digraph {
graph [overlap=false]
subgraph cluster_Bio_Roary_External_ProteinMuscleAlignmentFromNucleotides {
	label="Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides";
	"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::meta";
	"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::BEGIN@88";
	"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::BEGIN@23";
}
subgraph cluster_Moose_Meta_Role_Application_ToRole {
	label="Moose::Meta::Role::Application::ToRole";
	"Moose::Meta::Role::Application::ToRole::meta";
}
subgraph cluster_Bio_Roary_Main_RoaryPostAnalysis {
	label="Bio::Roary::Main::RoaryPostAnalysis";
	"Bio::Roary::Main::RoaryPostAnalysis::BEGIN@17";
}
subgraph cluster_Moose_Meta_Role_Application_ToInstance {
	label="Moose::Meta::Role::Application::ToInstance";
	"Moose::Meta::Role::Application::ToInstance::meta";
}
subgraph cluster_Class_MOP_Mixin_HasMethods {
	label="Class::MOP::Mixin::HasMethods";
	"Class::MOP::Mixin::HasMethods::_full_method_map";
	"Class::MOP::Mixin::HasMethods::_add_meta_method";
	"Class::MOP::Mixin::HasMethods::get_method";
	"Class::MOP::Mixin::HasMethods::_code_is_mine";
	"Class::MOP::Mixin::HasMethods::has_method";
	"Class::MOP::Mixin::HasMethods::update_package_cache_flag";
	"Class::MOP::Mixin::HasMethods::add_method";
	"Class::MOP::Mixin::HasMethods::method_metaclass";
	"Class::MOP::Mixin::HasMethods::_get_maybe_raw_method";
	"Class::MOP::Mixin::HasMethods::remove_method";
	"Class::MOP::Mixin::HasMethods::wrapped_method_metaclass";
	"Class::MOP::Mixin::HasMethods::_method_map";
	"Class::MOP::Mixin::HasMethods::wrap_method_body";
}
subgraph cluster_Package_Stash_XS {
	label="Package::Stash::XS";
	"Package::Stash::XS::new";
	"Package::Stash::XS::get_symbol";
	"Package::Stash::XS::has_symbol";
	"Package::Stash::XS::remove_symbol";
	"Package::Stash::XS::list_all_symbols";
	"Package::Stash::XS::add_symbol";
	"Package::Stash::XS::get_or_add_symbol";
}
subgraph cluster_Moose {
	label="Moose";
	"Moose::BEGIN@32";
	"Moose::BEGIN@26";
	"Moose::init_meta";
	"Moose::import";
	"Moose::unimport";
	"Moose::BEGIN@38";
	"Moose::BEGIN@34";
	"Moose::BEGIN@35";
	"Moose::BEGIN@24";
	"Moose::BEGIN@40";
	"Moose::BEGIN@36";
	"Moose::BEGIN@33";
	"Moose::BEGIN@25";
}
subgraph cluster_Eval_Closure_Sandbox_306 {
	label="Eval::Closure::Sandbox_306";
	"Eval::Closure::Sandbox_306::CORE:match";
}
subgraph cluster_Eval_Closure_Sandbox_281 {
	label="Eval::Closure::Sandbox_281";
	"Eval::Closure::Sandbox_281::CORE:match";
}
subgraph cluster_Bio_Roary_CommandLine_Common {
	label="Bio::Roary::CommandLine::Common";
	"Bio::Roary::CommandLine::Common::BEGIN@12";
	"Bio::Roary::CommandLine::Common::BEGIN@38";
}
subgraph cluster_List_Util {
	label="List::Util";
	"List::Util::all";
	"List::Util::any";
}
subgraph cluster_Moose_Meta_TypeConstraint_Registry {
	label="Moose::Meta::TypeConstraint::Registry";
	"Moose::Meta::TypeConstraint::Registry::type_constraints";
	"Moose::Meta::TypeConstraint::Registry::has_type_constraint";
	"Moose::Meta::TypeConstraint::Registry::meta";
	"Moose::Meta::TypeConstraint::Registry::add_type_constraint";
	"Moose::Meta::TypeConstraint::Registry::get_type_constraint";
}
subgraph cluster_Moose_Meta_Instance {
	label="Moose::Meta::Instance";
	"Moose::Meta::Instance::_new";
}
subgraph cluster_parent {
	label="parent";
	"parent::import";
}
subgraph cluster_Moose_Meta_Role_Attribute {
	label="Moose::Meta::Role::Attribute";
	"Moose::Meta::Role::Attribute::original_role";
	"Moose::Meta::Role::Attribute::associated_role";
	"Moose::Meta::Role::Attribute::original_options";
	"Moose::Meta::Role::Attribute::attribute_for_class";
	"Moose::Meta::Role::Attribute::_original_role";
}
subgraph cluster_Eval_Closure_Sandbox_388 {
	label="Eval::Closure::Sandbox_388";
	"Eval::Closure::Sandbox_388::CORE:match";
}
subgraph cluster_UNIVERSAL {
	label="UNIVERSAL";
	"UNIVERSAL::isa";
	"UNIVERSAL::can";
}
subgraph cluster_Moose_Meta_TypeConstraint_Class {
	label="Moose::Meta::TypeConstraint::Class";
	"Moose::Meta::TypeConstraint::Class::__ANON__[Moose/Meta/TypeConstraint/Class.pm:25]";
	"Moose::Meta::TypeConstraint::Class::meta";
	"Moose::Meta::TypeConstraint::Class::class";
	"Moose::Meta::TypeConstraint::Class::_new";
}
subgraph cluster_Class_MOP_Method_Wrapped {
	label="Class::MOP::Method::Wrapped";
	"Class::MOP::Method::Wrapped::__ANON__[Class/MOP/Method/Wrapped.pm:158]";
	"Class::MOP::Method::Wrapped::wrap";
}
subgraph cluster_Moose_Meta_Class {
	label="Moose::Meta::Class";
	"Moose::Meta::Class::add_role";
	"Moose::Meta::Class::_process_new_attribute";
	"Moose::Meta::Class::_inline_check_required_attr";
	"Moose::Meta::Class::immutable_trait";
	"Moose::Meta::Class::CORE:sort";
	"Moose::Meta::Class::_inline_triggers";
	"Moose::Meta::Class::roles";
	"Moose::Meta::Class::_eval_environment";
	"Moose::Meta::Class::excludes_role";
	"Moose::Meta::Class::add_role_application";
	"Moose::Meta::Class::_inline_init_attr_from_default";
	"Moose::Meta::Class::superclasses";
	"Moose::Meta::Class::_inline_init_attr_from_constructor";
	"Moose::Meta::Class::_inline_slot_initializer";
	"Moose::Meta::Class::constructor_class";
	"Moose::Meta::Class::_inline_BUILDARGS";
	"Moose::Meta::Class::destructor_class";
	"Moose::Meta::Class::_get_role_applications";
}
subgraph cluster_Bio_Roary_AnnotateGroups {
	label="Bio::Roary::AnnotateGroups";
	"Bio::Roary::AnnotateGroups::groups_filename";
	"Bio::Roary::AnnotateGroups::CORE:sort";
	"Bio::Roary::AnnotateGroups::_groups_to_id_names";
	"Bio::Roary::AnnotateGroups::_ids_to_product";
	"Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
	"Bio::Roary::AnnotateGroups::_ids_to_groups";
	"Bio::Roary::AnnotateGroups::output_filename";
	"Bio::Roary::AnnotateGroups::__ANON__[lib/Bio/Roary/AnnotateGroups.pm:31]";
	"Bio::Roary::AnnotateGroups::BEGIN@21";
	"Bio::Roary::AnnotateGroups::BEGIN@325";
	"Bio::Roary::AnnotateGroups::_generate__ids_to_groups";
	"Bio::Roary::AnnotateGroups::reannotate";
	"Bio::Roary::AnnotateGroups::_build__output_fh";
	"Bio::Roary::AnnotateGroups::_groups";
	"Bio::Roary::AnnotateGroups::BEGIN@19";
	"Bio::Roary::AnnotateGroups::_ids_to_gene_names";
	"Bio::Roary::AnnotateGroups::new";
	"Bio::Roary::AnnotateGroups::_ids_grouped_by_gene_name_for_group";
	"Bio::Roary::AnnotateGroups::consensus_product_for_id_names";
	"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names";
	"Bio::Roary::AnnotateGroups::_generate_groups_to_consensus_gene_names";
	"Bio::Roary::AnnotateGroups::meta";
	"Bio::Roary::AnnotateGroups::gff_files";
	"Bio::Roary::AnnotateGroups::BUILD";
	"Bio::Roary::AnnotateGroups::_builder__groups_to_id_names";
	"Bio::Roary::AnnotateGroups::_filtered_gff_files";
	"Bio::Roary::AnnotateGroups::_split_groups";
	"Bio::Roary::AnnotateGroups::DESTROY";
	"Bio::Roary::AnnotateGroups::_build__filtered_gff_files";
	"Bio::Roary::AnnotateGroups::_output_fh";
	"Bio::Roary::AnnotateGroups::_group_default_prefix";
}
subgraph cluster_Moose_Meta_Method_Destructor {
	label="Moose::Meta::Method::Destructor";
	"Moose::Meta::Method::Destructor::_generate_DEMOLISHALL";
	"Moose::Meta::Method::Destructor::_initialize_body";
}
subgraph cluster_Moose_Meta_TypeConstraint_DuckType {
	label="Moose::Meta::TypeConstraint::DuckType";
	"Moose::Meta::TypeConstraint::DuckType::meta";
}
subgraph cluster_Eval_Closure_Sandbox_309 {
	label="Eval::Closure::Sandbox_309";
	"Eval::Closure::Sandbox_309::CORE:match";
}
subgraph cluster_Bio_Roary_GroupStatistics {
	label="Bio::Roary::GroupStatistics";
	"Bio::Roary::GroupStatistics::_files_to_groups";
	"Bio::Roary::GroupStatistics::BEGIN@202";
	"Bio::Roary::GroupStatistics::DESTROY";
	"Bio::Roary::GroupStatistics::_build__files_to_groups";
	"Bio::Roary::GroupStatistics::create_spreadsheet";
	"Bio::Roary::GroupStatistics::_row";
	"Bio::Roary::GroupStatistics::annotate_groups_obj";
	"Bio::Roary::GroupStatistics::_build__output_fh";
	"Bio::Roary::GroupStatistics::_output_fh";
	"Bio::Roary::GroupStatistics::output_filename";
	"Bio::Roary::GroupStatistics::_text_csv_obj";
	"Bio::Roary::GroupStatistics::_groups_to_files";
	"Bio::Roary::GroupStatistics::_header";
	"Bio::Roary::GroupStatistics::meta";
	"Bio::Roary::GroupStatistics::_sorted_file_names";
	"Bio::Roary::GroupStatistics::BEGIN@19";
	"Bio::Roary::GroupStatistics::new";
	"Bio::Roary::GroupStatistics::_verbose";
	"Bio::Roary::GroupStatistics::analyse_groups_obj";
	"Bio::Roary::GroupStatistics::_build__text_csv_obj";
	"Bio::Roary::GroupStatistics::groups_to_contigs";
	"Bio::Roary::GroupStatistics::_build__groups_to_files";
	"Bio::Roary::GroupStatistics::_build__sorted_file_names";
	"Bio::Roary::GroupStatistics::_non_unique_name_for_group";
}
subgraph cluster_Class_MOP_Method_Meta {
	label="Class::MOP::Method::Meta";
	"Class::MOP::Method::Meta::wrap";
}
subgraph cluster_Class_MOP_Method_Generated {
	label="Class::MOP::Method::Generated";
	"Class::MOP::Method::Generated::is_inline";
	"Class::MOP::Method::Generated::_generate_description";
	"Class::MOP::Method::Generated::definition_context";
}
subgraph cluster_Devel_GlobalDestruction {
	label="Devel::GlobalDestruction";
	"Devel::GlobalDestruction::BEGIN@3";
	"Devel::GlobalDestruction::BEGIN@8";
	"Devel::GlobalDestruction::BEGIN@23";
	"Devel::GlobalDestruction::BEGIN@4";
}
subgraph cluster_Class_MOP_Instance {
	label="Class::MOP::Instance";
	"Class::MOP::Instance::create_instance";
	"Class::MOP::Instance::associated_metaclass";
	"Class::MOP::Instance::_class_name";
	"Class::MOP::Instance::new";
}
subgraph cluster_Sub_Exporter_Progressive {
	label="Sub::Exporter::Progressive";
	"Sub::Exporter::Progressive::__ANON__[Sub/Exporter/Progressive.pm:40]";
}
subgraph cluster_Bio_Roary_JobRunner_Role {
	label="Bio::Roary::JobRunner::Role";
	"Bio::Roary::JobRunner::Role::BEGIN@12";
}
subgraph cluster_Module_Runtime {
	label="Module::Runtime";
	"Module::Runtime::import";
	"Module::Runtime::module_notional_filename";
}
subgraph cluster_Eval_Closure_Sandbox_426 {
	label="Eval::Closure::Sandbox_426";
	"Eval::Closure::Sandbox_426::CORE:match";
}
subgraph cluster_Class_MOP_Method_Constructor {
	label="Class::MOP::Method::Constructor";
	"Class::MOP::Method::Constructor::_eval_environment";
	"Class::MOP::Method::Constructor::_generate_constructor_method_inline";
	"Class::MOP::Method::Constructor::_initialize_body";
	"Class::MOP::Method::Constructor::options";
	"Class::MOP::Method::Constructor::associated_metaclass";
}
subgraph cluster_Bio_Roary_GroupLabels {
	label="Bio::Roary::GroupLabels";
	"Bio::Roary::GroupLabels::_group_default_prefix";
	"Bio::Roary::GroupLabels::new";
	"Bio::Roary::GroupLabels::add_labels";
	"Bio::Roary::GroupLabels::CORE:close";
	"Bio::Roary::GroupLabels::output_filename";
	"Bio::Roary::GroupLabels::_build__input_fh";
	"Bio::Roary::GroupLabels::_build__output_fh";
	"Bio::Roary::GroupLabels::_input_fh";
	"Bio::Roary::GroupLabels::meta";
	"Bio::Roary::GroupLabels::CORE:readline";
	"Bio::Roary::GroupLabels::BEGIN@59";
	"Bio::Roary::GroupLabels::BEGIN@18";
	"Bio::Roary::GroupLabels::DESTROY";
	"Bio::Roary::GroupLabels::CORE:open";
	"Bio::Roary::GroupLabels::groups_filename";
	"Bio::Roary::GroupLabels::CORE:print";
	"Bio::Roary::GroupLabels::_output_fh";
}
subgraph cluster_Moose_Meta_TypeConstraint_Role {
	label="Moose::Meta::TypeConstraint::Role";
	"Moose::Meta::TypeConstraint::Role::__ANON__[Moose/Meta/TypeConstraint/Role.pm:27]";
	"Moose::Meta::TypeConstraint::Role::_new";
	"Moose::Meta::TypeConstraint::Role::meta";
	"Moose::Meta::TypeConstraint::Role::role";
}
subgraph cluster_Moose_Meta_TypeCoercion_Union {
	label="Moose::Meta::TypeCoercion::Union";
	"Moose::Meta::TypeCoercion::Union::meta";
}
subgraph cluster_Eval_Closure_Sandbox_434 {
	label="Eval::Closure::Sandbox_434";
	"Eval::Closure::Sandbox_434::CORE:match";
}
subgraph cluster_Exporter {
	label="Exporter";
	"Exporter::import";
}
subgraph cluster_Bio_Roary_Output_NumberOfGroups {
	label="Bio::Roary::Output::NumberOfGroups";
	"Bio::Roary::Output::NumberOfGroups::create_output_files";
	"Bio::Roary::Output::NumberOfGroups::_total_genes";
	"Bio::Roary::Output::NumberOfGroups::DESTROY";
	"Bio::Roary::Output::NumberOfGroups::BEGIN@17";
	"Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:31]";
	"Bio::Roary::Output::NumberOfGroups::output_raw_filename_new_genes";
	"Bio::Roary::Output::NumberOfGroups::meta";
	"Bio::Roary::Output::NumberOfGroups::group_statistics_obj";
	"Bio::Roary::Output::NumberOfGroups::BEGIN@116";
	"Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:34]";
	"Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:32]";
	"Bio::Roary::Output::NumberOfGroups::_unique_genes";
	"Bio::Roary::Output::NumberOfGroups::output_raw_filename_total_genes";
	"Bio::Roary::Output::NumberOfGroups::number_of_iterations";
	"Bio::Roary::Output::NumberOfGroups::_conserved_genes";
	"Bio::Roary::Output::NumberOfGroups::new";
	"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion";
	"Bio::Roary::Output::NumberOfGroups::_shuffle_input_files";
	"Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:33]";
	"Bio::Roary::Output::NumberOfGroups::_new_genes";
	"Bio::Roary::Output::NumberOfGroups::output_raw_filename_conserved_genes";
	"Bio::Roary::Output::NumberOfGroups::output_raw_filename_unique_genes";
}
subgraph cluster_Class_MOP_Attribute {
	label="Class::MOP::Attribute";
	"Class::MOP::Attribute::_inline_instance_get";
	"Class::MOP::Attribute::associated_methods";
	"Class::MOP::Attribute::try {...} ";
	"Class::MOP::Attribute::has_value";
	"Class::MOP::Attribute::get_value";
	"Class::MOP::Attribute::slots";
	"Class::MOP::Attribute::new";
	"Class::MOP::Attribute::associated_class";
	"Class::MOP::Attribute::_inline_instance_has";
	"Class::MOP::Attribute::_inline_instance_clear";
	"Class::MOP::Attribute::install_accessors";
	"Class::MOP::Attribute::_set_initial_slot_value";
	"Class::MOP::Attribute::_accessor_description";
	"Class::MOP::Attribute::remove_accessors";
	"Class::MOP::Attribute::_inline_instance_set";
	"Class::MOP::Attribute::get_raw_value";
	"Class::MOP::Attribute::_process_accessors";
}
subgraph cluster_Bio_Roary_Output_GroupsMultifastasNucleotide {
	label="Bio::Roary::Output::GroupsMultifastasNucleotide";
	"Bio::Roary::Output::GroupsMultifastasNucleotide::BEGIN@23";
	"Bio::Roary::Output::GroupsMultifastasNucleotide::meta";
	"Bio::Roary::Output::GroupsMultifastasNucleotide::BEGIN@19";
	"Bio::Roary::Output::GroupsMultifastasNucleotide::BEGIN@75";
}
subgraph cluster_Class_MOP_MiniTrait {
	label="Class::MOP::MiniTrait";
	"Class::MOP::MiniTrait::apply";
}
subgraph cluster_Class_MOP_Class_ {
	label="Class::MOP::Class:";
	"Class::MOP::Class:::around";
}
subgraph cluster_Bio_Roary_PostAnalysis {
	label="Bio::Roary::PostAnalysis";
	"Bio::Roary::PostAnalysis::output_statistics_filename";
	"Bio::Roary::PostAnalysis::BEGIN@14";
	"Bio::Roary::PostAnalysis::input_files";
	"Bio::Roary::PostAnalysis::_number_of_groups_obj";
	"Bio::Roary::PostAnalysis::output_multifasta_files";
	"Bio::Roary::PostAnalysis::_build__group_labels_obj";
	"Bio::Roary::PostAnalysis::_create_embl_files";
	"Bio::Roary::PostAnalysis::DESTROY";
	"Bio::Roary::PostAnalysis::accessory_ordering_key";
	"Bio::Roary::PostAnalysis::BEGIN@20";
	"Bio::Roary::PostAnalysis::BEGIN@16";
	"Bio::Roary::PostAnalysis::_output_inflate_clusters_filename";
	"Bio::Roary::PostAnalysis::run";
	"Bio::Roary::PostAnalysis::_annotate_groups_obj";
	"Bio::Roary::PostAnalysis::clusters_filename";
	"Bio::Roary::PostAnalysis::BEGIN@18";
	"Bio::Roary::PostAnalysis::dont_split_groups";
	"Bio::Roary::PostAnalysis::fasta_files";
	"Bio::Roary::PostAnalysis::_input_cd_hit_groups_file";
	"Bio::Roary::PostAnalysis::BEGIN@19";
	"Bio::Roary::PostAnalysis::_group_labels_obj";
	"Bio::Roary::PostAnalysis::_analyse_groups_obj";
	"Bio::Roary::PostAnalysis::dont_create_rplots";
	"Bio::Roary::PostAnalysis::BEGIN@21";
	"Bio::Roary::PostAnalysis::accessory_tab_output_filename";
	"Bio::Roary::PostAnalysis::_output_group_labels_filename";
	"Bio::Roary::PostAnalysis::_order_genes_obj";
	"Bio::Roary::PostAnalysis::_build__split_groups_obj";
	"Bio::Roary::PostAnalysis::_build__annotate_groups_obj";
	"Bio::Roary::PostAnalysis::new";
	"Bio::Roary::PostAnalysis::_build__group_statistics_obj";
	"Bio::Roary::PostAnalysis::_inflate_clusters_obj";
	"Bio::Roary::PostAnalysis::_build__inflate_clusters_obj";
	"Bio::Roary::PostAnalysis::BEGIN@22";
	"Bio::Roary::PostAnalysis::BEGIN@15";
	"Bio::Roary::PostAnalysis::meta";
	"Bio::Roary::PostAnalysis::verbose_stats";
	"Bio::Roary::PostAnalysis::_build__number_of_groups_obj";
	"Bio::Roary::PostAnalysis::core_accessory_tab_output_filename";
	"Bio::Roary::PostAnalysis::BEGIN@13";
	"Bio::Roary::PostAnalysis::_group_statistics_obj";
	"Bio::Roary::PostAnalysis::BEGIN@11";
	"Bio::Roary::PostAnalysis::BEGIN@17";
	"Bio::Roary::PostAnalysis::_build__analyse_groups_obj";
	"Bio::Roary::PostAnalysis::_delete_intermediate_files";
	"Bio::Roary::PostAnalysis::BEGIN@225";
	"Bio::Roary::PostAnalysis::output_filename";
	"Bio::Roary::PostAnalysis::_output_mcl_filename";
	"Bio::Roary::PostAnalysis::_output_inflate_unsplit_clusters_filename";
	"Bio::Roary::PostAnalysis::core_accessory_ordering_key";
	"Bio::Roary::PostAnalysis::_split_groups_obj";
	"Bio::Roary::PostAnalysis::dont_delete_files";
	"Bio::Roary::PostAnalysis::_build__order_genes_obj";
}
subgraph cluster_Package_DeprecationManager {
	label="Package::DeprecationManager";
	"Package::DeprecationManager::__ANON__[Package/DeprecationManager.pm:61]";
}
subgraph cluster_Bio_Roary_AnalyseGroups {
	label="Bio::Roary::AnalyseGroups";
	"Bio::Roary::AnalyseGroups::_freq_groups_per_genome";
