Fig. 3. Phylogenetic analysis of this dataset using two typing schemes. (a) Phylogenetic tree generated using the wgSNP typing scheme. The scale bar represents Hamming distance. (b) Phylogenetic tree generated using the gp60 sequences. The scale bar represents substitutions per site. (c) PCoA carried out using a Hamming distance matrix generated from the wgSNP set. Marker shapes represent gp60 subtypes. Coloured by country of isolation. (d) Correlation analysis of typing schemes generated using the pairwise distance of each pair of samples within the dataset, R2=0.14, P<0.01. Cluster markers are placed by the root node in tree (a) for each cluster and used to annotate the PCoA plot.
