etetoolkit SKILL.md skillA
etetoolkit from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/etetoolkit@v3.0Pins v3.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/etetoolkit/SKILL.md- Versions recorded
- 7
- Latest version
- v3.0, committed Oct 1, 2026
- First version recorded
- May 27, 2026
- Size
- 13,286 bytes
- Repository stars
- 53,159
- License
- MIT
Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports 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. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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 September 30, 2026. Core, phylogeny, local synthetic taxonomy and helper checks target this released package, not unreleased upstream changes. See [`references/review.md`](references/review.md) for executed coverage and limitations. Use `https://etetoolkit.github.io/ete/` for ETE 4 documentation. The …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/etetoolkit@sha256:da2e57c0e3677a42The line at the top of this page pins the label v3.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_feq5ixhkgspwo6j2)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 7 versions of this file, between May 27, 2026 and Oct 1, 2026, about one every 21 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v3.0 latest | 2026-10-01 | a92663a | 13,286 B | A | view · diff |
| v2.2 | 2026-09-30 | ce9e6e9 | 11,999 B | A | view · diff |
| v2.1 | 2026-09-02 | 1e5eeff | 11,692 B | A | view · diff |
| v2.0 | 2026-07-26 | b085e11 | 10,734 B | A | view · diff |
| v2.0 | 2026-07-23 | 53c5897 | 10,754 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 17,904 B | A | view · diff |
| v1.0 | 2026-05-27 | 0936740 | 17,899 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (13286 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
k-dense-ai/scientific-agent-skills · 53,159 stars · license MIT · pushed 2026-10-19 · 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/da2e57c0e3677a4219d0629a2c1392470f20bc3ade2809c1f0334fd84441da08
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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