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.