etetoolkit

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

## 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)