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I am looking for a software that can plot graphs in the spirit of Graph Thing.

I have been using a little bit this software and I enjoyed the few possibilities that are offered.

Some good points:

  • It is possible to ask for basic graph predicates
  • One can either draw the graphs in WYSIWIG style or by providing adjacency in simple text style

Some bad points:

  • It has not been updated for years
  • There are some bugs with the save/open option
  • It is not possible to simply provide the adjacency matrix of the graph and ask the software to plot it. Hence, working with graphs with more than a dozen of vertices is a bit tricky, especially if one wants to get a nice picture of the graph.

Is there any such software, apart of Mathematica?

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Sage should be the canonical answer. It's free and it's awesome. You can generate a graph by

  • Giving its graph6 string
  • Giving its adjacency matrix
  • Specifying its edges
  • Other

There are many built-in graphs that you can use without much work at all. For a few basic examples,

g = graphs.CompleteGraph(10)
g = graphs.PathGraph(6)
g = graphs.PetersenGraph()
g = graphs.RandomGNP(12, 0.5)

You can then add or delete vertices or edges to any of these graphs. Or, you can use graphs already constructed to build new ones in other ways, like the line graph of a graph or a product (various types of products built-in) of two graphs.

There is also a graph editor which allows you to add and delete edges and vertices to already existing graphs with a mouse, and you can move the vertices around to make it look nice as well. And, the graphics it outputs as PDFs are high quality vector graphics.

And, you can do more than just draw graphs. You can get information about the graphs, because the graphs are Sage objects.

See here and scroll down to the second video, "William Stein explains Graph Theory in Sage", to learn more about this.

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Graph Vis is the canonical answer. (Google it.)

I'm not really aware of any other similar software. (Though it would be useful if I was!)

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