bio-phylo-tree-manipulation
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees. Includes rooting method decision guidance.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tree-manipulation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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. ## Rooting Method Decision | Method | Mechanism | When to Use | Pitfalls | |--------|-----------|-------------|----------| | Outgroup | External taxon(a) known to be sister to ingroup | **Default method** when a suitable outgroup exists | Too-distant outgroup causes LBA; single outgroup has ~50% misplacement risk | | Midpoint | Root halfway between most divergent taxa | Quick exploratory; when outgroup is unknow
- Version Compatibility
- Rooting Method Decision
- Required Import
- Rooting Trees
- Root with Outgroup (Preferred)
- Root at Midpoint
- MAD Rooting (CLI Alternative)
- Check Rooting Status
- Ladderizing
- Pruning Trees
- Remove Specific Taxa
- Keep Only Specified Taxa
- Collapsing Clades
- Extracting Subtrees
What does the bio-phylo-tree-manipulation skill do?
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees. Includes rooting method decision guidance.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tree-manipulation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.