Homework 1

This is a long-term homework, with weekly deliveries. You must read and reproduce the following paper:

Dayhoff, M. O., and R. M. Schwartz. “A Model of Evolutionary Change in Proteins.” In Atlas of Protein Sequence and Structure. Washington, DC: National Biomedical Research Foundation, 1978. https://doi.org/10.1.1.145.4315.

You must show your partial advances every week. No excuses will be accepted. On the other hand, we welcome incomplete or wrong answers.

Homework 2

This is a straight application of phylogenetic methods. We assume that five sequences have been aligned using Clustal or any other similar multiple-sequence aligner. From that alignment, the Hamming distance can be calculated. The result is summarized in the following table.

In Class 13 we showed how to build a dendrogram using the UPGMA method, and we outlined how to do the same using WPGMA and Neighbor Joining. Your mission is to complete all these dendrograms using the same distance matrix:

• UPGMA
• WPGMA
• Neighbor Joining

This is not hard, and should be delivered before Thursday’s class.

Homework 3

I distributed four papers among the students. The idea is to form groups of two people and make a summary of each paper. It is good to discuss the document with your classmate, so you can both understand it. Nevertheless, the answers should be personal. It is important that each person writes their own text. Scientists are writers.

This is again a long-term homework. The only short-term task is to send me the names of each two-person team and the title of the paper. Send this information now.

Quiz 2

Please answer the questions published online.