The simplest script¶
Section author: Gavin Huttley
This is just about the simplest possible cogent3
script for evolutionary modelling. 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.evolve.models import HKY85
>>> from cogent3 import load_aligned_seqs, make_tree
>>> 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)
>>> print(lf)
Likelihood function statistics
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
------------------------------------