EZ-PHASE v1.10

Easy Haplotype Phasing - Advanced GUI for PHASE 2.1.1

A modern, user-friendly graphical interface for the PHASE haplotype reconstruction software, featuring enhanced file management, parallel processing, and advanced parameter control.

🌟 Features

Core Functionality

• Intuitive GUI for PHASE 2.1.1 haplotype phasing
• Batch Processing - Handle multiple .inp files simultaneously
• Real-time Progress Tracking with file-by-file status updates
• Advanced Parameter Control - Full access to PHASE options including:
  • Recombination models (MR0, MR1, MR2, MR3, MR4)
  • Mutation models for multi-allelic loci
  • Custom priors and thresholds
  • Hotspot detection and analysis

Enhanced Workflow

• Parallel Processing with auto-detection of optimal thread count
• Smart File Management with status indicators (pending/processing/completed/error)
• Process Control - Start, stop, and monitor PHASE executions
• Command Preview - See exactly what commands will be executed
• Comprehensive Output - Organized results with detailed logging

User Experience

• Cross-platform support (macOS, Windows, Linux)
• No Installation Required for PHASE binary - specify your own
• Modern Interface with responsive design and real-time feedback
• Error Handling with informative messages and recovery options

📋 Requirements

• PHASE 2.1.1 binary (download separately from Stephens Lab)
• Operating System: macOS 10.14+, Windows 10+, or Linux (Ubuntu 18.04+)
• Memory: 4GB RAM minimum (8GB+ recommended for large datasets)

📦 Installation

Download Pre-built Binaries

Latest Release: v1.10.0

Platform	Download	Instructions
macOS	EZ-PHASE-1.10.0.dmg	Download, mount, and drag to Applications
Windows	EZ-PHASE Setup 1.10.0.exe	Download and run installer
Linux	EZ-PHASE-1.10.0.AppImage	Download, make executable, and run

First Launch

1. Download PHASE 2.1.1 from the official source
2. Launch EZ-PHASE and use "Browse" to locate your PHASE binary
3. Select your .inp files and configure parameters
4. Run analysis with real-time monitoring

🚀 Quick Start

Basic Workflow

1. Select PHASE Binary - Browse to your PHASE 2.1.1 executable
2. Choose Input Files - Select one or more .inp files for analysis
3. Configure Parameters - Set iterations, burn-in, advanced options
4. Review Command - Check the generated command preview
5. Execute - Run with real-time progress tracking

Advanced Features

• Parallel Processing: Set thread count or use auto-detection
• Recombination Models: Choose from MR0-MR4 based on your data
• Hotspot Analysis: Detect and analyze recombination hotspots
• Custom Parameters: Fine-tune priors, thresholds, and mutation models

📊 Input File Format

EZ-PHASE supports standard PHASE input format:

NumberOfIndividuals
NumberOfLoci
P Position(1) Position(2) ... Position(NumberOfLoci)
LocusType(1) LocusType(2) ... LocusType(NumberOfLoci)
ID(1)
Genotype(1) row 1
Genotype(1) row 2
ID(2)
Genotype(2) row 1
Genotype(2) row 2
...

• S = SNP/biallelic locus
• M = Microsatellite/multi-allelic locus
• Missing data: ? for SNPs, -1 for microsatellites

🔧 Development

Building from Source

# Clone repository
git clone https://github.com/JSBarrington/ez-phase.git
cd ez-phase

# Install dependencies
npm install

# Run development version
npm start

# Build for all platforms
npm run build-all

Project Structure

ez-phase/
├── main.js              # Electron main process
├── renderer.js          # Frontend logic
├── preload.js           # IPC bridge
├── index.html           # Main interface
├── package.json         # Project configuration
└── assets/             # Icons and resources

📈 What's New in v1.10

Major Enhancements

• Enhanced File Management with visual status tracking
• Improved Process Control with robust stop/cancel functionality
• Auto-detect Parallel Processing for optimal performance
• Advanced Parameter UI with full MR model support
• Real-time Progress Updates with per-file status
• Better Error Handling and recovery mechanisms

Technical Improvements

• More reliable process management and cleanup
• Enhanced cross-platform compatibility
• Improved memory usage for large datasets
• Better handling of PHASE output parsing
• Streamlined build and distribution pipeline

📚 Documentation

• PHASE Manual: See included PDF documentation for PHASE 2.1.1 parameters
• Input Format: Detailed specifications in the PHASE documentation
• Parameter Guide: Comprehensive parameter explanations in the GUI tooltips

🤝 Contributing

Contributions welcome! Please see our contribution guidelines and:

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Commit changes (git commit -m 'Add amazing feature')
4. Push to branch (git push origin feature/amazing-feature)
5. Open a Pull Request

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

Note: PHASE 2.1.1 is separate software with its own license terms. Please review the PHASE license for commercial use restrictions.

🙏 Acknowledgments

• Matthew Stephens and colleagues for developing PHASE
• Stephens Lab at University of Chicago for maintaining PHASE
• Electron Community for the excellent application framework
• Bioinformatics Community for feedback and testing

📞 Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Email: jsbarrington@github.com

📊 Citation

If you use EZ-PHASE in your research, please cite:

Barrington, J.S. (2024). EZ-PHASE: A Modern GUI for PHASE Haplotype Reconstruction. 
GitHub repository: https://github.com/JSBarrington/ez-phase

And the original PHASE software:

Stephens, M., Smith, N.J., and Donnelly, P. (2001). A new statistical method for 
haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978–989.

---

<<<<<<< HEAD Made with ❤️ for the bioinformatics community ⭐ Star this repository if EZ-PHASE helps your research!