├── .gitignore ├── .gitmodules ├── License.txt ├── README.md ├── advanced_options.md ├── data └── TestSet │ ├── NC_000908.gbk │ ├── NC_018495.gbk │ ├── NC_018496.gbk │ └── NC_018497.gbk ├── link-to-server.py ├── metadata ├── country2region.tsv ├── meta_config.tsv └── metainfo.tsv ├── panX-environment.yml ├── panX-pipeline.png ├── panX.py ├── requirements.txt ├── run-TestSet.sh ├── scripts ├── cluster_collective_processing.py ├── help_concatenate-core-alignments.py ├── help_gene_presence_absence_matrix.py ├── help_pack_genes_for_download.py ├── helper_functions.py ├── pangenome_computation.py ├── sf_RNAcluster_align_makeTree.py ├── sf_association.py ├── sf_cluster_RNA.py ├── sf_cluster_protein.py ├── sf_cluster_protein_divide_conquer.py ├── sf_coreTree_json.py ├── sf_core_SNP_matrix.py ├── sf_core_diversity.py ├── sf_core_tree_build.py ├── sf_extract_metadata.py ├── sf_extract_sequences.py ├── sf_fetch_refseq.py ├── sf_gain_loss.py ├── sf_geneCluster_align_makeTree.py ├── 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