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.. jupyter-execute::
:hide-code:
import set_working_directory
The simplest script
===================
.. sectionauthor:: Gavin Huttley
We use a canned nucleotide substitution model (the ``HKY85`` model) on just three primate species. As there is only one unrooted tree possible, the sequence names are all that's required to make the tree.
.. jupyter-execute::
from cogent3 import load_aligned_seqs, make_tree
from cogent3.evolve.models import get_model
model = get_model("HKY85")
aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
tree = make_tree(tip_names=aln.names)
lf = model.make_likelihood_function(tree)
lf.set_alignment(aln)
lf.optimise(show_progress=False)
lf
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