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.. jupyter-execute::
:hide-code:
import set_working_directory
Make a neighbor joining tree
============================
.. sectionauthor:: Gavin Huttley
An example of how to calculate the pairwise distances for a set of sequences.
.. jupyter-execute::
from cogent3 import load_aligned_seqs
from cogent3.evolve import distance
from cogent3.phylo import nj
Import a substitution model (or create your own)
.. jupyter-execute::
from cogent3.evolve.models import get_model
Load the alignment.
.. jupyter-execute::
al = load_aligned_seqs("data/long_testseqs.fasta")
Create a pairwise distances object calculator for the alignment, providing a substitution model instance.
.. jupyter-execute::
d = distance.EstimateDistances(al, submodel=get_model("HKY85"))
d.run(show_progress=False)
Now use this matrix to build a neighbour joining tree.
.. jupyter-execute::
mytree = nj.nj(d.get_pairwise_distances(), show_progress=False)
print(mytree.ascii_art())
We can save this tree to file.
.. jupyter-execute::
mytree.write("test_nj.tree")
.. clean up
.. jupyter-execute::
:hide-code:
import os
os.remove("test_nj.tree")
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