Figure 2
![Figure 2](http://media.springernature.com/full/springer-static/image/art%3A10.1186%2F1471-2105-8-213/MediaObjects/12859_2007_Article_1585_Fig2_HTML.jpg)
3DPE main view mode for COG1222, ATP-dependent 26S proteasome regulatory subunit. 3DPE projects evolutionary information onto three spatial axes: each species is mapped to a unique location of on the X-axis; each orthologous group is assigned a unique plane on the Z-axis; and the Y-axis represents evolutionary distance. This can both yield valuable insights and reveal potential problems with the tree; e.g. the absence of paralogs in the Archaea suggests that these paralogs were created after the divergence of Eukaryota and Archaea, and thus that the tree's root should actually be at the node marked with an asterisk (*). Thus, 3DPE can make it easier to spot potential errors in the tree, which could be tested using other methods such as outgroup analysis. Genes are represented as hexagonal boxes and each species has its distinct color. Species (Taxonomy IDs): 2234, 145262, 190192, 2190, 29292, 53953, 188937, 56636, 2287, 64091, 4932, 4896, and 6035. Text size in VRML2 object is small not to interfere with other VRML2 objects. One can easily zoom in and read annotations from 3DPE 3D layout. All 3D objects are clickable to show additional information.