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Bioinformatics Advance Access originally published online on September 10, 2007
Bioinformatics 2007 23(21):2947-2948; doi:10.1093/bioinformatics/btm404
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Clustal W and Clustal X version 2.0

M.A. Larkin 1, G. Blackshields 1, N.P. Brown 3, R. Chenna 3, P.A. McGettigan 1, H. McWilliam 4, F. Valentin 4, I.M. Wallace 1, A. Wilm 1, R. Lopez 4, J.D. Thompson 2, T.J. Gibson 3 and D.G. Higgins 1,*

1The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland, 2Laboratoire de Biologie et Genomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France, 3European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and 4EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK

*To whom correspondence should be addressed.


   Abstract

Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.

Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/

Contact: clustalw{at}ucd.ie

Associate Editor: Alex Bateman


Received on June 27, 2007; revised on August 3, 2007; accepted on August 3, 2007

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J. R. Shak, J. J. Dick, R. J. Meinersmann, G. I. Perez-Perez, and M. J. Blaser
Repeat-Associated Plasticity in the Helicobacter pylori RD Gene Family
J. Bacteriol., November 15, 2009; 191(22): 6900 - 6910.
[Abstract] [Full Text] [PDF]


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DevelopmentHome page
P. Kahlem and S. J. Newfeld
Informatics approaches to understanding TGF{beta} pathway regulation
Development, November 15, 2009; 136(22): 3729 - 3740.
[Abstract] [Full Text] [PDF]


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J. Cell Sci.Home page
R. Nachat, S. Cipolat, L. M. Sevilla, M. Chhatriwala, K. R. Groot, and F. M. Watt
KazrinE is a desmosome-associated liprin that colocalises with acetylated microtubules
J. Cell Sci., November 15, 2009; 122(22): 4035 - 4041.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
M. Baud'huin, L. Duplomb, S. Teletchea, C. Charrier, M. Maillasson, M. Fouassier, and D. Heymann
Factor VIII-von Willebrand Factor Complex Inhibits Osteoclastogenesis and Controls Cell Survival
J. Biol. Chem., November 13, 2009; 284(46): 31704 - 31713.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
M. M. O. Pena, S. P. Melo, Y.-Y. Xing, K. White, K. W. Barbour, and F. G. Berger
The Intrinsically Disordered N-terminal Domain of Thymidylate Synthase Targets the Enzyme to the Ubiquitin-independent Proteasomal Degradation Pathway
J. Biol. Chem., November 13, 2009; 284(46): 31597 - 31607.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
S. J. Maerkl and S. R. Quake
Experimental determination of the evolvability of a transcription factor
PNAS, November 3, 2009; 106(44): 18650 - 18655.
[Abstract] [Full Text] [PDF]


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JCBHome page
N. R. Stevens, J. Dobbelaere, A. Wainman, F. Gergely, and J. W. Raff
Ana3 is a conserved protein required for the structural integrity of centrioles and basal bodies
J. Cell Biol., November 2, 2009; 187(3): 355 - 363.
[Abstract] [Full Text] [PDF]


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jvdiHome page
S. J. Schatzberg, Q. Li, B. F. Porter, R. M. Barber, M. K. Claiborne, J. M. Levine, G. J. Levine, S. K. Israel, B. D. Young, M. Kiupel, et al.
Broadly reactive pan-paramyxovirus reverse transcription polymerase chain reaction and sequence analysis for the detection of Canine distemper virus in a case of canine meningoencephalitis of unknown etiology
J Vet Diagn Invest, November 1, 2009; 21(6): 844 - 849.
[Abstract] [Full Text] [PDF]


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Brief BioinformHome page
M. D. Wilkerson, Y. Ru, and V. P. Brendel
Common introns within orthologous genes: software and application to plants
Brief Bioinform, November 1, 2009; 10(6): 631 - 644.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
M. Sakamoto, N. Suzuki, N. Matsunaga, K. Koshihara, M. Seki, H. Komiya, and Y. Benno
Parabacteroides gordonii sp. nov., isolated from human blood cultures
Int J Syst Evol Microbiol, November 1, 2009; 59(11): 2843 - 2847.
[Abstract] [Full Text] [PDF]


