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The Phylogenetic Handbook
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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.
Book Synopsis The Phylogenetic Handbook by : Philippe Lemey
Download or read book The Phylogenetic Handbook written by Philippe Lemey and published by Cambridge University Press. This book was released on 2009-03-26 with total page 763 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 2003-08-27 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sample Text
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 444 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.
Book Synopsis Phylogenetic Trees Made Easy by : Barry G. Hall
Download or read book Phylogenetic Trees Made Easy written by Barry G. Hall and published by . This book was released on 2004 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Book Synopsis Bayesian Evolutionary Analysis with BEAST by : Alexei J. Drummond
Download or read book Bayesian Evolutionary Analysis with BEAST written by Alexei J. Drummond and published by Cambridge University Press. This book was released on 2015-08-06 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Phylogenetic Comparative Methods in R by : Liam J. Revell
Download or read book Phylogenetic Comparative Methods in R written by Liam J. Revell and published by Princeton University Press. This book was released on 2022-07-12 with total page 441 pages. Available in PDF, EPUB and Kindle. Book excerpt: An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in R Explains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualization Features a wealth of exercises and challenge problems Serves as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areas Written by two of today’s leading developers of phylogenetic comparative methods
Book Synopsis Handbook of Trait-Based Ecology by : Francesco de Bello
Download or read book Handbook of Trait-Based Ecology written by Francesco de Bello and published by Cambridge University Press. This book was released on 2021-03-11 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.
Book Synopsis Homology and Systematics by : Robert Scotland
Download or read book Homology and Systematics written by Robert Scotland and published by CRC Press. This book was released on 2014-04-21 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: When looking at groups of organisms, shared characteristics (homologues) provide the raw data from which hypotheses of common ancestry may be suggested. In order to explore the relationship between homologues and particular hypotheses of common ancestry, complex matrices are devised, where homologues are coded, allowing theories of homology to be developed and tested. Practically nothing has been written about this matrix-building process, which is fundamental to our understanding of diversity and evolutionary history. This book fills the gap by discussing the ways observations are coded and the consequences for resulting hypotheses using case studies and theoretical examples.
Book Synopsis The Handbook of Historical Linguistics, Volume II by : Richard D. Janda
Download or read book The Handbook of Historical Linguistics, Volume II written by Richard D. Janda and published by John Wiley & Sons. This book was released on 2020-09-15 with total page 705 pages. Available in PDF, EPUB and Kindle. Book excerpt: An entirely new follow-up volume providing a detailed account of numerous additional issues, methods, and results that characterize current work in historical linguistics. This brand-new, second volume of The Handbook of Historical Linguistics is a complement to the well-established first volume first published in 2003. It includes extended content allowing uniquely comprehensive coverage of the study of language(s) over time. Though it adds fresh perspectives on several topics previously treated in the first volume, this Handbook focuses on extensions of diachronic linguistics beyond those key issues. This Handbook provides readers with studies of language change whose perspectives range from comparisons of large open vs. small closed corpora, via creolistics and linguistic contact in general, to obsolescence and endangerment of languages. Written by leading scholars in their respective fields, new chapters are offered on matters such as the origin of language, evidence from language for reconstructing human prehistory, invocations of language present in studies of language past, benefits of linguistic fieldwork for historical investigation, ways in which not only biological evolution but also field biology can serve as heuristics for research into the rise and spread of linguistic innovations, and more. Moreover, it: offers novel and broadened content complementing the earlier volume so as to provide the fullest available overview of a wholly engrossing field includes 23 all-new contributed chapters, treating some familiar themes from fresh perspectives but mostly covering entirely new topics features expanded discussion of material from language families other than Indo-European provides a multiplicity of views from numerous specialists in linguistic diachrony. The Handbook of Historical Linguistics, Volume II is an ideal book for undergraduate and graduate students in linguistics, researchers and professional linguists, as well as all those interested in the history of particular languages and the history of language more generally.
Book Synopsis Handbook of Computational Molecular Biology by : Srinivas Aluru
Download or read book Handbook of Computational Molecular Biology written by Srinivas Aluru and published by Chapman and Hall/CRC. This book was released on 2005-12-21 with total page 1104 pages. Available in PDF, EPUB and Kindle. Book excerpt: The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology offers comprehensive, systematic coverage of the various techniques and methodologies currently available. Accomplished researcher Srinivas Aluru leads a team of experts from around the world to produce this groundbreaking, authoritative reference. With discussions ranging from fundamental concepts to practical applications, this book details the algorithms necessary to solve novel problems and manage the massive amounts of data housed in biological databases throughout the world. Divided into eight sections for convenient searching, the handbook covers methods and algorithms for sequence alignment, string data structures, sequence assembly and clustering, genome-scale computational methods in comparative genomics, evolutionary and phylogenetic trees, microarrays and gene expression analysis, computational methods in structural biology, and bioinformatics databases and data mining. The Handbook of Computational Molecular Biology is the first resource to integrate coverage of the broad spectrum of topics in computational biology and bioinformatics. It supplies a quick-reference guide for easy implementation and provides a strong foundation for future discoveries in the field.
Book Synopsis Handbook of Self and Identity by : Mark R. Leary
Download or read book Handbook of Self and Identity written by Mark R. Leary and published by Guilford Press. This book was released on 2012-01-01 with total page 770 pages. Available in PDF, EPUB and Kindle. Book excerpt: Widely regarded as the authoritative reference in the field, this volume comprehensively reviews theory and research on the self. Leading investigators address this essential construct at multiple levels of analysis, from neural pathways to complex social and cultural dynamics. Coverage includes how individuals gain self-awareness, agency, and a sense of identity; self-related motivation and emotion; the role of the self in interpersonal behavior; and self-development across evolutionary time and the lifespan. Connections between self-processes and psychological problems are also addressed. New to This Edition *Incorporates significant theoretical and empirical advances. *Nine entirely new chapters. *Coverage of the social and cognitive neuroscience of self-processes; self-regulation and health; self and emotion; and hypoegoic states, such as mindfulness.
Book Synopsis Handbook of Milk Composition by : Bozzano G Luisa
Download or read book Handbook of Milk Composition written by Bozzano G Luisa and published by Elsevier. This book was released on 1995-10-23 with total page 947 pages. Available in PDF, EPUB and Kindle. Book excerpt: This informative treatise offers a concise collection of existing, expert data summarizing the composition of milk. The Handbook of Milk Composition summarizes current information on all aspects of human and bovine milk, including: sampling, storage, composition, as well as specific chapters on major and minor components such as protein, carbohydrates, lipids, electrolytes, minerals, vitamins and hormones. The book also features comprehensive coverage of compartmentation, host-defense components, factors affecting composition, composition of commercial formulas, and contaminants.* Reliable data on the composition of human and bovine milks.* Discusses the many factors affecting composition.* Composition tables make up 25-30% of the total book.* Problems concerning sampling and analysis are described.* Should appeal equally to industry and academia.* Also of interest to developing countries in need of information on infant nutrition and agricultural development
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.
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.
Book Synopsis Handbook of Statistical Genomics by : David J. Balding
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1740 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
