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Phylogenetic Trees Made Easy

Phylogenetic Trees Made Easy

ISBN 9781605357102
Edition 5
Publication Date
Publisher Oxford University Press
Author(s)
Overview
Helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data.Phylogenetic Trees Made Easy, Fifth Edition leads the reader, step by step, through identifying and acquiring the sequences to be included in a tree, aligning the sequences, estimating the tree by one of several methods, and drawing the tree for presentation to an intended audience. 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.New to This Edition:The release of this edition was prompted by the development of a new version of the phylogenetic software MEGA. MEGA7 has several capabilities that were not present in MEGA5.Three new chapters address important advanced topics: Minimum Spanning Trees (Chapter 14), an alternative to phylogenetic trees when they are not suitable; Time Trees (Chapter 15), a new feature of MEGA7 that permits estimation of the divergence times of the interior nodes of trees; and an alignment-free method for Estimating Phylogenetic Trees from Whole Genome Sequences (Chapter 18).The chapter on Bayesian Inference is now illustrated using the program BEAST (Bayesian Evolutionary Analysis Sampling Trees), a WYSIWYG program with a familiar application environment.Three new Appendices discuss text editors, the many command-line programs that are available, and facilitating the installation of those programs 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.This edition is organised into 19 (versus 16) chapters, to better isolate important topics.
Overview
Helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data.Phylogenetic Trees Made Easy, Fifth Edition leads the reader, step by step, through identifying and acquiring the sequences to be included in a tree, aligning the sequences, estimating the tree by one of several methods, and drawing the tree for presentation to an intended audience. 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.New to This Edition:The release of this edition was prompted by the development of a new version of the phylogenetic software MEGA. MEGA7 has several capabilities that were not present in MEGA5.Three new chapters address important advanced topics: Minimum Spanning Trees (Chapter 14), an alternative to phylogenetic trees when they are not suitable; Time Trees (Chapter 15), a new feature of MEGA7 that permits estimation of the divergence times of the interior nodes of trees; and an alignment-free method for Estimating Phylogenetic Trees from Whole Genome Sequences (Chapter 18).The chapter on Bayesian Inference is now illustrated using the program BEAST (Bayesian Evolutionary Analysis Sampling Trees), a WYSIWYG program with a familiar application environment.Three new Appendices discuss text editors, the many command-line programs that are available, and facilitating the installation of those programs 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.This edition is organised into 19 (versus 16) chapters, to better isolate important topics.

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