Graphthing

http://graph.seul.org/

GraphThing is a tool that allows you to create, manipulate and study graphs.

These “graphs” are mathematical objects (Graph Theory) that describe relationships between sets; they are not 2D plots, charts, or anything similar to that.

GraphThing is Free Software, licensed under the terms of the GNU GPL. That means that not only does it cost you nothing, but you also have the freedom to redistribute it or modify it however you please, so long as you also give these freedoms to others.