The Treekin program
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
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:
Efficient computation of RNA folding dynamics
J. Phys. A: Math. Gen. 37 4731, doi:10.1088/0305-4470/37/17/005
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
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
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 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 firstname.lastname@example.org