The Phylogenetic Handbook

Author: Philippe Lemey
Editor: Cambridge University Press
ISBN: 9781139478618
Size: 16,93 MB
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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.

The Phylogenetic Handbook

Author: Philippe Lemey
Editor: Cambridge University Press
ISBN: 0521877105
Size: 13,43 MB
Format: PDF, Docs
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A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

The Phylogenetic Handbook

Author: Marco Salemi
Editor:
ISBN: 9780511517037
Size: 16,91 MB
Format: PDF, Mobi
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A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

The Phylogenetic Handbook

Author: Marco Salemi
Editor: Cambridge University Press
ISBN: 9780521803908
Size: 17,75 MB
Format: PDF, ePub, Docs
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Introduction to the theory and practice of phylogenetic analysis for molecular evolution students and professionals.

Phylogenetics

Author: E. O. Wiley
Editor: John Wiley & Sons
ISBN: 1118017870
Size: 17,21 MB
Format: PDF, Kindle
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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.

Bayesian Evolutionary Analysis With Beast

Author: Alexei J. Drummond
Editor: Cambridge University Press
ISBN: 1107019656
Size: 15,75 MB
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Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.

Computational Molecular Evolution

Author: Ziheng Yang
Editor: Oxford University Press
ISBN: 0198566999
Size: 15,15 MB
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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.

Molecular Evolution And Phylogenetics

Author: Masatoshi Nei
Editor: Oxford University Press
ISBN: 0199881227
Size: 16,78 MB
Format: PDF, Docs
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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.

Inferring Phylogenies

Author: Joseph Felsenstein
Editor: Sinauer Associates Incorporated
ISBN: 9780878931774
Size: 10,40 MB
Format: PDF, Mobi
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Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.

Tree Thinking

Author: David A. Baum
Editor: Roberts & Company
ISBN: 9781936221165
Size: 16,84 MB
Format: PDF, Kindle
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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.