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:** ```python 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: ```bash # Display tree statistics python scripts/tree_operations.py stats t...