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Rapid Miner has it :

http://docs.rapidminer.com/studio/operators/data_transformation/filtering/sampling/sample_kennard_stone.html

R has it :

http://soilspec.r-forge.r-project.org/ken.sto.html

Weka i dunno ...

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Just a word of caution : with a simple KS procedure, your training and test sets will not be independent (which may be of very little significance in practice but will ruin many theoretical approaches) ; the KS procedure can be modified so as to build independent samples while keeping the uniformity property ; see DUPLEX

http://www.mff.cuni.cz/veda/konference/wds/proc/pdf10/WDS10_105_i1_Reitermanova.pdf

(the above link is a short introduction to data-splitting)

.R.D. Snee, Validation of regression models: methods and examples, Technometrics 19 (1977) 415-428

(the original paper)

R has it :

http://finzi.psych.upenn.edu/library/prospectr/html/duplex.html

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Weka has the requested feature.

Please see http://weka.sourceforge.net/doc.dev/weka/classifiers/Evaluation.html