Java Dot Plot Alignments

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.

Please note that Java has enhanced security on all web applications and is now requiring all apps to be signed by a certificate from a trusted authority. We are currently updating all of our apps to a new certificate and in the mean time are using a self-signed certificate. Any application with a self-signed certificate is blocked by default on your computer unless your Java Security Settings are set to ‘Medium’ or our URL is added to the Exception Site List. There may also a pop-up window on start up of the app where you will have to accept the risks regarding the certificate. Please bear with us as we fix this!

For instructions on how to add our URL to the Exception Site List and more information regarding the new security settings look here:


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 1.5. Please see Java Web Start Setup and Java Web Start Tips for help.


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