data/roary-3.13.0+dfsg/.gitignore: ASCII text data/roary-3.13.0+dfsg/.travis.yml: ASCII text data/roary-3.13.0+dfsg/AUTHORS: ASCII text data/roary-3.13.0+dfsg/CHANGELOG.md: UTF-8 Unicode text data/roary-3.13.0+dfsg/Dockerfile: ASCII text data/roary-3.13.0+dfsg/GPL-LICENSE: ASCII text data/roary-3.13.0+dfsg/README.md: ASCII text, with very long lines data/roary-3.13.0+dfsg/bin/create_pan_genome_plots.R: a /usr/bin/env Rscript script, ASCII text executable data/roary-3.13.0+dfsg/bin/roary-create_pan_genome_plots.R: a /usr/bin/env Rscript script, ASCII text executable data/roary-3.13.0+dfsg/bin/create_pan_genome: Perl script text executable data/roary-3.13.0+dfsg/bin/extract_proteome_from_gff: Perl script text executable data/roary-3.13.0+dfsg/bin/iterative_cdhit: Perl script text executable data/roary-3.13.0+dfsg/bin/pan_genome_assembly_statistics: Perl script text executable data/roary-3.13.0+dfsg/bin/pan_genome_core_alignment: Perl script text executable data/roary-3.13.0+dfsg/bin/pan_genome_post_analysis: Perl script text executable data/roary-3.13.0+dfsg/bin/pan_genome_reorder_spreadsheet: Perl script text executable data/roary-3.13.0+dfsg/bin/parallel_all_against_all_blastp: Perl script text executable data/roary-3.13.0+dfsg/bin/protein_alignment_from_nucleotides: Perl script text executable data/roary-3.13.0+dfsg/bin/query_pan_genome: Perl script text executable data/roary-3.13.0+dfsg/bin/roary: Perl script text executable data/roary-3.13.0+dfsg/bin/roary-pan_genome_reorder_spreadsheet: Perl script text executable data/roary-3.13.0+dfsg/bin/roary-query_pan_genome: Perl script text executable data/roary-3.13.0+dfsg/bin/roary-unique_genes_per_sample: Perl script text executable data/roary-3.13.0+dfsg/bin/transfer_annotation_to_groups: Perl script text executable data/roary-3.13.0+dfsg/deployment_process: ASCII text data/roary-3.13.0+dfsg/install_dependencies.sh: Bourne-Again shell script, ASCII text executable data/roary-3.13.0+dfsg/lib/Bio/Roary/AccessoryBinaryFasta.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/AccessoryClustering.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/AnalyseGroups.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/AnnotateGroups.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/AssemblyStatistics.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ChunkFastaFile.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ClustersRole.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CombinedProteome.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Common.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/CreatePanGenome.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/IterativeCdhit.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/QueryRoary.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Exceptions.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Blastp.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Cdhit.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/CheckTools.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Fasttree.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/IterativeCdhit.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Mafft.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Makeblastdb.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Mcl.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/PostAnalysis.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/External/Prank.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFFs.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/FilterFullClusters.pm: Perl5 module source, ASCII text 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ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/OrderGenes.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/BlastIdentityFrequency.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/DifferenceBetweenSets.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/EMBLHeaderCommon.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/EmblGroups.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupMultifasta.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastas.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/NumberOfGroups.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/Output/QueryGroups.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ParseGFFAnnotationRole.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/PrepareInputFiles.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/PresenceAbsenceMatrix.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/QC/Report.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ReformatInputGFFs.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/ReorderSpreadsheet.pm: Perl5 module source, UTF-8 Unicode text data/roary-3.13.0+dfsg/lib/Bio/Roary/SampleOrder.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/SequenceLengths.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/SortFasta.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/SplitGroups.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/SpreadsheetRole.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/UniqueGenesPerSample.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary/PostAnalysis.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/lib/Bio/Roary.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/QueryRoary.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/Roary.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/Blastp.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/Cdhit.