Evidence for an episodic model of protein sequence evolution.
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[1] R. Nielsen,et al. Patterns of Positive Selection in Six Mammalian Genomes , 2008, PLoS genetics.
[2] Asger Hobolth,et al. Comparative analysis of protein coding sequences from human, mouse and the domesticated pig , 2005, BMC Biology.
[3] Xun Gu,et al. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family , 2002, Bioinform..
[4] Adi Stern,et al. Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes , 2008, PLoS Comput. Biol..
[5] D. Liberles,et al. The quest for natural selection in the age of comparative genomics , 2007, Heredity.
[6] Gerard Talavera,et al. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.
[7] Wei Qian,et al. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.
[8] Julien Dutheil,et al. Detecting groups of coevolving positions in a molecule: a clustering approach , 2007, BMC Evolutionary Biology.
[9] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[10] Jianzhi Zhang,et al. Frequent false detection of positive selection by the likelihood method with branch-site models. , 2004, Molecular biology and evolution.
[11] Flavien Russier,et al. Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. , 2008, Molecular biology and evolution.
[12] Marie Sémon,et al. Consequences of genome duplication. , 2007, Current opinion in genetics & development.
[13] P. Phillips,et al. Relaxed Selection Among Duplicate Floral Regulatory Genes in Lamiales , 2006, Journal of Molecular Evolution.
[14] Tal Pupko,et al. A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[15] Ziheng Yang,et al. Computational Molecular Evolution , 2006 .
[16] R. Nielsen,et al. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. , 2002, Molecular biology and evolution.
[17] Jianzhi Zhang,et al. More genes underwent positive selection in chimpanzee evolution than in human evolution , 2007, Proceedings of the National Academy of Sciences.
[18] Stéphane Guindon,et al. Modeling the site-specific variation of selection patterns along lineages. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[19] M. Suchard,et al. Alignment Uncertainty and Genomic Analysis , 2008, Science.
[20] Ziheng Yang,et al. The power of phylogenetic comparison in revealing protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[21] Jörg Schultz,et al. Variation in structural location and amino acid conservation of functional sites in protein domain families , 2005, BMC Bioinformatics.
[22] C. Seoighe,et al. Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. , 2003, Molecular biology and evolution.
[23] Mario A. Fares,et al. CAPS: coevolution analysis using protein sequences , 2006, Bioinform..
[24] Hervé Philippe,et al. Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. , 2003, Molecular biology and evolution.
[25] H. Philippe,et al. Heterotachy and Functional Shift in Protein Evolution , 2003, IUBMB life.
[26] Mario A. Fares,et al. Why Should We Care About Molecular Coevolution? , 2008, Evolutionary bioinformatics online.
[27] Ziheng Yang,et al. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. , 2002, Molecular biology and evolution.
[28] J. Gillespie. The causes of molecular evolution , 1991 .
[29] Peter Andolfatto,et al. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. , 2007, Genome research.
[30] Xun Gu,et al. A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. , 2006, Molecular biology and evolution.
[31] P. Sanseau,et al. Drug discovery and computational evolutionary analysis. , 2007, Drug discovery today.
[32] Sébastien Moretti,et al. Selectome: a database of positive selection , 2008, Nucleic Acids Res..
[33] L. Duret,et al. Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. , 2008, Genome research.
[34] Joaquín Dopazo,et al. Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome , 2006, PLoS Comput. Biol..
[35] A. Meyer,et al. Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. , 2006, Molecular biology and evolution.
[36] T. Pupko,et al. Airing the word on pollution. , 1996, Environmental health perspectives.
[37] X. Gu,et al. Statistical methods for testing functional divergence after gene duplication. , 1999, Molecular biology and evolution.
[38] Kenneth H. Wolfe,et al. Turning a hobby into a job: How duplicated genes find new functions , 2008, Nature Reviews Genetics.
[39] E. Record,et al. Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family , 2006, BMC Evolutionary Biology.
[40] R. Nielsen,et al. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. , 2005, Molecular biology and evolution.
[41] Elisabeth R. M. Tillier,et al. The accuracy of several multiple sequence alignment programs for proteins , 2006, BMC Bioinformatics.
[42] Richard D Emes,et al. The role of positive selection in determining the molecular cause of species differences in disease , 2008, BMC Evolutionary Biology.
[43] Maria Anisimova,et al. Investigating protein-coding sequence evolution with probabilistic codon substitution models. , 2009, Molecular biology and evolution.
[44] John D. Storey,et al. Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[45] Z. Yang,et al. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. , 1998, Molecular biology and evolution.
[46] Lawrence P. Wackett,et al. Melamine Deaminase and Atrazine Chlorohydrolase: 98 Percent Identical but Functionally Different , 2001, Journal of bacteriology.
[47] Adam Eyre-Walker,et al. The genomic rate of adaptive evolution. , 2006, Trends in ecology & evolution.
[48] Julien Dutheil,et al. Detecting Site-Specific Biochemical Constraints Through Substitution Mapping , 2008, Journal of Molecular Evolution.
[49] Richard J. Edwards,et al. BADASP: predicting functional specificity in protein families using ancestral sequences , 2005, Bioinform..
[50] Mark D. Adams,et al. Human PAML browser: a database of positive selection on human genes using phylogenetic methods , 2007, Nucleic Acids Res..
[51] V. Laudet,et al. Fast Evolution of Interleukin-2 in Mammals and Positive Selection in Ruminants , 2000, Journal of Molecular Evolution.
[52] D. McNally,et al. In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae , 2007, BMC Evolutionary Biology.
[53] D. Liberles. Ancestral sequence reconstruction , 2007 .