Data and code for multi-layer comparative genomics of Lautropia mirabilis

This record contains organized genome files, annotations, metadata, scripts, intermediate outputs, final workbooks, figures, logs, and supplementary analysis folders supporting a multi-layer comparative genomic analysis of Lautropia mirabilis. The release includes genome FASTA files, GFF annotations, protein FASTA files, GenBank/GBFF files, assembly reports, metadata, logs, QUAST assembly-quality outputs, oral-cancer metadata, GTDB-Tk taxonomy audit outputs, FastANI analyses, Gubbins recombination-aware phylogenomics, high-quality candidate selection, pangenome analysis, Microbializer orthogroup outputs, protein annotation, AAI, phylogenomics, genomic-island analyses, PhaWeb phage/prophage analyses, HPIDB/PHI-base/DIAMOND host-interaction analyses, IntAct host-microbe interaction network files, DeepHPi outputs, Cytoscape network files, eggNOG-mapper annotation, and KEGG module completeness analysis.