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 AndyZhuang/Opentest --skill tooluniverse-phylogeneticsgit clone --depth 1 https://github.com/AndyZhuang/OpentestWrote 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/andyzhuang/opentest/tooluniverse-phylogenetics)<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-phylogenetics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-phylogenetics/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/andyzhuang/opentest/tooluniverse-phylogenetics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-phylogenetics.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 | $0.00177 | $0.04507 |
| Opus 5 | $0.00088 | $0.02253 |
| Sonnet 5 | $0.00035 | $0.00901 |
| Haiku 4.5 | $0.00018 | $0.00451 |
Grade A, and why
tooluniverse-phylogenetics scanned grade A with 0 findings 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 8d 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 462 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Phylogenetics and Sequence Analysis
Comprehensive phylogenetics and sequence analysis using PhyKIT, Biopython, and DendroPy. Designed for bioinformatics questions about multiple sequence alignments, phylogenetic trees, parsimony, molecular evolution, and comparative genomics.
IMPORTANT: This skill handles complex phylogenetic workflows. Most implementation details have been moved to references/ for progressive disclosure. This document focuses on high-level decision-making and workflow orchestration.
When to Use This Skill
Apply when users:
- Have FASTA alignment files and ask about parsimony informative sites, gaps, or alignment quality
- Have Newick tree files and ask about treeness, tree length, evolutionary rate, or DVMC
- Ask about treeness/RCV, RCV, or relative composition variability
- Need to compare phylogenetic metrics between groups (fungi vs animals, etc.)
- Ask about PhyKIT functions (treeness, rcv, dvmc, evo_rate, parsimony_informative, tree_length)
- Have gene family data with paired alignments and trees
- Need Mann-Whitney U tests or other statistical comparisons of phylogenetic metrics
- Ask about bootstrap support, branch lengths, or tree topology
- Need to build trees (NJ, UPGMA, parsimony) from alignments
- Ask about Robinson-Foulds distance or tree comparison
BixBench Coverage: 33 questions across 8 projects (bix-4, bix-11, bix-12, bix-25, bix-35, bix-38, bix-45, bix-60)
NOT for (use other skills instead):
- Multiple sequence alignment generation → Use external tools (MUSCLE, MAFFT, ClustalW)
- Maximum Likelihood tree construction → Use IQ-TREE, RAxML, or PhyML
- Bayesian phylogenetics → Use MrBayes or BEAST
- Ancestral state reconstruction → Use separate tools
Core Principles
- Data-first approach - Discover and validate all input files (alignments, trees) before any analysis
- PhyKIT-compatible - Use PhyKIT functions for treeness, RCV, DVMC, parsimony, evolutionary rate (matches BixBench expected outputs)
- Format-flexible - Support FASTA, PHYLIP, Nexus, Newick, and auto-detect formats
- Batch processing - Process hundreds of gene alignments/trees in a single analysis
- Statistical rigor - Mann-Whitney U, medians, percentiles, standard deviations with scipy.stats
- Precision awareness - Match rounding to 4 decimal places (PhyKIT default) or as requested
- Group comparison - Compare metrics between taxa groups (e.g., fungi vs animals)
- Question-driven - Parse exactly what is asked and return the specific number/statistic
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.
- 8d ago First seen · 462 lines · 177 tokens per session scan A 01c633b088d2
tooluniverse-phylogenetics is a skill published in the GitHub repository AndyZhuang/Opentest (22 stars, last pushed 6mo ago), licensed MIT. It adds 177 tokens to every session and 4,507 once invoked, about $0.0009 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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