Part I. Introduction: 1. Basic concepts of molecular evolution Anne-Mieke Vandamme; Part II. Data Preparation: 2. Sequence databases and database searching Guy Bottu, Marc Van Ranst and Philippe Lemey; 3. Multiple sequence alignment Des Higgins and Philippe Lemey; Part III. Phylogenetic Inference: 4. Nucleotide substitution models Korbinian Strimmer, Arndt von Haeseler and Marco Salemi; 5. Phylogenetic inference based on distance methods Yves Van de Peer and Marco Salemi; 6. Phylogenetic inference using maximum likelihood methods Heiko A. Schmidt and Arndt von Haeseler; 7. Bayesian phylogenetic analysis using MRBAYES Fredrik Ronquist, Paul van der Mark and John P. Huelsenbeck; 8. Phylogeny inference based on parsimony and other methods using PAUP* David L. Swofford and Jack Sullivan; 9. Phylogenetic analysis using protein sequences Fred R. Opperdoes and Philippe Lemey; Part IV. Testing Models and Trees: 10. Selecting models of evolution David Posada; 11. Molecular clock analysis Philippe Lemey and David Posada; 12. Testing tree topologies Heiko Schmidt; Part V. Molecular Adaptation: 13. Natural selection and adaptation of molecular sequences Oliver G. Pybus and Beth Shapiro; 14. Estimating selection pressures on alignments of coding sequences Sergei L. Kosakovsky Pond, Art F. Y. Poon, and Simon D. W. Frost; Part VI. Recombination: 15. Introduction to recombination detection Philippe Lemey and David Posada; 16. Detecting and characterizing individual recombination events Mika Salminen and Darren Martin; Part VII. Population Genetics: 17. The coalescent: population genetic inference using genealogies Allen Rodrigo; 18. Bayesian evolutionary analysis by sampling trees Alexei Drummond and Andrew Rambaut; 19. LAMARC: estimating population genetic parameters from molecular data Mary K. Kuhner; Part VIII. Additional Topics: 20. Assessing substitution saturation with DAMBE Xuhua Xia and Philippe Lemey; 21. Split networks: a tool for exploring complex evolutionary relationships in molecular data Vincent Moulton and Katharina T. Huber.