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.IX Title "SIMPLEGRAPH 1"
.TH SIMPLEGRAPH 1 2024-11-09 "perl v5.40.0" "User Contributed Perl Documentation"
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.SH NAME
simplegraph.pl \- Provides dotplot/chaos style plot of murasaki alignments
.SH SYNOPSIS
.IX Header "SYNOPSIS"
simplegraph.pl <murasaki ailgnment file> [\-output=<output prefix>]
.SH OPTIONS
.IX Header "OPTIONS"
.IP "\fBmurasaki alignment file\fR The main one outputted by murasaki." 8
.IX Item "murasaki alignment file The main one outputted by murasaki."
.PD 0
.IP "\-\-output Prefix for output files." 8
.IX Item "--output Prefix for output files."
.IP "\-\-nostitch Don't draw lines for stitch file breaks." 8
.IX Item "--nostitch Don't draw lines for stitch file breaks."
.IP \-\-signed 8
.IX Item "--signed"
.PD
Leave signedness alone (otherwise absolute coordinates are drawn)
.IP \-\-keepplot 8
.IX Item "--keepplot"
Keep the file containing the gnuplot commands (helpful if you want to run gnuplot interactively).
.IP \-\-interactive=<S> 8
.IX Item "--interactive=<S>"
Run gnuplot interactively for some set of sequences <S> (default all)
.IP "\-\-order=<S> Reorder input sequences on the fly (or consider only a subset)" 8
.IX Item "--order=<S> Reorder input sequences on the fly (or consider only a subset)"
<S> can be specified as a simple permutation like 201 (which would
mean sequence 2, then 0, then 1), or if you have more than 10 sequences you can separate
digits with any non-digit character (eg: "2,0,1").
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Draws graphs of murasaki alignments.