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/CheckTools.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/Mafft.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/Makeblastdb.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/Mcl.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/External/Prank.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/DifferenceBetweenSets.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/GroupsMultifastaProtein.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/GroupsMultifastas.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/NumberOfGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/Output/QueryGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/QC/Report.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/AccessoryBinaryFasta.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/AccessoryClustering.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/AnalyseGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/AnnotateGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/AssemblyStatistics.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ChunkFastaFile.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/CombinedProteome.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ContigsToGeneIDsFromGFF.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/EmblGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ExtractProteomeFromGFFs.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/FilterFullClusters.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/GeneNamesFromGFF.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/GroupLabels.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/GroupStatistics.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/InflateClusters.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/OrderGenes.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ParallelAllAgainstAllBlast.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/PrepareInputFiles.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/PresenceAbsenceMatrix.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ReformatInputGFFs.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/ReorderSpreadsheet.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/SampleOrder.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/SequenceLengths.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/SortFasta.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/SplitGroups.t: Perl script text executable data/roary-3.13.0+dfsg/t/Bio/Roary/UniqueGenesPerSample.t: Perl script text executable data/roary-3.13.0+dfsg/t/bin/dummy_blastp: Perl script text executable data/roary-3.13.0+dfsg/t/bin/dummy_cd-hit: Perl script text executable data/roary-3.13.0+dfsg/t/bin/dummy_makeblastdb: Perl script text executable data/roary-3.13.0+dfsg/t/bin/dummy_mcl: Perl script text executable data/roary-3.13.0+dfsg/t/bin/dummy_mcxdeblast: Perl script text executable data/roary-3.13.0+dfsg/t/bin/dummy_segmasker: Perl script text executable data/roary-3.13.0+dfsg/t/data/accessory_graphs/core_deletion: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/core_island: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/file_1.fa: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/file_1.gff: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/file_2.fa: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/file_2.gff: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/file_3.fa: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/file_3.gff: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/no_accessory: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/one_branch: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/one_bubble: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/single_gene_contig: ASCII text data/roary-3.13.0+dfsg/t/data/accessory_graphs/two_graphs: ASCII text data/roary-3.13.0+dfsg/t/data/allow_no_fasta_delimiter/annotation_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/allow_no_fasta_delimiter/annotation_1.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/allow_no_fasta_delimiter/annotation_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/allow_no_fasta_delimiter/annotation_2.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/blast_results: ASCII text data/roary-3.13.0+dfsg/t/data/clustered_proteins: ASCII text data/roary-3.13.0+dfsg/t/data/clustered_proteins_pan_genome: ASCII text data/roary-3.13.0+dfsg/t/data/clustered_proteins_post_analysis: ASCII text data/roary-3.13.0+dfsg/t/data/clusters_input.fa: ASCII text data/roary-3.13.0+dfsg/t/data/clusters_to_inflate: ASCII text data/roary-3.13.0+dfsg/t/data/clusters_to_inflate.mcl: ASCII text data/roary-3.13.0+dfsg/t/data/clusters_to_inflate_original_input.fa: ASCII text data/roary-3.13.0+dfsg/t/data/clustersfile: ASCII text data/roary-3.13.0+dfsg/t/data/core_alignment.csv: CSV text data/roary-3.13.0+dfsg/t/data/core_alignment/argF.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/core_alignment/hly.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/core_alignment/speH.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/core_alignment_core0.66.csv: CSV text data/roary-3.13.0+dfsg/t/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln: ASCII text data/roary-3.13.0+dfsg/t/data/core_alignment_gene_lookup/query_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/core_alignment_gene_lookup/query_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/core_alignment_gene_lookup/query_3.