Agent skill

Tooluniverse Phylogenetics

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Phylogenetics

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-phylogenetics --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio/tooluniverse-phylogenetics .claude/skills/tooluniverse-phylogenetics && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "tooluniverse-phylogenetics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics into .claude/skills/tooluniverse-phylogenetics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-phylogenetics", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-phylogenetics --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio/tooluniverse-phylogenetics .agents/skills/tooluniverse-phylogenetics && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "tooluniverse-phylogenetics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics into .agents/skills/tooluniverse-phylogenetics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-phylogenetics", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-phylogenetics --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio/tooluniverse-phylogenetics .cursor/skills/tooluniverse-phylogenetics && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "tooluniverse-phylogenetics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics into .cursor/skills/tooluniverse-phylogenetics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-phylogenetics", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/wu-yc/LabClaw.git --path skills/bio/tooluniverse-phylogenetics

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-phylogenetics --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio/tooluniverse-phylogenetics .gemini/skills/tooluniverse-phylogenetics && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "tooluniverse-phylogenetics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics into .gemini/skills/tooluniverse-phylogenetics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-phylogenetics", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-phylogenetics

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio/tooluniverse-phylogenetics .github/skills/tooluniverse-phylogenetics && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "tooluniverse-phylogenetics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics into .github/skills/tooluniverse-phylogenetics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-phylogenetics", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-phylogenetics --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio/tooluniverse-phylogenetics .opencode/skills/tooluniverse-phylogenetics && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "tooluniverse-phylogenetics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-phylogenetics into .opencode/skills/tooluniverse-phylogenetics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-phylogenetics", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: tooluniverse-phylogenetics
GitHub stars: 1.1k
Used in: 2 other repos
Token cost: ~4.2k tokens
SKILL.md length: 987 words
Files: 1
Skills in repo: 68
Repo updated: Mar 19, 2026
First seen: Oct 7, 2026
Licence: None found

At a glance

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.

Works in 8 steps: Data-first approach - Discover and… → PhyKIT-compatible - Use PhyKIT functions… → Format-flexible - Support FASTA, PHYLIP,… → …
Processing FASTA/PHYLIP/Nexus/Newick files
SKILL.md covers When to Use This Skill, Core Principles, Required Python Packages and High-Level Workflow Decision…, plus 12 more sections
Calls pip

What it does

Tooluniverse Phylogenetics is an agent skill from wu-yc/LabClaw. Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval…

Its SKILL.md is about 4.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics. It works with Biopython, Ensembl, NCBI and UniProt. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists).

When your agent uses it

Processing FASTA/PHYLIP/Nexus/Newick files
Computing phylogenetic metrics
Comparing taxa groups
Answering questions about alignments

Example prompts

“/tooluniverse-phylogenetics”

Requirements

Python 3

Workflow steps

8 steps, taken from the first numbered list in SKILL.md.

Data-first approach - Discover and validate all input files (alignments, trees) before any analysis
PhyKIT-compatible - Use PhyKIT functions for treeness, RCV, DVMC, parsimony, evolutionary rate (matches BixBench expected outputs)
Format-flexible - Support FASTA, PHYLIP, Nexus, Newick, and auto-detect formats
Batch processing - Process hundreds of gene alignments/trees in a single analysis
Statistical rigor - Mann-Whitney U, medians, percentiles, standard deviations with scipy.stats
Precision awareness - Match rounding to 4 decimal places (PhyKIT default) or as requested
Group comparison - Compare metrics between taxa groups (e.g., fungi vs animals)
Question-driven - Parse exactly what is asked and return the specific number/statistic

What it can do on your machine

Read from SKILL.md and the folder at commit df37802. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- jlsteenwyk.com
- biopython.org
- dendropy.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Tooluniverse Phylogenetics loads about 4.2k tokens when it runs. Until then it costs about 195 tokens; SKILL.md has 987 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~195
When it runs · the whole SKILL.md, loaded when a task matches: ~4.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 987 words (~4,176 tokens).

“Comprehensive phylogenetics and sequence analysis using PhyKIT, Biopython, and DendroPy. Designed for bioinformatics questions about multiple sequence alignments, phylogenetic trees, parsimony, molecular evolution, and comparative genomics.”

