TOC for all levels
ensembl-compara
ensembl-compara::docs
ensembl-compara::modules
ensembl-compara::modules::Algorithm
ensembl-compara::modules::Bio
ensembl-compara::modules::Bio::Das
ensembl-compara::modules::Bio::Das::ProServer
ensembl-compara::modules::Bio::Das::ProServer::SourceAdaptor
ensembl-compara::modules::Bio::EnsEMBL
ensembl-compara::modules::Bio::EnsEMBL::Compara
ensembl-compara::modules::Bio::EnsEMBL::Compara::AlignSlice
ensembl-compara::modules::Bio::EnsEMBL::Compara::DBSQL
ensembl-compara::modules::Bio::EnsEMBL::Compara::Filter
ensembl-compara::modules::Bio::EnsEMBL::Compara::Graph
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production::DBSQL
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production::EPOanchors
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production::GenomicAlignBlock
ensembl-compara::modules::Bio::EnsEMBL::Compara::RunnableDB
ensembl-compara::modules::t
ensembl-compara::scripts
ensembl-compara::scripts::BLAT
ensembl-compara::scripts::blastz
ensembl-compara::scripts::compare
ensembl-compara::scripts::das
ensembl-compara::scripts::domain
ensembl-compara::scripts::dumps
ensembl-compara::scripts::examples
ensembl-compara::scripts::examples::exercise_answers
ensembl-compara::scripts::family
ensembl-compara::scripts::gen_malign
ensembl-compara::scripts::hcr
ensembl-compara::scripts::homology
ensembl-compara::scripts::initialize
ensembl-compara::scripts::misc
ensembl-compara::scripts::phusion
ensembl-compara::scripts::pipeline
ensembl-compara::scripts::synteny
ensembl-compara::scripts::taxonomy
ensembl-compara::scripts::tree
ensembl-compara::scripts::view_alignment
ensembl-compara::sql
ensembl-comparaTop
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ensembl-compara::docsTop
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ensembl-compara::modulesTop
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ensembl-compara::modules::AlgorithmTop
DiffCompute `intelligent' differences between two files / lists
ensembl-compara::modules::BioTop
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ensembl-compara::modules::Bio::DasTop
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ensembl-compara::modules::Bio::Das::ProServerTop
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ensembl-compara::modules::Bio::Das::ProServer::SourceAdaptorTop
comparaExtension of the ProServer for e! genomic alignments and synteny block.
conservation_scoreExtension of the ProServer for e! conservation scores
ensembl-compara::modules::Bio::EnsEMBLTop
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ensembl-compara::modules::Bio::EnsEMBL::ComparaTop
AlignSliceAn AlignSlice can be used to map genes and features from one species onto another one
AlignedMemberDESCRIPTION of Object
Attribute
BaseRelation
ConservationScoreStores conservation scores
ConstrainedElementconstrained element data produced by Gerp
DnaFragDefines the DNA sequences used in the database.
DnaFragRegiondnafrag region on one species
Domain
Family
GenomeDBDESCRIPTION of Object
GenomicAlignDefines one of the sequences involved in a genomic alignment
GenomicAlignBlockAlignment of two or more pieces of genomic DNA
GenomicAlignGroupDefines groups of genomic aligned sequences
GenomicAlignTreeDESCRIPTION of Object
HomologyHomology between two proteins
Member
MethodLinkSpeciesSetRelates every method_link with the species_set for which it has been used
NCBITaxonDESCRIPTION of Object
NestedSetDESCRIPTION of Object
PeptideAlignFeature
ProteinTreeDESCRIPTION of Object
SitewiseOmegaDESCRIPTION of Object
SubsetDESCRIPTION of Object
SyntenyRegionSynteny region
TaxonDESCRIPTION of Object
ensembl-compara::modules::Bio::EnsEMBL::Compara::AlignSliceTop
ExonDescription
SliceThese objects contain all the information needed for mapping features through genomic alignments
TranslationExtension of the Bio::EnsEMBL::Translation module for the translations mapped on the AlignSlices
ensembl-compara::modules::Bio::EnsEMBL::Compara::DBSQLTop
AlignSliceAdaptorAn AlignSlice can be used to map genes from one species onto another one. This adaptor is used to fetch all the data needed for an AlignSlice from the database.
