# Quick usage

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

- **[Complete biological systems prediction workflow](pansystems.md)** — the `pansystems` command chains gene family
  annotation, system detection, and results writing into a single all-in-one run.
- **[Pangenome comparison analysis](quick_compare.md)** — 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.

```{toctree}
:maxdepth: 2

pansystems
quick_compare
```