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/core_group_statistics.csv: CSV text data/roary-3.13.0+dfsg/t/data/empty_file: empty data/roary-3.13.0+dfsg/t/data/example_1.faa: ASCII text data/roary-3.13.0+dfsg/t/data/example_2.faa: ASCII text data/roary-3.13.0+dfsg/t/data/example_3.faa: ASCII text data/roary-3.13.0+dfsg/t/data/example_annotation.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/example_annotation.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/example_annotation_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/example_annotation_no_fasta_line.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/example_groups: ASCII text data/roary-3.13.0+dfsg/t/data/example_groups_without_labels: ASCII text data/roary-3.13.0+dfsg/t/data/exp_qc_report.csv: CSV text data/roary-3.13.0+dfsg/t/data/exp_qc_report_real.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_0.seq: ASCII text data/roary-3.13.0+dfsg/t/data/expected_5.seq: ASCII text data/roary-3.13.0+dfsg/t/data/expected_accessory_binary_genes.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_accessory_binary_genes_bounded.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_clustered_proteins: ASCII text data/roary-3.13.0+dfsg/t/data/expected_clusters_to_inflate: ASCII text data/roary-3.13.0+dfsg/t/data/expected_combined_proteome.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_combined_proteome_with_filtering.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_complement_of_groups.gg: ASCII text data/roary-3.13.0+dfsg/t/data/expected_complement_of_groups_core0.66.gg: ASCII text data/roary-3.13.0+dfsg/t/data/expected_core_60_summary_statistics.txt: ASCII text data/roary-3.13.0+dfsg/t/data/expected_core_gene_alignment.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_core_gene_alignment_core0.66.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_create_pan_genome.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_example_annotation_1.faa: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/expected_filtered_original_input.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_g2_g5_pan_genome_reference.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_gene_presence_and_absence.Rtab: ASCII text, with CRLF line terminators data/roary-3.13.0+dfsg/t/data/expected_gff_set_difference_common_set_statistics.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_group_labels: ASCII text data/roary-3.13.0+dfsg/t/data/expected_group_statitics.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_group_statitics_missing_genes.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_group_statitics_verbose.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_inflated_results: ASCII text data/roary-3.13.0+dfsg/t/data/expected_intersection_of_groups.gg: ASCII text data/roary-3.13.0+dfsg/t/data/expected_intersection_of_groups_core0.66.gg: ASCII text data/roary-3.13.0+dfsg/t/data/expected_intersection_of_groups_paralogs.gg: ASCII text data/roary-3.13.0+dfsg/t/data/expected_mafft_input.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_mafft_real_data_core_gene_alignment.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_nnn_at_end.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_nuc_multifasta.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_nuc_multifasta.faa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_nuc_multifasta_mafft.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_number_of_conserved_genes.tab: ASCII text data/roary-3.13.0+dfsg/t/data/expected_number_of_conserved_genes_0.6.tab: ASCII text data/roary-3.13.0+dfsg/t/data/expected_number_of_genes_in_pan_genome.tab: ASCII text data/roary-3.13.0+dfsg/t/data/expected_number_of_new_genes.tab: ASCII text data/roary-3.13.0+dfsg/t/data/expected_number_of_unique_genes.tab: ASCII text data/roary-3.13.0+dfsg/t/data/expected_one_gene_presence_and_absence.Rtab: ASCII text, with CRLF line terminators data/roary-3.13.0+dfsg/t/data/expected_out_of_order_fasta.fa.sorted.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_core_missing_genes.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_filtered.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_groups: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_groups_cdhit: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_groups_group_2.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_groups_group_2_multi.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_groups_group_5.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_groups_group_5_multi.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_merged.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_output_merged_sparse.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_pan_genome.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_pan_genome_one_gene_per_fasta.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_pan_genome_reference.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_prank_input.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_query_1.fna: ASCII text data/roary-3.13.0+dfsg/t/data/expected_query_2.fna: ASCII text data/roary-3.13.0+dfsg/t/data/expected_real_data_core_gene_alignment.aln: ASCII text data/roary-3.13.0+dfsg/t/data/expected_reannotated_groups_file: ASCII text data/roary-3.13.0+dfsg/t/data/expected_sample_weights_accessory_graph.dot: ASCII text data/roary-3.13.0+dfsg/t/data/expected_sample_weights_core_accessory_graph.dot: ASCII text data/roary-3.13.0+dfsg/t/data/expected_set_difference_common_set: ASCII text data/roary-3.13.0+dfsg/t/data/expected_set_difference_common_set_statistics.