Using a codon 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.

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.

Note

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

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.

Warning

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

Any cogent3 codon substitution model can be used. (See cogent3.available_models().)

Note

If you provide parameter values, those must be consistent with the model definition.

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