Gapped k-mer support vector machine (gkmSVM) can predict stage-specific enhancers. (A) Topological illustration of the phylogenetic relationships between the three Drosophila species used to detect positive selection on enhancers. We want to detect positive selection that occurred on the lineage of D. melanogaster after divergence from D. simulans, as indicated by the red branch. Drosophila yakuba is the outgroup used to infer enhancer sequence in the ancestor of D. melanogaster and D. simulans. (B1–B5) Receiver operating characteristic (ROC) curves for gkmSVM classification performance on stage-specific enhancers. AUC values represent areas under the ROC curve and provide an overall measure of predictive power.