MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Briefings in Bioinformatics
Kazutaka KatohKazunori D Yamada

Abstract

This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

References

Jan 1, 1987·Journal of Molecular Evolution·D F Feng, R F Doolittle
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Jan 1, 1984·Journal of Molecular Evolution·P Hogeweg, B Hesper
Jul 31, 1998·Bioinformatics·C NotredameD G Higgins
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Aug 30, 2007·BMC Bioinformatics·Rodrigo Gouveia-OliveiraAnders G Pedersen
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Oct 29, 2009·BMC Bioinformatics·Mira V Han, Christian M Zmasek
May 18, 2010·Algorithms for Molecular Biology : AMB·Gordon BlackshieldsDesmond G Higgins
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
Jun 4, 2011·Bioinformatics·Simon A Berger, Alexandros Stamatakis
Oct 11, 2011·Bioinformatics·Siavash Mirarab, Tandy Warnow
Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Apr 19, 2012·Nature Reviews. Genetics·Mark Yandell, Daniel Ence
Oct 2, 2012·Bioinformatics·Kazutaka Katoh, Martin C Frith
Nov 10, 2012·Nature Biotechnology·Debora S MarksChris Sander
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 23, 2013·Bioinformatics·Fabian SieversDesmond G Higgins
Jul 19, 2013·Database : the Journal of Biological Databases and Curation·Alinda Nagy, László Patthy
Sep 7, 2013·Proceedings of the National Academy of Sciences of the United States of America·Hetunandan KamisettyDavid Baker
Jul 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Kieran BoyceDesmond G Higgins
Oct 6, 2014·BMC Bioinformatics·Fabian SieversDesmond G Higgins
Dec 31, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Siavash MirarabTandy Warnow
Jan 8, 2015·Proceedings of the National Academy of Sciences of the United States of America·Ge TanChristophe Dessimoz
Jun 17, 2015·Genome Biology·Nam-Phuong D NguyenTandy Warnow
May 18, 2016·Molecular Biology and Evolution·Oscar RobinsonChristophe Dessimoz

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Citations

Mar 6, 2018·Bioinformatics·Tsukasa NakamuraKazutaka Katoh
Apr 26, 2018·American Journal of Botany·Mark FishbeinAaron Liston
Jan 13, 2018·Frontiers in Microbiology·María P CortésAlejandro Maass
Jun 26, 2018·International Journal of Systematic and Evolutionary Microbiology·Martin W HahnElke Lang
Aug 29, 2018·Evolution; International Journal of Organic Evolution·Rohan MaddamsettiJustin R Meyer
Aug 21, 2018·Environmental Microbiology Reports·Raquel CantosAsunción Contreras
Sep 25, 2018·Microbial Genomics·Charlotte J HouldcroftAnkur Mutreja
Aug 12, 2018·Applied and Environmental Microbiology·Laura TeichmannErhard Bremer
Jan 4, 2019·International Journal of Systematic and Evolutionary Microbiology·Masaharu TsujiMasaki Uchida
Nov 23, 2018·International Journal of Systematic and Evolutionary Microbiology·Matthias HoetzingerMartin W Hahn
Dec 12, 2018·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Jean L MbisaUNKNOWN UK HIV Drug Resistance Database
Feb 15, 2019·ELife·Stephen M Hinshaw, Stephen C Harrison
Feb 7, 2019·Molecular Biology and Evolution·Timothy Q DuBucMark Q Martindale
Dec 7, 2018·The ISME Journal·Carlos A Aguilar-TriguerosMatthias C Rillig
Apr 29, 2018·Biology Direct·Michael MelesseIgor B Zhulin
May 1, 2019·Nature Chemical Biology·Liam DoyleChris Whitfield
Jun 9, 2018·Fungal biology and biotechnology·Sonia ChadhaPrasun K Mukherjee
May 28, 2019·Molecular Biology and Evolution·Maria Y SachkovaYehu Moran
Jun 12, 2019·FEMS Microbiology Ecology·José F Cobo-DíazAdeline Picot
Aug 6, 2019·Microbiology·Thomas E WoodAlain Filloux
Sep 4, 2019·Nature Microbiology·Thomas C FungElaine Y Hsiao
Aug 24, 2019·Evolution; International Journal of Organic Evolution·Jonas O WolffMarie E Herberstein
Jun 23, 2019·Plants·Ivete MaquiaAna I Ribeiro-Barros

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Software Mentioned

Phylo
Clustal Omega
UPP
MaxAlign
aLeaves
hmmalign
MSAViewer
PaPaRa
FastSP
UPGMA

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