Files

• AUTHORS
• GPL-LICENSE
• LICENSE
• MANIFEST
• META.yml
• Makefile.PL
• README
• README.md
• bin/create_pan_genome
• bin/create_pan_genome_plots.R
• bin/extract_proteome_from_gff
• bin/iterative_cdhit
• bin/pan_genome_assembly_statistics
• bin/pan_genome_core_alignment
• bin/pan_genome_post_analysis
• bin/pan_genome_reorder_spreadsheet
• bin/parallel_all_against_all_blastp
• bin/protein_alignment_from_nucleotides
• bin/query_pan_genome
• bin/roary
• bin/transfer_annotation_to_groups
• binaries/darwin/bedtools
• binaries/darwin/blastp
• binaries/darwin/cd-hit
• binaries/darwin/fasttree
• binaries/darwin/makeblastdb
• binaries/darwin/mcl
• binaries/darwin/mcxdeblast
• binaries/darwin/parallel
• binaries/darwin/prank
• binaries/linux/FastTree
• binaries/linux/bedtools
• binaries/linux/blastp
• binaries/linux/cd-hit
• binaries/linux/makeblastdb
• binaries/linux/mcl
• binaries/linux/mcxdeblast
• binaries/linux/parallel
• binaries/linux/prank
• contrib/roary2svg/roary2svg.pl
• contrib/roary_plots/README.md
• contrib/roary_plots/roary.html
• contrib/roary_plots/roary_files/MathJax.js
• contrib/roary_plots/roary_files/jquery.min.js
• contrib/roary_plots/roary_files/require.min.js
• contrib/roary_plots/roary_plots.ipynb
• contrib/roary_plots/roary_plots.py
• deployment_process
• dist.ini
• install_dependencies.sh
• lib/Bio/Roary.pm
• lib/Bio/Roary/AccessoryBinaryFasta.pm
• lib/Bio/Roary/AccessoryClustering.pm
• lib/Bio/Roary/AnalyseGroups.pm
• lib/Bio/Roary/AnnotateGroups.pm
• lib/Bio/Roary/AssemblyStatistics.pm
• lib/Bio/Roary/BedFromGFFRole.pm
• lib/Bio/Roary/ChunkFastaFile.pm
• lib/Bio/Roary/ClustersRole.pm
• lib/Bio/Roary/CombinedProteome.pm
• lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
• lib/Bio/Roary/CommandLine/Common.pm
• lib/Bio/Roary/CommandLine/CreatePanGenome.pm
• lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm
• lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm
• lib/Bio/Roary/CommandLine/IterativeCdhit.pm
• lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm
• lib/Bio/Roary/CommandLine/QueryRoary.pm
• lib/Bio/Roary/CommandLine/Roary.pm
• lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm
• lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm
• lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm
• lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm
• lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm
• lib/Bio/Roary/Exceptions.pm
• lib/Bio/Roary/External/Blastp.pm
• lib/Bio/Roary/External/Cdhit.pm
• lib/Bio/Roary/External/CheckTools.pm
• lib/Bio/Roary/External/Fasttree.pm
• lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm
• lib/Bio/Roary/External/IterativeCdhit.pm
• lib/Bio/Roary/External/Mafft.pm
• lib/Bio/Roary/External/Makeblastdb.pm
• lib/Bio/Roary/External/Mcl.pm
• lib/Bio/Roary/External/PostAnalysis.pm
• lib/Bio/Roary/External/Prank.pm
• lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm
• lib/Bio/Roary/ExtractProteomeFromGFF.pm
• lib/Bio/Roary/ExtractProteomeFromGFFs.pm
• lib/Bio/Roary/FilterFullClusters.pm
• lib/Bio/Roary/FilterUnknownsFromFasta.pm
• lib/Bio/Roary/GeneNamesFromGFF.pm
• lib/Bio/Roary/GroupLabels.pm
• lib/Bio/Roary/GroupStatistics.pm
• lib/Bio/Roary/InflateClusters.pm
• lib/Bio/Roary/IterativeCdhit.pm
• lib/Bio/Roary/JobRunner/Local.pm
