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RNALOCMIN(1)			 User Commands			  RNALOCMIN(1)

       RNAlocmin - manual page for RNAlocmin 2.1.0

       RNAlocmin [OPTIONS]... [FILES]...

       RNAlocmin 2.1.0

   Calculate local minima from structures via gradient walks. Example usage:
	      RNAsubopt	-p 10000 < "sequence.txt" > "suboptp.txt" RNAlocmin -s
	      "sequence.txt" [OPTIONS] < "suboptp.txt"

       -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:
       -s, --seq=STRING
	      Sequence file in FASTA format. If	the sequence is	the first line
	      of the input file, this is not needed  (default=`seq.txt')

       -p, --previous=STRING
	      Previously  found	 LM  (output  from  RNAlocmin or barriers), if
	      specified	does not need --seq option

       -m, --move=STRING
	      Move set:	I ==> insertion	& deletion of base pairs  S  ==>  I&D&
	      switch of	base pairs  (possible values="I", "S" default=`I')

       -n, --min-num=INT
	      Maximal  number  of local	minima returned	(0 == unlimited)  (de-

	      Maximal number of	local minima  found  (default  =  unlimited  -
	      crawl through whole input	file)

       -v, --verbose-lvl=INT
	      Level  of	verbosity (0 = nothing,	4 = full) WARNING: higher ver-
	      bose levels increase the computation time	 (default=`0')

	      Depth of findpath	search (higher value  increases	 running  time
	      linearly)	 (default=`10')

	      Print  only  minima  with	energy barrier greater than this  (de-

	      When flooding with --minh	option,	search for only	saddle (do not
	      search  for  a  LM  that is lower).  Increases efficiency	a tiny
	      bit, but when turned on, the results may omit  some  non-shallow
	      minima, especially with higher --minh value.  (default=off)

       -w, --walk=STRING
	      Walking method used D ==>	gradient descent F ==> use first found
	      lower energy structure R ==> use random lower  energy  structure
	      (does  not  work	with  --noLP  and -m S options)	(possible val-
	      ues="D", "F", "R"	default=`D')

       --noLP Work only	with  canonical	 RNA  structures  (w/o	isolated  base
	      pairs,  cannot  be  combined  with ranodm	walk (-w R option) and
	      shift move set (-m S))  (default=off)

       -e, --useEOS
	      Use energy_of_structure_pt calculation instead of	energy_of_move
	      (slower, it should not affect results)  (default=off)

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

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


	      With -d1 only unpaired bases can participate in at most one dan-
	      gling end, this is the default for mfe folding  but  unsupported
	      for the partition	function folding.

	      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 partition function folding (-p).  The
	      option -d0 ignores dangling ends altogether (mostly  for	debug-
	      ging).   With -d3	mfe folding will allow coaxial stacking	of ad-
	      jacent 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.

	      Note that	by default (as well as with -d1	and -d3)  pf  and  mfe
	      folding  treat dangling ends differently.	Use -d2	in addition to
	      -p to ensure that	both algorithms	use the	same energy model.

	      Fix barrier file for interior loops (just	recompute if all LM in
	      barrier  output  are  LM),  if  specified, does not need neither
	      --previous nor --seq option

       -k, --pseudoknots
	      Allow for	pseudoknots according to "gfold" model - H, K, L,  and
	      M	types (genus one) of pseudoknots are allowed (increases	compu-
	      tation time greatly), cannot be combined with shift move set (-m
	      S)  (default=off)

	      Do  not  expect  input from stdin, just do postprocessing.  (de-

       -N, --neighborhood
	      Use the Neighborhood routines to perform gradient	descend.  Can-
	      not be combined with shift move set (-m S) and pseudoknots (-k).
	      Test option.  (default=off)

	      Do not deal with degeneracy, select the lexicographically	 first
	      from the same energy neighbors.  (default=off)

	      Do not store the minima and optimize, just compute directly min-
	      ima and output them. Output file can contain  duplicates.	  (de-

   Barrier tree:
       -b, --bartree
	      Generate an approximate barrier tree.  (default=off)

	      Name  of	barrier	 tree  output file, switches on	-b flag.  (de-

   Kinetics (rates for treekin program):
	      File for saddle heights between LM (simulates the	output	format
	      of barriers program)

       -r, --rates
	      Create rates for treekin	(default=off)

       -f, --rates-file=STRING
	      File   where   to	  write	  rates,  switches  on	-r  flag  (de-

       -T, --temp=DOUBLE
	      Temperature in Celsius (only for rates) (default=`37.0')

   Flooding parameters (flooding occurs	only with -r, -b, or --minh option):
	      Fraction of minima to flood (floods first	minima with low	number
	      of  inwalking sample structures) (0.0 -> no flood; 1.0 ->	try to
	      flood all) Usable	only with -r or	-b options.  (default=`0.95')

	      Flood cap	- how many structures to  flood	 in  one  basin	  (de-

	      Number of	intervals for Jing's visualisation (default=`0')

	      Report  only  LM,	which energy is	in range <MFE (or lowest found
	      LM), MFE+eRange> in kcal/mol.

	      Filename where to	output the  allegiance	of  structures.	 Works
	      properly only with RNAsubopt -e list.

RNAlocmin 2.1.0			   July	2017			  RNALOCMIN(1)


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