Phylogenetic Trees Made Easy A How-To Manual

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.

Note: 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 via the Ancillary Resource Center link on this page.

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.

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