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.. jupyter-execute::
:hide-code:
import set_working_directory
``natsel_neutral`` – a test for selective neutrality
----------------------------------------------------
We employ codon models to test hypotheses regarding the mode of natural selection that has operated on a gene.
Noting that ω (omega) is the ratio of nonsynonymous substitutions to synonymous substitutions, ω=1 is indicative a gene is evolving neutrally.
.. warning:: I’m setting ``optimise_motif_probs=False`` to speed up execution of the examples, not because it’s a good idea!
.. jupyter-execute::
from cogent3 import get_app
loader = get_app("load_aligned", format="fasta", moltype="dna")
aln = loader("data/primate_brca1.fasta")
omega_eq_1 = get_app("natsel_neutral",
"GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
)
result = omega_eq_1(aln)
type(result)
.. jupyter-execute::
result
.. jupyter-execute::
result.alt.lf
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