Phylogenetics

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Phylogenetics

Author : E. O. Wiley
Publisher : John Wiley & Sons
ISBN 13 : 0470905964
Total Pages : 444 pages
Book Rating : 4.4/5 (79 download)

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Book Synopsis Phylogenetics by : E. O. Wiley

Download or read book Phylogenetics written by E. O. Wiley and published by John Wiley & Sons. This book was released on 2011-06-07 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Analysis of Phylogenetics and Evolution with R

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
ISBN 13 : 0387351000
Total Pages : 221 pages
Book Rating : 4.3/5 (873 download)

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Book Synopsis Analysis of Phylogenetics and Evolution with R by : Emmanuel Paradis

Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Phylogenetics

Author : Charles Semple
Publisher : Oxford University Press on Demand
ISBN 13 : 9780198509424
Total Pages : 258 pages
Book Rating : 4.5/5 (94 download)

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Book Synopsis Phylogenetics by : Charles Semple

Download or read book Phylogenetics written by Charles Semple and published by Oxford University Press on Demand. This book was released on 2003 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: 'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics. It is a flourishing area of intereaction between mathematics, statistics, computer science and biology.The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species. However, the methods are also relevant to a diverse range of fields including epidemiology, ecology, medicine, as well as linguistics and cognitive psychologyThis graduate-level book, based on the authors lectures at The University of Canterbury, New Zealand, focuses on the mathematical aspects of phylogenetics. It brings together the central results of the field (providing proofs of the main theorem), outlines their biological significance,and indicateshow algorithms may be derived. The presentation is self-contained and relies on discrete mathematics with some probability theory. A set of exercises and at least one specialist topic ends each chapter.This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics.'Phylogenetics' in the 24th volume in the Oxford Lecture Series in Mathematics and its Applications. This series contains short books suitable for graduate students and researchers who want a well-written account of mathematics that is fundamental to current to research. The series emphasises futuredirections of research and focuses on genuine applications of mathematics to finance, engineering and the physical and biological sciences.

Molecular Evolution and Phylogenetics

Author : Masatoshi Nei
Publisher : Oxford University Press
ISBN 13 : 0199881227
Total Pages : 352 pages
Book Rating : 4.1/5 (998 download)

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Book Synopsis Molecular Evolution and Phylogenetics by : Masatoshi Nei

Download or read book Molecular Evolution and Phylogenetics written by Masatoshi Nei and published by Oxford University Press. This book was released on 2000-07-27 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

Bayesian Phylogenetics

Author : Ming-Hui Chen
Publisher : CRC Press
ISBN 13 : 1466500794
Total Pages : 398 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Bayesian Phylogenetics by : Ming-Hui Chen

Download or read book Bayesian Phylogenetics written by Ming-Hui Chen and published by CRC Press. This book was released on 2014-05-27 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

The Phylogenetic Handbook

Author : Marco Salemi
Publisher : Cambridge University Press
ISBN 13 : 0521877105
Total Pages : 750 pages
Book Rating : 4.5/5 (218 download)

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Book Synopsis The Phylogenetic Handbook by : Marco Salemi

Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Computational Phylogenetics

Author : Tandy Warnow
Publisher : Cambridge University Press
ISBN 13 : 1107184711
Total Pages : 399 pages
Book Rating : 4.1/5 (71 download)

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Book Synopsis Computational Phylogenetics by : Tandy Warnow

Download or read book Computational Phylogenetics written by Tandy Warnow and published by Cambridge University Press. This book was released on 2017-11-02 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.

Tree Thinking: An Introduction to Phylogenetic Biology

Author : David A. Baum
Publisher : Roberts
ISBN 13 : 9781936221165
Total Pages : 0 pages
Book Rating : 4.2/5 (211 download)

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Book Synopsis Tree Thinking: An Introduction to Phylogenetic Biology by : David A. Baum

Download or read book Tree Thinking: An Introduction to Phylogenetic Biology written by David A. Baum and published by Roberts. This book was released on 2012-08-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.” However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives. Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.

A Mathematical Primer of Molecular Phylogenetics

Author : Xuhua Xia
Publisher : CRC Press
ISBN 13 : 0429759312
Total Pages : 366 pages
Book Rating : 4.4/5 (297 download)

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Book Synopsis A Mathematical Primer of Molecular Phylogenetics by : Xuhua Xia

Download or read book A Mathematical Primer of Molecular Phylogenetics written by Xuhua Xia and published by CRC Press. This book was released on 2020-04-13 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, A Mathematical Primer of Molecular Phylogenetics, offers a unique perspective on a number of phylogenetic issues that have not been covered in detail in previous publications. The volume provides sufficient mathematical background for young mathematicians and computational scientists, as well as mathematically inclined biology students, to make a smooth entry into the expanding field of molecular phylogenetics. The book will also provide sufficient details for researchers in phylogenetics to understand the workings of existing software packages used. The volume offers comprehensive but detailed numerical illustrations to render difficult mathematical and computational concepts in molecular phylogenetics accessible to a variety of readers with different academic background. The text includes examples of solved problems after each chapter, which will be particularly helpful for fourth-year undergraduates, postgraduates, and postdoctoral students in biology, mathematics and computer sciences. Researchers in molecular biology and evolution will find it very informative as well.

