20 points
Assigned Thursday, January 22
Due Thursday, January 29 by 11:59pm
In this mini-homework, you are to come up with a set of five protein sequences (each consisting of about 20 amino acids), along with an evolutionary tree for those sequences. First, define a rooted tree with five nodes. Then, define a sequence (of length 20) to be at the root of the tree. This will be the ancestor of all the other sequences. Then, for each child of the root, evolve a sequence for that node by performing substitutions, insertions, and deletions on the root sequence. (Each child is evolved independently of the others, and both substitutions and indels must be used at some point.) If any of those children has children, then repeat the process until each node has a sequence. You may use a probabilistic process to evolve each new sequence, or do it deterministically. Either way, you must briefly describe the evolutionary process you used.
Draw your tree with each node's assigned sequence, and write the pairwise alignment for each parent-child pair in your set of sequences (i.e., four alignments total). Put these and your evolutionary process description in your personal wiki, which is already linked in from the course wiki. Note that to edit the course wiki, you need a CSE Wiki account, which is distinct from your CSE login account. See the CSE Wiki Main Page for information on how to get this account.