Building phylogenies#

Building A Phylogenetic Tree From Pairwise Distances#

Directly via alignment.quick_tree()#

Both the ArrayAlignment and Alignment classes support this.

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

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

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

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)