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RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. The underlying theory of MAP refinement is given in a scientific publication: Scheres, JMB (2011) (DOI: 10.1016/j.jmb.2011.11.010). If RELION is useful in your work, please cite this paper. 

The documentation of RELION is stored on the following Wiki page:
http://www2.mrc-lmb.cam.ac.uk/relion