# Configuration Guide

BABAPPA uses YAML or TOML configuration.

Example YAML structure:

```yaml
qc:
  max_gap_fraction: 0.35
  max_ambiguity_fraction: 0.10
representation:
  projection_dim: 16
  projection_seed: 0
  smoothing_bandwidth: 0.15
null_model:
  model_name: mg94_neutral
  kappa: 2.0
  omega: 1.0
  codon_frequency_mode: f3x4
fit:
  null_replicates_train: 200
  ridge: 1.0e-4
score:
  null_replicates_score: 999
  two_sided: false
runtime:
  jobs: 1
  seed: 1
```

All settings are explicit in run manifests.
