Nucleic Acids Research, Vol 25, Issue 24 4876-4882, Copyright © 1997 by Oxford University Press
JD Thompson, TJ Gibson, F Plewniak, F Jeanmougin and DG Higgins
CLUSTAL X is a new windows interface for the widely-used progressive
multiple sequence alignment program CLUSTAL W. The new system is easy to
use, providing an integrated system for performing multiple sequence and
profile alignments and analysing the results. CLUSTAL X displays the
sequence alignment in a window on the screen. A versatile sequence
colouring scheme allows the user to highlight conserved features in the
alignment. Pull-down menus provide all the options required for traditional
multiple sequence and profile alignment. New features include: the ability
to cut-and-paste sequences to change the order of the alignment, selection
of a subset of the sequences to be realigned, and selection of a sub-range
of the alignment to be realigned and inserted back into the original
alignment. Alignment quality analysis can be performed and low-scoring
segments or exceptional residues can be highlighted. Quality analysis and
realignment of selected residue ranges provide the user with a powerful
tool to improve and refine difficult alignments and to trap errors in input
sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon
Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs,
Linux ELF for x86 PCs, and Macintosh PowerMac.
ARTICLES
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
Institut de Genetique et de Biologie Moleculaire et Cellulaire (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France.
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X. Guo, X.-Y. You, L.-J. Liu, J.-Y. Zhang, S.-J. Liu, and C.-Y. Jiang Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2415 - 2420. [Abstract] [Full Text] [PDF]
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S. Qin, G.-Z. Zhao, J. Li, W.-Y. Zhu, L.-H. Xu, and W.-J. Li Actinomadura flavalba sp. nov., an endophytic actinomycete isolated from leaves of Maytenus austroyunnanensis Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2453 - 2457. [Abstract] [Full Text] [PDF]
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M. Cai, S.-K. Tang, Y.-G. Chen, Y. Li, Y.-Q. Zhang, and W.-J. Li Streptomonospora amylolytica sp. nov. and Streptomonospora flavalba sp. nov., two novel halophilic actinomycetes isolated from a salt lake Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2471 - 2475. [Abstract] [Full Text] [PDF]
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J.-Y. Zhang, X.-Y. Liu, and S.-J. Liu Nocardioides terrae sp. nov., isolated from forest soil Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2444 - 2448. [Abstract] [Full Text] [PDF]
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P. Kampfer, H.-J. Busse, and H. C. Scholz Chromobacterium piscinae sp. nov. and Chromobacterium pseudoviolaceum sp. nov., from environmental samples Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2486 - 2490. [Abstract] [Full Text] [PDF]
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K. Houf, S. L. W. On, T. Coenye, L. Debruyne, S. De Smet, and P. Vandamme Arcobacter thereius sp. nov., isolated from pigs and ducks Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2599 - 2604. [Abstract] [Full Text] [PDF]
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Y.-P. Xiao, W. Hui, Q. Wang, S. W. Roh, X.-Q. Shi, J.-H. Shi, and Z.-X. Quan Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2594 - 2598. [Abstract] [Full Text] [PDF]
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S.-Y. Sheu, T. F. Chiu, J.-H. Chou, D.-S. Sheu, A. B. Arun, C.-C. Young, C. A. Chen, J.-T. Wang, and W.-M. Chen Andreprevotia lacus sp. nov., isolated from a fish-culture pond Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2482 - 2485. [Abstract] [Full Text] [PDF]
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S.-Y. Sheu, T. F. Chiu, N.-T. Cho, J.-H. Chou, D.-S. Sheu, A. B. Arun, C.-C. Young, C. A. Chen, J.-T. Wang, and W.-M. Chen Flectobacillus roseus sp. nov., isolated from freshwater in Taiwan Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2546 - 2551. [Abstract] [Full Text] [PDF]
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A. B. Arun, C.-C. Young, W.-M. Chen, M.-H. Hung, W.-A. Lai, J.-H. Chou, P. D. Rekha, F.-T. Shen, and S. P. Su Belliella pelovolcani sp. nov., isolated from a mud-volcano in Taiwan Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2534 - 2537. [Abstract] [Full Text] [PDF]
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S. Qin, J. Li, Y.-Q. Zhang, W.-Y. Zhu, G.-Z. Zhao, L.-H. Xu, and W.-J. Li Plantactinospora mayteni gen. nov., sp. nov., a member of the family Micromonosporaceae Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2527 - 2533. [Abstract] [Full Text] [PDF]
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Y.-G. Chen, Y.-Q. Zhang, Z.-X. Liu, D.-C. Zhuang, H.-P. Klenk, S.-K. Tang, X.-L. Cui, and W.-J. Li Halobacillus salsuginis sp. nov., a moderately halophilic bacterium from a subterranean brine Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2505 - 2509. [Abstract] [Full Text] [PDF]
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J. Xiao, Y. Wang, Y. Luo, S.-J. Xie, J.-S. Ruan, and J. Xu Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2624 - 2628. [Abstract] [Full Text] [PDF]
