Full Class List

Exhaustive list of all classes in the code

Bio::EnsEMBL::Compara::StableId::Adaptor
Bio::EnsEMBL::Compara::Graph::Algorithms
Bio::EnsEMBL::Compara::AlignedMember
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentChains
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentChains
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentNets
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing
Bio::EnsEMBL::Compara::AlignSlice
Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor
Bio::EnsEMBL::Compara::PipeConfig::AncestralMerge_conf
Bio::EnsEMBL::Compara::Production::EPOanchors::AnchorAlign
Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor
Bio::EnsEMBL::Compara::Production::DBSQL::AnchorAlignAdaptor
Bio::EnsEMBL::Compara::DBSQL::AnchorSeqAdaptor
Bio::EnsEMBL::Compara::Production::DBSQL::AnchorSeqAdaptor
Bio::EnsEMBL::Compara::Attribute
Bio::EnsEMBL::Compara::DBSQL::AttributeAdaptor
Bio::EnsEMBL::Compara::BaseGenomicAlignSet
Bio::EnsEMBL::Compara::BaseRelation
Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor
Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable
Bio::EnsEMBL::Compara::Production::Projection::Writer::BaseWriter
Bio::EnsEMBL::Compara::Graph::BaseXMLWriter
Bio::EnsEMBL::Compara::Filter::BestHit
Bio::EnsEMBL::Compara::RunnableDB::Families::BlastAndParseDistances
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastFactory
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastpWithReuse
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::BlastZ
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::Blat
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Blat
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BuildHMM
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFEAnalysis
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFETable
Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor
Bio::EnsEMBL::Compara::CAFETreeNode
Bio::EnsEMBL::Compara::Graph::CGObject
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FromScratch::CheckGenomeReuse
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::CheckReuseDB
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ChunkAndGroupDna
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::ChunkAndGroupDna
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::ChunkDnafrags
Bio::EnsEMBL::Compara::Production::EPOanchors::ChunkRefDnafrags
Bio::Das::ProServer::SourceAdaptor::compara
Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Compress
Bio::EnsEMBL::Compara::Graph::ConnectedComponentGraphs
Bio::EnsEMBL::Compara::Graph::ConnectedComponents
Bio::EnsEMBL::Compara::RunnableDB::Families::ConsensifyAfamily
Bio::Das::ProServer::SourceAdaptor::conservation_score
Bio::EnsEMBL::Compara::ConservationScore
Bio::EnsEMBL::Compara::DBSQL::ConservationScoreAdaptor
Bio::Das::ProServer::SourceAdaptor::constrained_element
Bio::EnsEMBL::Compara::ConstrainedElement
Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreateAlignmentChainsJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateAlignmentChainsJobs
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreateAlignmentNetsJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateAlignmentNetsJobs
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::CreateChrJobs
Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::CreateDefaultPairwiseMlss
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreateFilterDuplicatesJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateFilterDuplicatesJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateLowCoverageJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateNeighbourNodesJobs
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::CreateOtherJobs
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreatePairAlignerJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreatePairAlignerJobs
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateRules
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateSimpleNetsJobs
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::CreateSuperJobs
Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DeleteAlignment
Algorithm::Diff
Bio::EnsEMBL::Compara::Production::Projection::DisplayProjection
Bio::EnsEMBL::Compara::Production::Projection::DisplayXrefProjectionEngine
Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor
Bio::EnsEMBL::Compara::Production::DnaCollection
Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor
Bio::EnsEMBL::Compara::DnaFrag
Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor
Bio::EnsEMBL::Compara::Production::DnaFragChunk
Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor
Bio::EnsEMBL::Compara::Production::DnaFragChunkSet
Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkSetAdaptor
Bio::EnsEMBL::Compara::DnaFragRegion
Bio::EnsEMBL::Compara::DBSQL::DnaFragRegionAdaptor
Bio::EnsEMBL::Compara::Domain
Bio::EnsEMBL::Compara::DBSQL::DomainAdaptor
Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML
Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllTreesOrthoXML
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::DumpDnaCollection
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpDnaCollection
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpLargeNibForChains
Bio::EnsEMBL::Compara::RunnableDB::DumpMemberSequencesIntoFasta
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign
Bio::EnsEMBL::Compara::PipeConfig::DumpMultiAlign_conf
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::DumpRepeats
