Bio Z620 - Phylogenetics

Section: 23415
Class Day and Times: MWF 11:15-12:05
Class Location: MY 209
Text: Inferring Phylogenies by Joseph Felsenstein
WEB Page:
Instructor: Elizabeth Housworth
Office and Office Hours: 371 Rawles Hall, Tuesday 8-9 am, Sunday 1-2 pm
Important dates: Last day for automatic withdrawals is Wednesday, October 26.

Grading: There will be weekly short homework assignments to make sure that you have some practice with the material. These will be due on the Wednesdays of the week following the assignment. I will average your grades on these assignments after dropping your lowest two grades and this average will be the basis for your grade in the course. You may talk to others about the homeworks but the work you turn in should be your own.

Tentative Syllabus

Date Lecture Reading Homework
Monday, August 29 Tree Types Chapter 3 Homework Assignment 1
Wednesday, August 31 Counting trees Chapter 3
Friday, September 2 Generating random trees Chapter 3
Monday, September 5 Parsimony for a given tree Chapter 1 Homework Assignment 2
Wednesday, September 7 Parsimony for a given tree Chapter 2
Friday, September 9 Searching tree space for the most parsimonious tree Chapter 4
Monday, September 12 Searching tree space for the most parsimonious tree Chapter 5 Homework Assignment 3
Wednesday, September 14 Branch and bound algorithms Chapter 5
Friday, September 16 Computer Demonstration Chapter 5
Monday, September 19 Ancestral States and Branch Lengths Chapter 6 Homework Assignment 4
Wednesday, September 21 Computer Demonstration Chapter 6
Friday, September 23 Compatibility and Computer Demonstration Chapter 8
Monday, September 26 Models for DNA evolution Chapter 13 Homework Assignment 5
Wednesday, September 28 Models for DNA evolution Chapter 13
Friday, September 30 Calculating the likelihood for a given tree Chapter 13
Monday, October 3 Finding the most likely tree Chapter 16 Homework Assignment 6
Wednesday, October 5 More algorithms for searching tree-space Chapter 16
Friday, October 7 Ancestral States, Branch Lengths, and Computer Demonstration Chapter 16
Monday, October 10 Is ML consistent? Chapter 16 Break in Homework - no HW 7
Wednesday, October 12 Is parsimony consistent? Chapter 9
Friday, October 14 Robustness and using likelihoods to compare trees Chapter 19
Monday, October 17 Computer demonstration using likelihoods to compare trees Chapter 19 Homework Assignment 8
Wednesday, October 19 Bootstrapping Chapter 20
Friday, October 21 Bootstrapping plus computer demonstration Chapter 20
Monday, October 24 The Bayesian philosophy Chapter 18 Homework Assignment 9 - No Homework
Wednesday, October 26 Baysean Monte-Carlo Markov chains for phylogenies Chapter 18
Friday, October 28 Computer Demonstration Chapter 18
Monday, October 31 Distance Methods Chapter 11 Homework Assignment 10 - due Monday, November 14
Wednesday, November 2 Distance methods Chapter 11
Friday, November 4 Computer Demonstration Chapter 11
Monday, November 7 Consensus versus Total Evidence Chapter 30 Homework Assignment 11
Wednesday, November 9 Selection of Phylogenetic Reconstruction technique Overview
Friday, November 11 Example 1 Example 2 Overview
Monday, November 14 Overview Second article for discussion Homework Assignment 12
Wednesday, November 16 Phylogenetic Comparative Methods Chapter 25
Friday, November 18 Phylogenetic Comparative Methods Chapter 25
Monday, November 21 Computer demonstration of phylogenetic comparative methods Chapter 26 Homework Assignment 13
Wednesday, November 23 Thanksgiving Break --
Friday, November 25 Thanksgiving Break --
Monday, November 28 Evaluations and plan for the rest of the term No reading no Homework
Wednesday, November 30 Ferns phylogeny Ferns paper
Friday, December 2 Boundary of Phylogenetics with Population Genetics Native American phylogeny and Asian phylogeny and
Monday, December 5 Incongruence Length Difference Test and Partition Homogeneity Test Chapter 20 and Original Farris paper and The Utility of the ILD Test No homework
Wednesday, December 7 Software for fitting models Chapter 19 and