Lectures for CS 581, Spring 2025

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 after the midterm, 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.

• January 21, 2025 (Overview of course)
  • (PPTX) (PDF)
• January 23, 2025 (Newick strings, additive matrices, Naive Quartet Method, distance-based tree estimation)
  • (PPTX) (PDF)
• January 28, 2025 (constructing rooted trees)
  • (PPTX) (PDF)
• January 30 to February 4, 2025 (constructing unrooted trees from subtrees and maximum parsimony).
  • (PPTX) (PDF) Note: Feb 4 will begin with slide 36
• February 6 (maximum likelihood and Bayesian estimation).
  • (PPTX) (PDF)
• February 11: Eleanor Wedell will review the homework #2 problems.
• February 13-20 (species tree estimation)
  • (PPTX) (PDF)
• Feb 25 (Divide and conquer tree estimation)
  • (PDF) (PPTX)
• Feb 27 (Introduction to Phylogenetic Networks)
  • (PPTX) (PDF)
• March 4 (Introduction to Multiple Sequence Alignment)
  • (Basics, PDF) (Needleman-Wunsch, PDF)
• March 6 (Profile Hidden Markov Models and MSAs) and MSA: what we learn from data
  • (profile HMMs PDF)
  • (MSA-what we learn from data -PPTX) (MSA-what we learn from data - PDF)
• March 11:
  • Phylogenetics for language families, part I (PDF)
• March 13: Midterm discussed
• March 25: Phylogenetic networks
• March 27: Student presentations of course project proposals
• April 1: Student presentations of papers. The-Anh will present: QR-Star. Cindy will present learnMSA2. See The-Anh's presentation and Cindy's presentationk.
• April 3: Student presentations of papers, by zoom. Prathik will present T-Coffee. Ian will present Towards the accurate alignment of over a million sequences. See Ian's presentation. See Prathik's presentation.
• April 8: Student presentations of papers. Sean will present Advances in estimating level-1 phylogenetic networks from unrooted SNPs. Utkarsh will present Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation See Sean's talk and Utkarsh's talk.
• April 10: Student presentations of papers. Boyang will present PASTA for Proteins. See this for Boyang's talk. Progress report on course project: The-Anh Vu-Le, Ian Chen, and Cindy Zeng.
• April 15: Progress reports on course projects: Boyang (and possibly others)
• April 17: Progress reports on course projects: Sean (and anyone with new data).
• April 22: Eleanor will present the DEPP paper (Jiang et al., Systematic Biology, (HTML), but the entire class will discuss. You may wish to watch Siavash's presentation of this work at this site. Utkarsh and Pratikh will do a project progress report.
• April 24: Project progress reports
• April 29: Students discuss Zhang, C., Nielsen, R., & Mirarab, S. (2025). CASTER: Direct species tree inference from whole-genome alignments. Science, 387(6737):eadk9688. https://doi.org/10.1126/science.adk9688. You may wish to watch the video at this page.
• May 1: Progress reports on course projects (all)
• May 6: Last day (course projects due)