WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / man / RNAplot.1

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+2.1.2
+
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
+.TH RNAPLOT "1" "July 2013" "RNAplot 2.1.2" "User Commands"
+.SH NAME
+RNAplot \- manual page for RNAplot 2.1.2
+.SH SYNOPSIS
+.B RNAplot
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAplot 2.1.2
+.PP
+Draw RNA Secondary Structures
+.PP
+The program reads RNA sequences and structures from stdin in the format as
+produced by RNAfold and produces drawings of the secondary structure graph.
+The coordinates are produced using either E. Bruccoleri's naview routines, or a
+simple radial layout method.
+.PP
+If the sequence was preceded by a line of the form
+.PP
+>name
+.PP
+the output file will be named "name_ss.ps" otherwise "rna.ps" is used.
+Existing files of the same name will be overwritten.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Print help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print version and exit
+.TP
+\fB\-t\fR, \fB\-\-layout\-type\fR=\fIINT\fR
+Choose the layout algorithm. Simple radial
+layout if 0, or naview if 1
+.IP
+(default=`1')
+.TP
+\fB\-o\fR, \fB\-\-output\-format\fR=\fIps\fR|gml|xrna|svg
+Specify output format. Available formats are:
+.IP
+PostScript (ps), Graph Meta Language (gml),
+Scalable Vector Graphics (svg), and XRNA save
+file (xrna). Output filenames will end in
+".ps" ".gml" ".svg" ".ss",
+respectively.
+.IP
+(default=`ps')
+.TP
+\fB\-\-pre\fR=\fIstring\fR
+Add annotation macros to postscript file, and
+add the postscript code in "string" just
+before the code to draw the structure. This
+is an easy way to add annotation.
+.TP
+\fB\-\-post\fR=\fIstring\fR
+Same as \fB\-\-pre\fR but in contrast to adding the
+annotation macros. E.g to mark position 15
+with circle use \fB\-\-post\fR "15 cmark"
+.SH AUTHOR
+
+Ivo L Hofacker, Ronny Lorenz
+.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
+.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.