• lib/Bio/Roary/JobRunner/Parallel.pm
• lib/Bio/Roary/JobRunner/Role.pm
• lib/Bio/Roary/LookupGeneFiles.pm
• lib/Bio/Roary/MergeMultifastaAlignments.pm
• lib/Bio/Roary/OrderGenes.pm
• lib/Bio/Roary/Output/BlastIdentityFrequency.pm
• lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm
• lib/Bio/Roary/Output/DifferenceBetweenSets.pm
• lib/Bio/Roary/Output/EMBLHeaderCommon.pm
• lib/Bio/Roary/Output/EmblGroups.pm
• lib/Bio/Roary/Output/GroupMultifasta.pm
• lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
• lib/Bio/Roary/Output/GroupsMultifastaProtein.pm
• lib/Bio/Roary/Output/GroupsMultifastas.pm
• lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm
• lib/Bio/Roary/Output/NumberOfGroups.pm
• lib/Bio/Roary/Output/QueryGroups.pm
• lib/Bio/Roary/ParallelAllAgainstAllBlast.pm
• lib/Bio/Roary/ParseGFFAnnotationRole.pm
• lib/Bio/Roary/PostAnalysis.pm
• lib/Bio/Roary/PrepareInputFiles.pm
• lib/Bio/Roary/PresenceAbsenceMatrix.pm
• lib/Bio/Roary/QC/Report.pm
• lib/Bio/Roary/ReformatInputGFFs.pm
• lib/Bio/Roary/ReorderSpreadsheet.pm
• lib/Bio/Roary/SampleOrder.pm
• lib/Bio/Roary/SequenceLengths.pm
• lib/Bio/Roary/SortFasta.pm
• lib/Bio/Roary/SplitGroups.pm
• lib/Bio/Roary/SpreadsheetRole.pm
• t/00_requires_external.t
• t/Bio/Roary/AccessoryBinaryFasta.t
• t/Bio/Roary/AccessoryClustering.t
• t/Bio/Roary/AnalyseGroups.t
• t/Bio/Roary/AnnotateGroups.t
• t/Bio/Roary/AssemblyStatistics.t
• t/Bio/Roary/ChunkFastaFile.t
• t/Bio/Roary/CombinedProteome.t
• t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t
• t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t
• t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t
• t/Bio/Roary/CommandLine/QueryRoary.t
• t/Bio/Roary/CommandLine/Roary.t
• t/Bio/Roary/CommandLine/RoaryCoreAlignment.t
• t/Bio/Roary/CommandLine/RoaryPostAnalysis.t
• t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t
• t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t
• t/Bio/Roary/ContigsToGeneIDsFromGFF.t
• t/Bio/Roary/EmblGroups.t
• t/Bio/Roary/External/Blastp.t
• t/Bio/Roary/External/Cdhit.t
• t/Bio/Roary/External/CheckTools.t
• t/Bio/Roary/External/Mafft.t
• t/Bio/Roary/External/Makeblastdb.t
• t/Bio/Roary/External/Mcl.t
• t/Bio/Roary/External/Prank.t
• t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t
• t/Bio/Roary/ExtractProteomeFromGFFs.t
• t/Bio/Roary/FilterFullClusters.t
• t/Bio/Roary/GeneNamesFromGFF.t
• t/Bio/Roary/GroupLabels.t
• t/Bio/Roary/GroupStatistics.t
• t/Bio/Roary/InflateClusters.t
• t/Bio/Roary/OrderGenes.t
• t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t
• t/Bio/Roary/Output/DifferenceBetweenSets.t
• t/Bio/Roary/Output/GroupsMultifastaProtein.t
• t/Bio/Roary/Output/GroupsMultifastas.t
• t/Bio/Roary/Output/GroupsMultifastasNucleotide.t
• t/Bio/Roary/Output/NumberOfGroups.t
• t/Bio/Roary/Output/QueryGroups.t
• t/Bio/Roary/ParallelAllAgainstAllBlast.t
• t/Bio/Roary/PrepareInputFiles.t
• t/Bio/Roary/PresenceAbsenceMatrix.t
• t/Bio/Roary/QC/Report.t
• t/Bio/Roary/ReformatInputGFFs.t
• t/Bio/Roary/ReorderSpreadsheet.t
• t/Bio/Roary/SampleOrder.t
• t/Bio/Roary/SequenceLengths.t
• t/Bio/Roary/SortFasta.t
• t/Bio/Roary/SplitGroups.t
• t/bin/dummy_blastp
• t/bin/dummy_cd-hit
• t/bin/dummy_makeblastdb
• t/bin/dummy_mcl
• t/bin/dummy_mcxdeblast
