RNA2Dfold 2.1.9: Compute MFE structure, partition function and representative sample structures of k,l neighborhoods. The program partitions the secondary structure space into (basepair)distance classes according to two fixed reference structures. It expects a sequence and two secondary structures in dot−bracket notation as its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free energy is computed. Additionally, a stochastic backtracking routine allows to produce samples of representative suboptimal secondary structures from each partition.

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