etetoolkit

ETE Toolkit Skill

Overview

ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.

Core Capabilities

1. Tree Manipulation and Analysis

Load, manipulate, and analyze hierarchical tree structures with support for:

• Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
• Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
• Topology modification: Prune, root, collapse nodes, resolve polytomies
• Distance calculations: Compute branch lengths and topological distances between nodes
• Tree comparison: Calculate Robinson-Foulds distances and identify topological differences

Common patterns:

from ete3 import Tree

# Load tree from file
tree = Tree("tree.nw", format=1)

# Basic statistics
print(f"Leaves: {len(tree)}")
print(f"Total nodes: {len(list(tree.traverse()))}")

# Prune to taxa of interest
taxa_to_keep = ["species1", "species2", "species3"]
tree.prune(taxa_to_keep, preserve_branch_length=True)

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

# Save modified tree
tree.write(outfile="rooted_tree.nw")

Use scripts/tree_operations.py for command-line tree manipulation:

# Display tree statistics
python scripts/tree_operations.py stats tree.nw

# Convert format
python scripts/tree_operations.py convert tree.nw output.nw --in-format 0 --out-format 1

# Reroot tree
python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint

# Prune to specific taxa
python scripts/tree_operations.py prune tree.nw pruned.nw --keep-taxa "sp1,sp2,sp3"

# Show ASCII visualization
python scripts/tree_operations.py ascii tree.nw

2. Phylogenetic Analysis

Analyze gene trees with evolutionary event detection:

• Sequence alignment integration: Link trees to multiple sequence alignments (FASTA, Phylip)
• Species naming: Automatic or custom species extraction from gene names
• Evolutionary events: Detect duplication and speciation events using Species Overlap or tree reconciliation
• Orthology detection: Identify orthologs and paralogs based on evolutionary events
• Gene family analysis: Split trees by duplications, collapse lineage-specific expansions