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_set_difference_unique_set_one: ASCII text data/roary-3.13.0+dfsg/t/data/expected_set_difference_unique_set_one_statistics.csv: ASCII text, with very long lines, with CRLF line terminators data/roary-3.13.0+dfsg/t/data/expected_set_difference_unique_set_two: ASCII text data/roary-3.13.0+dfsg/t/data/expected_set_difference_unique_set_two_statistics.csv: CSV text data/roary-3.13.0+dfsg/t/data/expected_some_different_output: ASCII text data/roary-3.13.0+dfsg/t/data/expected_summary_statistics.txt: ASCII text data/roary-3.13.0+dfsg/t/data/expected_uneven_sequences.fa: ASCII text data/roary-3.13.0+dfsg/t/data/expected_union_of_groups.gg: ASCII text data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank1.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank2.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank3.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank3.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/genbank_gbff/genbank_gene_presence_absence.csv: CSV text data/roary-3.13.0+dfsg/t/data/gene_category_count.csv: ASCII text, with very long lines, with CR line terminators data/roary-3.13.0+dfsg/t/data/gene_name_field/annotation_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/gene_name_field/annotation_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/gene_name_field/expected_reannotated_groups_file: ASCII text data/roary-3.13.0+dfsg/t/data/gene_name_field/groups: ASCII text data/roary-3.13.0+dfsg/t/data/group_1.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/group_9.fa: ASCII text data/roary-3.13.0+dfsg/t/data/input_accessory_binary.fa: ASCII text data/roary-3.13.0+dfsg/t/data/input_block_spreadsheet.csv: CSV text data/roary-3.13.0+dfsg/t/data/kraken_report.txt: ASCII text data/roary-3.13.0+dfsg/t/data/kraken_test/database.idx: data data/roary-3.13.0+dfsg/t/data/kraken_test/database.jdb: data data/roary-3.13.0+dfsg/t/data/kraken_test/database.kdb: data data/roary-3.13.0+dfsg/t/data/kraken_test/taxonomy/names.dmp: ASCII text data/roary-3.13.0+dfsg/t/data/kraken_test/taxonomy/nodes.dmp: ASCII text data/roary-3.13.0+dfsg/t/data/large_accessory_binary_genes.fa: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_3.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_5.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/locus_tag_gffs/query_5.gff.proteome.faa.expected: ASCII text data/roary-3.13.0+dfsg/t/data/mafft_input.fa: ASCII text data/roary-3.13.0+dfsg/t/data/mcl_file: ASCII text data/roary-3.13.0+dfsg/t/data/mdoH.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/mdoH_mafft.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/multfasta1.aln: ASCII text data/roary-3.13.0+dfsg/t/data/multfasta2.aln: ASCII text data/roary-3.13.0+dfsg/t/data/multfasta3.aln: ASCII text data/roary-3.13.0+dfsg/t/data/multfasta4.aln: ASCII text data/roary-3.13.0+dfsg/t/data/multfasta5.aln: ASCII text data/roary-3.13.0+dfsg/t/data/multifasta_files/expected_output.embl: ASCII text data/roary-3.13.0+dfsg/t/data/nnn_at_end.fa: ASCII text data/roary-3.13.0+dfsg/t/data/nnn_at_end.fa.sorted.fa: ASCII text data/roary-3.13.0+dfsg/t/data/nuc_multifasta.fa: ASCII text data/roary-3.13.0+dfsg/t/data/nuc_to_be_aligned.fa: ASCII text data/roary-3.13.0+dfsg/t/data/out_of_order_fasta.fa: ASCII text data/roary-3.13.0+dfsg/t/data/out_of_order_fasta.fa.sorted.fa: ASCII text data/roary-3.13.0+dfsg/t/data/overall_gene_presence_absence.csv: CSV text data/roary-3.13.0+dfsg/t/data/pan_genome_sequences/argF.fa: ASCII text data/roary-3.13.0+dfsg/t/data/pan_genome_sequences/hly.fa: ASCII text data/roary-3.13.0+dfsg/t/data/pan_genome_sequences/speH.fa: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/_clustered.clstr: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/_combined_files: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/_combined_files.groups: empty data/roary-3.13.0+dfsg/t/data/post_analysis/_fasta_files: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/_gff_files: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/_uninflated_mcl_groups: empty data/roary-3.13.0+dfsg/t/data/post_analysis/query_1.gff.proteome.faa: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/query_2.gff.proteome.faa: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis/query_6.gff.proteome.faa: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis_expected/accessory.header.embl: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis_expected/accessory.tab: empty data/roary-3.13.0+dfsg/t/data/post_analysis_expected/core_accessory.header.embl: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis_expected/core_accessory.tab: ASCII text data/roary-3.13.0+dfsg/t/data/post_analysis_expected/gene_presence_absence.csv: CSV text data/roary-3.13.0+dfsg/t/data/prank_input.fa: ASCII text data/roary-3.13.0+dfsg/t/data/proteome_with_and_without_descriptions.faa: ASCII text data/roary-3.13.0+dfsg/t/data/query_1.fa: ASCII text data/roary-3.13.0+dfsg/t/data/query_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_1_alternative_patterns.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_2.fa: ASCII text data/roary-3.13.0+dfsg/t/data/query_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_3.fa: ASCII text data/roary-3.13.0+dfsg/t/data/query_3.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_4_missing_genes.fa: ASCII text data/roary-3.13.0+dfsg/t/data/query_4_missing_genes.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_5.