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Updated checkamg download to retrieve and extract a pre-built, standardized CheckAMG database containing all required profile HMMs and cutoff files, rather than downloading individual databases from their original sources.
This ensures reproducibility across CheckAMG and database versions and avoids failures caused by upstream download links changing or disappearing.
Added the notebook build_checkamg_db.ipynb, which documents how the standardized CheckAMG database is assembled, including data sources and formatting steps.
