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:
Barrier Trees of Degenerate Landscapes
Zeitschrift für Physikalische Chemie: Vol. 216, Issue 2, pp. 155, doi:10.1524/zpch.2002.216.2.155
Important: With version 1.7.0, the default move set for RNA graphs changed to noShift. Therefore, to obtain the same results as with version prior to 1.7.0, you might need to supply the
-M Shiftcommand line option.
Get the latest Barriers program
Compile from Source Code
Installing from sourcecode is the recommended way to get most out of Barriers. For best portability Barriers uses the GNU autoconf and automake tools and can thus be compiled and installed on almost every computer platform. See the INSTALL instructions for details.
Install precompiled Binary Package
For those unable to compile the Treekin program, or who simply don't want to, we also provide precompiled binary packages for several Linux distributions and operating systems. Packages are mainly build using the openSUSE Build Service. install system.
The packages listed above are meant for installation in RedHat derived Linux distributions with enabled Extra Packages for Enterprise Linux (EPEL) repository. They should work without problems in distributions such as CentOS, RedHat Enterprise Linux, and Scientific Linux.
There should rarely be a good reason to use any but the latest version of our software. However if you want to look up the old bugs, here's a list with most of the older releases for download.
Just click on the version numbers below to display the corresponding Barriers releases.
Comments and Bug Reports
If in doubt our program is right, nature is at fault.
Comments and bug reports should be sent to firstname.lastname@example.org