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RELIABI...-PROFILE(1)  User Contributed Perl Documentation RELIABI...-PROFILE(1)

NAME
     reliability-profile.pl

SYNOPSIS
     reliability-profile.pl [options] <locarna-output-dir>

DESCRIPTION
     reliability-profile.pl  generates	a reliability profile plot of a multiple
     alignment generated by mlocarna --probabilistic.

OPTIONS
     --help
	 Brief help message

     --man
	 Full documentation

     --seqname=seqname
	 Project to sequence name

     --dont-predict
	 Turn off predicting. (def=on)

     --fit-penalty=penalty
	 Penalty for on/off switching in fit

     --position-penalty
	 Position dependent penalty for calculating fit.

     --fit-once-on
	 Restrict fitting to being exactly once on

     --title=title
	 Title of plot

     --out=filename
	 Output filename

     --offset=pos
	 Offset of sequence in genome

     --signals=list
	 List of (from,to,orientation) triples.  Show signals in plot  and  com-
	 pared	infered signal to them.  Give list as string "from0 to0 orienta-
	 tion0;from1 to1 orientation1 ..." Specify multi-range signals by from0a
	 to0a from0b to0b ...

     --structure-weight=w
	 Weight of structure against sequence (1.0)

     --position-penalty-weight=pos_w
	 Weight of the position penalty

     --show-sw
	 Show the influence of structure weight in the plot

     --beta=f
	 Inverse temperature beta

     --dont-plot
	 Skip plotting, only output

     --write-R-script=file
	 Write the R script to file

     --revcompl
	 Plot and fit a reverse complement

     --write-subseq
	 Write the subsequence of fit

     --output-format=f
	 Output format (f = pdf or png, def=pdf)

     --show-fitonoff
	 Show the on/off values for the fit

     --use-consistency
	 Uses the file generated by the --consistency command e.g.  result.bmre-
	 liability-cbt

     The  target directory of mlocarna is required for obtaining the reliability
     information. Optionally, the reliability plot will be projected to the  se-
     quence with given sequence name (or containing "seqname" as prefix).

perl v5.38.2			   2022-10-04		   RELIABI...-PROFILE(1)

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