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# Using a nucleotide model

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

Note

We use an app loader, but since this is just a single file we could have used the `cogent3.load_unaligned_seqs()` function.

## Nucleotide alignment with default settings

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

Note

If you specify `unique_guides=True`, a guide tree will be estimated for every alignment.

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

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

## Providing a guide tree

Warning

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

## Specifying the substitution model

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

## Alignment settings provenance

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

The file from which the alignment was derived (the provenance) is on the `.source` attribute.