Lectures for CS 581
- August 28, 2018
(Overview of course, also parts of Chapter 1)
- August 30, 2018 (Chapters 1, 5.1, 5.3-5.5, and 8.1-8.2)
- September 4, 2018 (Chapters 2 and 3.1-3.3)
- September 6, 2018
(Chapters 3.4, 3.5, 4.1-4.4, 4.7, and 8.8)
-
(PPTX)
(PDF)
- Note: Homework #1 due today, covering Chapters 1 and 2
- September 11, 2018 (Chapters 4.1-4.4, 4.7, 8.6, and 8.8)
- September 13, 2018 (Chapter 8.5-8.8)
-
Discussion about statistical models of sequence
evolution.
-
Note: Homework #2 due today, covering Chapters 3 and 4
- September 18, 2018 (Chapter 9.1-9.5, 9.12)
-
Pairwise sequence alignment, Needleman-Wunsch,
MSA optimization criteria, and progressive alignment
(PDF).
- September 20, 2018
(Chapter 9.5)
-
The generalized tree alignment problem
(PDF).
and profile HMMs
(PDF)
-
Note: Homework #3 due today, covering Chapters 5 and 8
-
September 25, 2018
(Chapter 9.6-9.15)
-
MSA estimation techniques
(PDF)
-
September 27, 2018
-
Wei Qian will review homework problems.
-
Note: Homework #4 due today, covering Chapter 9
-
October 2-4, 2018
-
What we learn from data about MSA estimation
(PDF).
(PPTX).
- October 4, 2018
-
Two papers about BAli-Phy (#140, #164 from list of papers).
Research project possibilities about alignment
-
Note: Homework #5 due today, covering Chapter 9
- October 9, 2018 (Chapter 10)
-
Introduction to species tree estimation in the presence of
Incomplete Lineage Sorting (ILS)
(PDF)
- October 11, 2018
- Species tree estimation methods
-
Note: Homework #6 due October 11, covering Chapter 6
- October 16, 2018
-
Supertree methods (PDF)
and their use in divide-and-conquer strategies
- October 18, 2018
- Divide-and-conquer without supertrees
(PDF)
-
Note: Homework #7 due October 18, covering Chapter 10
- October 23, 2018
- Historical linguistics
(PDF)
- October 25, 2018
- Guest lecture by Mohammed El-Kebir
-
Note: Homework #8 due today, covering Chapter 7 and 10
- October 30, 2018
- Student presentations:
- Palash will present "QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data"
(paper)
(presentation)
-
Yuanyuan will present
"Quartet Inference from SNP Data Under the Coalescent Model"
(paper)
(presentation)
- Vlad will present "Clustering by Passing Messages
Between Data Points"
(paper)
(presentation)
- November 1, 2018
- Student presentations of papers
-
Bryce Kille will present
"On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics)", SICOMP 1998, https://doi.org/10.1137/S0097539795296334.
(talk)
-
Sayantani Basu will present "Collecting reliable clades using the Greedy Strict Consensus Merger (https://peerj.com/articles/2172.pdf).
(talk)
-
Sarah Schieferstein will present
"Horses or farmers? The tower of Babel and confidence in trees"
(paper)
(talk)
- November 6, 2018
- November 8, 2018
- Midterm distributed in class
(followed by discussion of the midterm questions)
- November 13, 2018
- November 15, 2018 - no class
- November 27, 2018
- Student presentations of papers
- Surbhi Jain will speak about
"A two-state model of tree evolution and its application to
Alu Retrotransposition"
(paper)
(talk)
-
Mia Schoening will present "IQ-Tree: A fast and effective stochastic algorithm for maximum-likelihood phylogenies"
(paper)
(talk)
-
Xilin Yu will present
"TreeShrink: fast and accurate detection of outlier long branches
in collections of phylogenetic trees",
(paper)
(talk)
- November 29, 2018
-
Thomas Cowell will present
"Phylogenetic Placement of Exact Amplicon Sequences Improves Associations
with Clinical Information",
(paper)
(talk)
-
Discussion about SEPP and similar techniques
(PDF)
(see also
(PDF) for
a second talk that goes into somewhat more detail)
- Note: Homework #9 (last one!) due today
- December 4, 2018
- Student presentations
of final projects
- December 6, 2018
- Student presentations
of final projects
- December 11, 2018
(LAST DAY)
- Student presentations
of final projects