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etetoolkit

etetoolkit is a skill for Claude Code from jimmc414/Kosmos. It costs 46 tokens per session (4,512 once invoked), scanned B, original, no licence file.

A toolkit for working with phylogenetic trees, diagrams that show how species or genes are related through evolution.

In plain words
What is it for?
Use it to manipulate Newick or NHX trees, study orthologs and paralogs, query NCBI taxonomy, detect evolutionary events, and create PDF or SVG visualizations.
Why use it?
It removes much of the manual work involved in editing tree files, detecting evolutionary events, and connecting genes with taxonomic information.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the scientific-skills plugin — 119 skills shipped together

not rated 605repo +1 28d ago B scan 46 tokens no licence

Good fit Use it to manipulate Newick or NHX trees, study orthologs and paralogs, query NCBI taxonomy, detect evolutionary events, and create PDF or SVG visualizations.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jimmc414/kosmos/etetoolkit
View source ↗ jimmc414/Kosmos
Install

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.

Any agent
npx skills add jimmc414/Kosmos --skill etetoolkit
Clone the repo
git clone --depth 1 https://github.com/jimmc414/Kosmos

Made for: Claude Code.

Or install scientific-skills, the plugin that ships this one along with the rest of its 119 skills.

Wrote 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.

agentmods badge for etetoolkit

README.md
[![agentmods](https://agentmods.dev/badge/skills/jimmc414/kosmos/etetoolkit/github.svg)](https://agentmods.dev/skills/jimmc414/kosmos/etetoolkit)
Your own site
<a href="https://agentmods.dev/skills/jimmc414/kosmos/etetoolkit"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/etetoolkit/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.

agentmods 80×15 button for etetoolkit

Your own site · 80×15
<a href="https://agentmods.dev/skills/jimmc414/kosmos/etetoolkit"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/etetoolkit.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,512 The whole file, excluding the scripts and references it only reads on demand.
Security scan B 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00046 $0.04512
Opus 5.5 $0.00018 $0.01805
Sonnet 5.5 $0.00009 $0.00902
Haiku 4.5 $0.00005 $0.00451

Measured 2mo ago against content hash 31fe1b501aee, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade B, and why

etetoolkit scanned grade B with 1 finding 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 2mo ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/quick_visualize.py, scripts/tree_operations.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Asks for rootmediumPrivilege escalation

A mod that escalates privileges can change anything on the machine, not only the project.

sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg
kosmos-claude-scientific-skills/scientific-skills/etetoolkit/SKILL.md · 618 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

5 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.

Changes

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.

  1. 2mo ago First seen · 618 lines · 46 tokens per session scan B 31fe1b501aee

Subscribe to this mod's changes

etetoolkit is a skill published in the GitHub repository jimmc414/Kosmos (605 stars, last pushed 28d ago), with no licence file. It adds 46 tokens to every session and 4,512 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it B with 1 finding (asks for root). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific
Related

etetoolkit compared with skills from other repositories

etetoolkit next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
etetoolkitjimmc414/KosmosSkill60528d agononeB46Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k2d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code