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.. jupyter-execute::
:hide-code:
import set_working_directory
Apply a non-stationary nucleotide model to an alignment with a tree
-------------------------------------------------------------------
We analyse an alignment with sequences from 6 primates.
.. jupyter-execute::
from cogent3 import get_app
loader = get_app("load_aligned", format="fasta", moltype="dna")
aln = loader("data/primate_brca1.fasta")
aln.names
Specify the tree via a tree instance
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3 import load_tree
from cogent3 import get_app
tree = load_tree("data/primate_brca1.tree")
gn = get_app("model", "GN", tree=tree)
gn
Specify the tree via a path.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
gn = get_app("model", "GN", tree="data/primate_brca1.tree")
gn
Apply the model to an alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
fitted = gn(aln)
fitted
In the above, no value is shown for ``unique_Q``. This can happen because of numerical precision issues.
.. note:: in the display of the ``lf`` below, the “length” parameter is not the ENS. It is, instead, just a scalar.
.. jupyter-execute::
fitted.lf
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