	"Bio::Roary::AnalyseGroups::_groups_to_genes";
	"Bio::Roary::AnalyseGroups::groups_filename";
	"Bio::Roary::AnalyseGroups::_builder__groups_to_genes";
	"Bio::Roary::AnalyseGroups::new";
	"Bio::Roary::AnalyseGroups::_count_num_files_in_group";
	"Bio::Roary::AnalyseGroups::BEGIN@19";
	"Bio::Roary::AnalyseGroups::fasta_files";
	"Bio::Roary::AnalyseGroups::_builder__files_to_genes";
	"Bio::Roary::AnalyseGroups::meta";
	"Bio::Roary::AnalyseGroups::_genes_to_groups";
	"Bio::Roary::AnalyseGroups::DESTROY";
	"Bio::Roary::AnalyseGroups::_files_to_genes";
	"Bio::Roary::AnalyseGroups::BEGIN@142";
	"Bio::Roary::AnalyseGroups::_builder__number_of_isolates";
	"Bio::Roary::AnalyseGroups::_genes_to_file";
	"Bio::Roary::AnalyseGroups::_builder__freq_groups_per_genome";
	"Bio::Roary::AnalyseGroups::_number_of_isolates";
	"Bio::Roary::AnalyseGroups::BUILD";
}
subgraph cluster_Moose_Meta_Role_Method_Required {
	label="Moose::Meta::Role::Method::Required";
	"Moose::Meta::Role::Method::Required::meta";
}
subgraph cluster_Moose_Meta_Attribute {
	label="Moose::Meta::Attribute";
	"Moose::Meta::Attribute::_eval_environment";
	"Moose::Meta::Attribute::_inline_generate_default";
	"Moose::Meta::Attribute::remove_accessors";
	"Moose::Meta::Attribute::_process_accessors";
	"Moose::Meta::Attribute::new";
	"Moose::Meta::Attribute::_inline_init_from_default";
	"Moose::Meta::Attribute::_inline_get_old_value_for_trigger";
	"Moose::Meta::Attribute::_inline_trigger";
	"Moose::Meta::Attribute::install_accessors";
	"Moose::Meta::Attribute::_inline_check_constraint";
	"Moose::Meta::Attribute::_inline_check_coercion";
	"Moose::Meta::Attribute::_inline_check_lazy";
	"Moose::Meta::Attribute::_inline_init_slot";
	"Moose::Meta::Attribute::_new";
	"Moose::Meta::Attribute::_auto_deref";
	"Moose::Meta::Attribute::_check_associated_methods";
	"Moose::Meta::Attribute::_writer_value_needs_copy";
	"Moose::Meta::Attribute::_inline_check_required";
	"Moose::Meta::Attribute::_inline_weaken_value";
}
subgraph cluster_Eval_Closure_Sandbox_433 {
	label="Eval::Closure::Sandbox_433";
	"Eval::Closure::Sandbox_433::CORE:match";
}
subgraph cluster_Class_MOP_Mixin_HasAttributes {
	label="Class::MOP::Mixin::HasAttributes";
	"Class::MOP::Mixin::HasAttributes::get_attribute";
	"Class::MOP::Mixin::HasAttributes::get_attribute_list";
	"Class::MOP::Mixin::HasAttributes::_attribute_map";
	"Class::MOP::Mixin::HasAttributes::remove_attribute";
	"Class::MOP::Mixin::HasAttributes::add_attribute";
	"Class::MOP::Mixin::HasAttributes::has_attribute";
	"Class::MOP::Mixin::HasAttributes::attribute_metaclass";
}
subgraph cluster_Bio_Roary_Output_GroupsMultifastaNucleotide {
	label="Bio::Roary::Output::GroupsMultifastaNucleotide";
	"Bio::Roary::Output::GroupsMultifastaNucleotide::BEGIN@17";
	"Bio::Roary::Output::GroupsMultifastaNucleotide::BEGIN@148";
	"Bio::Roary::Output::GroupsMultifastaNucleotide::meta";
}
subgraph cluster_Moose_Meta_Method_Accessor {
	label="Moose::Meta::Method::Accessor";
	"Moose::Meta::Method::Accessor::_eval_environment";
	"Moose::Meta::Method::Accessor::_instance_is_inlinable";
}
subgraph cluster_Moose_Meta_TypeConstraint {
	label="Moose::Meta::TypeConstraint";
	"Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:89]";
	"Moose::Meta::TypeConstraint::meta";
	"Moose::Meta::TypeConstraint::_inline_check";
	"Moose::Meta::TypeConstraint::_set_constraint";
	"Moose::Meta::TypeConstraint::has_message";
	"Moose::Meta::TypeConstraint::_has_compiled_type_constraint";
	"Moose::Meta::TypeConstraint::_has_inlined_type_constraint";
	"Moose::Meta::TypeConstraint::_compiled_type_constraint";
	"Moose::Meta::TypeConstraint::equals";
	"Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:36]";
	"Moose::Meta::TypeConstraint::new";
	"Moose::Meta::TypeConstraint::_inline_environment";
	"Moose::Meta::TypeConstraint::has_coercion";
	"Moose::Meta::TypeConstraint::is_subtype_of";
	"Moose::Meta::TypeConstraint::inline_environment";
	"Moose::Meta::TypeConstraint::_new";
	"Moose::Meta::TypeConstraint::parent";
	"Moose::Meta::TypeConstraint::_default_message";
	"Moose::Meta::TypeConstraint::can_be_inlined";
	"Moose::Meta::TypeConstraint::compile_type_constraint";
	"Moose::Meta::TypeConstraint::name";
	"Moose::Meta::TypeConstraint::has_parent";
	"Moose::Meta::TypeConstraint::constraint";
	"Moose::Meta::TypeConstraint::inlined";
}
subgraph cluster_Bio_Roary_ParseGFFAnnotationRole {
	label="Bio::Roary::ParseGFFAnnotationRole";
	"Bio::Roary::ParseGFFAnnotationRole::_gff_fh_input_string";
	"Bio::Roary::ParseGFFAnnotationRole::_build__awk_filter";
	"Bio::Roary::ParseGFFAnnotationRole::BEGIN@10";
}
subgraph cluster_Eval_Closure_Sandbox_171 {
	label="Eval::Closure::Sandbox_171";
	"Eval::Closure::Sandbox_171::CORE:match";
}
subgraph cluster_Moose_Meta_Role_Composite {
	label="Moose::Meta::Role::Composite";
	"Moose::Meta::Role::Composite::meta";
}
subgraph cluster_Class_MOP_Module {
	label="Class::MOP::Module";
	"Class::MOP::Module::_instantiate_module";
	"Class::MOP::Module::create";
}
subgraph cluster_warnings {
	label="warnings";
	"warnings::unimport";
	"warnings::import";
}
subgraph cluster_Moose_Exporter {
	label="Moose::Exporter";
	"Moose::Exporter::_get_caller";
	"Moose::Exporter::BEGIN@8";
	"Moose::Exporter::build_import_methods";
	"Moose::Exporter::_remove_keywords";
	"Moose::Exporter::_strip_metaclass";
	"Moose::Exporter::_strip_meta_name";
	"Moose::Exporter::_apply_metaroles";
	"Moose::Exporter::_strip_traits";
	"Moose::Exporter::__ANON__[Moose/Exporter.pm:140]";
}
subgraph cluster_Moose_Meta_TypeConstraint_Enum {
	label="Moose::Meta::TypeConstraint::Enum";
	"Moose::Meta::TypeConstraint::Enum::meta";
}
subgraph cluster_Moose_Meta_Role {
	label="Moose::Meta::Role";
	"Moose::Meta::Role::BEGIN@13";
	"Moose::Meta::Role::get_after_method_modifiers_map";
	"Moose::Meta::Role::get_required_methods_map";
	"Moose::Meta::Role::_new";
	"Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:351]";
	"Moose::Meta::Role::initialize";
	"Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:305]";
	"Moose::Meta::Role::get_method_modifier_list";
	"Moose::Meta::Role::get_override_method_modifiers_map";
	"Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:398]";
	"Moose::Meta::Role::BEGIN@11";
	"Moose::Meta::Role::add_attribute";
	"Moose::Meta::Role::applied_attribute_metaclass";
	"Moose::Meta::Role::method_metaclass";
	"Moose::Meta::Role::get_required_method_list";
	"Moose::Meta::Role::get_excluded_roles_list";
	"Moose::Meta::Role::application_to_class_class";
	"Moose::Meta::Role::CORE:match";
	"Moose::Meta::Role::meta";
	"Moose::Meta::Role::apply";
	"Moose::Meta::Role::get_before_method_modifiers_map";
	"Moose::Meta::Role::get_excluded_roles_map";
	"Moose::Meta::Role::get_around_method_modifiers_map";
	"Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:84]";
	"Moose::Meta::Role::BEGIN@14";
}
subgraph cluster_Moose_Util_TypeConstraints {
	label="Moose::Util::TypeConstraints";
	"Moose::Util::TypeConstraints::list_all_type_constraints";
	"Moose::Util::TypeConstraints::BEGIN@30";
	"Moose::Util::TypeConstraints::BEGIN@28";
	"Moose::Util::TypeConstraints::BEGIN@25";
	"Moose::Util::TypeConstraints::BEGIN@34";
	"Moose::Util::TypeConstraints::import";
	"Moose::Util::TypeConstraints::BEGIN@26";
	"Moose::Util::TypeConstraints::BEGIN@29";
	"Moose::Util::TypeConstraints::BEGIN@31";
}
subgraph cluster_Class_MOP_Method_Inlined {
	label="Class::MOP::Method::Inlined";
	"Class::MOP::Method::Inlined::_expected_method_class";
	"Class::MOP::Method::Inlined::can_be_inlined";
}
subgraph cluster_Bio_Roary_ContigsToGeneIDsFromGFF {
	label="Bio::Roary::ContigsToGeneIDsFromGFF";
	"Bio::Roary::ContigsToGeneIDsFromGFF::meta";
	"Bio::Roary::ContigsToGeneIDsFromGFF::contig_to_ids";
	"Bio::Roary::ContigsToGeneIDsFromGFF::new";
	"Bio::Roary::ContigsToGeneIDsFromGFF::CORE:match";
	"Bio::Roary::ContigsToGeneIDsFromGFF::BEGIN@17";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_awk_filter";
	"Bio::Roary::ContigsToGeneIDsFromGFF::CORE:close";
	"Bio::Roary::ContigsToGeneIDsFromGFF::CORE:readline";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_min_nucleotide_overlap_percentage";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_build_overlapping_hypothetical_protein_ids";
	"Bio::Roary::ContigsToGeneIDsFromGFF::BEGIN@142";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_tags_to_filter";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_build__awk_filter";
	"Bio::Roary::ContigsToGeneIDsFromGFF::DESTROY";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids";
	"Bio::Roary::ContigsToGeneIDsFromGFF::gff_file";
	"Bio::Roary::ContigsToGeneIDsFromGFF::overlapping_hypothetical_protein_ids";
	"Bio::Roary::ContigsToGeneIDsFromGFF::__ANON__[lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm:24]";
	"Bio::Roary::ContigsToGeneIDsFromGFF::_genes_annotation";
	"Bio::Roary::ContigsToGeneIDsFromGFF::CORE:open";
}
subgraph cluster_Moose_Util_TypeConstraints_Builtins {
	label="Moose::Util::TypeConstraints::Builtins";
	"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:60]";
	"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:170]";
	"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:284]";
	"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:77]";
}
subgraph cluster_Moose_Meta_TypeConstraint_Parameterized {
	label="Moose::Meta::TypeConstraint::Parameterized";
	"Moose::Meta::TypeConstraint::Parameterized::meta";
	"Moose::Meta::TypeConstraint::Parameterized::_new";
	"Moose::Meta::TypeConstraint::Parameterized::BEGIN@10";
	"Moose::Meta::TypeConstraint::Parameterized::_inline_check";
	"Moose::Meta::TypeConstraint::Parameterized::has_type_parameter";
	"Moose::Meta::TypeConstraint::Parameterized::inline_environment";
	"Moose::Meta::TypeConstraint::Parameterized::compile_type_constraint";
	"Moose::Meta::TypeConstraint::Parameterized::has_parameterized_from";
	"Moose::Meta::TypeConstraint::Parameterized::parameterized_from";
	"Moose::Meta::TypeConstraint::Parameterized::can_be_inlined";
	"Moose::Meta::TypeConstraint::Parameterized::type_parameter";
}
subgraph cluster_Moose_Meta_Role_Application_RoleSummation {
	label="Moose::Meta::Role::Application::RoleSummation";
	"Moose::Meta::Role::Application::RoleSummation::meta";
}
subgraph cluster_Moose_Meta_Mixin_AttributeCore {
	label="Moose::Meta::Mixin::AttributeCore";
	"Moose::Meta::Mixin::AttributeCore::has_trigger";
	"Moose::Meta::Mixin::AttributeCore::should_auto_deref";
	"Moose::Meta::Mixin::AttributeCore::type_constraint";
	"Moose::Meta::Mixin::AttributeCore::is_required";
	"Moose::Meta::Mixin::AttributeCore::should_coerce";
	"Moose::Meta::Mixin::AttributeCore::has_handles";
	"Moose::Meta::Mixin::AttributeCore::is_lazy";
	"Moose::Meta::Mixin::AttributeCore::has_type_constraint";
	"Moose::Meta::Mixin::AttributeCore::is_weak_ref";
}
subgraph cluster_Eval_Closure_Sandbox_431 {
	label="Eval::Closure::Sandbox_431";
	"Eval::Closure::Sandbox_431::CORE:match";
}
subgraph cluster_Scalar_Util {
	label="Scalar::Util";
	"Scalar::Util::blessed";
}
subgraph cluster_Bio_Roary_SplitGroups {
	label="Bio::Roary::SplitGroups";
	"Bio::Roary::SplitGroups::max_recursion";
	"Bio::Roary::SplitGroups::BEGIN@318";
	"Bio::Roary::SplitGroups::_set_genes_to_groups";
	"Bio::Roary::SplitGroups::fasta_files";
	"Bio::Roary::SplitGroups::_analyse_groups_obj";
	"Bio::Roary::SplitGroups::BEGIN@11";
	"Bio::Roary::SplitGroups::_genes_to_files";
	"Bio::Roary::SplitGroups::_genes_to_groups";
	"Bio::Roary::SplitGroups::_parse_gene_neighbourhood";
	"Bio::Roary::SplitGroups::meta";
	"Bio::Roary::SplitGroups::__ANON__[lib/Bio/Roary/SplitGroups.pm:38]";
	"Bio::Roary::SplitGroups::_pre_filter_fasta_files";
	"Bio::Roary::SplitGroups::split_groups";
	"Bio::Roary::SplitGroups::_update_genes_to_groups";
	"Bio::Roary::SplitGroups::new";
	"Bio::Roary::SplitGroups::_make_tmp_dir";
	"Bio::Roary::SplitGroups::DESTROY";
	"Bio::Roary::SplitGroups::groupfile";
	"Bio::Roary::SplitGroups::_gene_files_temp_dir_obj";
	"Bio::Roary::SplitGroups::_find_paralogs";
	"Bio::Roary::SplitGroups::_same_group";
	"Bio::Roary::SplitGroups::outfile";
	"Bio::Roary::SplitGroups::_tmp_dir";
	"Bio::Roary::SplitGroups::_build__genes_to_files";
	"Bio::Roary::SplitGroups::_true_orthologs";
	"Bio::Roary::SplitGroups::_build__analyse_groups_obj";
	"Bio::Roary::SplitGroups::_do_sorting";
	"Bio::Roary::SplitGroups::_neighbourhood_size";
}
subgraph cluster_Bio_Roary_InflateClusters {
	label="Bio::Roary::InflateClusters";
	"Bio::Roary::InflateClusters::inflate";
	"Bio::Roary::InflateClusters::CORE:close";
	"Bio::Roary::InflateClusters::_output_fh";
	"Bio::Roary::InflateClusters::cdhit_groups_filename";
	"Bio::Roary::InflateClusters::_build__mcl_fh";
	"Bio::Roary::InflateClusters::_mcl_fh";
	"Bio::Roary::InflateClusters::_clustered_genes";
	"Bio::Roary::InflateClusters::CORE:open";
	"Bio::Roary::InflateClusters::BEGIN@19";
	"Bio::Roary::InflateClusters::BEGIN@106";
	"Bio::Roary::InflateClusters::DESTROY";
	"Bio::Roary::InflateClusters::_build__output_fh";
	"Bio::Roary::InflateClusters::_inflate_gene";
	"Bio::Roary::InflateClusters::CORE:print";
	"Bio::Roary::InflateClusters::CORE:readline";
	"Bio::Roary::InflateClusters::meta";
	"Bio::Roary::InflateClusters::mcl_filename";
	"Bio::Roary::InflateClusters::new";
	"Bio::Roary::InflateClusters::_clusters_fh";
	"Bio::Roary::InflateClusters::clusters_filename";
	"Bio::Roary::InflateClusters::output_file";
}
subgraph cluster_Eval_Closure_Sandbox_295 {
	label="Eval::Closure::Sandbox_295";
	"Eval::Closure::Sandbox_295::CORE:match";
}
subgraph cluster_Class_MOP_Mixin {
	label="Class::MOP::Mixin";
	"Class::MOP::Mixin::meta";
}
subgraph cluster_Class_MOP_Mixin_HasOverloads {
	label="Class::MOP::Mixin::HasOverloads";
	"Class::MOP::Mixin::HasOverloads::is_overloaded";
}
subgraph cluster_Class_MOP_Method_Accessor {
	label="Class::MOP::Method::Accessor";
	"Class::MOP::Method::Accessor::_generate_accessor_method_inline";
	"Class::MOP::Method::Accessor::_generate_predicate_method";
	"Class::MOP::Method::Accessor::_generate_writer_method_inline";
	"Class::MOP::Method::Accessor::_generate_accessor_method";
	"Class::MOP::Method::Accessor::_generate_clearer_method_inline";
	"Class::MOP::Method::Accessor::_initialize_body";
	"Class::MOP::Method::Accessor::accessor_type";
	"Class::MOP::Method::Accessor::_generate_reader_method";
	"Class::MOP::Method::Accessor::_generate_reader_method_inline";
	"Class::MOP::Method::Accessor::_generate_writer_method";
	"Class::MOP::Method::Accessor::associated_attribute";
	"Class::MOP::Method::Accessor::_generate_clearer_method";
	"Class::MOP::Method::Accessor::_generate_predicate_method_inline";
}
subgraph cluster_Sub_Exporter {
	label="Sub::Exporter";
	"Sub::Exporter::__ANON__[Sub/Exporter.pm:337]";
}
subgraph cluster_Moose_Meta_TypeConstraint_Parameterizable {
	label="Moose::Meta::TypeConstraint::Parameterizable";
	"Moose::Meta::TypeConstraint::Parameterizable::has_inline_generator";
	"Moose::Meta::TypeConstraint::Parameterizable::inline_generator";
	"Moose::Meta::TypeConstraint::Parameterizable::constraint_generator";
	"Moose::Meta::TypeConstraint::Parameterizable::parameterize";
	"Moose::Meta::TypeConstraint::Parameterizable::meta";
	"Moose::Meta::TypeConstraint::Parameterizable::generate_inline_for";
	"Moose::Meta::TypeConstraint::Parameterizable::_new";
	"Moose::Meta::TypeConstraint::Parameterizable::has_constraint_generator";
	"Moose::Meta::TypeConstraint::Parameterizable::generate_constraint_for";
}
subgraph cluster_Class_MOP_Object {
	label="Class::MOP::Object";
	"Class::MOP::Object::meta";
}
subgraph cluster_strict {
	label="strict";
	"strict::import";
	"strict::unimport";
}
subgraph cluster_Class_MOP_Class {
	label="Class::MOP::Class";
	"Class::MOP::Class::linearized_isa";
	"Class::MOP::Class::find_attribute_by_name";
	"Class::MOP::Class::class_precedence_list";
	"Class::MOP::Class::_inline_constructor";
	"Class::MOP::Class::_inline_slot_initializer";
	"Class::MOP::Class::_inline_fallback_constructor";
	"Class::MOP::Class::__ANON__[Class/MOP/Class.pm:1082]";
	"Class::MOP::Class::get_all_attributes";
	"Class::MOP::Class::_immutable_metaclass";
	"Class::MOP::Class::immutable_trait";
	"Class::MOP::Class::_construct_instance";
	"Class::MOP::Class::_inline_default_value";
	"Class::MOP::Class::_single_metaclass_is_compatible";
	"Class::MOP::Class::_inline_preserve_weak_metaclasses";
	"Class::MOP::Class::create";
	"Class::MOP::Class::instance_metaclass";
	"Class::MOP::Class::superclasses";
	"Class::MOP::Class::constructor_name";
	"Class::MOP::Class::_immutable_options";
	"Class::MOP::Class::CORE:sort";
	"Class::MOP::Class::_check_metaclass_compatibility";
	"Class::MOP::Class::_inline_init_attr_from_constructor";
	"Class::MOP::Class::initialize";
	"Class::MOP::Class::_inline_init_attr_from_default";
	"Class::MOP::Class::destructor_class";
	"Class::MOP::Class::_construct_class_instance";
	"Class::MOP::Class::_real_ref_name";
	"Class::MOP::Class::_single_metaclass_can_be_made_compatible";
	"Class::MOP::Class::_inline_destructor";
	"Class::MOP::Class::get_all_methods";
	"Class::MOP::Class::_create_meta_instance";
	"Class::MOP::Class::_superclasses_updated";
	"Class::MOP::Class::constructor_class";
	"Class::MOP::Class::new_object";
}
subgraph cluster_Bio_Roary_CommandLine_RoaryPostAnalysis {
