HPV18 tree topology and pairwise comparisons of individual complete genomes.

<p>Phylogenetic trees were inferred from global alignment of complete genome nucleotide sequences (the other alpha-7 HPV reference prototypes were set as the outgroup). Numbers on or near branches indicate support indices in the following order: maximum likelihood (ML) bootstrap percentages using RAxML MPI v 7.2.8.27 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072565#B42" target="_blank">42</a>] and PhyML MPI v 1.4.3 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072565#B43" target="_blank">43</a>], and Bayesian credibility value percentage using MrBayes v 3.1.2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072565#B44" target="_blank">44</a>]. An asterisk (*) indicates 100% agreement between methods. “NA” indicates disagreement between a method and the reference RAxML tree at a given node. Thus, one tree is shown, but three different methods of tree construction were used to estimate the support of the provided tree, as explained above. Distinct variant lineages (i.e., termed A, B, and C) are classified according to the topology and nucleotide sequence differences from > 1% to < 10%; distinct sublineages (e.g., termed A1 and A2) were also inferred from the tree topology and nucleotide sequence differences in the > 0.5% to < 1% range. The percent nucleotide differences for each isolate compared to all other isolates (i.e., 1 x 1 comparisons) are shown in the panel to the right of the phylogeny. Values for each comparison of a given isolate are connected by lines and the comparison to self is indicated by the 0% difference point. Symbols and colored lines are used to distinguish each isolate.