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Nucleic Acids Research, 2003, Vol. 31, No. 13 3497-3500
© 2003 Oxford University Press

Multiple sequence alignment with the Clustal series of programs

Ramu Chenna, Hideaki Sugawara1, Tadashi Koike1, Rodrigo Lopez2, Toby J. Gibson, Desmond G. Higgins3 and Julie D. Thompson*,4

European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany 1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-Ken 411-8540, Japan 2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3 Department of Biochemistry, University College Cork, Cork, Ireland 4 Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, (CNRS/INSERM/ULP), BP 10142, 67404 Illkirch Cedex, France

*To whom correspondence should be addressed. Tel: +33 388653200; Fax: +33 388653276; Email: julie{at}igbmc.u-strasbg.fr

The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).


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Genetics, October 1, 2008; 180(2): 905 - 920.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
A. V. Ritchie, S. van Es, C. Fouquet, and P. Schaap
From Drought Sensing to Developmental Control: Evolution of Cyclic AMP Signaling in Social Amoebas
Mol. Biol. Evol., October 1, 2008; 25(10): 2109 - 2118.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
T. F. Wright, E. E. Schirtzinger, T. Matsumoto, J. R. Eberhard, G. R. Graves, J. J. Sanchez, S. Capelli, H. Muller, J. Scharpegge, G. K. Chambers, et al.
A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous
Mol. Biol. Evol., October 1, 2008; 25(10): 2141 - 2156.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
C. A. Lozupone, M. Hamady, B. L. Cantarel, P. M. Coutinho, B. Henrissat, J. I. Gordon, and R. Knight
The convergence of carbohydrate active gene repertoires in human gut microbes
PNAS, September 30, 2008; 105(39): 15076 - 15081.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
S. Horowitz Brown, R. Zarnowski, W. C. Sharpee, and N. P. Keller
Morphological Transitions Governed by Density Dependence and Lipoxygenase Activity in Aspergillus flavus
Appl. Envir. Microbiol., September 15, 2008; 74(18): 5674 - 5685.
[Abstract] [Full Text] [PDF]


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Infect. Immun.Home page
P. T. Beernink, J. A. Welsch, M. Bar-Lev, O. Koeberling, M. Comanducci, and D. M. Granoff
Fine Antigenic Specificity and Cooperative Bactericidal Activity of Monoclonal Antibodies Directed at the Meningococcal Vaccine Candidate Factor H-Binding Protein
Infect. Immun., September 1, 2008; 76(9): 4232 - 4240.
[Abstract] [Full Text] [PDF]


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J. Bacteriol.Home page
M. Letek, A. A. Ocampo-Sosa, M. Sanders, U. Fogarty, T. Buckley, D. P. Leadon, P. Gonzalez, M. Scortti, W. G. Meijer, J. Parkhill, et al.
Evolution of the Rhodococcus equi vap Pathogenicity Island Seen through Comparison of Host-Associated vapA and vapB Virulence Plasmids
J. Bacteriol., September 1, 2008; 190(17): 5797 - 5805.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
A. Just, F. Butter, M. Trenkmann, T. Heitkam, M. Morl, and H. Betat
A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme
Nucleic Acids Res., September 1, 2008; 36(16): 5212 - 5220.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
V. Mustonen, J. Kinney, C. G. Callan Jr, and M. Lassig
Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites
PNAS, August 26, 2008; 105(34): 12376 - 12381.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
C. G. Grummitt, F. M. Townsley, C. M. Johnson, A. J. Warren, and M. Bycroft
Structural Consequences of Nucleophosmin Mutations in Acute Myeloid Leukemia
J. Biol. Chem., August 22, 2008; 283(34): 23326 - 23332.
[Abstract] [Full Text] [PDF]


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J. Virol.Home page
L. Pache, S. Venkataraman, V. S. Reddy, and G. R. Nemerow
Structural Variations in Species B Adenovirus Fibers Impact CD46 Association
J. Virol., August 15, 2008; 82(16): 7923 - 7931.
[Abstract] [Full Text] [PDF]


