Files

• 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/pan_genome_post_analysis
• bin/pan_genome_reorder_spreadsheet
• bin/parallel_all_against_all_blastp
• bin/plot_pan_genome_groups
• bin/query_pan_genome
• bin/transfer_annotation_to_groups
• dist.ini
• lib/Bio/PanGenome.pm
• lib/Bio/PanGenome/AnalyseGroups.pm
• lib/Bio/PanGenome/AnnotateGroups.pm
• lib/Bio/PanGenome/ChunkFastaFile.pm
• lib/Bio/PanGenome/ClustersRole.pm
• lib/Bio/PanGenome/CombinedProteome.pm
• lib/Bio/PanGenome/CommandLine/CreatePanGenome.pm
• lib/Bio/PanGenome/CommandLine/ExtractProteomeFromGff.pm
• lib/Bio/PanGenome/CommandLine/PanGenomePostAnalysis.pm
• lib/Bio/PanGenome/CommandLine/PanGenomeReorderSpreadsheet.pm
• lib/Bio/PanGenome/CommandLine/ParallelAllAgainstAllBlastp.pm
• lib/Bio/PanGenome/CommandLine/PlotPanGenomeGroups.pm
• lib/Bio/PanGenome/CommandLine/QueryPanGenome.pm
• lib/Bio/PanGenome/CommandLine/TransferAnnotationToGroups.pm
• lib/Bio/PanGenome/Exceptions.pm
• lib/Bio/PanGenome/External/Blastp.pm
• lib/Bio/PanGenome/External/Cdhit.pm
• lib/Bio/PanGenome/External/Makeblastdb.pm
• lib/Bio/PanGenome/External/Mcl.pm
• lib/Bio/PanGenome/External/Muscle.pm
• lib/Bio/PanGenome/External/PostAnalysis.pm
• lib/Bio/PanGenome/External/Segmasker.pm
• lib/Bio/PanGenome/ExtractProteomeFromGFF.pm
• lib/Bio/PanGenome/ExtractProteomeFromGFFs.pm
• lib/Bio/PanGenome/FilterFullClusters.pm
• lib/Bio/PanGenome/FilterUnknownsFromFasta.pm
• lib/Bio/PanGenome/GeneNamesFromGFF.pm
• lib/Bio/PanGenome/GroupLabels.pm
• lib/Bio/PanGenome/GroupStatistics.pm
• lib/Bio/PanGenome/InflateClusters.pm
• lib/Bio/PanGenome/JobRunner/LSF.pm
• lib/Bio/PanGenome/JobRunner/Local.pm
• lib/Bio/PanGenome/JobRunner/Role.pm
• lib/Bio/PanGenome/Output/DifferenceBetweenSets.pm
• lib/Bio/PanGenome/Output/GroupMultifasta.pm
• lib/Bio/PanGenome/Output/GroupTabFiles.pm
• lib/Bio/PanGenome/Output/GroupsMultifastaNucleotide.pm
• lib/Bio/PanGenome/Output/GroupsMultifastas.pm
• lib/Bio/PanGenome/Output/GroupsMultifastasNucleotide.pm
• lib/Bio/PanGenome/Output/NumberOfGroups.pm
• lib/Bio/PanGenome/Output/OneGenePerGroupFasta.pm
• lib/Bio/PanGenome/Output/QueryGroups.pm
• lib/Bio/PanGenome/ParallelAllAgainstAllBlast.pm
• lib/Bio/PanGenome/Plot/FreqOfGenes.pm
• lib/Bio/PanGenome/PostAnalysis.pm
• lib/Bio/PanGenome/PrepareInputFiles.pm
• lib/Bio/PanGenome/ReorderSpreadsheet.pm
• lib/Bio/PanGenome/SampleOrder.pm
• lib/Bio/PanGenome/SequenceLengths.pm
• t/Bio/PanGenome/AnalyseGroups.t
• t/Bio/PanGenome/AnnotateGroups.t
• t/Bio/PanGenome/ChunkFastaFile.t
• t/Bio/PanGenome/CombinedProteome.t
• t/Bio/PanGenome/CommandLine/CreatePanGenome.t
• t/Bio/PanGenome/CommandLine/ExtractProteomeFromGff.t
• t/Bio/PanGenome/CommandLine/PanGenomeReorderSpreadsheet.t
• t/Bio/PanGenome/CommandLine/ParallelAllAgainstAllBlastp.t
• t/Bio/PanGenome/CommandLine/QueryPanGenome.t
• t/Bio/PanGenome/CommandLine/TransferAnnotationToGroups.t
• t/Bio/PanGenome/External/Blastp.t