	label="Bio::Roary::CommandLine::RoaryPostAnalysis";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::group_limit";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::dont_create_rplots";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::CORE:readline";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::output_statistics_filename";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@188";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::verbose_stats";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::clusters_filename";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::cpus";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::_read_file_into_array";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::fasta_files";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::core_definition";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::meta";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::DESTROY";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@15";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::run";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::input_files";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::job_runner";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::output_filename";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::help";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::_error_message";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::CORE:open";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::output_multifasta_files";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::translation_table";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::output_pan_geneome_filename";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::new";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::dont_delete_files";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::args";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::dont_split_groups";
	"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD";
}
subgraph cluster_Class_MOP {
	label="Class::MOP";
	"Class::MOP::store_metaclass_by_name";
	"Class::MOP::__ANON__[Class/MOP.pm:499]";
	"Class::MOP::__ANON__[Class/MOP.pm:139]";
	"Class::MOP::__ANON__[Class/MOP.pm:270]";
	"Class::MOP::__ANON__[Class/MOP.pm:184]";
	"Class::MOP::__ANON__[Class/MOP.pm:290]";
	"Class::MOP::__ANON__[Class/MOP.pm:211]";
	"Class::MOP::get_metaclass_by_name";
	"Class::MOP::__ANON__[Class/MOP.pm:243]";
}
subgraph cluster_Bio_Roary_OrderGenes {
	label="Bio::Roary::OrderGenes";
	"Bio::Roary::OrderGenes::meta";
	"Bio::Roary::OrderGenes::groups_to_contigs";
	"Bio::Roary::OrderGenes::_build__groups_to_file_contigs";
	"Bio::Roary::OrderGenes::_reorder_connected_components";
	"Bio::Roary::OrderGenes::new";
	"Bio::Roary::OrderGenes::CORE:sort";
	"Bio::Roary::OrderGenes::BEGIN@352";
	"Bio::Roary::OrderGenes::__ANON__[lib/Bio/Roary/OrderGenes.pm:33]";
	"Bio::Roary::OrderGenes::_build_groups_to_contigs";
	"Bio::Roary::OrderGenes::_percentage_of_largest_weak_threshold";
	"Bio::Roary::OrderGenes::_create_accessory_graph";
	"Bio::Roary::OrderGenes::gff_files";
	"Bio::Roary::OrderGenes::_remove_weak_edges_from_graph";
	"Bio::Roary::OrderGenes::analyse_groups_obj";
	"Bio::Roary::OrderGenes::_build_number_of_files";
	"Bio::Roary::OrderGenes::DESTROY";
	"Bio::Roary::OrderGenes::group_graphs";
	"Bio::Roary::OrderGenes::group_order";
	"Bio::Roary::OrderGenes::_groups_to_file_contigs";
	"Bio::Roary::OrderGenes::_groups_qc";
	"Bio::Roary::OrderGenes::_add_groups_to_graph";
	"Bio::Roary::OrderGenes::number_of_files";
	"Bio::Roary::OrderGenes::BEGIN@18";
	"Bio::Roary::OrderGenes::_build_group_order";
	"Bio::Roary::OrderGenes::BEGIN@21";
	"Bio::Roary::OrderGenes::_build_group_graphs";
}
subgraph cluster_Eval_Closure_Sandbox_432 {
	label="Eval::Closure::Sandbox_432";
	"Eval::Closure::Sandbox_432::CORE:match";
}
subgraph cluster_Moose_Meta_Role_Method {
	label="Moose::Meta::Role::Method";
	"Moose::Meta::Role::Method::_new";
}
subgraph cluster_Moose_Meta_Method {
	label="Moose::Meta::Method";
	"Moose::Meta::Method::_new";
}
subgraph cluster_Class_MOP_Class_Immutable_Class_MOP_Class {
	label="Class::MOP::Class::Immutable::Class::MOP::Class";
	"Class::MOP::Class::Immutable::Class::MOP::Class::_method_map";
	"Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance";
	"Class::MOP::Class::Immutable::Class::MOP::Class::get_all_attributes";
	"Class::MOP::Class::Immutable::Class::MOP::Class::is_immutable";
	"Class::MOP::Class::Immutable::Class::MOP::Class::linearized_isa";
}
subgraph cluster_Moose_Role {
	label="Moose::Role";
	"Moose::Role::BEGIN@18";
	"Moose::Role::import";
	"Moose::Role::init_meta";
}
subgraph cluster_main {
	label="main";
	"main::NULL";
	"main::RUNTIME";
}
subgraph cluster_Bio_Roary_GeneNamesFromGFF {
	label="Bio::Roary::GeneNamesFromGFF";
	"Bio::Roary::GeneNamesFromGFF::CORE:close";
	"Bio::Roary::GeneNamesFromGFF::gff_file";
	"Bio::Roary::GeneNamesFromGFF::BEGIN@65";
	"Bio::Roary::GeneNamesFromGFF::CORE:open";
	"Bio::Roary::GeneNamesFromGFF::CORE:readline";
	"Bio::Roary::GeneNamesFromGFF::BEGIN@17";
	"Bio::Roary::GeneNamesFromGFF::_tags_to_filter";
	"Bio::Roary::GeneNamesFromGFF::__ANON__[lib/Bio/Roary/GeneNamesFromGFF.pm:23]";
	"Bio::Roary::GeneNamesFromGFF::meta";
	"Bio::Roary::GeneNamesFromGFF::ids_to_product";
	"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name";
	"Bio::Roary::GeneNamesFromGFF::_awk_filter";
	"Bio::Roary::GeneNamesFromGFF::CORE:match";
	"Bio::Roary::GeneNamesFromGFF::new";
	"Bio::Roary::GeneNamesFromGFF::CORE:subst";
	"Bio::Roary::GeneNamesFromGFF::ids_to_gene_name";
	"Bio::Roary::GeneNamesFromGFF::DESTROY";
}
subgraph cluster_Class_MOP_Package {
	label="Class::MOP::Package";
	"Class::MOP::Package::get_package_symbol";
	"Class::MOP::Package::initialize";
	"Class::MOP::Package::BEGIN@8";
	"Class::MOP::Package::BEGIN@171";
	"Class::MOP::Package::has_package_symbol";
	"Class::MOP::Package::BEGIN@9";
	"Class::MOP::Package::BEGIN@12";
	"Class::MOP::Package::remove_package_symbol";
	"Class::MOP::Package::list_all_package_symbols";
	"Class::MOP::Package::BEGIN@10";
	"Class::MOP::Package::_new";
	"Class::MOP::Package::BEGIN@95";
	"Class::MOP::Package::BEGIN@7";
	"Class::MOP::Package::add_package_symbol";
	"Class::MOP::Package::BEGIN@5";
	"Class::MOP::Package::_package_stash";
	"Class::MOP::Package::name";
	"Class::MOP::Package::create";
	"Class::MOP::Package::get_or_add_package_symbol";
	"Class::MOP::Package::BEGIN@4";
}
subgraph cluster_Bio_Roary_Output_EmblGroups {
	label="Bio::Roary::Output::EmblGroups";
	"Bio::Roary::Output::EmblGroups::_build__groups_to_files";
	"Bio::Roary::Output::EmblGroups::_annotation_type";
	"Bio::Roary::Output::EmblGroups::_sorted_file_names";
	"Bio::Roary::Output::EmblGroups::_build__sorted_file_names";
	"Bio::Roary::Output::EmblGroups::annotate_groups_obj";
	"Bio::Roary::Output::EmblGroups::CORE:print";
	"Bio::Roary::Output::EmblGroups::create_files";
	"Bio::Roary::Output::EmblGroups::CORE:match";
	"Bio::Roary::Output::EmblGroups::new";
	"Bio::Roary::Output::EmblGroups::CORE:sort";
	"Bio::Roary::Output::EmblGroups::_output_header_fh";
	"Bio::Roary::Output::EmblGroups::_output_fh";
	"Bio::Roary::Output::EmblGroups::_fragment_blocks";
	"Bio::Roary::Output::EmblGroups::output_filename";
	"Bio::Roary::Output::EmblGroups::CORE:subst";
	"Bio::Roary::Output::EmblGroups::BEGIN@239";
	"Bio::Roary::Output::EmblGroups::_build__output_header_fh";
	"Bio::Roary::Output::EmblGroups::meta";
	"Bio::Roary::Output::EmblGroups::_block";
	"Bio::Roary::Output::EmblGroups::BEGIN@19";
	"Bio::Roary::Output::EmblGroups::_header_block";
	"Bio::Roary::Output::EmblGroups::_build__output_fh";
	"Bio::Roary::Output::EmblGroups::output_header_filename";
	"Bio::Roary::Output::EmblGroups::CORE:close";
	"Bio::Roary::Output::EmblGroups::ordering_key";
	"Bio::Roary::Output::EmblGroups::_build_output_header_filename";
	"Bio::Roary::Output::EmblGroups::groups_to_contigs";
	"Bio::Roary::Output::EmblGroups::DESTROY";
	"Bio::Roary::Output::EmblGroups::CORE:open";
	"Bio::Roary::Output::EmblGroups::analyse_groups_obj";
	"Bio::Roary::Output::EmblGroups::_groups_to_files";
}
subgraph cluster_Bio_Roary_ClustersRole {
	label="Bio::Roary::ClustersRole";
	"Bio::Roary::ClustersRole::_build__clusters_fh";
	"Bio::Roary::ClustersRole::BEGIN@11";
	"Bio::Roary::ClustersRole::_build__clustered_genes";
}
subgraph cluster_Class_MOP_Mixin_AttributeCore {
	label="Class::MOP::Mixin::AttributeCore";
	"Class::MOP::Mixin::AttributeCore::predicate";
	"Class::MOP::Mixin::AttributeCore::has_builder";
	"Class::MOP::Mixin::AttributeCore::has_initializer";
	"Class::MOP::Mixin::AttributeCore::has_default";
	"Class::MOP::Mixin::AttributeCore::has_accessor";
	"Class::MOP::Mixin::AttributeCore::name";
	"Class::MOP::Mixin::AttributeCore::clearer";
	"Class::MOP::Mixin::AttributeCore::has_reader";
	"Class::MOP::Mixin::AttributeCore::_set_insertion_order";
	"Class::MOP::Mixin::AttributeCore::definition_context";
	"Class::MOP::Mixin::AttributeCore::has_writer";
	"Class::MOP::Mixin::AttributeCore::reader";
	"Class::MOP::Mixin::AttributeCore::accessor";
	"Class::MOP::Mixin::AttributeCore::has_clearer";
	"Class::MOP::Mixin::AttributeCore::has_predicate";
	"Class::MOP::Mixin::AttributeCore::writer";
	"Class::MOP::Mixin::AttributeCore::init_arg";
	"Class::MOP::Mixin::AttributeCore::builder";
}
subgraph cluster_Class_MOP_Method {
	label="Class::MOP::Method";
	"Class::MOP::Method::name";
	"Class::MOP::Method::clone";
	"Class::MOP::Method::associated_metaclass";
	"Class::MOP::Method::body";
	"Class::MOP::Method::wrap";
	"Class::MOP::Method::package_name";
	"Class::MOP::Method::_set_original_method";
}
subgraph cluster_Moose_Meta_TypeConstraint_Union {
	label="Moose::Meta::TypeConstraint::Union";
	"Moose::Meta::TypeConstraint::Union::meta";
}
subgraph cluster_Moose_Meta_TypeCoercion {
	label="Moose::Meta::TypeCoercion";
	"Moose::Meta::TypeCoercion::BEGIN@8";
	"Moose::Meta::TypeCoercion::meta";
}
subgraph cluster_Moose_Meta_Role_Application {
	label="Moose::Meta::Role::Application";
	"Moose::Meta::Role::Application::new";
	"Moose::Meta::Role::Application::is_method_excluded";
	"Moose::Meta::Role::Application::get_method_aliases";
	"Moose::Meta::Role::Application::is_method_aliased";
	"Moose::Meta::Role::Application::get_method_exclusions";
	"Moose::Meta::Role::Application::meta";
	"Moose::Meta::Role::Application::__ANON__[Moose/Meta/Role/Application.pm:16]";
	"Moose::Meta::Role::Application::__ANON__[Moose/Meta/Role/Application.pm:23]";
}
subgraph cluster_Moose_Meta_Role_Application_ToClass {
	label="Moose::Meta::Role::Application::ToClass";
	"Moose::Meta::Role::Application::ToClass::meta";
	"Moose::Meta::Role::Application::ToClass::check_required_methods";
	"Moose::Meta::Role::Application::ToClass::_new";
	"Moose::Meta::Role::Application::ToClass::check_role_exclusions";
	"Moose::Meta::Role::Application::ToClass::apply_methods";
}
subgraph cluster_Eval_Closure_Sandbox_352 {
	label="Eval::Closure::Sandbox_352";
	"Eval::Closure::Sandbox_352::CORE:match";
}
"Bio::Roary::AnalyseGroups::BUILD" -> "Bio::Roary::AnalyseGroups::_freq_groups_per_genome";
"Bio::Roary::OrderGenes::BEGIN@21" -> "Bio::Roary::ContigsToGeneIDsFromGFF::meta";
"Bio::Roary::SplitGroups::_build__analyse_groups_obj" -> "Bio::Roary::SplitGroups::fasta_files";
"Bio::Roary::SplitGroups::_pre_filter_fasta_files" -> "Bio::Roary::SplitGroups::fasta_files";
"Moose::Meta::Role::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:184]";
"Bio::Roary::OrderGenes::number_of_files" -> "Eval::Closure::Sandbox_306::CORE:match";
"Bio::Roary::ParseGFFAnnotationRole::_gff_fh_input_string" -> "Bio::Roary::GeneNamesFromGFF::gff_file";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::cpus";
"Moose::Meta::Attribute::_inline_init_from_default" -> "Class::MOP::Mixin::AttributeCore::has_default";
"Moose::Meta::Attribute::_eval_environment" -> "Class::MOP::Mixin::AttributeCore::has_default";
"Moose::Meta::Attribute::_inline_generate_default" -> "Class::MOP::Mixin::AttributeCore::has_default";
"Moose::Meta::Class::_inline_check_required_attr" -> "Class::MOP::Mixin::AttributeCore::has_default";
"Class::MOP::Class::_inline_default_value" -> "Class::MOP::Mixin::AttributeCore::has_default";
"Bio::Roary::GroupLabels::_build__output_fh" -> "Bio::Roary::GroupLabels::output_filename";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::fasta_files";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::fasta_files";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::core_definition";
"Class::MOP::Class::find_attribute_by_name" -> "Class::MOP::Class::Immutable::Class::MOP::Class::linearized_isa";
"Class::MOP::Class::get_all_attributes" -> "Class::MOP::Class::Immutable::Class::MOP::Class::linearized_isa";
"Bio::Roary::PostAnalysis::_build__inflate_clusters_obj" -> "Bio::Roary::PostAnalysis::clusters_filename";
"Moose::Meta::TypeConstraint::Parameterized::_inline_check" -> "Moose::Meta::TypeConstraint::Parameterized::parameterized_from";
"Moose::Meta::TypeConstraint::Parameterized::can_be_inlined" -> "Moose::Meta::TypeConstraint::Parameterized::parameterized_from";
"Moose::Meta::TypeConstraint::Parameterized::inline_environment" -> "Moose::Meta::TypeConstraint::Parameterized::parameterized_from";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::Output::EmblGroups::CORE:subst";
"Bio::Roary::Output::EmblGroups::_build_output_header_filename" -> "Bio::Roary::Output::EmblGroups::CORE:subst";
"Class::MOP::Mixin::HasAttributes::add_attribute" -> "Class::MOP::Mixin::AttributeCore::_set_insertion_order";
"Class::MOP::Mixin::HasMethods::add_method" -> "Class::MOP::Method::package_name";
"Class::MOP::MiniTrait::apply" -> "Class::MOP::Method::package_name";
"Bio::Roary::Output::EmblGroups::_output_fh" -> "Bio::Roary::Output::EmblGroups::_build__output_fh";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::dont_create_rplots";
"Moose::Meta::Attribute::_inline_check_lazy" -> "Moose::Meta::Mixin::AttributeCore::is_lazy";
"Moose::Meta::Class::_inline_init_attr_from_default" -> "Moose::Meta::Mixin::AttributeCore::is_lazy";
"Bio::Roary::InflateClusters::_clustered_genes" -> "Bio::Roary::ClustersRole::_build__clustered_genes";
"Class::MOP::Package::BEGIN@7" -> "Exporter::import";
"Class::MOP::Package::BEGIN@8" -> "Exporter::import";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::translation_table";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::ContigsToGeneIDsFromGFF::DESTROY";
"Bio::Roary::CommandLine::RoaryPostAnalysis::core_definition" -> "Eval::Closure::Sandbox_433::CORE:match";
"Class::MOP::Attribute::_process_accessors" -> "Class::MOP::Class::instance_metaclass";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Class::MOP::Class::instance_metaclass";
"Class::MOP::Class::_single_metaclass_is_compatible" -> "Class::MOP::Class::instance_metaclass";
"Class::MOP::Class::_create_meta_instance" -> "Class::MOP::Class::instance_metaclass";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Class::MOP::Class::instance_metaclass";
"List::Util::all" -> "Class::MOP::Class::instance_metaclass";
"Moose::Meta::Method::Accessor::_instance_is_inlinable" -> "Class::MOP::Class::instance_metaclass";
"Bio::Roary::PostAnalysis::_split_groups_obj" -> "Bio::Roary::PostAnalysis::_build__split_groups_obj";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::PostAnalysis::new";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::Parameterizable::_new";
"Bio::Roary::AnalyseGroups::_builder__freq_groups_per_genome" -> "Bio::Roary::AnalyseGroups::_number_of_isolates";
"Class::MOP::Class::_immutable_options" -> "Class::MOP::Class::constructor_name";
"Moose::BEGIN@26" -> "Moose::Meta::TypeCoercion::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::TypeCoercion::meta";
"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names" -> "Bio::Roary::GeneNamesFromGFF::ids_to_gene_name";
"Bio::Roary::Output::EmblGroups::_build__groups_to_files" -> "Bio::Roary::Output::EmblGroups::analyse_groups_obj";
"Bio::Roary::Output::EmblGroups::_build__sorted_file_names" -> "Bio::Roary::Output::EmblGroups::analyse_groups_obj";
"Moose::Meta::Attribute::_inline_generate_default" -> "Class::MOP::Mixin::AttributeCore::builder";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::_inflate_clusters_obj";
"Class::MOP::Class::superclasses" -> "Class::MOP::Class::_check_metaclass_compatibility";
"Bio::Roary::AnalyseGroups::BUILD" -> "Bio::Roary::AnalyseGroups::_groups_to_genes";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::output_raw_filename_new_genes";
"parent::import" -> "Class::MOP::Package::BEGIN@171";
"Moose::Meta::TypeConstraint::can_be_inlined" -> "Moose::Meta::TypeConstraint::_has_inlined_type_constraint";
"Bio::Roary::Output::NumberOfGroups::new" -> "Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:34]";
"Bio::Roary::Output::NumberOfGroups::new" -> "Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:32]";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::_unique_genes";
"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion" -> "Bio::Roary::Output::NumberOfGroups::_unique_genes";
"Class::MOP::Package::create" -> "Module::Runtime::module_notional_filename";
"Moose::Meta::Role::Application::is_method_excluded" -> "Moose::Meta::Role::Application::get_method_exclusions";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::core_accessory_tab_output_filename";
"Bio::Roary::GroupLabels::add_labels" -> "Bio::Roary::GroupLabels::_input_fh";
"parent::import" -> "Class::MOP::Package::BEGIN@9";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::SplitGroups::DESTROY";
"Bio::Roary::SplitGroups::_build__analyse_groups_obj" -> "Bio::Roary::SplitGroups::groupfile";