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J.-H. Chou, Y.-J. Chou, A. B. Arun, C.-C. Young, C. A. Chen, J.-T. Wang, and W.-M. Chen Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2629 - 2632. [Abstract] [Full Text] [PDF]
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J. Mayer and A. M. Cook Homotaurine Metabolized to 3-Sulfopropanoate in Cupriavidus necator H16: Enzymes and Genes in a Patchwork Pathway J. Bacteriol., October 1, 2009; 191(19): 6052 - 6058. [Abstract] [Full Text] [PDF]
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S. Qin, J. Li, H.-H. Chen, G.-Z. Zhao, W.-Y. Zhu, C.-L. Jiang, L.-H. Xu, and W.-J. Li Isolation, Diversity, and Antimicrobial Activity of Rare Actinobacteria from Medicinal Plants of Tropical Rain Forests in Xishuangbanna, China Appl. Envir. Microbiol., October 1, 2009; 75(19): 6176 - 6186. [Abstract] [Full Text] [PDF]
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 R. Schwarz, P. N. Seibel, S. Rahmann, C. Schoen, M. Huenerberg, C. Muller-Reible, T. Dandekar, R. Karchin, J. Schultz, and T. Muller Detecting species-site dependencies in large multiple sequence alignments Nucleic Acids Res., October 1, 2009; 37(18): 5959 - 5968. [Abstract] [Full Text] [PDF]
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 B. Hou, F. Li, X. Yang, and G. Hong A small functional intramolecular region of NodD was identified by mutation Acta Biochim Biophys Sin, October 1, 2009; 41(10): 822 - 830. [Abstract] [Full Text] [PDF]
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 M. Teramoto, M. Suzuki, F. Okazaki, A. Hatmanti, and S. Harayama Oceanobacter-related bacteria are important for the degradation of petroleum aliphatic hydrocarbons in the tropical marine environment Microbiology, October 1, 2009; 155(10): 3362 - 3370. [Abstract] [Full Text] [PDF]
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 Y.-Y. Shen, P. Shi, Y.-B. Sun, and Y.-P. Zhang Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability Genome Res., October 1, 2009; 19(10): 1760 - 1765. [Abstract] [Full Text] [PDF]
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 F. Bringaud, M. Berriman, and C. Hertz-Fowler Trypanosomatid Genomes Contain Several Subfamilies of ingi-Related Retroposons Eukaryot. Cell, October 1, 2009; 8(10): 1532 - 1542. [Abstract] [Full Text] [PDF]
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P. Rada, O. Smid, R. Sutak, P. Dolezal, J. Pyrih, V. Zarsky, J.-J. Montagne, I. Hrdy, J.-M. Camadro, and J. Tachezy The Monothiol Single-Domain Glutaredoxin Is Conserved in the Highly Reduced Mitochondria of Giardia intestinalis Eukaryot. Cell, October 1, 2009; 8(10): 1584 - 1591. [Abstract] [Full Text] [PDF]
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H. Shan, L. Zahn, S. Guindon, P. K. Wall, H. Kong, H. Ma, C. W. dePamphilis, and J. Leebens-Mack Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene Duplications Mol. Biol. Evol., October 1, 2009; 26(10): 2229 - 2244. [Abstract] [Full Text] [PDF]
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D.-D. Wu, G.-D. Wang, D. M Irwin, and Y.-P. Zhang A Profound Role for the Expansion of Trypsin-Like Serine Protease Family in the Evolution of Hematophagy in Mosquito Mol. Biol. Evol., October 1, 2009; 26(10): 2333 - 2341. [Abstract] [Full Text] [PDF]
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K. Denger, J. Mayer, M. Buhmann, S. Weinitschke, T. H. M. Smits, and A. M. Cook Bifurcated Degradative Pathway of 3-Sulfolactate in Roseovarius nubinhibens ISM via Sulfoacetaldehyde Acetyltransferase and (S)-Cysteate Sulfolyase J. Bacteriol., September 15, 2009; 191(18): 5648 - 5656. [Abstract] [Full Text] [PDF]
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J. van Ingen, R. de Zwaan, R. Dekhuijzen, M. Boeree, and D. van Soolingen Region of Difference 1 in Nontuberculous Mycobacterium Species Adds a Phylogenetic and Taxonomical Character J. Bacteriol., September 15, 2009; 191(18): 5865 - 5867. [Abstract] [Full Text] [PDF]
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B. J. Watson, H. Zhang, A. G. Longmire, Y. H. Moon, and S. W. Hutcheson Processive Endoglucanases Mediate Degradation of Cellulose by Saccharophagus degradans J. Bacteriol., September 15, 2009; 191(18): 5697 - 5705. [Abstract] [Full Text] [PDF]
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 A. F. P. Cheung, S. Kondo, O. Abdel-Mannan, R. A. Chodroff, T. M. Sirey, L. E. Bluy, N. Webber, J. DeProto, S. J. Karlen, L. Krubitzer, et al. The Subventricular Zone Is the Developmental Milestone of a 6-Layered Neocortex: Comparisons in Metatherian and Eutherian Mammals Cereb Cortex, September 2, 2009; (2009) bhp168v1. [Abstract] [Full Text] [PDF]
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 L. E. de Vries, H. Christensen, R. L. Skov, F. M. Aarestrup, and Y. Agerso Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- and Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals J. Antimicrob. Chemother., September 1, 2009; 64(3): 490 - 500. [Abstract] [Full Text] [PDF]
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M. Coscolla and F. Gonzalez-Candelas Direct Sequencing of Legionella pneumophila from Respiratory Samples for Sequence-Based Typing Analysis J. Clin. Microbiol., September 1, 2009; 47(9): 2901 - 2905. [Abstract] [Full Text] [PDF]
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