Bayesian Phylogenetics
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Bayesian Phylogenetics
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Author : Ming-Hui Chen
language : en
Publisher: CRC Press
Release Date : 2014-05-27
Bayesian Phylogenetics written by Ming-Hui Chen and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-05-27 with Mathematics categories.
Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of c
Bayesian Phylogenetics
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Author : Ming-Hui Chen
language : en
Publisher:
Release Date : 2015-01-01
Bayesian Phylogenetics written by Ming-Hui Chen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-01-01 with categories.
Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.
Bayesian Phylogenetics
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Author : Ming-Hui Chen
language : en
Publisher:
Release Date : 2014
Bayesian Phylogenetics written by Ming-Hui Chen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Bayesian statistical decision theory categories.
Bayesian Phylogenetics
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Author : Ming-Hui Chen
language : en
Publisher: CRC Press
Release Date : 2014-05-27
Bayesian Phylogenetics written by Ming-Hui Chen and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-05-27 with Mathematics categories.
Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.
Bayesian Phylogenetics
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Author : Ming-Hui Chen
language : en
Publisher: Chapman & Hall/CRC
Release Date : 2022-06
Bayesian Phylogenetics written by Ming-Hui Chen and has been published by Chapman & Hall/CRC this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-06 with categories.
Suitable for graduate-level researchers in statistics and biology, this book presents a snapshot of current trends in Bayesian phylogenetic research. It emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. The book discusses new approaches to improve mixing in Bayesian phylogenetic analyses in whi
Bayesian Evolutionary Analysis With Beast
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Author : Alexei J. Drummond
language : en
Publisher: Cambridge University Press
Release Date : 2015-08-06
Bayesian Evolutionary Analysis With Beast written by Alexei J. Drummond and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-08-06 with Computers categories.
Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.
Elucidating The Re Emergence Of Human Pathogens With Bayesian Phylogenetics
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Author : Luis Roger Esquivel Gómez
language : de
Publisher:
Release Date : 2024*
Elucidating The Re Emergence Of Human Pathogens With Bayesian Phylogenetics written by Luis Roger Esquivel Gómez and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024* with categories.
The (re-)emergence of an infectious disease is a complex phenomenon that requires the interplay of multiple factors involving the pathogen (e.g. virulence, transmissibility, immune scape capacity), host species (e.g. population size, mobility, immunity level) and the environment (e.g. climatic conditions, hygiene conditions). In the manuscripts included in this thesis, I employed Bayesian phylogenetic models to elucidate the (re-)emergence of three human pathogens that occurred under different conditions and at distinct time points. At the start of the timeline, represented by the analyzed datasets, I investigated, in manuscript C, the emergence of human-adapted Salmonella enterica enterica serovars and its connection to animal domestication, by performing a molecular dating analysis using modern samples and ancient genomes up to 5500 years old. Moving forward in the timeline, in Manuscript A, I studied the migration dynamics of the bacterium Yersinia pestis in Madagascar to elucidate the factors that led to the re-emergence of plague in the city of Mahajanga during the 1990s. Lastly, in Manuscript B, I performed a recombination-aware phylogenetic analysis to clarify the role of genetic recombination in the emergence of SARS-CoV-2, the latest human pathogen to cause a severe pandemic, which started in 2019. Altogether the three manuscripts provide new knowledge about the (re-)emergence of viral and bacterial pathogens that have left an indelible mark on human history. Furthermore, I showed that Bayesian phylogenetic models can be applied to perform molecular dating analyses of datasets with very different time windows and to disentangle the role of pathogens mobility and recombination on disease (re-) emergence.
Understanding The Tripartite Approach To Bayesian Divergence Time Estimation
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Author : Rachel C. M. Warnock
language : en
Publisher: Cambridge University Press
Release Date : 2021-02-04
Understanding The Tripartite Approach To Bayesian Divergence Time Estimation written by Rachel C. M. Warnock and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-02-04 with Science categories.
Placing evolutionary events in the context of geological time is a fundamental goal in paleobiology and macroevolution. In this Element we describe the tripartite model used for Bayesian estimation of time calibrated phylogenetic trees. The model can be readily separated into its component models: the substitution model, the clock model and the tree model. We provide an overview of the most widely used models for each component and highlight the advantages of implementing the tripartite model within a Bayesian framework.
Phylogenetics
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Author : E. O. Wiley
language : en
Publisher: John Wiley & Sons
Release Date : 2011-06-07
Phylogenetics written by E. O. Wiley and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-06-07 with Science categories.
The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.
The Phylogenetic Handbook
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Author : Philippe Lemey
language : en
Publisher: Cambridge University Press
Release Date : 2009-03-26
The Phylogenetic Handbook written by Philippe Lemey and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-03-26 with Science categories.
The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.