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_6.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/query_groups: ASCII text data/roary-3.13.0+dfsg/t/data/query_groups_all_merged: ASCII text, with no line terminators data/roary-3.13.0+dfsg/t/data/query_groups_missing_genes: ASCII text data/roary-3.13.0+dfsg/t/data/query_groups_paralogs: ASCII text data/roary-3.13.0+dfsg/t/data/query_groups_reference: ASCII text data/roary-3.13.0+dfsg/t/data/raxml.tre: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/real_data_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/real_data_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/real_data_core_gene_alignment.aln: ASCII text data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/expected_fixed_query_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/expected_fixed_query_3.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/expected_real_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/query_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/query_2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/query_3.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reformat_input_gffs/real_1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/reorder_isolates.tre: ASCII text, with no line terminators data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_breadth_alpha.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_breadth_creation.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_breadth_height.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_breadth_revalpha.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_depth_alpha.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_depth_creation.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_depth_height.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_expected_output_depth_revalpha.csv: CSV text data/roary-3.13.0+dfsg/t/data/reorder_isolates_input.csv: CSV text data/roary-3.13.0+dfsg/t/data/sequences_with_unknowns.faa: ASCII text data/roary-3.13.0+dfsg/t/data/shred1.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/shred1.shred.fa: ASCII text data/roary-3.13.0+dfsg/t/data/shred2.gff: ASCII text, with very long lines data/roary-3.13.0+dfsg/t/data/shred2.shred.fa: ASCII text data/roary-3.13.0+dfsg/t/data/sopB.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/speH.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_clusters1: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_clusters2: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_clusters3: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_clusters4: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_exp_clusters1: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_exp_clusters2: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_exp_clusters3: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralog_exp_clusters4: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralogs1.fa: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralogs2.fa: ASCII text data/roary-3.13.0+dfsg/t/data/split_groups/paralogs3.fa: ASCII text data/roary-3.13.0+dfsg/t/data/split_pan_genome_sequences/argF.fa: ASCII text data/roary-3.13.0+dfsg/t/data/split_pan_genome_sequences/different.fa: ASCII text data/roary-3.13.0+dfsg/t/data/split_pan_genome_sequences/hly.fa: ASCII text data/roary-3.13.0+dfsg/t/data/split_pan_genome_sequences/reannotated_groups_file: ASCII text data/roary-3.13.0+dfsg/t/data/split_pan_genome_sequences/speH.fa: ASCII text data/roary-3.13.0+dfsg/t/data/uneven_sequences.fa: ASCII text data/roary-3.13.0+dfsg/t/data/uneven_sequences.fa.sorted.fa: ASCII text data/roary-3.13.0+dfsg/t/data/unique_genes_per_sample/clustered_proteins_valid: ASCII text data/roary-3.13.0+dfsg/t/data/unique_genes_per_sample/expected_unique_genes_per_sample.tsv: ASCII text data/roary-3.13.0+dfsg/t/data/variable_core/gene_1.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/variable_core/gene_2.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/variable_core/gene_3.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/variable_core/gene_4.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/data/variable_core/gene_5.fa.aln: ASCII text data/roary-3.13.0+dfsg/t/lib/TestHelper.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/t/00_requires_external.t: Perl script text executable data/roary-3.13.0+dfsg/t/dummy_blastp: Perl script text executable data/roary-3.13.0+dfsg/t/dummy_cd-hit: Perl script text executable data/roary-3.13.0+dfsg/t/dummy_makeblastdb: Perl script text executable data/roary-3.13.0+dfsg/debian/changelog: ASCII text data/roary-3.13.0+dfsg/debian/compat: ASCII text data/roary-3.13.0+dfsg/debian/control: ASCII text data/roary-3.13.0+dfsg/debian/copyright: UTF-8 Unicode text data/roary-3.13.0+dfsg/debian/lintian-overrides: ASCII text data/roary-3.13.0+dfsg/debian/patches/new-bioperl-require.patch: unified diff output, ASCII text data/roary-3.13.0+dfsg/debian/patches/rename_R_script.patch: unified diff output, ASCII text data/roary-3.13.0+dfsg/debian/patches/series: ASCII text data/roary-3.13.0+dfsg/debian/patches/use-debian-perl-path.patch: unified diff output, ASCII text data/roary-3.13.0+dfsg/debian/patches/use-dz-starter.patch: unified diff output, ASCII text data/roary-3.13.0+dfsg/debian/rules: a /usr/bin/make -f script, ASCII text executable data/roary-3.13.0+dfsg/debian/source/format: ASCII text data/roary-3.13.0+dfsg/debian/source/lintian-overrides: ASCII text data/roary-3.13.0+dfsg/debian/tests/control: ASCII text data/roary-3.13.0+dfsg/debian/tests/expected_files.out: ASCII text data/roary-3.13.0+dfsg/debian/tests/test-installed: POSIX shell script, ASCII text executable data/roary-3.13.0+dfsg/debian/upstream/metadata: ASCII text data/roary-3.13.0+dfsg/debian/watch: ASCII text data/roary-3.13.0+dfsg/.pc/.version: ASCII text data/roary-3.13.0+dfsg/.pc/.quilt_patches: ASCII text data/roary-3.13.0+dfsg/.pc/.quilt_series: ASCII text data/roary-3.13.0+dfsg/.pc/applied-patches: ASCII text data/roary-3.13.0+dfsg/.pc/rename_R_script.patch/lib/Bio/Roary/PostAnalysis.