ShapeSorter the first computational method for detecting functional RNA structure features that are supported both by evolutionary evidence and experimental SHAPE-probing evidence. ShapeSorter is capable of capturing RNA structure features due to RNA structure heterogeneity, transient RNA structure features as well as features of pseudo-knotted RNA structures. ShapeSorter employs a purely probabilistic framework that seamlessly integrates both evolutionary as well experimental SHAPE-probing evidence. It returns as output helices (i.e. stretches of consecutive base-pairs) that can be readily ranked by their estimated p-values.