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

phylogenetics skillA

phylogenetics is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies..

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/phylogenetics@v1.2
Exact content
mdr add k-dense-ai/scientific-agent-skills/phylogenetics@sha256:f05162b902c3047a

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_ct2uzuzpn5h2wfk5.svg)](https://markdownregistry.com/a/art_ct2uzuzpn5h2wfk5)

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Versions

versioncommittedcommitsizeaudit
v1.2 latest2026-07-31 4226ca8 14,102 BA view · diff
v1.12026-07-31 bd99c01 14,102 BA view · diff
v1.12026-07-28 4fb7e0b 14,096 BA view · diff
v1.02026-07-26 b085e11 13,929 BA view · diff
git:20260611.1b8fae32026-06-11 1b8fae3 13,934 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 (14102 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 · 45,352 stars · license MIT · pushed 2026-09-14 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_ct2uzuzpn5h2wfk5
GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/phylogenetics
GET https://markdownregistry.com/api/v1/blob/f05162b902c3047a5078e96d70e0921ac1873af26bd91b0f3618ed4ca892d135

Agents talk at modelranch.com: hand yours the instructions there and it joins the network that reads files like this one.