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# Modelling sequence evolution

`cogent3` possesses unique capabilities for molecular evolutionary analyses. Of particular significance are our non-stationary model classes and the associated measurement of genetic distance from these. That said, we also implement most of the conventional substitution models. See `cogent3.available_models()` for a display of the built-in models.

You can use these models either through the general `model` app, or some task specific apps. Both are described in the following “how-tos”.

- Apply a non-stationary nucleotide model to an alignment with 3 sequences
- Apply a non-stationary nucleotide model to an alignment with a tree
- Specifying a non-stationary model with time-heterogeneous parameters
- Extracting maximum likelihood estimates from a `model_result`
- Reconstructing ancestral states
- Applying a discrete-time, non-stationary nucleotide model
- Applying a time-reversible nucleotide model
- Applying GNC, a non-stationary codon model
- Applying a time-reversible codon model