biopython

# 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 - 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-package...