• t/bin/dummy_segmasker
• t/data/accessory_graphs/core_deletion
• t/data/accessory_graphs/core_island
• t/data/accessory_graphs/file_1.fa
• t/data/accessory_graphs/file_1.gff
• t/data/accessory_graphs/file_2.fa
• t/data/accessory_graphs/file_2.gff
• t/data/accessory_graphs/file_3.fa
• t/data/accessory_graphs/file_3.gff
• t/data/accessory_graphs/no_accessory
• t/data/accessory_graphs/one_branch
• t/data/accessory_graphs/one_bubble
• t/data/accessory_graphs/single_gene_contig
• t/data/accessory_graphs/two_graphs
• t/data/blast_results
• t/data/clustered_proteins
• t/data/clustered_proteins_pan_genome
• t/data/clustered_proteins_post_analysis
• t/data/clusters_input.fa
• t/data/clusters_to_inflate
• t/data/clusters_to_inflate.mcl
• t/data/clusters_to_inflate_original_input.fa
• t/data/clustersfile
• t/data/core_alignment.csv
• t/data/core_alignment/argF.fa.aln
• t/data/core_alignment/hly.fa.aln
• t/data/core_alignment/speH.fa.aln
• t/data/core_alignment_core0.66.csv
• t/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln
• t/data/core_alignment_gene_lookup/query_1.gff
• t/data/core_alignment_gene_lookup/query_2.gff
• t/data/core_alignment_gene_lookup/query_3.gff
• t/data/core_group_statistics.csv
• t/data/empty_file
• t/data/example_1.faa
• t/data/example_2.faa
• t/data/example_3.faa
• t/data/example_annotation.gff
• t/data/example_annotation.gff.proteome.faa.expected
• t/data/example_annotation_2.gff
• t/data/example_groups
• t/data/example_groups_without_labels
• t/data/exp_qc_report.csv
• t/data/exp_qc_report_real.csv
• t/data/expected_0.seq
• t/data/expected_5.seq
• t/data/expected_accessory_binary_genes.fa
• t/data/expected_accessory_binary_genes_bounded.fa
• t/data/expected_clustered_proteins
• t/data/expected_clusters_to_inflate
• t/data/expected_combined_proteome.fa
• t/data/expected_combined_proteome_with_filtering.fa
• t/data/expected_complement_of_groups.gg
• t/data/expected_complement_of_groups_core0.66.gg
• t/data/expected_core_60_summary_statistics.txt
• t/data/expected_core_gene_alignment.aln
• t/data/expected_core_gene_alignment_core0.66.aln
• t/data/expected_create_pan_genome.fa
• t/data/expected_example_annotation_1.faa
• t/data/expected_filtered_original_input.fa
• t/data/expected_g2_g5_pan_genome_reference.fa
• t/data/expected_gene_presence_and_absence.Rtab
• t/data/expected_gff_set_difference_common_set_statistics.csv
• t/data/expected_group_labels
• t/data/expected_group_statitics.csv
• t/data/expected_group_statitics_missing_genes.csv
• t/data/expected_group_statitics_verbose.csv
• t/data/expected_inflated_results
• t/data/expected_intersection_of_groups.gg
• t/data/expected_intersection_of_groups_core0.66.gg
• t/data/expected_intersection_of_groups_paralogs.gg
• t/data/expected_mafft_input.fa.aln
• t/data/expected_mafft_real_data_core_gene_alignment.aln
• t/data/expected_nnn_at_end.fa
• t/data/expected_nuc_multifasta.fa.aln
• t/data/expected_nuc_multifasta.faa
• t/data/expected_nuc_multifasta_mafft.fa.aln
• t/data/expected_number_of_conserved_genes.tab
• t/data/expected_number_of_conserved_genes_0.6.tab
• t/data/expected_number_of_genes_in_pan_genome.tab
• t/data/expected_number_of_new_genes.tab
• t/data/expected_number_of_unique_genes.tab
• t/data/expected_one_gene_presence_and_absence.Rtab
