biopython
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
npx skills add FreedomIntelligence/OpenClaw-Medical-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 1.85** (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 computation
- 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
Find information about specific functions grep -n "SeqIO.parse" references/sequence_io.md Find examples of specific tasks grep -n "BLAST" references/blast.md Find information about specific concepts grep -n "alignment" references/alignment.md Search for specific functions grep -n "function_name" references/*.md grep -n "example" references/sequence_io.md Find all occurrences of a module
What does the biopython skill do?
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.