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copied!<p>In principle, Mathematica 8 should be able to handle your problem with its new <a href="http://reference.wolfram.com/search.html?query=Graph&lang=en&forward=off" rel="nofollow noreferrer">Graph</a> object. I say, "in principle", because I have trouble imagining how a cluster of almost 5 million nodes (or vertices) will look when printed on screen or on paper. It will be crucial that you choose a suitable GraphLayout, as this comparison from <a href="http://www2.research.att.com/~yifanhu/PUB/graph_draw_small.pdf" rel="nofollow noreferrer">Hu</a> shows: <img src="https://i.stack.imgur.com/S7iOG.png" alt="3 graphs"></p> <p>They are 3 depictions of the same graph (936 vertices), with the poorest rendering (of course) on the left. The article contains a rendering of a graph with 225k vertices that has a somewhat discernible structure.</p> <p>Anyway, it can handle input in the form of adjacency matrix or list of edges, among others. Edges may be directed or not. You can show and label all or some or none of the vertices and edges. You can also remove the clusters (GraphComponents) and display them alone or in combination. It also gives you various GraphLayout options: CircularEmbedding, SpiralEmbedding, HighDimensionalEmbedding, LargeNetwork, etc. There are a variety of GraphStyles. </p> <p>There is a command called NeighborhoodGraph that you may find useful for that huge cluster. Neighborhood[g,v,n] generates a subgraph of all nodes within n steps from vertex v. You can also simplify things by asking for a Subgraph with a predetermined list of edges, vertices or both.</p> <p>Beware that some of the Graph documentation will refer to Combinatorica, which though excellent and useful for many purposes, does not render graphs with as much precision, in my view, as the version 8 Graph object will.</p> <p>Some of the issues regarding graph layout for huge graphs are discussed <a href="http://www2.research.att.com/~yifanhu/PUB/graph_draw_small.pdf" rel="nofollow noreferrer">here</a>. There is also a <a href="https://stackoverflow.com/questions/238724/visualizing-undirected-graph-thats-too-large-for-graphviz">SO discussion</a> about plotting large graphs in which various software solutions are compared.</p>

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