For Fall 2022, CMSC892A meets on Tuesdays and Thursdays from 11:00am - 12:15pm. A tentative course schedule is below.

Week Day Date Class Notes Associated Reading
1 Tu Aug 30th Preliminaries 1 Lecture: Class overview and some biological background [1_biol.pdf] CP Appendix B (for those looking to review algorithms)
Th Sep 1st Preliminaries 2 Lecture: Inputs, Outputs, and Data Processing as well as Basic Definitions for Phylogenetic Trees (e.g., clade, bipartition, contraction, refinement, etc.) [2_data.pdf] [3_trees.pdf] CP Sections 2.1-2.2.2, 2.3-2.3.4, 2.5-2.6, and 2.10
2 Tu Sep 6th Genome Assembly and Metagenomics Guest lecture by Prof. Mihai Pop NA (Not on exam)
Th Sep 8th Profiling Structural Variants in Cancer Guest lecture by Dr. Mikhail (Misha) Kolmogorov [5_cancer_svs.pdf] NA (Not on exam)
3 Tu Sep 13th Multiple Sequence Alignment Lecture: Pairwise alignment (review) and then multiple sequence alignment, specifically generalized tree alignment problem, sum-of-pairs (SOP) alignment problem, STAR alignment [6_msa_part1.pdf] CP Sections 9.1-9.5.3 and 9.12
Th Sep 15th Modern MSA Lecture: Consistency and maximum weight trace (MWT) problem, sequence profiles, aligning alignments, progressive alignment, iterative refinement, divide-and-conquer, popular MSA methods (Clustal W/Omega, T-Coffee, MAFFT, MUSCLE, PASTA) [7_msa_part2.pdf] CP Sections 9.6-9.74, 9.10-9.16
4 Tu Sep 20th Profile Hidden Markov Models (HMMs) Lecture: Supervised training (Maximum Likelihood), decoding (Viterbi algorithm) (also of interest is unsupervised training with Baum-Welch algorithm and posterior decoding with Forward and Background algorithms) [8_profile_hmms.pdf] BSA Sections 5.1-5.8
Th Sep 22nd Reading Group (MSA) Small group discussion

Homework assignment released!
5 Tu Sep 27th Presentations and large group discussion
Th Sep 29th Compatibility Lecture: Constructing trees from clades (Hasse diagram approach), clade compatibility, bipartition compatibility, homoplasy, character compatibility, perfect phylogeny problem, maximum compatibility problem, infinite sites assumption [9_compatibility.pdf] CP Sections 2.1-2.5, 4.4
6 Tu Oct 4th Parsimony Lecture: Maximum parsimony problem (small and large), Fitch's algorithm, branch-and-bound, randomized taxon addition, search moves (NNI, SPR, TBR), consensus trees [10_parsimony.pdf] CP Sections 4.1-4.3, 4.6-4.7, 6.1-6.2.3, Example 6.7
Th Oct 6th CFN model and Maximum likelihood Lecture: How to generate data under Cavendar-Farris-Neyman (CFN) model, How to compute probability of characters under CFN model, Felsenstein's Pruning Algorithm, Maximum Likelihood problem, statistical consistency [11_finite_sites.pdf] CP Sections 1.1-1.4, 8.1, 8.5-8.6, 8.8
7 Tu Oct 11th Practice Talk Lecture: Recent advances and open challenges in estimating evolutionary histories from low-homoplasy markers NA (Not on exam)
Deadline Homework assignment due today (Tuesday, October 11th at 11:59 PM ET)!
Th Oct 13th Molecular Sequence Evolution Models and Applications (Class on Zoom!) Lecture: Time-continuous Markov Chains, Jukes-Cantor model, Generalized Time Reversible (GTR) model, SHR assumptions as well as practical issues: insertions/deletions (missing data), model violations, varying rates across sites (CAT and GAMMA models), taxon sampling, uncertainty quantification (bootstrapping vs. Bayesian), phylogenetic placement and applications to taxonomic identification CP Sections 8.2,
8 Tu Oct 18th Population-level processes Lecture: Population-level processes (coalescent and recombination), Multi-Species Coalescent (MSC) model, concatenation vs. coalescent methods, practical issues (recombination ratchet, gene tree estimation error, missing data, etc.) [12_species_tree_msc.pdf] CP Sections 10.1-10.5.2 (skipping 10.5.1)
Th Oct 20th Reading Group (SARS-CoV-2) Small group discussion
9 Tu Oct 25th Presentations and large group discussion
Th Oct 27th Triplet Methods Lecture: Triplet methods for species tree estimation under MSC model - includes tree edit operations, compatibility supertrees, ASSU algorithm, STELAR, MP-EST [13_triplet_methods.pdf] CP Section 10.5.1
Deadline Project proposal due today (Tuesday, October 27th at 11:59 PM ET)!
10 Tu Nov 1st Distance and Quartet Methods Lecture: Quartet methods for species tree estimation under MSC model (includes All Quartets algorithm and ASTRAL), average gene tree internode distances, p-distances and model-corrected distances), additive and nearly additive, ultrametric, Naive Quartet method, UPGMA, and Neighbor Joining [14_quartet_and_distance_methods.pdf] CP Sections 10.5.1 (quartet methods), 7.7, 10.5.1 (distance methods) 5.1, 5.3-5.5.1, 8.4, 5.2, 5.6-5.10
Th Nov 3rd Reading group (tumor phylogeny) Small group discussion
11 Tu Nov 8th Presentations and large group discussion
Th Nov 10th Exam Review A running list of review questions and practice problems can be downloaded here: [exam-study-guide.pdf].
12 Tu Nov 15th Exam In-class today (Tuesday, November 15th in IRB-2207 from 11:00am-12:15pm ET)!
Th Nov 17th Logistics Check in about exam, projects, etc.
13 Tu Nov 22nd Hybridization and admixture Lecture: Phylogenetic networks, Wright-Fisher model, admixture graphs (Note this will be 30-minute lecture to prepare for reading groups. After I will have office hours about class projects.)
Th Nov 24th No class!
14 Tu Nov 29th Reading group (phylogenetic networks) Small group discussion
Th Dec 1st Presentations and large-group discussion
15 Tu Dec 6th Project Presentations
Th Dec 8th Project Presentations
17 Su Dec 18th Deadline Project reports due today (Sunday, December 18th at 11:59PM ET)!