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Is there any java file that I can use to perform "agglomerative clustering" Result should provide me every level nodes id help.................

A: 

Have you looked at Weka's HierarchicalClusterer class?

In any case, the agglomerative hierarchical clustering algorithm is fairly straightforward, assuming you have a function that yields the distance value between two clusters.

For a standard example, Kruskal's minimum spanning tree algorithm proceeds by clustering nearby nodes.

Jeffrey Hantin