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RNALOCMIN(1)			 User Commands			  RNALOCMIN(1)

NAME
       RNAlocmin - manual page for RNAlocmin 2.1.0

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

DESCRIPTION
       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

       --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:
       -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-
	      fault=`100000')

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

       --minh=DOUBLE
	      Print  only  minima  with	energy barrier greater than this  (de-
	      fault=`0.0')

       --minh-lite
	      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

	      (default=`2')

	      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-barriers=STRING
	      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)

       --just-read
	      Do  not  expect  input from stdin, just do postprocessing.  (de-
	      fault=off)

       -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)

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

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

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

       --barr-name=STRING
	      Name  of	barrier	 tree  output file, switches on	-b flag.  (de-
	      fault=`treeRNAloc.ps')

   Kinetics (rates for treekin program):
       --barrier-file=STRING
	      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-
	      fault=`rates.out')

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

   Flooding parameters (flooding occurs	only with -r, -b, or --minh option):
       --floodPortion=DOUBLE
	      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')

       --floodMax=INT
	      Flood cap	- how many structures to  flood	 in  one  basin	  (de-
	      fault=`1000')

   Miscelaneous:
       --numIntervals=INT
	      Number of	intervals for Jing's visualisation (default=`0')

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

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

RNAlocmin 2.1.0			   July	2017			  RNALOCMIN(1)

NAME | SYNOPSIS | DESCRIPTION

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