User Documentation

Get Started:

• Installation Guide 🦮
  • Latest version
  • Development Version
  • Troubleshooting
• Quick usage 🦅
  • Complete Biological Systems Prediction Workflow
  • Pangenome Comparison Analysis
• Reporting Issues and Suggesting Features 💬
  • Reporting a Bug 🐛
  • Suggesting a New Feature 💡
  • Enhancement Suggestion ✨
  • Asking Questions or Sharing Ideas 💭
  • What Happens Next?
  • Getting Help 🆘

Biological system Prediction:

• Gene Family annotation
  • Annotation Modes
  • Command Line Usage
  • Annotation Workflow
  • HMM Search Details
  • Minimal example
• System Detection Based on Models
  • Model Detection Workflow
  • Command Line Usage
  • Key Options
  • Output
• Systems analysis output 📊
  • System Projection on Genomes
  • System Association with Pangenome Elements
  • System Partition Analysis

Pangenomes comparison:

• Conserved Spots Comparison Across Pangenomes
  • Conserved Spots Detection Workflow
  • Compare spots command Line Usage
  • Output
  • Individual Conserved Spot Files
• Systems Comparison Across Pangenomes
  • Systems Comparison Workflow
  • System comparison command Line Usage
  • Output

PANORAMA utilities:

• Extract and Visualize Pangenome Information ℹ️
  • Info command line usage ️
  • Output
  • Key options
  • Exploring the Reports
• Gene Family Alignment Across Pangenomes
  • Alignment Workflow
  • Alignment command Line Usage
  • Parameter Guidelines
  • Output Files
• Gene Family Clustering Across Pangenomes
  • Clustering Workflow
  • Clustering command Line Usage
  • Clustering Methods Comparison
  • Parameter Guidelines
  • Output Files