NAME

       simplegraph.pl - Provides dotplot/chaos style plot of murasaki alignments

SYNOPSIS

       simplegraph.pl <murasaki ailgnment file> [-output=<output prefix>]

OPTIONS

       murasaki alignment file The main one outputted by murasaki.
       --output Prefix for output files.
       --nostitch Don't draw lines for stitch file breaks.
       --signed
               Leave signedness alone (otherwise absolute coordinates are drawn)

       --keepplot
               Keep the file containing the gnuplot commands (helpful if you want to run gnuplot
               interactively).

       --interactive=<S>
               Run gnuplot interactively for some set of sequences <S> (default all)

       --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").

DESCRIPTION

       Draws graphs of murasaki alignments.