Overview
biopython is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformati…”. The project has 46k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/biopython`.
What biopython does
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 1.87** (released 30 March 2026). It supports **Python 3.10-3.14** and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses **CVE-2025-68463** in `Bio.Entrez.Parser` when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.
What’s inside
The SKILL.md for biopython is organised into these sections:
- Overview
- When to Use This Skill
- Core Capabilities
- Installation and Setup
- Using This Skill
- 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
- 2. Alignment Analysis (Bio.Align & Bio.AlignIO)
- 3. Database Access (Bio.Entrez)
- 4. BLAST Operations (Bio.Blast)
- 5. Structural Bioinformatics (Bio.PDB)
- 6. Phylogenetics (Bio.Phylo)
- 7. Advanced Features
Installation
Add biopython to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/biopythonReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
biopython is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 45,887 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 12,066 GitHub stars over the last 34 days
Author
Topics
Frequently asked questions
- What does biopython do?
- Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
- How do I install biopython?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/biopython in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is biopython free to use?
- Yes. biopython is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does biopython come from?
- biopython ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 45,887 GitHub stars apply to that whole collection, not to this skill on its own.