The present invention is directed to a system and methods for analyzing dependencies. The dependencies that may be analyzed include, for example, dependencies among methods or procedures in software source code, or in system configuration or deployment. A layered system is provided, comprising a back-end layer, abstraction layer and user interface layer are used to derive dependency information from third-party tools, and present the information through uniform interfaces to a user-interface layer. The system maintains a dependency model as a hierarchical graph structure in computer memory, and provides a plurality of user views which may be manipulated actively or passively by the user. Active manipulations are propogated through the back-end layer to modify the system analyzed, and passive manipulations affect the user views without changing the analyzed system. The system provides advantages to users seeking to understand complex systems with many dependencies.