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LOCARNA_RNAFOLD_PP(1)		 User Commands		 LOCARNA_RNAFOLD_PP(1)

NAME
       locarna_rnafold_pp - manual page	for locarna_rnafold_pp (LocARNA	2.0.0)

DESCRIPTION
       locarna_rnafold_pp  --  compute	RNA  pair  probabilities  and write in
       pp-format USAGE:	locarna_rnafold_pp [options]

       Folds RNA sequences by calling the  Vienna  RNA	library	 and  directly
       writes LocARNA's	pp 2.0 format.	In many	cases this program can replace
       a  call to RNAfold or RNAalifold	followed by a conversion of its	output
       to pp format. mlocarna uses this	script wherever	 possible.  This  tool
       allows  moreover	precomputing "in-loop" probabilities as	used by	SPARSE
       and ExpaRNA-p.

OPTIONS
       -h, --help
	      Help

       -V, --version
	      Version info

       -v, --verbose
	      Verbose

       -C, --use-struct-constraints
	      Use structural constraints

       --noLP No lonely	pairs

       --maxBPspan=<span>(-1)
	      Limit maximum base pair span (default=off)

       --stacking
	      Compute stacking terms

       --dangling=<param>(2)
	      Dangling option value

       --in-loop
	      Compute in-loop probabilities

       -p, --min-prob=<prob>(0.001)
	      Minimal probability

       --p_unpaired_in_loop=<threshold>(0.0005)
	      Threshold	for prob_unpaired_in_loop

       --p_basepair_in_loop=<threshold>(0.0005)
	      Threshold	for prob_basepair_in_loop

       -o, --output=<filename>()
	      Output file

       --force-alifold
	      Force alifold for	single sequences

locarna_rnafold_pp (LocARNA 2... November 2022		 LOCARNA_RNAFOLD_PP(1)

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