Lectures

 

Schedule

Old handouts (some will move up some will replaced)

25 Aug 2009

Introduction to population genetics: Wright-Fisher model
[Handout 0] [Handout 1]

27 Aug 2009

Introduction to population genetics: Canning model, Moran model, effective population size,
[Handout 1] [Handout 2]

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

Mutation models: DNA models, protein models
[Handout 5] [Handout 6]

15 Sep 2009

Mutation models: Microsatellite model, Infinite allele model, ....
[Handout 7] [Handout 8 (not discussed)]

17 Sep 2009

Substitutions versus mutations, site rate variation, and general introductions of trees as constructs to represent relationships (algorithms to represent, traverse etc).
[Handout 5][Handout 7] [Handout 9]

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

Stochastic mutation models 2: protein models
[Handout 5]

Stochastic mutation models 3: microsatellites and other models

[Handout 6]

20 Sep 2011

Stochastic mutation models 3: microsatellites and other models (cont.)

Stochastic mutation models 4: Morphology

[Handout 7]

22 Sep 2011

Process heterogeneity across sites and trees

[Handout 8]

27 Sep 2011

Introduction to likelihood

[Paul Lewis’ MOLEVOL likelihood lecture]

[Handout 9]

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

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]