SIMPLEGRAPH

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.