Verifying relations between programs arises as a task in various verification contexts such as optimizing transformations, relating new versions of programs with older versions (regression verification), and noninterference. However, relational verification for programs acting on dynamically allocated mutable state is not well supported by existing tools, which provide a high level of automation at the cost of restricting the programs considered. Auto-active tools, on the other hand, require more user interaction but enable verification of a broader class of programs. This article presents WhyRel, a tool for the auto-active verification of relational properties of pointer programs based on relational region logic. WhyRel is evaluated through verification case studies, relying on SMT solvers orchestrated by the Why3 platform on which it builds. Case studies include establishing representation independence of ADTs, showing noninterference, and challenge problems from recent literature.