Java Dot Plot Alignments

NOTE: This tool requires Java Version 8. Download it here: Java Runtime Environment.
Java Dot Plot Alignments (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.

With this program, you can:

  • create whole-genome, sub-genome or protein dot plots from user-supplied sequences;
  • quickly load pre-calculated plots of complete genomes from VOCs database;
  • view and navigate the plots to pinpoint insertions/deletions and evaluate overall genome similarity;
  • print/save dot plots in JDotter or JPEG format.


Getting Started

If you’re new to JDotter, click on the launch button (on the right) and use the Quick Start Page to learn the basics (or if you’re like us…  just start clicking!).

The VBRC also provides additional help resources for JDotter:


If you use this resource please cite the relevant papers (publication list).
Brodie, R., R. L. Roper, and C. Upton. 2004
JDotter: A Java Interface to Multiple DotPlots Generated by Dotter. Bioinformatics, 20, 279-281.
Papers which have cited JDotter


If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.8. Please see Java Web Start Setup and Java Web Start Tips for help.