Computational Molecular Evolution

Ziheng Yang, October 2006, Oxford University Press (376 pages, numerous figures and tables)

ISBN-10: 0-19-856702-2
ISBN-13: 978-0-19-856702-8

The book can be ordered at

Reviews of the book

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

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



Example data files and answers to questions

The example data files and a few C programs are availabe in this archive (CME2006data.tgz). Save the file with the correct name before double-clicking.

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

Description from OUP web site The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. The increasing availability of large genomic data sets requires powerful statistical methods to analyse and interpret them, generating both computational and conceptual challenges for the field.

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)

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

Ziheng Yang's research group page