# This file was automatically generated by Dist::Zilla::Plugin::Manifest v5.033.
10060_5#2.gff.proteome.faa
10060_5#3.gff.proteome.faa
10060_5#4.gff.proteome.faa
10060_5#5.gff.proteome.faa
10209_5#1.gff.proteome.faa
10209_5#10.gff.proteome.faa
10209_5#11.gff.proteome.faa
10209_5#12.gff.proteome.faa
AUTHORS
GPL-LICENSE
LICENSE
MANIFEST
META.yml
Makefile.PL
README
README.md
_blast_results
_clustered
_clustered.clstr
_combined_files
_combined_files.groups
_fasta_files
_gff_files
_inflated_mcl_groups
_inflated_unsplit_mcl_groups
_labeled_mcl_groups
_uninflated_mcl_groups
accessory.header.embl
accessory.tab
bin/create_pan_genome
bin/create_pan_genome_plots.R
bin/extract_proteome_from_gff
bin/iterative_cdhit
bin/merge_multifasta_alignments
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/common/revtrans.py
binaries/darwin/bedtools
binaries/darwin/blastp
binaries/darwin/cd-hit
binaries/darwin/makeblastdb
binaries/darwin/mcl
binaries/darwin/mcxdeblast
binaries/darwin/muscle
binaries/darwin/parallel
binaries/linux/bedtools
binaries/linux/blastp
binaries/linux/cd-hit
binaries/linux/makeblastdb
binaries/linux/mcl
binaries/linux/mcxdeblast
binaries/linux/muscle
binaries/linux/parallel
blast_identity_frequency.Rtab
clustered_proteins
core_accessory.header.embl
core_accessory.tab
database_masking.asnb
deployment_process
dist.ini
gene_presence_absence.csv
lib/Bio/Roary.pm
lib/Bio/Roary/AnalyseGroups.pm
lib/Bio/Roary/AnnotateGroups.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/MergeMultipleFastaAlignments.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/Muscle.pm
lib/Bio/Roary/External/PostAnalysis.pm
lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm
lib/Bio/Roary/External/Revtrans.pm
lib/Bio/Roary/External/Segmasker.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/Kraken.pm
lib/Bio/Roary/QC/Report.pm
lib/Bio/Roary/QC/ShredAssemblies.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
number_of_conserved_genes.Rtab
number_of_genes_in_pan_genome.Rtab
number_of_new_genes.Rtab
number_of_unique_genes.Rtab
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