A Python toolkit for biological computing, including DNA, RNA, and protein data.

Reading and converting biology files, querying NCBI, running or parsing BLAST searches, aligning sequences, and analysing proteins or phylogenetic trees.

It helps developers work with common biology file formats, databases, sequence analysis, structures, and evolutionary trees.

biopython — Skill for Claude Code and Codex by tmolavi

Install

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.

Any agent

npx skills add tmolavi/mcp-agent-skills-hub --skill biopython

Clone the repo

git clone --depth 1 https://github.com/tmolavi/mcp-agent-skills-hub

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/tmolavi/mcp-agent-skills-hub/biopython/github.svg)](https://agentmods.dev/skills/tmolavi/mcp-agent-skills-hub/biopython)

Your own site

<a href="https://agentmods.dev/skills/tmolavi/mcp-agent-skills-hub/biopython"><img src="https://agentmods.dev/badge/skills/tmolavi/mcp-agent-skills-hub/biopython/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/tmolavi/mcp-agent-skills-hub/biopython"><img src="https://agentmods.dev/badge/skills/tmolavi/mcp-agent-skills-hub/biopython.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 49 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,424 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin 86% copy Near-identical to another mod in the catalogue.

Token cost

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	$0.00049	$0.03424
Opus 5.5	$0.00020	$0.01370
Sonnet 5.5	$0.00010	$0.00685
Haiku 4.5	$0.00005	$0.00342

Measured 2mo ago against content hash 335491aae8fb, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

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 2mo 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.

Origin

This is a copy

86% identical to biopython — 19 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.

skills/biopython/SKILL.md · 448 lines

How it starts

The opening of the file, as written. The whole thing — 448 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):

Read the full file on GitHub · 448 lines

Changes

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.

2mo ago First seen · 448 lines · 49 tokens per session scan A 335491aae8fb

Subscribe to this mod's changes

biopython is a skill published in the GitHub repository tmolavi/mcp-agent-skills-hub (9 stars, last pushed 1mo ago), licensed MIT. It adds 49 tokens to every session and 3,424 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 86% identical to biopython, differing in 19 lines, and is treated as a copy.

Languages Python Scientific ai-agents antigravity claude codex cursor geo

biopython next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
biopythontmolavi/mcp-agent-skills-hub	Skill	9	1mo ago	MIT	A	49	Claude Code, Codex
numpyG1Joshi/Agent-Skills	Skill	15	1mo ago	MIT	A	37	Claude Code, Codex
torchtalk-analyzeropendatahub-io/ai-helpers	Skill	39	3d ago	Apache-2.0	A	58	Claude Code
torchtalk-traceopendatahub-io/ai-helpers	Skill	39	3d ago	Apache-2.0	A	24	Claude Code
daskG1Joshi/Agent-Skills	Skill	15	1mo ago	MIT	A	40	Claude Code, Codex
pytorchG1Joshi/Agent-Skills	Skill	15	1mo ago	MIT	A	39	Claude Code, Codex
scikit-learnG1Joshi/Agent-Skills	Skill	15	1mo ago	MIT	A	38	Claude Code, Codex