AbstractMotivationTertiary structure alignment is one of the main challenges in the computer-aided comparative study of molecular structures. Its aim is to optimally overlay the 3D shapes of two or more molecules in space to find the correspondence between their nucleotides. Alignment is the starting point for most algorithms that assess structural similarity or find common substructures. Thus, it has applications in solving a variety of bioinformatics problems, e.g. in the search for structural patterns, structure clustering, identifying structural redundancy, and evaluating the prediction accuracy of 3D models. To date, several tools have been developed to align 3D structures of RNA. However, most of them are not applicable to arbitrarily large structures and do not allow users to parameterize the optimization algorithm.ResultsWe present two customizable heuristics for flexible alignment of 3D RNA structures, geometric search (GEOS), and genetic algorithm (GENS). They work in sequence-dependent/independent mode and find the suboptimal alignment of expected quality (below a predefined RMSD threshold). We compare their performance with those of state-of-the-art methods for aligning RNA structures. We show the results of quantitative and qualitative tests run for all of these algorithms on benchmark sets of RNA structures.Availability and implementationSource codes for both heuristics are hosted athttps://github.com/RNApolis/rnahugs.