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()
.