• Bio::Roary::GroupLabels
• Bio::Roary::GroupStatistics
• Bio::Roary::InflateClusters
• Bio::Roary::IterativeCdhit
• Bio::Roary::JobRunner::Local
• Bio::Roary::JobRunner::Parallel
• Bio::Roary::JobRunner::Role
• Bio::Roary::LookupGeneFiles
• Bio::Roary::MergeMultifastaAlignments
• Bio::Roary::OrderGenes
• Bio::Roary::Output::BlastIdentityFrequency
• Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL
• Bio::Roary::Output::DifferenceBetweenSets
• Bio::Roary::Output::EmblGroups
• Bio::Roary::Output::EMBLHeaderCommon
• Bio::Roary::Output::GroupMultifasta
• Bio::Roary::Output::GroupsMultifastaNucleotide
• Bio::Roary::Output::GroupsMultifastaProtein
• Bio::Roary::Output::GroupsMultifastas
• Bio::Roary::Output::GroupsMultifastasNucleotide
• Bio::Roary::Output::NumberOfGroups
• Bio::Roary::Output::QueryGroups
• Bio::Roary::ParallelAllAgainstAllBlast
• Bio::Roary::ParseGFFAnnotationRole
• Bio::Roary::PostAnalysis
• Bio::Roary::PrepareInputFiles
• Bio::Roary::PresenceAbsenceMatrix
• Bio::Roary::QC::Report
• Bio::Roary::ReformatInputGFFs
• Bio::Roary::ReorderSpreadsheet
• Bio::Roary::SampleOrder
• Bio::Roary::SequenceLengths
• Bio::Roary::SortFasta
• Bio::Roary::SplitGroups
• Bio::Roary::SpreadsheetRole
• Bio::Root::Build
• Bio::Root::Exception
• Bio::Root::HTTPget
• Bio::Root::IO
• Bio::Root::Root
• Bio::Root::RootI
• Bio::Root::Storable
• Bio::Root::Test
• Bio::Root::Test::Warn
• Bio::Root::Utilities
• Bio::Root::Version
• Bio::SCF
• Bio::Search::BlastStatistics
• Bio::Search::BlastUtils
• Bio::Search::DatabaseI
• Bio::Search::GenericDatabase
• Bio::Search::GenericStatistics
• Bio::Search::Hit::BlastHit
• Bio::Search::Hit::BlastPullHit
• Bio::Search::Hit::Fasta
• Bio::Search::Hit::GenericHit
• Bio::Search::Hit::HitFactory
• Bio::Search::Hit::HitI
• Bio::Search::Hit::hmmer3Hit
• Bio::Search::Hit::HMMERHit
• Bio::Search::Hit::HmmpfamHit
• Bio::Search::Hit::ModelHit
• Bio::Search::Hit::PsiBlastHit
• Bio::Search::Hit::PullHitI
• Bio::Search::HSP::BlastHSP
• Bio::Search::HSP::BlastPullHSP
• Bio::Search::HSP::FastaHSP
• Bio::Search::HSP::GenericHSP
• Bio::Search::HSP::hmmer3HSP
• Bio::Search::HSP::HMMERHSP