--- /dev/null
+# Name of your program
+package "RNALalifold" # don't use package if you're using automake
+purpose "calculate locally stable secondary structures for a set of aligned RNAs"
+usage "RNALalifold [options] <file1.aln>"
+
+# 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=RNALalifold_cmdl --include-getopt --default-optional --unamed-opts --func-name=RNALalifold_cmdline_parser --arg-struct-name=RNALalifold_args_info"
+
+description "reads aligned RNA sequences from stdin or file.aln and calculates\
+ locally stable RNA secondary structure with a maximal base pair span. For a sequence\
+ of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and\
+ O(n*L*L) CPU time. Thus it is practical to \"scan\" very large genomes for short RNA
+ structures.\n"
+
+# Options
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n"
+
+option "span" L
+"Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with\
+ j-i>span will be allowed.\n\n"
+int
+default="70"
+optional
+
+option "csv" -
+"Create comma seperated output (csv)\n\n"
+flag
+off
+
+section "Algorithms"
+sectiondesc="Select additional algorithms which should be included in the calculations.\nThe Minimum free energy\
+ (MFE) and a structure representative are calculated in any case.\n\n"
+
+option "partfunc" p
+"Calculate the partition function and base pairing probability matrix in addition to the mfe structure."
+details="Default is calculation of mfe structure only. In addition to the MFE structure we print a coarse\
+ representation of the pair probabilities in form of a pseudo bracket notation, followed by the ensemble\
+ free energy, as well as the centroid structure derived from the pair probabilities together with\
+ its free energy and distance to the ensemble. Finally it prints the frequency of the mfe structure.\n\nAn\
+ additionally passed value to this option changes the behavior of partition function calculation:\n-p0\
+ \tCalculate the partition function but not the pair probabilities, saving about 50% in runtime. This\
+ prints the ensemble free energy -kT ln(Z).\n\n"
+int
+default="1"
+argoptional
+optional
+
+option "cutoff" c
+"Report only base pairs with an average probability > cutoff in the dot plot\n\n"
+float
+default="0.01"
+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).\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 "mis" -
+"Output \"most informative sequence\" instead of simple consensus: For each column of the alignment\
+ output the set of nucleotides with frequence greater than average in IUPAC notation.\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 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 "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
+
+option "energyModel" e
+"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.\n\n"
+int
+optional
+hidden
+
+option "cfactor" -
+"Set the weight of the covariance term in the energy function\n\n"
+default="1.0"
+double
+optional
+
+option "nfactor" -
+"Set the penalty for non-compatible sequences in the covariance term of the energy function\n\n"
+default="1.0"
+double
+optional
+
+option "ribosum_file" R
+"use specified Ribosum Matrix instead of normal energy model. Matrixes to use should be 6x6 matrices,\
+ the order of the terms is AU, CG, GC, GU, UA, UG.\n\n"
+string
+typestr="ribosumfile"
+optional
+
+option "ribosum_scoring" r
+"use ribosum scoring matrix. The matrix is chosen according to the minimal and maximal pairwise\
+ identities of the sequences in the file.\n\n"
+flag
+off
+
+
+text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"
git://source.jalview.org / jabaws.git / blobdiff