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Phylogenetic Trees Made Easy

A How-To Manual

Fifth Edition

Barry G. Hall

October 2017

ISBN: 9781605357102

368 pages
Paperback

In Stock

Price: £69.99

Helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data. If you are a lecturer interested in adopting this title for your course, please contact your Oxford representative to arrange a local price.

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Description

Published by Sinauer Associates, an imprint of Oxford University Press.

Phylogenetic Trees Made Easy, Fifth Edition helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data. Although aimed at molecular and cell biologists, who may not be familiar with phylogenetic or evolutionary theory, it also serves students who have a theoretical understanding of phylogenetics but need guidance in transitioning to a practical application of the methodology.

  • "Learn More" boxes present background on the various concepts and methods.
  • Files needed for working through the tutorials in the text, as well as additional software that facilitates some of the methods discussed, are provided on a Companion Website.

New to this edition

  • The release of this edition was prompted by the development of a new version of the phylogenetic software MEGA, and takes into account the new capabilities present in MEGA7
  • Three new chapters (Minimum Spanning Trees; Time Trees; and Estimating Phylogenetic Trees from Whole Genome Sequences) address important advanced topics
  • Three new Appendices discuss text editors, the many command-line programmes that are available, and facilitating the installation of those programmes in the Windows, Mac, and Linux environments
  • New screen shots throughout show the current versions of all software. These illustrations are in full colour, enabling readers to more easily identify elements in which colour plays an important informational role

About the Author(s)

Barry G. Hall, Director, Bellingham Research Institute

Barry G. Hall is Director of the Bellingham Research Institute, Adjunct Professor of Genomics and Bioinformatics at the Allegheny-Singer Research Institute's Center for Genomic Sciences, and Professor Emeritus of Biology, University of Rochester. A founding member of the Society for Molecular Biology and Evolution, he has served as Editor-in-Chief of its journal, Molecular Biology and Evolution, and on the Editorial Boards of Genetics, the Journal of Molecular Evolution, and the Journal of Bacteriology. His current research interests include the molecular epidemiology of bacterial pathogens and application of genomic analysis to rapid prediction of antibiotic sensitivity in clinical applications. He has continued to publish 2-3 papers a year since his retirement in 2003.

Table of Contents

    1:Read Me First!
    2:Tutorial: Estimate a Tree
    3:Acquiring the Sequences
    4:Aligning the Sequences
    5:Major Methods for Estimating Phylogenetic Trees
    6:Neighbor Joining Trees
    7:Drawing Phylogenetic Trees
    8:Parsimony
    9:Maximum Likelihood
    10:Bayesian Inference of Trees Using BEAST
    11:Which Method Should You Use?
    12:Working with Various Computer Platforms
    13:Phylogenetic Networks
    14:Minimum Spanning Trees
    15:Time Trees
    16:Reconstructing Ancestral Sequences
    17:Detecting Adaptive Evolution
    18:Estimating Phylogenetic Trees from Whole Genome Sequences
    19:Some Final Advice: Learn to Program

Additional Resources

Files needed for working through the tutorials in the text, as well as additional software that facilitates some of the methods discussed, can be accessed online.

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