Inferred tumor phylogeny for Patient 2 from Gawad et al. (2014) with (A) SCITE and (B) B-SCITE. The coloring of the trees is motivated by the colors used for SCITE and B-SCITE in the previous figures. B-SCITE's use of VAFs alter the tree topology by moving the mutation in CMTM8 higher up in the tree. B-SCITE also reorders the mutations in genes in the linear topology identified by SCITE rooted at FGD4 —primarily according to their VAFs.