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Installation

PhyloForester can be installed in several ways depending on your needs and platform.

Installing Pre-built Binaries

The easiest way to install PhyloForester is to download pre-built binaries from the GitHub releases page.

Windows

  1. Go to the releases page

  2. Download the latest PhyloForester-Setup-vX.Y.Z.exe installer

  3. Run the installer and follow the installation wizard

  4. Launch PhyloForester from the Start Menu or Desktop shortcut

Portable Version:

Alternatively, download the ZIP file (PhyloForester-Windows-vX.Y.Z-buildN.zip):

  1. Extract the ZIP to any folder

  2. Run PhyloForester.exe from the extracted folder

  3. No installation required - run from USB drives

macOS

  1. Go to the releases page

  2. Download the latest PhyloForester-macOS-vX.Y.Z-buildN.zip

  3. Extract the ZIP file

  4. Drag PhyloForester to your Applications folder (optional)

  5. Double-click to run

Note: On first launch, you may need to right-click → Open to bypass Gatekeeper.

Linux

  1. Go to the releases page

  2. Download the latest PhyloForester-Linux-vX.Y.Z-buildN.tar.gz

  3. Extract the tarball:

    tar -xzf PhyloForester-Linux-vX.Y.Z-buildN.tar.gz
cd PhyloForester

  4. Run the application:

    ./PhyloForester

System Dependencies:

On some Linux distributions, you may need to install Qt5 libraries:

# Ubuntu/Debian
sudo apt-get install libqt5gui5 libqt5core5a libqt5widgets5

# Fedora/RHEL
sudo dnf install qt5-qtbase qt5-qtbase-gui

Installing from Source

Prerequisites

  • Python 3.9 or higher

  • pip (Python package manager)

  • Git (optional, for cloning repository)

Steps

  1. Clone or Download the Repository

    git clone https://github.com/jikhanjung/PhyloForester.git
cd PhyloForester

    Or download and extract the ZIP from GitHub.

  2. Create a Virtual Environment (Recommended)

    # Windows
python -m venv venv
venv\\Scripts\\activate

# macOS/Linux
python3 -m venv venv
source venv/bin/activate

  3. Install Dependencies

    pip install -r requirements.txt

  4. Run PhyloForester

    python PhyloForester.py

Development Installation

For development, install additional dependencies:

pip install -r requirements-ci.txt

This includes testing tools (pytest, pytest-qt) and code quality tools (ruff).

Installing External Analysis Software

PhyloForester integrates with external phylogenetic software for analysis. These are optional but required for their respective analysis types.

TNT (Parsimony Analysis)

  1. Download TNT from http://www.lillo.org.ar/phylogeny/tnt/

  2. Extract the executable

  3. In PhyloForester, go to Edit → Preferences

  4. Set the path to the TNT executable

IQTree (Maximum Likelihood)

  1. Download IQTree from http://www.iqtree.org/

  2. Extract the executable

  3. In PhyloForester, go to Edit → Preferences

  4. Set the path to the IQTree executable

MrBayes (Bayesian Inference)

  1. Download MrBayes from https://nbisweden.github.io/MrBayes/

  2. Install following the platform-specific instructions

  3. In PhyloForester, go to Edit → Preferences

  4. Set the path to the MrBayes executable

Verifying Installation

To verify PhyloForester is installed correctly:

  1. Launch the application

  2. The main window should appear with an empty project tree

  3. Check Help → About to see the version number

  4. Try creating a new project (Ctrl+N)

If you encounter issues, see the Troubleshooting guide.

Updating PhyloForester

Binary Installation

  1. Download the latest version from the releases page

  2. Install over the existing installation (Windows installer)

  3. Or replace the old files with the new ones (portable/macOS/Linux)

Your data is stored in a separate database location and will not be affected:

  • Windows: C:\\Users\\<username>\\PaleoBytes\\PhyloForester\\PhyloForester.db

  • macOS/Linux: ~/PaleoBytes/PhyloForester/PhyloForester.db

Source Installation

cd PhyloForester
git pull origin main
pip install -r requirements.txt --upgrade

Uninstalling

Windows (Installer)

  1. Go to Settings → Apps → Installed Apps

  2. Find “PhyloForester”

  3. Click Uninstall

Windows (Portable) / macOS / Linux

Simply delete the PhyloForester folder.

Removing User Data:

If you want to completely remove all PhyloForester data:

  • Windows: Delete C:\\Users\\<username>\\PaleoBytes

  • macOS/Linux: Delete ~/PaleoBytes

This will remove all projects, datamatrices, and analyses.

Next Steps

After installation, see the User Guide to get started with your first phylogenetic analysis.