Lectures for CS 581, Fall 2022

The lectures in the first part of course (up to the take-home midterm) cover the basis of the material. The second part of the course will be decided based on student interests, and will include presentations by students and some guest lectures.

Starting October 20, each student will be assigned to present a paper and lead a discussion. All students will be required to read the papers that are presented, and submit homework based on the papers.

• August 23, 2022 (Overview of course)
  • (PPTX)
• August 25, 2022 (Newick strings, additive matrices, Naive Quartet Method, distance-based tree estimation)
  • (PPTX)
• August 30, 2022 (constructing rooted trees)
  • (PPTX)
• September 1, 2022 (constructing unrooted trees from subtrees).
  • (PPTX)
• September 6-8, 2022 (maximum parsimony and maximum likelihood)
  • Maximum parsimony (PPTX) (9/6: slides 1-15, 9/8: slides 16-29, 9/13: slides 30-end)
  • Maximum likelihood (PPTX)
• September 13, 2022 (Supertrees, DTMs, and divide-and-conquer)
  • Introduction to supertree methods (PDF)
  • DTM pipelines (PPTX)
• September 15-20 2022 (species tree estimation, Yasamin lectures)
  • (PPTX).
• September 22, 2021: constrained optimization tree construction
  • (PDF)
• September 27: Multiple sequence alignment
  • Introduction to Multiple Sequence Alignment (PDF)
  • Needleman-Wunsch (PDF)
• September 29: Profile Hidden Markov Models and MSAs
  • (PDF)
• October 4: Discussing Homework 6, and specifically the papers that were assigned and read.
• October 6: What we learn from data about MSA methods. Also, handing out the midterm.
  • (PPTX)
• October 11. Discussed midterm.
• October 13. Yasamin Tabatabaee will talk about rooting species trees. (PPTX)
• October 18. Computational phylogenetics for language families (PDF)
• October 20: Invited lecture (Marc Canby) (PDF)
• October 25: Student paper presentation. Akhil will talk about Triplets MaxCut (HTML). His talk is available (HERE)
• October 27: Student paper presentation. Nicole will present the paper titled "Bayesian phylogenetic analysis of linguistic data using BEAST" (HTML). Her talk is available (HERE).
• November 1: Student paper presentation. Stefan will talk about QuCo: quartet-based co-estimation of species trees and gene trees. (HTML). His talk is available here.
• November 3: Student paper presentation. Kel will talk about INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores (HTML). Her talk is available (here).
• November 8: Campus holiday (no lecture)
• November 10: Student paper presentation (Chloe). Chloe will present "Parallel SuperFine--A tool for fast and accurate supertree estimation: Features and limitations", available at (HTML). Her talk is available (here).
• November 15: Guest lecture: Dan Gusfield will talk about the Buneman Steiner theorem (PDF). The Buneman-Steiner theorem states that for every matrix M, there is an optimal Steiner Tree for M that is contained in the Buneman graph for M. Published proofs for this theorem are difficult to understand, and Dan will try to provide a simple proof.
• November 17: Student paper presentation. Vikram will present PASTASpark: (HTML). His presentation is here.
• November 19-27, Fall Break (no lectures)
• November 29: Student paper presentation. Jiayue will present the paper "Hobgoblin of phylogenetics?", available at (HTML). See assigned reading for additional papers to read on this subject (homework). Her presentation is (here).
• December 1: Student presentations of course projects. Students: Nicole (PDF), Kel (PPTX), Stefan (PDF), and Vikram (PPTX).
• December 6, Last day: Student presentations of course projects. Students: Jiayue, Akhil, and Chloe.