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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Time-stamped phylogenies

So far, all of our trees have been in units of genetic divergence. We are often most interested in calendar time. If we can either assume or estimate an evolutionary rate, we can root the tree and change the scale to real time.