This thesis introduces, develops and applies methods for analysing nonlinear systems with the multiple challenges of time-varying, non-polynomial, uncertain or large-scale proper- ties. Both computational and analytic methods using Lyapunov functions are developed and the methods are applied to a range of examples. Generalised Absolute stability is introduced, which is a method of treating polynomial systems with non polynomial, uncertain or time-varying feedback. Analysis is completed with Sum of Squares programming, and this method extends both the applicability of sum of squares as well as existing absolute stability theory. Perturbation methods for invariant Sum of Squares and Semidefinite programs are introduced, which significantly improves scalability of computations and al- lows sum of squares programming to be used for large scale systems. Finally, invariance principles are introduced for nonlinear, time-varying systems. The concept of trajectories leaving sets uniformly in time is introduced, which allows a non-autonomous version of Barbashin-Krasovskii theorem.