"Bio::Roary::SplitGroups::split_groups" -> "Bio::Roary::SplitGroups::groupfile";
"Bio::Roary::PostAnalysis::BEGIN@21" -> "Bio::Roary::Output::EmblGroups::meta";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::GroupStatistics::new";
"parent::import" -> "Class::MOP::Package::BEGIN@10";
"Class::MOP::Class::superclasses" -> "Class::MOP::Class::_superclasses_updated";
"Bio::Roary::GroupStatistics::_text_csv_obj" -> "Bio::Roary::GroupStatistics::_build__text_csv_obj";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::has_clearer";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Mixin::AttributeCore::has_clearer";
"Bio::Roary::OrderGenes::new" -> "Eval::Closure::Sandbox_309::CORE:match";
"Moose::Util::TypeConstraints::import" -> "Moose::Exporter::_strip_meta_name";
"Moose::import" -> "Moose::Exporter::_strip_meta_name";
"Moose::Role::import" -> "Moose::Exporter::_strip_meta_name";
"Moose::BEGIN@40" -> "Moose::Util::TypeConstraints::import";
"Moose::Role::BEGIN@18" -> "Moose::Util::TypeConstraints::import";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Class::MOP::Mixin::HasMethods::method_metaclass";
"Class::MOP::Class::_single_metaclass_is_compatible" -> "Class::MOP::Mixin::HasMethods::method_metaclass";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Class::MOP::Mixin::HasMethods::method_metaclass";
"List::Util::all" -> "Class::MOP::Mixin::HasMethods::method_metaclass";
"Class::MOP::Mixin::HasMethods::wrap_method_body" -> "Class::MOP::Mixin::HasMethods::method_metaclass";
"Bio::Roary::PostAnalysis::_build__inflate_clusters_obj" -> "Bio::Roary::PostAnalysis::_output_inflate_unsplit_clusters_filename";
"Bio::Roary::PostAnalysis::_build__split_groups_obj" -> "Bio::Roary::PostAnalysis::_output_inflate_unsplit_clusters_filename";
"Class::MOP::Module::create" -> "Class::MOP::Package::create";
"Class::MOP::Class::superclasses" -> "Class::MOP::Package::get_or_add_package_symbol";
"Class::MOP::Package::BEGIN@8" -> "Devel::GlobalDestruction::BEGIN@8";
"Bio::Roary::GroupLabels::add_labels" -> "Bio::Roary::GroupLabels::_group_default_prefix";
"Moose::Util::TypeConstraints::BEGIN@30" -> "Moose::Meta::TypeConstraint::Enum::meta";
"Bio::Roary::InflateClusters::_clusters_fh" -> "Bio::Roary::ClustersRole::_build__clusters_fh";
"Moose::Meta::Role::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:270]";
"Moose::Util::TypeConstraints::BEGIN@25" -> "Moose::Meta::TypeConstraint::Union::meta";
"Moose::Meta::Role::Application::ToClass::_new" -> "Moose::Meta::Role::Application::__ANON__[Moose/Meta/Role/Application.pm:23]";
"Bio::Roary::SplitGroups::new" -> "Bio::Roary::SplitGroups::__ANON__[lib/Bio/Roary/SplitGroups.pm:38]";
"Moose::Meta::TypeConstraint::Parameterized::compile_type_constraint" -> "Moose::Meta::TypeConstraint::Parameterized::has_type_parameter";
"Moose::Meta::TypeConstraint::Parameterized::inline_environment" -> "Moose::Meta::TypeConstraint::Parameterized::has_type_parameter";
"Moose::BEGIN@35" -> "Moose::Meta::Role::Application::RoleSummation::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Application::RoleSummation::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::group_limit" -> "Eval::Closure::Sandbox_432::CORE:match";
"Bio::Roary::GroupStatistics::_build__groups_to_files" -> "Bio::Roary::GroupStatistics::annotate_groups_obj";
"Bio::Roary::GroupStatistics::_non_unique_name_for_group" -> "Bio::Roary::GroupStatistics::annotate_groups_obj";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::GroupStatistics::annotate_groups_obj";
"Bio::Roary::GroupStatistics::create_spreadsheet" -> "Bio::Roary::GroupStatistics::annotate_groups_obj";
"Bio::Roary::Output::EmblGroups::_annotation_type" -> "Bio::Roary::Output::EmblGroups::CORE:match";
"Bio::Roary::Main::RoaryPostAnalysis::BEGIN@17" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::meta";
"Bio::Roary::GroupStatistics::create_spreadsheet" -> "Bio::Roary::GroupStatistics::_text_csv_obj";
"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::CORE:readline";
"Bio::Roary::Output::EmblGroups::_build__sorted_file_names" -> "Bio::Roary::Output::EmblGroups::CORE:sort";
"Bio::Roary::Output::EmblGroups::_fragment_blocks" -> "Bio::Roary::Output::EmblGroups::CORE:sort";
"Bio::Roary::ContigsToGeneIDsFromGFF::meta" -> "Scalar::Util::blessed";
"Bio::Roary::OrderGenes::new" -> "Scalar::Util::blessed";
"Bio::Roary::GroupStatistics::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::TypeCoercion::Union::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_analyse_groups_obj" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::_new" -> "Scalar::Util::blessed";
"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Application::ToClass::meta" -> "Scalar::Util::blessed";
"Bio::Roary::ContigsToGeneIDsFromGFF::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Parameterizable::_new" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::new" -> "Scalar::Util::blessed";
"Bio::Roary::InflateClusters::new" -> "Scalar::Util::blessed";
"Moose::Meta::TypeCoercion::meta" -> "Scalar::Util::blessed";
"Bio::Roary::GeneNamesFromGFF::DESTROY" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_inflate_clusters_obj" -> "Scalar::Util::blessed";
"Bio::Roary::GroupLabels::new" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Parameterized::_new" -> "Scalar::Util::blessed";
"Class::MOP::Mixin::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::meta" -> "Scalar::Util::blessed";
"Bio::Roary::ContigsToGeneIDsFromGFF::new" -> "Scalar::Util::blessed";
"Bio::Roary::GroupLabels::meta" -> "Scalar::Util::blessed";
"Bio::Roary::CommandLine::RoaryPostAnalysis::DESTROY" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_group_statistics_obj" -> "Scalar::Util::blessed";
"Bio::Roary::SplitGroups::new" -> "Scalar::Util::blessed";
"Bio::Roary::GroupStatistics::meta" -> "Scalar::Util::blessed";
"Bio::Roary::SplitGroups::DESTROY" -> "Scalar::Util::blessed";
"Bio::Roary::Output::EmblGroups::meta" -> "Scalar::Util::blessed";
"Bio::Roary::GroupStatistics::new" -> "Scalar::Util::blessed";
"Bio::Roary::OrderGenes::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::Role::meta" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Parameterizable::meta" -> "Scalar::Util::blessed";
"Bio::Roary::GroupLabels::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Method::Required::meta" -> "Scalar::Util::blessed";
"Bio::Roary::Output::GroupsMultifastasNucleotide::meta" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Enum::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Method::_new" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Union::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Role::_new" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Role::_new" -> "Scalar::Util::blessed";
"Bio::Roary::SplitGroups::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Instance::_new" -> "Scalar::Util::blessed";
"Bio::Roary::AnalyseGroups::new" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_number_of_groups_obj" -> "Scalar::Util::blessed";
"Bio::Roary::Output::NumberOfGroups::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Application::RoleSummation::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Composite::meta" -> "Scalar::Util::blessed";
"Bio::Roary::Output::NumberOfGroups::meta" -> "Scalar::Util::blessed";
"Bio::Roary::CommandLine::RoaryPostAnalysis::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_annotate_groups_obj" -> "Scalar::Util::blessed";
"Bio::Roary::GroupStatistics::_text_csv_obj" -> "Scalar::Util::blessed";
"Bio::Roary::AnnotateGroups::new" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Role::meta" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Parameterized::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_group_labels_obj" -> "Scalar::Util::blessed";
"Bio::Roary::AnnotateGroups::meta" -> "Scalar::Util::blessed";
"Bio::Roary::OrderGenes::group_graphs" -> "Scalar::Util::blessed";
"Bio::Roary::AnalyseGroups::DESTROY" -> "Scalar::Util::blessed";
"Bio::Roary::GeneNamesFromGFF::new" -> "Scalar::Util::blessed";
"Bio::Roary::Output::GroupsMultifastaNucleotide::meta" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Class::_new" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Class::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_order_genes_obj" -> "Scalar::Util::blessed";
"Bio::Roary::CommandLine::RoaryPostAnalysis::new" -> "Scalar::Util::blessed";
"Bio::Roary::InflateClusters::meta" -> "Scalar::Util::blessed";
"Bio::Roary::Output::EmblGroups::DESTROY" -> "Scalar::Util::blessed";
"Bio::Roary::OrderGenes::meta" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::meta" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::Registry::meta" -> "Scalar::Util::blessed";
"Class::MOP::Object::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Application::ToRole::meta" -> "Scalar::Util::blessed";
"Bio::Roary::Output::EmblGroups::new" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Application::meta" -> "Scalar::Util::blessed";
"Bio::Roary::Output::NumberOfGroups::new" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Application::ToClass::_new" -> "Scalar::Util::blessed";
"Bio::Roary::GeneNamesFromGFF::meta" -> "Scalar::Util::blessed";
"Bio::Roary::AnalyseGroups::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Attribute::_new" -> "Scalar::Util::blessed";
"Bio::Roary::InflateClusters::DESTROY" -> "Scalar::Util::blessed";
"Bio::Roary::AnnotateGroups::DESTROY" -> "Scalar::Util::blessed";
"Moose::Meta::TypeConstraint::DuckType::meta" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Method::_new" -> "Scalar::Util::blessed";
"Moose::Meta::Role::Application::ToInstance::meta" -> "Scalar::Util::blessed";
"Bio::Roary::PostAnalysis::_split_groups_obj" -> "Scalar::Util::blessed";
"Bio::Roary::GeneNamesFromGFF::new" -> "Bio::Roary::GeneNamesFromGFF::__ANON__[lib/Bio/Roary/GeneNamesFromGFF.pm:23]";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::output_raw_filename_total_genes";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Class::MOP::Mixin::HasMethods::wrapped_method_metaclass";
"Class::MOP::Class::__ANON__[Class/MOP/Class.pm:1082]" -> "Class::MOP::Mixin::HasMethods::wrapped_method_metaclass";
"Class::MOP::Class::_single_metaclass_is_compatible" -> "Class::MOP::Mixin::HasMethods::wrapped_method_metaclass";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Class::MOP::Mixin::HasMethods::wrapped_method_metaclass";
"List::Util::all" -> "Class::MOP::Mixin::HasMethods::wrapped_method_metaclass";
"Moose::Meta::Role::Application::ToClass::_new" -> "Moose::Meta::Role::Application::__ANON__[Moose/Meta/Role/Application.pm:16]";
"Moose::Meta::Role::Attribute::attribute_for_class" -> "Moose::Meta::Role::applied_attribute_metaclass";
"Class::MOP::Method::Constructor::_initialize_body" -> "Class::MOP::Method::Generated::is_inline";
"Class::MOP::Method::Accessor::_initialize_body" -> "Class::MOP::Method::Generated::is_inline";
"Bio::Roary::AnalyseGroups::_builder__files_to_genes" -> "Bio::Roary::AnalyseGroups::fasta_files";
"Bio::Roary::GroupStatistics::_build__sorted_file_names" -> "Bio::Roary::AnalyseGroups::fasta_files";
"Bio::Roary::Output::EmblGroups::_build__sorted_file_names" -> "Bio::Roary::AnalyseGroups::fasta_files";
"Bio::Roary::AnalyseGroups::_builder__number_of_isolates" -> "Bio::Roary::AnalyseGroups::fasta_files";
"Bio::Roary::PostAnalysis::_build__analyse_groups_obj" -> "Bio::Roary::PostAnalysis::fasta_files";
"Bio::Roary::PostAnalysis::_build__split_groups_obj" -> "Bio::Roary::PostAnalysis::fasta_files";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::_conserved_genes";
"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion" -> "Bio::Roary::Output::NumberOfGroups::_conserved_genes";
"Class::MOP::Package::has_package_symbol" -> "Package::Stash::XS::has_symbol";
"Moose::Meta::Role::Application::ToClass::check_role_exclusions" -> "Moose::Meta::Role::get_excluded_roles_list";
"Moose::Util::TypeConstraints::BEGIN@26" -> "Moose::Meta::TypeConstraint::Parameterized::meta";
"Moose::Meta::Role::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:211]";
"Bio::Roary::OrderGenes::_add_groups_to_graph" -> "Bio::Roary::OrderGenes::group_graphs";
"Bio::Roary::OrderGenes::_build_groups_to_contigs" -> "Bio::Roary::OrderGenes::group_graphs";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::AnalyseGroups::DESTROY";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::Class::_new";
"Moose::Meta::Role::get_excluded_roles_list" -> "Moose::Meta::Role::get_excluded_roles_map";
"Bio::Roary::GroupStatistics::_sorted_file_names" -> "Bio::Roary::GroupStatistics::_build__sorted_file_names";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Class::MOP::Class::superclasses";
"Class::MOP::Class::create" -> "Class::MOP::Class::superclasses";
"Class::MOP::Class::_superclasses_updated" -> "Class::MOP::Class::superclasses";
"Moose::Meta::Class::superclasses" -> "Class::MOP::Class::superclasses";
"Bio::Roary::Output::NumberOfGroups::new" -> "Eval::Closure::Sandbox_281::CORE:match";
"Moose::BEGIN@25" -> "Moose::Meta::TypeConstraint::meta";
"Bio::Roary::SplitGroups::new" -> "Eval::Closure::Sandbox_352::CORE:match";
"Bio::Roary::Output::EmblGroups::_sorted_file_names" -> "Bio::Roary::Output::EmblGroups::_build__sorted_file_names";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::verbose_stats";
"Class::MOP::Package::get_or_add_package_symbol" -> "Package::Stash::XS::get_or_add_symbol";
"Moose::Exporter::BEGIN@8" -> "Class::MOP::Object::meta";
"Class::MOP::Method::Meta::wrap" -> "Class::MOP::Object::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Class::MOP::Object::meta";
"Moose::Meta::TypeCoercion::BEGIN@8" -> "Class::MOP::Object::meta";
"Moose::Meta::Attribute::new" -> "Class::MOP::Object::meta";
"Moose::BEGIN@24" -> "Class::MOP::Object::meta";
"Class::MOP::Class::_immutable_metaclass" -> "Class::MOP::Object::meta";
"Class::MOP::Class::_construct_class_instance" -> "Class::MOP::Object::meta";
"Moose::Meta::Role::_new" -> "Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:305]";
"Bio::Roary::GroupStatistics::_output_fh" -> "Bio::Roary::GroupStatistics::_build__output_fh";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Application::ToRole::meta";
"Moose::Meta::Role::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:290]";
"Bio::Roary::AnalyseGroups::_number_of_isolates" -> "Eval::Closure::Sandbox_171::CORE:match";
"Moose::Meta::TypeConstraint::Role::__ANON__[Moose/Meta/TypeConstraint/Role.pm:27]" -> "Moose::Meta::TypeConstraint::Role::role";
"Class::MOP::Package::get_package_symbol" -> "Package::Stash::XS::get_symbol";
"Class::MOP::Method::Constructor::_generate_constructor_method_inline" -> "Class::MOP::Method::Constructor::options";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::reader";
"Class::MOP::Mixin::HasMethods::_full_method_map" -> "Class::MOP::Package::list_all_package_symbols";
"Bio::Roary::PostAnalysis::BEGIN@14" -> "Bio::Roary::AnalyseGroups::meta";
"Moose::Meta::Role::apply" -> "Moose::Meta::Role::application_to_class_class";
"Class::MOP::Package::list_all_package_symbols" -> "Package::Stash::XS::list_all_symbols";
"Class::MOP::Attribute::new" -> "Moose::Meta::Attribute::_new";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::help";
"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::CORE:match";
"Moose::Util::TypeConstraints::BEGIN@31" -> "Moose::Meta::TypeConstraint::DuckType::meta";
"parent::import" -> "Class::MOP::Package::BEGIN@5";
"Bio::Roary::AnnotateGroups::_filtered_gff_files" -> "Bio::Roary::AnnotateGroups::_build__filtered_gff_files";
"Bio::Roary::OrderGenes::_build_groups_to_contigs" -> "Bio::Roary::OrderGenes::_groups_qc";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::OrderGenes::_groups_qc";
"Bio::Roary::ContigsToGeneIDsFromGFF::contig_to_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids";
"Bio::Roary::AnalyseGroups::_builder__files_to_genes" -> "Bio::Roary::AnalyseGroups::_genes_to_file";
"Bio::Roary::Output::EmblGroups::_build__groups_to_files" -> "Bio::Roary::AnalyseGroups::_genes_to_file";
"Bio::Roary::SplitGroups::_build__genes_to_files" -> "Bio::Roary::AnalyseGroups::_genes_to_file";
"Bio::Roary::GroupStatistics::_build__groups_to_files" -> "Bio::Roary::AnalyseGroups::_genes_to_file";
"Bio::Roary::AnalyseGroups::_count_num_files_in_group" -> "Bio::Roary::AnalyseGroups::_genes_to_file";
"Moose::Util::TypeConstraints::import" -> "Moose::Exporter::_apply_metaroles";
"Moose::import" -> "Moose::Exporter::_apply_metaroles";
"Moose::Role::import" -> "Moose::Exporter::_apply_metaroles";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::core_accessory_ordering_key";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Moose::Meta::Class::constructor_class";
"Class::MOP::Class::_single_metaclass_is_compatible" -> "Moose::Meta::Class::constructor_class";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Moose::Meta::Class::constructor_class";
"Class::MOP::Class::_immutable_options" -> "Moose::Meta::Class::constructor_class";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::dont_create_rplots";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::dont_create_rplots";
"Bio::Roary::OrderGenes::_reorder_connected_components" -> "Bio::Roary::OrderGenes::CORE:sort";
"Bio::Roary::PostAnalysis::_group_labels_obj" -> "Bio::Roary::PostAnalysis::_build__group_labels_obj";
"Moose::Meta::Attribute::_inline_init_from_default" -> "Class::MOP::Mixin::AttributeCore::has_builder";
