TreeCraft

A cross-platform phylogenetic tree visualization and analysis tool. The goal of this program is a way to quickly generate and modify phylogenetic trees without having to edit lots of FASTA files manually.

Version 1.0

By Alan Rockefeller - 4/21/2025

What is TreeCraft?

TreeCraft helps you create, visualize, and analyze phylogenetic trees from DNA sequence data. It combines powerful tree-building algorithms with an easy-to-use interface.

Features

Sequence Handling

• Import sequences from FASTA/FASTQ files with automatic validation
• Fix common sequence formatting issues automatically
• Edit sequence names directly within the application
• Align sequences using integrated alignment tools

Tree Building

• Build trees using multiple methods:
  • Quick methods: UPGMA, Neighbor Joining
  • Advanced methods: Maximum Likelihood (RAxML)
• Assess tree reliability with bootstrap support
• Find the best evolutionary model for your data using ModelTest-NG or IQ-TREE

Visualization

• Interactive tree display with drag-and-drop rearrangement
• Customize tree appearance (branch widths, colors, fonts)
• Highlight important branches or taxonomic groups
• View aligned sequences alongside the tree
• Easily remove branches from the tree
• Toggle between dark and light mode

Export & Sharing

• Save trees in standard formats (Newick, Nexus, PhyloXML)
• Export tree visualizations as high-quality images (PNG, JPG, SVG)
• Export alignments for use in other applications

How TreeCraft Works

1. Load your sequences - Import your DNA/RNA sequences from FASTA or FASTQ files
2. Align your sequences - Use integrated alignment tools (MUSCLE, MAFFT) or import pre-aligned data
3. Build your tree - Choose from multiple tree-building algorithms with customizable parameters
4. Visualize and edit - Interact with your tree, customize its appearance, and make adjustments
5. Export and share - Save your tree in various formats for publication or further analysis

External Tool Integration

TreeCraft integrates with popular bioinformatics tools:

• Alignment: MUSCLE, MAFFT
• Alignment trimming: trimAl, Gblocks
• Model testing: ModelTest-NG, IQ-TREE
• Tree inference: RAxML/RAxML-NG, MrBayes

Note: These tools are optional - TreeCraft will use them if available but provides built-in alternatives.

Installation

1. Clone this repository
2. Install the required dependencies:

   pip install PyQt6 biopython matplotlib numpy
   

3. Optionally install RaxML, IQ-Tree and ModelTest-NG
4. Run TreeCraft:

   ./run_treecraft.sh
   

   or

   python3 treecraft.py
   

Directory Structure

• treecraft/gui/: GUI components (windows, dialogs, visualization)
• treecraft/core/: Core functionality (tree building, file handling)
• treecraft/utils/: Utility functions (external tool integration)

Development

If you find any bugs or have suggestions contact Alan Rockefeller, or make the changes yourself and do a pull request.

https://github.com/AlanRockefeller/Treecraft

License

GNU General Public License 3.0