Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.

For each virus family nucleotide sequences were first translated to amino acid data using Seqotron v.1.0.1 [32] , aligned with MUSCLE v.3.8 [33] , and poorly aligned regions then eliminated using trimAl [34] , ensuring that all remaining sequences were at least 100 amino acids in length (Table 1) . Amino acid sequences were aligned because there is widespread substitutional saturation at the nucleotide level. Although our data sets utilize single genes, we ensured that they were free of inter-specific virus recombination using RAT [35] . To estimate phylogenetic trees for the virus data sets we selected the optimal amino acid substitution model identified using the Bayesian Information Criterion as implemented in Modelgenerator v0.85 [36] and analyzed the data using PhyML v3.1 [37] , employing the SPR branch-swapping tree search algorithm (see Table 1 for the substitution models used). We assessed the support for individual nodes using the approximate likelihood ratio test (aLRT) implemented in PhyML v3.1 [38] , with aLRT values ranging between 0 (no support) and 1 (strong support). Studies involving simulations and empirical data have demonstrated that this statistic has similar false-positive rates to other metrics, such as the non-parametric bootstrap [39] .