# Using a nucleotide model

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

## Nucleotide alignment with default settings

The default setting for “nucleotide” is a HKY85 model.

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

For the nucleotide case, you can use TN93 or paralinear.

## Providing a guide tree

Note

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

## Specifying the substitution model

You can use any nucleotide substitution model. For a list of all available, see `cogent3.available_models()`.

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