This course will introduce students to current analytical methods for answering applied questions in evolution and epidemiology based on pathogen genetic data. Topics will include tree building, molecular clocks, inferring demographic histories using coalescent approaches, ancestral state reconstruction and phylogeography; focusing on the widely used software BEAST as well as other computer programs.

The course will be offered over five half days that will combine lectures (1 hour per day) and practical computer labs (2 hours per day.

None.

Students will submit practical exercises to gauge their depth of understanding and engagement with the skills learned in each of the practical sessions. The work will be assessed not only on completion of the assigned tasks but on interpretation and self reflection of the theories learned (40%). The remaining 60% will be based on a particular applied research problem in pathogen evolution and epidemiology for which the students are asked to analyse a provided data set using the tools learned in the course and write up a scientific report based on their findings (2000-3000 words).

To provide students with the conceptual background and hands-on training for analysing and interpreting genetic data to answer applied questions in evolutionary biology and epidemiology through the use of relevant specialised computer software and critical evaluation of the scientific literature.

By the end of this course students will be able to:

- Critically discuss, with respect to the primary literature, the use of various types of genetic data used in evolutionary analysis and epidemiology and their suitability for addressing specific research questions

- Conduct basic analyses on such data using contemporary software (including program BEAST and others) and to diagnose and troubleshoot problems encountered during analysis

- Critically interpret and synthesise results of these analyses and make specific research and management recommendations on their basis with reference to the evidence base

Students must submit at least 75% by weight of the components (including examinations) of the course's summative assessment.