simplegraph.pl(1) 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.