The system's background operation and user interaction. The arrows represent the flow of data and controls across the system's modules (boxes) and are labelled according to their order of execution. The system starts by receiving the user's choice of start and end points for the pipeline which represent, respectively, the type of input file that the user has and the format into which the user wants to transform the original file. In accordance with the combination of these start and end points, the system determines the input files (module 'Determine Input') that the user needs to provide in order to complete the chosen path through the pipeline. The required input files are presented to the user as a Web page tailored by the 'Generate HTML' module. The user can then upload the input files that need to be converted to the format required for a specific population genetics program. These files are received by the system's 'Coordination Module', which controls the execution of all required steps through the pipeline, including a verification step (the 'Verification module') for checking whether the provided input files are in their correct formats. Depending on the combination chosen by the user for start and end points, different scripts are invoked by the 'Coordination Module'. These scripts generate outputs that are presented to the user through the 'Format Output Module'.