Introduction
1. Background
2. Retrieving sequences
- 2.1. Theory
- 2.2. Practice
3. Sequence alignment
- 3.1. Theory
- 3.2. Practice
4. Distance-based analyses
- 4.1. Theory
- 4.2. Practice
  - 4.2.1. Neighbour joining example
  - 4.2.2. Exercise
5. Recombination
- 5.1. Theory
- 5.2. Practice
  - 5.2.1. Exercise
6. Maximum likelihood based analyses
- 6.1. Theory
- 6.2. Practice
7. Visualising trees
- 7.1. Practice
  - 7.1.1. Exercise
8. Time-stamped phylogenies
- 8.1. Theory
- 8.2. Practice
  - 8.2.1. Fixing the maximum likelihood tree
  - 8.2.2. Time tree exercise
9. Bayesian reconstruction of time trees
- 9.1. Theory
- 9.2. Practice
  - 9.2.1. MrBayes example
10. Effective population size estimation
- 10.1. Theory
- 10.2. Practice
  - 10.2.1. Fitting skyline
  - 10.2.2. Exercise
11. Structured populations
- 11.1. Theory
- 11.2. Practice
  - 11.2.1. 'Mugration' exercise
12. References
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Visualising trees

Now that you have some trees, you want to plot them. In this section, I'll outline some of the packages that allow you to plot trees. No theory in this section, all practice!