The best reference for WEKA 3.8 and 3.9 is the online appendix on the WEKA workbench for the fourth edition of "Data Mining: Practical Machine Learning Tools and Techniques" by I.H. Witten, Eibe Frank, Mark A. Hall, and Chris J. Pal. The citation is
Eibe Frank, Mark A. Hall, and Ian H. Witten (2016). The WEKA Workbench. Online Appendix for "Data Mining: Practical Machine Learning Tools and Techniques", Morgan Kaufmann, Fourth Edition, 2016.
You may also want to consider the SIGKDD Explorations paper covering WEKA 3.6. The citation is
Mark Hall, Eibe Frank, Geoffrey Holmes, Bernhard Pfahringer, Peter Reutemann, and Ian H. Witten (2009). The WEKA Data Mining Software: An Update. SIGKDD Explorations, Volume 11, Issue 1.
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