This file contains all custom scripts used for data processing, alignment, trimming, phylogenetic tree reconstruction, site-wise and gene-wise likelihood analyses, model adequacy tests, and branch‑length calculations for this study. All scripts were developed for reproducible phylogenomic workflows following current best practices in systematic biology. All scripts are organized according to major analytical steps, from BUSCO gene extraction to alignment, trimming, gene‑tree inference, matrix construction, phylogenetic hypothesis testing, and systematic‑error diagnosis (LBA, compositional heterogeneity, ILS, GTEE). Unless otherwise specified, these scripts require standard command‑line tools (bash ≥ 4.0, GNU parallel) and widely used phylogenetic software packages (IQ‑TREE, PhyKIT, MAFFT, TrimAl, ClipKIT, BMGE, ASTRAL, SeqKit, etc.).
Zhan et al. (Tue,) studied this question.