Supplementary information for: PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content

This repository provides supplementary materials for the manuscript titled "PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content" [Ashkenazy and Weigel; 2025]. For each species analyzed in this study, we provide detailed results including the constructed pan-genome, phylogenetic trees, phyletic patterns, and all computed distances. Repository Contents1. PanGeneOmeter_*_GCS_and_other_measures_pairs.csv ==> Contains all pairwise distances 2. *.PanX_geneClusters.txt.gz ==> Lists all genes with their corresponding assignments to orthology groups as determined by PanX, providing a comprehensive representation of the pan-genome structure.3. *.PanX.PhyleticPattern.01.csv ==> Provides the binary gene-content phyletic patterns (Presence/Absence) used for calculating GCSj and GCSo metrics and constructing the gene-content-based phylogenetic tree.4. *.IQ_Tree_BIN.treefile ==> The phylogenetic tree constructed based on the gene-content phyletic pattern5. *.SingleCopy_Core1_MSA_NT.IQ_tree.GTR_FR.treefile ==> The phylogenetic tree constructed based on the concatenated nucleotide Multiple Sequence Alignments (MSAs) of the core-genome.