Lectures
Lectures
Schedule
Old handouts (some will move up some will replaced)
25 Aug 2009
27 Aug 2009
1 Sep 2009
Coalescence theory: Introduction
[Handout 3]
3 Sep 2009
Coalescence theory: Variance, Extensions
[Handout 4]
© Peter Beerli 2011 Tallahassee
8 Sep 2009
Mutation models: introduction, DNA models
[Handout 5]
10 Sep 2009
15 Sep 2009
Mutation models: Microsatellite model, Infinite allele model, ....
[Handout 7] [Handout 8 (not discussed)]
17 Sep 2009
29 Aug 2011
Trees as constructs to represent relationships (algorithms to represent, traverse etc).
[Handout 1]
2 Sep 2011
Parsimony methods
[Handout 2]
29 Sep 2009
Counting trees.
[Handout 11]
1 Oct 2009
Likelihood calculations (general and on trees)
[Handout 12]
6 Oct 2009
Likelihood calculations on trees
[Handout 13]
6 Sep 2011
Best Tree: exhaustive,Branch-and-Bound, heuristic searches
[Handout 3]
8 Sep 2011
Stochastic mutation models 1: nucleotide models
[Handout 4]
13 Sep 2011
Stochastic mutation models 1: nucleotide models (cont.)
15 Sep 2011
20 Sep 2011
Stochastic mutation models 3: microsatellites and other models (cont.)
Stochastic mutation models 4: Morphology
22 Sep 2011
Process heterogeneity across sites and trees
27 Sep 2011
29 Sep 2011
Calculation of likelihood on a tree (a very simple one)
[Handout 10] and a Python example, the file contains two tests use it as a memo and notepad in class
04 Oct 2011
Bayesian inference [Handout 11] [Paul Lewis’ MOLEVOL Bayesian lecture]
06 Oct 2011
Markov chain Monte Carlo [Handout 12] [Paul Lewis’ MOLEVOL Bayesian lecture]
11 Oct 2011
Markov chain Monte Carlo in practice, see Python program mcmc.py [Handout 12] [Paul Lewis’ MOLEVOL Bayesian lecture]
13 Oct 2011
Tree models [Handout 13]
18 Oct 2011
Population genetics [Handout 14] [Handout 15]
20 Oct 2011
Population genetics [Handout 15]
20 Oct 2011
Population genetics [Handout 15]
25 Oct 2011
Coalescence theory [MOLEVOL slides]
25 Oct 2011
Coalescence theory [Handout 16]
25 Oct 2011
Coalescence theory [Handout 17]