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RNALALIFOLD(1)			 User Commands			RNALALIFOLD(1)

NAME
       RNALalifold - manual page for RNALalifold 2.4.14

SYNOPSIS
       RNALalifold [options] _file1.aln_

DESCRIPTION
       RNALalifold 2.4.14

       calculate locally stable	secondary structures for a set of aligned RNAs

       reads  aligned  RNA sequences from stdin	or file.aln and	calculates lo-
       cally 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

	      structures.

       -h, --help
	      Print help and exit

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

       --full-help
	      Print help, including hidden options, and	exit

       -V, --version
	      Print version and	exit

   General Options:
	      Command  line  options  which alter the general behavior of this
	      program

       -v, --verbose
	      Be verbose.

	      (default=off)

       -q, --quiet
	      Be quiet.	 (default=off)

	      This option can be used to minimize the output of	additional in-
	      formation	 and  non-severe  warnings  which otherwise might spam
	      stdout/stderr.

       --noconv
	      Do not automatically substitute nucleotide "T" with "U"

	      (default=off)

       -f, --input-format=C|S|F|M
	      File format of the input multiple	sequence alignment (MSA).

	      If this parameter	is set,	the input is considered	 to  be	 in  a
	      particular  file	format.	Otherwise, the program tries to	deter-
	      mine the file format automatically, if an	input  file  was  pro-
	      vided  in	 the  set of parameters. In case the input MSA is pro-
	      vided in interactive mode, or from a terminal  (TTY),  the  pro-
	      grams default is to assume CLUSTALW format.  Currently, the fol-
	      lowing formats are available: ClustalW (C), Stockholm  1.0  (S),
	      FASTA/Pearson (F), and MAF (M).

       --csv  Create comma separated output (csv)

	      (default=off)

       --aln[=prefix]
	      Produce output alignments	and secondary structure	plots for each
	      hit found.

	      This option tells	the program to produce,	for each hit,  a  col-
	      ored and structure annotated (sub)alignment and secondary	struc-
	      ture plot	in PostScript format. It also  adds  the  subalignment
	      hit  into	 a  multi-Stockholm  formatted	file  "RNALalifold_re-
	      sults.stk".   The	  postscript	output	  file	  names	   are
	      "aln_start_end.eps"  and	"ss_start_end.eps".  All files will be
	      created in the current directory.	The optional  argument	string
	      can  be  used  to	set a specific prefix that is used to name the
	      output   files.	The   file    names    then    become	 "pre-
	      fix_aln_start_end.eps",	"prefix_ss_start_end.eps",  and	 "pre-
	      fix.stk".	Note: Any special characters in	the prefix will	be re-
	      placed  by the filename delimiter, hence there is	no way to pass
	      an entire	directory path through this option yet.	(See also  the
	      "--filename-delim" parameter)

       --aln-EPS[=prefix]
	      Produce  colored	and  structure annotated subalignment for each
	      hit

	      The default file name used for the output	is "aln_start_end.eps"
	      where  "start" and "end" denote the first	and last column	of the
	      subalignment relative to the input (1-based). Users  may	change
	      the  filename  to	 "prefix_aln_start_end.eps"  by	specifying the
	      prefix as	optional argument.  Files will be create in  the  cur-
	      rent  directory. Note: Any special characters in the prefix will
	      be replaced by the filename delimiter, hence there is no way  to
	      pass an entire directory path through this option	yet. (See also
	      the "--filename-delim" parameter)

       --aln-EPS-cols=INT
	      Number of	columns	in colored EPS alignment output.

	      (default=`60')

	      A	value less than	1 indicates that  the  output  should  not  be
	      wrapped at all.

       --aln-EPS-ss[=prefix]
	      Produce  colored	consensus  secondary  structure	plots in Post-
	      Script format

	      The default file name used for the output	is  "ss_start_end.eps"
	      where  "start" and "end" denote the first	and last column	of the
	      subalignment relative to the input (1-based). Users  may	change
	      the filename to "prefix_ss_start_end.eps"	by specifying the pre-
	      fix as optional argument.	 Files will be create in  the  current
	      directory.  Note:	 Any  special characters in the	prefix will be
	      replaced by the filename delimiter, hence	there  is  no  way  to
	      pass an entire directory path through this option	yet. (See also
	      the "--filename-delim" parameter)

       --aln-stk[=prefix]
	      Add hits to a multi-Stockholm formatted output file.

