├── .github └── workflows │ ├── black_lint.yml │ ├── check_doc.yml │ ├── check_recipes.yml │ ├── main.yml │ └── pypi.yml ├── .readthedocs.yaml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── VERSION ├── docs ├── Makefile ├── _static │ ├── drawspot_example.png │ ├── evolution.png │ ├── gephi.gif │ ├── logo.png │ ├── projection.png │ ├── proksee_exemple_A_baumannii_AYE.png │ ├── proksee_metadata_example.png │ ├── resampling.png │ ├── runtimes.png │ ├── tile_plot_dendro.png │ ├── tile_plot_no_dendro.png │ ├── tutorial │ │ ├── U-shape.gif │ │ └── tile_plot.png │ ├── u_plot.png │ └── workflow.png ├── api │ ├── api_ref.md │ ├── indice_and_table.md │ ├── ppanggolin.RGP.md │ ├── ppanggolin.align.md │ ├── ppanggolin.annotate.md │ ├── ppanggolin.cluster.md │ ├── ppanggolin.context.md │ ├── ppanggolin.figures.md │ ├── ppanggolin.formats.md │ ├── ppanggolin.graph.md │ ├── ppanggolin.info.md │ ├── ppanggolin.md │ ├── ppanggolin.meta.md │ ├── ppanggolin.metrics.md │ ├── ppanggolin.mod.md │ ├── ppanggolin.nem.md │ ├── ppanggolin.projection.md │ ├── ppanggolin.utility.md │ └── ppanggolin.workflow.md ├── conf.py ├── dev │ ├── buildDoc.md │ └── contribute.md ├── index.md ├── make.bat └── user │ ├── MSA.md │ ├── Modules │ ├── moduleAnalyses.md │ ├── moduleOutputs.md │ └── modulePrediction.md │ ├── PangenomeAnalyses │ ├── pangenomeAnalyses.md │ ├── pangenomeAnnotation.md │ ├── pangenomeCluster.md │ ├── pangenomeFigures.md │ ├── pangenomeGraph.md │ ├── pangenomeGraphOut.md │ ├── pangenomeInfo.md │ ├── pangenomeMetric.md │ ├── pangenomePartition.md │ ├── pangenomeStat.md │ └── pangenomeWorkflow.md │ ├── QuickUsage │ ├── quickAnalyses.md │ ├── quickOutputs.md │ └── quickWorkflow.md │ ├── RGP │ ├── rgpAnalyses.md │ ├── rgpClustering.md │ ├── rgpOutputs.md │ └── rgpPrediction.md │ ├── align.md │ ├── genomicContext.md │ ├── install.md │ ├── metadata.md │ ├── practicalInformation.md │ ├── projection.md │ ├── writeFasta.md │ └── writeGenomes.md ├── ppanggolin ├── RGP │ ├── __init__.py │ ├── genomicIsland.py │ ├── rgp_cluster.py │ └── spot.py ├── __init__.py ├── align │ ├── __init__.py │ └── alignOnPang.py ├── annotate │ ├── __init__.py │ ├── annotate.py │ ├── rRNA_DB │ │ ├── RF00001.cm │ │ ├── RF00177.cm │ │ ├── RF01959.cm │ │ ├── RF02540.cm │ │ ├── RF02541.cm │ │ ├── rRNA_arch.cm │ │ ├── rRNA_arch.cm.i1f │ │ ├── rRNA_arch.cm.i1i │ │ ├── rRNA_arch.cm.i1m │ │ ├── rRNA_arch.cm.i1p │ │ ├── rRNA_bact.cm │ │ ├── rRNA_bact.cm.i1f │ │ ├── rRNA_bact.cm.i1i │ │ ├── rRNA_bact.cm.i1m │ │ └── rRNA_bact.cm.i1p │ └── synta.py ├── cluster │ ├── __init__.py │ └── cluster.py ├── context │ ├── __init__.py │ └── searchGeneContext.py ├── edge.py ├── figures │ ├── __init__.py │ ├── draw_spot.py │ ├── drawing.py │ ├── tile_plot.py │ └── ucurve.py ├── formats │ ├── __init__.py │ ├── readBinaries.py │ ├── writeAnnotations.py │ ├── writeBinaries.py │ ├── writeFlatGenomes.py │ ├── writeFlatMetadata.py │ ├── writeFlatPangenome.py │ ├── writeMSA.py │ ├── writeMetadata.py │ ├── writeSequences.py │ └── write_proksee.py ├── geneFamily.py ├── genetic_codes.py ├── genome.py ├── graph │ ├── __init__.py │ └── makeGraph.py ├── info │ ├── __init__.py │ └── info.py ├── main.py ├── meta │ ├── __init__.py │ └── meta.py ├── metadata.py ├── metrics │ ├── __init__.py │ ├── fluidity.py │ └── metrics.py ├── mod │ ├── __init__.py │ └── module.py ├── nem │ ├── NEM │ │ ├── genmemo.c │ │ ├── genmemo.h │ │ ├── lib_io.c │ │ ├── lib_io.h │ │ ├── nem_alg.c │ │ ├── nem_alg.h │ │ ├── nem_exe.c │ │ ├── nem_exe.h │ │ ├── nem_hlp.c │ │ ├── nem_hlp.h │ │ ├── nem_mod.c │ │ ├── nem_mod.h │ │ ├── nem_nei.c │ │ ├── nem_nei.h │ │ ├── nem_rnd.c │ │ ├── nem_rnd.h │ │ ├── nem_stats.pyx │ │ ├── nem_typ.h │ │ ├── nem_ver.c │ │ └── nem_ver.h │ ├── __init__.py │ ├── partition.py │ └── rarefaction.py ├── pangenome.py ├── projection │ ├── __init__.py │ └── projection.py ├── region.py ├── utility │ ├── __init__.py │ └── utils.py ├── utils.py └── workflow │ ├── __init__.py │ ├── all.py │ ├── panModule.py │ ├── panRGP.py │ └── workflow.py ├── ppanggolin_env.yaml ├── pyproject.toml ├── setup.py ├── testingDataset ├── FASTA │ ├── GCF_000026905.1_ASM2690v1_genomic.fna.gz │ ├── GCF_000092665.1_ASM9266v1_genomic.fna.gz │ ├── GCF_000092685.1_ASM9268v1_genomic.fna.gz │ ├── GCF_000092685.1_ASM9268v1_genomic_MANUALLY_FRAGMENTED_top34_contigs.fna.gz │ ├── GCF_000093005.1_ASM9300v1_genomic.fna.gz │ ├── GCF_000173495.1_ASM17349v1_genomic.fna.gz │ ├── GCF_000210495.1_ASM21049v1_genomic.fna.gz │ ├── GCF_000220105.1_ASM22010v1_genomic.fna.gz │ ├── GCF_000226605.1_ASM22660v1_genomic.fna.gz │ ├── GCF_000304515.1_Cm_FSW4_genomic.fna.gz │ ├── GCF_000318545.1_ASM31854v1_genomic.fna.gz │ ├── GCF_000318785.1_ASM31878v1_genomic.fna.gz │ ├── GCF_000318805.1_ASM31880v1_genomic.fna.gz │ ├── GCF_000318825.1_ASM31882v1_genomic.fna.gz │ ├── GCF_000318865.1_ASM31886v1_genomic.fna.gz │ ├── GCF_000318925.1_ASM31892v1_genomic.fna.gz │ ├── GCF_000318945.1_ASM31894v1_genomic.fna.gz │ ├── GCF_000319105.1_ASM31910v1_genomic.fna.gz │ ├── GCF_000441655.1_ASM44165v1_genomic.fna.gz │ ├── GCF_000441775.1_ASM44177v1_genomic.fna.gz │ ├── GCF_000472205.1_E_CS88_f__genomic.fna.gz │ ├── GCF_000590575.1_ASM59057v1_genomic.fna.gz │ ├── GCF_000590635.1_ASM59063v1_genomic.fna.gz │ ├── GCF_000590695.1_ASM59069v1_genomic.fna.gz │ ├── GCF_001183765.1_ASM118376v1_genomic.fna.gz │ ├── GCF_001183805.1_ASM118380v1_genomic.fna.gz │ ├── GCF_001183825.1_ASM118382v1_genomic.fna.gz │ ├── GCF_001183845.1_ASM118384v1_genomic.fna.gz │ ├── GCF_001213045.1_5082_8_5_genomic.fna.gz │ ├── GCF_001293965.1_ASM129396v1_genomic.fna.gz │ ├── GCF_001317785.1_7396_3_13_genomic.fna.gz │ ├── GCF_001398135.1_7501_6_52_genomic.fna.gz │ ├── GCF_001398215.1_7501_6_50_genomic.fna.gz │ ├── GCF_001398295.1_7396_3_21_genomic.fna.gz │ ├── GCF_001729845.1_ASM172984v1_genomic.fna.gz │ ├── GCF_001729905.1_ASM172990v1_genomic.fna.gz │ ├── GCF_002088315.1_ASM208831v1_genomic.fna.gz │ ├── GCF_002192615.1_ASM219261v1_genomic.fna.gz │ ├── GCF_002776845.1_ASM277684v1_genomic.fna.gz │ ├── GCF_002776885.1_ASM277688v1_genomic.fna.gz │ ├── GCF_002776935.1_ASM277693v1_genomic.fna.gz │ ├── GCF_002776955.1_ASM277695v1_genomic.fna.gz │ ├── GCF_002777015.1_ASM277701v1_genomic.fna.gz │ ├── GCF_002777095.1_ASM277709v1_genomic.fna.gz │ ├── GCF_002777115.1_ASM277711v1_genomic.fna.gz │ ├── GCF_002777155.1_ASM277715v1_genomic.fna.gz │ ├── GCF_003788785.1_ct114V1_genomic.fna.gz │ ├── GCF_003788895.1_sc110_genomic.fna.gz │ ├── GCF_006508185.1_ASM650818v1_genomic.fna.gz │ ├── GCF_006508235.1_ASM650823v1_genomic.fna.gz │ └── GCF_006508265.1_ASM650826v1_genomic.fna.gz ├── GBFF │ ├── GCF_000026905.1_ASM2690v1_genomic.gbff.gz │ ├── GCF_000092665.1_ASM9266v1_genomic.gbff.gz │ ├── GCF_000092685.1_ASM9268v1_genomic.gbff.gz │ ├── GCF_000093005.1_ASM9300v1_genomic.gff.gz │ ├── GCF_000173495.1_ASM17349v1_genomic.gbff.gz │ ├── GCF_000210495.1_ASM21049v1_genomic.gbff.gz │ ├── GCF_000220105.1_ASM22010v1_genomic.gbff.gz │ ├── GCF_000226605.1_ASM22660v1_genomic.gbff.gz │ ├── GCF_000304515.1_Cm_FSW4_genomic.gbff.gz │ ├── GCF_000318545.1_ASM31854v1_genomic.gbff.gz │ ├── GCF_000318785.1_ASM31878v1_genomic.gbff.gz │ ├── GCF_000318805.1_ASM31880v1_genomic.gbff.gz │ ├── GCF_000318825.1_ASM31882v1_genomic.gbff.gz │ ├── GCF_000318865.1_ASM31886v1_genomic.gbff.gz │ ├── GCF_000318925.1_ASM31892v1_genomic.gbff.gz │ ├── GCF_000318945.1_ASM31894v1_genomic.gbff.gz │ ├── GCF_000319105.1_ASM31910v1_genomic.gbff.gz │ ├── GCF_000441655.1_ASM44165v1_genomic.gbff.gz │ ├── GCF_000441775.1_ASM44177v1_genomic.gbff.gz │ ├── GCF_000472205.1_E_CS88_f__genomic.gbff.gz │ ├── GCF_000590575.1_ASM59057v1_genomic.gbff.gz │ ├── GCF_000590635.1_ASM59063v1_genomic.gbff.gz │ ├── GCF_000590695.1_ASM59069v1_genomic.gbff.gz │ ├── GCF_001183765.1_ASM118376v1_genomic.gbff.gz │ ├── GCF_001183805.1_ASM118380v1_genomic.gbff.gz │ ├── GCF_001183825.1_ASM118382v1_genomic.gbff.gz │ ├── GCF_001183845.1_ASM118384v1_genomic.gbff.gz │ ├── GCF_001213045.1_5082_8_5_genomic.gbff.gz │ ├── GCF_001293965.1_ASM129396v1_genomic.gbff.gz │ ├── GCF_001317785.1_7396_3_13_genomic.gbff.gz │ ├── GCF_001398135.1_7501_6_52_genomic.gbff.gz │ ├── GCF_001398215.1_7501_6_50_genomic.gbff.gz │ ├── GCF_001398295.1_7396_3_21_genomic.gbff.gz │ ├── GCF_001729845.1_ASM172984v1_genomic.gbff.gz │ ├── GCF_001729905.1_ASM172990v1_genomic.gbff.gz │ ├── GCF_002088315.1_ASM208831v1_genomic.gff3.gz │ ├── GCF_002192615.1_ASM219261v1_genomic.gbff.gz │ ├── GCF_002776845.1_ASM277684v1_genomic.gbff.gz │ ├── GCF_002776885.1_ASM277688v1_genomic.gbff.gz │ ├── GCF_002776935.1_ASM277693v1_genomic.gbff.gz │ ├── GCF_002776955.1_ASM277695v1_genomic.gbff.gz │ ├── GCF_002777015.1_ASM277701v1_genomic.gbff.gz │ ├── GCF_002777095.1_ASM277709v1_genomic.gbff.gz │ ├── GCF_002777115.1_ASM277711v1_genomic.gbff.gz │ ├── GCF_002777155.1_ASM277715v1_genomic.gbff.gz │ ├── GCF_003788785.1_ct114V1_genomic.gbff.gz │ ├── GCF_003788785.1_ct114V1_genomic_prodigal_annotation.gff.gz │ ├── GCF_003788895.1_sc110_genomic.gbff.gz │ ├── GCF_006508185.1_ASM650818v1_genomic.gbff.gz │ ├── GCF_006508235.1_ASM650823v1_genomic.gbff.gz │ ├── GCF_006508265.1_ASM650826v1_genomic.gbff.gz │ ├── NC_000117.1.gbk.gz │ ├── NC_010287.1.gff.gz │ ├── PROKKA_12132021.gbk.gz │ ├── PROKKA_12132021.gff.gz │ ├── plasmid_GCF_000093005.1_ASM9300v1.fna.gz │ ├── plasmid_GCF_000093005.1_ASM9300v1.gff.gz │ ├── plasmid_NC_017433.1_pyrodigal.gbk.gz │ └── plasmid_NZ_CP007132_with_manually_added_chevrons.gff.gz ├── compare_results.py ├── expected_info_files │ ├── checksum.txt │ ├── expected_hashes.json │ ├── myannopang_info.yaml │ ├── mybasicpangenome_info.yaml │ ├── panrgp_from_existing_cluster_info.yaml │ └── stepbystep_info.yaml ├── genomes.fasta.list ├── genomes.gbff.list ├── metadata │ ├── metadata_contigs.tsv │ ├── metadata_families.tsv │ ├── metadata_genes.tsv │ ├── metadata_genomes.tsv │ ├── metadata_modules.tsv │ └── metadata_rgps.tsv ├── some_chlam_families.txt └── some_chlam_proteins.fasta └── tests ├── __init__.py ├── conftest.py ├── functional_tests ├── test_align_cmd.py ├── test_config_files.py ├── test_context_cmd.py ├── test_draw.py ├── test_fasta.py ├── test_fasta_all_wf.py ├── test_gbff_basic_wf.py ├── test_metadata_pan.py ├── test_msa.py ├── test_projection.py ├── test_rarefaction.py ├── test_rgp_clustering.py ├── test_stepbystep.py ├── test_wf_from_clusters.py ├── test_write_genomes.py └── test_write_pangenome.py ├── pytest.ini ├── unit_tests ├── align │ └── test_align.py ├── annotate │ └── test_annotate.py ├── context │ └── test_context.py ├── formats │ └── test_writeFlatGenomes.py ├── region │ ├── test_genomicIsland.py │ └── test_rgp_cluster.py ├── test_edge.py ├── test_genefamily.py ├── test_genome.py ├── test_metadata.py ├── test_pangenome.py ├── test_region.py └── utils │ └── test_utilities.py └── utils ├── cache_utils.py ├── checksum.py ├── file_compare.py └── run_ppanggolin.py /.github/workflows/black_lint.yml: 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