In the case of vibration analysis I know how to perform an eigenvalue analysis to obtain the frequencies and vibration mode shapes, but I do not have any idea about nonlinear vibration.
It depends on what non-linearity is, i.e. what is its mathematical form. In any case you can calculate a so called fixed point od the equation, for which the dependant variable is a constant, and then you can linearize the equation around this point. The result will be a linear pde equation, which you can solve. The solution would represent vibrational modes and frequencies in close vicinity of a particular solution, i.e. constant solution. There is no general procedure to solve non-linear wave equation, only a few examples of true non-linear waves are known.