MBT/Genetics 541 Homework Assignment 3

Due Friday Apr. 20

• Write a program which takes the DNA sequences for a number of species and computes a table of Jukes-Cantor distances between them. Check it by having Dnatree simulate a tree and the sequences, using a Transition/Transversion ratio of 0.50001, which is the value that will yield the JC model. Use your program to compute the distances, then check them (by hand is OK) against the total branch length separating the species on the true tree. For this you will need to save the true tree into a file and look at that to get the branch lengths. The current version (1.0) of Dnatree does not write branch lengths onto the tree file, but I will in the next day replace it by a version, 1.1, which does.
• Email me (joe@genetics) the branch lengths as output by Dnatree, and your program's output of the pairwise distances.