biopython

1# Biopython: Computational Molecular Biology in Python
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3## Overview
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5Biopython 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. These examples target **Biopython 1.88** (released 6 August 2026), tested here on Python 3.13. It requires Python 3.10+ and NumPy; Python 3.10 support is deprecated. Upgrade to 1.88 for its `Bio.Nexus` parser security fix, in addition to the Entrez XML fix in 1.87. See the [release notes](https://github.com/biopython/biopython/blob/biopython-188/NEWS.rst). Local example checks and external-service limits are recorded in `references/review.md`; examples requiring user files or external programs are illustrative unless listed there as exercised.
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7## When to Use This Skill
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9Use this skill when:
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11- Working with biological sequences (DNA, RNA, or protein)
12- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
13- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
14- Running BLAST searches or parsing BLAST results
15- Performing sequence alignments (pairwise or multiple sequence alignments)
16- Analyzing protein structures from PDB files
17- Creating, manipulating, or visualizing phylogenetic trees
18- Finding sequence motifs or analyzing motif patterns
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