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We consider stochastic networks with pairwise transition rates of the formwhere the temperatureTis a small parameter. Such networks arise in physics and chemistry and serve as mathematically tractable models of complex systems. Typically, such networks contain large numbers of states and widely varying pairwise transition rates. We present a methodology for spectral analysis and clustering of such networks that takes advance of the small parameterTand consists of two steps: (1) computing zero-temperature asymptotics for eigenvalues and the collection of quasi-invariant sets, and (2) finite temperature continuation. Step (1) is reducible to a sequence of optimisation problems on graphs. A novel single-sweep algorithm for solving them is introduced. Its mathematical justification is provided. This algorithm is valid for both time-reversible and time-irreversible networks. For time-reversible networks, a finite temperature continuation technique combining lumping and truncation with Rayleigh quotient iteration is developed. The proposed methodology is applied to the network representing the energy landscape of the Lennard-Jones-75 cluster containing 169523 states and 226377 edges. The transition process between its two major funnels is analysed. The corresponding eigenvalue is shown to have a kink at the solid–solid phase transition temperature. [ABSTRACT FROM AUTHOR]