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 agentmods add skills/thesecondfox/skill/biopythonnpx skills add thesecondfox/skill --skill biopythongit clone --depth 1 https://github.com/thesecondfox/skillWrote 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/thesecondfox/skill/biopython)<a href="https://agentmods.dev/skills/thesecondfox/skill/biopython"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/biopython.svg" alt="Measured on agentmods" 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 | $0.00076 | $0.03369 |
| Opus 5 | $0.00038 | $0.01684 |
| Sonnet 5 | $0.00015 | $0.00674 |
| Haiku 4.5 | $0.00008 | $0.00337 |
Grade A, and why
biopython 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 2d 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.
This is a copy
91% identical to biopython — 7 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 442 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Biopython: Computational Molecular Biology in Python
Overview
Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is Biopython 1.85 (released January 2025), which supports Python 3 and requires NumPy.
When to Use This Skill
Use this skill when:
- Working with biological sequences (DNA, RNA, or protein)
- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
- Running BLAST searches or parsing BLAST results
- Performing sequence alignments (pairwise or multiple sequence alignments)
- Analyzing protein structures from PDB files
- Creating, manipulating, or visualizing phylogenetic trees
- Finding sequence motifs or analyzing motif patterns
- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
- Performing structural bioinformatics tasks
- Working with population genetics data
- Any other computational molecular biology task
Core Capabilities
Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:
- Sequence Handling - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
- Alignment Analysis - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
- Database Access - Bio.Entrez for programmatic access to NCBI databases
- BLAST Operations - Bio.Blast for running and parsing BLAST searches
- Structural Bioinformatics - Bio.PDB for working with 3D protein structures
- Phylogenetics - Bio.Phylo for phylogenetic tree manipulation and visualization
- Advanced Features - Motifs, population genetics, sequence utilities, and more
Installation and Setup
Install Biopython using pip (requires Python 3 and NumPy):
What ships with it
7 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.
- 2d ago First seen · 442 lines · 76 tokens per session scan A bee6b6274224
biopython is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 76 tokens to every session and 3,369 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. It is 91% identical to biopython, differing in 7 lines, and is treated as a copy.
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