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bio-phylo-tree-manipulation

Maintainer FreedomIntelligence · Last updated April 1, 2026

Root, prune, reorder, and annotate phylogenetic trees.

OpenClawNanoClawAnalysisReproductionbio-phylo-tree-manipulation🧠 bioos extended suitebioos extended bioinformatics suiteroot

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-phylo-tree-manipulation

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Modify phylogenetic tree structure: rooting, pruning, ladderizing, and subtree extraction.
tree.root_with_outgroup({'name': 'Outgroup'}).

Source Doc

Excerpt From SKILL.md

Root with Outgroup

tree = Phylo.read('tree.nwk', 'newick')

## Root with multiple taxa (must be monophyletic)

outgroup = [{'name': 'TaxonA'}, {'name': 'TaxonB'}]
if tree.is_monophyletic(outgroup):
    tree.root_with_outgroup(*outgroup)
else:
    print('Outgroup is not monophyletic')

Check if tree is rooted (bifurcating at root)

print(f'Is bifurcating: {tree.is_bifurcating()}')

Use cases

Use bio-phylo-tree-manipulation for genomics and bioinformatics workflows.
Apply bio-phylo-tree-manipulation to sequencing, variant, or omics analysis tasks.