# 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] " # 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." int default="70" optional option "csv" - "Create comma seperated output (csv)\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" 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" 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" 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." flag off section "Model Details" option "temp" T "Rescale energy parameters to a temperature of temp C. Default is 37C.\n" double optional option "noTetra" 4 "Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\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" 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" flag off option "noGU" - "Do not allow GU pairs\n" flag off option "noClosingGU" - "Do not allow GU pairs at the end of helices\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" 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" 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" int optional hidden option "cfactor" - "Set the weight of the covariance term in the energy function" default="1.0" double optional option "nfactor" - "Set the penalty for non-compatible sequences in the covariance term of the energy function" 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" 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" flag off text "Written by:\n\nIvo L Hofacker\n\n" text "Report bugs:\n\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\ rna@tbi.univie.ac.at.\n"