# Biopython

Comprehensive molecular biology toolkit.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Engineering
- License: Unknown
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill biopython -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill biopython -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill biopython -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill biopython -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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:

1. **Sequence Handling** - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
2. **Alignment Analysis** - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
3. **Database Access** - Bio.Entrez for programmatic access to NCBI databases
4. **BLAST Operations** - Bio.Blast for running and parsing BLAST searches
5. **Structural Bioinformatics** - Bio.PDB for working with 3D protein structures
6. **Phylogenetics** - Bio.Phylo for phylogenetic tree manipulation and visualization
7. **Advanced Features** - Motifs, population genetics, sequence utilities, and more

## Installation and Setup

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/biopython/SKILL.md