User Documentation

PANORAMA is organised around three main workflows: biological system prediction (annotate gene families, detect systems, write results), pangenome comparison (compare conserved spots and detected systems across pangenomes), and a set of utilities (pangenome info, alignment, clustering) that support both. If you are new to PANORAMA, start with the installation guide and the quick usage page below, then jump into the workflow that matches your goal.

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
• How to Cite
  • Cite PANORAMA
  • Cite PPanGGOLiN
  • Cite PPanGGOLiN tools used by PANORAMA

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 Identification 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
  • 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