CATs are Conversion and Analysis Tools. These tools are intended for manipulation and analysis of AMBER topology, coordinates, and trajectories. Operations can be performed on the whole structure or on a subset defined by a mask. The mask syntax is fully compatible with the AMBER with several extensions. CATs support parallel processing of AMBER trajectories together with management of obtained data. It also provides tools for simple virtual screening. Moreover, the package also contains a scripting environment based on JavaScript, which opens ways for advanced analysis.