H5N1 Influenza A Virus Genomes: Codon Usage, Host Adaptation, and Temporal-Geographic Metadata n=139,000

This dataset contains 139,000 complete H5N1 influenza A virus sequences sourced from NCBI, processed using local Python and Bioinformatics scripts. Sequences were filtered for completeness, aligned with MAFFT (using --parttree --retree 1 --maxiterate 0 for scalability), and trimmed using custom gap-based methods.
Codon usage metrics including ENc, CAI (relative to human and avian reference sets), GC3, RSCU, CPB, PR2, and mutation burden were computed per sequence.
Temporal (year) and geographic (country/city) metadata were extracted from FASTA headers. Includes aligned FASTA, codon metrics CSV, QC reports, and plots for our upcoming journal article.
Now being shared via: https://figshare.com/s/036ddf020b4b479db080