Date
|
Topic
|
Reading
|
| |
|
|
| 4/1 |
What is a phylogeny? Parsimony - a small example |
Chapter 1 |
| 3 |
Parsimony algorithms - small parsimony problem |
Chapter 2 |
| 5 |
Exact enumeration - the number of trees |
Chapter 3 |
| |
|
|
| 4/8 |
Searching tree space heuristically |
Chapter 4 |
| 10 |
Branch and bound |
Chapter 5 |
| 12 |
Reconstruction of ancestral character states. Branch lengths |
Chapter 6 |
| |
|
|
| 4/15 |
Variants of parsimony |
Chapter 7 |
| 17 |
Compatibility |
Chapter 8 |
| 19 |
Inconsistency and parsimony |
Chapter 9 |
| |
|
|
| 4/22 |
" " " |
" " |
| 24 |
A brief discussion of philosophy, parsimony, history etc. |
Chapter 10 |
| 26 |
Distance matrix methods: UPGMA, Fitch-Margoliash |
Chapter 11 |
| |
|
|
| 4/29 |
" " " : Neighbor-joining,
Minimum evolution, etc. |
Chapter 11 |
| 5/1 |
DNA distances incl. rate variation among sites, |
Chapter 13 |
| 3 |
Protein distances and models |
Chapter 14 |
| |
|
|
| 5/6 |
Restriction sites, RAPDs, microsatellites, etc. |
Chaps. 14, 15 |
| 8 |
Likelihood methods |
Chapter 16 |
| 10 |
Bayesian inference |
Chapter 18 |
| |
|
|
| 5/13 |
Testing trees, clocks, etc. by likelihood ratio tests |
Chapter 19 |
| 15 |
The bootstrap, the jackknife, etc. |
Chapter 20 |
| 17 |
" " " |
" " |
| |
|
|
| 5/20 |
The KHT test(s) |
Chapter 21 |
| 20 |
Invariants ("evolutionary parsimony") |
Chapter 22 |
| 22 |
Trees from continuous characters and gene frequencies |
Chaps. 23, 24 |
| |
|
|
| 5/27 |
HOLIDAY (Memorial Day; last day of NW Folk Life Festival) |
|
| 29 |
Comparative methods |
Chapter 25 |
| 31 |
Another kind of tree: Coalescents |
Chapter 26 |
| |
|
|
| 6/3 |
Likelihoods on coalescents |
Chapter 27 |
| 5 |
Consensus trees. Tree distances. |
Chapter 33 |
| 7 |
Tests based on tree shape. Drawing rooted and unrooted trees |
Chaps. 33, 34 |