# Using a codon model

We load the unaligned sequences we will use in our examples.

## Codon alignment with default settings

The default settings will result in estimation of a guide tree (using percent identity between the sequences). The default “codon” model is MG94HKY.

The parameters used to construct the alignment, including the guide tree and substitution model, are record in the `info` attribute.

Note

If can also specify `unique_guides=True`, which means a guide tree will be estimated for every alignment.

## Specify a different distance measure for estimating the guide tree

The distance measures available are the same as for the nucleotide case (percent, TN93 or paralinear).

Note

An estimated guide tree has its branch lengths scaled so they are consistent with usage in a codon model.

## Providing a guide tree

Note

The guide tree needs to have branch lengths, otherwise a `ValueError` is raised.

## Specifying the gap parameters

## Specifying the substitution model and parameters

Any codon substitution model can be used. (See `cogent3.available_models()`.) If you provide parameter values, those must be consistent with the model definition.

## Alignment settings and file provenance are recorded in the `info` attribute