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...A probabilistic modeling approach is applied by solving the master equation in mitochondrial quality state space in the presence of fusion-fission events, decay of functional quality, mitophagy and mitochondrial biogenesis, as well as molecular damage originating from a random source or from infectious events during fusion and fission. The provided source code is written in C and performs the time integration of the master equation for the time-evolution of the probability to find mitochondria in states of quality q at time t. Output is generated in terms of data files and the graphical visualization of readout parameters is automatically performed using the Graphical Layout Engine (GLE; see: http://glx.sourceforge.net/). Please, send email to thilo.figge<at>hki-jena.de to request a copy of the source code.