  We extend recent methods for parametric sequence alignment to the parameter
space for scoring RNA folds. This involves the construction of an RNA polytope.
A vertex of this polytope corresponds to RNA secondary structures with common
branching. We use this polytope and its normal fan to study the effect of
varying three parameters in the free energy model that are not determined
experimentally. Our results indicate that variation of these specific
parameters does not have a dramatic effect on the structures predicted by the
free energy model. We additionally map a collection of known RNA secondary
structures to the RNA polytope.
