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 userInner/SKILLS --skill etetoolkit-k-dense-ai-scientific-agent-skillsgit clone --depth 1 https://github.com/userInner/SKILLSWrote 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/userinner/skills/etetoolkit-k-dense-ai-scientific-agent-skills)<a href="https://agentmods.dev/skills/userinner/skills/etetoolkit-k-dense-ai-scientific-agent-skills"><img src="https://agentmods.dev/badge/skills/userinner/skills/etetoolkit-k-dense-ai-scientific-agent-skills/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/userinner/skills/etetoolkit-k-dense-ai-scientific-agent-skills"><img src="https://agentmods.dev/badge/skills/userinner/skills/etetoolkit-k-dense-ai-scientific-agent-skills.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00091 | $0.02838 |
| Opus 5 | $0.00046 | $0.01419 |
| Sonnet 5 | $0.00018 | $0.00568 |
| Haiku 4.5 | $0.00009 | $0.00284 |
Grade A, and why
etetoolkit 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 12d 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.
This is a copy
100% identical to etetoolkit — 19 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 328 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ETE Toolkit 4
Scope
Use ETE 4 to work with an existing tree:
- Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write Newick trees
- Compare topologies and calculate phylogenetic distances
- Find repeated subtree topologies with
TreePattern - Analyze gene trees with
PhyloTree - Query local NCBI or GTDB taxonomy databases
- Explore large trees interactively with SmartView
- Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview
ETE does not replace sequence alignment or phylogenetic inference software. For raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or another inference tool; then load the resulting tree into ETE.
Current Target
This skill targets ETE 4.4.0, released September 3, 2025 and verified as the current PyPI release on July 23, 2026.
Use https://etetoolkit.github.io/ete/ for ETE 4 documentation. The
etetoolkit.org/docs/latest pages are legacy ETE 3 documentation despite the
URL name.
Do not silently translate these examples back to ETE 3:
- Package and import:
ete4, notete3 - File input: pass an open file object; use strings for Newick text and do not rely on path-string heuristics retained in ETE 4.4.0
- Newick selection:
parser=, notformat= - Node metadata:
props,add_prop(), andadd_props() - Iteration:
leaves(),descendants(), and related methods return iterators - Predicates:
node.is_leafandnode.is_rootare properties, not methods - Node lookup:
tree["name"], nottree & "name"
For porting older code, load
references/migration-ete3-to-ete4.md.
Installation
Install the pinned base package:
uv pip install "ete4==4.4.0"
Add only the visualization extra required by the workflow:
# SmartView static PNG screenshots
uv pip install "ete4[render-sm]==4.4.0"
# Legacy Qt renderer for PNG, PDF, and SVG
uv pip install "ete4[treeview]==4.4.0"
Confirm the active environment:
What ships with it
10 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.
- effecta.manifest.json 1022 B
- LICENSE 1.0 KB
- NOTICE.effecta 337 B
- references/api_reference.md 14 KB
- references/migration-ete3-to-ete4.md 11 KB
- references/taxonomy.md 8.8 KB
- references/visualization.md 12 KB
- references/workflows.md 15 KB
- scripts/quick_visualize.py 15 KB runs code
- scripts/tree_operations.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.
- 12d ago First seen · 328 lines · 91 tokens per session scan A e9637685939b
etetoolkit is a skill published in the GitHub repository userInner/SKILLS (3 stars, last pushed 5d ago), licensed Apache-2.0. It adds 91 tokens to every session and 2,838 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. It is 100% identical to etetoolkit, differing in 19 lines, and is treated as a copy.
Other skills, from other repositories
experiment-planner
Use when exploring, continuing, or accepting a deep-learning or computer-science research idea. Converts claims into pilot-first experiment matrices covering diagnostics, failure analysis, authorized execution, evaluation, and paper-story viability.
paper-refinement-skills
Use when refining research-paper prose or section logic, including abstracts, introductions, related work, methods, captions, conclusions, and rebuttals. Improves clarity, concision, transitions, terminology, notation, and venue-appropriate style without inventing evidence.
paper-visual-craft
Use when designing, redrawing, or validating research-paper figures and tables, including Matplotlib plots, LaTeX tables, benchmarks, captions, legends, annotations, color, and typography. Preserves exact evidence and checks rendered PDFs for clipping, overlap, and readability.
paper-framework-figure-studio-pro
Use when planning a source-grounded method overview, architecture, pipeline, system/data-flow, mechanism, or agent-workflow figure for a CS or deep-learning paper. Produces an editable figure brief before image generation or manual redrawing; not for plots, tables, or general prose.
paper-section-playbook
Use when planning, drafting, or restructuring the Abstract, Introduction, Related Work, Method, Experiments, or Conclusion of a computer-vision, 3D-perception, or autonomous-driving paper. Provides section- and paragraph-level methodology; use paper-refinement-skills for sentence-level polish.
arxiv-reader
A paper-reading tool for arXiv, a website where researchers share scientific papers. Give it an arXiv ID or URL and it uses an AI agent to classify the paper and print detailed reading notes.