--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAPALN "1" "July 2013" "RNApaln 2.1.2" "User Commands"
+.SH NAME
+RNApaln \- manual page for RNApaln 2.1.2
+.SH SYNOPSIS
+.B RNApaln
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNApaln 2.1.2
+.PP
+RNA alignment based on sequence base pairing propensities
+.PP
+Uses string\-alignment techniques to perform fast pairwise structural alignments
+of RNAs. Similar to RNApdist secondary structure is incorporated in an
+approximate manner by computing base pair probabilities, which are then reduced
+to a vector holding the probability that a base is paired upstream, downstream,
+or remains unpaired. Such pair propsensity vectors can then be compared using
+standard alignment algorithms. In contrast to RNApdist, RNApaln performs
+similarity (instead of distance) alignments, considers both sequence and
+structure information, and uses affine (rather than linear) gap costs. RNApaln
+can perform semi\-local alignments by using free end gaps, a true local
+alignment mode is planned.
+.PP
+The same approach has since been used in the StraL program from Gerhard
+Steeger's group. Since StraL has optimized parameters and a multiple alignment
+mode, it be be currently the better option.
+.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\-B\fR, \fB\-\-printAlignment\fR[=\fIfilename\fR]
+Print an "alignment" with gaps of the
+.IP
+profiles
+The aligned structures are written to
+filename, if specified
+Otherwise output is written to stdout, unless
+the \fB\-Xm\fR option is set in which case
+"backtrack.file" is used.
+.IP
+(default=`stdout')
+.IP
+The following symbols are used:
+.TP
+(
+) essentially upstream (downstream) paired bases
+.TP
+{
+} weakly upstream (downstream) paired bases
+.TP
+|
+strongly paired bases without preference
+.TP
+,
+weakly paired bases without preference
+.TP
+\&.
+essentially unpaired bases.
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide
+"T" with "U"
+.IP
+(default=off)
+.SS "Algorithms:"
+.IP
+Select additional algorithms which should be included in the calculations.
+.TP
+\fB\-X\fR, \fB\-\-mode\fR=\fIpmfc\fR
+Set the alignment mode to be used
+.IP
+The alignment mode is passed as a single character value. The following
+options are available:
+\&'p' \- Compare the structures pairwise, that is first with 2nd, third with 4th
+etc. This is the default.
+.TP
+\&'m'
+\- Calculate the distance matrix between all structures. The output is
+.IP
+formatted as a lower triangle matrix.
+.IP
+\&'f' \- Compare each structure to the first one.
+.IP
+\&'c' \- Compare continuously, that is i\-th with (i+1)th structure.
+.SS "Model Details:"
+.TP
+\fB\-\-gapo\fR=\fIopen\fR
+Set the gap open penalty
+.TP
+\fB\-\-gape\fR=\fIext\fR
+Set the gap extension penalty
+.TP
+\fB\-\-seqw\fR=\fIw\fR
+Set the weight of sequence (compared to
+structure) in the scoring function.
+.TP
+\fB\-\-endgaps\fR
+Use free end\-gaps
+.IP
+(default=off)
+.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 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.
+.SH AUTHOR
+
+Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer
+.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
+
+
+Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P (1993),
+"RNA multi-structure landscapes",
+Euro Biophys J: 22, pp 13-24
+
+.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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