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PhyloForester Documentation

Welcome to PhyloForester’s documentation!

PhyloForester is a PyQt5-based desktop application for phylogenetic analysis. It provides a graphical interface for managing phylogenetic projects, datamatrices, and running various tree reconstruction analyses (Parsimony, Maximum Likelihood, and Bayesian inference).

Contents:

Features

  • Project Management: Organize phylogenetic analyses in a hierarchical structure

  • Datamatrix Editor:

    • Excel-style editing with copy/paste support

    • Undo/redo functionality (Ctrl+Z/Y)

    • Clear and fill operations

    • Reorder taxa and characters with drag and drop

  • Multiple Analysis Types:

    • Parsimony Analysis: TNT (Tree analysis using New Technology)

    • Maximum Likelihood: IQTree

    • Bayesian Inference: MrBayes

  • Tree Visualization:

    • SVG-based phylogenetic tree rendering

    • Character state mapping

    • Synapomorphy visualization

    • Ancestral state reconstruction (Fitch algorithm)

  • Data Import/Export:

    • Nexus format support

    • Phylip format support

    • TNT format support

    • Tree file import (Newick, Nexus)

  • Database Storage: All data persisted in SQLite with Peewee ORM

Quick Start

Installation

Download the latest version from the releases page.

For Windows:

Download and run the installer (PhyloForester-Setup-vX.Y.Z.exe)

For macOS:

Download and extract the ZIP file, then run PhyloForester

For Linux:

Download and extract the tarball, then run ./PhyloForester

From Source:
git clone https://github.com/jikhanjung/PhyloForester.git
cd PhyloForester
pip install -r requirements.txt
python PhyloForester.py

Basic Usage

  1. Create a New Project

    Click “New Project” or press Ctrl+N to create a project for your phylogenetic study.

  2. Create or Import a Datamatrix

    • Create new: Right-click project → “New Datamatrix”

    • Import: Drag and drop Nexus/Phylip/TNT files

  3. Edit Datamatrix

    • Double-click to open the datamatrix editor

    • Add/remove taxa and characters

    • Fill in character states (0, 1, 2, ?, etc.)

    • Use Excel-style editing: Ctrl+C, Ctrl+V, Ctrl+Z

  4. Configure Analysis

    • Right-click datamatrix → “New Analysis”

    • Choose analysis type (Parsimony/ML/Bayesian)

    • Set parameters (search settings, models, etc.)

  5. Run Analysis

    • Click “Start Analysis” button

    • Monitor progress in real-time

    • View results in the Analysis tab

  6. View Results

    • Examine tree topologies

    • Map character states on trees

    • Export results

Keyboard Shortcuts:

  • Ctrl+N - New Project

  • Ctrl+S - Save changes

  • Ctrl+Z - Undo

  • Ctrl+Y - Redo

  • Ctrl+C - Copy

  • Ctrl+V - Paste

  • Delete - Clear selection / Delete items

For more detailed instructions, see the User Guide.

Technology Stack

  • Language: Python 3.9+

  • GUI Framework: PyQt5

  • Core Libraries:

    • Database ORM: Peewee

    • Numerical/Scientific: NumPy, Matplotlib

    • Bioinformatics: BioPython

    • Tree Reconstruction: TNT, IQTree, MrBayes (external)

System Requirements

Minimum Requirements:

  • OS: Windows 10+, macOS 10.14+, or Linux (Ubuntu 20.04+)

  • RAM: 4GB

  • Disk Space: 500MB

  • Display: 1280x720

Recommended:

  • RAM: 8GB or more

  • Display: 1920x1080 or higher

External Software (Optional):

  • TNT for parsimony analysis

  • IQTree for maximum likelihood

  • MrBayes for Bayesian inference

Indices and tables