JIDT: Java Information Dynamics Toolkit for studying information-theoretic measures of computation in complex systems. JIDT provides a stand-alone, open-source code Java implementation (also usable in Matlab, Octave, Python, R, Julia and Clojure) of information-theoretic measures of distributed computation in complex systems: i.e. information storage, transfer and modification. JIDT includes implementations: principally for the measures transfer entropy, mutual information, and their conditional variants, as well as active information storage, entropy, etc; for both discrete and continuous-valued data; using various types of estimators (e.g. Kraskov-Stögbauer-Grassberger estimators, box-kernel estimation, linear-Gaussian). JIDT ships with a large number of demos, and includes a GUI app for automatic push-button analysis as well as code template generation to get you started.