"Moose::Meta::Attribute::_inline_generate_default" -> "Class::MOP::Mixin::AttributeCore::has_builder";
"Moose::Meta::Class::_inline_check_required_attr" -> "Class::MOP::Mixin::AttributeCore::has_builder";
"Class::MOP::Class::_inline_default_value" -> "Class::MOP::Mixin::AttributeCore::has_builder";
"Bio::Roary::PostAnalysis::_build__split_groups_obj" -> "Bio::Roary::PostAnalysis::_output_inflate_clusters_filename";
"Bio::Roary::PostAnalysis::_build__group_labels_obj" -> "Bio::Roary::PostAnalysis::_output_inflate_clusters_filename";
"Class::MOP::Method::Constructor::_generate_constructor_method_inline" -> "Class::MOP::Method::Constructor::associated_metaclass";
"Class::MOP::Method::Constructor::_eval_environment" -> "Class::MOP::Method::Constructor::associated_metaclass";
"Class::MOP::Method::Inlined::can_be_inlined" -> "Class::MOP::Method::Constructor::associated_metaclass";
"Moose::Exporter::__ANON__[Moose/Exporter.pm:140]" -> "Class::MOP::Package::has_package_symbol";
"Moose::Exporter::build_import_methods" -> "Class::MOP::Package::has_package_symbol";
"Moose::Meta::Attribute::_process_accessors" -> "Class::MOP::Package::has_package_symbol";
"Bio::Roary::Output::EmblGroups::create_files" -> "Bio::Roary::Output::EmblGroups::_output_fh";
"Bio::Roary::ParseGFFAnnotationRole::_gff_fh_input_string" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_awk_filter";
"Moose::Meta::TypeConstraint::Parameterized::compile_type_constraint" -> "Moose::Meta::TypeConstraint::Parameterized::type_parameter";
"Moose::Meta::TypeConstraint::Parameterized::_inline_check" -> "Moose::Meta::TypeConstraint::Parameterized::type_parameter";
"Moose::Meta::TypeConstraint::Parameterized::can_be_inlined" -> "Moose::Meta::TypeConstraint::Parameterized::type_parameter";
"Moose::Meta::TypeConstraint::Parameterized::inline_environment" -> "Moose::Meta::TypeConstraint::Parameterized::type_parameter";
"Moose::Meta::TypeConstraint::Parameterizable::generate_constraint_for" -> "Moose::Meta::TypeConstraint::Parameterized::type_parameter";
"Bio::Roary::AnnotateGroups::_ids_grouped_by_gene_name_for_group" -> "Bio::Roary::AnnotateGroups::_ids_to_gene_names";
"Bio::Roary::AnnotateGroups::BUILD" -> "Bio::Roary::AnnotateGroups::_ids_to_gene_names";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::_clustered_genes";
"Bio::Roary::InflateClusters::_inflate_gene" -> "Bio::Roary::InflateClusters::_clustered_genes";
"Moose::Meta::TypeConstraint::Parameterizable::generate_inline_for" -> "Moose::Meta::TypeConstraint::Parameterizable::inline_generator";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::AnalyseGroups::_genes_to_groups";
"Bio::Roary::AnalyseGroups::_builder__groups_to_genes" -> "Bio::Roary::AnalyseGroups::_genes_to_groups";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::job_runner";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::_new";
"Bio::Roary::Output::EmblGroups::_build__output_header_fh" -> "Bio::Roary::Output::EmblGroups::output_header_filename";
"Bio::Roary::AnnotateGroups::_groups_to_id_names" -> "Bio::Roary::AnnotateGroups::_builder__groups_to_id_names";
"Bio::Roary::InflateClusters::_output_fh" -> "Bio::Roary::InflateClusters::_build__output_fh";
"Class::MOP::Instance::_class_name" -> "Class::MOP::Instance::associated_metaclass";
"Moose::Meta::Role::Application::ToClass::apply_methods" -> "Class::MOP::Method::name";
"Class::MOP::MiniTrait::apply" -> "Class::MOP::Method::name";
"Class::MOP::Method::Inlined::can_be_inlined" -> "Class::MOP::Method::name";
"Class::MOP::Class::get_all_methods" -> "Class::MOP::Method::name";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::output_raw_filename_conserved_genes";
"Bio::Roary::PostAnalysis::_build__annotate_groups_obj" -> "Bio::Roary::PostAnalysis::_output_group_labels_filename";
"Bio::Roary::PostAnalysis::_build__group_labels_obj" -> "Bio::Roary::PostAnalysis::_output_group_labels_filename";
"Bio::Roary::ParseGFFAnnotationRole::_gff_fh_input_string" -> "Bio::Roary::ContigsToGeneIDsFromGFF::gff_file";
"Bio::Roary::AnalyseGroups::_freq_groups_per_genome" -> "Bio::Roary::AnalyseGroups::_builder__freq_groups_per_genome";
"Bio::Roary::AnalyseGroups::_freq_groups_per_genome" -> "UNIVERSAL::can";
"Bio::Roary::InflateClusters::_output_fh" -> "UNIVERSAL::can";
"Bio::Roary::SplitGroups::_genes_to_files" -> "UNIVERSAL::can";
"Bio::Roary::GroupStatistics::_output_fh" -> "UNIVERSAL::can";
"Bio::Roary::Output::EmblGroups::_output_fh" -> "UNIVERSAL::can";
"Bio::Roary::ContigsToGeneIDsFromGFF::_awk_filter" -> "UNIVERSAL::can";
"Bio::Roary::AnnotateGroups::_ids_to_gene_names" -> "UNIVERSAL::can";
"Bio::Roary::InflateClusters::_clustered_genes" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_analyse_groups_obj" -> "UNIVERSAL::can";
"Bio::Roary::Output::EmblGroups::output_header_filename" -> "UNIVERSAL::can";
"Bio::Roary::OrderGenes::_groups_to_file_contigs" -> "UNIVERSAL::can";
"Bio::Roary::ContigsToGeneIDsFromGFF::overlapping_hypothetical_protein_ids" -> "UNIVERSAL::can";
"Bio::Roary::AnalyseGroups::_number_of_isolates" -> "UNIVERSAL::can";
"Bio::Roary::GeneNamesFromGFF::ids_to_gene_name" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_inflate_clusters_obj" -> "UNIVERSAL::can";
"Bio::Roary::AnalyseGroups::_groups_to_genes" -> "UNIVERSAL::can";
"Bio::Roary::ContigsToGeneIDsFromGFF::contig_to_ids" -> "UNIVERSAL::can";
"Bio::Roary::OrderGenes::groups_to_contigs" -> "UNIVERSAL::can";
"Moose::import" -> "UNIVERSAL::can";
"Bio::Roary::GroupLabels::_input_fh" -> "UNIVERSAL::can";
"Bio::Roary::Output::EmblGroups::_output_header_fh" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_group_statistics_obj" -> "UNIVERSAL::can";
"Bio::Roary::OrderGenes::group_order" -> "UNIVERSAL::can";
"Bio::Roary::AnnotateGroups::_filtered_gff_files" -> "UNIVERSAL::can";
"Bio::Roary::AnnotateGroups::_output_fh" -> "UNIVERSAL::can";
"Moose::Util::TypeConstraints::import" -> "UNIVERSAL::can";
"Bio::Roary::InflateClusters::_clusters_fh" -> "UNIVERSAL::can";
"Bio::Roary::GroupStatistics::_files_to_groups" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_number_of_groups_obj" -> "UNIVERSAL::can";
"Bio::Roary::AnnotateGroups::_groups_to_id_names" -> "UNIVERSAL::can";
"Bio::Roary::InflateClusters::_mcl_fh" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_annotate_groups_obj" -> "UNIVERSAL::can";
"Bio::Roary::GroupStatistics::_text_csv_obj" -> "UNIVERSAL::can";
"Bio::Roary::GroupStatistics::_sorted_file_names" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_group_labels_obj" -> "UNIVERSAL::can";
"Bio::Roary::OrderGenes::group_graphs" -> "UNIVERSAL::can";
"Bio::Roary::AnalyseGroups::_files_to_genes" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_order_genes_obj" -> "UNIVERSAL::can";
"Bio::Roary::Output::EmblGroups::_sorted_file_names" -> "UNIVERSAL::can";
"Bio::Roary::SplitGroups::_analyse_groups_obj" -> "UNIVERSAL::can";
"Bio::Roary::GroupStatistics::_groups_to_files" -> "UNIVERSAL::can";
"Bio::Roary::GeneNamesFromGFF::_awk_filter" -> "UNIVERSAL::can";
"Moose::Role::import" -> "UNIVERSAL::can";
"Bio::Roary::OrderGenes::number_of_files" -> "UNIVERSAL::can";
"Bio::Roary::PostAnalysis::_split_groups_obj" -> "UNIVERSAL::can";
"Bio::Roary::Output::EmblGroups::_groups_to_files" -> "UNIVERSAL::can";
"Bio::Roary::GroupLabels::_output_fh" -> "UNIVERSAL::can";
"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::CORE:subst";
"Bio::Roary::PostAnalysis::_build__inflate_clusters_obj" -> "Bio::Roary::InflateClusters::new";
"Bio::Roary::ClustersRole::_build__clusters_fh" -> "Bio::Roary::InflateClusters::clusters_filename";
"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names" -> "Bio::Roary::GeneNamesFromGFF::DESTROY";
"Bio::Roary::PostAnalysis::_build__number_of_groups_obj" -> "Bio::Roary::OrderGenes::groups_to_contigs";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::OrderGenes::groups_to_contigs";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::OrderGenes::groups_to_contigs";
"Bio::Roary::PostAnalysis::_build__group_labels_obj" -> "Bio::Roary::GroupLabels::new";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::Parameterized::_new";
"Class::MOP::Package::BEGIN@171" -> "strict::unimport";
"Bio::Roary::OrderGenes::_groups_to_file_contigs" -> "Bio::Roary::OrderGenes::_build__groups_to_file_contigs";
"Bio::Roary::Output::NumberOfGroups::new" -> "Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:31]";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::has_accessor";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Mixin::AttributeCore::has_accessor";
"Moose::Meta::Role::get_method_modifier_list" -> "Moose::Meta::Role::get_override_method_modifiers_map";
"Class::MOP::Class::Immutable::Class::MOP::Class::_method_map" -> "Class::MOP::Method::Wrapped::__ANON__[Class/MOP/Method/Wrapped.pm:158]";
"Class::MOP::Class::Immutable::Class::MOP::Class::get_all_attributes" -> "Class::MOP::Method::Wrapped::__ANON__[Class/MOP/Method/Wrapped.pm:158]";
"Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance" -> "Class::MOP::Method::Wrapped::__ANON__[Class/MOP/Method/Wrapped.pm:158]";
"Class::MOP::Class::Immutable::Class::MOP::Class::linearized_isa" -> "Class::MOP::Method::Wrapped::__ANON__[Class/MOP/Method/Wrapped.pm:158]";
"Class::MOP::Class::Immutable::Class::MOP::Class::is_immutable" -> "Class::MOP::Method::Wrapped::__ANON__[Class/MOP/Method/Wrapped.pm:158]";
"Moose::Meta::Role::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:243]";
"Class::MOP::Package::BEGIN@8" -> "Sub::Exporter::Progressive::__ANON__[Sub/Exporter/Progressive.pm:40]";
"Bio::Roary::PostAnalysis::_build__number_of_groups_obj" -> "Bio::Roary::PostAnalysis::_group_statistics_obj";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::_group_statistics_obj";
"Bio::Roary::PostAnalysis::_build__split_groups_obj" -> "Bio::Roary::SplitGroups::new";
"Moose::Meta::Role::Attribute::original_role" -> "Moose::Meta::Role::Attribute::_original_role";
"Moose::Meta::Attribute::_eval_environment" -> "Moose::Meta::Mixin::AttributeCore::has_trigger";
"Moose::Meta::Attribute::_inline_get_old_value_for_trigger" -> "Moose::Meta::Mixin::AttributeCore::has_trigger";
"Moose::Meta::Class::_inline_triggers" -> "Moose::Meta::Mixin::AttributeCore::has_trigger";
"Moose::Meta::Attribute::_inline_trigger" -> "Moose::Meta::Mixin::AttributeCore::has_trigger";
"Moose::Meta::Class::_eval_environment" -> "Moose::Meta::Mixin::AttributeCore::has_trigger";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::CORE:open";
"Bio::Roary::InflateClusters::_build__mcl_fh" -> "Bio::Roary::InflateClusters::CORE:open";
"Bio::Roary::InflateClusters::_build__output_fh" -> "Bio::Roary::InflateClusters::CORE:open";
"Moose::Util::TypeConstraints::import" -> "Moose::Exporter::_get_caller";
"Moose::import" -> "Moose::Exporter::_get_caller";
"Moose::Role::import" -> "Moose::Exporter::_get_caller";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::_error_message";
"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names" -> "Bio::Roary::GeneNamesFromGFF::ids_to_product";
"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::ids_to_product";
"Bio::Roary::AnnotateGroups::new" -> "Bio::Roary::AnnotateGroups::BUILD";
"Moose::import" -> "warnings::import";
"Moose::Util::TypeConstraints::import" -> "warnings::import";
"Moose::Role::import" -> "warnings::import";
"Class::MOP::Package::BEGIN@5" -> "warnings::import";
"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names" -> "Bio::Roary::AnnotateGroups::_filtered_gff_files";
"Bio::Roary::GroupLabels::_build__output_fh" -> "Bio::Roary::GroupLabels::CORE:open";
"Bio::Roary::GroupLabels::_build__input_fh" -> "Bio::Roary::GroupLabels::CORE:open";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::GroupLabels::DESTROY";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::GroupStatistics::groups_to_contigs";
"Moose::Meta::Role::_new" -> "Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:84]";
"Bio::Roary::ClustersRole::_build__clustered_genes" -> "Bio::Roary::InflateClusters::_clusters_fh";
"Moose::Meta::Method::_new" -> "Class::MOP::Class::new_object";
"Class::MOP::Instance::create_instance" -> "Class::MOP::Instance::_class_name";
"Class::MOP::Mixin::HasMethods::_get_maybe_raw_method" -> "Class::MOP::Package::get_package_symbol";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_statistics_filename";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_statistics_filename";
"Bio::Roary::CommandLine::RoaryPostAnalysis::_read_file_into_array" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::CORE:readline";
"Class::MOP::Package::initialize" -> "Moose::Meta::Role::_new";
"Moose::Meta::Role::get_required_method_list" -> "Moose::Meta::Role::get_required_methods_map";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::Role::_new";
"Moose::Meta::Class::_inline_check_required_attr" -> "Moose::Meta::Mixin::AttributeCore::is_required";
"Moose::Meta::Attribute::_inline_check_required" -> "Moose::Meta::Mixin::AttributeCore::is_required";
"Bio::Roary::PostAnalysis::BEGIN@22" -> "Bio::Roary::SplitGroups::meta";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::output_multifasta_files";
"Class::MOP::Instance::new" -> "Moose::Meta::Instance::_new";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::PostAnalysis::DESTROY";
"Moose::Util::TypeConstraints::import" -> "Moose::Exporter::_strip_metaclass";
"Moose::import" -> "Moose::Exporter::_strip_metaclass";
"Moose::Role::import" -> "Moose::Exporter::_strip_metaclass";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
"Bio::Roary::Output::EmblGroups::_header_block" -> "Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
"Bio::Roary::AnnotateGroups::reannotate" -> "Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
"Bio::Roary::Output::EmblGroups::_fragment_blocks" -> "Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
"Bio::Roary::AnnotateGroups::_split_groups" -> "Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::AnnotateGroups::_groups_to_consensus_gene_names";
"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion" -> "Bio::Roary::Output::NumberOfGroups::group_statistics_obj";
"Bio::Roary::Output::NumberOfGroups::_shuffle_input_files" -> "Bio::Roary::Output::NumberOfGroups::group_statistics_obj";
"Bio::Roary::PostAnalysis::BEGIN@19" -> "Bio::Roary::Output::NumberOfGroups::meta";
"Moose::Meta::Role::_new" -> "Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:398]";
"Class::MOP::Method::Accessor::_generate_accessor_method_inline" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_writer_method_inline" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_predicate_method" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_accessor_method" -> "Class::MOP::Method::Accessor::associated_attribute";
"Moose::Meta::Method::Accessor::_eval_environment" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_clearer_method_inline" -> "Class::MOP::Method::Accessor::associated_attribute";
"Moose::Meta::Method::Accessor::_instance_is_inlinable" -> "Class::MOP::Method::Accessor::associated_attribute";
"Moose::Meta::Attribute::_process_accessors" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_reader_method_inline" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_reader_method" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_writer_method" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_clearer_method" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Method::Accessor::_generate_predicate_method_inline" -> "Class::MOP::Method::Accessor::associated_attribute";
"Class::MOP::Mixin::HasMethods::has_method" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Mixin::HasMethods::_full_method_map" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Mixin::HasMethods::add_method" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Mixin::HasMethods::_get_maybe_raw_method" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Class:::around" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Mixin::HasMethods::remove_method" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Mixin::HasMethods::get_method" -> "Class::MOP::Mixin::HasMethods::_method_map";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::clearer";
"Bio::Roary::PostAnalysis::_build__annotate_groups_obj" -> "Bio::Roary::AnnotateGroups::new";
"Bio::Roary::Output::NumberOfGroups::_shuffle_input_files" -> "Bio::Roary::GroupStatistics::_sorted_file_names";
"Bio::Roary::GroupStatistics::_header" -> "Bio::Roary::GroupStatistics::_sorted_file_names";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::GroupStatistics::_sorted_file_names";
"Moose::Meta::TypeConstraint::Parameterizable::generate_constraint_for" -> "Moose::Meta::TypeConstraint::Parameterizable::has_constraint_generator";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_overlapping_hypothetical_protein_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_min_nucleotide_overlap_percentage";
"Bio::Roary::PostAnalysis::BEGIN@16" -> "Bio::Roary::AnnotateGroups::meta";
"Bio::Roary::AnalyseGroups::BUILD" -> "Bio::Roary::AnalyseGroups::_files_to_genes";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build__awk_filter" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_tags_to_filter";
"Moose::Meta::Class::_process_new_attribute" -> "Class::MOP::Mixin::HasAttributes::attribute_metaclass";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Class::MOP::Mixin::HasAttributes::attribute_metaclass";
