Data and code for mobile-accessory genome architecture in the Mycobacterium gordonae complex

This record contains organized data, scripts, compressed analysis folders, intermediate outputs, final workbooks, figures, documentation files, and supplementary resources supporting a comparative genomic analysis of the Mycobacterium gordonae complex. The release is organized by analytical layer, including genome resources, annotation, phylogeny, ANI and in silico DNA-DNA relatedness, pangenome and orthology, lineage-specific protein annotation, genomic island analysis, PhaBOX/prophage analysis, mobile-accessory genome analysis, ancestral gain/loss reconstruction, synteny and enrichment outputs, MetaGraph recovery analysis, PathogenFinder2 candidate integration, and reproducible scripts. Analysis scripts are retained inside their corresponding folders to preserve computational context and reproducibility.