ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-phylogeneticsgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-phylogenetics)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-phylogenetics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-phylogenetics/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-phylogenetics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-phylogenetics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00155 | $0.07243 |
| Opus 5 | $0.00077 | $0.03622 |
| Sonnet 5 | $0.00031 | $0.01449 |
| Haiku 4.5 | $0.00015 | $0.00724 |
Grade A, and why
tooluniverse-phylogenetics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 513 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Phylogenetics and Sequence Analysis
RULE ZERO — Check for pre-computed results FIRST
Before following any instruction below, scan the data folder for:
scogs_fungi.zip/scogs_animals.zip(BUSCO single-copy ortholog phylogenetics) → these contain the pre-computed alignments (*.faa.mafft.clipkit) and trees (*.faa.mafft.clipkit.treefile) from the original analysis. Use these directly with PhyKIT (see "BUSCO scogs questions" below). Re-running BUSCO → MAFFT → IQ-TREE from*.busco.zipfiles takes 1–6 hours AND produces slightly different numbers due to seed/version drift.*_executed.ipynb→ read withtu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'and cite its cell outputs as the authoritative answer- Pre-computed result files (CSV/TSV with names like
*results*,*tree*,*phykit*,*saturation*,*treeness*) → read directly and report the requested value - Canonical analysis scripts (
analysis.R,run_*.py,find_*.R,*.Rmd) → execute as-is and read the output
Only follow this skill's re-analysis recipe below if none of the above exist. Re-running from raw data produces different numbers than the published answer and is much slower (often 5–10× turn count).
BUSCO scogs questions (multi-species phylogenomics)
data folders with scogs_fungi.zip and/or scogs_animals.zip ship
pre-computed per-ortholog alignments (and sometimes trees). The
question asks for a metric per group, or a Mann-Whitney U / median /
ratio comparison between groups.
PRIMARY SCRIPT — both groups in one pass (use this FIRST)
When the question compares animals vs fungi (Mann-Whitney U, ratio, fold-change, paired difference), the bundled paired-comparison script extracts both zips, computes the metric per ortholog for each group, and emits ALL of: per-group summary, two-tailed Mann-Whitney U + p-value (in both orderings since U is asymmetric), paired-ortholog median diff, paired-ortholog median ratio, group-median ratio, and lowest-non-zero ratios — in one run, no aggregation step needed:
What ships with it
12 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- .env.template 234 B
- QUICK_START.md 7.8 KB
- references/parsimony_analysis.md 16 KB
- references/sequence_alignment.md 11 KB
- references/tree_building.md 14 KB
- references/troubleshooting.md 13 KB
- scripts/busco_target_orthologs.py 8.5 KB runs code
- scripts/format_alignment.py 14 KB runs code
- scripts/phykit_batch.py 8.2 KB runs code
- scripts/scogs_paired_compare.py 21 KB runs code
- scripts/scogs_phykit_pipeline.py 10 KB runs code
- scripts/tree_statistics.py 15 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 513 lines · 155 tokens per session scan A 933a9d5c6a82
tooluniverse-phylogenetics is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,680 stars, last pushed 2d ago), licensed Apache-2.0. It adds 155 tokens to every session and 7,243 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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