The first step in such an analysis is to generate a de novo multiple sequence alignment using software such as Clustal, MUSCLE, or MAFFT.”
The sooty moulds (2014, methodology): “For this review, large subunit ribosomal RNA (LSU rRNA) gene sequences from 46 isolates from sooty mould taxa belonging to the families Antennulariellaceae, Capnodiaceae, Chaetothyriaceae, Euantennariaceae and Trichomeriaceae were downloaded from GenBank and aligned using MAFFT version 7 (Katoh et a”
Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata) (2014, methodology): “Phylogenetic analyses Multiple sequence alignments were performed using mafft (Katoh et al., 2009) under default parameters.”
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic (2020, methodology): “Sequences were aligned by MAFTT (Katoh et al., 2009), with a final alignment length of 30927, and used in the analyses below.”
Ancient hybridizations among the ancestral genomes of bread wheat (2014, methodology): “A phylogenyaware sequence alignment pipeline modified from (19) was implemented in R language usingMAFFT (29) to construct multiple sequence alignments, GUIDANCE (30) to assess sequence alignment quality, and phangorn (31) to construct maximum likelihood topologies, which were used to evaluate ortho”
Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence (2016, methodology): “Sequences of each locus were aligned using the program MAFFT v7 (Katoh et al. 2009; Katoh and Toh 2008).”
Elemental stoichiometry of Fungi and Bacteria strains from grassland leaf litter (2014, methodology): “For phylogenetic analyses, the ITS portions of each sequence were removed and 558 bp of the 28S rRNA were aligned using the local pairwise alignment setting of MAFFT (Katoh et al., 2009) with the Chytrid Spizellomyces punctatus added as an outgroup.”
A new bioinformatics analysis tools framework at EMBL–EBI (2010, background): “These include sequence similarity search services (http://www.ebi.ac .uk/Tools/similarity.html), such as FASTA (3), BLAST (4,5) and InterProScan (6) and multiple sequence alignment tools (http://www.ebi.ac.uk/Tools/sequence.html), such as ClustalW (7), T-Coffee (8), MUSCLE (9), Kalign (10) and MAFFT”
Phylogeny of the Lobariaceae (lichenized Ascomycota: Peltigerales), with a reappraisal of the genus Lobariella (2013, methodology): “Final alignments were made with MAFFT 6.850b (Katoh et al. 2002, 2009) using the –auto option.”
The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday (2017, methodology): “The SSU, LSU, TEF1 and RPB2 data sets were aligned separately using MAFFT (Katoh et al. 2009) and checked manually using Bioedit (Hall 1999).”
Phylogenetic tree building in the genomic age (2020, positive): “Orthology is a special type of homology in which genes in different species have diverged from each other due to speciation 15,16 .”
A Molecular Phylogeny of Living Primates (2011, methodology): “DNA Sequence Analyses Multiple sequence files for each gene segment amplified were aligned by MAFFT version 6 [69,70], imported into Se-Al ver Figure 2.”