Table of Contents

1. Maximum Likelihood 1
2. Maximum Likelihood 2
3. Maximum Likelihood Tree Reconstruction 1
4. Maximum Likelihood Tree Reconstruction 1
5. Maximum Likelihood Tree Reconstruction 2
6. Maximum Likelihood Tree Reconstruction 3
7. Maximum Likelihood Tree Reconstruction 4
8. Typical Assumptions of ML Substitution Models
9. Maximum Likelihood Models 1
10. Maximum Likelihood Models 2
11. A case study in phylogenetic analysis
12. A four taxon problem for Deinococcus and Thermus (Thermus, Deinococcus, Bacillus, Aquifex)
13. The Jukes and Cantor Model
14. Output of JC ML analysis for (Thermus, Deinococcus, Bacillus, Aquifex)
15. 16s rRNA base frequencies of Aquifex, Bacillus, Deinococcus and Thermus
16. Models can be made more parameter rich to increase their realism 1
17. A gamma distribution can be used to model site rate heterogeneity 
18. Models can be made more parameter rich to increase their realism 2
19. Models can be made more parameter rich to increase their realism 3
20. The GTR model of sequence evolution
21. The 16S rRNA sequences of Aquifex, Bacillus, Deinococcus, Thermus and Thermus ruber
22. Output of GTR-inv sites ML analysis for (Deinococcus, Bacillus, Aquifex, thermus and Thermus ruber)
23. Estimation of ML substitution model parameters
24. Parameter estimates using the "tree scores" command in PAUP*
25. ML Parameter Estimates over a Parsimony Tree in PAUP*
26. ML tree
27. ML - Advantages
28. ML - Disadvantages

Email: tme@nhm.ac.uk

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