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J. Virol.Home page
A. M. Land, T. B. Ball, M. Luo, R. Pilon, P. Sandstrom, J. E. Embree, C. Wachihi, J. Kimani, and F. A. Plummer
Human Immunodeficiency Virus (HIV) Type 1 Proviral Hypermutation Correlates with CD4 Count in HIV-Infected Women from Kenya
J. Virol., August 15, 2008; 82(16): 8172 - 8182.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
C. J. Plante, K. M. Coe, and R. G. Plante
Isolation of Surfactant-Resistant Bacteria from Natural, Surfactant-Rich Marine Habitats
Appl. Envir. Microbiol., August 15, 2008; 74(16): 5093 - 5099.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
R. M. Vanacore, A.-J. L. Ham, J.-P. Cartailler, M. Sundaramoorthy, P. Todd, V. Pedchenko, Y. Sado, D.-B. Borza, and B. G. Hudson
A Role for Collagen IV Cross-links in Conferring Immune Privilege to the Goodpasture Autoantigen: STRUCTURAL BASIS FOR THE CRYPTICITY OF B CELL EPITOPES
J. Biol. Chem., August 15, 2008; 283(33): 22737 - 22748.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
R. Becker, B. Loll, and A. Meinhart
Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II
J. Biol. Chem., August 15, 2008; 283(33): 22659 - 22669.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
P. D. Kiely, J. O'Callaghan, A. Abbas, and F. O'Gara
Genetic analysis of genes involved in dipeptide metabolism and cytotoxicity in Pseudomonas aeruginosa PAO1
Microbiology, August 1, 2008; 154(8): 2209 - 2218.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
M. Hadjifrangiskou and T. M. Koehler
Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters
Microbiology, August 1, 2008; 154(8): 2501 - 2512.
[Abstract] [Full Text] [PDF]


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J EndocrinolHome page
E. H Stolte, A. F de Mazon, K. M Leon-Koosterziel, M. Jesiak, N. R Bury, A. Sturm, H. F J Savelkoul, B M L. V. van Kemenade, and G. Flik
Corticosteroid receptors involved in stress regulation in common carp, Cyprinus carpio
J. Endocrinol., August 1, 2008; 198(2): 403 - 417.
[Abstract] [Full Text] [PDF]


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J. Clin. Microbiol.Home page
J. F. Staropoli and J. A. Branda
Cord Formation in a Clinical Isolate of Mycobacterium marinum
J. Clin. Microbiol., August 1, 2008; 46(8): 2814 - 2816.
[Abstract] [Full Text] [PDF]


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Cancer Res.Home page
S. Das, Y. Hahn, D. A. Walker, S. Nagata, M. C. Willingham, D. M. Peehl, T. K. Bera, B. Lee, and I. Pastan
Topology of NGEP, a Prostate-Specific Cell:Cell Junction Protein Widely Expressed in Many Cancers of Different Grade Level
Cancer Res., August 1, 2008; 68(15): 6306 - 6312.
[Abstract] [Full Text] [PDF]


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J. Bacteriol.Home page
F. Bagnoli, M. Moschioni, C. Donati, V. Dimitrovska, I. Ferlenghi, C. Facciotti, A. Muzzi, F. Giusti, C. Emolo, A. Sinisi, et al.
A Second Pilus Type in Streptococcus pneumoniae Is Prevalent in Emerging Serotypes and Mediates Adhesion to Host Cells
J. Bacteriol., August 1, 2008; 190(15): 5480 - 5492.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
J. R. Hall, K. R. Mitchell, O. Jackson-Weaver, A. S. Kooser, B. R. Cron, L. J. Crossey, and C. D. Takacs-Vesbach
Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes
Appl. Envir. Microbiol., August 1, 2008; 74(15): 4910 - 4922.
[Abstract] [Full Text] [PDF]


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Mol. Biol. CellHome page
H. S. Jung, S. Komatsu, M. Ikebe, and R. Craig
Head-Head and Head-Tail Interaction: A General Mechanism for Switching Off Myosin II Activity in Cells
Mol. Biol. Cell, August 1, 2008; 19(8): 3234 - 3242.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
J. L. Knies, K. K. Dang, T. J. Vision, N. G. Hoffman, R. Swanstrom, and C. L. Burch
Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites
Mol. Biol. Evol., August 1, 2008; 25(8): 1778 - 1787.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
L. Deluc, J. Bogs, A. R. Walker, T. Ferrier, A. Decendit, J.-M. Merillon, S. P. Robinson, and F. Barrieu
The Transcription Factor VvMYB5b Contributes to the Regulation of Anthocyanin and Proanthocyanidin Biosynthesis in Developing Grape Berries
Plant Physiology, August 1, 2008; 147(4): 2041 - 2053.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
S. Puthiyaveetil, T. A. Kavanagh, P. Cain, J. A. Sullivan, C. A. Newell, J. C. Gray, C. Robinson, M. van der Giezen, M. B. Rogers, and J. F. Allen
The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts
PNAS, July 22, 2008; 105(29): 10061 - 10066.
[Abstract] [Full Text] [PDF]


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Antimicrob. Agents Chemother.Home page
M. Stoczko, J.-M. Frere, G. M. Rossolini, and J.-D. Docquier
Functional Diversity among Metallo-{beta}-Lactamases: Characterization of the CAR-1 Enzyme of Erwinia carotovora
Antimicrob. Agents Chemother., July 1, 2008; 52(7): 2473 - 2479.
[Abstract] [Full Text] [PDF]



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