biopython

Biopython (v1.85+) delivers a comprehensive Python library for biological data analysis. It requires Python 3 and NumPy, providing modular components for sequences, alignments, database access, BLAST, structures, and phylogenetics.

| Sequence Operations | Create, modify, translate DNA/RNA/protein sequences | | File Format Handling | Parse or convert FASTA, GenBank, FASTQ, PDB, mmCIF | | NCBI Database Access | Query GenBank, PubMed, Protein, Gene, Taxonomy | | Similarity Searches | Execute BLAST locally or via NCBI, parse results |

| Alignment Work | Pairwise or multiple sequence alignments | | Structural Analysis | Parse PDB files, compute distances, DSSP assignment | | Tree Construction | Build, manipulate, visualize phylogenetic trees | | Motif Discovery | Find and score sequence patterns | | Sequence Statistics | GC content, molecular weight, melting temperature |