• t/Bio/PanGenome/External/Cdhit.t
• t/Bio/PanGenome/External/Makeblastdb.t
• t/Bio/PanGenome/External/Mcl.t
• t/Bio/PanGenome/External/Segmasker.t
• t/Bio/PanGenome/ExtractProteomeFromGFFs.t
• t/Bio/PanGenome/FilterFullClusters.t
• t/Bio/PanGenome/GeneNamesFromGFF.t
• t/Bio/PanGenome/GroupLabels.t
• t/Bio/PanGenome/GroupStatistics.t
• t/Bio/PanGenome/InflateClusters.t
• t/Bio/PanGenome/Output/DifferenceBetweenSets.t
• t/Bio/PanGenome/Output/GroupsMultifastas.t
• t/Bio/PanGenome/Output/GroupsMultifastasNucleotide.t
• t/Bio/PanGenome/Output/NumberOfGroups.t
• t/Bio/PanGenome/Output/OneGenePerGroupFasta.t
• t/Bio/PanGenome/Output/QueryGroups.t
• t/Bio/PanGenome/ParallelAllAgainstAllBlast.t
• t/Bio/PanGenome/PrepareInputFiles.t
• t/Bio/PanGenome/ReorderSpreadsheet.t
• t/Bio/PanGenome/SampleOrder.t
• t/Bio/PanGenome/SequenceLengths.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/00002-speH.fa.aln
• t/data/00003-group_9.fa
• t/data/00006-group_1.fa.aln
• t/data/blast_results
• t/data/clustered_proteins
• t/data/clustered_proteins_pan_genome
• 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/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/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_create_pan_genome.fa
• t/data/expected_example_annotation_1.faa
• t/data/expected_filtered_original_input.fa
• t/data/expected_group_labels
• t/data/expected_group_statitics.csv
• t/data/expected_group_statitics_missing_genes.csv
• t/data/expected_inflated_results
• t/data/expected_intersection_of_groups.gg
• t/data/expected_number_of_conserved_genes.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_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_pan_genome.fa
• t/data/expected_pan_genome_one_gene_per_fasta.fa
• 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_union_of_groups.gg
• t/data/mcl_file
• t/data/overall_group_statisics.csv
• t/data/pan_genome_sequences/00001-group_6.fa
• t/data/pan_genome_sequences/00001-group_7.fa
• t/data/pan_genome_sequences/00001-yfnB.fa
• t/data/pan_genome_sequences/00002-argF.fa
• t/data/pan_genome_sequences/00002-speH.fa
• t/data/pan_genome_sequences/00003-hly.fa
• t/data/proteome_with_and_without_descriptions.faa
• t/data/query_1.fa
• t/data/query_1.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_6.gff
• t/data/query_groups
• t/data/query_groups_all_merged
• t/data/query_groups_missing_genes
• t/data/raxml.tre
• t/data/reorder_isolates.tre
• t/data/reorder_isolates_expected_output.csv
• t/data/reorder_isolates_input.csv
• t/data/sequences_with_unknowns.faa
• t/data/split_pan_genome_sequences/00002-argF.fa
• t/data/split_pan_genome_sequences/00002-hly.fa
• t/data/split_pan_genome_sequences/00002-speH.fa
• t/data/split_pan_genome_sequences/00006-different.fa
• t/data/split_pan_genome_sequences/reannotated_groups_file
• t/dummy_blastp
• t/dummy_cd-hit
• t/dummy_makeblastdb
• t/lib/TestHelper.pm
• t/requires_external.t