---
name: "simplegraph.pl"
section: "1"
platform: "linux"
package: "murasaki-common"
version: "1.68.6-14"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/simplegraph.pl"
---

# simplegraph.pl(1)

Provides dotplot/chaos style plot of murasaki alignments

## 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.