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Marcus-Levich-Jortner (MLJ) theory is one of the most commonly used methods for including nuclear quantum effects into the calculation of electron-transfer rates and for interpreting experimental data. It divides the molecular problem into a subsystem treated quantum-mechanically by Fermi's golden rule and a solvent bath treated by classical Marcus theory. As an extension of this idea, we here present a "reduced" semiclassical instanton theory, which is a multiscale method for simulating quantum tunnelling of the subsystem in molecular detail in the presence of a harmonic bath. We demonstrate that instanton theory is typically significantly more accurate than the cumulant expansion or the semiclassical Franck-Condon sum, which can give orders-of-magnitude errors and in general do not obey detailed balance. As opposed to MLJ theory, which is based on wavefunctions, instanton theory is based on path integrals and thus does not require solutions of the Schrödinger equation, nor even global knowledge of the ground- and excited-state potentials within the subsystem. It can thus be efficiently applied to complex, anharmonic multidimensional subsystems without making further approximations. In addition to predicting accurate rates, instanton theory gives a high level of insight into the reaction mechanism by locating the dominant tunnelling pathway as well as providing information on the reactant and product vibrational states involved in the reaction and the activation energy in the bath similarly to what would be found with MLJ theory.