1. Bootstrapping in MEGA:
Open the file Crab_rRNA.meg
Select Phylogeny > Neighbor-Joining
->
Bootstrapping can be done for each method

2. Bootstrap values are presented for internal branches

3. Construct a NJ tree with bootstrap values for the cytochrome c oxidase subunit II protein sequences in cyt2.fas
Who is the closest relative of humans?
How confident are you at this result?

4. Construct a NJ tree with bootstrap values for the cytochrome c oxidase subunit II protein sequences in cyt2.fas
Who is the closest relative of humans?
How confident are you at this result?

5. Consensus Implementation of the consensus program in Mega.
Use the flu.fas data from class 7 and build a maximum parsimony tree.

6. How many different trees can be found using maximum parsimony?

7. Given the consensus tree found when using a 30% cutoff do you expect something to change if we use a 100% cutoff ?

8. 100% cutoff

9. 30% cutoff