Introduction |

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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Lecture notes, examples, and exercises for 'Molecular Epidemiology of Viruses in R'.

These notes were generated using Gitbook (Pesse and O'Mullan, 2014), knitr (Xie, 2015), and knitcitations (Boettiger, 2014).

Given that this work has benefited so much from open source software, all text and figures are licensed under the Creative Commons CC0 1.0 Universal license, and all code is licensed under the MIT License. Share and enjoy!