--- /dev/null
+# Name of your program
+package "RNAsubopt" # don't use package if you're using automake
+purpose "calculate suboptimal secondary structures of RNAs"
+#usage "RNAsubopt [options]\n"
+
+# Version of your program
+#version "2.0" # don't use version if you're using automake
+
+
+# command line options passed to gengetopt
+args "--file-name=RNAsubopt_cmdl --include-getopt --default-optional --func-name=RNAsubopt_cmdline_parser --arg-struct-name=RNAsubopt_args_info"
+
+
+description "reads RNA sequences from stdin and (in the default -e mode) calculates all suboptimal secondary\
+ structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal\
+ structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of\
+ structures returned grows exponentially with both sequence length and energy range.\n\nAlternatively, when\
+ used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.\n"
+
+# Options
+
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n"
+
+option "constraint" C
+"Calculate structures subject to constraints.\n"
+details="The program reads first the\
+ sequence, then a string containing constraints on the structure encoded with the symbols:\n\n. (no constraint\
+ for this base)\n\n| (the corresponding base has to be paired\n\nx (the base is unpaired)\n\n< (base i is paired with\
+ a base j>i)\n\n> (base i is paired with a base j<i)\n\nand matching brackets ( ) (base i pairs base j)\n\nWith the\
+ exception of \"|\", constraints will disallow all pairs conflicting with the constraint. This is usually\
+ sufficient to enforce the constraint, but occasionally a base may stay unpaired in spite of constraints. PF\
+ folding ignores constraints of type \"|\".\n\n"
+flag
+off
+
+option "noconv" -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+section "Algorithms"
+sectiondesc="Select the algorithms which should be applied to the given RNA sequence.\n"
+
+option "deltaEnergy" e
+"Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol).\
+ Default is calculation of mfe structure only.\n\n"
+float
+typestr="range"
+optional
+
+option "deltaEnergyPost" -
+"Only print structures with energy within range of the mfe after post reevaluation of energies.\n"
+details="Useful in conjunction with -logML, -d1 or -d3: while the -e option specifies the range\
+ before energies are re-evaluated, this option specifies the maximum energy after re-evaluation.\n\n"
+float
+typestr="range"
+optional
+
+option "sorted" s
+"Sort the suboptimal structures by energy.\n"
+details="Since the sort in is done in memory, this becomes impractical when the number of structures produced\
+ goes into millions. In such cases better pipe the output through \"sort +1n\".\n\n"
+flag
+off
+
+option "stochBT" p
+"Instead of producing all suboptimals in an energy range, produce a random sample of suboptimal structures,\
+ drawn with probabilities equal to their Boltzmann weights via stochastic backtracking in the partition\
+ function. The -e and -p options are mutually exclusive.\n\n"
+int
+typestr="number"
+optional
+
+option "pfScale" S
+"In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid\
+ overflows). Needed by stochastic backtracking\n"
+details="The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed\
+ for long sequences.\nYou can also recompile the program to use double precision (see the README file).\n\n"
+double
+typestr="scaling factor"
+optional
+hidden
+
+option "circ" c
+"Assume a circular (instead of linear) RNA molecule.\n\n"
+flag
+off
+
+option "dos" D
+"Compute density of states instead of secondary structures\n"
+details="This option enables the evaluation of the number of secondary structures in certain energy bands arround\
+ the MFE.\n"
+flag
+off
+
+option "zuker" z
+"Compute Zuker suboptimals instead of all suboptimal structures within an engery band arround the MFE.\n\n"
+flag
+off
+
+section "Model Details"
+
+option "temp" T
+"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
+double
+optional
+
+option "noTetra" 4
+"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
+flag
+off
+
+option "dangles" d
+"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
+details="\nWith -d1 only unpaired bases can participate in at most one dangling end, this is the\
+ default for mfe folding but unsupported for the partition function folding.\n\nWith -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 partition function folding (-p).\nThe option -d0 ignores dangling ends altogether (mostly for\
+ debugging).\nWith -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.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
+ treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
+ energy model.\n\n"
+int
+default="2"
+optional
+
+option "noLP" -
+"Produce structures without lonely pairs (helices of length 1).\n"
+details="For partition function folding this only disallows pairs that can only occur isolated. Other\
+ pairs may still occasionally occur as helices of length 1.\n\n"
+flag
+off
+
+option "noGU" -
+"Do not allow GU pairs\n\n"
+flag
+off
+
+option "noClosingGU" -
+"Do not allow GU pairs at the end of helices\n\n"
+flag
+off
+
+option "logML" -
+"Recalculate energies of structures using a logarithmic energy function for multi-loops before output."
+details="This option does not effect structure generation, only the energies that are printed out.\
+ Since logML lowers energies somewhat, some structures may be missing.\n\n"
+flag
+off
+
+option "betaScale" -
+"Set the scaling of the Boltzmann factors\n"
+details="The argument provided with this option enables to scale the thermodynamic temperature\
+ used in the Boltzmann factors independently from the temperature used to scale the individual\
+ energy contributions of the loop types. The Boltzmann factors then become exp(-dG/(kT*betaScale))\
+ where k is the Boltzmann constant, dG the free energy contribution of the state and T the\
+ absolute temperature.\n\n"
+double
+default="1."
+optional
+dependon="stochBT"
+hidden
+
+option "paramFile" P
+"Read energy parameters from paramfile, instead of using the default parameter set.\n"
+details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
+ documentation for details on the file format.\n\n"
+string
+typestr="paramfile"
+optional
+
+option "nsp" -
+"Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
+details="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.\ne.g.\
+ RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
+ energy.\n\n"
+string
+optional
+hidden
+
+text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"
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