# Command Reference

## `babappa init`
Create project scaffold.

## `babappa validate`
Validate codon alignments and tree compatibility.

## `babappa fit-null`
Simulate null data, fit/freeze energy model, write `null_bundle.json`.

## `babappa score`
Score genes with frozen bundle and exact Monte Carlo p-values.

## `babappa adjust`
Apply BH/BY/Bonferroni correction.

## `babappa report`
Generate HTML report and plots.

## `babappa benchmark`
Run simulation + real-data benchmark tracks.

## `babappa demo`
Run complete packaged example pipeline.

## `babappa doctor`
Check environment/dependencies/optional comparator availability.
