Quick usage

These two pages guide you through analyses in the fewest commands:

• Complete biological systems prediction workflow — the pansystems command chains gene family annotation, system detection, and results writing into a single all-in-one run.

• Pangenome comparison analysis — the compare_spots and compare_systems commands for comparing conserved spots and detected systems across multiple pangenomes.

For finer-grained control over each step, see the dedicated guides linked from the sections below.

• Complete Biological Systems Prediction Workflow
  • Pansystems Workflow
  • Command Line Usage
  • Key Arguments
  • Output Structure
  • When to Use Pansystems vs Individual Commands
  • Integration Notes
• Pangenome Comparison Analysis
  • Compare spots across pangenomes
  • Compare systems across pangenomes
  • GFRR Metrics Overview
  • Output Summary
  • Prerequisites