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

Philippe Lemey is a FWO postdoctoral researcher at the Rega Institute, Katholieke Universiteit Leuven, Belgium, where he completed his PhD in Medical Sciences. He has been an EMBO fellow and a Marie-Curie fellow in the Evolutionary Biology Group at the Department of Zoology, University of Oxford. His research focuses on molecular evolution of viruses by integrating molecular biology and computational approaches.

Marco Salemi is a postdoctoral scientist in the Medical Faculty at the Katholieke Universiteit, Belgium. He currently holds a research position at the University of California, Irvine, where he works on epidemiological virology and phylogenetic analysis, focusing on the molecular epidemiology of human pathogenic viruses, such as HIV and HCV. He is supported by the Fund for Scientific Research - Flanders, Belgium.

Anne-Mieke Vandamme is a Full Professor in the Medical Faculty at the Katholieke Universiteit, Belgium, working in the field of clinical and epidemiological virology. Her laboratory investigates treatment responses in HIV-infected patients and is respected for its scientific and clinical contributions on virus-drug resistance. Her laboratory also studies the evolution and molecular epidemiology of human viruses such as HIV and HTLV.