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In the 20th century, newly invented technical artifacts were connected to form large-scale complex engineering systems. Furthermore, the interactions found within these networked systems has grown in both degree as well as heterogeneity. Consequently, these already complex engineering systems have converged in what is now called systems-of-systems. The analysis, design, planning, and operation of these engineering systems from a holistic perspective has necessitated ever-more sophisticated modeling techniques. Despite significant advancements in model-based systems engineering and network science, these seemingly disparate fields have experienced similar limitations in addressing the complexity of engineering systems. Hetero-Functional Graph Theory (HFGT) has emerged as a means to address some of these limitations. This paper serves as a user guide to a recently developed Hetero-functional Graph Theory Toolbox which facilitates the computation of HFGT mathematical models. It is written in the MATLAB language and has been tested with v9.6 (R2019a). It is openly available on GitHub together with a sample input file for straightforward re-use. The paper details the syntax and semantics of the input file, the principal data structure of the toolbox, and the functions used to construct and populate this data structure. The toolbox has been fully validated against several peer-review HFGT publications.