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::DumpSubsetCreateBlastDB
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpSubsetIntoFasta
Bio::EnsEMBL::Compara::PipeConfig::DumpTrees_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Emf2Maf
Bio::EnsEMBL::Compara::PipeConfig::EPO_conf
Bio::EnsEMBL::Compara::PipeConfig::EpoLowCoverage_conf
Bio::EnsEMBL::Compara::AlignSlice::Exon
Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors
Bio::EnsEMBL::Compara::Production::Projection::FakeXrefHolder
Bio::EnsEMBL::Compara::PipeConfig::Families_conf
Bio::EnsEMBL::Compara::Family
Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor
Bio::EnsEMBL::Compara::Production::EPOanchors::FilterAnchors
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::FilterDuplicates
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::FilterDuplicates
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::FilterStack
Bio::EnsEMBL::Compara::RunnableDB::FindCoreRegionLength
Bio::EnsEMBL::Compara::Production::EPOanchors::FindPairwiseOverlaps
Bio::EnsEMBL::Compara::RunnableDB::FindPartialGenesOnTree
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::FindRepeatGabs
Bio::EnsEMBL::Compara::RunnableDB::FindSingleGenesOnTree
Bio::EnsEMBL::Compara::RunnableDB::FindSplitGenesOnTree
Bio::EnsEMBL::Compara::Production::EPOanchors::FindStrand
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FlowMemberSeq
Bio::EnsEMBL::Compara::FormatTree
Bio::EnsEMBL::Compara::PipeConfig::GenerateAnchors_conf
Bio::EnsEMBL::Compara::StableId::Generator
Bio::EnsEMBL::Compara::Production::GeneSet
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GeneStoreNCMembers
Bio::EnsEMBL::Compara::GeneTree
Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor
Bio::EnsEMBL::Compara::GeneTreeMember
Bio::EnsEMBL::Compara::GeneTreeNode
Bio::EnsEMBL::Compara::PipeConfig::GeneTreesStableIdAndTreefamXrefs_conf
Bio::EnsEMBL::Compara::GenomeDB
Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GenomePrepareNCMembers
Bio::EnsEMBL::Compara::GenomicAlign
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor
Bio::EnsEMBL::Compara::GenomicAlignBlock
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor
Bio::EnsEMBL::Compara::GenomicAlignGroup
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor
Bio::EnsEMBL::Compara::GenomicAlignTree
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor
Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp
Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps
Bio::EnsEMBL::Compara::Production::Projection::GOAProjectionEngine
Bio::EnsEMBL::Compara::Filter::Greedy
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::GroupGenomesUnderTaxa
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterParseOutput
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterPrepare
Bio::EnsEMBL::Compara::RunnableDB::HealthCheck
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMerAnchors
Bio::EnsEMBL::Compara::PipeConfig::HmmerConstrainedElements_conf
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::HMMsearch
Bio::EnsEMBL::Compara::Homology
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Homology_dNdS
Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor
Bio::EnsEMBL::Compara::RunnableDB::HomologyGroupingFactory
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyGroupingFactory
Bio::EnsEMBL::Compara::Production::HomologySet
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::ImportAlignment
Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportChains
Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportNets
Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Infernal
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::InitJobs
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Ktreedist
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Lagan
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::LastZ
Bio::EnsEMBL::Compara::PipeConfig::Lastz_conf
Bio::EnsEMBL::Compara::PipeConfig::Lastz_primate_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMaster_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMasterConf_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMasterCore_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMasterReg_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::LastzNoMaster_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::LastzNoMasterConf_conf
Bio::EnsEMBL::Compara::Graph::Link
Bio::EnsEMBL::Compara::PipeConfig::LoadAllMasterGenomeDB_conf
Bio::EnsEMBL::Compara::PipeConfig::LoadCertainGenomeDB_conf
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::LoadConsEles
Bio::EnsEMBL::Compara::RunnableDB::LoadMembers
Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB
Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtEntries
Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtIndex
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::LowCoverageGenomeAlignment
Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment
Bio::EnsEMBL::Compara::RunnableDB::Families::MafftAfamily
Bio::EnsEMBL::Compara::RunnableDB::MakeSpeciesTree
Bio::EnsEMBL::Compara::StableId::Map
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mavid
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::MD5SUM
Bio::EnsEMBL::Compara::Member
Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor
Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::MercatorFileFactory
Bio::EnsEMBL::Compara::PipeConfig::MercatorPecan_conf
Bio::EnsEMBL::Compara::PipeConfig::MergeHomologyIntoRelease_conf
Bio::EnsEMBL::Compara::PipeConfig::MergeHomologySideTogether_conf
