Legacy Genomic codon usage Computational Demonstration and Data: Depreciated

Genomic codon usage reveals First-Classness: Computational Demonstration and Data This deposit contains Iteration 1 of the Genetic Code Analysis project. The aim of this iteration is to establish, in a fully reproducible and operational manner, the structural organisation of the standard genetic code as revealed through codon-orbit structure and First-Classness (FC) measures, independently of chemical or biochemical interpretation. Using aggregated RefSeq codon-usage data drawn from 70,425 species, the included pipeline computes ENC and FC compliance metrics across the full dataset and generates the figures reported in the accompanying paper. The core FC compliance metric — the ratio of within-orbit to between-orbit codon-usage variance — is evaluated against a 10,000-permutation null model, yielding the Z-score and empirical P-value reported in the manuscript. An orbit-by-orbit analysis characterises FC compliance across all 21 degeneracy families, demonstrating a systematic structural gradient consistent with the mathematical constraints of the κ/ρ orbit framework. A Serine/Leucine tension analysis and a paired ciliate nuclear/mitochondrial comparison are included as auxiliary analyses corroborating the primary structural result. This package has been depreciated and replaced with a cut down version for publication