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An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

Figure 4

A simulation scenario example.

One of the simulation scenarios used to asses our detection method with the results over replicates (scenario 5/close in Table 2). The query sequence (2) was simulated to move from reference lineage 1 to reference lineage 3 every 400 bp as shown in the tree panel. The clustering chart depicts model and replicate averaged support for assigning the query sequence to a particular reference lineage, as estimated by the genetic algorithm over 100 simulated data replicates, whereas black impulse plots indicate the inferred placements of breakpoints. The y-axis does not reach because each replicate contributes the model averaged support for the best inferred mosaic type–a value that is ; the upper limit on the y-axis is, therefore, the mean (over replicates) model-averaged support for the best-fitting mosaic (0.92 in this case).

Figure 4