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The Visual Understanding Environment (VUE) is an Open Source project based at Tufts University. One can classify nodes and edges informally with keywords sorted into categories or use full-fledged ontologies. It is possible to hierarchically nest nodes inside other nodes. The display quality and styling options are good but could be improved. There are no import/export filters to established graph description languages, and VUE lacks the analysis tools of Gephi, while being generally more stable (both are programmed in Java).
VUE can produce presentations based on marking paths (with alternatives) on your graph.
VUE development is not very transparent although it seems that the next version will be available in a git repository. A very successful plugin that allowed one to map a literature database in Zotero is now unmaintained and it is impossible to obtain a statement from the developers on whether it will be fixed or left to rot.