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I've had a lot of luck with Gephi for fairly complex graphs (~10000 nodes and edges), in particular it has some very powerful layout algorithms. It can be very

by nurbl 4y ago

I've had a lot of luck with Gephi for fairly complex graphs (~10000 nodes and edges), in particular it has some very powerful layout algorithms. It can be very helpful to have immediate visual feedback when untangling something like that. Nice to see that development is ongoing, the GUI used to feel a bit clunky but 0.10 seems a lot better!

anigbrowl 4y ago
Seconding this. Get Gephi, install as many plugins as possible, and dig into the plugin pages to find the underlying papers. Also true for Cytoscape, but that tool focuses a little more on connectivity to bio databases and extremely specific stuff like proteomics.