Table of Contents

1. Phylogenetic inference from Proteins
2. Why protein phylogenies?
3. Proteins were the first molecular sequences to be used for phylogenetics
4. Phylogenies from proteins
5. Evolutionary models for amino acid changes
6. Phylogenetic trees from protein alignments
7. Character states in DNA and protein alignments
8. DNA->Protein: the code
9. DNA->Protein
10. Codon degeneracy: protein alignments as a guide for DNA alignments
11. Evolutionary models for amino acid changes
12. Evolutionary models for amino acid changes
13. Amino acid physico-chemical properties
14. Amino acid physico-chemical properties
15. Amino acids categories 1: Doolittle (1985). Sci. Am. 253, 74-85.
16. Amino acids categories 2
17. Phylogenetic trees from protein alignments
18. Trees from protein alignment: Parsimony methods - cost matrices
19. Parsimony: unweighted matrix for amino acid changes
20. Parsimony: weighted matrix for amino acid changes 1: minimal changes of amino acids
21. Weighting matrix based on minimal amino acid changes - PROTPARS
22. Phylogenetic trees from protein alignments
23. Protein similarity measurements: scoring matrices
24. Amino acid substitution matrices (MDMs)
25. Protein similarity measurements with scoring matrices
26. How is an MDM inferred?
27. MDM - An example
28. How is an MDM inferred?
29. Log-odds matrices
30. The PAM and JTT matrices
31. The BLOSUM matrices
32. BLOSUM62 Amino Acid Substitution Matrix
33. Pairwise distance estimation
34. Pairwise distance estimates for divergent Sequences
35. Ideally each pairwise comparison would have its own specific model
36. Phylogenetic trees from protein alignments
37. Protein phylogenies: some software
38. PHYLIP
39. PUZZLE4.0
40. PUZZLE4.0
41. PUZZLE4.0
42. PUZZLE4.0
43. PUZZLE4.0
44. PROTML2.2
45. PROTML2.2
46. PROTML2.2
47. PROTML2.2
48. Summary

Email: rch@nhm.ac.uk

Home Page: http://www.nhm.ac.uk/zoology/home/hirt.htm