2 package "RNAdistance" # don't use package if you're using automake
4 purpose "Calculate distances between RNA secondary structures"
6 #usage "RNAfold [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=RNAdistance_cmdl --include-getopt --default-optional --func-name=RNAdistance_cmdline_parser --arg-struct-name=RNAdistance_args_info"
14 description "This program reads RNA secondary structures from stdin and calculates one or more\
15 measures for their dissimilarity, based on tree or string editing\
16 (alignment). In addition it calculates a \"base pair distance\" given by the\
17 number of base pairs present in one structure, but not the other. For\
18 structures of different length base pair distance is not recommended.\n"
22 "Specify the distance representation to be used in calculations.\n"
23 details="Use the full, HIT, weighted coarse, or coarse representation to\
24 calculate the distance. Capital letters indicate string alignment\
25 otherwise tree editing is used.\nAny combination of distances can be\
33 "Specify the comparison directive.\n"
34 details="Possible arguments for this option are: -Xp compare the structures\
35 pairwise (p), i.e. first with 2nd, third with 4th etc.\n-Xm calculate the\
36 distance matrix between all structures. The output is formatted as a lower\
37 triangle matrix.\n-Xf compare each structure to the first one.\n-Xc compare\
38 continuously, that is i-th with (i+1)th structure.\n\n"
45 "Use the Bruce Shapiro's cost matrix for comparing coarse structures.\n\n"
50 "Print an \"alignment\" with gaps of the structures, to show matching\
51 substructures. The aligned structures are written to <filename>, if\
53 details="If <filename> is not specified, the output is written to stdout,\
54 unless the -Xm option is set in which case \"backtrack.file\" is used.\n\n"
64 text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
65 rna@tbi.univie.ac.at.\n"