Figure 1.

2D vs. 3DPE views of the same tree. In standard (2D) phylogeny layout it is not always easy to distinguish gene duplication events (paralogs) from speciation branching (species), because only one spatial axis (labelled "genes" in the diagram above) is available to show the mix of these two kinds of information. By contrast, they can be distinguished at a glance in 3DPE, because it projects them onto two orthogonal axes; species (X) vs. paralogs (Z). For example, whereas the evolution of a large number of paralogs is visually obvious in the 3DPE view (in the three eukaryote species, on the right), this pattern is less clear in the 2D representation. Both trees represent COG1222, and 2D tree was downloaded from the COG database.