Part II: Distance matrix methods 1. Answer the following questions: What is the general approach used by distance matrix methods to construct a phylogeny? a. b. 2. 3. 4. a. 5.

a. b. 6. What are the main differences between UPGMA and neighbor-joining methods? Take your protein sequences from the links page and import them into Mega. Align them via Clustal W and save the alignment. Use your alignment to construct UGMA and Neighbor-Joining Trees. What are the differences and similarities between the trees? Repeat the above with an alignment based on MUSCLE instead of ClustalW. How does this change the results? Why do you think the results are different? Include labeled screen shots of your different trees.