A link simulation tool for simulating high-speed communications link systems is provided. Communications links may include link subsystems such as transmit (TX) circuitry, receive (TX) circuitry, oscillator circuits that provide reference clock signals to the TX and RX circuitry, and channels that link the TX and RX circuitry. The link simulation tool may model each of the subsystems using behavioral models. The behavioral models may include characteristic functions such as transfer functions, probability density functions, and eye characteristics. The link simulation tool may have a link analysis engine that is capable of performing two-dimensional (two-variable) convolution operations and in applying dual-domain (frequency-time) transformations on the characteristic functions provided by the behavioral models to simulate the performance of the link system. The link simulation tool may have an input screen that allows a user to specify desired link parameters and a data display screen that display simulated results.