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

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

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+2.1.2
+
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
+.TH RNADISTANCE "1" "July 2013" "RNAdistance 2.1.2" "User Commands"
+.SH NAME
+RNAdistance \- manual page for RNAdistance 2.1.2
+.SH SYNOPSIS
+.B RNAdistance
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAdistance 2.1.2
+.PP
+Calculate distances between RNA secondary structures
+.PP
+This program reads RNA secondary structures from stdin and calculates one or
+more measures for their dissimilarity, based on tree or string editing
+(alignment). In addition it calculates a "base pair distance" given by the
+number of base pairs present in one structure, but not the other. For
+structures of different length base pair distance is not recommended.
+.PP
+
+RNAdistance accepts structures in bracket format, where matching brackets
+symbolize base pairs and unpaired bases are represented by a dot ".",
+or coarse grained representations where hairpins, interior loops,
+bulges, multiloops, stacks and external bases are represented by
+(H), (I), (B), (M), (S), and (E), respectively. These can be optionally
+weighted. Full structures can be represented in the same fashion using
+the identifiers (U) and (P) for unpaired and paired bases, respectively.
+We call this the HIT representation (you don't want to know what this means).
+For example the following structure consists of 2 hairpins joined by
+a multiloop:
+
+.nf
+.ft CW
+  .((..(((...)))..((..)))).       full structure (usual format);
+  (U)((U2)((U3)P3)(U2)((U2)P2)P2) HIT structure;
+  ((H)(H)M)  or
+  ((((H)S)((H)S)M)S)              coarse grained structure;
+  (((((H3)S3)((H2)S2)M4)S2)E2)    weighted coarse grained.
+.ft
+.fi
+
+The program will continue to read new structures until a line consisting
+of the single character @ or an end of file condition is encountered. Input
+lines neither containing a valid structure nor starting with > are ignored.
+.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\-V\fR, \fB\-\-version\fR
+Print version and exit
+.TP
+\fB\-D\fR, \fB\-\-distance\fR=\fIfhwcFHWCP\fR
+Specify the distance representation to be used
+in calculations.
+.IP
+(default=`f')
+.IP
+Use the full, HIT, weighted coarse, or coarse representation to calculate the
+distance. Capital letters indicate string alignment otherwise tree editing is
+used.
+Any combination of distances can bespecified.
+.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\-S\fR, \fB\-\-shapiro\fR
+Use the Bruce Shapiro's cost matrix for
+comparing coarse structures.
+.IP
+(default=off)
+.TP
+\fB\-B\fR, \fB\-\-backtrack[=\fR<filename>]
+Print an "alignment" with gaps of the
+structures, to show matching substructures.
+The aligned structures are written to
+<filename>, if specified.
+.IP
+(default=`none')
+.IP
+If <filename> is not specified, the output is written to stdout, unless the
+\fB\-Xm\fR option is set in which case "backtrack.file" is used.
+.SH AUTHOR
+
+Walter Fontana, Ivo L Hofacker, Peter F Stadler
+.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
+
+B.A. Shapiro (1988),
+"An algorithm for comparing multiple RNA secondary structures"
+CABIOS: 4, pp 381-393
+
+B.A. Shapiro, K. Zhang (1990),
+"Comparing multiple RNA secondary structures using tree comparison",
+CABIOS: 6, pp 309-318
+
+W. Fontana, D.A.M. Konings, P.F. Stadler and P. Schuster P (1993),
+"Statistics of RNA secondary structures",
+Biopolymers: 33, pp 1389-1404
+.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.