Respectfully, I will be appreciative if you inform me what is the best software for analyzing a huge graph with more than about 10^4 nodes?
What type of analysis do you wish to perform on this graph? Depending on the task the complexity may vary quite a lot! :-)
Try cytoscape
http://cytoscape.org/
Hey Mahdieh!
Gephi is thought to be used for very large graphs (see link).
Greetings, David
https://gephi.org/
Pajek is another software used for large graphs. Here is the link:
http://vlado.fmf.uni-lj.si/pub/networks/pajek/howto.htm
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