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RNAPDIST(1)			 User Commands			   RNAPDIST(1)

       RNApdist	- manual page for RNApdist 2.4.14

       RNApdist	[OPTIONS]...

       RNApdist	2.4.14

       Calculate  distances between thermodynamic RNA secondary	structures en-

       This program reads RNA sequences	from stdin  and	 calculates  structure
       distances between the thermodynamic ensembles of	their secondary	struc-

       To do this the partition	function and matrix of base pairing probabili-
       ties is computed	for each sequence. The probability matrix is then con-
       densed into a vector holding for	each base the probabilities  of	 being
       unpaired,  paired  upstream,  or	paired downstream, respectively. These
       profiles	are compared by	a standard alignment algorithm.

       The base	pair probabilities are also saved as  postscript  "dot	plots"
       (as  in	RNAfold) in the	files  "", where name	is the name of
       the sequence, or	a number if unnamed.

       -h, --help
	      Print help and exit

	      Print help, including all	details	and hidden options, and	exit

	      Print help, including hidden options, and	exit

       -V, --version
	      Print version and	exit

   General Options:
	      Do not automatically substitude nucleotide "T" with "U"


       -X, --compare=p|m|f|c
	      Specify the comparison directive.	 (default=`p')

	      Possible arguments for this option are: -Xp compare  the	struc-
	      tures  pairwise  (p),  i.e.  first with 2nd, third with 4th etc.
	      -Xm calculate the	distance matrix	between	 all  structures.  The
	      output  is  formatted  as	 a lower triangle matrix.  -Xf compare
	      each structure to	the first one.	-Xc compare continuously, that
	      is i-th with (i+1)th structure.

       -B, --backtrack[=<filename>]
	      Print  an	 "alignment"  with  gaps  of the profiles. The aligned
	      structures are written to	<filename>, if specified.


	      Within the profile output, the following symbols will be used:

       ()     essentially upstream (downstream)	paired bases

       {}     weakly upstream (downstream) paired bases

       |      strongly paired bases without preference

       ,      weakly paired bases without preference

       .      essentially unpaired bases.

	      If <filename> is not specified, the output is written to stdout,
	      unless the

	      "-Xm" option is set in which case	"backtrack.file" is used.

   Model Details:
       -T, --temp=DOUBLE
	      Rescale energy parameters	to a temperature of temp C. Default is

       -4, --noTetra
	      Do not include special tabulated stabilizing energies for	 tri-,
	      tetra- and hexaloop hairpins. Mostly for testing.


       -d, --dangles=INT
	      set energy model for treatment of	dangling bases

	      (possible	values="0", "2"	default=`2')

       --noLP Produce structures without lonely	pairs (helices of length 1).


	      For  partition  function	folding	this only disallows pairs that
	      can only occur isolated. Other pairs may still occasionally  oc-
	      cur as helices of	length 1.

       --noGU Do not allow GU pairs


	      Do not allow GU pairs at the end of helices


       -P, --paramFile=paramfile
	      Read  energy parameters from paramfile, instead of using the de-
	      fault parameter set.

	      Different	sets of	energy parameters for RNA and DNA  should  ac-
	      company your distribution.  See the RNAlib documentation for de-
	      tails on the file	format.	When passing the placeholder file name
	      "DNA",  DNA  parameters  are loaded without the need to actually
	      specify any input	file.

	      Allow other pairs	in addition to the usual AU,GC,and GU pairs.

	      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 -nsp -GA  will	 allow
	      GA and AG	pairs. Nonstandard pairs are given 0 stacking energy.

       -e, --energyModel=INT
	      Rarely used option to fold sequences from	the artificial ABCD...
	      alphabet,	where A	pairs B, C-D etc.  Use the  energy  parameters
	      for GC (-e 1) or AU (-e 2) pairs.

       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	Struc-
       tures", Monatshefte f. Chemie: 125, pp 167-188

       R.  Lorenz,  I.L. Hofacker, P.F.	Stadler	(2016),	"RNA folding with hard
       and soft	constraints", Algorithms for Molecular Biology 11:1 pp 1-13

       S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster	 (1993),  "RNA
       multi-structure landscapes", Euro Biophys J:22, pp 13-24

       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  modifica-
       tion 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

       Peter F Stadler,	Ivo L Hofacker,	Sebastian Bonhoeffer.

       If in doubt our program is right, nature	is at fault.  Comments	should
       be sent to

RNApdist 2.4.14			  August 2019			   RNAPDIST(1)


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