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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.
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
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
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.