Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-phylo-tree-io

Maintainer FreedomIntelligence · Last updated April 1, 2026

Read/write phylogenetic trees in Newick, Nexus, PhyloXML formats.

OpenClawNanoClawAnalysisReproductionbio-phylo-tree-io🧠 bioos extended suitebioos extended bioinformatics suiteread

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Parse, write, and convert phylogenetic tree files in various formats.
tree = Phylo.read('tree.nwk', 'newick').

Source Doc

Excerpt From SKILL.md

Supported Formats

Format	Extension	Description
`newick`	.nwk, .tre, .tree	Standard format with branch lengths
`nexus`	.nex, .nxs	Rich format with annotations (PAUP, MrBayes)
`phyloxml`	.xml	XML format with metadata support
`nexml`	.nexml	Modern XML format
`cdao`	.rdf	RDF format (limited use)

Read multiple trees from file

trees = list(Phylo.parse('bootstrap_trees.nwk', 'newick')) print(f'Loaded {len(trees)} trees')

Read from string

tree_string = '((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);' tree = Phylo.read(StringIO(tree_string), 'newick')

Use cases

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

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

tree-visualization - Draw and export tree figures
tree-manipulation - Root, prune, and modify tree structure
distance-calculations - Compute distances and build trees from alignments
alignment/alignment-io - Read MSA files for tree construction

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