Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(5):676-679; doi:10.1093/bioinformatics/bti079
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HyPhy: hypothesis testing using phylogenies
1 Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
2 Bioinformatics Research Center, North Carolina State University Raleigh NC 27695-7566, USA
*To whom correspondence should be addressed.
Summary: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.
Availability: http://www.hyphy.org
Contact: muse{at}stat.ncsu.edu
Supplementary information: HyPhydocumentation and tutorials are available at http://www.hyphy.org
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R. A. Zufall, C. L. McGrath, S. V. Muse, and L. A. Katz Genome Architecture Drives Protein Evolution in Ciliates Mol. Biol. Evol., September 1, 2006; 23(9): 1681 - 1687. [Abstract] [Full Text] [PDF]
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L. M. Turner and H. E. Hoekstra Adaptive Evolution of Fertilization Proteins within a Genus: Variation in ZP2 and ZP3 in Deer Mice (Peromyscus) Mol. Biol. Evol., September 1, 2006; 23(9): 1656 - 1669. [Abstract] [Full Text] [PDF]
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M. Tapio, N. Marzanov, M. Ozerov, M. Cinkulov, G. Gonzarenko, T. Kiselyova, M. Murawski, H. Viinalass, and J. Kantanen Sheep Mitochondrial DNA Variation in European, Caucasian, and Central Asian Areas Mol. Biol. Evol., September 1, 2006; 23(9): 1776 - 1783. [Abstract] [Full Text] [PDF]
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A. S. Mikheyev, U. G. Mueller, and P. Abbot Cryptic sex and many-to-one coevolution in the fungus-growing ant symbiosis PNAS, July 11, 2006; 103(28): 10702 - 10706. [Abstract] [Full Text] [PDF]
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 E. Schuettpelz and K. M. Pryer Reconciling Extreme Branch Length Differences: Decoupling Time and Rate through the Evolutionary History of Filmy Ferns Syst Biol, June 1, 2006; 55(3): 485 - 502. [Abstract] [Full Text] [PDF]
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I. Braasch, W. Salzburger, and A. Meyer Asymmetric Evolution in Two Fish-Specifically Duplicated Receptor Tyrosine Kinase Paralogons Involved in Teleost Coloration Mol. Biol. Evol., June 1, 2006; 23(6): 1192 - 1202. [Abstract] [Full Text] [PDF]
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B. Wrobel, M. Torres-Puente, N. Jimenez, M. A. Bracho, I. Garcia-Robles, A. Moya, and F. Gonzalez-Candelas Analysis of the Overdispersed Clock in the Short-Term Evolution of Hepatitis C Virus: Using the E1/E2 Gene Sequences to Infer Infection Dates in a Single Source Outbreak Mol. Biol. Evol., June 1, 2006; 23(6): 1242 - 1253. [Abstract] [Full Text] [PDF]
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J. Kusumi, A. Sato, and H. Tachida Relaxation of Functional Constraint on Light-Independent Protochlorophyllide Oxidoreductase in Thuja Mol. Biol. Evol., May 1, 2006; 23(5): 941 - 948. [Abstract] [Full Text] [PDF]
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Y.-J. Won, Y. Wang, A. Sivasundar, J. Raincrow, and J. Hey Nuclear Gene Variation and Molecular Dating of the Cichlid Species Flock of Lake Malawi Mol. Biol. Evol., April 1, 2006; 23(4): 828 - 837. [Abstract] [Full Text] [PDF]
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T. Gesell and A. von Haeseler In silico sequence evolution with site-specific interactions along phylogenetic trees Bioinformatics, March 15, 2006; 22(6): 716 - 722. [Abstract] [Full Text] [PDF]
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M. S. Bulmer and R. H. Crozier Variation in Positive Selection in Termite GNBPs and Relish Mol. Biol. Evol., February 1, 2006; 23(2): 317 - 326. [Abstract] [Full Text] [PDF]
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K. D. Crow, P. F. Stadler, V. J. Lynch, C. Amemiya, and G. P. Wagner The "Fish-Specific" Hox Cluster Duplication Is Coincident with the Origin of Teleosts Mol. Biol. Evol., January 1, 2006; 23(1): 121 - 136. [Abstract] [Full Text] [PDF]
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S. D. W. Frost, T. Wrin, D. M. Smith, S. L. K. Pond, Y. Liu, E. Paxinos, C. Chappey, J. Galovich, J. Beauchaine, C. J. Petropoulos, et al. Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection PNAS, December 20, 2005; 102(51): 18514 - 18519. [Abstract] [Full Text] [PDF]
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M. Mondragon-Palomino and B. S. Gaut Gene Conversion and the Evolution of Three Leucine-Rich Repeat Gene Families in Arabidopsis thaliana Mol. Biol. Evol., December 1, 2005; 22(12): 2444 - 2456. [Abstract] [Full Text] [PDF]
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F. Ren, H. Tanaka, and Z. Yang An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction Syst Biol, October 1, 2005; 54(5): 808 - 818. [Abstract] [Full Text] [PDF]
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Y.-L. Guo and S. Ge Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes Am. J. Botany, September 1, 2005; 92(9): 1548 - 1558. [Abstract] [Full Text] [PDF]
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C. T. T. Edwards, K. J. Pfafferott, P. J. R. Goulder, R. E. Phillips, and E. C. Holmes Intrapatient Escape in the A*0201-Restricted Epitope SLYNTVATL Drives Evolution of Human Immunodeficiency Virus Type 1 at the Population Level J. Virol., July 15, 2005; 79(14): 9363 - 9366. [Abstract] [Full Text] [PDF]
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S. L. Kosakovsky Pond and S. D. W. Frost Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection Mol. Biol. Evol., May 1, 2005; 22(5): 1208 - 1222. [Abstract] [Full Text] [PDF]
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