--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNA2DFOLD "1" "July 2013" "RNA2Dfold 2.1.2" "User Commands"
+.SH NAME
+RNA2Dfold \- manual page for RNA2Dfold 2.1.2
+.SH SYNOPSIS
+.B RNA2Dfold
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNA2Dfold 2.1.2
+.PP
+Compute MFE structure, partition function and representative sample structures
+of k,l neighborhoods
+.PP
+The program partitions the secondary structure space into (basepair)distance
+classes according to two fixed reference structures. It expects a sequence and
+two secondary structures in dot\-bracket notation as its inputs. For each
+distance class, the MFE representative, Boltzmann probabilities and Gibbs free
+energy is computed. Additionally, a stochastic backtracking routine allows to
+produce samples of representative suboptimal secondary structures from each
+partition
+.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
+.SS "General Options:"
+.IP
+Below are command line options which alter the general behavior of this
+program
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide
+"T" with "U"
+.IP
+(default=off)
+.TP
+\fB\-j\fR, \fB\-\-numThreads\fR=\fIINT\fR
+Set the number of threads used for calculations
+(only available when compiled with OpenMP
+support)
+.SS "Algorithms:"
+.TP
+\fB\-p\fR, \fB\-\-partfunc\fR
+calculate partition function and thus,
+Boltzmann probabilities and Gibbs free energy
+.IP
+(default=off)
+.TP
+\fB\-\-stochBT\fR=\fIINT\fR
+backtrack a certain number of Boltzmann samples
+from the appropriate k,l neighborhood(s)
+.TP
+\fB\-\-neighborhood=\fR<k>:<l>
+backtrack structures from certain
+k,l\-neighborhood only, can be specified
+multiple times (<k>:<l>,<m>:<n>,...)
+.TP
+\fB\-S\fR, \fB\-\-pfScale\fR=\fIDOUBLE\fR
+scaling factor for pf to avoid overflows
+.TP
+\fB\-\-noBT\fR
+do not backtrack structures, calculate energy
+contributions only
+.IP
+(default=off)
+.TP
+\fB\-c\fR, \fB\-\-circ\fR
+Assume a circular (instead of linear) RNA
+molecule.
+.IP
+(default=off)
+.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\-K\fR, \fB\-\-maxDist1\fR=\fIINT\fR
+maximum distance to first reference structure
+.IP
+If this value is set all structures that exhibit a basepair distance greater
+than maxDist1 will be thrown into a distance class denoted by K=L=\-1
+.TP
+\fB\-L\fR, \fB\-\-maxDist2\fR=\fIINT\fR
+maximum distance to second reference structure
+.IP
+If this value is set all structures that exhibit a basepair distance greater
+than maxDist1 will be thrown into a distance class denoted by K=L=\-1
+.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\-P\fR, \fB\-\-parameterFile\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\-d\fR, \fB\-\-dangles\fR=\fIINT\fR
+How to treat "dangling end" energies for
+bases adjacent to helices in free ends and
+multi\-loops
+.IP
+(possible values="0", "2" default=`2')
+.IP
+With \fB\-d2\fR dangling energies will be added for the bases adjacent to a helix on
+both sides
+.IP
+in any case.
+.IP
+The option \fB\-d0\fR ignores dangling ends altogether (mostly for debugging).
+.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)
+.SH AUTHOR
+
+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
+
+R. Lorenz, C. Flamm, I.L. Hofacker (2009),
+"2D Projections of RNA folding Landscapes",
+GI, Lecture Notes in Informatics, German Conference on Bioinformatics 2009: 157, pp 11-20
+
+M. Zuker, P. Stiegler (1981),
+"Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information",
+Nucl Acid Res: 9, pp 133-148
+
+J.S. McCaskill (1990),
+"The equilibrium partition function and base pair binding probabilities for RNA secondary structures",
+Biopolymers: 29, pp 1105-1119
+
+I.L. Hofacker and P.F. Stadler (2006),
+"Memory Efficient Folding Algorithms for Circular RNA Secondary Structures",
+Bioinformatics
+
+D. Adams (1979),
+"The hitchhiker's guide to the galaxy",
+Pan Books, London
+
+The calculation of mfe structures is based on dynamic programming algorithm originally developed by M. Zuker and P. Stiegler. The partition function algorithm is based on work by J.S. McCaskill.
+
+.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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