Date | Topic | Reading |
| 3/27 | What is a phylogeny? Parsimony - a small example | Chapter 1 |
| 29 | Parsimony algorithms - small parsimony problem | Chapter 2 |
| 31 | Exact enumeration - the number of trees | Chapter 3 |
| 4/3 | Searching tree space heuristically | Chapter 4 |
| 5 | Branch and bound | Chapter 5 |
| 7 | Reconstruction of ancestral character states. Branch lengths | Chapter 6 |
| 4/10 | Variants of parsimony | Chapter 7 |
| 12 | Compatibility | Chapter 8 |
| 14 | Inconsistency and parsimony | Chapter 9 |
| 4/17 | A brief discussion of philosophy, parsimony, history etc. | Chapter 10 |
| 19 | Distance matrix methods: UPGMA, Fitch-Margoliash | Chapter 11 |
| 21 | " " " : Neighbor-joining, Minimum evolution, etc. | Chapter 11 |
| 4/24 | DNA distances incl. rate variation among sites, | Chapter 13 |
| 26 | Protein distances and models, Restriction sites and RAPD | Chaps. 14, 15 |
| 28 | Guest lecture (Richard Olmstead, Botany Dept.) | |
| 5/1 | Guest lecture (Scott Edwards, Zoology Dept.) | |
| 3 | Microsatellite distances and models | Chapter 15 |
| 5 | Likelihood methods | Chapter 16 |
| 5/8 | " " | Chapter 16 |
| 10 | Testing trees, clocks, etc. by likelihood ratio tests | Chapter 17 |
| 12 | The bootstrap, the jackknife, etc. | Chapter 18 |
| 5/15 | The KHT test(s) | |
| 17 | Invariants ("evolutionary parsimony") | Chapter 20 |
| 19 | Trees from continuous characters and gene frequencies | Chaps. 21, 22 |
| 5/22 | Comparative methods | |
| 24 | Other kinds of trees: Coalescents | Chapter 24 |
| 26 | Likelihoods on coalescents | Chapter 25 |
| 5/29 | HOLIDAY (Memorial Day; last day of Folk Life Festival) | |
| 31 | Tree distances. Consensus trees | Chapter 28 |
| 6/2 | Tests based on tree shape. Drawing rooted and unrooted trees |
2:30-4:30 Wednesday, June 7 in J280 HSB
Felsenstein, J. 2000. Inferring Phylogenies. ASUW Publishing, Seattle. (available at their office in HUB 113, price about $20).