bio-phylo-tree-manipulation - Modify Phylogenetic Tree Structure
Modify phylogenetic tree structure using Biopython
Tags
Updated: 2026-05-11Capabilities
Typical Inputs
Typical Outputs
What this skill does
- root tree with outgroup
- root tree at midpoint
- ladderize tree
- prune taxon
- collapse clade
- extract subtree
- traverse tree nodes
- find clade
- get path between nodes
- check tree properties
- modify branch length
- rename taxon
- count nodes
- get tree depths
- split clade
- generate random tree
Inputs
- Newick tree file
- outgroup taxa
- target taxon names
- branch length threshold
- confidence threshold
- name mapping
Outputs
- modified Newick tree file
- rooted tree
- ladderized tree
- pruned tree
- collapsed tree
- subtree
- ASCII tree representation
Requirements
- Python environment
- Biopython library