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:

And here is a somewhat dense 50-node graph:

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:

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:

And here is a somewhat dense 50-node graph:

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:

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:        And here is a somewhat dense 50-node graph:       
 Both were produced this without giving Mathematica any advice: . Like most such tools, it has options for applying different methods, e.g., SpringEmbedding.