	      (default=`RNALalifold_results')

	      The default file name used for the  output  is  "RNALalifold_re-
	      sults.stk".   Users  may	change the filename to "prefix.stk" by
	      specifying the prefix as optional	argument.  The	file  will  be
	      create in	the current directory if it does not already exist. In
	      case the file already exists, output will	 be  appended  to  it.
	      Note:  Any  special characters in	the prefix will	be replaced by
	      the filename delimiter, hence there is no	way to pass an	entire
	      directory	 path  through this option yet.	(See also the "--file-
	      name-delim" parameter)

       --auto-id
	      Automatically generate an	ID for each alignment.

	      (default=off)

	      The default mode of RNALalifold is to automatically determine an
	      ID  from	the input alignment if the input file format allows to
	      do that. Alignment IDs  are,  for	 instance,  usually  given  in
	      Stockholm	 1.0 formatted input. If this flag is active, RNALali-
	      fold ignores any IDs retrieved from the input and	 automatically
	      generates	an ID for each alignment.

       --id-prefix=prefix
	      Prefix  for  automatically generated IDs (as used	in output file
	      names)

	      (default=`alignment')

	      If this parameter	is set,	each alignment will be	prefixed  with
	      the  provided string. Hence, the output files will obey the fol-
	      lowing naming scheme: "prefix_xxxx_ss.ps"	 (secondary  structure
	      plot), "prefix_xxxx_dp.ps" (dot-plot), "prefix_xxxx_aln.ps" (an-
	      notated alignment), etc. where xxxx is the alignment number  be-
	      ginning with the second alignment	in the input. Use this setting
	      in conjunction with the --continuous-ids flag to assign IDs  be-
	      ginning with the first input alignment.

       --id-delim=delimiter
	      Change  the  delimiter  between prefix and increasing number for
	      automatically generated IDs (as used in output file names)

	      (default=`_')

	      This parameter can be used to change the default	delimiter  "_"
	      between

	      the  prefix  string  and the increasing number for automatically
	      generated	ID.

       --id-digits=INT
	      Specify the number of digits of  the  counter  in	 automatically
	      generated	alignment IDs.

	      (default=`4')

	      When alignments IDs are automatically generated, they receive an
	      increasing number, starting with 1. This number will  always  be
	      left-padded  by  leading	zeros, such that the number takes up a
	      certain width. Using this	parameter, the width can be  specified
	      to the users need. We allow numbers in the range [1:18].

       --id-start=LONG
	      Specify  the  first  number in automatically generated alignment
	      IDs.

	      (default=`1')

	      When alignment IDs are automatically generated, they receive  an
	      increasing  number,  usually starting with 1. Using this parame-
	      ter, the first number can	be specified  to  the  users  require-
	      ments.  Note:  negative  numbers are not allowed.	 Note: Setting
	      this parameter implies continuous	alignment IDs, i.e.  it	 acti-
	      vates the	--continuous-ids flag.

       --filename-delim=delimiter
	      Change the delimiting character that is used

	      for sanitized filenames

	      (default=`ID-delimiter')

	      This  parameter  can  be used to change the delimiting character
	      used while sanitizing filenames, i.e. replacing invalid  charac-
	      ters. Note, that the default delimiter ALWAYS is the first char-
	      acter of the "ID delimiter" as supplied through  the  --id-delim
	      option. If the delimiter is a whitespace character or empty, in-
	      valid characters will be simply removed rather than substituted.
	      Currently, we regard the following characters as illegal for use
	      in filenames: backslash '\', slash '/', question mark '?',  per-
	      cent  sign '%', asterisk '*', colon ':', pipe symbol '|',	double
	      quote '"', triangular brackets '<' and '>'.

       --split-contributions
	      Split the	free energy contributions into separate	parts

	      (default=off)

	      By default, only the total energy	contribution for each  hit  is
	      returned.	  Using	 this  option, this contribution is split into
	      individual parts,	i.e. the Nearest Neighbor  model  energy,  the
	      covariance  pseudo energy, and if	applicable, a remaining	pseudo
	      energy derived from special constraints, such as probing signals
	      like SHAPE.

   Structure Constraints:
	      Command  line options to interact	with the structure constraints
	      feature of this program

       --shape=file1,file2
	      Use SHAPE	reactivity data	to guide structure predictions

	      Multiple shapefiles for the individual sequences in  the	align-
	      ment  may	 be  specified	as a comma separated list. An optional
	      association of particular	shape files to a specific  sequence in
	      the alignment can	be expressed by	prepending the sequence	number
	      to the filename,	e.g.  "5=seq5.shape,3=seq3.shape" will	assign
	      the  reactivity  values  from  file seq5.shape to	 the fifth se-
	      quence in	the alignment, and the values from file	seq3.shape  to
	      sequence	3. If  no assignment is	specified, the reactivity val-
	      ues are assigned to corresponding	sequences in  the  order  they
	      are given.

