Enterprise architecture advocates for model-based decision-making on enterprise-wide information system issues. In order to provide decision-making support, enterprise architecture models should not only be descriptive but also enable analysis. This paper presents a software tool, currently under development, for the evaluation of enterprise architecture models. In particular, the paper focuses on how to encode scientific theories so that they can be used for model-based analysis and reasoning under uncertainty. The tool architecture is described, and a case study shows how the tool supports the process of enterprise architecture analysis.