XML were created in BEAUti v1.5.4 for analysis in BEAST v1.7.4, as described in Hedge et al. 2013 (Drummond & Rambaut, 2007, Drummond et al. 2012). Each file specifies the EpiFlu accession numbers of the segments concatenated into the whole-genome sequences and used as input data for the analysis (http://platform.gisaid.org/). Each file is labelled with the name of the last month during which sequences included in the analysis were sampled and the growth modelled employed. For example, June.exp.xml comprises EpiFlu accession numbers of sequences sampled from the start of the pandemic until June 2009 and specifies the use of an exponential growth model. Details of the substitution, clock and coalescent models are provided along with the priors placed on the model parameters. An additional block implementing the estimation of the marginal likelihood of the model using path-sampling is given after the Markov chain Monte Carlo (MCMC) block (Baele et al. 2012)