       --shapeMethod=D[mX][bY]
	      Specify  the  method  how	 to  convert  SHAPE reactivity data to
	      pseudo energy contributions

	      (default=`D')

	      Currently, the only data conversion method available is that  of
	      to  Deigan et al 2009.  This method is the default and is	recog-
	      nized  by	 a  capital  'D'  in  the  provided  parameter,	 i.e.:
	      --shapeMethod="D"	is the default setting.	 The slope 'm' and the
	      intercept	'b' can	be set to a  non-default value	if  necessary.
	      Otherwise	 m=1.8 and b=-0.6 as stated in the paper mentionen be-
	      fore.  To	alter these parameters,	e.g. m=1.9 and b=-0.7,	use  a
	      parameter	 string	like this: --shapeMethod="Dm1.9b-0.7". You may
	      also  provide  only   one	  of   the   two    parameters	 like:
	      --shapeMethod="Dm1.9" or --shapeMethod="Db-0.7".

   Algorithms:
	      Select  additional  algorithms  which  should be included	in the
	      calculations.  The Minimum free energy  (MFE)  and  a  structure
	      representative are calculated in any case.

       -L, --maxBPspan=INT
	      Set  the maximum allowed separation of a base pair to span. I.e.
	      no pairs (i,j) with j-i>span will	be allowed.

	      (default=`70')

       --threshold=DOUBLE
	      Energy threshold in kcal/mol per	nucleotide  above  which  sec-
	      ondary structure hits are	omitted	in the output.

	      (default=`-0.1')

       --mis  Output  "most informative	sequence" instead of simple consensus:
	      For each column of the alignment output the set  of  nucleotides
	      with frequency greater than average in IUPAC notation.

	      (default=off)

       -g, --gquad
	      Incoorporate  G-Quadruplex  formation into the structure predic-
	      tion algorithm

	      (default=off)

   Model Details:
       -T, --temp=DOUBLE
	      Rescale energy parameters	to a temperature of temp C. Default is
	      37C.

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

	      (default=off)

       -d, --dangles=INT
	      How to treat "dangling end" energies for bases adjacent  to  he-
	      lices in free ends and multi-loops

	      (default=`2')

	      With -d1 only unpaired bases can participate in at most one dan-
	      gling end.  With -d2 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	 mfe  and  partition  function
	      folding  (-p).   The option -d0 ignores dangling ends altogether
	      (mostly for debugging).  With -d3	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	 inte-
	      rior pairs in a loop of degree 3 and works only for mfe folding.

	      Note that	with -d1 and -d3 only the MFE computations will	be us-
	      ing this setting while partition function	uses -d2 setting, i.e.
	      dangling ends will be treated differently.

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

	      (default=off)

	      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

	      (default=off)

       --noClosingGU
	      Do not allow GU pairs at the end of helices

	      (default=off)

       -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.

       --nsp=STRING
	      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.

       --cfactor=DOUBLE
	      Set the weight of	the covariance term in the energy function

	      (default=`1.0')

       --nfactor=DOUBLE
	      Set  the	penalty	for non-compatible sequences in	the covariance
	      term of the energy function

	      (default=`1.0')

       -R, --ribosum_file=ribosumfile
	      use specified Ribosum Matrix instead of normal

       energy model. Matrixes to use should be 6x6
	      matrices,	the order of the terms is AU, CG, GC, GU, UA, UG.

       -r, --ribosum_scoring
	      use ribosum scoring matrix. The matrix is	 chosen	 according  to
	      the  minimal and maximal pairwise	identities of the sequences in
	      the file.

	      (default=off)

REFERENCES
       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

       I.L.  Hofacker,	B.  Priwitzer, and P.F.	Stadler	(2004),	"Prediction of
       Locally Stable  RNA  Secondary  Structures  for	Genome-Wide  Surveys",
       Bioinformatics: 20, pp 186-190

       Stephan	H.  Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gru-
       ber, and	Peter  F.  Stadler  (2008),  "RNAalifold:  Improved  consensus
       structure prediction for	RNA alignments", BMC Bioinformatics: 9,	pp 474

       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

AUTHOR
       Ivo L Hofacker, Ronny Lorenz

REPORTING BUGS
       If in doubt our program is right, nature	is at fault.  Comments	should
       be sent to rna@tbi.univie.ac.at.

RNALalifold 2.4.14		  August 2019			RNALALIFOLD(1)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS

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