├── .gitignore ├── .travis.yml ├── AUTHORS ├── CHANGELOG.md ├── Dockerfile ├── GPL-LICENSE ├── README.md ├── bin ├── create_pan_genome ├── create_pan_genome_plots.R ├── extract_proteome_from_gff ├── iterative_cdhit ├── pan_genome_assembly_statistics ├── pan_genome_core_alignment ├── pan_genome_post_analysis ├── pan_genome_reorder_spreadsheet ├── parallel_all_against_all_blastp ├── protein_alignment_from_nucleotides ├── query_pan_genome ├── roary ├── roary-create_pan_genome_plots.R ├── roary-pan_genome_reorder_spreadsheet ├── roary-query_pan_genome ├── roary-unique_genes_per_sample └── transfer_annotation_to_groups ├── contrib ├── roary2svg │ └── roary2svg.pl └── roary_plots │ ├── README.md │ ├── roary.html │ ├── roary_files │ ├── MathJax.js │ ├── jquery.min.js │ └── require.min.js │ ├── roary_plots.ipynb │ └── roary_plots.py ├── deployment_process ├── dist.ini ├── install_dependencies.sh ├── lib └── Bio │ ├── Roary.pm │ └── Roary │ ├── AccessoryBinaryFasta.pm │ ├── AccessoryClustering.pm │ ├── AnalyseGroups.pm │ ├── AnnotateGroups.pm │ ├── AssemblyStatistics.pm │ ├── BedFromGFFRole.pm │ ├── ChunkFastaFile.pm │ ├── ClustersRole.pm │ ├── CombinedProteome.pm │ ├── CommandLine │ ├── AssemblyStatistics.pm │ ├── Common.pm │ ├── CreatePanGenome.pm │ ├── ExtractProteomeFromGff.pm │ ├── GeneAlignmentFromNucleotides.pm │ ├── IterativeCdhit.pm │ ├── ParallelAllAgainstAllBlastp.pm │ ├── QueryRoary.pm │ ├── Roary.pm │ ├── RoaryCoreAlignment.pm │ ├── RoaryPostAnalysis.pm │ ├── RoaryReorderSpreadsheet.pm │ ├── TransferAnnotationToGroups.pm │ └── UniqueGenesPerSample.pm │ ├── ContigsToGeneIDsFromGFF.pm │ ├── Exceptions.pm │ ├── External │ ├── Blastp.pm │ ├── Cdhit.pm │ ├── CheckTools.pm │ ├── Fasttree.pm │ ├── GeneAlignmentFromNucleotides.pm │ ├── IterativeCdhit.pm │ ├── Mafft.pm │ ├── Makeblastdb.pm │ ├── Mcl.pm │ ├── PostAnalysis.pm │ └── Prank.pm │ ├── ExtractCoreGenesFromSpreadsheet.pm │ ├── ExtractProteomeFromGFF.pm │ ├── ExtractProteomeFromGFFs.pm │ ├── FilterFullClusters.pm │ ├── FilterUnknownsFromFasta.pm │ ├── GeneNamesFromGFF.pm │ ├── GroupLabels.pm │ ├── GroupStatistics.pm │ ├── InflateClusters.pm │ ├── IterativeCdhit.pm │ ├── JobRunner │ ├── Local.pm │ ├── Parallel.pm │ └── Role.pm │ ├── LookupGeneFiles.pm │ ├── MergeMultifastaAlignments.pm │ ├── OrderGenes.pm │ ├── Output │ ├── BlastIdentityFrequency.pm │ ├── CoreGeneAlignmentCoordinatesEMBL.pm │ ├── DifferenceBetweenSets.pm │ ├── EMBLHeaderCommon.pm │ ├── EmblGroups.pm │ ├── GroupMultifasta.pm │ ├── GroupsMultifastaNucleotide.pm │ ├── GroupsMultifastaProtein.pm │ ├── GroupsMultifastas.pm │ ├── GroupsMultifastasNucleotide.pm │ ├── NumberOfGroups.pm │ └── QueryGroups.pm │ ├── ParallelAllAgainstAllBlast.pm │ ├── ParseGFFAnnotationRole.pm │ ├── PostAnalysis.pm │ ├── PrepareInputFiles.pm │ ├── PresenceAbsenceMatrix.pm │ ├── QC │ └── Report.pm │ ├── ReformatInputGFFs.pm │ ├── ReorderSpreadsheet.pm │ ├── SampleOrder.pm │ ├── SequenceLengths.pm │ ├── SortFasta.pm │ ├── SplitGroups.pm │ ├── SpreadsheetRole.pm │ └── UniqueGenesPerSample.pm └── t ├── 00_requires_external.t ├── Bio └── Roary │ ├── AccessoryBinaryFasta.t │ ├── AccessoryClustering.t │ ├── AnalyseGroups.t │ ├── AnnotateGroups.t │ ├── AssemblyStatistics.t │ ├── ChunkFastaFile.t │ ├── CombinedProteome.t │ ├── CommandLine │ ├── ExtractProteomeFromGff.t │ ├── GeneAlignmentFromNucleotides.t │ ├── ParallelAllAgainstAllBlastp.t │ ├── QueryRoary.t │ ├── Roary.t │ ├── RoaryCoreAlignment.t │ ├── RoaryPostAnalysis.t │ ├── RoaryReorderSpreadsheet.t │ └── TransferAnnotationToGroups.t │ ├── ContigsToGeneIDsFromGFF.t │ ├── EmblGroups.t │ ├── External │ ├── Blastp.t │ ├── Cdhit.t │ ├── CheckTools.t │ ├── Mafft.t │ ├── Makeblastdb.t │ ├── Mcl.t │ └── Prank.t │ ├── ExtractCoreGenesFromSpreadsheet.t │ ├── ExtractProteomeFromGFFs.t │ ├── FilterFullClusters.t │ ├── GeneNamesFromGFF.t │ ├── GroupLabels.t │ ├── GroupStatistics.t │ ├── InflateClusters.t │ ├── OrderGenes.t │ ├── Output │ ├── CoreGeneAlignmentCoorindatesEMBL.t │ ├── DifferenceBetweenSets.t │ ├── GroupsMultifastaProtein.t │ ├── GroupsMultifastas.t │ ├── GroupsMultifastasNucleotide.t │ ├── NumberOfGroups.t │ └── QueryGroups.t │ ├── ParallelAllAgainstAllBlast.t │ ├── PrepareInputFiles.t │ ├── PresenceAbsenceMatrix.t │ ├── QC │ └── Report.t │ ├── ReformatInputGFFs.t │ ├── ReorderSpreadsheet.t │ ├── SampleOrder.t │ ├── SequenceLengths.t │ ├── SortFasta.t │ ├── SplitGroups.t │ └── UniqueGenesPerSample.t ├── bin ├── dummy_blastp ├── dummy_cd-hit ├── dummy_makeblastdb ├── dummy_mcl ├── dummy_mcxdeblast └── dummy_segmasker ├── data ├── accessory_graphs │ ├── core_deletion │ ├── core_island │ ├── file_1.fa │ ├── file_1.gff │ ├── file_2.fa │ ├── file_2.gff │ ├── file_3.fa │ ├── file_3.gff │ ├── no_accessory │ ├── one_branch │ ├── one_bubble │ ├── single_gene_contig │ └── two_graphs ├── allow_no_fasta_delimiter │ ├── annotation_1.gff │ ├── annotation_1.gff.proteome.faa.expected │ ├── annotation_2.gff │ └── annotation_2.gff.proteome.faa.expected ├── blast_results ├── clustered_proteins ├── clustered_proteins_pan_genome ├── clustered_proteins_post_analysis ├── clusters_input.fa ├── clusters_to_inflate ├── clusters_to_inflate.mcl ├── clusters_to_inflate_original_input.fa ├── clustersfile ├── core_alignment.csv ├── core_alignment │ ├── argF.fa.aln │ ├── hly.fa.aln │ └── speH.fa.aln ├── core_alignment_core0.66.csv ├── core_alignment_gene_lookup │ ├── expected_core_gene_alignment.aln │ ├── query_1.gff │ ├── query_2.gff │ └── query_3.gff ├── core_group_statistics.csv ├── empty_file ├── example_1.faa ├── example_2.faa ├── example_3.faa ├── example_annotation.gff ├── example_annotation.gff.proteome.faa.expected ├── example_annotation_2.gff ├── example_annotation_no_fasta_line.gff ├── example_groups ├── example_groups_without_labels ├── exp_qc_report.csv ├── exp_qc_report_real.csv ├── expected_0.seq ├── expected_5.seq ├── expected_accessory_binary_genes.fa ├── expected_accessory_binary_genes_bounded.fa ├── expected_clustered_proteins ├── expected_clusters_to_inflate ├── expected_combined_proteome.fa ├── expected_combined_proteome_with_filtering.fa ├── expected_complement_of_groups.gg ├── expected_complement_of_groups_core0.66.gg ├── expected_core_60_summary_statistics.txt ├── expected_core_gene_alignment.aln ├── expected_core_gene_alignment_core0.66.aln ├── expected_create_pan_genome.fa ├── expected_example_annotation_1.faa ├── expected_filtered_original_input.fa ├── expected_g2_g5_pan_genome_reference.fa ├── expected_gene_presence_and_absence.Rtab ├── expected_gff_set_difference_common_set_statistics.csv ├── expected_group_labels ├── expected_group_statitics.csv ├── expected_group_statitics_missing_genes.csv ├── expected_group_statitics_verbose.csv ├── expected_inflated_results ├── expected_intersection_of_groups.gg ├── expected_intersection_of_groups_core0.66.gg ├── expected_intersection_of_groups_paralogs.gg ├── expected_mafft_input.fa.aln ├── expected_mafft_real_data_core_gene_alignment.aln ├── expected_nnn_at_end.fa ├── expected_nuc_multifasta.fa.aln ├── expected_nuc_multifasta.faa ├── expected_nuc_multifasta_mafft.fa.aln ├── expected_number_of_conserved_genes.tab ├── expected_number_of_conserved_genes_0.6.tab ├── expected_number_of_genes_in_pan_genome.tab ├── expected_number_of_new_genes.tab ├── expected_number_of_unique_genes.tab ├── expected_one_gene_presence_and_absence.Rtab ├── expected_out_of_order_fasta.fa.sorted.fa ├── expected_output_core_missing_genes.aln ├── expected_output_filtered.fa ├── expected_output_groups ├── expected_output_groups_cdhit ├── expected_output_groups_group_2.fa ├── expected_output_groups_group_2_multi.fa ├── expected_output_groups_group_5.fa ├── expected_output_groups_group_5_multi.fa ├── expected_output_merged.aln ├── expected_output_merged_sparse.aln ├── expected_pan_genome.fa ├── expected_pan_genome_one_gene_per_fasta.fa ├── expected_pan_genome_reference.fa ├── expected_prank_input.fa.aln ├── expected_query_1.fna ├── expected_query_2.fna ├── expected_real_data_core_gene_alignment.aln ├── expected_reannotated_groups_file ├── expected_sample_weights_accessory_graph.dot ├── expected_sample_weights_core_accessory_graph.dot ├── expected_set_difference_common_set ├── expected_set_difference_common_set_statistics.csv ├── expected_set_difference_unique_set_one ├── expected_set_difference_unique_set_one_statistics.csv ├── expected_set_difference_unique_set_two ├── expected_set_difference_unique_set_two_statistics.csv ├── expected_some_different_output ├── expected_summary_statistics.txt ├── expected_uneven_sequences.fa ├── expected_union_of_groups.gg ├── genbank_gbff │ ├── genbank1.gff │ ├── genbank1.gff.proteome.faa.expected │ ├── genbank2.gff │ ├── genbank2.gff.proteome.faa.expected │ ├── genbank3.gff │ ├── genbank3.gff.proteome.faa.expected │ └── genbank_gene_presence_absence.csv ├── gene_category_count.csv ├── gene_name_field │ ├── annotation_1.gff │ ├── annotation_2.gff │ ├── expected_reannotated_groups_file │ └── groups ├── group_1.fa.aln ├── group_9.fa ├── input_accessory_binary.fa ├── input_block_spreadsheet.csv ├── kraken_report.txt ├── kraken_test │ ├── database.idx │ ├── database.jdb │ ├── database.kdb │ └── taxonomy │ │ ├── names.dmp │ │ └── nodes.dmp ├── large_accessory_binary_genes.fa ├── locus_tag_gffs │ ├── query_1.gff │ ├── query_1.gff.proteome.faa.expected │ ├── query_2.gff │ ├── query_2.gff.proteome.faa.expected │ ├── query_3.gff │ ├── query_3.gff.proteome.faa.expected │ ├── query_5.gff │ └── query_5.gff.proteome.faa.expected ├── mafft_input.fa ├── mcl_file ├── mdoH.fa.aln ├── mdoH_mafft.fa.aln ├── multfasta1.aln ├── multfasta2.aln ├── multfasta3.aln ├── multfasta4.aln ├── multfasta5.aln ├── multifasta_files │ └── expected_output.embl ├── nnn_at_end.fa ├── nnn_at_end.fa.sorted.fa ├── nuc_multifasta.fa ├── nuc_to_be_aligned.fa ├── out_of_order_fasta.fa ├── out_of_order_fasta.fa.sorted.fa ├── overall_gene_presence_absence.csv ├── pan_genome_sequences │ ├── argF.fa │ ├── hly.fa │ └── speH.fa ├── post_analysis │ ├── _clustered.clstr │ ├── _combined_files │ ├── _combined_files.groups │ ├── _fasta_files │ ├── _gff_files │ ├── _uninflated_mcl_groups │ ├── query_1.gff.proteome.faa │ ├── query_2.gff.proteome.faa │ └── query_6.gff.proteome.faa ├── post_analysis_expected │ ├── accessory.header.embl │ ├── accessory.tab │ ├── core_accessory.header.embl │ ├── core_accessory.tab │ └── gene_presence_absence.csv ├── prank_input.fa ├── proteome_with_and_without_descriptions.faa ├── query_1.fa ├── query_1.gff ├── query_1_alternative_patterns.gff ├── query_2.fa ├── query_2.gff ├── query_3.fa ├── query_3.gff ├── query_4_missing_genes.fa ├── query_4_missing_genes.gff ├── query_5.gff ├── query_6.gff ├── query_groups ├── query_groups_all_merged ├── query_groups_missing_genes ├── query_groups_paralogs ├── query_groups_reference ├── raxml.tre ├── real_data_1.gff ├── real_data_2.gff ├── real_data_core_gene_alignment.aln ├── reformat_input_gffs │ ├── expected_fixed_query_2.gff │ ├── expected_fixed_query_3.gff │ ├── expected_real_1.gff │ ├── query_1.gff │ ├── query_2.gff │ ├── query_3.gff │ └── real_1.gff ├── reorder_isolates.tre ├── reorder_isolates_expected_output.csv ├── reorder_isolates_expected_output_breadth_alpha.csv ├── reorder_isolates_expected_output_breadth_creation.csv ├── reorder_isolates_expected_output_breadth_height.csv ├── reorder_isolates_expected_output_breadth_revalpha.csv ├── reorder_isolates_expected_output_depth_alpha.csv ├── reorder_isolates_expected_output_depth_creation.csv ├── reorder_isolates_expected_output_depth_height.csv ├── reorder_isolates_expected_output_depth_revalpha.csv ├── reorder_isolates_input.csv ├── sequences_with_unknowns.faa ├── shred1.gff ├── shred1.shred.fa ├── shred2.gff ├── shred2.shred.fa ├── sopB.fa.aln ├── speH.fa.aln ├── split_groups │ ├── paralog_clusters1 │ ├── paralog_clusters2 │ ├── paralog_clusters3 │ ├── paralog_clusters4 │ ├── paralog_exp_clusters1 │ ├── paralog_exp_clusters2 │ ├── paralog_exp_clusters3 │ 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