Hi, I'm Gephi main developper.

I think Gephi fits to your needs because it can handle very large graphs,
and propose innovative layout algorithms. On our 8gb ram machine, we handle
300K nodes and 1.5M edges, rendering is slow but it's still fine.

But the problem you're describing is a layout issue. With traditionnal
Spring repulsion or Fruchterman-Reingold algorithm, you have a O(N²)
algorithm. Scaled to millions of nodes and edges, computing require hours
for each algorithm pass. In Gephi we recently implement Yifan Hu's layout
algorithm, that has a 0(nlog(n)) complexity. I recommed you to try this out.
This problem is often references as multilevel graph layout algorithm.

Cheers
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