--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAALIFOLD "1" "July 2013" "RNAalifold 2.1.2" "User Commands"
+.SH NAME
+RNAalifold \- manual page for RNAalifold 2.1.2
+.SH SYNOPSIS
+.B RNAalifold
+[\fIoptions\fR] \fI<file1.aln>\fR
+.SH DESCRIPTION
+RNAalifold 2.1.2
+.PP
+calculate secondary structures for a set of aligned RNAs
+.PP
+Read aligned RNA sequences from stdin or file.aln and calculate their minimum
+free energy (mfe) structure, partition function (pf) and base pairing
+probability matrix. Currently, the input alignment has to be in CLUSTAL format.
+It returns the mfe structure in bracket notation, its energy, the free energy
+of the thermodynamic ensemble and the frequency of the mfe structure in the
+ensemble to stdout. It also produces Postscript files with plots of the
+resulting secondary structure graph ("alirna.ps") and a "dot plot" of the
+base pairing matrix ("alidot.ps"). The file "alifold.out" will contain a
+list of likely pairs sorted by credibility, suitable for viewing with
+"AliDot.pl". Be warned that output file will overwrite any existing files of
+the same name.
+.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.
+The constraining structure will be read from
+\&'stdin', the alignment has to be given as a
+file name on the command line.
+.IP
+(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\-\-color\fR
+Produce a colored version of the consensus
+strcture plot "alirna.ps" (default b&w
+only)
+.IP
+(default=off)
+.TP
+\fB\-\-aln\fR
+Produce a colored and structure annotated
+alignment in PostScript format in the file
+"aln.ps" in the current directory.
+.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.
+.IP
+An additionally passed value to this option changes the behavior of partition
+function calculation:
+\fB\-p0\fR deactivates the calculation of the pair probabilities, saving about 50%
+in runtime. This prints the ensemble free energy \fB\-kT\fR ln(Z).
+.TP
+\fB\-\-MEA\fR[=\fIgamma\fR]
+Calculate an MEA (maximum expected accuracy)
+structure.
+.IP
+(default=`1.')
+.IP
+If gamma is not specified a default of gamma=1 is used.
+Using \fB\-\-MEA\fR implies \fB\-p\fR
+See also RNAfold man page for details.
+.TP
+\fB\-\-mis\fR
+Output "most informative sequence" instead of
+simple consensus: For each column of the
+alignment output the set of nucleotides with
+frequence greater than average in IUPAC
+notation.
+.IP
+(default=off)
+.TP
+\fB\-s\fR, \fB\-\-stochBT\fR=\fIINT\fR
+Stochastic backtrack. Compute a certain number
+of random structures with a probability
+dependend on the partition function. See \fB\-p\fR
+option in RNAsubopt.
+.TP
+\fB\-\-stochBT_en\fR=\fIINT\fR
+same as "\-s" but also print out the energies
+and probabilities of the backtraced
+structures.
+.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\-c\fR, \fB\-\-circ\fR
+Assume a circular (instead of linear) RNA
+molecule.
+.IP
+(default=off)
+.TP
+\fB\-\-bppmThreshold=\fR<value>
+Set the threshold for base pair probabilities
+included in the postscript output
+.IP
+(default=`1e\-6')
+.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 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\-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\-\-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\-\-cfactor\fR=\fIDOUBLE\fR
+Set the weight of the covariance term in the
+energy function
+.IP
+(default=`1.0')
+.TP
+\fB\-\-nfactor\fR=\fIDOUBLE\fR
+Set the penalty for non\-compatible sequences in
+the covariance term of the energy function
+.IP
+(default=`1.0')
+.TP
+\fB\-E\fR, \fB\-\-endgaps\fR
+Score pairs with endgaps same as gap\-gap pairs.
+.IP
+(default=off)
+.TP
+\fB\-R\fR, \fB\-\-ribosum_file\fR=\fIribosumfile\fR
+use specified Ribosum Matrix instead of normal
+.IP
+energy model. Matrixes to use should be 6x6
+matrices, the order of the terms is AU, CG,
+GC, GU, UA, UG.
+.TP
+\fB\-r\fR, \fB\-\-ribosum_scoring\fR
+use ribosum scoring matrix. The matrix is
+chosen according to the minimal and maximal
+pairwise identities of the sequences in the
+file.
+.IP
+(default=off)
+.TP
+\fB\-\-old\fR
+use old energy evaluation, treating gaps as
+characters.
+.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/(kTn*betaScale)) where k is the
+Boltzmann constant, dG the free energy contribution of the state, T the
+absolute temperature and n the number of sequences.
+.PP
+Caveats:
+.PP
+Sequences are not weighted. If possible, do not mix very similar and dissimilar
+sequences. Duplicate sequences, for example, can distort the prediction.
+.SH AUTHOR
+
+Ivo L Hofacker, 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
+
+
+The algorithm is a variant of the dynamic programming algorithms of M. Zuker and P. Stiegler (mfe)
+and J.S. McCaskill (pf) adapted for sets of aligned sequences with covariance information.
+
+Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler (2002),
+"Secondary Structure Prediction for Aligned RNA Sequences",
+J.Mol.Biol.: 319, pp 1059-1066.
+
+Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler (2008),
+"RNAalifold: Improved consensus structure prediction for RNA alignments",
+BMC Bioinformatics: 9, pp 474
+
+
+.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.
+.SH "SEE ALSO"
+
+The ALIDOT package http://www.tbi.univie.ac.at/RNA/ALIDOT/
git://source.jalview.org / jabaws.git / blobdiff