show/hide this revision's text 4 punctuation to remove ambiguity

You might start by exploring the various tools that are available. For example, Mathematica's GraphPlot3D[] does a nice job with small graphs. Here is a 5-node graph:
      Graph 3D
And here is a somewhat dense 50-node graph:
      Graph Random 50

Both were produced without giving Mathematica any advice. Like most such tools, it has options for applying different methods, e.g., SpringEmbedding.

Edit. As requested by Surikator, here are some more sparse random, more-sparse, 50-node graphs:
Sparse graphs
show/hide this revision's text 3 Added some sparse graphs.

You might start by exploring the various tools that are available. For example, Mathematica's GraphPlot3D[] does a nice job with small graphs. Here is a 5-node graph:
      Graph 3D
And here is a somewhat dense 50-node graph:
      Graph Random 50

Both were produced without giving Mathematica any advice. Like most such tools, it has options for applying different methods, e.g., SpringEmbedding.

Edit. As requested by Surikator, here are some more sparse 50-node graphs:
Sparse graphs
show/hide this revision's text 2 Added 50-node graph.

You might start by exploring the various tools that are available. For example, Mathematica's GraphPlot3D[ GraphPlot3D[] does a nice job with small graphs. I just Here is a 5-node graph:
      Graph 3D
And here is a somewhat dense 50-node graph:
      Graph Random 50

Both were produced this without giving Mathematica any advice: . Like most such tools, it has options for applying different methods, e.g., SpringEmbedding.
show/hide this revision's text 1