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