Agent Skill
Biopython skill
biopythonforyourhealth111-pixel/Vibe-Skillsbundled/skills/biopython/SKILL.md
Primary retained Python toolkit for molecular biology sequence work. Preferred for sequence manipulation, FASTA/FASTQ/GenBank parsing, Bio.Entrez, BLAST workflows, alignments, structures, and phylogenetics. For biological database evidence lookup, use bio-database-evidence. For single-cell workflows use scanpy. For direct literature REST API, use pubmed-database.
always on
81 tokname + description
once used
3,339 tokSKILL.md body
bundled files
779 KB
repo stars
3.8kGitHub
Install the Biopython skill
Skills CLI (Claude Code, Codex, Cursor and others)
npx skills add https://github.com/foryourhealth111-pixel/Vibe-Skills --skill biopython
Claude Code, by hand (all projects)
git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git /tmp/Vibe-Skills mkdir -p ~/.claude/skills cp -R /tmp/Vibe-Skills/bundled/skills/biopython ~/.claude/skills/biopython
For one project only, copy the folder into .claude/skills/ in that project instead. The agent picks it up when a task matches its description.
What it costs your context
Agent Skills load in three steps. Tokens counted with the o200k tokenizer; your model's count will differ a little.
| When | What loads | Cost |
|---|---|---|
| Every session | Name and description | 81 tok |
| When the agent uses it | The SKILL.md instructions | 3,339 tok |
| Only if opened | 7 bundled files (79 KB) | varies |
Until it is used, biopython costs about 17× less than the median MCP server we measured (1,363 tokens on every turn). Installing all 150 skills from foryourhealth111-pixel/Vibe-Skills would load 9,038 tokens of descriptions. Skills vs MCP study
Checks
Our checks found nothing to flag: it follows the Agent Skills specification's naming and size guidelines and doesn't pipe downloads into a shell.
Checked 2026-10-22 · method
What's inside
The headings of its SKILL.md. Read the full file on GitHub.
- Biopython: Computational Molecular Biology in Python
- 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
- General Workflow Guidelines
- Reading Documentation
- Writing Biopython Code
- Common Patterns
- Pattern 1: Fetch Sequence from GenBank
- Pattern 2: Sequence Analysis Pipeline
- Pattern 3: BLAST and Fetch Top Hits
- Pattern 4: Build Phylogenetic Tree from Sequences
- Best Practices
- Troubleshooting Common Issues
- Issue: "No handlers could be found for logger 'Bio.Entrez'"
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