# This file was automatically generated by Dist::Zilla::Plugin::Manifest v5.036.
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_core_alignment
bin/pan_genome_post_analysis
bin/pan_genome_reorder_spreadsheet
bin/parallel_all_against_all_blastp
bin/protein_muscle_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/makeblastdb
binaries/darwin/mcl
binaries/darwin/mcxdeblast
binaries/darwin/parallel
binaries/darwin/prank
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/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/AnalyseGroups.pm
lib/Bio/Roary/AnnotateGroups.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/Common.pm
lib/Bio/Roary/CommandLine/CreatePanGenome.pm
lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm
lib/Bio/Roary/CommandLine/IterativeCdhit.pm
lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm
lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.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/IterativeCdhit.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/External/ProteinMuscleAlignmentFromNucleotides.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/DifferenceBetweenSets.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/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
t/Bio/Roary/AnalyseGroups.t
t/Bio/Roary/AnnotateGroups.t
t/Bio/Roary/ChunkFastaFile.t
t/Bio/Roary/CombinedProteome.t
t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t
t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t
t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.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/External/Blastp.t
t/Bio/Roary/External/Cdhit.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/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/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_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_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_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_nnn_at_end.fa
t/data/expected_nuc_multifasta.fa.aln
t/data/expected_nuc_multifasta.faa
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_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_reannotated_groups_file
t/data/expected_set_difference_common_set
t/data/expected_set_difference_common_set_plot.png
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_plot.png
t/data/expected_set_difference_unique_set_two_statistics.csv
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/group_1.fa.aln
t/data/group_9.fa
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/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/mcl_file
t/data/mdoH.fa.aln
t/data/multfasta1.aln
t/data/multfasta2.aln
t/data/multfasta3.aln
t/data/multfasta4.aln
t/data/multfasta5.aln
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/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
t/requires_external.t
