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Try using this knn.jar, it has both trees as an option. Although that one isn't using my latest tree, you should be able to figure out how to change which tree it is using.

Seriously, the different in performance between RedGen3 and Skil are pretty negligible. You'd be better off putting the time into figuring out how to reduce a dimension of the data you're storing, or something like that, which will actually provide a speedup.

how do i change which tree its using

You'll need to extract the .jar file, and make a new wrapper class in net/robowiki/knn/implementations directory, similar to the other ones there. Then at the top of net/robowiki/knn/implementations/KNNBenchmark.java you'll need to add a reference to the tree you want to test, like the others are referenced.

how do i make a new knn.jar with the latest skilgannon kd-tree

You don't need to. Just run the KNNBenchmark by java KNNBenchmark.class

it doesn't work