I don't know which platform you're working on, but on most modern platforms, all culling and clipping happens after vertex transformations, but before fragment shading.
You can do some custom pre-culling, and not issue draw commands for objects you know won't be visible, but once you ask some triangles to be drawn, it's not until you apply view and projection matrices that you know which vertices are eligible for culling and clipping.
This graph, which I don't know who drew it first, but is the first result when you google image search "Direct3D 9 pipeline" is very useful for understanding where everything fits.
