Comparisons of approaches of GeneTree and OrthoParaMap. The top tree is a clade from the middle of the MAGE phylogeny in Figure 1. The bottom tree shows the "reconciled" species and gene family tree predicted by GeneTree . Gene duplications in the GeneTree prediction are indicated with small squares, and all other nodes are predicted speciations. Inferred sequence losses are shown in gray. The two procedures provide complementary results: OPM identifies which genes are part of synteny blocks or clusters, and GeneTree predicts some additional gene duplications or losses based on speciation and gene family trees.