Good Java graph algorithm library?

Summary:

• JGraphT if you are more interested in data structures and algorithms.
• JGraph if your primary focus is visualization.
• Jung, yWorks, and BFG are other things people tried using.
• Prefuse is a no no since one has to rewrite most of it.
• Google Guava if you need good datastructures only.
• Apache Commons Graph. Currently dormant, but provides implementations for many algorithms. See https://issues.apache.org/jira/browse/SANDBOX-458 for a list of implemented algorithms, also compared with Jung, GraphT, Prefuse, jBPT

Check out JGraphT for a very simple and powerful Java graph library that is pretty well done and, to allay any confusion, is different than JGraph. Some sample code:

UndirectedGraph<String, DefaultEdge> g =
        new SimpleGraph<String, DefaultEdge>(DefaultEdge.class);

    String v1 = "v1";
    String v2 = "v2";
    String v3 = "v3";
    String v4 = "v4";

    // add the vertices
    g.addVertex(v1);
    g.addVertex(v2);
    g.addVertex(v3);
    g.addVertex(v4);

    // add edges to create a circuit
    g.addEdge(v1, v2);
    g.addEdge(v2, v3);
    g.addEdge(v3, v4);
    g.addEdge(v4, v1);

If you were using JGraph, you should give a try to JGraphT which is designed for algorithms. One of its features is visualization using the JGraph library. It's still developed, but pretty stable. I analyzed the complexity of JGraphT algorithms some time ago. Some of them aren't the quickest, but if you're going to implement them on your own and need to display your graph, then it might be the best choice. I really liked using its API, when I quickly had to write an app that was working on graph and displaying it later.