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The Treekin program

treekin example The program  treekin  computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix). For detailed instructions see the man page.

In case you are using our software for your publications you may want to cite:

Michael T Wolfinger, W Andreas Svrcek-Seiler, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
Efficient computation of RNA folding dynamics
J. Phys. A: Math. Gen. 37 4731, doi:10.1088/0305-4470/37/17/005

News

  • The new version 0.4 is up! The changes include: improvement of numerical stability, additional options including the Quasi-steady-state removal, and several bug fixes. The input format and some default options have changed, so take care using your old scripts. (18-Dec-2015)

Get the latest Treekin program

The latest stable release is Version 0.4 from February, 5th 2016

Get the source code and compile it yourself Compile from Source Code

Installing from sourcecode is the recommended way to get most out of Treekin. For best portability Treekin 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 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.

Simply select your Linux distribution or operating system by clicking on the corresponding icon below, and download the binary packages that best suite your needs from the corresponding list.

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.

Just click on the version numbers below to display the corresponding Treekin releases.

Comments and Bug Reports

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