--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAPDIST "1" "July 2013" "RNApdist 2.1.2" "User Commands"
+.SH NAME
+RNApdist \- manual page for RNApdist 2.1.2
+.SH SYNOPSIS
+.B RNApdist
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNApdist 2.1.2
+.PP
+Calculate distances between thermodynamic RNA secondary structures ensembles
+.PP
+This program reads RNA sequences from stdin and calculates structure distances
+between the thermodynamic ensembles of their secondary structures.
+.PP
+To do this the partition function and matrix of base pairing probabilities is
+computed for each sequence. The probability matrix is then condensed into a
+vector holding for each base the probabilities of being unpaired, paired
+upstream, or paired downstream, respectively. These profiles are compared
+by a standard alignment algorithm.
+
+The base pair probabilities are also saved as postscript "dot plots" (as in
+RNAfold) in the files "name_dp.ps", where name is the name of the sequence,
+or a number if unnamed.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Print help and exit
+.TP
+\fB\-\-detailed\-help\fR
+Print help, including all details and hidden
+options, and exit
+.TP
+\fB\-\-full\-help\fR
+Print help, including hidden options, and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print version and exit
+.SS "General Options:"
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide
+"T" with "U"
+.IP
+(default=off)
+.SS "Algorithms:"
+.TP
+\fB\-X\fR, \fB\-\-compare\fR=\fIp\fR|m|f|c
+Specify the comparison directive.
+(default=`p')
+.IP
+Possible arguments for this option are: \fB\-Xp\fR compare the structures pairwise
+(p), i.e. first with 2nd, third with 4th etc.
+\fB\-Xm\fR calculate the distance matrix between all structures. The output is
+formatted as a lower triangle matrix.
+\fB\-Xf\fR compare each structure to the first one.
+\fB\-Xc\fR compare continuously, that is i\-th with (i+1)th structure.
+.TP
+\fB\-B\fR, \fB\-\-backtrack[=\fR<filename>]
+Print an "alignment" with gaps of the
+profiles. The aligned structures are written
+to <filename>, if specified.
+.IP
+(default=`none')
+.IP
+Within the profile output, the following symbols will be used:
+.TP
+()
+essentially upstream (downstream) paired bases
+.TP
+{}
+weakly upstream (downstream) paired bases
+.TP
+|
+strongly paired bases without preference
+.TP
+,
+weakly paired bases without preference
+.TP
+\&.
+essentially unpaired bases.
+.IP
+If <filename> is not specified, the output is written to stdout, unless the
+.IP
+"\-Xm" option is set in which case "backtrack.file" is used.
+.SS "Model Details:"
+.TP
+\fB\-T\fR, \fB\-\-temp\fR=\fIDOUBLE\fR
+Rescale energy parameters to a temperature of
+temp C. Default is 37C.
+.TP
+\fB\-4\fR, \fB\-\-noTetra\fR
+Do not include special tabulated stabilizing
+energies for tri\-, tetra\- and hexaloop
+hairpins. Mostly for testing.
+.IP
+(default=off)
+.TP
+\fB\-d\fR, \fB\-\-dangles\fR=\fIINT\fR
+set energy model for treatment of dangling
+bases
+.IP
+(possible values="0", "2" default=`2')
+.TP
+\fB\-\-noLP\fR
+Produce structures without lonely pairs
+(helices of length 1).
+.IP
+(default=off)
+.IP
+For partition function folding this only disallows pairs that can only occur
+isolated. Other pairs may still occasionally occur as helices of length 1.
+.TP
+\fB\-\-noGU\fR
+Do not allow GU pairs
+.IP
+(default=off)
+.TP
+\fB\-\-noClosingGU\fR
+Do not allow GU pairs at the end of helices
+.IP
+(default=off)
+.TP
+\fB\-P\fR, \fB\-\-paramFile\fR=\fIparamfile\fR
+Read energy parameters from paramfile, instead
+of using the default parameter set.
+.IP
+A sample parameter file should accompany your distribution.
+See the RNAlib documentation for details on the file format.
+.TP
+\fB\-\-nsp\fR=\fISTRING\fR
+Allow other pairs in addition to the usual
+AU,GC,and GU pairs.
+.IP
+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.
+e.g. RNAfold \fB\-nsp\fR \fB\-GA\fR will allow GA and AG pairs. Nonstandard pairs are
+given 0 stacking energy.
+.TP
+\fB\-e\fR, \fB\-\-energyModel\fR=\fIINT\fR
+Rarely used option to fold sequences from the
+artificial ABCD... alphabet, where A pairs B,
+C\-D etc. Use the energy parameters for GC
+(\fB\-e\fR 1) or AU (\fB\-e\fR 2) pairs.
+.SH AUTHOR
+
+Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer.
+.SH REFERENCES
+.I If you use this program in your work you might want to cite:
+
+R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011),
+"ViennaRNA Package 2.0",
+Algorithms for Molecular Biology: 6:26
+
+I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994),
+"Fast Folding and Comparison of RNA Secondary Structures",
+Monatshefte f. Chemie: 125, pp 167-188
+
+
+S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster (1993),
+"RNA multi-structure landscapes",
+Euro Biophys J:22, pp 13-24
+
+.I The energy parameters are taken from:
+
+D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004),
+"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure",
+Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292
+
+D.H Turner, D.H. Mathews (2009),
+"NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure",
+Nucleic Acids Research: 38, pp 280-282
+.SH "REPORTING BUGS"
+If in doubt our program is right, nature is at fault.
+.br
+Comments should be sent to rna@tbi.univie.ac.at.
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