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/.pc/use-dz-starter.patch/dist.ini: ASCII text data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/create_pan_genome: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/extract_proteome_from_gff: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/iterative_cdhit: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/pan_genome_assembly_statistics: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/pan_genome_core_alignment: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/pan_genome_post_analysis: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/pan_genome_reorder_spreadsheet: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/parallel_all_against_all_blastp: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/protein_alignment_from_nucleotides: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/query_pan_genome: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/roary: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/roary-pan_genome_reorder_spreadsheet: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/roary-query_pan_genome: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/roary-unique_genes_per_sample: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/bin/transfer_annotation_to_groups: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/00_requires_external.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/AccessoryBinaryFasta.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/AccessoryClustering.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/AnalyseGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/AnnotateGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/AssemblyStatistics.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ChunkFastaFile.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CombinedProteome.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/QueryRoary.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/Roary.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ContigsToGeneIDsFromGFF.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/EmblGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/Blastp.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/Cdhit.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/CheckTools.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/Mafft.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/Makeblastdb.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/Mcl.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/External/Prank.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ExtractProteomeFromGFFs.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/FilterFullClusters.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/GeneNamesFromGFF.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/GroupLabels.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/GroupStatistics.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/InflateClusters.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/OrderGenes.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/DifferenceBetweenSets.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/GroupsMultifastaProtein.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/GroupsMultifastas.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/NumberOfGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/Output/QueryGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ParallelAllAgainstAllBlast.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/PrepareInputFiles.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/PresenceAbsenceMatrix.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/QC/Report.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ReformatInputGFFs.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/ReorderSpreadsheet.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/SampleOrder.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/SequenceLengths.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/SortFasta.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/SplitGroups.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/Bio/Roary/UniqueGenesPerSample.t: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_blastp: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_cd-hit: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_makeblastdb: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_mcl: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_mcxdeblast: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_segmasker: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/dummy_blastp: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/dummy_cd-hit: Perl script text executable data/roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/dummy_makeblastdb: Perl script text executable data/roary-3.13.0+dfsg/.pc/new-bioperl-require.patch/lib/Bio/Roary.pm: Perl5 module source, ASCII text data/roary-3.13.0+dfsg/dist.ini: ASCII text