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MLSSIDFactory
Bio::EnsEMBL::Compara::Production::Projection::Writer::MultipleWriter
Bio::EnsEMBL::Compara::PipeConfig::MyISAMiseTables_conf
Bio::EnsEMBL::Compara::StableId::NamedClusterSet
Bio::EnsEMBL::Compara::StableId::NamedClusterSetLink
Bio::EnsEMBL::Compara::NCBITaxon
Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicAlignment
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicTree
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCRecoverEPO
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCRecoverSearch
Bio::EnsEMBL::Compara::PipeConfig::ncRNAtrees_conf
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCSecStructTree
Bio::EnsEMBL::Compara::DBSQL::NCTreeAdaptor
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCTreeBestMMerge
Bio::EnsEMBL::Compara::NestedSet
Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor
Bio::EnsEMBL::Compara::Graph::NewickParser
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML
Bio::EnsEMBL::Compara::Graph::Node
Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory
Bio::EnsEMBL::Compara::RunnableDB::Ortheus
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Ortheus
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree
Bio::EnsEMBL::Compara::Graph::OrthoXMLWriter
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OtherParalogs
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OverallGroupsetQC
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::PairAligner
Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::PairAlignerConfig
Bio::EnsEMBL::Compara::RunnableDB::PairwiseSynteny
Bio::EnsEMBL::Compara::Production::EPOanchors::ParseEnredo
Bio::EnsEMBL::Compara::RunnableDB::Families::ParseMCLintoFamilies
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf
Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Pecan
Bio::EnsEMBL::Compara::PeptideAlignFeature
Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor
Bio::EnsEMBL::Compara::RunnableDB::PeptideMemberGroupingFactory
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::PerGenomeGroupsetQC
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons
Bio::EnsEMBL::Compara::Graph::PhyloXMLWriter
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::PrepareSecStructModels
Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDBEntryWriter
Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedDisplayXrefWriter
Bio::EnsEMBL::Compara::Production::Projection::Writer::ProjectedFileWriter
Bio::EnsEMBL::Compara::Production::Projection::Projection
Bio::EnsEMBL::Compara::Production::Projection::ProjectionEngine
Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::ProjectOntologyXref
Bio::EnsEMBL::Compara::DBSQL::ProteinTreeAdaptor
Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf
Bio::EnsEMBL::Compara::PipeConfig::ProteinTreesFromFASTA_conf
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak
Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::RemoveAlignmentDataInconsistencies
Bio::EnsEMBL::Compara::Production::EPOanchors::RemoveAnchorOverlaps
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMLoadModels
Bio::EnsEMBL::Compara::Production::Projection::RunnableDB::RunnableLogger
Bio::EnsEMBL::Compara::RunnableDB::SearchHMM
Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::SecStructModelTree
Bio::EnsEMBL::Compara::DBSQL::SequenceAdaptor
Bio::EnsEMBL::Compara::Production::EPOanchors::SetGenomeDBLocator
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::SetInternalIds
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes
Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::SetNeighbourNodes
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SimpleNets
Bio::EnsEMBL::Compara::SitewiseOmega
Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor
Bio::EnsEMBL::Compara::AlignSlice::Slice
Bio::EnsEMBL::Compara::SpeciesSet
Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor
Bio::EnsEMBL::Compara::DBSQL::SpeciesTreeAdaptor
Bio::EnsEMBL::Compara::PipeConfig::SplitAndPartialGenesOnTrees_conf
Bio::EnsEMBL::Compara::PipeConfig::SplitAndPartialGenesOnTrees_ensembl_genomes_conf
Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::SplitCeIds
Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FromScratch::StoreMembersSequence
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::StoreSequence
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::StoreSequence
Bio::EnsEMBL::Compara::Subset
Bio::EnsEMBL::Compara::DBSQL::SubsetAdaptor
Bio::EnsEMBL::Compara::SyntenyRegion
Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor
Bio::EnsEMBL::Compara::DBSQL::TagAdaptor
Bio::EnsEMBL::Compara::Taggable
Bio::EnsEMBL::Compara::PipeConfig::TBlat_conf
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Threshold_on_dS
Bio::EnsEMBL::Compara::AlignSlice::Translation
Bio::EnsEMBL::Compara::RunnableDB::TreefamXrefMapper
Bio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign
Bio::EnsEMBL::Compara::Production::EPOanchors::TrimStoreAnchors
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscChainFactory
Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping
Bio::EnsEMBL::Compara::Production::EPOanchors::UpdateMaxAlignmentLength
Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::UpdateMaxAlignmentLength
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::UpdateMaxAlignmentLength
Bio::EnsEMBL::Compara::PipeConfig::Example::VegaProteinTrees_conf
Bio::EnsEMBL::Compara::PipeConfig::Example::WormProteinTrees_conf