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A disk based production quality RTree based upon Guttmans quadratic split algorithm having following features:
Buffering with dirty write,
Index joins,
Tree Seeding,
Window and NN queries,
Runtime STR Packing capability,
Completely Thread safe.
geoLucene is an extension of Lucene that allows to effectively index and search documents that contain locational information (longitude/latitude). It uses R-tree as a spacial index. See http://www.gossamer-threads.com/lists/lucene/java-dev/53378.