Chapter 1. Read Me First!Chapter 2. Tutorial: Estimate a TreeChapter 3. Acquiring the SequencesChapter 4. Aligning the SequencesChapter 5. Major Methods for Estimating Phylogenetic TreesChapter 6. Neighbor Joining TreesChapter 7. Drawing Phylogenetic TreesChapter 8. ParsimonyChapter 9. Maximum LikelihoodChapter 10. Bayesian Inference of Trees Using BEASTChapter 11. Which Method Should You Use?Chapter 12. Working with Various Computer PlatformsChapter 13. Phylogenetic NetworksChapter 14. Minimum Spanning TreesChapter 15. Time TreesChapter 16. Reconstructing Ancestral SequencesChapter 17. Detecting Adaptive EvolutionChapter 18. Estimating Phylogenetic Trees from Whole Genome SequencesChapter 19. Some Final Advice: Learn to Program Appendix I: File Formats and Their InterconversionAppendix II: Text EditorsAppendix III: The Command-Line EnvironmentAppendix IV: Installing and Running Command-Line ProgramsAppendix V: Additional ProgramsAppendix VI: Frequently Asked Questions
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.