A method of semi-automatic data collection, data analysis and model generation for performance analysis of computer networks and software is provided. The invention provides a graphical user interface which indicates the overall data flow in the performance analysis process and guides the user through the proper sequence of steps in that process. Underneath the graphical user interface, the invention provides software tools which include novel data pipeline for transformation of network traces, resource data and application data into organized hash tables, and further into spreadsheets for introduction into computer network simulation programs. The invention also provides novel algorithms for recognizing transaction and parentage between transactions from low level network trace data. The invention further provides novel methods of visualization of trace data and transaction and parentage associations.