Newick Format

The Newick format is the standard text representation for phylogenetic trees. This skill covers parsing, manipulating, and visualizing Newick trees.

Newick Format Syntax

# Basic formats:
(A,B);                          # Unrooted, no lengths
(A:0.1,B:0.2);                  # With branch lengths
(A:0.1,B:0.2):0.3;             # With root branch length
((A,B),C);                      # Nested clades
((A:0.1,B:0.2):0.3,C:0.4);     # Full format
((A,B)0.95:0.3,(C,D)0.99:0.2); # With support values

BioPython Phylo Module

from Bio import Phylo
from io import StringIO

# Read tree from file
tree = Phylo.read('tree.nwk', 'newick')

# Read tree from string
newick_str = "((A:0.1,B:0.2):0.3,(C:0.1,D:0.2):0.3);"
tree = Phylo.read(StringIO(newick_str), 'newick')

# ASCII visualization
Phylo.draw_ascii(tree)

# Write tree
Phylo.write(tree, 'output.nwk', 'newick')

Tree Navigation

# Get all terminal nodes (leaves)
terminals = tree.get_terminals()
for term in terminals:
    print(f"Leaf: {term.name}")

# Get all internal nodes
internals = tree.get_nonterminals()

# Find specific clade
clade = tree.find_any(name='A')

# Get path between two nodes
path = tree.get_path('A', 'B')

# Calculate distances
distance = tree.distance('A', 'B')

# Get common ancestor
common = tree.common_ancestor('A', 'B')

Tree Manipulation

from Bio.Phylo import BaseTree

# Root/unroot tree
tree.root_with_outgroup('A')
tree.root_at_midpoint()

# Collapse branches
def collapse_short_branches(tree, threshold=0.01):
    for clade in tree.find_clades():
        if clade.branch_length and clade.branch_length < threshold:
            clade.branch_length = 0
    return tree

# Prune taxa
def prune_taxa(tree, taxa_to_remove):
    for taxon in taxa_to_remove:
        tree.prune(taxon)
    return tree

# Rename tips
for tip in tree.get_terminals():
    tip.name = tip.name.replace('_', ' ')

Using ete3 Library

from ete3 import Tree

# Read tree
tree = Tree('tree.nwk')
# Or from string
tree = Tree('((A:0.1,B:0.2):0.3,(C:0.1,D:0.2):0.3);')

# Tree traversal
for node in tree.traverse('preorder'):  # or 'postorder', 'levelorder'
    print(node.name, node.dist)

# Get leaf names
leaves = tree.get_leaf_names()

# Calculate Robinson-Foulds distance between trees
tree1 = Tree('((A,B),(C,D));')
tree2 = Tree('((A,C),(B,D));')
rf, max_rf, common, parts1, parts2, set1, set2 = tree1.robinson_foulds(tree2)
print(f"RF distance: {rf}")

# Midpoint rooting
midpoint = tree.get_midpoint_outgroup()
tree.set_outgroup(midpoint)

Tree Visualization

from Bio import Phylo
import matplotlib.pyplot as plt

# Basic plot
fig, ax = plt.subplots(figsize=(10, 8))
Phylo.draw(tree, axes=ax)
plt.savefig('tree.png', dpi=150)

# Circular tree with ete3
from ete3 import Tree, TreeStyle, NodeStyle

tree = Tree('((A,B),(C,D));')
ts = TreeStyle()
ts.mode = 'c'  # Circular
ts.show_leaf_name = True
ts.show_branch_length = True

tree.render('circular_tree.png', tree_style=ts)

# Customize node styles
for node in tree.traverse():
    nstyle = NodeStyle()
    if node.is_leaf():
        nstyle['fgcolor'] = 'blue'
        nstyle['size'] = 10
    node.set_style(nstyle)

Tree Statistics

def tree_statistics(tree):
    """Calculate basic tree statistics."""
    from Bio import Phylo

    terminals = tree.get_terminals()
    internals = tree.get_nonterminals()

    # Branch lengths
    branch_lengths = [c.branch_length for c in tree.find_clades()
                     if c.branch_length is not None]

    # Tree depth
    depths = tree.depths()
    max_depth = max(depths.values()) if depths else 0

    return {
        'num_tips': len(terminals),
        'num_internal': len(internals),
        'total_branch_length': sum(branch_lengths),
        'mean_branch_length': sum(branch_lengths) / len(branch_lengths) if branch_lengths else 0,
        'max_depth': max_depth
    }

stats = tree_statistics(tree)
print(f"Tips: {stats['num_tips']}")
print(f"Total branch length: {stats['total_branch_length']:.4f}")

Converting Between Formats

from Bio import Phylo

# Newick to Nexus
tree = Phylo.read('tree.nwk', 'newick')
Phylo.write(tree, 'tree.nex', 'nexus')

# Newick to PhyloXML
Phylo.write(tree, 'tree.xml', 'phyloxml')

# Convert multiple trees
trees = Phylo.parse('bootstrap_trees.nwk', 'newick')
Phylo.write(trees, 'bootstrap_trees.nex', 'nexus')

Bootstrap Support Values

def add_bootstrap_support(main_tree, bootstrap_trees):
    """Map bootstrap support values to main tree."""
    from Bio.Phylo.Consensus import get_support

    support_tree = get_support(main_tree, bootstrap_trees)
    return support_tree

# Read bootstrap trees
boot_trees = list(Phylo.parse('bootstrap.nwk', 'newick'))
main_tree = Phylo.read('best_tree.nwk', 'newick')

# Add support
supported_tree = add_bootstrap_support(main_tree, boot_trees)