Bioinformatics and Phylogenetics

Author : Tandy Warnow
Publisher : Springer
ISBN 13 : 3030108376
Total Pages : 410 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Bioinformatics and Phylogenetics by : Tandy Warnow

Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.

An Introduction to Molecular Evolution and Phylogenetics

Author : Lindell Bromham
Publisher : Oxford University Press
ISBN 13 : 0191070696
Total Pages : 479 pages
Book Rating : 4.1/5 (91 download)

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Book Synopsis An Introduction to Molecular Evolution and Phylogenetics by : Lindell Bromham

Download or read book An Introduction to Molecular Evolution and Phylogenetics written by Lindell Bromham and published by Oxford University Press. This book was released on 2016-10-14 with total page 479 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA can be extracted and sequenced from a diverse range of biological samples, providing a vast amount of information about evolution and ecology. The analysis of DNA sequences contributes to evolutionary biology at all levels, from dating the origin of the biological kingdoms to untangling family relationships. An Introduction to Molecular Evolution and Phylogenetics presents the fundamental concepts and intellectual tools you need to understand how the genome records information about evolutionary past and processes, how that information can be "read", and what kinds of questions we can use that information to answer. Starting with evolutionary principles, and illustrated throughout with biological examples, it is the perfect starting point on the journey to an understanding of the way molecular data is used in modern biology. Online Resource Centre The Online Resource Centre features: For registered adopters of the book: - Class plans for one-hour hands-on sessions associated with each chapter - Figures from the textbook to view and download

Phylogenetic Systematics

Author : Olivier Rieppel
Publisher : CRC Press
ISBN 13 : 1138032158
Total Pages : 514 pages
Book Rating : 4.1/5 (38 download)

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Book Synopsis Phylogenetic Systematics by : Olivier Rieppel

Download or read book Phylogenetic Systematics written by Olivier Rieppel and published by CRC Press. This book was released on 2016-07-06 with total page 514 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetic Systematics: Haeckel to Hennig traces the development of phylogenetic systematics against the foil of idealistic morphology through 100 years of German biology. It starts with the iconic Ernst Haeckel-the German Darwin from Jena-and the evolutionary morphology he developed. It ends with Willi Hennig, the founder of modern phylogenetic

Molecular Evolution

Author : Roderick D.M. Page
Publisher : John Wiley & Sons
ISBN 13 : 1444313363
Total Pages : 352 pages
Book Rating : 4.4/5 (443 download)

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Book Synopsis Molecular Evolution by : Roderick D.M. Page

Download or read book Molecular Evolution written by Roderick D.M. Page and published by John Wiley & Sons. This book was released on 2009-07-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Author : László Zsolt Garamszegi
Publisher : Springer
ISBN 13 : 3662435500
Total Pages : 552 pages
Book Rating : 4.6/5 (624 download)

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Book Synopsis Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology by : László Zsolt Garamszegi

Download or read book Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology written by László Zsolt Garamszegi and published by Springer. This book was released on 2014-07-29 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.

Phylogenetic Systematics

Author : Willi Hennig
Publisher : University of Illinois Press
ISBN 13 : 9780252068140
Total Pages : 284 pages
Book Rating : 4.0/5 (681 download)

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Book Synopsis Phylogenetic Systematics by : Willi Hennig

Download or read book Phylogenetic Systematics written by Willi Hennig and published by University of Illinois Press. This book was released on 1999 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetic Systematics, first published in 1966, marks a turning point in the history of systematic biology. Willi Hennig's influential synthetic work, arguing for the primacy of the phylogenetic system as the general reference system in biology, generated significant controversy and opened possibilities for evolutionary biology that are still being explored.

Cultural Phylogenetics

Author : Larissa Mendoza Straffon
Publisher : Springer
ISBN 13 : 3319259288
Total Pages : 202 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis Cultural Phylogenetics by : Larissa Mendoza Straffon

Download or read book Cultural Phylogenetics written by Larissa Mendoza Straffon and published by Springer. This book was released on 2016-02-10 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores the potential and challenges of implementing evolutionary phylogenetic methods in archaeological research, by discussing key concepts and presenting concrete applications of these approaches. The volume is divided into two parts: The first covers the theoretical and conceptual implications of using evolution-based models in the sociocultural domain, illustrates the sorts of questions that these methods can help answer, and invites the reader to reflect on the opportunities and limitations of these perspectives. The second part comprises case studies that address relevant empirical issues, such as inferring patterns and rates of cultural transmission, detecting selective pressures in cultural evolution, and explaining the nature of cultural variation. This book will appeal to archaeologists interested in applying evolutionary thinking and inferential methods to their field, and to anyone interested in cultural evolution studies.

Essential Bioinformatics

Author : Jin Xiong
Publisher : Cambridge University Press
ISBN 13 : 113945062X
Total Pages : 360 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Essential Bioinformatics by : Jin Xiong

Download or read book Essential Bioinformatics written by Jin Xiong and published by Cambridge University Press. This book was released on 2006-03-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.