Phylogenetic Networks

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Publisher : Cambridge University Press
ISBN 13 : 9780521755962
Total Pages : 376 pages
Book Rating : 4.7/5 (559 download)

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Book Synopsis Phylogenetic Networks by : Daniel H. Huson

Download or read book Phylogenetic Networks written by Daniel H. Huson and published by Cambridge University Press. This book was released on 2010-12-02 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

Phylogenetic Networks

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Publisher : Cambridge University Press
ISBN 13 : 113949287X
Total Pages : 375 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Phylogenetic Networks by : Daniel H. Huson

Download or read book Phylogenetic Networks written by Daniel H. Huson and published by Cambridge University Press. This book was released on 2010-12-02 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

ReCombinatorics

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Publisher : MIT Press
ISBN 13 : 0262027526
Total Pages : 601 pages
Book Rating : 4.2/5 (62 download)

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Book Synopsis ReCombinatorics by : Dan Gusfield

Download or read book ReCombinatorics written by Dan Gusfield and published by MIT Press. This book was released on 2014-07-03 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: When a Philadelphia girl intercepts a message about an impending British attack against her father's regiment, commanded by General Washington, in White Marsh, she travels alone by horseback to warn the Patriot army.

Bioinformatics and Phylogenetics

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Publisher : Springer
ISBN 13 : 3030108376
Total Pages : 426 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 426 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.

Analysis of Biological Networks

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Publisher : John Wiley & Sons
ISBN 13 : 1118209915
Total Pages : 278 pages
Book Rating : 4.1/5 (182 download)

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Book Synopsis Analysis of Biological Networks by : Björn H. Junker

Download or read book Analysis of Biological Networks written by Björn H. Junker and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.

Phylogeny

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Publisher : SIAM
ISBN 13 : 161197447X
Total Pages : 302 pages
Book Rating : 4.6/5 (119 download)

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Book Synopsis Phylogeny by : Mike Steel

Download or read book Phylogeny written by Mike Steel and published by SIAM. This book was released on 2016-09-29 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetics is a topical and growing area of research. Phylogenies (phylogenetic trees and networks) allow biologists to study and graph evolutionary relationships between different species. These are also used to investigate other evolutionary processes?for example, how languages developed or how different strains of a virus (such as HIV or influenza) are related to each other. This self-contained book addresses the underlying mathematical theory behind the reconstruction and analysis of phylogenies. The theory is grounded in classical concepts from discrete mathematics and probability theory as well as techniques from other branches of mathematics (algebra, topology, differential equations). The biological relevance of the results is highlighted throughout. The author supplies proofs of key classical theorems and includes results not covered in existing books, emphasizes relevant mathematical results derived over the past 20 years, and provides numerous exercises, examples, and figures.

Basic Phylogenetic Combinatorics

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Publisher : Cambridge University Press
ISBN 13 : 0521768322
Total Pages : 277 pages
Book Rating : 4.5/5 (217 download)

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Book Synopsis Basic Phylogenetic Combinatorics by : Andreas Dress

Download or read book Basic Phylogenetic Combinatorics written by Andreas Dress and published by Cambridge University Press. This book was released on 2012 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first book to systematically introduce the emerging area of phylogenetic combinatorics.

Mathematics of Evolution and Phylogeny

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Publisher : OUP Oxford
ISBN 13 : 9780191513732
Total Pages : 444 pages
Book Rating : 4.5/5 (137 download)

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Book Synopsis Mathematics of Evolution and Phylogeny by : Olivier Gascuel

Download or read book Mathematics of Evolution and Phylogeny written by Olivier Gascuel and published by OUP Oxford. This book was released on 2005-02-24 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

The Phylogenetic Handbook

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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.

Creole Studies – Phylogenetic Approaches

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Publisher : John Benjamins Publishing Company
ISBN 13 : 9027265739
Total Pages : 426 pages
Book Rating : 4.0/5 (272 download)

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Book Synopsis Creole Studies – Phylogenetic Approaches by : Peter Bakker

Download or read book Creole Studies – Phylogenetic Approaches written by Peter Bakker and published by John Benjamins Publishing Company. This book was released on 2017-05-31 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book launches a new approach to creole studies founded on phylogenetic network analysis. Phylogenetic approaches offer new visualisation techniques and insights into the relationships between creoles and non-creoles, creoles and other contact varieties, and between creoles and lexifier languages. With evidence from creole languages in Africa, Asia, the Americas, and the Pacific, the book provides new perspectives on creole typology, cross-creole comparisons, and creole semantics. The book offers an introduction for newcomers to the fields of creole studies and phylogenetic analysis. Using these methods to analyse a variety of linguistic features, both structural and semantic, the book then turns to explore old and new questions and problems in creole studies. Original case studies explore the differences and similarities between creoles, and propose solutions to the problems of how to classify creoles and how they formed and developed. The book provides a fascinating glimpse into the unity and heterogeneity of creoles and the areal influences on their development. It also provides metalinguistic discussions of the “creole” concept from different perspectives. Finally, the book reflects critically on the findings and methods, and sets new agendas for future studies. Creole Studies has been written for a broad readership of scholars and students in the fields of contact linguistics, biolinguistics, sociolinguistics, language typology, and semantics.

Phylogenetics

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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.

Phylogenetics

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Publisher : John Wiley & Sons
ISBN 13 : 1118017870
Total Pages : 444 pages
Book Rating : 4.1/5 (18 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 2011-10-11 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.

6th International Conference on Practical Applications of Computational Biology & Bioinformatics

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Publisher : Springer Science & Business Media
ISBN 13 : 3642288391
Total Pages : 283 pages
Book Rating : 4.6/5 (422 download)

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Book Synopsis 6th International Conference on Practical Applications of Computational Biology & Bioinformatics by : Miguel P. Rocha

Download or read book 6th International Conference on Practical Applications of Computational Biology & Bioinformatics written by Miguel P. Rocha and published by Springer Science & Business Media. This book was released on 2012-03-05 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘12 hopes to contribute to this effort promoting this fruitful interaction. PACBB'12 technical program included 32 papers from a submission pool of 61 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.

Biodiversity Conservation and Phylogenetic Systematics

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Publisher : Springer
ISBN 13 : 3319224611
Total Pages : 396 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis Biodiversity Conservation and Phylogenetic Systematics by : Roseli Pellens

Download or read book Biodiversity Conservation and Phylogenetic Systematics written by Roseli Pellens and published by Springer. This book was released on 2016-02-24 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about phylogenetic diversity as an approach to reduce biodiversity losses in this period of mass extinction. Chapters in the first section deal with questions such as the way we value phylogenetic diversity among other criteria for biodiversity conservation; the choice of measures; the loss of phylogenetic diversity with extinction; the importance of organisms that are deeply branched in the tree of life, and the role of relict species. The second section is composed by contributions exploring methodological aspects, such as how to deal with abundance, sampling effort, or conflicting trees in analysis of phylogenetic diversity. The last section is devoted to applications, showing how phylogenetic diversity can be integrated in systematic conservation planning, in EDGE and HEDGE evaluations. This wide coverage makes the book a reference for academics, policy makers and stakeholders dealing with biodiversity conservation.

Tree Thinking: An Introduction to Phylogenetic Biology

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Author :
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.

Phylogenetic Trees Made Easy

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Publisher :
ISBN 13 : 9780878933129
Total Pages : 221 pages
Book Rating : 4.9/5 (331 download)

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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:

Molecular Evolution

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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.