Phylogenetics at RSABG

This semester we are studying computational phylogenetics. Many of the students haven’t used the R statistics environment before and learning to conduct analyses in R is one of the primary goals of lab this year, so I try to incorporate exercises in R as much as possible.

Prelab 2
Lab 2. Tree estimation (search & summary) and character evolution
Homework 2. Follow-up to Lab 2

Prelab 3
Lab 3. Multivariate statistics for examining taxonomic differentiation
Homework 3. Follow-up to Lab3

Prelab 4
Lab 4. Characteristics of molecular data: modelling variation

Lab 5. Models of molecular evolution and maximum likelihood

Lab 6. DNA sequence alignment, model estimation, and Bayesian inference
Homework 6. Follow-up to Lab 6

Lab 7. Bayesian analyses and post hoc analyses

Lab 8. Statistical tests on phylogenies: discordance among hypotheses

Lab 9. Gene trees in species trees