JDotter- A Java Dot Plot Viewer 6.0

JDotter — A Java Dot Plot Viewer

JDotter is a cross-platform desktop application for visualizing pairwise sequence similarity with dot plots. It helps researchers and students explore relationships between DNA, RNA, or protein sequences, revealing conserved regions, repeats, inversions, and rearrangements at a glance. Built in Java, it runs on Windows, macOS, and Linux with minimal setup.

Key features:

• Load sequences (for example, FASTA) or precomputed comparison data
• Create self- and pairwise dot plots for nucleotides or proteins
• Zoom, pan, and inspect coordinates for fine-grained exploration
• Adjust sensitivity (e.g., window size and score threshold) to reduce noise and highlight signal
• View forward and reverse-complement strands to detect inversions
• Optionally overlay or link sequence annotations when available
• Export plots as images for reports and publications

Common use cases include visualizing synteny between genomes or contigs, identifying tandem repeats and duplications, and inspecting domain-level similarities in proteins.

JDotter- A Java Dot Plot Viewer is developed by Dr. Chris Upton, University of Victoria. The most popular version of this product among our users is 6.0.