Phylogenetic Trees Made Easy

A How-To Manual

Fifth Edition

Barry G. Hall

"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

Phylogenetic Trees Made Easy

A How-To Manual

Fifth Edition

Barry G. Hall

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. The reader is led, 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. "Learn More" boxes present background on the various concepts and methods.

Phylogenetic Trees Made Easy

A How-To Manual

Fifth Edition

Barry G. Hall

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

Phylogenetic Trees Made Easy

A How-To Manual

Fifth Edition

Barry G. Hall

Author Information

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.