Bayesian phylogenetics : methods, algorithms, and applications /: methods, algorithms, and applications. (2014)

• Record Type: Book
• Further Information: Note: Edited by Ming-Hui Chen, Lynn Kuo and Paul O. Lewis.
• Other Names: Chen, Ming-Hui, 1961-; Kuo, Lynn, 1949-; Lewis, Paul O, 1961-
• Contents: Bayesian phylogenetics: methods, computational algorithms, and applications; Introduction; Overview Priors in Bayesian phylogenetics Ying Wang and Ziheng Yang ; Introduction; Estimation of distance between two sequences; Priors on model parameters in Bayesian phylogenetics; Priors on the tree topology; Priors on times and rates for estimation of divergence times; Summary IDR for marginal likelihood in Bayesian phylogenetics Serena Arima and Luca Tardella ; Introduction; Substitution models: a brief overview; Bayesian model choice; Computational tools for Bayesian model evidence; Marginal likelihood for phylogenetic data; Discussion Bayesian model selection in phylogenetics and genealogy-based population genetics Guy Baele and Philippe Lemey ; Introduction; Prior and posterior-based estimators; Path sampling approaches; Simulation study: uncorrelated relaxed clocks; Practical example on demographic Variable tree topology stepping-stone marginal likelihood estimation Mark T. Holder, Paul O. Lewis, David L. Swofford, and David Bryant ; Introduction; The generalized stepping-stone (GSS) method; Reference distribution for tree topology; Example; Summary; Funding; Acknowledgements Consistency of marginal likelihood estimation when topology varies Rui Wu, Ming-Hui Chen, Lynn Kuo, and Paul O. Lewis ; Introduction; Notation and definitions; Empirical example; Discussion; Funding; Acknowledgements Bayesian phylogeny analysis Sooyoung Cheon and Faming Liang ; Introduction; Bayesian phylogeny inference; Monte Carlo methods for Bayesian phylogeny inference; Summary Sequential Monte Carlo (SMC) for Bayesian phylogenetics Alexandre Bouchard-Côté ; Using phylogenetic SMC samplers; How phylogenetic SMC works; Extensions and implementation issues; Discussion Population model comparison using multi-locus datasets Michal Palczewski and Peter Beerli ; Introduction; Bayesian inference of independent loci; Model comparison using our independent marginal likelihood sampler; Conclusion Bayesian methods in the presence of recombination Mary K. Kuhner ; Introduction to non-treelike phylogenies; Describing the ARG; Inference of the ARG; Mechanics of sampling ARGs; Hazards of Bayesian inference in the presence of recombination; Directions for future research; Open questions; Conclusions Bayesian nonparametric phylodynamics Julia A. Palacios, Mandev S. Gill, Marc A. Suchard, and Vladimir N. Minin ; Introduction; General model formulation; Priors on effective population size trajectory; Examples; Extensions and future directions Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution Asger Hobolth and Jeffrey L. Thorne ; Introduction; Independent sites models and summary statistics; Dependent{site models and Markov chain Monte Carlo; Future directions for sequence paths with dependence models Bayesian inference of species divergence times Tracy A. Heath and Brian R. Moore ; Introduction; Priors on branch rates; Priors on node times; Priors for calibrating divergence times; Practical issues for estimating divergence times; Summary and prospectus Index
• Publisher Details: Boca Raton : CRC Presss, an imprint of the Taylor & Francis Group
• Publication Date: 2014
• Extent: 1 online resource
• Subjects: 576.8/8; Phylogeny; Biometry; Molecular genetics; Bayesian statistical decision theory; Bayesian statistical decision theory; Biometry; Molecular genetics; Phylogeny
• Languages: English
• ISBNs: 9781466500822; 1466500824
• Related ISBNs: 9781466500792; 1466500794
• Notes: Note: Includes bibliographical references.; Note: Print version record.; Note: Online resource; title from digital title page (viewed on June 23, 2014).
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