Pathogen evolution, selection and immunity


H3N2 influenza undergoes frequent antigenic drift in which a new variant emerges and takes over the viral population. Here, we will investigate phylogenetic and coalescent patterns of variant emergence and spread. This tutorial walks through how to use BEAST and associated software to infer spatiotemporal dynamics from viral sequence data.

Required software

  • BEAST is used to infer evolutionary dynamics from sequence data. Download here.
  • BEAGLE is a helper library that allows faster and more advanced functions to be run in BEAST. For this practical, it is not necessary to install CUDA drivers (step 2 in the BEAGLE installation). Download here.
  • Tracer is used to analyze parameter estimates from BEAST.
  • FigTree is used to analyze phylogeny estimates from BEAST.


  1. Compile sequence data
  2. Prepare BEAST analysis
  3. Run BEAST analysis
  4. Examine MCMC output
  5. Examine tree output
  6. Analyze vaccine strain choice

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