alterlab-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**, 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: - 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 ...