Phylogenetic Trees Made Easy

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, USA. He was a founding member of the Society for Molecular Biology and Evolution and has been Editor-in-Chief of the journal Molecular Biology and Evolution, and on the Editorial Boards of Genetica, the Journal of Molecular Evolution, and the Journal of Bacteriology.

Read Me First!.- Tutorial: Estimate a Tree.- Acquiring the Sequences.- Aligning the Sequences.- Major Methods for Estimating Phylogenetic Trees.- Neighbor-Joining Trees.- Drawing Phylogenetic Trees.- Parsimony.- Maximum Likelihood.- Bayesian Inference of Trees Using MrBayes.- Working with Various Computer Platforms.- Advanced Alignment Using GUIDANCE.- Reconstructing Ancestral Sequences.- Detecting Adaptive Evolution.- Phylogenetic Networks.- Some Final Advice: Learn to Program.- Appendix I. File Formats and Their Interconversion.- Appendix II. Additional Programs.- Appendix III. Frequently Asked Questions.