Scientists recently involved in Network Alignment Topic at Bioinformatic's Networks. People are trying to both find alignments in one path. At another path, people are involved in better visualization outputs. Today, I found a graph for alignment at Milenkovic et al's, "Optimal Network Alignment with Graphlet Degree Vectors". Here, they found shared PPI interactions and nodes of two species. They provide as simple force directed layout output. See the following image:
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