"Class::MOP::Class::_single_metaclass_is_compatible" -> "Class::MOP::Mixin::HasAttributes::attribute_metaclass";
"Class::MOP::Mixin::HasAttributes::add_attribute" -> "Class::MOP::Mixin::HasAttributes::attribute_metaclass";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Class::MOP::Mixin::HasAttributes::attribute_metaclass";
"List::Util::all" -> "Class::MOP::Mixin::HasAttributes::attribute_metaclass";
"Moose::Meta::Attribute::_eval_environment" -> "Class::MOP::Package::name";
"Class::MOP::Class::linearized_isa" -> "Class::MOP::Package::name";
"Moose::Meta::Role::Application::ToClass::check_role_exclusions" -> "Class::MOP::Package::name";
"Class::MOP::Instance::_class_name" -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasMethods::_full_method_map" -> "Class::MOP::Package::name";
"Class::MOP::Class::class_precedence_list" -> "Class::MOP::Package::name";
"Moose::Meta::Method::Destructor::_initialize_body" -> "Class::MOP::Package::name";
"Moose::init_meta" -> "Class::MOP::Package::name";
"Class::MOP::Attribute::try {...} " -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasMethods::_add_meta_method" -> "Class::MOP::Package::name";
"Class::MOP::Class::_inline_constructor" -> "Class::MOP::Package::name";
"Class::MOP::Module::_instantiate_module" -> "Class::MOP::Package::name";
"Class::MOP::Class::_inline_fallback_constructor" -> "Class::MOP::Package::name";
"Class::MOP::Class::__ANON__[Class/MOP/Class.pm:1082]" -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasMethods::update_package_cache_flag" -> "Class::MOP::Package::name";
"Class::MOP::Class::_construct_instance" -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasMethods::wrap_method_body" -> "Class::MOP::Package::name";
"Class::MOP::Class::_inline_destructor" -> "Class::MOP::Package::name";
"Moose::Role::init_meta" -> "Class::MOP::Package::name";
"Class::MOP::Class::_inline_preserve_weak_metaclasses" -> "Class::MOP::Package::name";
"Moose::Meta::Class::_eval_environment" -> "Class::MOP::Package::name";
"Class::MOP::Attribute::_accessor_description" -> "Class::MOP::Package::name";
"Class::MOP::Attribute::_process_accessors" -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasMethods::_code_is_mine" -> "Class::MOP::Package::name";
"Class::MOP::Package::_package_stash" -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasMethods::add_method" -> "Class::MOP::Package::name";
"Class::MOP::Mixin::HasOverloads::is_overloaded" -> "Class::MOP::Package::name";
"Class::MOP::Class::superclasses" -> "Class::MOP::Package::name";
"Class::MOP::Package::create" -> "Class::MOP::Package::name";
"Class::MOP::Method::Inlined::can_be_inlined" -> "Class::MOP::Package::name";
"Class::MOP::Class::new_object" -> "Class::MOP::Package::name";
"Moose::Meta::TypeConstraint::Parameterized::can_be_inlined" -> "Moose::Meta::TypeConstraint::Parameterized::has_parameterized_from";
"Moose::Meta::TypeConstraint::Parameterized::inline_environment" -> "Moose::Meta::TypeConstraint::Parameterized::has_parameterized_from";
"Moose::Meta::Class::add_role_application" -> "Moose::Meta::Class::_get_role_applications";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::Output::EmblGroups::DESTROY";
"Bio::Roary::PostAnalysis::_group_statistics_obj" -> "Bio::Roary::PostAnalysis::_build__group_statistics_obj";
"Bio::Roary::OrderGenes::group_graphs" -> "Bio::Roary::OrderGenes::_build_group_graphs";
"Bio::Roary::SplitGroups::_set_genes_to_groups" -> "Bio::Roary::SplitGroups::_genes_to_groups";
"Bio::Roary::SplitGroups::_same_group" -> "Bio::Roary::SplitGroups::_genes_to_groups";
"Bio::Roary::SplitGroups::_update_genes_to_groups" -> "Bio::Roary::SplitGroups::_genes_to_groups";
"Moose::Meta::Attribute::_check_associated_methods" -> "Class::MOP::Attribute::associated_methods";
"Bio::Roary::GroupStatistics::_files_to_groups" -> "Bio::Roary::GroupStatistics::_build__files_to_groups";
"Bio::Roary::Output::GroupsMultifastasNucleotide::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::ContigsToGeneIDsFromGFF::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Enum::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Method::_new" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Union::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::SplitGroups::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Application::RoleSummation::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Composite::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::Output::NumberOfGroups::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::CommandLine::RoaryPostAnalysis::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Role::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Parameterized::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeCoercion::Union::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::AnnotateGroups::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::Output::GroupsMultifastaNucleotide::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Application::ToClass::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Class::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::InflateClusters::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeCoercion::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::OrderGenes::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Registry::meta" -> "Class::MOP::Class::initialize";
"Class::MOP::Mixin::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::PostAnalysis::meta" -> "Class::MOP::Class::initialize";
"Class::MOP::Object::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Application::ToRole::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::GroupLabels::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Application::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::GroupStatistics::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::Output::EmblGroups::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::GeneNamesFromGFF::meta" -> "Class::MOP::Class::initialize";
"Bio::Roary::AnalyseGroups::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::Parameterizable::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::TypeConstraint::DuckType::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Application::ToInstance::meta" -> "Class::MOP::Class::initialize";
"Moose::Meta::Role::Method::Required::meta" -> "Class::MOP::Class::initialize";
"Class::MOP::Package::create" -> "Class::MOP::Class::initialize";
"Class::MOP::Method::Generated::_generate_description" -> "Class::MOP::Method::Generated::definition_context";
"Bio::Roary::PostAnalysis::_number_of_groups_obj" -> "Bio::Roary::PostAnalysis::_build__number_of_groups_obj";
"Moose::Meta::TypeConstraint::compile_type_constraint" -> "Moose::Meta::TypeConstraint::_compiled_type_constraint";
"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:284]" -> "Moose::Meta::TypeConstraint::_compiled_type_constraint";
"Moose::Meta::Class::_eval_environment" -> "Moose::Meta::TypeConstraint::_compiled_type_constraint";
"Moose::Meta::Role::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:139]";
"Bio::Roary::GroupStatistics::_build__files_to_groups" -> "Bio::Roary::GroupStatistics::_groups_to_files";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::GroupStatistics::_groups_to_files";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::Output::EmblGroups::new";
"Bio::Roary::Output::EmblGroups::_build_output_header_filename" -> "Bio::Roary::Output::EmblGroups::output_filename";
"Bio::Roary::Output::EmblGroups::_build__output_fh" -> "Bio::Roary::Output::EmblGroups::output_filename";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::CORE:close";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::accessor";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Mixin::AttributeCore::accessor";
"Bio::Roary::SplitGroups::_make_tmp_dir" -> "Bio::Roary::SplitGroups::_tmp_dir";
"Bio::Roary::PostAnalysis::_build__analyse_groups_obj" -> "Bio::Roary::PostAnalysis::output_filename";
"Bio::Roary::PostAnalysis::_build__annotate_groups_obj" -> "Bio::Roary::PostAnalysis::output_filename";
"parent::import" -> "Class::MOP::Package::BEGIN@95";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::InflateClusters::DESTROY";
"Moose::Meta::Attribute::install_accessors" -> "Moose::Meta::Mixin::AttributeCore::has_handles";
"Moose::Meta::Attribute::remove_accessors" -> "Moose::Meta::Mixin::AttributeCore::has_handles";
"Class::MOP::Mixin::HasMethods::_get_maybe_raw_method" -> "Class::MOP::Class::Immutable::Class::MOP::Class::_method_map";
"Class::MOP::Mixin::HasMethods::get_method" -> "Class::MOP::Class::Immutable::Class::MOP::Class::_method_map";
"Class::MOP::Package::_package_stash" -> "Package::Stash::XS::new";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Application::ToInstance::meta";
"Moose::BEGIN@38" -> "Moose::Meta::Role::Application::ToInstance::meta";
"Bio::Roary::OrderGenes::_reorder_connected_components" -> "Bio::Roary::OrderGenes::number_of_files";
"Bio::Roary::OrderGenes::_create_accessory_graph" -> "Bio::Roary::OrderGenes::number_of_files";
"Moose::Util::TypeConstraints::import" -> "strict::import";
"Moose::import" -> "strict::import";
"Moose::Role::import" -> "strict::import";
"Class::MOP::Package::BEGIN@4" -> "strict::import";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::_split_groups_obj";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::Output::EmblGroups::_groups_to_files";
"Bio::Roary::InflateClusters::_build__output_fh" -> "Bio::Roary::InflateClusters::output_file";
"Bio::Roary::GroupLabels::add_labels" -> "Bio::Roary::GroupLabels::_output_fh";
"parent::import" -> "Class::MOP::Package::BEGIN@4";
"Moose::Meta::TypeConstraint::Registry::has_type_constraint" -> "Moose::Meta::TypeConstraint::Registry::type_constraints";
"Moose::Util::TypeConstraints::list_all_type_constraints" -> "Moose::Meta::TypeConstraint::Registry::type_constraints";
"Moose::Meta::TypeConstraint::Registry::add_type_constraint" -> "Moose::Meta::TypeConstraint::Registry::type_constraints";
"Moose::Meta::TypeConstraint::Registry::get_type_constraint" -> "Moose::Meta::TypeConstraint::Registry::type_constraints";
"Bio::Roary::SplitGroups::split_groups" -> "Bio::Roary::SplitGroups::max_recursion";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::predicate";
"Class::MOP::Package::BEGIN@9" -> "Module::Runtime::import";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::_output_fh";
"Class::MOP::Class::_immutable_metaclass" -> "Moose::Meta::Class::immutable_trait";
"Class::MOP::Class::_immutable_options" -> "Moose::Meta::Class::immutable_trait";
"Moose::Meta::Mixin::AttributeCore::has_trigger" -> "Class::MOP::Attribute::has_value";
"Moose::Meta::Mixin::AttributeCore::has_type_constraint" -> "Class::MOP::Attribute::has_value";
"Moose::Meta::Mixin::AttributeCore::has_handles" -> "Class::MOP::Attribute::has_value";
"Bio::Roary::AnnotateGroups::_build__output_fh" -> "Bio::Roary::AnnotateGroups::output_filename";
"Class::MOP::Method::Constructor::_generate_constructor_method_inline" -> "Class::MOP::Method::associated_metaclass";
"Class::MOP::Method::Constructor::_eval_environment" -> "Class::MOP::Method::associated_metaclass";
"Moose::Meta::Method::Destructor::_generate_DEMOLISHALL" -> "Class::MOP::Method::associated_metaclass";
"Moose::Meta::Method::Destructor::_initialize_body" -> "Class::MOP::Method::associated_metaclass";
"Class::MOP::Method::Inlined::can_be_inlined" -> "Class::MOP::Method::associated_metaclass";
"Bio::Roary::GroupStatistics::_build__output_fh" -> "Bio::Roary::GroupStatistics::output_filename";
"Bio::Roary::GroupStatistics::create_spreadsheet" -> "Bio::Roary::GroupStatistics::_output_fh";
"Moose::Meta::Attribute::_inline_init_from_default" -> "Moose::Meta::Mixin::AttributeCore::has_type_constraint";
"Moose::Meta::Attribute::_eval_environment" -> "Moose::Meta::Mixin::AttributeCore::has_type_constraint";
"Moose::Meta::Attribute::_inline_check_constraint" -> "Moose::Meta::Mixin::AttributeCore::has_type_constraint";
"parent::import" -> "Class::MOP::Package::BEGIN@12";
"Moose::Meta::TypeConstraint::inline_environment" -> "Moose::Meta::TypeConstraint::_inline_environment";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::input_files";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::input_files";
"Bio::Roary::SplitGroups::split_groups" -> "Bio::Roary::SplitGroups::outfile";
"Class::MOP::Package::BEGIN@12" -> "parent::import";
"Bio::Roary::GroupStatistics::_header" -> "Bio::Roary::GroupStatistics::_verbose";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::GroupStatistics::_verbose";
"Bio::Roary::PostAnalysis::_build__order_genes_obj" -> "Bio::Roary::PostAnalysis::_analyse_groups_obj";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::PostAnalysis::_analyse_groups_obj";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::_analyse_groups_obj";
"Bio::Roary::GroupStatistics::_build__sorted_file_names" -> "Bio::Roary::GroupStatistics::analyse_groups_obj";
"Bio::Roary::GroupStatistics::_build__groups_to_files" -> "Bio::Roary::GroupStatistics::analyse_groups_obj";
"Bio::Roary::GroupStatistics::create_spreadsheet" -> "Bio::Roary::GroupStatistics::analyse_groups_obj";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::GroupStatistics::analyse_groups_obj";
"parent::import" -> "Class::MOP::Package::BEGIN@7";
"Bio::Roary::ContigsToGeneIDsFromGFF::_awk_filter" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_build__awk_filter";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::has_predicate";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Mixin::AttributeCore::has_predicate";
"Class::MOP::Package::BEGIN@95" -> "warnings::unimport";
"Moose::Meta::TypeConstraint::Registry::add_type_constraint" -> "Moose::Meta::TypeConstraint::name";
"Moose::Meta::TypeConstraint::Parameterizable::parameterize" -> "Moose::Meta::TypeConstraint::name";
"Moose::Meta::TypeConstraint::Parameterizable::generate_constraint_for" -> "Moose::Meta::TypeConstraint::name";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::name";
"Bio::Roary::SplitGroups::_analyse_groups_obj" -> "Bio::Roary::SplitGroups::_build__analyse_groups_obj";
"Bio::Roary::SplitGroups::_true_orthologs" -> "Bio::Roary::SplitGroups::_do_sorting";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::args";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::ContigsToGeneIDsFromGFF::overlapping_hypothetical_protein_ids";
"Class::MOP::Class::_inline_slot_initializer" -> "Class::MOP::Mixin::AttributeCore::init_arg";
"Moose::Meta::Class::_inline_check_required_attr" -> "Class::MOP::Mixin::AttributeCore::init_arg";
"Class::MOP::Class::_inline_init_attr_from_constructor" -> "Class::MOP::Mixin::AttributeCore::init_arg";
"Moose::Meta::Attribute::new" -> "Class::MOP::Mixin::AttributeCore::init_arg";
"Moose::Meta::Class::_inline_init_attr_from_constructor" -> "Class::MOP::Mixin::AttributeCore::init_arg";
"Moose::Meta::TypeConstraint::_inline_check" -> "Moose::Meta::TypeConstraint::inlined";
"Bio::Roary::PostAnalysis::_inflate_clusters_obj" -> "Bio::Roary::PostAnalysis::_build__inflate_clusters_obj";
"Moose::Meta::Attribute::_new" -> "Class::MOP::__ANON__[Class/MOP.pm:499]";
"Moose::Meta::Role::Attribute::original_role" -> "Moose::Meta::Role::Attribute::associated_role";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::ContigsToGeneIDsFromGFF::contig_to_ids";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_overlapping_hypothetical_protein_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::contig_to_ids";
"Bio::Roary::InflateClusters::_mcl_fh" -> "Bio::Roary::InflateClusters::_build__mcl_fh";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13" -> "Bio::Roary::PostAnalysis::meta";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::PostAnalysis::verbose_stats";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::ContigsToGeneIDsFromGFF::new";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Class::MOP::Class::destructor_class";
"List::Util::all" -> "Class::MOP::Class::destructor_class";
"Class::MOP::Class::_immutable_options" -> "Class::MOP::Class::destructor_class";
"Bio::Roary::PostAnalysis::BEGIN@15" -> "Bio::Roary::GroupLabels::meta";
"main::NULL" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::DESTROY";
"Bio::Roary::CommandLine::RoaryPostAnalysis::new" -> "Eval::Closure::Sandbox_434::CORE:match";
"Moose::Meta::TypeConstraint::Parameterized::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:36]";
"Moose::Meta::TypeConstraint::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:36]";
"Bio::Roary::PostAnalysis::BEGIN@17" -> "Bio::Roary::GroupStatistics::meta";
"Bio::Roary::OrderGenes::number_of_files" -> "Bio::Roary::OrderGenes::_build_number_of_files";
"Class::MOP::Mixin::HasMethods::remove_method" -> "Class::MOP::Package::remove_package_symbol";
"Bio::Roary::CommandLine::RoaryPostAnalysis::cpus" -> "Eval::Closure::Sandbox_426::CORE:match";
"Moose::Meta::Role::add_attribute" -> "Moose::Meta::Role::CORE:match";
"Moose::BEGIN@32" -> "Moose::Meta::Role::meta";
"Class::MOP::Method::Meta::wrap" -> "Moose::Meta::Role::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::meta";
"Moose::Meta::Class::add_role" -> "Moose::Meta::Class::roles";
"Moose::Meta::Class::excludes_role" -> "Moose::Meta::Class::roles";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_filename";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_filename";
"Bio::Roary::OrderGenes::_remove_weak_edges_from_graph" -> "Bio::Roary::OrderGenes::group_order";
