We consider the effect of self-phase modulation and cross-phase modulation on the joint spectral amplitude of photon pairs generated by spontaneous four-wave mixing. In particular, the purity of a heralded photon from a pair is considered, in the context of schemes that aim to maximise the purity and minimise correlation in the joint spectral amplitude using birefringent phase-matching and short pump pulses. We find that non-linear phase modulation effects will be detrimental, and will limit the quantum interference visibility that can be achieved at a given generation rate. An approximate expression for the joint spectral amplitude with phase modulation is found by considering the group velocity walk-off between each photon and the pump, but neglecting the group-velocity dispersion at each wavelength. The group-velocity dispersion can also be included with a numerical calculation, and it is shown that it only has a small effect on the purity for the realistic parameters considered.
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