Two types of ambiguities can be distinguished. Parse tree ambiguity and structural ambiguity. Structural ambiguity does not affect thermodynamic approaches as the optimal structure selection is always on the basis of lowest free energy scores. Parse tree ambiguity concerns the existence of multiple parse trees per sequence. Such an ambiguity can reveal all possible base-paired structures for the sequence by generating all possible parse trees then finding the optimal one. In the case of structural ambiguity multiple parse trees describe the same secondary structure. This obscures the CYK algorithm decision on finding an optimal structure as the correspondence between the parse tree and the structure is not unique. Grammar ambiguity can be checked for by the conditional-inside algorithm.