|1||Jan 21, 23||Introduction|
|Felsenstein Chapters 1-3, 9|
(We may come back to Chapter 4.)
Due by 6:00AM, Sunday, January 25: Email me two questions about the reading.
|Due Friday, January 30: Homework 1|
|2||Jan 26, 28, 30||Parsimony||Felsenstein Chapters 4 and 11|
Due by 6:00AM, Sunday, February 1: Email me two questions about the reading.
|3||Feb 2, 4, 6||Distance Methods|
Continuous-time Markov chains
|Felsenstein Chapter 13|
Due by 6:00AM, Sunday, February 8: Email me two questions about the reading.
|Due Friday, February 13: Homework 2|
|4||Feb 9, 11, 13||Continuous-time Markov chains|
|Felsenstein Chapter 16|
Due by 6:00AM, Sunday, February 15: Email me two questions about the reading.
|5||Feb 16, 18, 20||Likelihood Methods||
Holder and Lewis (2003). Nature Review: Genetics|
Note: Please read the articles, but you need not send questions for this reading. You may defer questions until the next week.
|6||Feb 23, 25, 27||Bayesian Phylogenetics||Felsenstein Chapter 18|
Due by 9:00PM, Monday, March 1: Email me two questions about the reading.
|Due Friday, March 5: Homework 3|
|7||Mar 1, 3, 5||Computation, Bayesian Phylogenetics, Bootstrap||Felsenstein Chapter 20||oneBranch.C|
|8||Mar 8, 10, 12||Bootstrapping Phylogenies||Susan Holmes (2003) Statistical Science|
Note: Please read Susan Holmes at some point (the early sections are especially clear).
Please give Newton a read by Friday (but do not become stressed about the details).
|Break||Mar 15, 17, 19|| || || |
|9||Mar 22, 24, 26||Bootstrapping, Reversible Jump MCMC, Model Selection||
Mark Pagel (1999) Systematic Biology|
Due by 6:00PM, Thursday, April 1: Email me two questions about the reading.
|10||Mar 29, 31, Apr 2||Reversible Jump MCMC|| || |
|11||Apr 5, 7, 9||Evolution of discrete characters|
Mapping mutations on phylogenies
| || |
|12||Apr 12, 14, 16||Goodness-of-fit Tests, Tests of Topology||Assigned reading for Monday|
Felsenstein Chapter 21.
Shimodaira and Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution.
Goldman, Anderson, and Rodrigo (2000). Likelihood-based tests of phylogenies in phylogenetics. Systematic Biology
Due by 6:00AM, Sunday, April 18: Email me two questions about the reading.
Other background reading (not assigned) Posada and Crandall (1998)
|13||Apr 19, 21, 23||Tests of Topology, Genome Arrangements|| || |
|14||Apr 26, 28, 30||Genome Arrangements (parsimony)|| || |
|15||May 3, 5, 7||Genome Arrangements (Bayesian)|| ||Due Friday, May 7: Homework 4|
Bret Larget, firstname.lastname@example.org