Biopython

If you're doing molecular biology work in Python, this is the standard toolkit. It handles the full range: parsing FASTA/GenBank/PDB files, querying NCBI databases through Bio.Entrez, running BLAST searches, manipulating sequences, analyzing protein structures, and building phylogenetic trees. The documentation here is well organized by module, so you can jump straight to sequence I/O, alignment, or structural bioinformatics depending on what you need. Version 1.85 as of January 2025. One thing to know: NCBI requires you to set your email address before making Entrez queries, and you'll want an API key if you're doing more than casual searches. The skill recommends gget for quick BLAST jobs instead.