XML of Eurasian AIV

XML were created in BEAUti v1.6.2 for analysis in BEAST v1.7.3 (Drummond & Rambaut, 2007, Drummond et al. 2012). For each file, one internal segment of the same 344 subsampled Eurasian AIV (specified with subtype, host, location and isolate dates) was used as input data, labelled with the segment name. Files labelled with “original” represent the original time-scaled phylogenies of different segments. The substitution, clock and coalescent models are provided along with the priors placed on the model parameters. The other files labelled “empirical” and “H, N or HN” were generated to estimate the transition rate among discrete subtypes (HA, NA or HA-NA combined), with the implementation of a discrete trait model and BSSVS (Lemey et al. 2009) using empirical trees for each segment. These other files contain additional XML code not generated by BEAUTi in order to allow the re-use of the previously generated empirical tree sets.