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J. Clin. Microbiol.Home page
L. Chen, J. R. Mediavilla, D. C. Oliveira, B. M. Willey, H. de Lencastre, and B. N. Kreiswirth
Multiplex Real-Time PCR for Rapid Staphylococcal Cassette Chromosome mec Typing
J. Clin. Microbiol., November 1, 2009; 47(11): 3692 - 3706.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
M. Rho and H. Tang
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes
Nucleic Acids Res., November 1, 2009; 37(21): e143 - e143.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
G. W. Wilson and D. R. Edgell
Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII
Nucleic Acids Res., November 1, 2009; 37(21): 7110 - 7123.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
R. M. Smith, J. Josephsen, and M. D. Szczelkun
An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI
Nucleic Acids Res., November 1, 2009; 37(21): 7231 - 7238.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
C. S. Mahon, A. J. O'Donoghue, D. H. Goetz, P. G. Murray, C. S. Craik, and M. G. Tuohy
Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii
Microbiology, November 1, 2009; 155(11): 3673 - 3682.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
K. Schirner and J. Errington
Influence of heterologous MreB proteins on cell morphology of Bacillus subtilis
Microbiology, November 1, 2009; 155(11): 3611 - 3621.
[Abstract] [Full Text] [PDF]


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J. Virol.Home page
Y. Sun, F. Xue, Y. Guo, M. Ma, N. Hao, X. C. Zhang, Z. Lou, X. Li, and Z. Rao
Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus Leader Protease Nsp1{alpha}
J. Virol., November 1, 2009; 83(21): 10931 - 10940.
[Abstract] [Full Text] [PDF]


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J MOLLUS STUDHome page
C. L. Elderkin
Intragenomic variation in the rDNA internal transcribed spacer (ITS1) in the freshwater mussel Cumberlandia monodonta (Say, 1828)
J. Mollus. Stud., November 1, 2009; 75(4): 419 - 421.
[Full Text] [PDF]


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Mol PlantHome page
S. K. A. Natesan, J. A. Sullivan, and J. C. Gray
Myosin XI Is Required for Actin-Associated Movement of Plastid Stromules
Mol Plant, November 1, 2009; 2(6): 1262 - 1272.
[Abstract] [Full Text] [PDF]


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J HeredHome page
K. Livingstone and S. Anderson
Patterns of Variation in the Evolution of Carotenoid Biosynthetic Pathway Enzymes of Higher Plants
J. Hered., November 1, 2009; 100(6): 754 - 761.
[Abstract] [Full Text] [PDF]


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J Exp BotHome page
K. Bouwmeester and F. Govers
Arabidopsis L-type lectin receptor kinases: phylogeny, classification, and expression profiles
J. Exp. Bot., November 1, 2009; 60(15): 4383 - 4396.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
R. Khanna, B. Kronmiller, D. R. Maszle, G. Coupland, M. Holm, T. Mizuno, and S.-H. Wu
The Arabidopsis B-Box Zinc Finger Family
PLANT CELL, November 1, 2009; 21(11): 3416 - 3420.
[Full Text] [PDF]


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Plant Physiol.Home page
G. Bannenberg, M. Martinez, M. J. Rodriguez, M. A. Lopez, I. Ponce de Leon, M. Hamberg, and C. Castresana
Functional Analysis of {alpha}-DOX2, an Active {alpha}-Dioxygenase Critical for Normal Development in Tomato Plants
Plant Physiology, November 1, 2009; 151(3): 1421 - 1432.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
Y. Nishiyama, S. Planque, Y. Mitsuda, G. Nitti, H. Taguchi, L. Jin, J. Symersky, S. Boivin, M. Sienczyk, M. Salas, et al.
Toward Effective HIV Vaccination: INDUCTION OF BINARY EPITOPE REACTIVE ANTIBODIES WITH BROAD HIV NEUTRALIZING ACTIVITY
J. Biol. Chem., October 30, 2009; 284(44): 30627 - 30642.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
L. A. Martin-Visscher, X. Gong, M. Duszyk, and J. C. Vederas
The Three-dimensional Structure of Carnocyclin A Reveals That Many Circular Bacteriocins Share a Common Structural Motif
J. Biol. Chem., October 16, 2009; 284(42): 28674 - 28681.
[Abstract] [Full Text] [PDF]



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