— opening of SKILL.md by wu-yc

name: tooluniverse-phylogenetics

Outline of SKILL.md

Phylogenetics and Sequence Analysis
When to Use This Skill
Core Principles
Required Python Packages
High-Level Workflow Decision Tree
Quick Reference: Common Metrics
Common Analysis Patterns (BixBench)
Pattern 1: Single Metric Across Groups
Pattern 2: Statistical Comparison
Pattern 3: Filtering + Metric
Pattern 4: Specific Gene Lookup
Choosing Methods: When to Use What
Alignment Methods
Tree Building Methods
Batch Processing
Discovering Gene Files
Computing Metrics in Batch
Statistical Analysis
Answer Extraction for BixBench
Rounding Rules
BixBench Question Coverage
ToolUniverse Integration
Sequence Retrieval
File Structure
Completeness Checklist
Next Steps
Support
License

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/bio/tooluniverse-phylogenetics of wu-yc/LabClaw.

Open the folder on GitHubat commit df37802

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in wu-yc/LabClaw, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Tooluniverse Phylogenetics next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Tooluniverse Phylogenetics compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Tooluniverse Phylogenetics this skillwu-yc/LabClaw	1.1k	2 repos	~4.2k	Automated safety check: Pass	None	6 mo ago
Ggetdavila7/claude-code-templates	33k	10 repos	~6.3k	Automated safety check: Pass	MIT	today
Biopythonlamm-mit/scienceclaw	246	—	~3.9k	Automated safety check: Pass	Apache-2.0	1 mo ago
Ggetaipoch/medical-research-skills	1.9k	—	~816	Automated safety check: Pass	MIT	24 days ago
Ena Databasejaechang-hits/SciAgent-Skills	374	1 repos	~5.3k	Automated safety check: Pass	Custom licence	12 days ago
Biopython Bioinformaticsaiming-lab/AutoResearchClaw	15k	—	~810	Automated safety check: Pass	MIT	1 mo ago

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Works with

Questions about Tooluniverse Phylogenetics

What does Tooluniverse Phylogenetics do?

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Tooluniverse Phylogenetics is an agent skill from wu-yc/LabClaw. Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.

When should I use Tooluniverse Phylogenetics?

Tooluniverse Phylogenetics fits situations like: processing FASTA/PHYLIP/Nexus/Newick files; computing phylogenetic metrics; comparing taxa groups; answering questions about alignments.

How do I install Tooluniverse Phylogenetics in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a claude-code`. Or copy the skill folder (skills/bio/tooluniverse-phylogenetics in wu-yc/LabClaw) into .claude/skills/tooluniverse-phylogenetics in your project. Claude Code loads it when a task matches its description.

How do I install Tooluniverse Phylogenetics in Codex?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a codex`. Or copy the skill folder (skills/bio/tooluniverse-phylogenetics in wu-yc/LabClaw) into .agents/skills/tooluniverse-phylogenetics in your project. Codex loads it when a task matches its description.

Can I use Tooluniverse Phylogenetics in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wu-yc/LabClaw --skill tooluniverse-phylogenetics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tooluniverse-phylogenetics, .gemini/skills/tooluniverse-phylogenetics, .github/skills/tooluniverse-phylogenetics and .opencode/skills/tooluniverse-phylogenetics in your project.

What does Tooluniverse Phylogenetics need to run?

Going by SKILL.md and its folder, Tooluniverse Phylogenetics needs the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Tooluniverse Phylogenetics access the network?

SKILL.md names 3 domains. As links in the text: jlsteenwyk.com, biopython.org and dendropy.org. This is read from the text; nothing was executed.

Is Tooluniverse Phylogenetics safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Tooluniverse Phylogenetics use?

No licence was found for Tooluniverse Phylogenetics or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Tooluniverse Phylogenetics use?

About 4.2k tokens (SKILL.md is roughly 17k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Tooluniverse Phylogenetics?

Skills that share tags, products or a category with Tooluniverse Phylogenetics: Gget (davila7/claude-code-templates, 33k stars), Biopython (lamm-mit/scienceclaw, 246 stars), Gget (aipoch/medical-research-skills, 1.9k stars) and Ena Database (jaechang-hits/SciAgent-Skills, 374 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse Phylogenetics?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,055 GitHub stars. The repository holds 68 skills in this directory. The repository was last updated on March 19, 2026.

Source: wu-yc/LabClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Tooluniverse Phylogenetics

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from wu-yc/LabClaw

Related

Questions about Tooluniverse Phylogenetics