Installation

CRAIC runs on macOS, Windows, and Linux. It needs Python 3.9 or newer.

The fast path is a prebuilt wheel from PyPI — no compiler or Rust toolchain required. The Rust acceleration core is bundled in the wheel; if you install from source without Rust, CRAIC still runs on a built-in NumPy fallback (the status bar shows core: numpy instead of core: rust).

Prefer a double-clickable app with no Python at all? See Download a ready-to-run app below.

Download a ready-to-run app

Each release includes standalone bundles that need no Python and no install — just download, unpack, and double-click:

Platform	Download	Run
macOS	CRAIC-macos.dmg	Open the .dmg, drag CRAIC to Applications
Windows	CRAIC-windows.zip	Unzip, open the folder, double-click CRAIC.exe
Linux	CRAIC-linux.tar.gz	Extract, then run ./CRAIC/CRAIC

These apps are not code-signed (that needs paid developer certificates), so the operating system shows a one-time warning the first time you open one. This is expected — here's how to get past it:

macOS — first launch

The app isn't signed by an Apple-registered developer, so macOS blocks it the first time ("Apple could not verify 'CRAIC' is free of malware…"). To allow it, once:

1. Drag CRAIC to Applications, double-click it, and click Done on the warning.
2. Open System Settings → Privacy & Security and scroll down to Security, where it says "CRAIC" was blocked. Click Open Anyway, enter your password, then click Open Anyway again.

After that it opens normally. (On macOS 14 and earlier, right-click the app and choose Open instead; macOS 15 removed that shortcut.)

No warning at all: if you have Python, install from PyPI (below) and run craic make-app. It builds the app on your own Mac, so macOS never marks it as downloaded.

If macOS says the app is "damaged" or won't open, clear the quarantine flag in Terminal (this is safe — it only removes the download-quarantine attribute):

xattr -dr com.apple.quarantine /Applications/CRAIC.app

Windows — first launch

Windows SmartScreen may say "Windows protected your PC". Click More info → Run anyway.

Linux

If the binary isn't executable after extracting, run chmod +x CRAIC/CRAIC.

If you'd rather avoid the warnings entirely, install from PyPI instead (below) — the pip route is never blocked by the OS.

Install from PyPI (recommended)

pip install craic-msa
craic                      # launch the GUI
craic path/to/alignment.fasta   # …or open a file straight away

We recommend installing into a virtual environment so CRAIC's dependencies (NumPy, Biopython, PySide6) don't clash with other tools:

python3 -m venv craic-env
# macOS / Linux:
source craic-env/bin/activate
# Windows (PowerShell):
craic-env\Scripts\Activate.ps1

pip install craic-msa
craic

Platform notes

• macOS — works on both Apple Silicon and Intel. If craic isn't found after install, make sure your virtual environment is activated, or launch with python -m craic.
• Windows — use the same commands in PowerShell or Command Prompt. If craic isn't on your PATH, use python -m craic.
• Linux — PySide6 needs a few system libraries for Qt. On Debian/Ubuntu:

sudo apt-get install -y libegl1 libgl1 libxkbcommon0 libdbus-1-3

Install from source

You'll need Rust to build the acceleration core (or skip it and use the NumPy fallback).

git clone https://github.com/mol-evol/craic
cd craic
python3 -m venv .venv && source .venv/bin/activate
pip install maturin
maturin develop --release        # compiles the Rust core into the venv
pip install -e .
craic examples/coding_genes.fasta

No Rust? Install just the Python dependencies and run on the NumPy fallback:

pip install numpy biopython PySide6
python -m craic examples/coding_genes.fasta

Optional: external aligners

CRAIC auto-detects these on your PATH and offers them in the engine menu and the multi-aligner disagreement map: MAFFT, MUSCLE, Clustal Omega, ProbCons, PRANK and ClustalW. None are required — the built-in aligner always works — but installing one or more gives you stronger alignments and a more informative disagreement comparison. All six are on Bioconda:

conda install -c bioconda mafft muscle clustalo probcons prank clustalw

Verifying the install

craic --version

Launch CRAIC and open examples/coding_genes.fasta. The status bar at the bottom shows the active core (core: rust or core: numpy) and confirms everything loaded.