"Bio::Roary::OrderGenes::_add_groups_to_graph" -> "Bio::Roary::OrderGenes::group_order";
"Bio::Roary::OrderGenes::_reorder_connected_components" -> "Bio::Roary::OrderGenes::group_order";
"Bio::Roary::OrderGenes::_create_accessory_graph" -> "Bio::Roary::OrderGenes::group_order";
"Bio::Roary::CommandLine::RoaryPostAnalysis::_read_file_into_array" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::CORE:open";
"Moose::Meta::TypeConstraint::Parameterized::BEGIN@10" -> "Moose::Meta::TypeConstraint::Parameterizable::meta";
"Bio::Roary::Output::NumberOfGroups::new" -> "Bio::Roary::Output::NumberOfGroups::__ANON__[lib/Bio/Roary/Output/NumberOfGroups.pm:33]";
"Bio::Roary::AnnotateGroups::reannotate" -> "Bio::Roary::AnnotateGroups::_output_fh";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_pan_geneome_filename";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_pan_geneome_filename";
"Moose::Util::TypeConstraints::import" -> "Moose::Exporter::_strip_traits";
"Moose::import" -> "Moose::Exporter::_strip_traits";
"Moose::Role::import" -> "Moose::Exporter::_strip_traits";
"Bio::Roary::InflateClusters::_build__mcl_fh" -> "Bio::Roary::InflateClusters::mcl_filename";
"Moose::Meta::Role::BEGIN@13" -> "Moose::Meta::Role::Method::Required::meta";
"Moose::Meta::Role::BEGIN@14" -> "Moose::Meta::Role::Method::Required::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Method::Required::meta";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::_total_genes";
"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion" -> "Bio::Roary::Output::NumberOfGroups::_total_genes";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::CORE:close";
"Bio::Roary::PostAnalysis::BEGIN@18" -> "Bio::Roary::Output::GroupsMultifastasNucleotide::meta";
"Class::MOP::Method::wrap" -> "Moose::Meta::Method::_new";
"Bio::Roary::AnalyseGroups::_builder__freq_groups_per_genome" -> "Bio::Roary::AnalyseGroups::groups_filename";
"Bio::Roary::AnalyseGroups::_builder__groups_to_genes" -> "Bio::Roary::AnalyseGroups::groups_filename";
"Moose::import" -> "Moose::init_meta";
"Bio::Roary::AnalyseGroups::_groups_to_genes" -> "Bio::Roary::AnalyseGroups::_builder__groups_to_genes";
"Moose::Meta::Role::_new" -> "Moose::Meta::Role::__ANON__[Moose/Meta/Role.pm:351]";
"Bio::Roary::AnnotateGroups::_ids_grouped_by_gene_name_for_group" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::Output::EmblGroups::_build__groups_to_files" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::AnnotateGroups::_generate_groups_to_consensus_gene_names" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::AnnotateGroups::CORE:sort" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::GroupStatistics::_row" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::GroupStatistics::create_spreadsheet" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::AnnotateGroups::reannotate" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::AnnotateGroups::_generate__ids_to_groups" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::GroupStatistics::_build__groups_to_files" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::AnnotateGroups::_groups" -> "Bio::Roary::AnnotateGroups::_groups_to_id_names";
"Bio::Roary::Output::EmblGroups::create_files" -> "Bio::Roary::Output::EmblGroups::CORE:print";
"Bio::Roary::Output::EmblGroups::_fragment_blocks" -> "Bio::Roary::Output::EmblGroups::CORE:print";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::Output::NumberOfGroups::DESTROY";
"Bio::Roary::GroupLabels::add_labels" -> "Bio::Roary::GroupLabels::CORE:close";
"Bio::Roary::ContigsToGeneIDsFromGFF::new" -> "Eval::Closure::Sandbox_295::CORE:match";
"Moose::Meta::Attribute::_eval_environment" -> "Moose::Meta::TypeConstraint::has_message";
"Moose::Meta::Class::_eval_environment" -> "Moose::Meta::TypeConstraint::has_message";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::has_message";
"Bio::Roary::OrderGenes::new" -> "Bio::Roary::OrderGenes::__ANON__[lib/Bio/Roary/OrderGenes.pm:33]";
"Moose::Meta::TypeConstraint::Parameterized::compile_type_constraint" -> "Moose::Meta::TypeConstraint::_set_constraint";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::_mcl_fh";
"parent::import" -> "Class::MOP::Package::BEGIN@8";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::_has_compiled_type_constraint";
"Bio::Roary::GroupLabels::_output_fh" -> "Bio::Roary::GroupLabels::_build__output_fh";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::dont_split_groups";
"Moose::Util::TypeConstraints::BEGIN@29" -> "Moose::Meta::TypeConstraint::Role::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::translation_table" -> "Eval::Closure::Sandbox_431::CORE:match";
"Class::MOP::Attribute::_process_accessors" -> "Class::MOP::Mixin::AttributeCore::definition_context";
"Class::MOP::Mixin::HasMethods::wrap_method_body" -> "Moose::Meta::Role::method_metaclass";
"Class::MOP::Package::initialize" -> "Class::MOP::store_metaclass_by_name";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::_group_labels_obj";
"Bio::Roary::AnnotateGroups::_build__filtered_gff_files" -> "Bio::Roary::AnnotateGroups::gff_files";
"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names" -> "Bio::Roary::GeneNamesFromGFF::new";
"Moose::Meta::Attribute::_eval_environment" -> "Moose::Meta::TypeConstraint::_default_message";
"Moose::Meta::Class::_eval_environment" -> "Moose::Meta::TypeConstraint::_default_message";
"Moose::Meta::TypeConstraint::new" -> "Moose::Meta::TypeConstraint::_default_message";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::accessory_tab_output_filename";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::Output::EmblGroups::ordering_key";
"Bio::Roary::Output::EmblGroups::_header_block" -> "Bio::Roary::Output::EmblGroups::ordering_key";
"Bio::Roary::Output::EmblGroups::_fragment_blocks" -> "Bio::Roary::Output::EmblGroups::ordering_key";
"Moose::Util::TypeConstraints::BEGIN@28" -> "Moose::Meta::TypeConstraint::Class::meta";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::writer";
"Bio::Roary::PostAnalysis::BEGIN@13" -> "Bio::Roary::InflateClusters::meta";
"Bio::Roary::SplitGroups::_parse_gene_neighbourhood" -> "Bio::Roary::SplitGroups::_neighbourhood_size";
"Bio::Roary::AnalyseGroups::new" -> "Bio::Roary::AnalyseGroups::BUILD";
"Bio::Roary::AnnotateGroups::_generate_groups_to_consensus_gene_names" -> "Bio::Roary::AnnotateGroups::_group_default_prefix";
"Bio::Roary::GroupStatistics::_non_unique_name_for_group" -> "Bio::Roary::AnnotateGroups::_group_default_prefix";
"Bio::Roary::CommandLine::RoaryPostAnalysis::new" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD";
"Bio::Roary::AnnotateGroups::_builder__groups_to_id_names" -> "Bio::Roary::AnnotateGroups::groups_filename";
"Bio::Roary::PostAnalysis::BEGIN@20" -> "Bio::Roary::OrderGenes::meta";
"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::CORE:close";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::group_limit";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::group_limit";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::Output::EmblGroups::_sorted_file_names";
"Moose::Meta::TypeConstraint::Class::__ANON__[Moose/Meta/TypeConstraint/Class.pm:25]" -> "Moose::Meta::TypeConstraint::Class::class";
"Moose::Meta::Attribute::_eval_environment" -> "Moose::Meta::Mixin::AttributeCore::type_constraint";
"Moose::Meta::Attribute::_inline_check_constraint" -> "Moose::Meta::Mixin::AttributeCore::type_constraint";
"Moose::Meta::Class::_eval_environment" -> "Moose::Meta::Mixin::AttributeCore::type_constraint";
"Bio::Roary::Output::EmblGroups::create_files" -> "Bio::Roary::Output::EmblGroups::annotate_groups_obj";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::Output::EmblGroups::annotate_groups_obj";
"Bio::Roary::Output::EmblGroups::_build__groups_to_files" -> "Bio::Roary::Output::EmblGroups::annotate_groups_obj";
"Bio::Roary::Output::EmblGroups::_header_block" -> "Bio::Roary::Output::EmblGroups::annotate_groups_obj";
"Bio::Roary::Output::EmblGroups::_fragment_blocks" -> "Bio::Roary::Output::EmblGroups::annotate_groups_obj";
"Bio::Roary::SplitGroups::BEGIN@318" -> "Moose::unimport";
"Bio::Roary::Output::GroupsMultifastasNucleotide::BEGIN@75" -> "Moose::unimport";
"Bio::Roary::GroupStatistics::BEGIN@202" -> "Moose::unimport";
"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::BEGIN@88" -> "Moose::unimport";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@188" -> "Moose::unimport";
"Bio::Roary::OrderGenes::BEGIN@352" -> "Moose::unimport";
"Bio::Roary::GeneNamesFromGFF::BEGIN@65" -> "Moose::unimport";
"Bio::Roary::Output::GroupsMultifastaNucleotide::BEGIN@148" -> "Moose::unimport";
"Bio::Roary::Output::NumberOfGroups::BEGIN@116" -> "Moose::unimport";
"Bio::Roary::AnnotateGroups::BEGIN@325" -> "Moose::unimport";
"Bio::Roary::Output::EmblGroups::BEGIN@239" -> "Moose::unimport";
"Bio::Roary::PostAnalysis::BEGIN@225" -> "Moose::unimport";
"Bio::Roary::GroupLabels::BEGIN@59" -> "Moose::unimport";
"Bio::Roary::ContigsToGeneIDsFromGFF::BEGIN@142" -> "Moose::unimport";
"Bio::Roary::InflateClusters::BEGIN@106" -> "Moose::unimport";
"Bio::Roary::AnalyseGroups::BEGIN@142" -> "Moose::unimport";
"Bio::Roary::CommandLine::Common::BEGIN@38" -> "Moose::unimport";
"Moose::Exporter::build_import_methods" -> "Class::MOP::Package::initialize";
"Moose::Meta::Role::initialize" -> "Class::MOP::Package::initialize";
"Bio::Roary::AnnotateGroups::new" -> "Bio::Roary::AnnotateGroups::__ANON__[lib/Bio/Roary/AnnotateGroups.pm:31]";
"Moose::BEGIN@34" -> "Moose::Meta::Role::Application::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Application::meta";
"Moose::Meta::Role::Application::new" -> "Moose::Meta::Role::Application::ToClass::_new";
"Bio::Roary::PostAnalysis::_build__number_of_groups_obj" -> "Bio::Roary::Output::NumberOfGroups::new";
"Bio::Roary::SplitGroups::_genes_to_files" -> "Bio::Roary::SplitGroups::_build__genes_to_files";
"Class::MOP::Method::Accessor::_initialize_body" -> "Class::MOP::Method::Accessor::accessor_type";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::output_multifasta_files";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::AnnotateGroups::DESTROY";
"Bio::Roary::AnalyseGroups::_number_of_isolates" -> "Bio::Roary::AnalyseGroups::_builder__number_of_isolates";
"Class::MOP::Method::wrap" -> "Moose::Meta::Role::Method::_new";
"Class::MOP::Class::_create_meta_instance" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_all_attributes";
"Class::MOP::Class::_construct_instance" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_all_attributes";
"Moose::Meta::Attribute::new" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_all_attributes";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::CORE:readline";
"Bio::Roary::PostAnalysis::_build__inflate_clusters_obj" -> "Bio::Roary::PostAnalysis::_output_mcl_filename";
"Bio::Roary::PostAnalysis::_delete_intermediate_files" -> "Bio::Roary::PostAnalysis::dont_delete_files";
"Bio::Roary::PostAnalysis::_build__split_groups_obj" -> "Bio::Roary::PostAnalysis::dont_delete_files";
"Bio::Roary::PostAnalysis::_order_genes_obj" -> "Bio::Roary::PostAnalysis::_build__order_genes_obj";
"Bio::Roary::Output::EmblGroups::output_header_filename" -> "Bio::Roary::Output::EmblGroups::_build_output_header_filename";
"Bio::Roary::Output::EmblGroups::_block" -> "Bio::Roary::Output::EmblGroups::groups_to_contigs";
"Bio::Roary::Output::EmblGroups::_header_block" -> "Bio::Roary::Output::EmblGroups::groups_to_contigs";
"Bio::Roary::Output::EmblGroups::_fragment_blocks" -> "Bio::Roary::Output::EmblGroups::groups_to_contigs";
"Bio::Roary::GroupLabels::add_labels" -> "Bio::Roary::GroupLabels::CORE:print";
"Class::MOP::Package::BEGIN@10" -> "Package::DeprecationManager::__ANON__[Package/DeprecationManager.pm:61]";
"Bio::Roary::ContigsToGeneIDsFromGFF::new" -> "Bio::Roary::ContigsToGeneIDsFromGFF::__ANON__[lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm:24]";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::dont_split_groups";
"Bio::Roary::PostAnalysis::_build__split_groups_obj" -> "Bio::Roary::PostAnalysis::input_files";
"Bio::Roary::PostAnalysis::_build__annotate_groups_obj" -> "Bio::Roary::PostAnalysis::input_files";
"Bio::Roary::PostAnalysis::_build__order_genes_obj" -> "Bio::Roary::PostAnalysis::input_files";
"Class::MOP::Class::_real_ref_name" -> "Class::MOP::Class::Immutable::Class::MOP::Class::is_immutable";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::cdhit_groups_filename";
"Bio::Roary::SplitGroups::_find_paralogs" -> "Bio::Roary::SplitGroups::_genes_to_files";
"Bio::Roary::SplitGroups::_parse_gene_neighbourhood" -> "Bio::Roary::SplitGroups::_genes_to_files";
"Class::MOP::Package::add_package_symbol" -> "Package::Stash::XS::add_symbol";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::GroupStatistics::DESTROY";
"Bio::Roary::PostAnalysis::_build__order_genes_obj" -> "Bio::Roary::OrderGenes::new";
"Class::MOP::Package::BEGIN@8" -> "Devel::GlobalDestruction::BEGIN@3";
"Bio::Roary::GroupLabels::_input_fh" -> "Bio::Roary::GroupLabels::_build__input_fh";
"Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::CORE:open";
"Class::MOP::Class::_immutable_metaclass" -> "Class::MOP::Class::immutable_trait";
"Class::MOP::Class::_immutable_options" -> "Class::MOP::Class::immutable_trait";
"Bio::Roary::GroupLabels::add_labels" -> "Bio::Roary::GroupLabels::CORE:readline";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::has_writer";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Mixin::AttributeCore::has_writer";
"Bio::Roary::PostAnalysis::_build__inflate_clusters_obj" -> "Bio::Roary::PostAnalysis::_input_cd_hit_groups_file";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::TypeCoercion::Union::meta";
"Moose::Meta::TypeConstraint::Parameterizable::generate_constraint_for" -> "Moose::Meta::TypeConstraint::Parameterizable::constraint_generator";
"Bio::Roary::OrderGenes::_build_group_order" -> "Bio::Roary::OrderGenes::_groups_to_file_contigs";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@15" -> "Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::meta";
"Moose::BEGIN@36" -> "Moose::Meta::Role::Application::ToClass::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Application::ToClass::meta";
"Class::MOP::Mixin::HasMethods::add_method" -> "Class::MOP::Package::add_package_symbol";
"Moose::Exporter::build_import_methods" -> "Class::MOP::Package::add_package_symbol";
"Bio::Roary::PostAnalysis::new" -> "Eval::Closure::Sandbox_388::CORE:match";
"Bio::Roary::InflateClusters::inflate" -> "Bio::Roary::InflateClusters::CORE:print";
"Class::MOP::Method::Inlined::can_be_inlined" -> "Class::MOP::Method::Inlined::_expected_method_class";
"Bio::Roary::Output::EmblGroups::_build__output_header_fh" -> "Bio::Roary::Output::EmblGroups::CORE:open";
"Bio::Roary::Output::EmblGroups::_build__output_fh" -> "Bio::Roary::Output::EmblGroups::CORE:open";
"Moose::Meta::TypeConstraint::Parameterized::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:89]";
"Moose::Meta::TypeConstraint::Parameterizable::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:89]";
"Moose::Meta::TypeConstraint::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:89]";
"Moose::Meta::TypeConstraint::Role::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:89]";
"Moose::Meta::TypeConstraint::Class::_new" -> "Moose::Meta::TypeConstraint::__ANON__[Moose/Meta/TypeConstraint.pm:89]";
"Bio::Roary::Output::EmblGroups::_groups_to_files" -> "Bio::Roary::Output::EmblGroups::_build__groups_to_files";
"Moose::Meta::Role::BEGIN@11" -> "Class::MOP::Mixin::meta";
"Moose::Exporter::BEGIN@8" -> "Class::MOP::Mixin::meta";
"Class::MOP::Method::Meta::wrap" -> "Class::MOP::Mixin::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Class::MOP::Mixin::meta";
"parent::import" -> "Class::MOP::Mixin::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::clusters_filename";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::clusters_filename";
"Bio::Roary::Output::GroupsMultifastasNucleotide::BEGIN@19" -> "Moose::import";
"Bio::Roary::SplitGroups::BEGIN@11" -> "Moose::import";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::import";
"Bio::Roary::Output::NumberOfGroups::BEGIN@17" -> "Moose::import";
"Bio::Roary::Output::GroupsMultifastaNucleotide::BEGIN@17" -> "Moose::import";
"Bio::Roary::CommandLine::Common::BEGIN@12" -> "Moose::import";
"Bio::Roary::GeneNamesFromGFF::BEGIN@17" -> "Moose::import";
"Bio::Roary::AnalyseGroups::BEGIN@19" -> "Moose::import";
"Bio::Roary::ContigsToGeneIDsFromGFF::BEGIN@17" -> "Moose::import";
"Bio::Roary::AnnotateGroups::BEGIN@19" -> "Moose::import";
"Bio::Roary::PostAnalysis::BEGIN@11" -> "Moose::import";
"Bio::Roary::GroupStatistics::BEGIN@19" -> "Moose::import";
"Bio::Roary::Output::EmblGroups::BEGIN@19" -> "Moose::import";
"Bio::Roary::InflateClusters::BEGIN@19" -> "Moose::import";
"Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides::BEGIN@23" -> "Moose::import";
"Bio::Roary::GroupLabels::BEGIN@18" -> "Moose::import";
"Bio::Roary::OrderGenes::BEGIN@18" -> "Moose::import";
"Moose::unimport" -> "Moose::Exporter::_remove_keywords";
