--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNALALIFOLD "1" "July 2013" "RNALalifold 2.1.2" "User Commands"
+.SH NAME
+RNALalifold \- manual page for RNALalifold 2.1.2
+.SH SYNOPSIS
+.B RNALalifold
+[\fIoptions\fR] \fI<file1.aln>\fR
+.SH DESCRIPTION
+RNALalifold 2.1.2
+.PP
+calculate locally stable secondary structures for a set of aligned RNAs
+.PP
+reads aligned RNA sequences from stdin or file.aln and calculates locally
+stable RNA secondary structure with a maximal base pair span. For a sequence of
+length n and a base pair span of L the algorithm uses only O(n+L*L) memory and
+O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for
+short RNA
+.IP
+structures.
+.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\-L\fR, \fB\-\-span\fR=\fIINT\fR
+Set the maximum allowed separation of a base
+pair to span. I.e. no pairs (i,j) with
+j\-i>span will be allowed.
+.IP
+(default=`70')
+.TP
+\fB\-\-csv\fR
+Create comma seperated output (csv)
+.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=`1')
+.IP
+Default is calculation of mfe structure only. 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 \etCalculate the partition function but not the pair probabilities, saving
+about 50% in runtime. This prints the ensemble free energy \fB\-kT\fR ln(Z).
+.TP
+\fB\-c\fR, \fB\-\-cutoff\fR=\fIFLOAT\fR
+Report only base pairs with an average
+probability > cutoff in the dot plot
+.IP
+(default=`0.01')
+.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\-\-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)
+.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 is 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\-\-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\-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)
+.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