--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNACOFOLD "1" "July 2013" "RNAcofold 2.1.2" "User Commands"
+.SH NAME
+RNAcofold \- manual page for RNAcofold 2.1.2
+.SH SYNOPSIS
+.B RNAcofold
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAcofold 2.1.2
+.PP
+calculate secondary structures of two RNAs with dimerization
+.PP
+The program works much like RNAfold, but allows to specify two RNA sequences
+wich are then allowed to form a dimer structure. RNA sequences are read from
+stdin in the usual format, i.e. each line of input corresponds to one sequence,
+except for lines starting with ">" which contain the name of the next
+sequence.
+To compute the hybrid structure of two molecules, the two sequences must be
+concatenated using the \e'&\e' character as separator.
+RNAcofold can compute minimum free energy (mfe) structures, as well as
+partition function (pf) and base pairing probability matrix (using the \fB\-p\fR
+switch)
+Since dimer formation is concentration dependent, RNAcofold can be used to
+compute equilibrium concentrations for all five monomer and (homo/hetero)\-dimer
+species, given input concentrations for the monomers.
+Output consists of the mfe structure in bracket notation as well as PostScript
+structure plots and "dot plot" files containing the pair probabilities, see
+the RNAfold man page for details. In the dot plots a cross marks the chain
+break between the two concatenated sequences.
+The program will continue to read new sequences until a line consisting of the
+single character @ or an end of file condition is encountered.
+.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:"
+.IP
+Below are command line options which alter the general behavior of this
+program
+.TP
+\fB\-C\fR, \fB\-\-constraint\fR
+Calculate structures subject to constraints.
+(default=off)
+.IP
+The program reads first the sequence, then a string containing constraints on
+the structure encoded with the symbols:
+.IP
+\&. (no constraint for this base)
+.IP
+| (the corresponding base has to be paired
+.IP
+x (the base is unpaired)
+.IP
+< (base i is paired with a base j>i)
+.IP
+\f(CW> (base i is paired with a base j<i)\fR
+.IP
+and matching brackets ( ) (base i pairs base j)
+.IP
+With the exception of "|", constraints will disallow all pairs conflicting
+with the constraint. This is usually sufficient to enforce the constraint,
+but occasionally a base may stay unpaired in spite of constraints. PF folding
+ignores constraints of type "|".
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide
+"T" with "U"
+.IP
+(default=off)
+.TP
+\fB\-\-noPS\fR
+Do not produce postscript output
+.IP
+(default=off)
+.SS "Algorithms:"
+.IP
+Select additional algorithms which should be included in the calculations.
+The Minimum free energy (MFE) and a structure representative are calculated
+in any case.
+.TP
+\fB\-p\fR, \fB\-\-partfunc\fR[=\fIINT\fR]
+Calculate the partition function and base
+pairing probability matrix in addition to the
+mfe structure. Default is calculation of mfe
+structure only.
+.IP
+(default=`1')
+.IP
+In addition to the MFE structure we print a coarse representation of the pair
+probabilities in form of a pseudo bracket notation, followed by the ensemble
+free energy, as well as the centroid structure derived from the pair
+probabilities together with its free energy and distance to the ensemble.
+Finally it prints the frequency of the mfe structure, and the structural
+diversity (mean distance between the structures in the ensemble).
+See the description of pf_fold() and mean_bp_dist() and centroid() in the
+RNAlib documentation for details.
+Note that unless you also specify \fB\-d2\fR or \fB\-d0\fR, the partition function and mfe
+calculations will use a slightly different energy model. See the discussion
+of dangling end options below.
+.IP
+An additionally passed value to this option changes the behavior of partition
+function calculation:
+.IP
+In order to calculate the partition function but not the pair probabilities
+.IP
+use the \fB\-p0\fR option and save about
+.IP
+50% in runtime. This prints the ensemble free energy \fB\-kT\fR ln(Z).
+.TP
+\fB\-a\fR, \fB\-\-all_pf\fR
+Compute the partition function and free
+energies not only of the hetero\-dimer
+consisting of the two input sequences (the
+"AB dimer"), but also of the homo\-dimers AA
+and BB as well as A and B monomers.
+.IP
+(default=off)
+.IP
+The output will contain the free energies for each of these species, as well
+as 5 dot plots containing the conditional pair probabilities, called
+ABname5.ps, AAname5.ps and so on. For later use, these dot plot files also
+contain the free energy of the ensemble as a comment. Using \fB\-a\fR automatically
+toggles the \fB\-p\fR option.
+.TP
+\fB\-c\fR, \fB\-\-concentrations\fR
+In addition to everything listed under the \fB\-a\fR
+option, read in initial monomer
+concentrations and compute the expected
+equilibrium concentrations of the 5 possible
+species (AB, AA, BB, A, B).
+.IP
+(default=off)
+.IP
+Start concentrations are read from stdin (unless the \fB\-f\fR option is used) in
+[mol/l], equilibrium concentrations are given realtive to the sum of the two
+inputs. An arbitrary number of initial concentrations can be specified (one
+pair of concentrations per line).
+.TP
+\fB\-f\fR, \fB\-\-concfile\fR=\fIfilename\fR
+Specify a file with initial concentrations for
+the to sequences.
+.IP
+The table consits of arbitrary many lines with just two numbers (the
+concentration of sequence A and B). This option will automatically toggle the
+\fB\-c\fR (and thus \fB\-a\fR and \fB\-p\fR) options (see above).
+.TP
+\fB\-S\fR, \fB\-\-pfScale\fR=\fIscaling\fR factor
+In the calculation of the pf use scale*mfe as
+an estimate for the ensemble free energy
+(used to avoid overflows).
+.IP
+The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for
+long sequences.
+You can also recompile the program to use double precision (see the README
+file).
+.TP
+\fB\-\-bppmThreshold=\fR<value>
+Set the threshold for base pair probabilities
+included in the postscript output
+.IP
+(default=`1e\-5')
+.IP
+By setting the threshold the base pair probabilities that are included in the
+output can be varied. By default only those exceeding 1e\-5 in probability
+will be shown as squares in the dot plot. Changing the threshold to any other
+value allows for increase or decrease of data.
+.TP
+\fB\-g\fR, \fB\-\-gquad\fR
+Incoorporate G\-Quadruplex formation into the
+structure prediction algorithm
+.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 stabilizing energies for
+certain tetra\-loops. 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 is the default for mfe folding but 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 and works only for mfe
+folding.
+.IP
+Note that by default (as well as with \fB\-d1\fR and \fB\-d3\fR) pf and mfe folding treat
+dangling ends differently. Use \fB\-d2\fR in addition to \fB\-p\fR to ensure that both
+algorithms use the same energy model.
+.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.
+.TP
+\fB\-\-betaScale\fR=\fIDOUBLE\fR
+Set the scaling of the Boltzmann factors
+(default=`1.')
+.IP
+The argument provided with this option enables to scale the thermodynamic
+temperature used in the Boltzmann factors independently from the temperature
+used to scale the individual energy contributions of the loop types. The
+Boltzmann factors then become exp(\fB\-dG\fR/(kT*betaScale)) where k is the
+Boltzmann constant, dG the free energy contribution of the state and T the
+absolute temperature.
+.SH AUTHOR
+
+Ivo L Hofacker, Peter F Stadler, Stephan Bernhart, 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
+
+
+S.H.Bernhart, Ch. Flamm, P.F. Stadler, I.L. Hofacker, (2006),
+"Partition Function and Base Pairing Probabilities of RNA Heterodimers",
+Algorithms Mol. Biol.
+
+.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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