bio-phylo-tree-io

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name: bio-phylo-tree-io description: Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees. tool_type: python primary_tool: Bio.Phylo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

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Tree I/O

Parse, write, and convert phylogenetic tree files in various formats.

Required Import

from Bio import Phylo
from io import StringIO

Supported Formats

Format	Extension	Description
newick	.nwk, .tre, .tree	Standard format with branch lengths
nexus	.nex, .nxs	Rich format with annotations (PAUP, MrBayes)
phyloxml	.xml	XML format with metadata support
nexml	.nexml	Modern XML format
cdao	.rdf	RDF format (limited use)

Reading Trees

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

# Read multiple trees from file
trees = list(Phylo.parse('bootstrap_trees.nwk', 'newick'))
print(f'Loaded {len(trees)} trees')

# Read from string
tree_string = '((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);'
tree = Phylo.read(StringIO(tree_string), 'newick')

# Read PhyloXML with metadata
tree = Phylo.read('annotated.xml', 'phyloxml')

# Read Nexus (often contains multiple trees)
trees = list(Phylo.parse('mrbayes.nex', 'nexus'))

Writing Trees

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

# Write multiple trees
Phylo.write(trees, 'all_trees.nwk', 'newick')

# Write to PhyloXML (preserves metadata)
Phylo.write(tree, 'output.xml', 'phyloxml')

# Write to Nexus
Phylo.write(tree, 'output.nex', 'nexus')

Serialize to String

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

# Get tree as string (useful for embedding, logging, or API responses)
newick_string = format(tree, 'newick')
print(newick_string)  # ((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);

# Alternative method
newick_string = tree.format('newick')

# Other formats work too
phyloxml_string = format(tree, 'phyloxml')

Format Conversion

# Direct file conversion
Phylo.convert('input.nwk', 'newick', 'output.xml', 'phyloxml')
Phylo.convert('mrbayes.nex', 'nexus', 'trees.nwk', 'newick')

# Convert with processing
tree = Phylo.read('input.nwk', 'newick')
tree.ladderize()  # Sort branches
Phylo.write(tree, 'sorted.nwk', 'newick')

Quick Tree Inspection

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

# Print ASCII representation
print(tree)

# ASCII tree diagram
Phylo.draw_ascii(tree)

# Basic tree properties
print(f'Total branch length: {tree.total_branch_length()}')
print(f'Number of terminals: {len(tree.get_terminals())}')
print(f'Is bifurcating: {tree.is_bifurcating()}')

Accessing Tree Structure

# Get all terminal (leaf) nodes
terminals = tree.get_terminals()
for term in terminals:
    print(f'{term.name}: branch_length={term.branch_length}')

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

# Get all clades (nodes)
all_clades = list(tree.find_clades())

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

Tree from Newick String Patterns

# Simple tree (no branch lengths)
tree = Phylo.read(StringIO('((A,B),(C,D));'), 'newick')

# With branch lengths
tree = Phylo.read(StringIO('((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);'), 'newick')

# With internal node names
tree = Phylo.read(StringIO('((A,B)AB,(C,D)CD)root;'), 'newick')

# With bootstrap values (internal node names)
tree = Phylo.read(StringIO('((A:0.1,B:0.2)95:0.3,(C:0.4,D:0.5)80:0.6);'), 'newick')

Working with PhyloXML Metadata

# PhyloXML supports rich annotations
tree = Phylo.read('annotated.xml', 'phyloxml')

for clade in tree.find_clades():
    if clade.confidences:
        print(f'{clade.name}: confidence={clade.confidences[0].value}')
    if hasattr(clade, 'taxonomy') and clade.taxonomy:
        print(f'{clade.name}: taxonomy={clade.taxonomy.scientific_name}')

# Convert Newick to PhyloXML (adds metadata capabilities)
newick_tree = Phylo.read('simple.nwk', 'newick')
phyloxml_tree = newick_tree.as_phyloxml()

Handling Multiple Trees

# Parse bootstrap or posterior trees
trees = list(Phylo.parse('bootstrap.nwk', 'newick'))
print(f'Loaded {len(trees)} bootstrap trees')

# Process each tree
for i, tree in enumerate(trees):
    print(f'Tree {i}: {len(tree.get_terminals())} taxa')

# Write subset of trees
Phylo.write(trees[:100], 'first_100.nwk', 'newick')

Iterating Over Large Tree Files

# Memory-efficient iteration (doesn't load all trees at once)
for tree in Phylo.parse('large_file.nwk', 'newick'):
    if tree.total_branch_length() > 1.0:
        print(f'Long tree: {tree.total_branch_length()}')

Common Newick Format Variations

Input	Description
(A,B,C);	Unrooted, no lengths
((A,B),C);	Rooted topology
(A:0.1,B:0.2);	With branch lengths
((A,B)X,C);	Internal node named X
((A,B):0.5[90],C);	Branch with bootstrap

Error Handling

from Bio import Phylo
from io import StringIO

# Check for valid newick
tree_string = '((A,B),(C,D));'
try:
    tree = Phylo.read(StringIO(tree_string), 'newick')
    print('Valid tree')
except Exception as e:
    print(f'Parse error: {e}')

# Handle missing branch lengths
tree = Phylo.read('tree.nwk', 'newick')
for clade in tree.find_clades():
    if clade.branch_length is None:
        clade.branch_length = 0.0  # Set default

Format-Specific Notes

Format	Strengths	Limitations
Newick	Universal, simple	No metadata
Nexus	PAUP/MrBayes compatible	Complex syntax
PhyloXML	Rich metadata, colors	Verbose
NeXML	Modern, extensible	Less common

Related Skills

• tree-visualization - Draw and export tree figures
• tree-manipulation - Root, prune, and modify tree structure
• distance-calculations - Compute distances and build trees from alignments
• alignment/alignment-io - Read MSA files for tree construction