Make a neighbor joining tree

Section author: Gavin Huttley

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"

An example of how to calculate the pairwise distances for a set of sequences.

from cogent3 import load_aligned_seqs
from cogent3.evolve import distance
from cogent3.phylo import nj

Import a substitution model (or create your own)

from cogent3.evolve.models import get_model

Load the alignment.

al = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna")

Create a pairwise distances object calculator for the alignment, providing a substitution model instance.

d = distance.EstimateDistances(al, submodel=get_model("HKY85"))
d.run(show_progress=False)

Now use this matrix to build a neighbour joining tree.

mytree = nj.nj(d.get_pairwise_distances(), show_progress=False)
print(mytree.ascii_art())

          /-DogFaced
         |
         |          /-Mouse
         |-edge.1--|
-root----|         |          /-Human
         |          \edge.0--|
         |                    \-HowlerMon
         |
          \-NineBande

We can save this tree to file.

mytree.write("test_nj.tree")