Lectures for CS 581, Spring 2018
 January 16.
Introduction to the course.
(PPTX)
(PDF)
 January 18.
Additive matrices and constructing trees using
the Naive Quartet Method.
Estimating trees under statistical models.
(Chapters 1 and 5.15.5)
(PPTX)
(PDF)

January 23.
Newick strings. Constructing
rooted trees from triplet trees using ASSU.
(Chapters 2 and 3.13.3.)
(PPTX)
(PDF)

January 25.
Constructing unrooted trees from bipartitions and
compatible binary characters.
Introduction to maximum parsimony.
(Chapter 4.)
(PPTX)
(PDF)

January 30.
Proving MP is not statistically consistent under the CFN model.
(Chapter 8.8.)
(PPTX)
(PDF)

February 1.
Maximum likelihood, Bayesian MCMC, and
distancebased tree estimation
(Chapter 8.68.7, 8.10)
(PPTX)
(PDF)

February 6. Pairwise sequence alignment, NeedlemanWunsch,
MSA optimization criteria, and progressive alignment
(PDF).
The generalized tree alignment problem
(PDF).
(Chapter 9.19.5)

February 8. Profile HMMs and probability calculations
(PDF)
and the Viterbi algorithm
(PDF)
(Chapter 9.69.7)

February 13.
MSA estimation techniques
(PDF)
(Chapter 9.89.15)

February 1520.
What we learn from data
(PDF).

February 22.
Discussion of the assigned MSA papers.
(PDF).

February 27.
Introduction to species tree estimation in the presence of
Incomplete Lineage Sorting (ILS)
(PDF)

March 1 and 6.
Coalescentbased species tree estimation
methods
(PDF)

March 8. Supertree methods
(Chapters 7.17.9)
(PDF)

March 13. Distancebased methods (advanced)
(Chapter 5)

March 15. Historical linguistics
(PDF)

March 20 and 22. SPRING BREAK

April 3. Students present papers
related to their final projects

April 5. Students present papers
related to their final projects

April 1017. Cancer Phylogeny
(Guest lecturer: Prof. Mohammed ElKebir)

April 19.
Midterm handed out.
(Due back April 23, noon, via Moodle.)

April 24. Review of Midterm.

April 26: Student presentations of final projects.

May 1. Students presentation of final projects
(Last day of class)