The Barriers program
The program barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt For each local minimum found it prints to stdout, 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 and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory.
For detailed instructions see the man page.
In case you are using our software for your publications you may want to cite:
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler und Michael T. Wolfinger
Barrier Trees of Degenerate Landscapes
Zeitschrift für Physikalische Chemie: Vol. 216, Issue 2, pp. 155, doi:10.1524/zpch.2002.216.2.155