MBT/Genetics 541 Homework Assignment 1

Due Wednesday Apr. 4

1. Read sections 7.1, 7.2 and 7.4 of Durbin et al.
2. Go to the site ftp://evolution.genetics.washington.edu/pub/dnatree/dnatree.html There you will find a program (available for Windows, Macs, and Unix) which does the following:
   1. Simulates the random branching of lineages to make an evolutionary tree,
   2. Evolves a stretch of DNA sequence along this tree.
   3. Shows you an arbitrary tree for those species and lets you rearrange it interactively to find the most parsimonious tree you can.
   Do these. You may need to try different settings for menu option 0 to get trees to be properly visibile. Use a rate of evolution of 0.1. Write down the true tree. Then look at the data, and then use the interactive rearrangement to try to find the most parsimonious tree. You will need to explore the options which are explained in the Web page. Send Joe (by e-mail:joe@genetics.washington.edu) a report on how it went and how close the most parsimonious tree was to the true tree. If you feel adventurous, try a higher rate of evolution like 1.0 and see what that does to the accuracy.