1. Parsimony methods -- 2. Counting evolutionary changes -- 3. How many trees are there? -- 4. Finding the best tree by heuristic search -- 5. Finding the best tree : branch and bound -- 6. Ancestral states and branch lengths -- 7. Variants of parsimony -- 8. Compatibility -- 9. Statistical properties of parsimony -- 10. A digression on history and philosophy -- 11. Distance matrix methods -- 12. Quartets of species -- 13. Models of DNA evolution -- 14. Models of protein evolution -- 15. Restriction sites, RAPDS, and microsatellites -- 16. Likelihood methods -- 17. Hadamard methods -- 18. Bayesian inference of phylogenies -- 19. Testing models, trees, and clocks -- 20. Bootstrap, jackknife, and permutation tests -- 21. Paired-sites tests -- 22. Invariants -- 23. Brownian motion and gene frequencies -- 24. Quantitative characters -- 25. Comparative methods -- 26. Coalescent trees -- 27. Likelihood calculations on coalescents -- 28. Coalescents and species trees -- 29. Alignment, genre families, and genomics -- 30. Consensus trees and distances between trees -- 31. Biogeography, hosts, and parasites -- 32. Phylogenies and paleontology -- 33. Tests based on tree shape -- 34. Drawing trees -- 35. Phylogeny software

1. Cladistic analysis -- Mathematics