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 5.1-5.5)
(PPTX)
(PDF)
-
January 23.
Newick strings. Constructing
rooted trees from triplet trees using ASSU.
(Chapters 2 and 3.1-3.3.)
(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
distance-based tree estimation
(Chapter 8.6-8.7, 8.10)
(PPTX)
(PDF)
-
February 6. Pairwise sequence alignment, Needleman-Wunsch,
MSA optimization criteria, and progressive alignment
(PDF).
The generalized tree alignment problem
(PDF).
(Chapter 9.1-9.5)
-
February 8. Profile HMMs and probability calculations
(PDF)
and the Viterbi algorithm
(PDF)
(Chapter 9.6-9.7)
-
February 13.
MSA estimation techniques
(PDF)
(Chapter 9.8-9.15)
-
February 15-20.
What we learn from data
(PDF).
-
February 22.
Discussion of the assigned MSA papers.
(PDF)
-
February 27 and March 1.
Introduction to species tree estimation in the presence of
Incomplete Lineage Sorting (ILS)
(PDF)
-
March 6. Supertree methods
(Chapters 7.1-7.9)
(PDF)
-
March 8. Absolute fast converging methods
(Chapters 8.12 and 11.10)
(PDF)
(PPT)
-
March 13. Triangulated graphs and phylogenies
(Chapter 11)
(PPTX)
(PDF)
- March 15. Historical linguistics
(PDF)
-
March 20 and 22. SPRING BREAK
-
March 27.
Genome rearrangement phylogeny estimation.
(PPTX)
- March 29. Students present papers
related to their final projects.
Presenters:
-
Srilakshmi (Roch and Snir (2013): "Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis", https://doi.org/10.1089/cmb.2012.0234),
(PDF)
-
Jinfeng
(Tan et al., Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference, Syst. Biol 2015, 10.1093/sysbio/syv033)
and
(PDF)
-
Wei (J. Castresana; Selection of Conserved Blocks from Multiple
Alignments for Their Use in Phylogenetic Analysis, Molecular
Biology and Evolution, Volume 17, Issue 4, 1 April 2000,
Pages 540-552, https://doi.org/10.1093/oxfordjournals.molbev.a026334)
(PDF)
-
April 3. Students present papers
related to their final projects.
Presenters:
-
Rishika (Higgins, Desmond G., and Paul M. Sharp. "CLUSTAL: a package for performing multiple sequence alignment
on a microcomputer." Gene
73.1 (1988): 237-244)
(PDF)
-
Aniket
(Blackshields et al., (2010): "Sequence embedding for fast
construction of guide trees for multiple sequence alignment",
https://doi.org/10.1186/1748-7188-5-21)
(PDF)
-
April 5. Students present papers
related to their final projects.
Presenters:
-
Omri (Redelings and Suchard, Joint Bayesian Estimation of Alignment and Phylogeny, doi:10.1080/10635150590947041)
(PDF)
-
Jeffrey (Li, W. & Godzik, A. (2006). Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22(13), 1658-1659. doi:10.1093/bioinformatics/btl158)
(PDF)
-
Dikshant
(Jiao, W., Vembu, S., Deshwar, A. G., Stein, L., and Morris, Q. (2014). Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinformatics,15(1), 35. doi:10.1186/1471-2105-15-35)
(PPTX)
-
April 10-17. Cancer Phylogeny
(Guest lecturer: Prof. Mohammed El-Kebir)
Lecture 1
Lecture 2
Lecture 3
-
April 19.
Midterm handed out.
(Due back April 24, noon, via Moodle.)
-
April 24. Review of Midterm.
-
April 26: Student presentations of final projects.
(Srilakshmi)
(Dikshant)
(BAli-Phy benchmarking)
-
May 1. Students presentation of final projects
(Last day of class)
(Rishika)
(Wei and Jinfen)
(Aniket)