The simplest script#
Section author: Gavin Huttley
Note
These docs now use the new_type core objects via the following setting.
import os
# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"
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.
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", moltype="dna")
tree = make_tree(tip_names=aln.names)
lf = model.make_likelihood_function(tree)
lf.set_alignment(aln)
lf.optimise(show_progress=False)
lf
HKY85
log-likelihood = -2494.9537
number of free parameters = 4
| kappa |
|---|
| 5.9589 |
| edge | parent | length |
|---|---|---|
| human | root | 0.0040 |
| macaque | root | 0.0384 |
| chimp | root | 0.0061 |
| A | C | G | T |
|---|---|---|---|
| 0.2439 | 0.2581 | 0.2428 | 0.2552 |