Grad Core Phylogenetics 2012

Syllabus Fall 2012:

Day 1

Topics:
Why phylo?
Continuous time Markov Chain finite state space
Doing this in Geiger: get exercise Discrete.R
Slides (PDF)

Day 2

Topics:
In class review quiz
Central limit theorem CLT.R
Brownian motion, Ornstein Uhlenbeck, Independent Contrasts
Slides (PDF)

Day 3

Topics:
In class review quiz
Likelihood vs Bayes redux
Model comparison exercise
Tree stretching
Tree stretching exercise
Slides (PDF)

Day 4

Topics:
In class review quiz
Working through homework. What did you conclude? What does it mean? (relevant R script is here)
Delve deeper into how to do an analysis.
Diversification
Slides (PDF)

Day 5

Topics:
Doing a good analysis
Slides (PDF)

Day 6

Topics
Continuing pair analyses

Final

Concatenation of all slides (PDF)
Study guide (PDF)