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