• t/data/expected_out_of_order_fasta.fa.sorted.fa
• t/data/expected_output_core_missing_genes.aln
• t/data/expected_output_filtered.fa
• t/data/expected_output_groups
• t/data/expected_output_groups_cdhit
• t/data/expected_output_groups_group_2.fa
• t/data/expected_output_groups_group_2_multi.fa
• t/data/expected_output_groups_group_5.fa
• t/data/expected_output_groups_group_5_multi.fa
• t/data/expected_output_merged.aln
• t/data/expected_output_merged_sparse.aln
• t/data/expected_pan_genome.fa
• t/data/expected_pan_genome_one_gene_per_fasta.fa
• t/data/expected_pan_genome_reference.fa
• t/data/expected_prank_input.fa.aln
• t/data/expected_query_1.fna
• t/data/expected_query_2.fna
• t/data/expected_real_data_core_gene_alignment.aln
• t/data/expected_reannotated_groups_file
• t/data/expected_sample_weights_accessory_graph.dot
• t/data/expected_sample_weights_core_accessory_graph.dot
• t/data/expected_set_difference_common_set
• t/data/expected_set_difference_common_set_statistics.csv
• t/data/expected_set_difference_unique_set_one
• t/data/expected_set_difference_unique_set_one_statistics.csv
• t/data/expected_set_difference_unique_set_two
• t/data/expected_set_difference_unique_set_two_statistics.csv
• t/data/expected_some_different_output
• t/data/expected_summary_statistics.txt
• t/data/expected_uneven_sequences.fa
• t/data/expected_union_of_groups.gg
• t/data/genbank_gbff/genbank1.gff
• t/data/genbank_gbff/genbank1.gff.proteome.faa.expected
• t/data/genbank_gbff/genbank2.gff
• t/data/genbank_gbff/genbank2.gff.proteome.faa.expected
• t/data/genbank_gbff/genbank3.gff
• t/data/genbank_gbff/genbank3.gff.proteome.faa.expected
• t/data/genbank_gbff/genbank_gene_presence_absence.csv
• t/data/gene_category_count.csv
• t/data/group_1.fa.aln
• t/data/group_9.fa
• t/data/input_accessory_binary.fa
• t/data/input_block_spreadsheet.csv
• t/data/kraken_report.txt
• t/data/kraken_test/database.idx
• t/data/kraken_test/database.jdb
• t/data/kraken_test/database.kdb
• t/data/kraken_test/taxonomy/names.dmp
• t/data/kraken_test/taxonomy/nodes.dmp
• t/data/large_accessory_binary_genes.fa
• t/data/locus_tag_gffs/query_1.gff
• t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected
• t/data/locus_tag_gffs/query_2.gff
• t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected
• t/data/locus_tag_gffs/query_3.gff
• t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected
• t/data/locus_tag_gffs/query_5.gff
• t/data/locus_tag_gffs/query_5.gff.proteome.faa.expected
• t/data/mafft_input.fa
• t/data/mcl_file
• t/data/mdoH.fa.aln
• t/data/mdoH_mafft.fa.aln
• t/data/multfasta1.aln
• t/data/multfasta2.aln
• t/data/multfasta3.aln
• t/data/multfasta4.aln
• t/data/multfasta5.aln
• t/data/multifasta_files/expected_output.embl
• t/data/nnn_at_end.fa
• t/data/nnn_at_end.fa.sorted.fa
• t/data/nuc_multifasta.fa
• t/data/nuc_to_be_aligned.fa
• t/data/out_of_order_fasta.fa
• t/data/out_of_order_fasta.fa.sorted.fa
• t/data/overall_gene_presence_absence.csv
• t/data/pan_genome_sequences/argF.fa
• t/data/pan_genome_sequences/hly.fa
• t/data/pan_genome_sequences/speH.fa
• t/data/post_analysis/_clustered
• t/data/post_analysis/_clustered.bak.clstr
• t/data/post_analysis/_clustered.clstr
• t/data/post_analysis/_combined_files
