Installation¶

Requirements¶

Python 3.12 – 3.14 (including free-threaded 3.14t)
Nothing else for a normal install — binary wheels are published for Linux (x86_64/aarch64), macOS (arm64/x86_64) and Windows, so pip never has to compile the Rust extension.
A Rust toolchain and maturin ≥ 1.0 only if you build from a checkout.

Install from PyPI¶

pip install dot-explorer

That gives you the library and the interactive HTML reports. To also run the browser app locally, add the app extra and use the console script:

pip install "dot-explorer[app]"
dot-explorer-app

dot-explorer-app starts the Shiny app on http://127.0.0.1:8000 and opens a browser. See Web App for the options.

Optional extras¶

Extra	Installs	Gives you
`app`	`shiny`	The local browser app (`dot-explorer-app`)
`cluster`	`sourmash ≥ 4.8`, `scipy ≥ 1.10`	Similarity metrics, clustering and trees
`docs`	`zensical`, `mkdocstrings-python`, `nbconvert`	Building these docs

Combine them as usual:

pip install "dot-explorer[app,cluster]"

Both are optional rather than core dependencies for concrete reasons: shiny pulls in orjson, which has no free-threaded wheel, so requiring it would make the package uninstallable on 3.14t; and scipy + sourmash add roughly 110 MB, more than doubling the install for users who only want dot plots.

Core dependencies¶

Installed automatically:

Package	Purpose
`matplotlib ≥ 3.5`	Dotplot visualisation
`numpy ≥ 1.21`	Array operations used by matplotlib
`pyfaidx`	Lazy, indexed FASTA access (pure Python, ~0.2 MB)

Install from a checkout¶

Use this if you want to modify the Rust core. It needs a Rust toolchain:

git clone https://github.com/Adamtaranto/dot-explorer.git
cd dot-explorer
pip install maturin
maturin develop --release

The --release flag enables full Rust compiler optimisations, which is strongly recommended for any non-trivial dataset. To work on the app as well:

pip install ".[app]"
dot-explorer-app

See the Development Guide for the full contributor setup.

Verify the installation¶

import dot_explorer
print(dot_explorer.__version__)  # e.g. 0.1.0

from dot_explorer import SequenceIndex
idx = SequenceIndex(k=10)
idx.add_sequence("test", "ACGTACGTACGT")
print(idx)  # SequenceIndex(k=10, sequences=1)