CMSC54610-1, Introduction to Bioinformatics, Spring quarter 2006.

Introduction to Bioinformatics: CMSC54610-1, Spring quarter 2006.

Chapter 5 homework

Do a phylogenetic study of mammals in the swiss-prot database, based on the HBA1 protein. You should generate both distance based (UPGMA and NJ) trees, and a parsimony tree.

1. Which of these algorithms generate rooted trees?
2. If you wanted to root the unrooted trees, what is the most reasonable outgroup? Justify your choice.
3. Generate a consensus tree based on these three phylogenies.

Hints.

The echidna is a mammal, the rockcod is a fish.
Clustalw can generate output files formatted for phylip, but a small amount of hand editing may be needed. Phylip can generate all three trees, and even draw them.