Optimized phylogenetic clustering of HIV-1 sequence data for public health applications
Fig 5
Concordance between predicted growth in phylogenetic clusters and the actual (simulated) transmission network.
The top and bottom barplots summarize phylogenetic clusters obtained under bootstrap thresholds of 0% and 95%, respectively. Bars correspond to the number of incident cases mapped to phylogenetic clusters, coloured by three distance thresholds: dmax = 0.01, the ΔAIC optimum, and dmax = 0.03. Distance in transmission network is the shortest path in the transmission network between the incident case and any member of the predicted cluster. A distance of zero means the actual source individual is in the cluster, and distances greater than zero indicate the actual source was not sampled. Unsampled indicates that none of the sampled infections in the transmission history of an incident case were members of the phylogenetic cluster. Discordant indicates that the actual source individual was sampled but does not appear in the predicted cluster.