Genomic codon usage reveals First-Classness: large-scale empirical validation across the tree of life

This record is a biological reproducibility archive for the empirical study Genomic codon usage is structurally consistent with First-Classness across the tree of life. It contains the code, curated input datasets, verification scripts, and figure-generation pipeline required to reproduce the reported biological analyses. The package reproduces the manuscript’s principal results on genome-scale codon usage across 70,950 RefSeq species and includes extended robustness analyses on 1,447,521 GenBank entries. In particular, it reproduces the within-family codon-usage uniformity analysis, the fine-structure analysis of the split six-fold families, and the family-balanced null-model comparison reported in the manuscript. The archive also contains the computational routines used to verify the FC-derived codon-family partition employed in the biological analyses. These components are included to document the provenance of the codon-family definitions used in the paper, but the primary purpose of this record is biological reproducibility rather than standalone mathematical exposition. No external downloads are required to run the archived verification workflow from the packaged materials. Full methodological details, verification logic, and script-level documentation are provided in the Supplementary Information, which should be treated as the authoritative technical record. The accompanying README serves as a practical quick-start guide only. This record is intended to support transparent review, verification, and reuse of the empirical codon-usage analyses.