I've been using Metanet (a Scilab toolbox) to manipulate graphs via scripts, but they lack nice visualizations resources as yEd does. So it would be nice if yEd could load/save the .graph and .xgraph formats, the only ones used by Metanet.
For now, I'm using some crappy scripts to load/save tgf files in Scilab, and then opening them on yEd for better visualization.