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.. jupyter-execute::
:hide-code:
import set_working_directory
``natsel_timehet`` – a test of branch heterogeneity
---------------------------------------------------
We employ codon models to test whether the mode of natural selection affecting human and chimpanzee lineages is distinctive. This is done by specifying the edges of interest (`Yang 1998 <https://www.ncbi.nlm.nih.gov/pubmed/9580986>`__).
.. 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")
hc_differ = get_app("natsel_timehet",
"GNC",
tree="data/primate_brca1.tree",
optimise_motif_probs=False,
tip1="Human",
tip2="Chimpanzee",
)
result = hc_differ(aln)
result
.. jupyter-execute::
result.alt.lf
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