bio-phylo-tree-visualization

Version Compatibility

Reference examples tested with: BioPython 1.83+, matplotlib 3.8+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Tree Visualization

"Create a publication-quality tree figure" → Draw and customize phylogenetic tree visualizations with colored branches, tip labels, and bootstrap support values using matplotlib.

• Python: Bio.Phylo.draw() with matplotlib customization

Draw phylogenetic trees using matplotlib integration.

Required Import

from Bio import Phylo
import matplotlib.pyplot as plt

ASCII Tree Display

tree = Phylo.read('tree.nwk', 'newick')

# Quick text representation
print(tree)

# ASCII art diagram
Phylo.draw_ascii(tree)

Basic Tree Drawing

tree = Phylo.read('tree.nwk', 'newick')

# Simple plot (opens interactive window)
Phylo.draw(tree)
plt.show()

# Save to file
fig, ax = plt.subplots(figsize=(10, 8))
Phylo.draw(tree, axes=ax)
plt.savefig('tree.png', dpi=300, bbox_inches='tight')
plt.close()

Customizing Tree Appearance

fig, ax = plt.subplots(figsize=(12, 10))
Phylo.draw(tree, axes=ax, do_show=False,
           branch_labels=lambda c: f'{c.branch_length:.2f}' if c.branch_length else '',
           label_func=lambda c: c.name if c.is_terminal() else '')

ax.set_title('Phylogenetic Tree')
plt.savefig('custom_tree.png', dpi=300, bbox_inches='tight')
plt.close()

Label Customization

# Custom label function
def custom_labels(clade):
    if clade.is_terminal():
        return clade.name
    elif clade.confidence:
        return f'{clade.confidence:.0f}'
    return ''

fig, ax = plt.subplots(figsize=(10, 8))
Phylo.draw(tree, axes=ax, label_func=custom_labels)
plt.savefig('labeled_tree.png', dpi=300)
plt.close()