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PP2DOT(1)	       User Contributed Perl Documentation	       PP2DOT(1)

NAME
     pp2dot

SYNOPSIS
     pp2dot [options] ]infile.pp outfile_dp.ps

DESCRIPTION
     Convert  an (extended) pp file to a dot plot file (like produced by RNAfold
     -p).  pp is a locarna proprietary format for representing dot plots.  Reads
     pp file from infile.pp and write dotplot file to outputfile_dp.ps

     A pp-file has the following structure

     [SCORE: X]

     <name1> <seq1> .  .  .  <nameK> <seqK>

     # <i1> <j1> <p1> [<p2> [<w1> [<w2>]]]

     The script accepts up to four weights per base pair in the pp file. Missing
     weights are considered to be 0.  The script draws p1 as the size of  a  dot
     in  the  upper right triangle and w1 as its color. p2 and w2 are visualized
     accordingly in the lower left triangle.

     The color palette is controlled by options.

OPTIONS
     --colors P
      Color palette. Use --colors2 to define a second palette for the lower-left
      triangle. Default: "black","cyan","green","yellow","red"

     --colors2 P
      Color palette for lower left triangle.

     --help
      Brief help message

     --man
      Full documentation

perl v5.38.2			   2022-11-17			       PP2DOT(1)

Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=pp2dot&sektion=1&manpath=FreeBSD+Ports+15.1.quarterly>

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