2 package "RNApdist" # don't use package if you're using automake
4 purpose "Calculate distances between thermodynamic RNA secondary structures ensembles"
6 #usage "RNApdist [options]\n"
7 #version "2.0" # don't use version if you're using automake
10 # command line options passed to gengetopt
11 args "--file-name=RNApdist_cmdl --include-getopt --default-optional --func-name=RNApdist_cmdline_parser --arg-struct-name=RNApdist_args_info"
14 description "This program reads RNA sequences from stdin and calculates structure\
15 distances between the thermodynamic ensembles of their secondary structures.\n"
18 section "General Options"
21 "Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
28 "Specify the comparison directive.\n"
29 details="Possible arguments for this option are: -Xp compare the structures\
30 pairwise (p), i.e. first with 2nd, third with 4th etc.\n-Xm calculate the\
31 distance matrix between all structures. The output is formatted as a lower\
32 triangle matrix.\n-Xf compare each structure to the first one.\n-Xc compare\
33 continuously, that is i-th with (i+1)th structure.\n\n"
40 "Print an \"alignment\" with gaps of the profiles. The aligned structures\
41 are written to <filename>, if specified.\n"
42 details="Within the profile output, the following symbols will be used:\n\n\
43 () essentially upstream (downstream) paired bases\n\n\
44 {} weakly upstream (downstream) paired bases\n\n\
45 | strongly paired bases without preference\n\n\
46 , weakly paired bases without preference\n\n\
47 . essentially unpaired bases.\n\n\
48 If <filename> is not specified, the output is written to stdout,\
49 unless the \"-Xm\" option is set in which case \"backtrack.file\" is used.\n\n"
56 section "Model Details"
59 "Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
64 "Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
69 "set energy model for treatment of dangling bases\n\n"
75 "Produce structures without lonely pairs (helices of length 1).\n"
76 details="For partition function folding this only disallows pairs that can only occur isolated. Other\
77 pairs may still occasionally occur as helices of length 1.\n\n"
82 "Do not allow GU pairs\n\n"
86 option "noClosingGU" -
87 "Do not allow GU pairs at the end of helices\n\n"
92 "Read energy parameters from paramfile, instead of using the default parameter set.\n"
93 details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
94 documentation for details on the file format.\n\n"
100 "Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
101 details="Its argument is a comma separated list of additionally allowed pairs. If the\
102 first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
103 RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
109 option "energyModel" e
110 "Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
111 A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.\n\n"
119 text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
120 rna@tbi.univie.ac.at.\n"