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.. jupyter-execute::
:hide-code:
import set_working_directory
``natsel_sitehet`` – a test of site heterogeneity
-------------------------------------------------
This app evaluates evidence for whether sites differ in their mode of
natural selection (`Nielsen and Yang
1998 <https://www.ncbi.nlm.nih.gov/pubmed/9539414>`__).
.. jupyter-execute::
from cogent3 import get_app
loader = get_app("load_aligned", format="fasta", moltype="dna")
aln = loader("data/primate_brca1.fasta")
sites_differ = get_app("natsel_sitehet",
"GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
)
result = sites_differ(aln)
result
The models have been constructed such that site-class bins have names indicating the mode of natural selection: -ve is purifying (oomega<1); neutral (omega=1); and +ve is positive natural selection (omega>1). The two parameters of interest relating to these are the ``bprobs`` (the maximum likelihood estimate of the frequency of the site-class) and the corresponding value of omega.
.. jupyter-execute::
result.alt.lf
Getting the individual site posterior probabilities
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I’m just displaying the posterior-probabilities from the first 20 positions only.
.. jupyter-execute::
bprobs = result.alt.lf.get_bin_probs()
bprobs[:, :20]
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