Circuits and systems for generating multiple frequencies are disclosed. In some embodiments, a circuit can include a first node, a second node, and a programmable phase rotator. The first node can receive a first signal having frequency f1, and the second node can output a second signal having frequency f2 that is different from f1. In some embodiments, a frequency divider can generate a third signal having frequency f3 based on the second signal. In some embodiments, a frequency divider can generate the first signal based on a reference signal having frequency f4. The programmable phase rotator can be capable of updating, at an update frequency that is substantially equal to f1 and/or f4, a phase difference between the first signal and the second signal. In some embodiments, the circuit can be part of a USB (Universal Serial Bus) 3.0 physical layer (PHY) circuit.