• t/data/post_analysis/_combined_files.groups
• t/data/post_analysis/_fasta_files
• t/data/post_analysis/_gff_files
• t/data/post_analysis/_uninflated_mcl_groups
• t/data/post_analysis/query_1.gff.proteome.faa
• t/data/post_analysis/query_2.gff.proteome.faa
• t/data/post_analysis/query_6.gff.proteome.faa
• t/data/post_analysis_expected/accessory.header.embl
• t/data/post_analysis_expected/accessory.tab
• t/data/post_analysis_expected/core_accessory.header.embl
• t/data/post_analysis_expected/core_accessory.tab
• t/data/post_analysis_expected/gene_presence_absence.csv
• t/data/prank_input.fa
• t/data/proteome_with_and_without_descriptions.faa
• t/data/query_1.fa
• t/data/query_1.gff
• t/data/query_1_alternative_patterns.gff
• t/data/query_2.fa
• t/data/query_2.gff
• t/data/query_3.fa
• t/data/query_3.gff
• t/data/query_4_missing_genes.fa
• t/data/query_4_missing_genes.gff
• t/data/query_5.gff
• t/data/query_6.gff
• t/data/query_groups
• t/data/query_groups_all_merged
• t/data/query_groups_missing_genes
• t/data/query_groups_paralogs
• t/data/query_groups_reference
• t/data/raxml.tre
• t/data/real_data_1.gff
• t/data/real_data_2.gff
• t/data/real_data_core_gene_alignment.aln
• t/data/reformat_input_gffs/expected_fixed_query_2.gff
• t/data/reformat_input_gffs/expected_fixed_query_3.gff
• t/data/reformat_input_gffs/expected_real_1.gff
• t/data/reformat_input_gffs/query_1.gff
• t/data/reformat_input_gffs/query_2.gff
• t/data/reformat_input_gffs/query_3.gff
• t/data/reformat_input_gffs/real_1.gff
• t/data/reorder_isolates.tre
• t/data/reorder_isolates_expected_output.csv
• t/data/reorder_isolates_expected_output_breadth_alpha.csv
• t/data/reorder_isolates_expected_output_breadth_creation.csv
• t/data/reorder_isolates_expected_output_breadth_height.csv
• t/data/reorder_isolates_expected_output_breadth_revalpha.csv
• t/data/reorder_isolates_expected_output_depth_alpha.csv
• t/data/reorder_isolates_expected_output_depth_creation.csv
• t/data/reorder_isolates_expected_output_depth_height.csv
• t/data/reorder_isolates_expected_output_depth_revalpha.csv
• t/data/reorder_isolates_input.csv
• t/data/sequences_with_unknowns.faa
• t/data/shred1.gff
• t/data/shred1.shred.fa
• t/data/shred2.gff
• t/data/shred2.shred.fa
• t/data/sopB.fa.aln
• t/data/speH.fa.aln
• t/data/split_groups/paralog_clusters1
• t/data/split_groups/paralog_clusters2
• t/data/split_groups/paralog_clusters3
• t/data/split_groups/paralog_clusters4
• t/data/split_groups/paralog_exp_clusters1
• t/data/split_groups/paralog_exp_clusters2
• t/data/split_groups/paralog_exp_clusters3
• t/data/split_groups/paralog_exp_clusters4
• t/data/split_groups/paralogs1.fa
• t/data/split_groups/paralogs2.fa
• t/data/split_groups/paralogs3.fa
• t/data/split_pan_genome_sequences/argF.fa
• t/data/split_pan_genome_sequences/different.fa
• t/data/split_pan_genome_sequences/hly.fa
• t/data/split_pan_genome_sequences/reannotated_groups_file
• t/data/split_pan_genome_sequences/speH.fa
• t/data/uneven_sequences.fa
• t/data/uneven_sequences.fa.sorted.fa
• t/data/variable_core/gene_1.fa.aln
• t/data/variable_core/gene_2.fa.aln
• t/data/variable_core/gene_3.fa.aln
• t/data/variable_core/gene_4.fa.aln
• t/data/variable_core/gene_5.fa.aln
• t/dummy_blastp
• t/dummy_cd-hit
• t/dummy_makeblastdb
• t/lib/TestHelper.pm