6. Give examples for each of these MSA methods: Progressive, Iterative, Consistency-based, Structure-based
7. What is a guide tree in MSA?
8. What are types of substitutions that can be hidden?
9. What is molecular hypothesis? What are its assumptions? What are the exceptions?
10. On a phylogenetic tree, show the following: OTU, taxon, node, leaf, root, common ancestor, outgroup, branch
11. What are the differences between distance-based and character-based trees?
12. Give examples to distance-based and character-based tree construction methods.
13. What are the steps of phylogenetic analysis?
14. Explain the differences between JC69, K80 and T92 models.
15. What does heuristic search algorithm mean? Why do we need to use it in character-based algorithms?
16. Why do we use GBLOCKS or BMGE in phylogeny analysis? What do they do?
17. What is bootstrapping? Where do we use it?
18. What is a Hamming distance? How do we estimate it?
19. Explain synonymous and nonsynonymous substitutions. How are they indicate positive or negative selection?
20. What is a Smart Model Selection (SMS)? Why do we use it?
21. Explain the levels of protein structure.
22. Give examples to secondary structure, super secondary structure, tertiary structure and quaternary structure.
23. What is a motif? What is a domain? How are they different?
24. Which amino acids are considered structurally special? Why?
25. What are the databases for motifs?