Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help 
RELIABI...-PROFILE(1) User Contributed Perl DocumentationRELIABI...-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
	   compared infered signal to them.  Give list as  string  "from0  to0
	   orientation0;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.bmreliability-cbt

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

perl v5.32.1			  2022-11-19		 RELIABI...-PROFILE(1)

Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=reliability-profile.pl&sektion=1&manpath=FreeBSD+Ports+15.0>

home | help