Molecular Evolution And Phylogenetics
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Molecular Evolution And Phylogenetics
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Author : Masatoshi Nei
language : en
Publisher: Oxford University Press
Release Date : 2000-07-27
Molecular Evolution And Phylogenetics written by Masatoshi Nei and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2000-07-27 with Science categories.
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.
An Introduction To Molecular Evolution And Phylogenetics
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Author : Lindell Bromham
language : en
Publisher: Oxford University Press
Release Date : 2016
An Introduction To Molecular Evolution And Phylogenetics written by Lindell Bromham and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with Medical categories.
The analysis of DNA sequences contributes to evolutionary biology at all levels, from dating the origin of the biological kingdoms to untangling family relationships. This introductory text presents the fundamental concepts and intellectual tools needed to understand how the genome records information about the 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 offers an ideal starting point on the journey to an understanding of the way molecular data is used in modern biology
Molecular Evolution
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Author : Roderick D.M. Page
language : en
Publisher: John Wiley & Sons
Release Date : 2009-07-14
Molecular Evolution written by Roderick D.M. Page 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 2009-07-14 with Science categories.
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.
Phylogenetic Trees And Molecular Evolution
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Author : David R. Bickel
language : en
Publisher: Springer Nature
Release Date : 2022-09-29
Phylogenetic Trees And Molecular Evolution written by David R. Bickel and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-09-29 with Science categories.
This book serves as a brief introduction to phylogenetic trees and molecular evolution for biologists and biology students. It does so by presenting the main concepts in a variety of ways: first visually, then in a history, next in a dice game, and finally in simple equations. The content is primarily designed to introduce upper-level undergraduate and graduate students of biology to phylogenetic tree reconstruction and the underlying models of molecular evolution. A unique feature also of interest to experienced researchers is the emphasis on simple ways to quantify the uncertainty in the results more fully than is possible with standard methods.
Molecular Evolution
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Author : Ziheng Yang
language : en
Publisher: OUP Oxford
Release Date : 2014-05-16
Molecular Evolution written by Ziheng Yang and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-05-16 with Science categories.
Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. Molecular Evolution: a statistical approach 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. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with 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. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology.
Computational Molecular Evolution
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Author : Ziheng Yang
language : en
Publisher: OUP Oxford
Release Date : 2006-10-05
Computational Molecular Evolution written by Ziheng Yang and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-10-05 with Science categories.
The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. The increasing availability of large genomic data sets requires powerful statistical methods to analyse and interpret them, generating both computational and conceptual challenges for the field. Computational Molecular Evolution provides an up-to-date and comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. Yang 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. The book emphasizes essential concepts rather than mathematical proofs. It includes detailed derivations and implementation details, as well as numerous illustrations, worked examples, and exercises. It will be of relevance and use to students and professional researchers (both empiricists and theoreticians) in the fields of molecular phylogenetics, evolutionary biology, population genetics, mathematics, statistics and computer science. Biologists who have used phylogenetic software programs to analyze their own data will find the book particularly rewarding, although it should appeal to anyone seeking an authoritative overview of this exciting area of computational biology.
Bioinformatics And Molecular Evolution
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Author : Paul G. Higgs
language : en
Publisher: John Wiley & Sons
Release Date : 2013-04-30
Bioinformatics And Molecular Evolution written by Paul G. Higgs 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 2013-04-30 with Science categories.
In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.
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.
Analysis Of Phylogenetics And Evolution With R
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Author : Emmanuel Paradis
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-11-25
Analysis Of Phylogenetics And Evolution With R written by Emmanuel Paradis and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-11-25 with Science categories.
As a result, the inference of phylogenies often seems divorced from any connection to other methods of analysis of scienti?c data. Felsenstein Once calculation became easy, the statistician’s energies could be - voted to understanding his or her dataset. Venables & Ripley The study of the evolution of life on Earth stands as one of the most complex ?elds in science. It involves observations from very di?erent sources, and has implications far beyond the domain of basic science. It is concerned with processes occurring on very long time spans, and we now know that it is also important for our daily lives as shown by the rapid evolution of many pathogens. As a ?eld ecologist, for a long time I was remotely interested in phylo- netics and other approaches to evolution. Most of the work I accomplished during my doctoral studies involved ?eld studies of small mammals and es- mation of demographic parameters. Things changed in 1996 when my interest was attracted by the question of the e?ect of demographic parameters on bird diversi?cation. This was a new issue for me, so I searched for relevant data analysis methods, but I failed to ?nd exactly what I needed. I started to conduct my own research on this problem to propose some, at least partial, solutions. This work made me realize that this kind of research critically - pends on the available software, and it was clear to me that what was o?ered to phylogeneticists at this time was inappropriate.
Mathematics Of Evolution And Phylogeny
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Author : Olivier Gascuel
language : en
Publisher: OUP Oxford
Release Date : 2005-02-24
Mathematics Of Evolution And Phylogeny written by Olivier Gascuel and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-02-24 with Mathematics categories.
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.