For Fall 2024, CMSC 702 meets on Mondays and Wednesdays from 3:30-4:45pm in IRB-2207 (unless otherwise indicated). A tentative course schedule is below. Check back frequently for updates on course assignments and due dates.

Week Day Date Class Associated Reading
1 Mon Aug 26 Lecture - Preliminaries CP Appendix A and B
Wed Aug 28 Lecture - Preliminaries, cont. [3_data.pdf]
  • Some more biology (high level)
  • Computational problems (high level)
  • Popular data processing pipelines
Problem set 1 released today
2 Mon Sep 2 No class - Labor Day Holiday
Wed Sep 4 Lecture - Multiple Sequence Alignment (MSA) [4_msa_part1.pdf]
  • Pairwise alignment (review from algorithms courses)
  • Generalized tree alignment (GTA) problem
  • Sum-of-pairs (SOP) alignment problem
  • STAR alignment
 CP Sections 9.1-9.5.3 and 9.12
Fri Sep 6 Problem set 1 DUE today
3 Mon Sep 9 Lecture - Advanced MSA [5_msa_part2.pdf]
  • Consistency
  • Maximum Weight Trace (MWT) problem
  • Sequence profiles
  • Aligning two alignments
  • Progressive alignment
  • Iterative refinement
  • Divide-and-conquer
  • Popular methods (Clustal Omega, T-Coffee, MAFFT, MUSCLE, SATe/PASTA)
 CP Sections 9.6-9.74, 9.10-9.16
Wed Sep 11 Lecture - Profile Hidden Markov Models (HMMs) [6_profile_hmms.pdf]
  • Supervised training (Maximum Likelihood)
  • Decoding profile HMMs (Viterbi algorithm)
 BSA Sections 5.1-5.8
4 Mon Sep 16 Reading Group 1
Small group paper discussions
Wed Sep 18 Presentations and large group discussion
5 Mon Sep 23 Reading Group 2
Small group paper discussions
Wed Sep 25 Presentations and large group discussions
6 Mon Sep 30 Lecture - Tree Basics [7_trees.pdf]
  • Newick strings
  • Rooted trees and clades
  • Unrooted trees and bipartitions
  • Contractions, refinements, homeomorphic subtrees
  • Tree error
  • Size of tree space
Problem set 2 released today 		CP Sections 2.1-2.2.2, 2.3-2.3.4, 2.5-2.6, and 2.10
Wed Oct 2 Lecture - Compatibility & Infinite Sites Model [8_compatibility.pdf]
  • Constructing trees from clades (Hasse diagram approach)
  • Clade compatibility, bipartition compatibility
  • Homoplasy
  • Character compatibility
  • Maximum compatibility problem
  • Perfect phylogeny problem
  • Infinite sites (IS) model
  • Applications
 CP Sections 2.1-2.5, 4.4
7 Mon Oct 7 Lecture - Parsimony [9_parsimony.pdf]
  • Parsimony criterion scores (Fitch, Dollo, Camin-Sokal, Star Homoplasy)
  • Small Maximum Parimsony Problem (Fitch's and Sankoff's Algorithms)
  • Large Maximum Parsimony problem
  • Branch-and-bound
  • Search heuristics - randomized taxon addition, edit moves (NNI, SPR, TBR)
  • Applications
 CP Sections 4.1-4.6, 4.6-4.7, 6.1-6.2.3, Example 6.7
Wed Oct 9 Lecture - Finite Sites Model & Likelihood [10_finite_sites.pdf]
  • Cavendar-Farris-Neyman (CFN) finite sites model
  • Small Maximum Likelihood (ML) problem (Felsenstein's Pruning Algorithm)
  • Maximum Likelihood problem
  • Statistical (in)consistency result for parsimony (Felsenstein Zone)
  • Taxon sampling and long branch attraction
 CP Sections 1.1-1.4, 8.1, 8.5-8.6, 8.8
Fri Oct 11 Problem set 2 DUE today
8 Mon Oct 14 Lecture - Distance Methods [13_distance_methods.pdf]
  • p-distances
  • CFN-corrected distances
  • Additive and nearly additive
  • Ultrametric
  • Naive Quartet method
  • UPGMA
  • Neighbor Joining (NJ)
  • Statistical (in)consistency results for UPGMA (Felsenstein Zone)
Problem set 3 released today 		CP Chapter 5
Wed Oct 16 Lecture - SuperTrees [12_supertrees.pdf]
  • Compatibility supertrees
  • Triplet compatibility supertrees & ASSU algorithm
  • Quartet compatibility supertrees & All Quartets algorithm
  • Optimization problems for triplets, quartets, and bipartitions (+ heursitics and consistency results)
 CP Chapter 7
9 Mon Oct 21 Lecture - Molecular Sequence Evolution [11_mol_seq_evol.pdf]
  • Continuous-time Markov chains and SHR assumptions (JC and GTR models)
  • Modeling variable rates across sites (CAT and GAMMA models)
  • Accounting for uncertainty via bootstrapping & consensus trees
  • Practical issues - Insertions/deletions (missing data), low phylogenetic signal (due to rate of evolution & sequence length)
  • Applications
 Chapter 8 (cont), Chapter 6
Wed Oct 23 Lecture - Overflow from previously classes
Fri Oct 25 Problem set 3 DUE today
10 Wed Oct 28 Lecture - Species/Population-level Evolution [14_species_trees_msc.pdf] [Github Activity]
  • Gene trees vs. species trees
  • Multi-Species Coalescent (MSC) model
  • Consistency results for triplets (rooted 3-leaf trees) and quartets (unrooted 4-leaf trees) under MSC
  • (In)consistency result for concatenation
  • Concatenation vs. coalescent methods
  • Practical issues - gene tree estimation error, missingness, etc.
 CP Chapter 10
Wed Oct 30 Lecture - Species/Population-level Evolution, cont.
11 Mon Nov 4 Lecture - Species/Population-level Evolution, cont, cont. [15_species_trees_msc_cont.pdf]
Wed Nov 6 Exam Review
12 Mon Nov 11 In Class Exam today at 3:30pm!
Wed Nov 13 Reading Group 3
Small group paper discussions
Mon Nov 15th Proposed methods for project due at 11:59pm!
13 Mon Nov 18 Presentations and large group discussions (zoom recordings due to conference travel)
Wed Nov 20 Reading Group 4
Small group paper discussions
14 Mon Nov 25 Presentations and large group discussion (zoom option)
Wed Nov 27 No class - Thanksgiving Holiday
15 Mon Dec 2 Project meeting time, extra office hours, chill
Wed Dec 4 Project Presentations (Teams: A, B, C, D)
16 Mon Dec 9 Project Presentations (Teams: E, F, G)
17 Mon Dec 16th Project reports due today at 11:59PM ET!