General Options:

--noconv

Do not automatically substitude nucleotide "T" with "U"

(default=off)

Algorithms:

-X, --compare=p|m|f|c

Specify the comparison directive. (default=`p')

Possible arguments for this option are: -Xp compare the structures pairwise (p), i.e. first with 2nd, third with 4th etc. -Xm calculate the distance matrix between all structures. The output is formatted as a lower triangle matrix. -Xf compare each structure to the first one. -Xc compare continuously, that is i-th with (i+1)th structure.

-B, --backtrack[=<filename>]

Print an "alignment" with gaps of the profiles. The aligned structures are written to <filename>, if specified.

(default=`none')

Within the profile output, the following symbols will be used:

()

essentially upstream (downstream) paired bases

{}

weakly upstream (downstream) paired bases

|

strongly paired bases without preference

,

weakly paired bases without preference

.

essentially unpaired bases.

If <filename> is not specified, the output is written to stdout, unless the

"-Xm" option is set in which case "backtrack.file" is used.

Model Details:

-T, --temp=DOUBLE

Rescale energy parameters to a temperature of temp C. Default is 37C.

-4, --noTetra

Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.

(default=off)

-d, --dangles=INT

set energy model for treatment of dangling bases

(possible values="0", "2" default=`2')

--noLP

Produce structures without lonely pairs (helices of length 1).

(default=off)

For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.

--noGU

Do not allow GU pairs

(default=off)

--noClosingGU

Do not allow GU pairs at the end of helices

(default=off)

-P, --paramFile=paramfile

Read energy parameters from paramfile, instead of using the default parameter set.

Different sets of energy parameters for RNA and DNA should accompany your distribution. See the RNAlib documentation for details on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file.

--nsp=STRING

Allow other pairs in addition to the usual AU,GC,and GU pairs.

Its argument is a comma separated list of additionally allowed pairs. If the first character is a "-" then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.

-e, --energyModel=INT

Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.