There are a few and they most typically rely on setting up a boundary value problem. You can find solutions to these in the AUTO continuation package, and the XPP package that provides a (partial) front end to it. However, you'll still have to understand how to set it up because it's not an automated process. There are tutorials for those packages that include that application, I believe.
Alternatively, my own package, PyDSTool, is meant for dynamical systems analysis and comes with a prototype (and somewhat naive) tool to compute separatrices -- in fact, any geometrically simple sub-manifold around a fixed point. It is described in graphic detail here. It uses the shooting method. A similar computation was achieved using my package's PyCont sub-package (uses AUTO internally), which is described here.
The shooting method will, however, struggle more if you need to cover a very large domain of the independent variable unless its geometry remains relatively "simple". E.g. it doesn't get tangled or squeezed close to other sub-manifolds. It should be a good starting point for further analysis, though.