Phylogenies and alignment
Materials for class on Monday, July 20, 2020
Contents
Slides
Action Items
- Assignment 4
Points of Reflection
Try to understand the long branch attraction problem.
Enumerate all the undirected graphs with 6 species.
Suppose you have an amino acid sequence of length 100. You apply the PAM_1 Markov model to each position. So some amino acids change, likely most don’t. We would expected 1% to change. Now apply the PAM_1 MM again. Do you expected to see that 2% of the amino acids have changed? Why or why not?
Why is PAM_250 considered the upper bound? What happens after PAM_250?