CMSC 702 meets on Mondays and Wednesdays from 2:00-3:15pm in IRB-1207, unless otherwise indicated. The schedule will cover much of the same material from 2024 with some exclusions and additions.
CP = Computational Phylogenetics (Warnow, 2017)
[UMD Library]
| Week | Day | Date | Class | Reading |
|---|---|---|---|---|
| 1 | Mon | Aug 31 |
No class - Recorded Lecture
Course overview and logistics [materials] Some biology basics [materials] |
CP Appendix A and B |
| Wed | Sep 2 |
Guest lecture by Junyan Dai
Is level-1 blob reconstruction under the network multispecies coalescent easy? [materials] |
NetCS paper | |
| 2 | Mon | Sep 7 | No class - Labor Day Holiday | |
| Wed | Sep 9 |
Phylogenetic Trees
Rooted trees and clades, unrooted trees and bipartitions, contractions, refinements, homemorphic subtrees, tree error, tree space, compatibility [materials] |
CP Chapter 2 | |
| 3 | Mon | Sep 14 |
Characters and Infinite Sites Model
Character compatibility, perfect phylogeny, homoplasy, single nucleotide variants, infinite sites + noise model, minimum error correction problem, applications in tumor phylogeny [materials] |
CP Sections 4.1, 4.2, 4.4 |
| Wed | Sep 16 |
Parsimony
Parsimony criterion scores (Fitch, Dollo, Camin-Sokal, Star Homoplasy), small and large maximum parsimony problems, branch-and-bound, tree space search heuristics (randomized taxon addition, edit moves e.g. NNI, SPR, TBR), consensus trees (may carry over to next Wed) [materials] |
CP Sections 4.3, 6.1-6.2 | |
| 4 | Mon | Sep 21 |
Maximum Likelihood and Finite Sites Model
Cavendar-Farris Neyman (CFN) model, Small maximum likelihood (ML) problem (Felsenstein's pruning algorithm), Large ML problem, Statistical (inconsisteny) of parsimony (Felsenstein Zone), Taxon sampling and Long branch attraction [materials] |
CP Sections 1.1-1.3, 5.1-5.5.2, 8.8 |
| Wed | Sep 24 |
Finite Sites cont.
GTR model, SHR assumptions, site rate heterogeneity, heterotachy, bootstrap
Supertrees Compatibility supertrees, ASSU, All Quartets, supertree optimization problems [materials] |
CP Sections 1.1, Chapter5, Chapter 8 | |
| Fri | Sep 26 | Problem set #1 due today! | ||
| 5 | Mon | Sep 28 | Distance Methods p-distance, distance correction, additive, ultrametric, Four Point Method, UPGMA, NJ, Balanced Minimum Evolution [materials] | CP Chapter 5 |
| Wed | Sep 30 | Multi-species Coalescent Model | TBD | |
| 6 | Mon | Oct 5 | Species Tree Reconstruction | TBD |
| Wed | Oct 7 | Species Network Reconstruction | TBD | |
| Fri | Oct 9 | Problem set #2 due today! | ||
| 7 | Mon | Oct 12 | No class - UMD Fall Break | |
| Wed | Oct 14 | Multiple Sequence Alignment (MSA) | TBD | |
| 8 | Mon | Oct 19 | From MSA to Whole Genome Alignment (WGA) | TBD |
| Wed | Oct 21 | Structural Variants | ||
| 9 | Mon | Oct 26 | Sequence conservation and hidden markov models | |
| Wed | Oct 28 | ML methods, connection to coalescent, etc | ||
| 10 | Mon | Nov 2 | Overflow day | |
| Wed | Nov 4 | Small reading group | ||
| 11 | Mon | Nov 9 | Large reading group | |
| Wed | Nov 11 | Exam Review | ||
| 12 | Mon | Nov 16 | Exam today in class at 2:00pm! | |
| Wed | Nov 18 | |||
| 13 | Mon | Nov 23 | ||
| Wed | Nov 25 | No class - Thanksgiving Holiday | ||
| 14 | Mon | Nov 30 | ||
| Wed | Dec 2 | |||
| 15 | Mon | Dec 7 | ||
| Wed | Dec 10 | |||
| 17 | Sun | Dec 20th | Project reports due today at 11:59PM ET! |