I/O Options:

Command line options for input and output (pre-)processing

--noconv

Do not automatically substitute nucleotide "T" with "U".

(default=off)

--log-level=level

Set log level threshold. (default=`2')

By default, any log messages are filtered such that only warnings (level 2) or errors (level 3) are printed. This setting allows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information.

--log-file[=filename]

Print log messages to a file instead of stderr. (default=`RNApdist.log')

--log-time

Include time stamp in log messages.

(default=off)

--log-call

Include file and line of log calling function.

(default=off)

Algorithms:

Select additional algorithms which should be included in the calculations.

-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.

Energy Parameters:

Energy parameter sets can be adapted or loaded from user-provided input files

-T, --temp=DOUBLE

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

(default=`37.0')

-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.

-4, --noTetra

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

(default=off)

Mostly for testing.

--salt=DOUBLE

Set salt concentration in molar (M). Default is 1.021M.

Model Details:

Tweak the energy model and pairing rules additionally using the following parameters

-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)

--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.

--energyModel=INT

Set energy model.

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

--helical-rise=FLOAT

Set the helical rise of the helix in units of Angstrom.

(default=`2.8')

Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded via -P DNA and no further value is provided.

--backbone-length=FLOAT

Set the average backbone length for looped regions in units of Angstrom.

(default=`6.0')

Use with caution! This value will be re-set automatically to 6.76 in case DNA parameters are loaded via -P DNA and no further value is provided.