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NAME − analyse dynamic RNA folding landscapes

SYNOPSIS [−T temp] [−4] [−d[0|1|2|3]] [−no[GU|CloseGU|LP]] [−logML]
[−P paramfile] [ [...]]


The program reads a series of bar files e.g for different length fragments in the order of the growing chain or for different temperatures in the order of the heating/cooling schedule, and computes which minima in successive barrier trees are equivalent. The program Outputs the correpondence table of minima to STDOUT .

Each column of the output corresponds to the minima of a bar file (last bar file is the right most gap-less column). The correspondence between minima of successive columns are calculated by a gradient walk. Within a row of the output the symbol −> indicates exact correspondence between the local minima in the succesive barrier trees while the symbol ~> indicates approximate correspondence with maximal similarity (= base pair distance). Approximate similarity arises if forinstance not all minima are listed in the bar file because the program "barriers" was used with the −minh option.



Set the "dangling end" energies for bases adjacent to helices in free ends and multi-loops: With −d1 only unpaired bases can participate in at most one dangling end. With −d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case. With −d | −d0 dangling ends are ignored altogether. With −d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3 and works only for mfe folding.

−h, −help

Display long help message.


Display man page.


With −noGU do not allow GU pairs. With −noCloseGU do not allow GU pairs at the end of helices. With −noLP disallow pairs that can only occur isolated.

−P paramfile

Read energy parameters from paramfile.

−T temp

Rescale energy parameters to a temperature of temp.


Turn off special stabilizing energies for certain tetra-loops.


Ivo L Hofacker, Peter F Stadler, Christoph Flamm


If in doubt our program is right, nature is at fault. Please send comments and bug reports to