20 points
Assigned Thursday, March 19
Due Thursday, April 2 by 11:59pm
In this mini-homework, you are to infer a phylogenetic tree of the five sequences you created in the prior mini-homeworks. To do this, you will choose a distance measure between sequences, e.g., Jukes-Cantor described in class (make sure you justify your choice of distance measure). Once you've selected a distance measure, you will apply the Neighbor Joining algorithm to build a tree. Describe the details of each step of Neighbor Joining (the values of Dij, dij, and ri at each step) and give an image of the final tree, with the edge lengths. Finally, briefly compare your new tree to the true evolutionary tree you built in Homework 0.5. For example, did closely-related sequences in the true tree appear near each other in the inferred tree?
Take your step-by-step description and your tree and add them to your sequence descriptions and alignments in your personal wiki, which is already linked in from the course wiki. Do not remove your previous results from your wiki; keep everything as a single, comprehensive document.