The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing

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.