got-dot-plot

An interactive DNA dot plot tool. Compares two FASTA files and produces a self-contained HTML file you can open in any browser — zoom, pan, and export without any server or extra software.

Built as a modern replacement for Re-dot-able, without the Java dependency headaches.

What is a dot plot?

A dot plot is a way to visually compare two DNA sequences. Each axis represents one sequence, and a diagonal line means that region is identical (or reverse-complementary) between the two. You can immediately see:

• Conserved regions — long diagonal lines
• Inversions — anti-diagonal lines (reverse-complement matches)
• Rearrangements — diagonal lines that are offset or out of order
• Duplications — multiple parallel diagonals

Installation

Install directly from GitHub. uv is the preferred Python environment + package manager, but pip and pyenv or other equivalent tools also work.

git clone https://github.com/ira-zibbu/got-dot-plot.git --depth=1
cd got-dot-plot
uv tool install --editable .

This makes got-dot-plot available as a command anywhere on your system.

Usage

got-dot-plot reference.fasta assembly.fasta

This writes dotplot.html to the current directory. Open it in your browser.

# Custom output file
got-dot-plot reference.fasta assembly.fasta -o myplot.html

# Increase minimum match length for cleaner plots on large genomes
got-dot-plot reference.fasta assembly.fasta -m 500

# Show verbose progress
got-dot-plot reference.fasta assembly.fasta -v

Options

Flag	Default	Description
-k, --kmer-size	10	K-mer size for seeding matches. Larger values are faster and more specific but miss divergent regions.
-m, --min-match	100	Minimum match length to display. Increase this to reduce HTML file size and improve browser performance.
-o, --output	dotplot.html	Output HTML file.
-v, --verbose	off	Show per-500 kbp progress messages during scanning.

How it works

Matching uses k-mer hashing — the same approach as MUMmer dot plots:

1. Every k-mer in the X sequence (both forward and reverse-complement strands) is indexed into a hash table.
2. Each k-mer in the Y sequence is looked up in the index.
3. On a hit, the match is extended in both directions until a mismatch or N is reached.
4. Matches shorter than --min-match are discarded.

Forward matches (same orientation) appear as blue diagonal lines. Reverse-complement matches (inversions) appear as red anti-diagonal lines.

Both FASTA files can contain multiple sequences. They are concatenated with N gaps for display, with sequence names labelled on the axes and dashed lines marking boundaries.

Tuning for performance

Genome size	Recommended -m
< 100 kbp	50
100 kbp – 10 Mbp	100–500
> 10 Mbp	500+

Increasing -k also speeds up the scan by reducing spurious k-mer hits, at the cost of missing matches that contain mismatches in the seed region.

Development

# Install dependencies including dev tools
uv sync --group dev

# Run tests
uv run pytest