etetoolkit SKILL.md skillA
etetoolkit from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/etetoolkit@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/etetoolkit/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 21,381 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene family evolution, annotated tree figures.
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: Phylogenetic Tree Analysis and Visualization ## Overview ETE Toolkit (ETE3) is a Python framework for phylogenetic tree exploration, manipulation, and publication-quality visualization. It supports reading and writing Newick, NHX, PhyloXML, and NeXML formats, rich node annotation, programmatic tree traversal, NCBI taxonomy integration, and a flexible rendering engine for customizable tree figures. ETE3 is widely used in comparative genomics, phylogenomics, and evolutionary biology workflows. ## When to Use - Parse phylogenetic trees from Newick, NHX, PhyloXML, or NeXML files and programmatically traverse or modify topology - Annotate tree nodes with metadata (bootstrap values, gene names, taxonomic ranks, expression data) for visualization or downstream analysis - Render publication-quality tree figures with custom node shapes, colors, branch widths, and face decorations using TreeStyle and NodeStyle - Map NCBI taxonomy IDs to lineage information, validate species names, or build taxonomy-aware trees - Compute evolutionary statistics: branch lengths, tree distances (Robinson-Foulds), LCA queries, monophyly tests …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/etetoolkit@sha256:947411838f544634The line at the top of this page pins the label git:20260428.81ea2d2, 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_udb7flncz3vdn3qk)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 34 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 21,381 B | A | view · diff |
| git:20260414.65bebbb | 2026-04-14 | 65bebbb | 21,513 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 21,192 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 (21381 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_udb7flncz3vdn3qk GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/etetoolkit GET https://markdownregistry.com/api/v1/blob/947411838f544634baeee1a564ded0990e50c9ebda0d7bb6e17c17bb0e2ead0e
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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