Modeling the site-specific variation of selection patterns along lineages.
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Stéphane Guindon | John P Huelsenbeck | Allen G Rodrigo | A. Rodrigo | J. Huelsenbeck | S. Guindon | K. Dyer | Kelly A Dyer | Stéphane Guindon
[1] D. Haydon,et al. Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates. , 2001, Genetics.
[2] B. Bainbridge,et al. Genetics , 1981, Experientia.
[3] Ziheng Yang. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.
[4] N. Goldman,et al. A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.
[5] J. Margolick,et al. Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection , 1999, Journal of Virology.
[6] Allen G. Rodrigo,et al. Immune-Mediated Positive Selection Drives Human Immunodeficiency Virus Type 1 Molecular Variation and Predicts Disease Duration , 2002, Journal of Virology.
[7] P. Sharp,et al. In search of molecular darwinism , 1997, Nature.
[8] Allen G. Rodrigo,et al. Computational and Evolutionary Analysis of HIV Molecular Sequences , 2001, Springer US.
[9] K. Liang,et al. Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions , 1987 .
[10] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.
[11] T. Ota,et al. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. , 1995, Molecular biology and evolution.
[12] M. Nei,et al. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection , 1988, Nature.
[13] M. Nei,et al. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.
[14] T. Ohta. Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication. , 1993, Genetics.
[15] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[16] W. Messier,et al. Episodic adaptive evolution of primate lysozymes , 1997, Nature.
[17] C. Luo,et al. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. , 1985, Molecular biology and evolution.
[18] J. Huelsenbeck,et al. Bayesian Estimation of Positively Selected Sites , 2004, Journal of Molecular Evolution.
[19] Ziheng Yang,et al. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[20] K. Crandall,et al. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. , 1999, Molecular biology and evolution.
[21] M. Steel,et al. Modeling the covarion hypothesis of nucleotide substitution. , 1998, Mathematical biosciences.
[22] Roald Forsberg,et al. A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. , 2003, Molecular biology and evolution.
[23] R. Nielsen,et al. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. , 2002, Molecular biology and evolution.
[24] Z. Yang,et al. Positive and negative selection in the DAZ gene family. , 2001, Molecular biology and evolution.
[25] N. Goldman,et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. , 2000, Genetics.
[26] Richard A. Goldstein,et al. Probabilistic reconstruction of ancestral protein sequences , 1996, Journal of Molecular Evolution.
[27] Z. Yang,et al. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.
[28] S. Yokoyama,et al. ADAPTIVE EVOLUTION OF PHOTORECEPTORS AND VISUAL PIGMENTS IN VERTEBRATES , 1996 .
[29] F. Ayala,et al. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[30] M. Adams,et al. Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios , 2003, Science.
[31] R. Nielsen,et al. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. , 1998, Genetics.