In a network that includes intermediary nodes, such as WAN accelerators, that transform messages between nodes, an end-to-end path of the messages is determined. The determined end-to-end path is used in subsequent analysis of message traces, to identify timing and other factors related to the performance of the network relative to the propagation of these messages, including the propagation of the transformed messages. A variety of techniques are presented for determining the path of the messages, depending upon the characteristics of the collected trace data. Upon determining the message path, the traces are synchronized in time and correlations between the connections along the path are determined, including causal relationships. In a preferred embodiment, a user identifies an application process between or among particular nodes of a network, and the system provides a variety of formats for viewing statistics related to the performance of the application on the network.