--- /dev/null
+# Name of your program
+package "RNApaln" # don't use package if you're using automake
+
+purpose "RNA alignment based on sequence base pairing propensities"
+
+#usage "RNApaln [options]\n"
+
+# 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=RNApaln_cmdl --include-getopt --default-optional --func-name=RNApaln_cmdline_parser --arg-struct-name=RNApaln_args_info"
+
+
+description "Uses string-alignment techniques to perform fast pairwise structural alignments of RNAs.\
+ Similar to RNApdist secondary structure is incorporated in an approximate manner by computing base pair\
+ probabilities, which are then reduced to a vector holding the probability that a base is paired upstream,\
+ downstream, or remains unpaired. Such pair propsensity vectors can then be compared using standard\
+ alignment algorithms. In contrast to RNApdist, RNApaln performs similarity (instead of distance) alignments,\
+ considers both sequence and structure information, and uses affine (rather than linear) gap costs. RNApaln\
+ can perform semi-local alignments by using free end gaps, a true local alignment mode is planned.\n\nThe\
+ same approach has since been used in the StraL program from Gerhard Steeger's group. Since StraL has\
+ optimized parameters and a multiple alignment mode, it be be currently the better option.\n"
+
+# Options
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n"
+
+option "printAlignment" B
+"Print an \"alignment\" with gaps of the profiles\nThe aligned structures are written\
+ to filename, if specified\nOtherwise output is written to stdout, unless the -Xm option\
+ is set in which case \"backtrack.file\" is used.\n"
+details="The following symbols are used:\n ( ) essentially upstream (downstream) paired bases\n
+ { } weakly upstream (downstream) paired bases\n | strongly paired bases without preference\n
+ , weakly paired bases without preference\n . essentially unpaired bases.\n\n"
+string
+default="stdout"
+typestr="filename"
+argoptional
+optional
+
+option "noconv" -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+section "Algorithms"
+sectiondesc="Select additional algorithms which should be included in the calculations.\n"
+
+option "mode" X
+"Set the alignment mode to be used\n"
+details="The alignment mode is passed as a single character value. The following options\
+ are available:\n'p' - Compare the structures pairwise, that is first with 2nd, third\
+ with 4th etc. This is the default.\n
+ 'm' - Calculate the distance matrix between all structures. The output is formatted\
+ as a lower triangle matrix.\n
+ 'f' - Compare each structure to the first one.\n
+ 'c' - Compare continuously, that is i-th with (i+1)th structure.\n\n"
+string
+typestr="pmfc"
+optional
+
+
+section "Model Details"
+
+option "gapo" -
+"Set the gap open penalty\n\n"
+float
+typestr="open"
+optional
+
+option "gape" -
+"Set the gap extension penalty\n\n"
+float
+typestr="ext"
+optional
+
+option "seqw" -
+"Set the weight of sequence (compared to structure) in the scoring function.\n\n"
+float
+typestr="w"
+optional
+
+option "endgaps" -
+"Use free end-gaps\n\n"
+flag
+off
+
+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 the\
+ default for mfe folding but 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
+
+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