├── Dockerfile ├── LICENSE.txt ├── PGG_User_Manual.docx ├── QUICKSTART ├── README.md └── pangenome ├── bin ├── BLAST2GO │ ├── plasmidDB2GO_lookup.txt │ ├── plasmid_finder_rep.pep │ ├── plasmid_finder_rep.pep.phr │ ├── plasmid_finder_rep.pep.pin │ ├── plasmid_finder_rep.pep.psq │ ├── plasmid_finder_rep.seq │ ├── plasmid_finder_rep.seq.nhr │ ├── plasmid_finder_rep.seq.nin │ └── plasmid_finder_rep.seq.nsq ├── FELIX │ ├── ANI_cluster.pl │ ├── ANI_redundant.pl │ ├── PGGanno_coverage_regions.pl │ ├── QSUB_ANNO_CMD │ ├── QSUB_ITER_CMD │ ├── QSUB_MA_CMD │ ├── attribute_compare.pl │ ├── cluster_ANI_mash.pl │ ├── compute_new_clusters.pl │ ├── compute_pgg_graph.pl │ ├── core_neighbor_finder.pl │ ├── filter_anomalies.pl │ ├── gff_nuc_natt.pl │ ├── iterate_pgg_graph.pl │ ├── iterate_pgg_graph_grid.pl │ ├── kmer_bucket_file_sort.c │ ├── low_coverage_regions.pl │ ├── make_hierarchy_file.pl │ ├── mask_lower_case.pl │ ├── medoid_blast_engineered.pl │ ├── medoid_blast_paralogs.pl │ ├── medoid_blast_search.pl │ ├── multi_attribute_overlaps.pl │ ├── multi_pgg_annotate_new.pl │ ├── orf_medoids.pl │ ├── parse_CALLS_blast.pl │ ├── parse_CALLS_fasta.pl │ ├── parse_covid_gb.pl │ ├── parse_cpustats.pl │ ├── pgg_annotate.pl │ ├── pgg_combine_edges.pl │ ├── pgg_edge_multifasta.pl │ ├── pgg_match_summary.pl │ ├── run_all_vs_all_mash.pl │ ├── run_multiple_mash.pl │ ├── run_sketches_mash.pl │ ├── run_type_vs_all_mash.pl │ ├── single_copy_core.pl │ ├── split_genomes.pl │ └── summarize_alignment.R ├── HMMER2GO │ ├── .gitignore │ ├── LICENSE │ ├── bin │ │ └── hmmer2go │ └── lib │ │ ├── App │ │ ├── Cmd.pm │ │ └── Cmd │ │ │ ├── ArgProcessor.pm │ │ │ ├── Command.pm │ │ │ ├── Command │ │ │ ├── commands.pm │ │ │ ├── help.pm │ │ │ └── version.pm │ │ │ ├── Plugin.pm │ │ │ ├── Setup.pm │ │ │ ├── Simple.pm │ │ │ ├── Subdispatch.pm │ │ │ ├── Subdispatch │ │ │ └── DashedStyle.pm │ │ │ ├── Tester.pm │ │ │ ├── Tester │ │ │ └── CaptureExternal.pm │ │ │ └── Tutorial.pod │ │ ├── HMMER2GO.pm │ │ ├── HMMER2GO │ │ ├── Command.pm │ │ └── Command │ │ │ ├── fetchmap.pm │ │ │ ├── getorf.pm │ │ │ ├── map2gaf.pm │ │ │ ├── mapterms.pm │ │ │ ├── mapterms.pm.orig │ │ │ ├── pfamsearch.pm │ │ │ └── run.pm │ │ ├── IPC │ │ └── System │ │ │ └── Simple.pm │ │ └── Module │ │ └── Pluggable │ │ └── Object.pm ├── Newick-ruby │ ├── newickAlphabetize │ ├── newickCompare │ ├── newickDist │ ├── newickDraw │ ├── newickReorder │ ├── newickReroot │ └── newickTaxa ├── UPGMA_tree_batch ├── align_clusters.pl ├── analysis │ ├── calculate_distance_matrix.pl │ ├── calculate_distance_matrix_paralogs.pl │ ├── cluster_number_variation.pl │ ├── cluster_synteny.pl │ ├── create_syntany_db.pl │ └── parse_panoct.pl ├── check_att_files.pl ├── check_combined_files.pl ├── choose_centroids.pl ├── clean_multifasta.pl ├── cluster_alt_genomes.R ├── cluster_consensus.pl ├── cluster_consensus_synteny.pl ├── cluster_genomes.R ├── cluster_size.pl ├── compute_pangenome.R ├── compute_pangenome_ani.pl ├── convert_att_file_to_hsh.pl ├── core.HMM ├── core_cluster_histogram.R ├── core_hmm_checker.pl ├── core_hmm_checker_post.pl ├── core_hmm_checker_prep.pl ├── create_meta_groupings.pl ├── create_mev_table.pl ├── download_ncbi_annotation.pl ├── ftp_download_ncbi_annotation.pl ├── gene_order.pl ├── genome_properties │ ├── evaluation_order │ └── genome_properties.pl ├── get_collection_date.pl ├── get_dna_for_loci.pl ├── get_go_annotations.pl ├── get_patric_files.pl ├── hclust_complete_newick.R ├── kmer_matrix_maker.pl ├── make_BSR_trees.sh ├── make_trees.R ├── map_annotation_to_fgis.pl ├── map_go_via_blast.pl ├── muscle ├── neighbor_joining_tree_batch ├── new_plot_pangenome.R ├── pan_chromosome │ ├── db2circle_rainbow.ph │ ├── db2circle_rainbow_flatfile.spl │ ├── fig2dev │ ├── graphical_elements_rainbow.pl │ ├── make_db2circle_genome_att.pl │ └── make_pan_chromosome_fig.sh ├── pangenome_statistics.pl ├── panoct.pl ├── panoct_multifasta.pl ├── paralog_matchtable.pl ├── parse_genbank_files.pl ├── plot_pangenome.R ├── rgi │ ├── .gitignore │ ├── _data │ │ └── card.json │ ├── _db │ │ ├── .gitignore │ │ ├── protein.db.dmnd │ │ ├── protein.db.phr │ │ ├── protein.db.pin │ │ ├── protein.db.psq │ │ └── proteindb.fsa │ ├── _docs │ │ ├── INSTALL │ │ ├── README │ │ └── rgi.py.diff │ ├── blastnsnp.py │ ├── clean.py │ ├── contigToORF.py │ ├── contigToProteins.py │ ├── convertJsonToTSV.py │ ├── create_gff3_file.py │ ├── filepaths.py │ ├── formatJson.py │ ├── fqToFsa.py │ ├── jcvi.rgi.py │ ├── load.py │ ├── orig.rgi.py │ ├── rgi.py │ ├── rrna.py │ └── tests │ │ └── protein.fasta ├── run_pangenome.pl ├── run_panoct.pl ├── sample_medioids.R ├── split_fasta.pl ├── sub_matrix.R └── summarize_fgis.pl ├── doc ├── OUT_FILE_DESCRIPTIONS └── gpl-2.0.txt └── lib ├── File ├── Slurp.pm └── Touch.pm ├── Pangenome ├── BLASTResult.pm ├── Cluster.pm ├── Clusterset.pm ├── Config.pm ├── ConsistencyChecks.pm ├── DB │ └── ProkSybase.pm ├── Download.pm ├── Method │ ├── PanOCT │ │ ├── Parser.pm │ │ └── Run.pm │ └── RunI.pm ├── 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