SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
CNRS UMR 5558, Biométrie, Génétique et Biologie des Populations. Université Claude Bernard Lyon 1, 43, Boulevard du 11 novembre 1918, 69622 Villeurbanne cedex. France
1To whom correspondence should be addressed. E-mail galtier{at}biomserv.univ-lyonl.fr
SEA VIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEA VIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyonl. fr/pub/ mol_phylogeny or http://acnuc.univ-lyonl.fr, or by e-mail to galtier{at}biomserv.univ-lyonl.fr.
Received on July 11, 1996; accepted on August 28, 1996
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B. Brindefalk, J. Viklund, D. Larsson, M. Thollesson, and S. G. E. Andersson Origin and Evolution of the Mitochondrial Aminoacyl-tRNA Synthetases Mol. Biol. Evol., March 1, 2007; 24(3): 743 - 756. [Abstract] [Full Text] [PDF]
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J. Zluvova, M. Nicolas, A. Berger, I. Negrutiu, and F. Moneger Premature arrest of the male flower meristem precedes sexual dimorphism in the dioecious plant Silene latifolia PNAS, December 5, 2006; 103(49): 18854 - 18859. [Abstract] [Full Text] [PDF]
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G. Plotz, C. Welsch, L. Giron-Monzon, P. Friedhoff, M. Albrecht, A. Piiper, R. M. Biondi, T. Lengauer, S. Zeuzem, and J. Raedle Mutations in the MutS{alpha} interaction interface of MLH1 can abolish DNA mismatch repair Nucleic Acids Res., December 2, 2006; 34(22): 6574 - 6586. [Abstract] [Full Text] [PDF]
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S. M. Turner, R. R. Chaudhuri, Z.-D. Jiang, H. DuPont, C. Gyles, C. W. Penn, M. J. Pallen, and I. R. Henderson Phylogenetic Comparisons Reveal Multiple Acquisitions of the Toxin Genes by Enterotoxigenic Escherichia coli Strains of Different Evolutionary Lineages J. Clin. Microbiol., December 1, 2006; 44(12): 4528 - 4536. [Abstract] [Full Text] [PDF]
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A. Aouacheria, C. Geourjon, N. Aghajari, V. Navratil, G. Deleage, C. Lethias, and J.-Y. Exposito Insights into Early Extracellular Matrix Evolution: Spongin Short Chain Collagen-Related Proteins Are Homologous to Basement Membrane Type IV Collagens and Form a Novel Family Widely Distributed in Invertebrates Mol. Biol. Evol., December 1, 2006; 23(12): 2288 - 2302. [Abstract] [Full Text] [PDF]
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B. Piegu, R. Guyot, N. Picault, A. Roulin, A. Saniyal, H. Kim, K. Collura, D. S. Brar, S. Jackson, R. A. Wing, et al. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice Genome Res., October 1, 2006; 16(10): 1262 - 1269. [Abstract] [Full Text] [PDF]
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A. Pareek, A. Singh, M. Kumar, H. R. Kushwaha, A. M. Lynn, and S. L. Singla-Pareek Whole-Genome Analysis of Oryza sativa Reveals Similar Architecture of Two-Component Signaling Machinery with Arabidopsis Plant Physiology, October 1, 2006; 142(2): 380 - 397. [Abstract] [Full Text] [PDF]
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G. Delhon, E. R. Tulman, C. L. Afonso, Z. Lu, J. J. Becnel, B. A. Moser, G. F. Kutish, and D. L. Rock Genome of invertebrate iridescent virus type 3 (mosquito iridescent virus). J. Virol., September 1, 2006; 80(17): 8439 - 8449. [Abstract] [Full Text] [PDF]
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M.-P. Egloff, H. Malet, A. Putics, M. Heinonen, H. Dutartre, A. Frangeul, A. Gruez, V. Campanacci, C. Cambillau, J. Ziebuhr, et al. Structural and Functional Basis for ADP-Ribose and Poly(ADP-Ribose) Binding by Viral Macro Domains. J. Virol., September 1, 2006; 80(17): 8493 - 8502. [Abstract] [Full Text] [PDF]
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E. R. Tulman, G. Delhon, C. L. Afonso, Z. Lu, L. Zsak, N. T. Sandybaev, U. Z. Kerembekova, V. L. Zaitsev, G. F. Kutish, and D. L. Rock Genome of horsepox virus. J. Virol., September 1, 2006; 80(18): 9244 - 9258. [Abstract] [Full Text] [PDF]
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F. G. Brunet, H. R. Crollius, M. Paris, J.-M. Aury, P. Gibert, O. Jaillon, V. Laudet, and M. Robinson-Rechavi Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes Mol. Biol. Evol., September 1, 2006; 23(9): 1808 - 1816. [Abstract] [Full Text] [PDF]
