bio-phylogenomics SKILL.md skillA
bio-phylogenomics from fmschulz/omics-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fmschulz/omics-skills/bio-phylogenomics@git:20261001.bf5afd6Pins git:20261001.bf5afd6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fmschulz/omics-skills
- Path
skills/bio-phylogenomics/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- Jul 12, 2026
- Size
- 6,932 bytes
- Repository stars
- 11
- License
- MIT
Build marker-gene alignments and ML trees and find closest relatives. Use when inferring phylogenies, placing genomes, choosing substitution models, or checking tree support.
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
# Bio Phylogenomics
Build marker-gene alignments and maximum-likelihood trees, identify closest relatives, and fetch the relative genomes that downstream comparisons need.
## Instructions
Tool guides, versions, and verified flags: [docs/README.md](docs/README.md).
1. Use the literature-derived analysis playbook to choose markers, reference sampling, rooting, and placement strategy for the inferred group.
2. Extract marker genes or SSU rRNA sequences for the queries and references.
3. Validate the marker and reference manifests and write a checksum-gated, fixed-seed plan; inspect `run_manifest.json`, then rerun with `--execute`:
```bash
uv run --script skills/bio-phylogenomics/scripts/run_phylogenomics.py \
markers.tsv --references references.tsv --seed 1729 \
--tree-tool veryfasttree --threads 4 --out results/bio-phylogenomics/trees
```
- `markers.tsv` columns: `marker_id fasta sequence_type` (`protein` or `nucleotide`); each FASTA holds the unaligned marker sequences.
- `references.tsv` columns: `accession path sha256`; every reference file must match its checksum before anything runs.
…Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-phylogenomics@sha256:8e6d84cc8003c5cbThe line at the top of this page pins the label git:20261001.bf5afd6, 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_2eafsensqpfzpjwp)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jul 12, 2026 and Oct 1, 2026, about one every 16 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261001.bf5afd6 latest | 2026-10-01 | bf5afd6 | 6,932 B | A | view · diff |
| git:20260905.3e49039 | 2026-09-05 | 3e49039 | 5,434 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 5,300 B | A | view · diff |
| git:20260825.bd47e68 | 2026-08-25 | bd47e68 | 5,807 B | A | view · diff |
| git:20260713.88e759d | 2026-07-13 | 88e759d | 5,683 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 5,544 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 (6932 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
fmschulz/omics-skills · 11 stars · license MIT · pushed 2026-10-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_2eafsensqpfzpjwp GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-phylogenomics GET https://markdownregistry.com/api/v1/blob/8e6d84cc8003c5cb2b9b82bcef50acb4e2a81f2c0037094b08bd894a7804b551
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.