General Options:

Below are command line options which alter the general behavior of this program

-B, --printAlignment[=filename]

Print an "alignment" with gaps of the

profiles

The aligned structures are written to filename, if specified Otherwise output is written to stdout, unless the -Xm option is set in which case "backtrack.file" is used.

(default=`stdout')

The following symbols are used:

(

) essentially upstream (downstream) paired bases

{

} weakly upstream (downstream) paired bases

|

strongly paired bases without preference

,

weakly paired bases without preference

.

essentially unpaired bases.

--noconv

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

(default=off)

Algorithms:

Select additional algorithms which should be included in the calculations.

-X, --mode=pmfc

Set the alignment mode to be used

The alignment mode is passed as a single character value. The following options are available: 'p' - Compare the structures pairwise, that is first with 2nd, third with 4th etc. This is the default.

'm'

- Calculate the distance matrix between all structures. The output is

formatted as a lower triangle matrix.

'f' - Compare each structure to the first one.

'c' - Compare continuously, that is i-th with (i+1)th structure.

Model Details:

--gapo=open

Set the gap open penalty

--gape=ext

Set the gap extension penalty

--seqw=w

Set the weight of sequence (compared to structure) in the scoring function.

--endgaps

Use free end-gaps

(default=off)

-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

How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops

(default=`2')

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; this is the default for mfe and partition function folding (-p). The option -d0 ignores dangling ends altogether (mostly for debugging). 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.

Note that with -d1 and -d3 only the MFE computations will be using this setting while partition function uses -d2 setting, i.e. dangling ends will be treated differently.

--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.