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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-phylogeneticsgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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/alterlab-ieu/alterlab-academic-skills/alterlab-phylogenetics)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-phylogenetics"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-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/alterlab-ieu/alterlab-academic-skills/alterlab-phylogenetics"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-phylogenetics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00152 | $0.04133 |
| Opus 5 | $0.00076 | $0.02067 |
| Sonnet 5 | $0.00030 | $0.00827 |
| Haiku 4.5 | $0.00015 | $0.00413 |
Grade A, and why
alterlab-phylogenetics 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 11d 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.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
result = subprocess.run(cmd, stdout=out, stderr=subprocess.PIPE, text=True) How it starts
The opening of the file, as written. The whole thing — 414 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Phylogenetics
Overview
Phylogenetic analysis reconstructs the evolutionary history of biological sequences (genes, proteins, genomes) by inferring the branching pattern of descent. This skill covers the standard pipeline:
- MAFFT — Multiple sequence alignment
- IQ-TREE 2 — Maximum likelihood tree inference with model selection
- FastTree — Fast approximate maximum likelihood (for large datasets)
- ETE3 — Python library for tree manipulation and visualization
Installation: The aligners and tree builders are compiled CLI tools (not on PyPI). Install the binaries via bioconda or Homebrew; install the Python visualization layer with uv.
# CLI binaries — bioconda (cross-platform) ...
conda install -c bioconda mafft iqtree fasttree trimal
# ... or Homebrew on macOS (Apple Silicon): IQ-TREE/TrimAl live in the brewsci/bio tap
brew install mafft fasttree
brew tap brewsci/bio && brew install brewsci/bio/iqtree brewsci/bio/trimal # iqtree formula ships the iqtree2 binary
# Python visualization layer
uv pip install "ete3==3.1.3" # also needs numpy<2 and PyQt5 for rendering
ETE3 (3.1.3) is the last ete3 release and can be fragile to install on Python ≥3.12 (pins old numpy/PyQt5). If
t.render()fails, fall back to writing the Newick tree and viewing it in FigTree/iTOL, or use the maintained successorete4(note: ete4 changed theTreeStyle/renderAPI, so the snippets below are ete3-specific).
When to Use This Skill
Use phylogenetics when:
- Evolutionary relationships: Which organism/gene is most closely related to my sequence?
- Viral phylodynamics: Trace outbreak spread and estimate transmission dates
- Protein family analysis: Infer evolutionary relationships within a gene family
- Horizontal gene transfer detection: Identify genes with discordant species/gene trees
- Ancestral sequence reconstruction: Infer ancestral protein sequences
- Molecular clock analysis: Estimate divergence dates using temporal sampling
- GWAS companion: Place variants in evolutionary context (e.g., SARS-CoV-2 variants)
- Microbiology: Species phylogeny from 16S rRNA or core genome phylogeny
What ships with it
3 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.
- 11d ago First seen · 414 lines · 152 tokens per session scan A c3ba902acd49
alterlab-phylogenetics is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 6d ago), licensed MIT. It adds 152 tokens to every session and 4,133 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
ob-hrm-scale-adaptor
A guide for adapting organisational behaviour and human-resources survey scales across languages and cultures. It covers permission checks, translation and back-translation, expert review, participant interviews, and tests of whether groups interpret the scale comparably.
r-spss-syntax-architect
A guide for turning research hypotheses into repeatable R or SPSS code for statistical analysis. It covers panel data, where the same companies or other units are observed over time, as well as interaction effects, curves, and mediation.
thesis-consistency-audit
A consistency audit for quantitative master’s and doctoral theses in management, finance, or strategy. It checks whether numbers, tables, analyses, and claims agree, and can inspect hidden author information in office documents.
management-figure
A chart-making toolkit for evidence-based management, finance, and strategy research. It creates publication-ready plots from regression results and tracking data, including coefficient, interaction, group-comparison, trend, and curved-relationship charts.
reproducibility-architect
A guide for packaging research so another person can rerun its data processing and analysis. A replication package is the project files, instructions, code, data guidance, and software details needed to reproduce published results.
journal-submission-scout
A research tool for choosing a journal for a completed paper. It searches for journals that publish similar work, compares public information such as citation data, fees, open-access listing, and review practices, and screens for warning signs of predatory journals, which charge authors without providing trustworthy publishing services.