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The Barriers program

barrier tree example 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 "" 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


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The latest stable release is Version 1.5.2

Get the source code and compile it yourself 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.

Barriers v1.5.2 (tar.gz, SourceCode) [323kB]

Use our prepared ArchLinux source package Install barriers package from AUR in ArchLinux

Installing Barriers in ArchLinux is quite easy since it is available through the ArchLinux User Repository (AUR). You can also just download the Arch Linux Source Package that we provide here

Barriers v1.5.2 (tar.gz, ArchLinux Source Package) [843b]

... and proceed with the following steps:

  1. Extract the downloaded tarball with
    $ tar xzf barriers.tar.gz
  2. Run makepkg in the directory you just created.
    $ makepkg -si
    This installs missing dependencies (-s option), downloads the code, compiles and packages it, and finally, performs the installation (-i option) of Barriers.

Alternatively, use an AUR repository tool like yaourt to install it directly from AUR::

$ yaourt -S barriers

Use our precompiled Debian binary packages (.deb) Install Debian GNU/Linux binary package

We also provide precompiled binary packages for Debian GNU/Linux.

Barriers v1.5.2-1 (deb, Debian/Ubuntu, 64bit) [45.5kB]

Use our precompiled Ubuntu binary packages (.deb) Install Debian GNU/Linux binary package

Our Debian GNU/Linux files should also work well with Ubuntu

Barriers v1.5.2-1 (deb, Debian/Ubuntu, 64bit) [45.5kB]

Older versions:

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.

Comments and Bug Reports

If in doubt our program is right, nature is at fault.
Comments and bug reports should be sent to