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JWalk   - Representation learning on graphs.
node2vec   - Scalable Feature Learning for Networks.
Pajek   - a (large) network analysis and visualization tool.
PEGASUS: Peta-Scale Graph Mining System  
SNAP   - means Stanford Network Analysis Platform (SNAP). It is a general purpose network analysis and graph mining library.
statnet   - a suite of software packages for network analysis that implement recent advances in the statistical modeling of networks.