--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAEVAL "1" "July 2013" "RNAeval 2.1.2" "User Commands"
+.SH NAME
+RNAeval \- manual page for RNAeval 2.1.2
+.SH SYNOPSIS
+.B RNAeval
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAeval 2.1.2
+.PP
+calculate energy of RNA sequences with given secondary structure
+.PP
+Evaluates the free energy of an RNA molecule in fixed secondary structure.
+Sequences and structures are read alternately from stdin. The energy in
+Kcal/Mol is written to stdout.
+The program will continue to read new sequences and structures until a line
+consisting of the single character "@" or an end of file condition is
+encountered.
+If the input sequence or structure contains the separator character "&" the
+program calculates the energy of the co\-folding of two RNA strands, where the
+"&" marks the boundary between the two strands.
+.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\-v\fR, \fB\-\-verbose\fR
+Print out energy contribution of each loop in the
+structure.
+.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\-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
+How to treat "dangling end" energies for bases
+adjacent to helices in free ends and multi\-loops
+.IP
+(default=`2')
+.IP
+With \fB\-d1\fR only unpaired bases can participate in at most one dangling end,
+this unsupported for the partition function folding.
+.IP
+With \fB\-d2\fR 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 (\fB\-p\fR).
+The option \fB\-d0\fR ignores dangling ends altogether (mostly for debugging).
+With \fB\-d3\fR 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.
+.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.
+.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\-c\fR, \fB\-\-circ\fR
+Assume a circular (instead of linear) RNA
+molecule.
+.IP
+(default=off)
+.TP
+\fB\-g\fR, \fB\-\-gquad\fR
+Incoorporate G\-Quadruplex formation into the
+structure prediction algorithm
+.IP
+(default=off)
+.TP
+\fB\-\-logML\fR
+Recalculate energies of structures using a
+logarithmic energy function for multi\-loops
+before output.
+.IP
+(default=off)
+.IP
+This option does not effect structure generation, only the energies that are
+printed out. Since logML lowers energies somewhat, some structures may be
+missing.
+.SH AUTHOR
+
+Ivo L Hofacker, Peter F Stadler, 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
+
+
+.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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