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L. Urios, H. Agogue, F. Lesongeur, E. Stackebrandt, and P. Lebaron Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1883 - 1887. [Abstract] [Full Text] [PDF]
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C. L. Afonso, E. R. Tulman, G. Delhon, Z. Lu, G. J. Viljoen, D. B. Wallace, G. F. Kutish, and D. L. Rock Genome of crocodilepox virus. J. Virol., May 1, 2006; 80(10): 4978 - 4991. [Abstract] [Full Text] [PDF]
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M. Sammeth, T. Griebel, F. Tille, and J. Stoye Panta rhei (QAlign2): an open graphical environment for sequence analysis Bioinformatics, April 1, 2006; 22(7): 889 - 890. [Abstract] [Full Text] [PDF]
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M. Novinec, D. Kordis, V. Turk, and B. Lenarcic Diversity and Evolution of the Thyroglobulin Type-1 Domain Superfamily Mol. Biol. Evol., April 1, 2006; 23(4): 744 - 755. [Abstract] [Full Text] [PDF]
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A. Schluter, S. Fourcade, R. Ripp, J. L. Mandel, O. Poch, and A. Pujol The Evolutionary Origin of Peroxisomes: An ER-Peroxisome Connection Mol. Biol. Evol., April 1, 2006; 23(4): 838 - 845. [Abstract] [Full Text] [PDF]
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W. I.L. Tameling, J. H. Vossen, M. Albrecht, T. Lengauer, J. A. Berden, M. A. Haring, B. J.C. Cornelissen, and F. L.W. Takken Mutations in the NB-ARC Domain of I-2 That Impair ATP Hydrolysis Cause Autoactivation Plant Physiology, April 1, 2006; 140(4): 1233 - 1245. [Abstract] [Full Text] [PDF]
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T. A. Fritz, J. Raman, and L. A. Tabak Dynamic Association between the Catalytic and Lectin Domains of Human UDP-GalNAc:Polypeptide {alpha}-N-Acetylgalactosaminyltransferase-2 J. Biol. Chem., March 31, 2006; 281(13): 8613 - 8619. [Abstract] [Full Text] [PDF]
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J.-P. Pichon, B. Bonnaud, P. Cleuziat, and F. Mallet Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling Nucleic Acids Res., March 22, 2006; 34(6): e46 - e46. [Abstract] [Full Text] [PDF]
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S. Eichler, R. Christen, C. Holtje, P. Westphal, J. Botel, I. Brettar, A. Mehling, and M. G. Hofle Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting. Appl. Envir. Microbiol., March 1, 2006; 72(3): 1858 - 1872. [Abstract] [Full Text] [PDF]
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A.-M. Grenier, G. Duport, S. Pages, G. Condemine, and Y. Rahbe The Phytopathogen Dickeya dadantii (Erwinia chrysanthemi 3937) Is a Pathogen of the Pea Aphid. Appl. Envir. Microbiol., March 1, 2006; 72(3): 1956 - 1965. [Abstract] [Full Text] [PDF]
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H. Tostivint, L. Joly, I. Lihrmann, C. Parmentier, A. Lebon, M. Morisson, A. Calas, M. Ekker, and H. Vaudry Comparative genomics provides evidence for close evolutionary relationships between the urotensin II and somatostatin gene families PNAS, February 14, 2006; 103(7): 2237 - 2242. [Abstract] [Full Text] [PDF]
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V. Rodriguez-Nava, A. Couble, G. Devulder, J.-P. Flandrois, P. Boiron, and F. Laurent Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species J. Clin. Microbiol., February 1, 2006; 44(2): 536 - 546. [Abstract] [Full Text] [PDF]
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A. G. Collins, P. Schuchert, A. C. Marques, T. Jankowski, M. Medina, and B. Schierwater Medusozoan Phylogeny and Character Evolution Clarified by New Large and Small Subunit rDNA Data and an Assessment of the Utility of Phylogenetic Mixture Models Syst Biol, February 1, 2006; 55(1): 97 - 115. [Abstract] [Full Text] [PDF]
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B. Anand, S. K. Verma, and B. Prakash Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding. Nucleic Acids Res., January 1, 2006; 34(8): 2196 - 2205. [Abstract] [Full Text] [PDF]
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V. Rodriguez-Nava, A. Couble, Z. U. Khan, M. Perouse de Montclos, L. Brasme, C. Villuendas, C. Molinard, P. Boiron, and F. Laurent Nocardia ignorata, a New Agent of Human Nocardiosis Isolated from Respiratory Specimens in Europe and Soil Samples from Kuwait J. Clin. Microbiol., December 1, 2005; 43(12): 6167 - 6170. [Abstract] [Full Text] [PDF]
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