Login
BioMart
Tools
Downloads
Help & Documentation
Blog
More
▼
Search terms
Ensembl search all species
Ensembl search this species
Ensembl genomes search
Vega search
EBI search
Sanger search
Home
Help & Documentation
Doxygen Perl documentation
Overview
Classes
Namespaces
Files
Directory Browser
Related Pages
Class Hierarchy
Class Index
Full Class List
Methods from all packages
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
All
Classes
Namespaces
Files
Functions
Custom Data