Computer-aided-design tools are provided that support real-time phase-locked loop reconfiguration with a single design compilation. Each design compilation may involve operations such as logic synthesis and place and route operations. A circuit designer who is designing an integrated circuit may supply circuit design data. The circuit design data may include design data for multiple configurations of a phase-locked loop. By using a phase-locked loop scan chain initialization file generator engine located in a CAD tool design input wizard, the computer-aided-design tools may produce multiple phase-locked loop initialization files without performing a design compilation. The CAD tools may process one or more initialization files and the circuit design data to produce output data. The output data may include configuration data to implement the circuit design. The output data may also include warning messages that indicate when phase-locked loop settings in an initialization file do not match settings in the circuit design.