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 and file provenance are recorded in the info attribute