The layout algorithm. In this example proteins with the same color are orthologous (if they are in different panels in rows 1, 3, or 4 of the figure) or paralogous (if they are in the same panel). The two networks in Ia) and Ib) are first merged to the graph in II). This graph is now laid out, as seen in III). This layout is assigned to the two individual networks as shown in IVa) and IVb). In the last step paralogs, that are still merged in the individual networks are laid out and the results are shown in Va) and Vb).