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Author : Alexei J. Drummond,Remco R. Bouckaert
Publisher : Cambridge University Press
Page : 263 pages
File Size : 54,6 Mb
Release : 2015-08-06
Category : Computers
ISBN : 9781107019652
Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.
Author : Alexei J. Drummond,Remco R. Bouckaert
Publisher : Cambridge University Press
Page : 263 pages
File Size : 50,7 Mb
Release : 2015-08-06
Category : Science
ISBN : 9781316298343
What are the models used in phylogenetic analysis and what exactly is involved in Bayesian evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you choose and apply these models, which parameterisations and priors make sense, and how can you diagnose Bayesian MCMC when things go wrong? These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. This practical guide: • Addresses the theoretical aspects of the field • Advises on how to prepare and perform phylogenetic analysis • Helps with interpreting analyses and visualisation of phylogenies • Describes the software architecture • Helps developing BEAST 2.2 extensions to allow these models to be extended further. With an accompanying website providing example files and tutorials (http://beast2.org/), this one-stop reference to applying the latest phylogenetic models in BEAST 2 will provide essential guidance for all users – from those using phylogenetic tools, to computational biologists and Bayesian statisticians.
Author : Ming-Hui Chen,Lynn Kuo,Paul O. Lewis
Publisher : CRC Press
Page : 398 pages
File Size : 55,5 Mb
Release : 2014-05-27
Category : Mathematics
ISBN : 9781466500792
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.
Author : Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
Publisher : Cambridge University Press
Page : 750 pages
File Size : 49,8 Mb
Release : 2009-03-26
Category : Science
ISBN : 9780521877107
A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Author : Ziheng Yang
Publisher : Oxford University Press
Page : 374 pages
File Size : 45,5 Mb
Release : 2006-10-05
Category : Medical
ISBN : 9780198566991
This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
Author : John C. Avise
Publisher : Cambridge University Press
Page : 17 pages
File Size : 53,8 Mb
Release : 2006-05-04
Category : Science
ISBN : 9781139455039
Reconstructing phylogenetic trees from DNA sequences has become a popular exercise in many branches of biology, and here the well-known geneticist John Avise explains why. Molecular phylogenies provide a genealogical backdrop for interpreting the evolutionary histories of many other types of biological traits (anatomical, behavioral, ecological, physiological, biochemical and even geographical). Guiding readers on a natural history tour along dozens of evolutionary pathways, the author describes how creatures ranging from microbes to elephants came to possess their current phenotypes. Essential reading for college students, professional biologists and anyone interested in natural history and biodiversity, this book is packed with fascinating examples of evolutionary puzzles from across the animal kingdom; how the toucan got its enormous bill, how reptiles grow back lost limbs and why Arctic fish don't freeze.
Author : Andreas Dress
Publisher : Cambridge University Press
Page : 277 pages
File Size : 46,5 Mb
Release : 2012
Category : Mathematics
ISBN : 9780521768320
The first book to systematically introduce the emerging area of phylogenetic combinatorics.
Author : Maria Anisimova
Publisher : Unknown
Page : 128 pages
File Size : 47,9 Mb
Release : 2012
Category : Evolutionary genetics
ISBN : 1617795828
Author : Marco Salemi,Anne-Mieke Vandamme
Publisher : Cambridge University Press
Page : 456 pages
File Size : 51,7 Mb
Release : 2003-08-27
Category : Computers
ISBN : 052180390X
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Author : Ziheng Yang
Publisher : Oxford University Press
Page : 509 pages
File Size : 46,6 Mb
Release : 2014
Category : Science
ISBN : 9780199602605
This book presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. The book offers numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative.
Author : Anna Marie Prentiss
Publisher : Springer
Page : 443 pages
File Size : 48,9 Mb
Release : 2019-06-03
Category : Social Science
ISBN : 9783030111175
Evolutionary Research in Archaeology seeks to provide a comprehensive overview of contemporary evolutionary research in archaeology. The book will provide a single source for introduction and overview of basic and advanced evolutionary concepts and research programs in archaeology. Content will be organized around four areas of critical research including microevolutionary and macroevolutionary process, human ecology studies (evolutionary ecology, demography, and niche construction), and evolutionary cognitive archaeology. Authors of individual chapters will address theoretical foundations, history of research, contemporary contributions and debates, and implications for the future for their respective topics. As appropriate, authors present or discuss short empirical case studies to illustrate key arguments.
Author : Olivier Gascuel
Publisher : OUP Oxford
Page : 444 pages
File Size : 51,6 Mb
Release : 2005-02-24
Category : Mathematics
ISBN : 0191513733
This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.
Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 221 pages
File Size : 40,8 Mb
Release : 2006-11-25
Category : Science
ISBN : 9780387351001
This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
Author : Guangchuang Yu
Publisher : Unknown
Page : 128 pages
File Size : 50,9 Mb
Release : 2022
Category : Phylogeny
ISBN : 1032245549
"Data Integration, Manipulation and Visualization of Phylogenetic Trees introduces and demonstrates data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio, ggtree and ggtreeExtra. Using the most comprehensive packages for phylogenetic data integration and visualization, contains numerous examples that can be used for teaching and learning. Ideal for undergraduate readers and researchers with a working knowledge of R and ggplot2"--
Author : S. Blair Hedges,Sudhir Kumar
Publisher : OUP Oxford
Page : 1237 pages
File Size : 53,9 Mb
Release : 2009-04-23
Category : Science
ISBN : 9780191608988
The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrialimpacts, and other features.The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routineestimation and utilization of these so-called 'time-trees' could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). Theycould help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology.This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects ofthe evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included. The book is complemented by an online database(www.timetree.net) which allows researchers to both deposit and retrieve data.