Building phylogenies

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"

Building A Phylogenetic Tree From Pairwise Distances

Directly via alignment.quick_tree()

from cogent3 import load_aligned_seqs

aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
tree = aln.quick_tree(calc="TN93")
tree = tree.balanced()  # purely for display
print(tree.ascii_art())

          /-Orangutan
         |
         |          /-Rhesus
         |-edge.2--|
         |         |          /-HowlerMon
-root----|          \edge.1--|
         |                    \-Galago
         |
         |                    /-Gorilla
         |          /edge.0--|
          \edge.3--|          \-Human
                   |
                    \-Chimpanzee

Directly via alignment.quick_tree() with a third-party hook

You can use the IQ-TREE rapid-NJ algorithm for quick_tree() by installing piqtree and setting use_hook="piqtree".

from cogent3 import load_aligned_seqs

aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
tree = aln.quick_tree(calc="TN93", use_hook="piqtree")
# dropping branch lengths to simplify display
dnd = tree.get_figure(contemporaneous=True, width=600, height=600)
dnd.show()

Using the DistanceMatrix object

from cogent3 import load_aligned_seqs

aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
dists = aln.distance_matrix(calc="TN93")
tree = dists.quick_tree()
tree = tree.balanced()  # purely for display
print(tree.ascii_art())

          /-Orangutan
         |
         |          /-Rhesus
         |-edge.2--|
         |         |          /-HowlerMon
-root----|          \edge.1--|
         |                    \-Galago
         |
         |                    /-Gorilla
         |          /edge.0--|
          \edge.3--|          \-Human
                   |
                    \-Chimpanzee

Explicitly via DistanceMatrix and cogent3.phylo.nj.nj()`

from cogent3 import load_aligned_seqs
from cogent3.phylo import nj

aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
dists = aln.distance_matrix(calc="TN93")
tree = nj.nj(dists, show_progress=False)
tree = tree.balanced()  # purely for display
print(tree.ascii_art())

          /-Orangutan
         |
         |          /-Rhesus
         |-edge.2--|
         |         |          /-HowlerMon
-root----|          \edge.1--|
         |                    \-Galago
         |
         |                    /-Gorilla
         |          /edge.0--|
          \edge.3--|          \-Human
                   |
                    \-Chimpanzee

Directly from a pairwise distance dict

from cogent3.phylo import nj

dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73}
tree = nj.nj(dists, show_progress=False)
print(tree.ascii_art())

          /-c
         |
-root----|--a
         |
          \-b

By Least-squares

We illustrate the phylogeny reconstruction by least-squares using the F81 substitution model. We use the advanced-stepwise addition algorithm to search tree space. Here a is the number of taxa to exhaustively evaluate all possible phylogenies for. Successive taxa are added to the top k trees (measured by the least-squares metric) and k trees are kept at each iteration.

from cogent3.phylo.least_squares import WLS
from cogent3.util.deserialise import deserialise_object

dists = deserialise_object("data/dists_for_phylo.json")
ls = WLS(dists)
stat, tree = ls.trex(a=5, k=5, show_progress=False)

Other optional arguments that can be passed to the trex method are: return_all, whether the k best trees at the final step are returned as a ScoredTreeCollection object; order, a series of tip names whose order defines the sequence in which tips will be added during tree building (this allows the user to randomise the input order).

By ML

We illustrate the phylogeny reconstruction using maximum-likelihood using the F81 substitution model. We use the advanced-stepwise addition algorithm to search tree space.

from cogent3 import load_aligned_seqs
from cogent3.evolve.models import F81
from cogent3.phylo.maximum_likelihood import ML

aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
ml = ML(F81(), aln)