Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill genome-distance-and-species-delineationgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/genome-distance-and-species-delineation)<a href="https://agentmods.dev/skills/gptomics/bioskills/genome-distance-and-species-delineation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/genome-distance-and-species-delineation/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/genome-distance-and-species-delineation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/genome-distance-and-species-delineation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00218 | $0.07502 |
| Opus 5 | $0.00109 | $0.03751 |
| Sonnet 5 | $0.00044 | $0.01500 |
| Haiku 4.5 | $0.00022 | $0.00750 |
Grade A, and why
bio-comparative-genomics-genome-distance-and-species-delineation scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_r220_data.tar.gz Copies of this mod
1 near-identical copy found in the catalogue:
- bio-comparative-genomics-genome-distance-and-species-delineation — 98% identical, 14 lines differ
How it starts
The opening of the file, as written. The whole thing — 438 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: skani 0.2.5+ (Shaw & Yu 2023 Nat Methods 20:1661; bluenote-1577/skani), FastANI 1.34+ (Jain 2018 Nat Commun 9:5114), pyani 0.3.0+ (Pritchard 2016 Anal Methods 8:12), pyskani 0.1+ (Larralde 2025), OrthoANI 1.40+ (Lee 2016 Int J Syst Evol Microbiol 66:1100), OrthoANIu 1.2+, GTDB-Tk 2.7.1+ (Chaumeil 2022 Bioinformatics 38:5315), GTDB release 220 (2024-Q3+), TYGS web (Meier-Kolthoff & Goker 2019 Nat Commun 10:2182), GGDC v3.0 (web), Mash 2.3+ (Ondov 2016 Genome Biol 17:132), Dashing 2 (Baker & Langmead 2023 Genome Res 33:1218), CompareM 0.1.2+ for AAI (Parks/Cherubini), pyANI 0.3.1+, BLAT 36+, DIAMOND 2.1+. JSpeciesWS web (Richter et al 2016 Bioinformatics 32:929).
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
skani --version;fastANI --version;gtdbtk --version;mash --version;pyani --version - Python:
pip show gtdbtk pyani
If code throws GTDB-Tk database not found, skani sketch incompatible, Mash sketch version, these tools have database-version coupling: GTDB-Tk requires the GTDB release matched to the binary version; Mash/skani sketches are forward-compatible but not always backward. Check gtdbtk check_install for database completeness.
Genome Distance and Species Delineation
"Are these genomes the same species, and what species are they?" -> Prokaryote species delineation has shifted from 16S rRNA identity (now considered insufficient at < 98.7%) to whole-genome ANI at a 95% threshold (Jain 2018 Nat Commun 9:5114; corroborating Goris 2007 and Konstantinidis 2005). The modern operational standard for taxonomy is GTDB-Tk (Chaumeil 2020/2022 Bioinformatics 38:5315), which assigns genomes to the Genome Taxonomy Database (GTDB) using ANI radius + marker-gene placement. skani (Shaw & Yu 2023 Nat Methods 20:1661) has replaced FastANI as the default ANI tool in GTDB-Tk 2.4+ for being 20-30x faster while maintaining accuracy. The 95% ANI threshold is robust but not absolute -- the species circumscription radius varies by genus (Parks 2018 Nat Biotech 36:996).
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 438 lines · 218 tokens per session scan A 5ab7a1216d36
bio-comparative-genomics-genome-distance-and-species-delineation is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 28d ago), licensed MIT. It adds 218 tokens to every session and 7,502 once invoked, about $0.0011 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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