Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data

Run the phylogeographic analysis

Open BEAST and select the file pandemic_geo.xml.

This analysis (because of the function to infer ancestral states) requires that BEAGLE be loaded.

Select ‘Use BEAGLE library if available’.

Generally, I turn on SSE as this should give a decent speed increase and set the ‘Rescaling scheme’ to ‘Dynamic’.


Click on ‘Run’.

This will produce the output files pandemic_geo.log, pandemic_geo.rates, pandemic_geo.root and pandemic_geo.trees. This analysis took ~24 hours to complete on a single cluster node.

I’ve included these files with the practical in the output/ directory.

Next section