Bio-Roary 3.12.0
Files
- AUTHORS
- Dockerfile
- GPL-LICENSE
- LICENSE
- MANIFEST
- META.json
- 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/roary-create_pan_genome_plots.R
- bin/roary-pan_genome_reorder_spreadsheet
- bin/roary-query_pan_genome
- bin/roary-unique_genes_per_sample
- bin/transfer_annotation_to_groups
- 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/CommandLine/UniqueGenesPerSample.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
- lib/Bio/Roary/UniqueGenesPerSample.pm
- t/00-report-prereqs.dd
- t/00-report-prereqs.t
- 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/Bio/Roary/UniqueGenesPerSample.t
- t/author-00-compile.t
- t/author-pod-syntax.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/allow_no_fasta_delimiter/annotation_1.gff
- t/data/allow_no_fasta_delimiter/annotation_1.gff.proteome.faa.expected
- t/data/allow_no_fasta_delimiter/annotation_2.gff
- t/data/allow_no_fasta_delimiter/annotation_2.gff.proteome.faa.expected
- 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_annotation_no_fasta_line.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/gene_name_field/annotation_1.gff
- t/data/gene_name_field/annotation_2.gff
- t/data/gene_name_field/expected_reannotated_groups_file
- t/data/gene_name_field/groups
- 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/unique_genes_per_sample/clustered_proteins_valid
- t/data/unique_genes_per_sample/expected_unique_genes_per_sample.tsv
- 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