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.本仓库为题为《PanGene-O-Meter：基于基因内容的种内多样性》[Ashkenazy与Weigel；2025]的学术手稿提供补充材料。 本研究针对各分析物种提供详尽结果，涵盖构建完成的泛基因组（pan-genome）、系统发育树、基因存在/缺失的系统发育模式（phyletic patterns）以及所有计算得到的距离数据。 仓库内容如下： 1. PanGeneOmeter_*_GCS_and_other_measures_pairs.csv：包含所有成对距离计算结果 2. *.PanX_geneClusters.txt.gz：收录所有基因及其经PanX鉴定的直系同源基因簇（orthology groups）归属信息，全面呈现泛基因组结构 3. *.PanX.PhyleticPattern.01.csv：提供用于计算GCSj与GCSo指标、构建基于基因内容的系统发育树的二进制基因存在/缺失系统发育模式 4. *.IQ_Tree_BIN.treefile：基于基因内容系统发育模式构建的系统发育树文件 5. *.SingleCopy_Core1_MSA_NT.IQ_tree.GTR_FR.treefile：基于核心基因组的串联核苷酸多序列比对（Multiple Sequence Alignments, MSA）构建的系统发育树文件