biopython
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.
npx skills add K-Dense-AI/scientific-agent-skills --skill biopython --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 1.87** (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. ## 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 -
- 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
uv pip install "biopython==1.87" Find information about specific functions rg -n "SeqIO.parse" references/sequence_io.md Find examples of specific tasks rg -n "BLAST" references/blast.md Find information about specific concepts rg -n "alignment" references/alignment.md Search for specific functions rg -n "function_name" references/*.md rg -n "example" references/sequence_io.md
What does the biopython skill 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 it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill biopython --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.