An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
The SCUEAL clustering plots present in this figure and Figures 7, 8 and 9 are conceptually analogous to bootscan plots, i.e. which reference sequence is the most likely sister lineage of the query sequence for a given site, but is based on model averaged support values instead of phylogenetic bootstrap. A partial reference tree with placed query is shown; color coding is consistent between the similarity plot and the tree. A phylogenetic tree with bootstrap support values and bootscan plot using the REGA alignment generated for the query sequence are shown.