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, which supports Python 3 and requires NumPy.

Version note (1.78+): The command-line application wrappers in Bio.Blast.Applications (Ncbiblastn/p/x...Commandline, NcbimakeblastdbCommandline) and Bio.Align.Applications (ClustalOmegaCommandline, MuscleCommandline) were deprecated in 1.78 and removed — they no longer import. Call BLAST+/aligner executables via subprocess instead (see references/blast.md and references/alignment.md). Bio.pairwise2 is deprecated; use Bio.Align.PairwiseAligner.

When to Use This Skill

Use this skill when: