# Name of your program package "RNAalifold" # don't use package if you're using automake purpose "calculate secondary structures for a set of aligned RNAs" usage "RNAalifold [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=RNAalifold_cmdl --include-getopt --default-optional --unamed-opts --func-name=RNAalifold_cmdline_parser --arg-struct-name=RNAalifold_args_info" description "Read aligned RNA sequences from stdin or file.aln and calculate\ their minimum free energy (mfe) structure, partition function (pf) and base\ pairing probability matrix. Currently, the input alignment has to be in\ CLUSTAL format. It returns the mfe structure in bracket notation, its\ energy, the free energy of the thermodynamic ensemble and the frequency of\ the mfe structure in the ensemble to stdout. It also produces Postscript\ files with plots of the resulting secondary structure graph (\"alirna.ps\")\ and a \"dot plot\" of the base pairing matrix (\"alidot.ps\"). The file\ \"alifold.out\" will contain a list of likely pairs sorted by credibility,\ suitable for viewing with \"AliDot.pl\". Be warned that output file will\ overwrite any existing files of the same name." # 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.\nThe constraining structure will be read from 'stdin',\ the alignment has to be given as a file name on the command line.\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