1. A method for non-intrusive real-time analysis of secure communications between a first application and a second application, wherein the first and second applications communicate through a communication channel, comprising the steps of: non-intrusively and securely capturing a plurality of secure communications between the first application and the second application substantially in real-time; processing the plurality of communications to form a first plurality of information units, each information unit comprising application level information substantially in real-time; analyzing a second plurality of information units up to an application layer, the second plurality comprising one or more of the first plurality of information units, to determine a plurality of dependencies among the second plurality of information units substantially in real-time; organizing the second plurality of information units into a hierarchical data structure according to the plurality of dependencies among the information units.