Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation
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Philippe Lemey | Guy Baele | Marc A Suchard | Paul Bastide | Mandev S Gill | Mandev S. Gill | M. Suchard | P. Lemey | G. Baele | P. Bastide | M. Gill
[1] S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .
[2] Alain Jean-Marie,et al. Markov-Modulated Markov Chains and the Covarion Process of Molecular Evolution , 2004, J. Comput. Biol..
[3] C. Viboud,et al. Explorer The genomic and epidemiological dynamics of human influenza A virus , 2016 .
[4] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[5] J. Huelsenbeck. Testing a covariotide model of DNA substitution. , 2002, Molecular biology and evolution.
[6] W. Fitch,et al. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution , 1970, Biochemical Genetics.
[7] Edward Susko,et al. PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis , 2009, BMC Evolutionary Biology.
[8] Z. Yang,et al. Among-site rate variation and its impact on phylogenetic analyses. , 1996, Trends in ecology & evolution.
[9] M. Suchard,et al. Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty. , 2016, Systematic biology.
[10] R. Murray,et al. The Family Deinococcaceae , 1992 .
[11] E. Holmes,et al. The evolution of base composition and phylogenetic inference. , 2000, Trends in ecology & evolution.
[12] Olivier Gascuel,et al. Modelling the Variability of Evolutionary Processes , 2007 .
[13] Carl E. Rasmussen,et al. Factorial Hidden Markov Models , 1997 .
[14] J. G. Burleigh,et al. Covarion structure in plastid genome evolution: a new statistical test. , 2005, Molecular biology and evolution.
[15] H. Kishino,et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.
[16] B. Ames,et al. Sunlight ultraviolet and bacterial DNA base ratios. , 1970, Science.
[17] Daniel L. Ayres,et al. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics , 2019, Systematic biology.
[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] Jan Irvahn,et al. Phylogenetic Stochastic Mapping , 2015 .
[20] Moshe Haviv,et al. Introduction to Markov Chains , 2013 .
[21] Ziheng Yang. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.
[22] Edward Susko,et al. Testing for covarion-like evolution in protein sequences. , 2007, Molecular biology and evolution.
[23] Ming-Hui Chen,et al. Choosing among Partition Models in Bayesian Phylogenetics , 2010, Molecular biology and evolution.
[24] Peter G Foster,et al. Modeling compositional heterogeneity. , 2004, Systematic biology.
[25] Guy Baele,et al. πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios , 2013, BMC Bioinformatics.
[26] Alexei J Drummond,et al. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. , 2006, Molecular biology and evolution.
[27] Esra Bas. An Introduction to Markov Chains , 2019 .
[28] M. Pagel,et al. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. , 2004, Systematic biology.
[29] M. Steel,et al. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. , 1998, Molecular biology and evolution.
[30] Guy Baele,et al. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST , 2017, Bioinform..
[31] Hervé Philippe,et al. A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests. , 2010, Molecular biology and evolution.
[32] Alexei J. Drummond,et al. Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments , 2012, Molecular biology and evolution.
[33] Thomas E. Stern,et al. Analysis of separable Markov-modulated rate models for information-handling systems , 1991, Advances in Applied Probability.
[34] H. Philippe,et al. Heterotachy, an important process of protein evolution. , 2002, Molecular biology and evolution.
[35] N. Galtier,et al. Maximum-likelihood phylogenetic analysis under a covarion-like model. , 2001, Molecular biology and evolution.
[36] Marc A. Suchard,et al. Many-core algorithms for statistical phylogenetics , 2009, Bioinform..
[37] Nicolas Lartillot,et al. A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution. , 2006, Molecular biology and evolution.
[38] S. Jeffery. Evolution of Protein Molecules , 1979 .
[39] R. H. Thomas,et al. Reduced thermophilic bias in the 16S rDNA sequence from Thermus ruber provides further support for a relationship between Thermus and Deinococcus , 1993 .
[40] Victor Y. Pan,et al. The complexity of the matrix eigenproblem , 1999, STOC '99.
[41] Michael D. Hendy,et al. Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution , 2001, Journal of Molecular Evolution.
[42] G. Serio,et al. A new method for calculating evolutionary substitution rates , 2005, Journal of Molecular Evolution.
[43] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[44] Wolfgang Fischer,et al. The Markov-Modulated Poisson Process (MMPP) Cookbook , 1993, Perform. Evaluation.
[45] Michael Worobey,et al. A synchronized global sweep of the internal genes of modern avian influenza virus , 2014, Nature.
[46] M. Steel,et al. Modeling the covarion hypothesis of nucleotide substitution. , 1998, Mathematical biosciences.
[47] Simon Whelan,et al. Spatial and temporal heterogeneity in nucleotide sequence evolution. , 2008, Molecular biology and evolution.
[48] Mike Steel,et al. Should phylogenetic models be trying to "fit an elephant"? , 2005, Trends in genetics : TIG.
[49] Xiang Ji,et al. A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast. , 2016, Molecular biology and evolution.
[50] Bernard W. Silverman,et al. The kernel method for multivariate data , 2018 .
[51] R. Nielsen. Mapping mutations on phylogenies. , 2002, Systematic biology.
[52] Vladimir N. Minin,et al. Phylogenetic Stochastic Mapping Without Matrix Exponentiation , 2014, J. Comput. Biol..
[53] M. Donoghue,et al. Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms. , 2013, Systematic biology.
[54] Daniel L. Ayres,et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.
[55] G. Yule,et al. A Mathematical Theory of Evolution Based on the Conclusions of Dr. J. C. Willis, F.R.S. , 1925 .