"Moose::Meta::Attribute::_eval_environment" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Class::MOP::Class::_inline_init_attr_from_constructor" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Class::MOP::Attribute::_set_initial_slot_value" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Moose::Meta::Attribute::_inline_init_slot" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"List::Util::any" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Moose::Meta::Class::_inline_init_attr_from_constructor" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Moose::Meta::Class::_inline_init_attr_from_default" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Class::MOP::Class::_inline_init_attr_from_default" -> "Class::MOP::Mixin::AttributeCore::has_initializer";
"Moose::Meta::Role::Application::is_method_aliased" -> "Moose::Meta::Role::Application::get_method_aliases";
"Bio::Roary::AnnotateGroups::_split_groups" -> "Bio::Roary::AnnotateGroups::_ids_to_groups";
"Bio::Roary::OrderGenes::_remove_weak_edges_from_graph" -> "Bio::Roary::OrderGenes::_percentage_of_largest_weak_threshold";
"Bio::Roary::OrderGenes::new" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_number_of_groups_obj" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_annotate_groups_obj" -> "UNIVERSAL::isa";
"Bio::Roary::GroupStatistics::_text_csv_obj" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_group_labels_obj" -> "UNIVERSAL::isa";
"Bio::Roary::OrderGenes::group_graphs" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_analyse_groups_obj" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_order_genes_obj" -> "UNIVERSAL::isa";
"Class::MOP::Class::superclasses" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_inflate_clusters_obj" -> "UNIVERSAL::isa";
"Bio::Roary::Output::EmblGroups::new" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_group_statistics_obj" -> "UNIVERSAL::isa";
"Bio::Roary::SplitGroups::new" -> "UNIVERSAL::isa";
"Bio::Roary::Output::NumberOfGroups::new" -> "UNIVERSAL::isa";
"Bio::Roary::GroupStatistics::new" -> "UNIVERSAL::isa";
"Bio::Roary::PostAnalysis::_split_groups_obj" -> "UNIVERSAL::isa";
"Bio::Roary::AnnotateGroups::_output_fh" -> "Bio::Roary::AnnotateGroups::_build__output_fh";
"Bio::Roary::Output::EmblGroups::create_files" -> "Bio::Roary::Output::EmblGroups::_output_header_fh";
"Class::MOP::Attribute::_inline_instance_has" -> "Class::MOP::Attribute::associated_class";
"Moose::Meta::Attribute::_eval_environment" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::_inline_instance_clear" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::_inline_instance_get" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::_accessor_description" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::try {...} " -> "Class::MOP::Attribute::associated_class";
"Moose::Meta::Method::Accessor::_instance_is_inlinable" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::_inline_instance_set" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Attribute::associated_class";
"Moose::Meta::Attribute::_process_accessors" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Attribute::_process_accessors" -> "Class::MOP::Attribute::associated_class";
"Class::MOP::Method::Accessor::_generate_reader_method" -> "Class::MOP::Attribute::associated_class";
"Moose::Meta::Attribute::_inline_weaken_value" -> "Class::MOP::Attribute::associated_class";
"Moose::Role::import" -> "Moose::Role::init_meta";
"Class::MOP::Attribute::install_accessors" -> "Class::MOP::Mixin::AttributeCore::has_reader";
"Class::MOP::Attribute::remove_accessors" -> "Class::MOP::Mixin::AttributeCore::has_reader";
"Bio::Roary::Output::EmblGroups::_output_header_fh" -> "Bio::Roary::Output::EmblGroups::_build__output_header_fh";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::OrderGenes::analyse_groups_obj";
"Bio::Roary::PostAnalysis::_analyse_groups_obj" -> "Bio::Roary::PostAnalysis::_build__analyse_groups_obj";
"Class::MOP::Class::_construct_instance" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance";
"Class::MOP::Attribute::has_value" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance";
"Moose::Meta::Attribute::_inline_weaken_value" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance";
"Class::MOP::Attribute::_inline_instance_set" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance";
"Class::MOP::Attribute::get_raw_value" -> "Class::MOP::Class::Immutable::Class::MOP::Class::get_meta_instance";
"Moose::Meta::Role::Application::ToClass::check_required_methods" -> "Moose::Meta::Role::get_required_method_list";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::OrderGenes::DESTROY";
"Moose::Meta::Attribute::_eval_environment" -> "Moose::Meta::TypeConstraint::has_coercion";
"Moose::Meta::Class::_eval_environment" -> "Moose::Meta::TypeConstraint::has_coercion";
"Moose::Meta::TypeConstraint::Parameterizable::generate_constraint_for" -> "Moose::Meta::TypeConstraint::has_coercion";
"Class::MOP::Package::remove_package_symbol" -> "Package::Stash::XS::remove_symbol";
"Bio::Roary::ContigsToGeneIDsFromGFF::overlapping_hypothetical_protein_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_build_overlapping_hypothetical_protein_ids";
"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:170]" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Meta::TypeConstraint::_inline_check" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Meta::TypeConstraint::inline_environment" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Meta::TypeConstraint::is_subtype_of" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:77]" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Meta::TypeConstraint::Parameterizable::parameterize" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Meta::TypeConstraint::can_be_inlined" -> "Moose::Meta::TypeConstraint::parent";
"Moose::Util::TypeConstraints::Builtins::__ANON__[Moose/Util/TypeConstraints/Builtins.pm:60]" -> "Moose::Meta::TypeConstraint::parent";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Class::MOP::Class::constructor_class";
"List::Util::all" -> "Class::MOP::Class::constructor_class";
"Class::MOP::Class::_immutable_options" -> "Class::MOP::Class::constructor_class";
"Moose::Meta::Role::get_method_modifier_list" -> "Moose::Meta::Role::get_before_method_modifiers_map";
"Bio::Roary::GroupLabels::_build__input_fh" -> "Bio::Roary::GroupLabels::groups_filename";
"Moose::Meta::TypeConstraint::_inline_check" -> "Moose::Meta::TypeConstraint::constraint";
"Moose::Meta::TypeConstraint::equals" -> "Moose::Meta::TypeConstraint::constraint";
"Moose::Meta::TypeConstraint::inline_environment" -> "Moose::Meta::TypeConstraint::constraint";
"Moose::Meta::TypeConstraint::can_be_inlined" -> "Moose::Meta::TypeConstraint::constraint";
"Class::MOP::Class::_check_metaclass_compatibility" -> "Moose::Meta::Class::destructor_class";
"Class::MOP::Class::_single_metaclass_is_compatible" -> "Moose::Meta::Class::destructor_class";
"Class::MOP::Class::_single_metaclass_can_be_made_compatible" -> "Moose::Meta::Class::destructor_class";
"Class::MOP::Class::_immutable_options" -> "Moose::Meta::Class::destructor_class";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_genes_annotation";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_overlapping_hypothetical_protein_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::_genes_annotation";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::CORE:open";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::PostAnalysis::output_statistics_filename";
"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion" -> "Bio::Roary::GroupStatistics::_files_to_groups";
"Class::MOP::Mixin::HasAttributes::get_attribute_list" -> "Class::MOP::Mixin::HasAttributes::_attribute_map";
"Class::MOP::Mixin::HasAttributes::get_attribute" -> "Class::MOP::Mixin::HasAttributes::_attribute_map";
"Class::MOP::Class::get_all_attributes" -> "Class::MOP::Mixin::HasAttributes::_attribute_map";
"Class::MOP::Mixin::HasAttributes::remove_attribute" -> "Class::MOP::Mixin::HasAttributes::_attribute_map";
"Class::MOP::Mixin::HasAttributes::add_attribute" -> "Class::MOP::Mixin::HasAttributes::_attribute_map";
"Class::MOP::Mixin::HasAttributes::has_attribute" -> "Class::MOP::Mixin::HasAttributes::_attribute_map";
"Class::MOP::Package::initialize" -> "Class::MOP::get_metaclass_by_name";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::_number_of_groups_obj";
"Bio::Roary::PostAnalysis::_build__analyse_groups_obj" -> "Bio::Roary::AnalyseGroups::new";
"Bio::Roary::SplitGroups::_build__analyse_groups_obj" -> "Bio::Roary::AnalyseGroups::new";
"Bio::Roary::AnnotateGroups::consensus_product_for_id_names" -> "Bio::Roary::AnnotateGroups::_ids_to_product";
"Bio::Roary::AnnotateGroups::_build__ids_to_gene_names" -> "Bio::Roary::AnnotateGroups::_ids_to_product";
"Moose::Meta::Attribute::_writer_value_needs_copy" -> "Moose::Meta::Mixin::AttributeCore::should_coerce";
"Moose::Meta::Attribute::_inline_check_coercion" -> "Moose::Meta::Mixin::AttributeCore::should_coerce";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::accessory_ordering_key";
"Moose::BEGIN@33" -> "Moose::Meta::Role::Composite::meta";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@11" -> "Moose::Meta::Role::Composite::meta";
"Class::MOP::Package::BEGIN@8" -> "Devel::GlobalDestruction::BEGIN@4";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::CORE:match";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_overlapping_hypothetical_protein_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::CORE:match";
"Bio::Roary::PostAnalysis::_build__number_of_groups_obj" -> "Bio::Roary::PostAnalysis::_annotate_groups_obj";
"Bio::Roary::PostAnalysis::run" -> "Bio::Roary::PostAnalysis::_annotate_groups_obj";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::PostAnalysis::_annotate_groups_obj";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::_annotate_groups_obj";
"Bio::Roary::ParseGFFAnnotationRole::_build__awk_filter" -> "Bio::Roary::GeneNamesFromGFF::_tags_to_filter";
"Moose::Meta::Attribute::_inline_generate_default" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Class::CORE:sort" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Class::_inline_check_required_attr" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::_inline_instance_get" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::has_value" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Attribute::_process_accessors" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::slots" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Class::CORE:sort" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::_inline_instance_has" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Attribute::_inline_check_constraint" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::_inline_instance_clear" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::_set_initial_slot_value" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::_accessor_description" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::_inline_instance_set" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Attribute::get_raw_value" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Role::Attribute::attribute_for_class" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Method::Accessor::_generate_reader_method_inline" -> "Class::MOP::Mixin::AttributeCore::name";
"Class::MOP::Mixin::HasAttributes::add_attribute" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Class::_inline_slot_initializer" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Attribute::_inline_check_required" -> "Class::MOP::Mixin::AttributeCore::name";
"Moose::Meta::Attribute::_inline_weaken_value" -> "Class::MOP::Mixin::AttributeCore::name";
"Bio::Roary::OrderGenes::_build_number_of_files" -> "Bio::Roary::OrderGenes::gff_files";
"Bio::Roary::OrderGenes::_build__groups_to_file_contigs" -> "Bio::Roary::OrderGenes::gff_files";
"Bio::Roary::AnnotateGroups::_ids_to_gene_names" -> "Bio::Roary::AnnotateGroups::_build__ids_to_gene_names";
"Bio::Roary::SplitGroups::_pre_filter_fasta_files" -> "Bio::Roary::SplitGroups::_gene_files_temp_dir_obj";
"Bio::Roary::SplitGroups::_parse_gene_neighbourhood" -> "Bio::Roary::SplitGroups::_gene_files_temp_dir_obj";
"Moose::import" -> "Sub::Exporter::__ANON__[Sub/Exporter.pm:337]";
"Moose::Role::import" -> "Sub::Exporter::__ANON__[Sub/Exporter.pm:337]";
"Moose::Util::TypeConstraints::import" -> "Sub::Exporter::__ANON__[Sub/Exporter.pm:337]";
"Bio::Roary::GeneNamesFromGFF::_awk_filter" -> "Bio::Roary::ParseGFFAnnotationRole::_build__awk_filter";
"Class::MOP::Package::initialize" -> "Class::MOP::Package::_new";
"Bio::Roary::GeneNamesFromGFF::ids_to_gene_name" -> "Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name";
"Bio::Roary::Output::GroupsMultifastasNucleotide::BEGIN@23" -> "Bio::Roary::Output::GroupsMultifastaNucleotide::meta";
"Bio::Roary::Output::EmblGroups::create_files" -> "Bio::Roary::Output::EmblGroups::CORE:close";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::_new_genes";
"Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion" -> "Bio::Roary::Output::NumberOfGroups::_new_genes";
"Moose::Meta::TypeConstraint::_inline_check" -> "Moose::Meta::TypeConstraint::has_parent";
"Moose::Meta::TypeConstraint::inline_environment" -> "Moose::Meta::TypeConstraint::has_parent";
"Moose::Meta::TypeConstraint::can_be_inlined" -> "Moose::Meta::TypeConstraint::has_parent";
"Bio::Roary::CommandLine::RoaryPostAnalysis::run" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::dont_delete_files";
"Bio::Roary::CommandLine::RoaryPostAnalysis::BUILD" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::dont_delete_files";
"Bio::Roary::PostAnalysis::_build__number_of_groups_obj" -> "Bio::Roary::PostAnalysis::_order_genes_obj";
"Bio::Roary::PostAnalysis::_build__group_statistics_obj" -> "Bio::Roary::PostAnalysis::_order_genes_obj";
"Bio::Roary::PostAnalysis::_create_embl_files" -> "Bio::Roary::PostAnalysis::_order_genes_obj";
"main::RUNTIME" -> "Bio::Roary::CommandLine::RoaryPostAnalysis::new";
"Bio::Roary::PostAnalysis::_annotate_groups_obj" -> "Bio::Roary::PostAnalysis::_build__annotate_groups_obj";
"Bio::Roary::OrderGenes::group_order" -> "Bio::Roary::OrderGenes::_build_group_order";
"Class::MOP::Method::clone" -> "Class::MOP::Method::_set_original_method";
"Moose::Meta::Attribute::_inline_weaken_value" -> "Moose::Meta::Mixin::AttributeCore::is_weak_ref";
"Moose::Util::TypeConstraints::BEGIN@34" -> "Moose::Meta::TypeConstraint::Registry::meta";
"Bio::Roary::SplitGroups::_build__genes_to_files" -> "Bio::Roary::SplitGroups::_analyse_groups_obj";
"Moose::Meta::Attribute::_auto_deref" -> "Moose::Meta::Mixin::AttributeCore::should_auto_deref";
"Moose::Meta::Role::get_method_modifier_list" -> "Moose::Meta::Role::get_after_method_modifiers_map";
"Moose::Meta::Mixin::AttributeCore::should_auto_deref" -> "Class::MOP::Attribute::get_value";
"Moose::Meta::Mixin::AttributeCore::is_required" -> "Class::MOP::Attribute::get_value";
"Moose::Meta::Mixin::AttributeCore::should_coerce" -> "Class::MOP::Attribute::get_value";
"Moose::Meta::Mixin::AttributeCore::is_lazy" -> "Class::MOP::Attribute::get_value";
"Moose::Meta::Mixin::AttributeCore::is_weak_ref" -> "Class::MOP::Attribute::get_value";
"Bio::Roary::OrderGenes::groups_to_contigs" -> "Bio::Roary::OrderGenes::_build_groups_to_contigs";
"Class::MOP::Package::BEGIN@8" -> "Devel::GlobalDestruction::BEGIN@23";
"Moose::Meta::Role::Attribute::attribute_for_class" -> "Moose::Meta::Role::Attribute::original_options";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::number_of_iterations";
"Bio::Roary::AnalyseGroups::_files_to_genes" -> "Bio::Roary::AnalyseGroups::_builder__files_to_genes";
"Moose::Meta::TypeConstraint::Parameterizable::generate_inline_for" -> "Moose::Meta::TypeConstraint::Parameterizable::has_inline_generator";
"Moose::Meta::TypeConstraint::Parameterized::can_be_inlined" -> "Moose::Meta::TypeConstraint::Parameterizable::has_inline_generator";
"Bio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids" -> "Bio::Roary::ContigsToGeneIDsFromGFF::CORE:readline";
"Class::MOP::Mixin::HasMethods::add_method" -> "Class::MOP::Method::body";
"Moose::Meta::Role::Application::ToClass::apply_methods" -> "Class::MOP::Method::body";
"Class::MOP::MiniTrait::apply" -> "Class::MOP::Method::body";
"Class::MOP::Method::Wrapped::wrap" -> "Class::MOP::Method::body";
"Class::MOP::Mixin::HasMethods::_method_map" -> "Class::MOP::Method::body";
"Moose::Meta::Class::_inline_BUILDARGS" -> "Class::MOP::Method::body";
"Bio::Roary::AnnotateGroups::BEGIN@21" -> "Bio::Roary::GeneNamesFromGFF::meta";
"Bio::Roary::ParseGFFAnnotationRole::_gff_fh_input_string" -> "Bio::Roary::GeneNamesFromGFF::_awk_filter";
"Bio::Roary::JobRunner::Role::BEGIN@12" -> "Moose::Role::import";
"Bio::Roary::ClustersRole::BEGIN@11" -> "Moose::Role::import";
"Bio::Roary::ParseGFFAnnotationRole::BEGIN@10" -> "Moose::Role::import";
"Moose::Meta::Role::get_method_modifier_list" -> "Moose::Meta::Role::get_around_method_modifiers_map";
"Class::MOP::Package::add_package_symbol" -> "Class::MOP::Package::_package_stash";
"Class::MOP::Package::remove_package_symbol" -> "Class::MOP::Package::_package_stash";
"Class::MOP::Package::list_all_package_symbols" -> "Class::MOP::Package::_package_stash";
"Class::MOP::Package::get_package_symbol" -> "Class::MOP::Package::_package_stash";
"Class::MOP::Package::has_package_symbol" -> "Class::MOP::Package::_package_stash";
"Class::MOP::Package::get_or_add_package_symbol" -> "Class::MOP::Package::_package_stash";
"Bio::Roary::Output::NumberOfGroups::create_output_files" -> "Bio::Roary::Output::NumberOfGroups::output_raw_filename_unique_genes";
"Bio::Roary::GroupStatistics::_groups_to_files" -> "Bio::Roary::GroupStatistics::_build__groups_to_files";
}
