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PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
Bioinformatics Institute and Allan Wilson Centre, University of Auckland Private Bag 92019, Auckland, New Zealand 1Projet Méthodes et Algorithmes pour la Bioinformatique, LIRMM-CNRS 161 Rue Ada, 34392-Montpellier Cedex 5, France
*To whom correspondence should be addressed. Tel: +33 4 67 41 85 47; Fax: +33 4 67 41 85 00; Email: gascuel{at}lirmm.fr
Received December 8, 2004. Accepted December 20, 2004.
PHYML Online is a web interface to PHYML, a software that implements a fast and accurate heuristic for estimating maximum likelihood phylogenies from DNA and protein sequences. This tool provides the user with a number of options, e.g. nonparametric bootstrap and estimation of various evolutionary parameters, in order to perform comprehensive phylogenetic analyses on large datasets in reasonable computing time. The server and its documentation are available at http://atgc.lirmm.fr/phyml.
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T. Nosenko, K. L. Lidie, F. M. Van Dolah, E. Lindquist, J.-F. Cheng, US Department of Energy-Joint Genome Institute, and D. Bhattacharya Chimeric Plastid Proteome in the Florida "Red Tide" Dinoflagellate Karenia brevis Mol. Biol. Evol., November 1, 2006; 23(11): 2026 - 2038. [Abstract] [Full Text] [PDF]
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T. A. Richards, J. B. Dacks, S. A. Campbell, J. L. Blanchard, P. G. Foster, R. McLeod, and C. W. Roberts Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot. Cell, September 1, 2006; 5(9): 1517 - 1531. [Abstract] [Full Text] [PDF]
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A M Tarrant, S R Greytak, G V Callard, and M E Hahn Estrogen receptor-related receptors in the killifish Fundulus heteroclitus: diversity, expression, and estrogen responsiveness. J. Mol. Endocrinol., August 1, 2006; 37(1): 105 - 120. [Abstract] [Full Text] [PDF]
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A. Shahsavarani, B. McNeill, F. Galvez, C. M. Wood, G. G. Goss, P.-P. Hwang, and S. F. Perry Characterization of a branchial epithelial calcium channel (ECaC) in freshwater rainbow trout (Oncorhynchus mykiss) J. Exp. Biol., May 15, 2006; 209(10): 1928 - 1943. [Abstract] [Full Text] [PDF]
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M. E. Schranz and T. Mitchell-Olds Independent Ancient Polyploidy Events in the Sister Families Brassicaceae and Cleomaceae PLANT CELL, May 1, 2006; 18(5): 1152 - 1165. [Abstract] [Full Text] [PDF]
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M. Salomao, X. An, X. Guo, W. B. Gratzer, N. Mohandas, and A. J. Baines Mammalian {alpha}I-spectrin is a neofunctionalized polypeptide adapted to small highly deformable erythrocytes PNAS, January 17, 2006; 103(3): 643 - 648. [Abstract] [Full Text] [PDF]
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P. Kosa, M. Valach, L. Tomaska, K. H. Wolfe, and J. Nosek Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants. Nucleic Acids Res., January 1, 2006; 34(8): 2472 - 2481. [Abstract] [Full Text] [PDF]
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