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.