For Fall 2023, CMSC892A meets on Tuesdays and Thursdays. A tentative course schedule is below. Typically, slides will be posted to ELMS right before the lecture and then linked here after (note that the slides linked well in advance of the lecture are being reposted from last year; these may be changed before the lecture).
Week  Day  Date  Class  Notes  Associated Reading 

1  Tu  Aug 29th  Preliminaries 1  Lecture: Class overview and some biological background [1_overview.pdf] [2_biol.pdf]  CP Appendix B (for those looking to review algorithms) 
Th  Aug 31st  Preliminaries 2  Lecture: Problems, Method Evaluation, and Data Processing (part 1); likely start the MSA module (see below) [3_probsmthdevalanddata.pdf]  
2  Tu  Sep 5th  Class canceled  
Th  Sep 7th  Multiple Sequence Alignment  Lecture: Pairwise alignment (review) and then multiple sequence alignment, specifically generalized tree alignment problem, sumofpairs (SOP) alignment problem, STAR alignment [4_msa_part1.pdf]  CP Sections 9.19.5.3 and 9.12  
3  Tu  Sep 12th  Modern MSA  Lecture: Consistency and maximum weight trace (MWT) problem, sequence profiles, aligning alignments, progressive alignment, iterative refinement, divideandconquer, popular MSA methods (Clustal W/Omega, TCoffee, MAFFT, MUSCLE, PASTA) [5_msa_part2.pdf]  CP Sections 9.69.74, 9.109.16 
Th  Sep 14th  Profile Hidden Markov Models (HMMs) 
Lecture: Supervised training (Maximum Likelihood), decoding (Viterbi algorithm) (also of interest is unsupervised training with BaumWelch algorithm and posterior decoding with Forward and Background algorithms)
[6_profile_hmms.pdf]

BSA Sections 5.15.8  
4  Tu  Sep 21st  Variant Calling and Tree Basics  Data Processing (part 2  variant calling); Tree Basics (e.g., clade, bipartition, contraction, refinement, etc.) [7_variant_calling.pdf] [8_trees.pdf] [8_trees_worksheet.pdf]  CP Sections 2.12.2.2, 2.32.3.4, 2.52.6, and 2.10 
Th  Sep 21st  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 2.12.5, 4.4  
5  Tu  Sep 26th  Parsimony  Lecture: Maximum parsimony problem (small and large), Fitch's algorithm, branchandbound, randomized taxon addition, search moves (NNI, SPR, TBR), consensus trees [10_parsimony.pdf]  CP Sections 4.14.3, 4.64.7, 6.16.2.3, Example 6.7 
Th  Sep 28th  CFN model and Maximum likelihood 
Lecture: How to generate data under CavendarFarrisNeyman (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 1.11.4, 8.1, 8.58.6, 8.8  
6  Tu  Oct 3rd  Molecular Sequence Evolution Models and Applications 
Lecture: Timecontinuous Markov Chains, JukesCantor 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 
Th  Oct 5th  Populationlevel processes  Lecture: Populationlevel processes (coalescent and recombination), MultiSpecies 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 10.110.5.2 (skipping 10.5.1)  
7  Tu  Oct 10th  Triplet Methods  Lecture: Triplet methods for species tree estimation under MSC model  includes tree edit operations, compatibility supertrees, ASSU algorithm, STELAR, MPEST [13_triplet_methods.pdf]  CP Section 10.5.1 
Th  Oct 12th  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, pdistances and modelcorrected 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, 5.35.5.1, 8.4, 5.2, 5.65.10  
8  Tu  Oct 17th  No lecture  Intentionally leaving free in case other lectures run long, review, + project discussion  
Th  Oct 19th  Tumor Phy I  Lecture by Dr. Salem Malikic: Overview of tumor evolution and Integer Linear Programming (ILP), Studying the history of tumor evolution from bulk sequencing data (method: CITUP)  CITUP paper  
9  Tu  Oct 24th  Tumor Phy II 
Lecture by Dr. Salem Malikic:
Inference of trees of tumor evolution from singlecell sequencing data under perfect phylogeny model (methods: SCITE and ScisTree).

SCITE paper and ScisTree paper 
Th  Oct 26th  Tumor Phy III  Lecture by Dr. Salem Malikic: Exact ILP formulations for tree inference from singlecell data under subperfect phylogeny and kDollo evolutionary models (methods: PhISCS and gpps)  PhISCS paper and gpps paper  
10  Tu  Oct 31st  Tumor Phy IV  Lecture by Dr. Cenk Sahinalp Branchandbound for subperfect phylogeny (method: PhISCSBnB), Identifying common evolutionary trajectories with ILP (method: CONETT)  PhISCSBnB paper and CONETT paper 
Th  Nov 2nd  Tumor Phy V 
Lecture by Dr. Cenk Sahinalp:
Quantifying uncertainy with partition function formulation, may also cover consensus trees


11  Tu  Nov 7th  Species vs. tumor phylo  Lecture by Yunheng Han Models + methods for species vs. tumor phylogenies  Preprint (accepted at WABI 2023); Also TREEQMC paper 
Th  Nov 9th  Exam Review 
See this exam study guide for a list of concepts and problems; also review the graded homework


12  Tu  Nov 14th  Species vs. tumor phylo, cont  Unpublished work (but will also review some core ideas for exam)  
Th  Nov 16th  Exam  Inclass exam TODAY (Thursday, November 16th in IRB2207 from 3:30pm4:45pm ET)!  
13  Tu  Nov 21st  No class! 
Extended thanksgiving break from classes


Th  Nov 23rd  No class!  Thanksgiving break  
14  Tu  Nov 28th  Phylo networks and Admixture graphs  Leveraging graph theoretic results for phylogenetics networks for admixture graph estimation  OrientAGraph paper 
Th  Nov 30th  Ancestral recombination graphs  
15  Tu  Dec 5th  Project Presentations  Schedule on ELMS  
Th  Dec 7th  Project Presentations  Schedule on ELMS  
17  Mo  Dec 18th  Deadline  Project reports due today (Monday, December 18th at 11:59PM ET)! 