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 1.85** (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 ...