Computational Molecular Evolution

The book can be ordered at

• OUP web site
• Amazon.co.uk
• OUP USA web site
• Amazon.com

Reviews of the book

• In summary, Ziheng Yang has presented a very interesting and readable book that highlights aspects of computational molecular evolution that are not mentioned in other contributions to the field. It also points out open problems that provide ample space for future research. The book covers essential topics in a logical order to progressively educate the reader. It describes topics in a high level of detail with appropriate biological motivations and is full of valuable discussions.
  The book is highly recommended to graduate computer scientists, mathematicians, and biologists. However, every novice in the field should be aware that a large degree of mathematical, statistical, and biological knowledge is necessary to follow the full argumentation in the book. Although Ziheng Yang provides a sometimes very personal view of computational molecular evolution, the book is a valuable source of thought-provoking aspects of the field.

Le Sy Vinh and Arndt von Haeseler in Systematic Biology 56: 1024-1026 (2007)

• What sets this book apart is the authority and thoughtfulness with which it is written, the thorough coverage of the relevant literature, and the great care that has been taken in the computational examples to compare different methods on the same set of data, and to present the results clearly. ... It will be an invaluable resource both for new graduate students and established researchers. ... In the field of molecular evolution, the topics covered in this volume have taken center stage. It will be a major source for insight and enormously helpful for anyone who wants to understand molecular phylogenies.

Joe Felsenstein in The Quarterly Review of Biology 83: 205-206 (2008)

Errata

• Errata I applies to the 2006 edition and has been incorporated into the 2007 reprint.
• Errata II applies to both the 2006 edition and the 2007 reprint, and has been incorporated into the 2008 reprint.
• Errata III applies to the 2006 edition, the 2007 reprint, and also the 2008 reprint.
• Errata IV applies to the 2006 edition, and the 2007, 2008, and 2010 reprints.

Translations

• Chinese (2008)
• Japanese (2009)

Example data files and answers to questions

If you use the book for teaching and would like a copy of the slides, please send me an email. I have powerpoint slides for some of the chapters.

The answers to selected questions are availabe in this pdf file, which also contains a proof of equation 2.19 about dS.

Book description and contents

• Authored by a world-renowned specialist in the field
• Adopts a statistical approach to phylogenetics
• Web-based example data sets used to clarify the theory
• Emphasises the models and methods designed for understanding the evolutionary process of genes and genomes
• Ideal graduate seminar course material

Computational Molecular Evolution provides an up-to-date and comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. Yang describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. The book emphasizes essential concepts rather than mathematical proofs. It includes detailed derivations and implementation details, as well as numerous illustrations, worked examples, and exercises. It will be of relevance and use to students and professional researchers (both empiricists and theoreticians) in the fields of molecular phylogenetics, evolutionary biology, population genetics, mathematics, statistics and computer science. Biologists who have used phylogenetic software programs to analyze their own data will find the book particularly rewarding, although it should appeal to anyone seeking an authoritative overview of this exciting area of computational biology.

Readership: An advanced textbook suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of molecular phylogenetics, evolutionary biology, mathematics and statistics.

Contents (Extensive table of sontents)

Preface
1. Models of Nucleotide Substitution
2. Models of Amino Acid and Codon Substitution
3. Phylogeny Reconstruction: Overview
4. Maximum Likelihood Methods
5. Bayesian Methods
6. Comparison of Methods and Tests on Trees
7. Molecular Clock and Estimation of Species Divergence Times
8. Neutral and Adaptive Protein Evolution
9. Simulating Molecular Evolution
10. Perspectives
Appendixes
Reference