# Biopython

Primary retained Python toolkit for molecular biology sequence work.

- Repository: https://github.com/foryourhealth111-pixel/Vibe-Skills (3789 stars)
- Category: Data and ML
- License: Apache-2.0
- Last updated: 2026-10-31
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add foryourhealth111-pixel/Vibe-Skills --skill biopython -g -a claude-code -y`
Codex: `npx skills add foryourhealth111-pixel/Vibe-Skills --skill biopython -g -a codex -y`
Cursor: `npx skills add foryourhealth111-pixel/Vibe-Skills --skill biopython -g -a cursor -y`
Gemini CLI: `npx skills add foryourhealth111-pixel/Vibe-Skills --skill biopython -g -a gemini-cli -y`

## Description

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.

## 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

Do not use this skill as a catch-all for single-cell analysis, bulk RNA-seq differential expression, biological database evidence tables, protein language model training, metabolic flux modeling, or flow-cytometry file parsing. Those surfaces are either owned by another retained bio-science skill or intentionally no longer exposed as separate bundled route owners.

## Core Capabilities

Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:

The rest: https://github.com/foryourhealth111-pixel/Vibe-Skills/blob/HEAD/bundled/skills/biopython/SKILL.md