Working with Phylogenetic Trees with Biopython

import requests
from Bio import Phylo

# Download all files used in this tutorial once
urls = {
    "opuntia.dnd": "https://raw.githubusercontent.com/biopython/biopython/master/Doc/examples/opuntia.dnd",
    "hedgehog.aln": "https://raw.githubusercontent.com/biopython/biopython/master/Tests/Clustalw/hedgehog.aln",
    "apaf.xml": "https://raw.githubusercontent.com/biopython/biopython/master/Tests/PhyloXML/apaf.xml",
}

for filename, url in urls.items():
    response = requests.get(url, timeout=30)
    response.raise_for_status()
    with open(filename, "w", encoding="utf-8") as f:
        f.write(response.text)

# Load a Newick tree file and inspect basic properties
tree = Phylo.read("opuntia.dnd", "newick")
print("Rooted:", tree.rooted)
print("Number of terminal clades:", len(tree.get_terminals()))
print("Terminal names:", [clade.name for clade in tree.get_terminals()])

from Bio import AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor

# Read a protein multiple sequence alignment in Clustal format
alignment = AlignIO.read("hedgehog.aln", "clustal")

# Compute pairwise distances using a protein substitution model
calculator = DistanceCalculator("blosum62")
distance_matrix = calculator.get_distance(alignment)

# Build a Neighbor-Joining tree from the distance matrix
constructor = DistanceTreeConstructor()
protein_tree = constructor.nj(distance_matrix)

print("Terminal clades:", len(protein_tree.get_terminals()))
print("First five terminal names:", [c.name for c in protein_tree.get_terminals()[:5]])

from Bio import Phylo

# Read Newick and PhyloXML trees from local files
newick_tree = Phylo.read("opuntia.dnd", "newick")
phyloxml_tree = Phylo.read("apaf.xml", "phyloxml")

# Write trees to different output formats
Phylo.write(newick_tree, "opuntia_copy.xml", "phyloxml")
Phylo.write(phyloxml_tree, "apaf_copy.nwk", "newick")

print("Wrote opuntia_copy.xml and apaf_copy.nwk")

from Bio import Phylo

# Load an unrooted/partially rooted tree
tree = Phylo.read("opuntia.dnd", "newick")

# Midpoint root is a practical default when no outgroup is available
tree.root_at_midpoint()
print("Rooted after midpoint rooting:", tree.rooted)

# Re-root using an explicit outgroup terminal if present
terminals = tree.get_terminals()
if terminals:
    tree.root_with_outgroup(terminals[0])
    print("Re-rooted with outgroup:", terminals[0].name)

from Bio import Phylo

# Load tree and get terminal labels
tree = Phylo.read("opuntia.dnd", "newick")
terminals = [clade.name for clade in tree.get_terminals()]

# Keep only a small panel of taxa by pruning the rest
keep = set(terminals[:4])
for clade in list(tree.get_terminals()):
    if clade.name not in keep:
        tree.prune(clade)

print("Remaining terminals after pruning:", [c.name for c in tree.get_terminals()])

from Bio import Phylo
from copy import deepcopy

# Read original tree and find an internal clade
tree = Phylo.read("opuntia.dnd", "newick")
internal_clades = [c for c in tree.find_clades() if not c.is_terminal()]

if not internal_clades:
    raise ValueError("No internal clades found for subtree extraction.")

target_clade = internal_clades[0]
subtree = deepcopy(target_clade)

# Wrap clade in a Tree object and export
subtree_tree = Phylo.BaseTree.Tree(root=subtree)
Phylo.write(subtree_tree, "opuntia_subtree.nwk", "newick")
print("Subtree terminals:", [c.name for c in subtree_tree.get_terminals()])
print("Wrote subtree to opuntia_subtree.nwk")

import matplotlib.pyplot as plt
from Bio import Phylo

# Read the tree object
visual_tree = Phylo.read("opuntia.dnd", "newick")

# ASCII view is useful in terminal-only environments
Phylo.draw_ascii(visual_tree)

# Matplotlib rendering gives publication-style visualization
plt.figure(figsize=(10, 6))
Phylo.draw(visual_tree, do_show=False)
plt.title("Opuntia Phylogenetic Tree")
plt.tight_layout()
plt.show()

# Save static files for reports and papers
plt.figure(figsize=(10, 6))
Phylo.draw(visual_tree, do_show=False)
plt.title("Opuntia Phylogenetic Tree")
plt.tight_layout()
plt.savefig("opuntia_tree.png", dpi=300)
plt.savefig("opuntia_tree.pdf")
print("Saved opuntia_tree.png and opuntia_tree.pdf")