Barriers
Barriers (Flamm et al., 2002) (Wolfinger et al., 2004) reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For each local minimum found it prints the conformation of the minimum, its energy, the number of the “parent”-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation, basin sizes, etc. can be gathered as well.
The barriers program is fundamental to compute global folding kinetics (using treekin) of RNA molecules.