Which Utilities are available?

b2ct	converts dot-bracket notation to Zukers mfold '.ct' file format
b2mt.pl	converts dot-bracket notation to x y values
cmount.pl	generates colored mountain plot
coloraln.pl	colorize an alirna.ps file
colorrna.pl	colorize a secondary structure with reliability annotation
ct2b.pl	converts Zukers mfold '.ct' file format to dot-bracket notation
dpzoom.pl	extract a portion of a dot plot
mountain.pl	generates mountain plot
popt	extract Zuker's p-optimal folds from subopt output
refold.pl	refold using consensus structure as constraint
relplot.pl	add reliability information to a RNA secondary structure plot
rotate_ss.pl	rotate the coordinates of an RNA secondary structure plot
switch.pl	describes RNA sequences that exhibit two almost equally stable structures

All programs in the ViennaRNA Package are documented in ``man pages'' that can be called up using the man command, e.g.

  $ man RNAalifold

or find it on the website http://www.tbi.univie.ac.at/~ronny/RNA/manpages.htmlThe path to the manpages are stored in the MANPATH environment variable.

There also is a helpful documentation in the share/doc/ViennaRNA-folder of the ViennaRNA Package.

Most Perl scripts carry embedded documentation that is displayed by typing

  $ perldoc coloraln.pl

in the folder where the script is located. All scripts and programs give short usage instructions when called with the -h command line option (e.g. RNAalifold -h).