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