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.. jupyter-execute::
:hide-code:
import set_working_directory
Applying GNC, a non-stationary codon model
------------------------------------------
See `Kaehler et al <https://www.ncbi.nlm.nih.gov/pubmed/28175284>`__ for the formal description of this model. Note that perform hypothesis testing using this model elsewhere.
We apply this to a sample alignment.
.. jupyter-execute::
from cogent3 import get_app
loader = get_app("load_aligned", format="fasta", moltype="dna")
aln = loader("data/primate_brca1.fasta")
The model is specified using it’s abbreviation.
.. jupyter-execute::
model = get_app("model", "GNC", tree="data/primate_brca1.tree")
result = model(aln)
result
.. jupyter-execute::
result.lf
We can obtain the tree with branch lengths as ENS
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If this tree is written to newick (using the ``write()`` method), the lengths will now be ENS.
.. jupyter-execute::
tree = result.tree
fig = tree.get_figure()
fig.scale_bar = "top right"
fig.show(width=500, height=500)
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