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biopython

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A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.

scientific-skills/Data Analysis/biopython/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

Use this skill when you need to:

- Batch-process DNA/RNA/protein sequences (translation, reverse complement, statistics) as part of a custom pipeline.
- Parse, validate, convert, or stream large bioinformatics files (FASTA/FASTQ/GenBank/PDB/mmCIF) without loading everything into memory.
- Programmatically query and download records from NCBI (GenBank, PubMed, Gene, Protein) via `Bio.Entrez`, respecting rate limits.
- Automate BLAST searches (web or local) and parse results to extract top hits and metadata.
- Build or manipulate phylogenetic trees from alignments or distance matrices (e.g., NJ trees) for downstream analysis.

> Note: For quick one-off queries, tools like **gget** may be more convenient; for multi-service API aggregation, **bioservices** may be a better fit.

## Key Features
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