k-dense-ai/scientific-agent-skills · skills/etetoolkit/SKILL.md

etetoolkit skillA

etetoolkit is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first..

Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.

How to install

Latest version
mdr add k-dense-ai/scientific-agent-skills/etetoolkit@v2.1
Exact content
mdr add k-dense-ai/scientific-agent-skills/etetoolkit@sha256:ad1649e47ef9a32b

Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_feq5ixhkgspwo6j2.svg)](https://markdownregistry.com/a/art_feq5ixhkgspwo6j2)

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Versions

versioncommittedcommitsizeaudit
v2.1 latest2026-09-02 1e5eeff 11,692 BA view · diff
v2.02026-07-26 b085e11 10,734 BA view · diff
v2.02026-07-23 53c5897 10,754 BA view · diff
git:20260611.1b8fae32026-06-11 1b8fae3 17,904 BA view · diff
v1.02026-05-27 0936740 17,899 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (11692 bytes)
  • pass: No zero-width or bidi control characters
  • pass: No instruction hidden inside an HTML comment
  • pass: No link to an exfiltration or paste host
  • pass: No credential-shaped string
  • pass: No instruction to send local credentials anywhere
  • pass: No text hidden with inline styles
  • pass: No prompt-injection phrasing
  • pass: No curl or wget piped into a shell
  • pass: No recursive delete of root, home or parent
  • pass: No instruction to read or print local credentials
  • pass: No base64 blob over 200 characters
  • pass: No link to a raw IP address
  • pass: No script tag

Source

GitHub

k-dense-ai/scientific-agent-skills · 43,331 stars · license MIT · pushed 2026-09-02 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_feq5ixhkgspwo6j2
GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/etetoolkit
GET https://markdownregistry.com/api/v1/blob/ad1649e47ef9a32ba442e2fbafd4a3be902f64480038b6ec6035f01d9da7dcaa