Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences
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Guy Baele | Stijn Vansteelandt | Yves Van de Peer | S. Vansteelandt | Y. van de Peer | G. Baele | Y. Van de Peer
[1] Christopher B. Burge,et al. DNA Sequence Evolution with Neighbor-Dependent Mutation , 2003, J. Comput. Biol..
[2] Eric D Green,et al. Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons. , 2006, Trends in genetics : TIG.
[3] J. Schafer,et al. Analysis of Incomplete Multivariate Data (Monographs on Statistics and Applied Probability, No. 72) , 2000 .
[4] D. Penny. Inferring Phylogenies.—Joseph Felsenstein. 2003. Sinauer Associates, Sunderland, Massachusetts. , 2004 .
[5] J. L. Jensen,et al. Probabilistic models of DNA sequence evolution with context dependent rates of substitution , 2000, Advances in Applied Probability.
[6] H. Philippe,et al. Assessing site-interdependent phylogenetic models of sequence evolution. , 2006, Molecular biology and evolution.
[7] C. H. Edwards,et al. Calculus with analytic geometry , 1994 .
[8] ben-Avraham,et al. Mean-field (n,m)-cluster approximation for lattice models. , 1992, Physical review. A, Atomic, molecular, and optical physics.
[9] Wanjun Gu,et al. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. , 2010, Molecular biology and evolution.
[10] Ziheng Yang. Estimating the pattern of nucleotide substitution , 1994, Journal of Molecular Evolution.
[11] K. J. Fryxell,et al. Cytosine deamination plays a primary role in the evolution of mammalian isochores. , 2000, Molecular biology and evolution.
[12] David T. Jones,et al. Protein evolution with dependence among codons due to tertiary structure. , 2003, Molecular biology and evolution.
[13] Jonathan P. Bollback,et al. Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.
[14] Mark Holder,et al. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. , 2004, Systematic biology.
[15] Mike Steel,et al. Should phylogenetic models be trying to "fit an elephant"? , 2005, Trends in genetics : TIG.
[16] G. Serio,et al. A new method for calculating evolutionary substitution rates , 2005, Journal of Molecular Evolution.
[17] B. Blaisdell,et al. Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding , 1985, Journal of Molecular Evolution.
[18] Michael T. Clegg,et al. Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome , 1995, Journal of Molecular Evolution.
[19] P. Green,et al. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[20] H. Philippe,et al. Computing Bayes factors using thermodynamic integration. , 2006, Systematic biology.
[21] Sylvia Richardson,et al. Markov Chain Monte Carlo in Practice , 1997 .
[22] W. Salser. Globin mRNA sequences: analysis of base pairing and evolutionary implications. , 1978, Cold Spring Harbor symposia on quantitative biology.
[23] B. Morton,et al. Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[24] G. G. Altman,et al. A search for patterns in the nucleotide sequence of the MS2 genome , 1979 .
[25] D. Haussler,et al. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. , 2003, Molecular biology and evolution.
[26] M. Clegg,et al. The Influence of Specific Neighboring Bases on Substitution Bias in Noncoding Regions of the Plant Chloroplast Genome , 1997, Journal of Molecular Evolution.
[27] W. Wong,et al. The calculation of posterior distributions by data augmentation , 1987 .
[28] P. Green,et al. Transcription-associated mutational asymmetry in mammalian evolution , 2003, Nature Genetics.
[29] B. Morton. The Influence of Neighboring Base Composition on Substitutions in Plant Chloroplast Coding Sequences , 1997 .
[30] Ziheng Yang,et al. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. , 2008, Molecular biology and evolution.
[31] Guy Baele,et al. A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. , 2008, Systematic biology.
[32] Guy Baele,et al. Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences , 2009, BMC Evolutionary Biology.
[33] Hervé Philippe,et al. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles , 2010, Proceedings of the National Academy of Sciences.