bio-phylo-tree-manipulation

Version Compatibility

Reference examples tested with: BioPython 1.83+

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 Manipulation

"Root and prune my phylogenetic tree" → Modify tree topology by rooting with outgroups or midpoint, pruning taxa, collapsing low-support clades, ladderizing branches, or extracting subtrees.

• Python: tree.root_with_outgroup(), tree.prune(), tree.ladderize() (Bio.Phylo)

Modify phylogenetic tree structure: rooting, pruning, ladderizing, and subtree extraction.

Required Import

from Bio import Phylo
from io import StringIO

Rooting Trees

Root with Outgroup

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

# Root with single taxon
tree.root_with_outgroup({'name': 'Outgroup'})

# Root with multiple taxa (must be monophyletic)
outgroup = [{'name': 'TaxonA'}, {'name': 'TaxonB'}]
if tree.is_monophyletic(outgroup):
    tree.root_with_outgroup(*outgroup)
else:
    print('Outgroup is not monophyletic')

Root at Midpoint

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

Check Rooting Status

# Check if tree is rooted (bifurcating at root)
print(f'Is bifurcating: {tree.is_bifurcating()}')

# Count children of root
root = tree.root
print(f'Root has {len(root.clades)} children')
# 2 children = rooted, 3+ children = unrooted

Ladderizing

Sort clades for consistent visual presentation.

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

# Larger clades at bottom
tree.ladderize()

# Larger clades at top
tree.ladderize(reverse=True)

Phylo.write(tree, 'ladderized.nwk', 'newick')

Pruning Trees

Remove Specific Taxa

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

# Find and remove a taxon
target = tree.find_any(name='TaxonToRemove')
if target:
    tree.prune(target)

# Remove multiple taxa
for name in ['TaxonA', 'TaxonB', 'TaxonC']:
    target = tree.find_any(name=name)
    if target:
        tree.prune(target)