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.. jupyter-execute::
:hide-code:
import set_working_directory
Make a UPGMA cluster
====================
.. sectionauthor:: Catherine Lozupone
An example of how to calculate the pairwise distances for a set of sequences.
.. note:: UPGMA should not be used for phylogenetic reconstruction.
.. jupyter-execute::
from cogent3 import load_aligned_seqs
from cogent3.cluster.UPGMA import upgma
from cogent3.evolve import distance
Import a substitution model (or create your own)
.. jupyter-execute::
from cogent3.evolve.models import HKY85
Load the alignment.
.. jupyter-execute::
al = load_aligned_seqs("data/test.paml")
Create a pairwise distances object calculator for the alignment, providing a substitution model instance.
.. jupyter-execute::
d = distance.EstimateDistances(al, submodel=HKY85())
d.run(show_progress=False)
Now use this matrix to build a UPGMA cluster.
.. jupyter-execute::
mycluster = upgma(d.get_pairwise_distances())
print(mycluster.ascii_art())
We demonstrate saving this UPGMA cluster to a file.
.. jupyter-execute::
mycluster.write("test_upgma.tree")
.. We don't actually want to keep that file now, so I'm importing the ``os`` module to delete it.
.. jupyter-execute::
:hide-code:
import os
os.remove("test_upgma.tree")
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