phylogenetics SKILL.md skillA
phylogenetics 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/phylogenetics@v1.5Pins v1.5 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/phylogenetics/SKILL.md- Versions recorded
- 8
- Latest version
- v1.5, committed Oct 1, 2026
- First version recorded
- Jun 11, 2026
- Size
- 9,393 bytes
- Repository stars
- 56,497
- License
- MIT
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.
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
# Phylogenetics ## When to use Use this workflow for an alignment of homologous loci or proteins, a gene tree, branch support, and an interpretable tree figure. Multi-locus partitioning, concordance factors, ancestral states and dating are covered in [IQ-TREE reference](references/iqtree_inference.md). A gene tree does not establish a species tree, transmission direction, or horizontal transfer by itself. Sampling dates alone do not justify a molecular clock. ## Versions and installation Reviewed against current official documentation on 2026-10-01. The executed smoke workflow used MAFFT **7.526**, IQ-TREE **3.1.4**, FastTree **2.2.0** and ETE3 **3.1.3** on Python 3.12. ETE3 remains deliberate for this helper; ETE4 is a separate API and is not a drop-in replacement. ETE3 imports `cgi`, removed in Python 3.13. The native executables are not Python packages. Illustrative installation commands; verify executable versions after installation: ```bash conda create -n phylo -c conda-forge -c bioconda mafft iqtree fasttree trimal conda activate phylo uv venv --python 3.12 .venv-phylo uv pip install --python .venv-phylo/bin/python ete3==3.1.3 numpy six …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/phylogenetics@sha256:eef2354a8fe6c51cThe line at the top of this page pins the label v1.5, 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_ct2uzuzpn5h2wfk5)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 8 versions of this file, between Jun 11, 2026 and Oct 1, 2026, about one every 16 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.5 latest | 2026-10-01 | a92663a | 9,393 B | A | view · diff |
| v1.4 | 2026-09-30 | a0aea74 | 14,130 B | A | view · diff |
| v1.3 | 2026-09-30 | ce9e6e9 | 14,130 B | A | view · diff |
| v1.2 | 2026-07-31 | 4226ca8 | 14,102 B | A | view · diff |
| v1.1 | 2026-07-31 | bd99c01 | 14,102 B | A | view · diff |
| v1.1 | 2026-07-28 | 4fb7e0b | 14,096 B | A | view · diff |
| v1.0 | 2026-07-26 | b085e11 | 13,929 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 13,934 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 (9393 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 · 56,497 stars · license MIT · pushed 2026-11-02 · 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/eef2354a8fe6c51c2ad8a506e512326553bda52c731952598adef677ae2d67d5
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.