AnchorAlignAdaptor(1)Bio::EnsEMBL::Compara::Production::DBSQL::AnchorAlignAdaptor
AnchorSeqAdaptor(1)
AttributeAdaptor
BaseRelationAdaptor
ConservationScoreAdaptorObject adaptor to access data in the conservation_score table
ConstrainedElementAdaptor
DBAdaptor(1)Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
DnaAlignFeatureAdaptorBio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor
DnaFragAdaptorBio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor
DnaFragRegionAdaptorDESCRIPTION of Object
DomainAdaptorDomainAdaptor
FamilyAdaptorDESCRIPTION of Object This object represents a family coming from a database of protein families.
GenomeDBAdaptorDESCRIPTION of Object
GenomicAlignAdaptorObject adaptor to access data in the genomic_align table
GenomicAlignBlockAdaptorBio::EnsEMBL::DBSQL::Compara::GenomicAlignBlockAdaptor
GenomicAlignGroupAdaptorObject to access data in genomic_align_group table
GenomicAlignTreeAdaptorObject used to store and retrieve GenomicAlignTrees to/from the databases
HomologyAdaptor
MemberAdaptor
MethodLinkSpeciesSetAdaptorObject to access data in the method_link_species_set and method_link tables
NCBITaxonAdaptorDESCRIPTION of Object
NestedSetAdaptorDESCRIPTION of Object
PeptideAlignFeatureAdaptorBio::EnsEMBL::Hive::DBSQL::PeptideAlignFeatureAdaptor
ProteinTreeAdaptorDESCRIPTION of Object
SequenceAdaptor
SitewiseOmegaAdaptorDESCRIPTION of Object
SubsetAdaptor
SyntenyRegionAdaptorObject to access data in the synteny_region and dnafrag_region tables
TaxonAdaptorDESCRIPTION of Object
ensembl-compara::modules::Bio::EnsEMBL::Compara::FilterTop
BestHit
Greedy
ensembl-compara::modules::Bio::EnsEMBL::Compara::GraphTop
AlgorithmsDESCRIPTION of Object
CGObjectDESCRIPTION of Object
ConnectedComponentGraphsBio::EnsEMBL::Compara::Graph::ConnectedComponentGraphs
ConnectedComponentsBio::EnsEMBL::Compara::Graph::ConnectedComponents
LinkDESCRIPTION of Object
NewickParserDESCRIPTION of Object
NodeDESCRIPTION of Object
ensembl-compara::modules::Bio::EnsEMBL::Compara::ProductionTop
DnaCollectionBio::EnsEMBL::Compara::Production::DnaCollection
DnaFragChunk
DnaFragChunkSetBio::EnsEMBL::Compara::Production::DnaFragChunkSet
GeneSetBio::EnsEMBL::Compara::Production::GeneSet
HomologySetBio::EnsEMBL::Compara::Production::HomologySet
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production::DBSQLTop
AnchorAlignAdaptor(2)Bio::EnsEMBL::Compara::Production::DBSQL::AnchorAlignAdaptor
AnchorSeqAdaptor(2)
DBAdaptor(2)Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
DnaCollectionAdaptorBio::EnsEMBL::Compara::Production::DnaCollectionAdaptor
DnaFragChunkAdaptorBio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor
DnaFragChunkSetAdaptor
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production::EPOanchorsTop
AnchorAlign
ExonerateAnchorsBio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors
FilterAnchorsBio::EnsEMBL::Compara::Production::GenomicAlignBlock::EPOanchors::FilterAnchors
GetBlastzOverlapsBio::EnsEMBL::Compara::Production::EPOanchors:GetBlastzOverlaps:
RemoveAnchorOverlapsBio::EnsEMBL::Compara::Production::EPOanchors::RemoveAnchorOverlaps
TrimAnchorAlignBio::EnsEMBL::Compara::Production::EPOanchors::TrimAnchorAlign
TrimStoreAnchorsBio::EnsEMBL::Compara::Production::EPOanchors::TrimStoreAnchors
ensembl-compara::modules::Bio::EnsEMBL::Compara::Production::GenomicAlignBlockTop
AlignmentChainsBio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentChains
AlignmentNetsBio::EnsEMBL::Compara::Production::GenomicAlign::AlignmentNets
AlignmentProcessingBio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing
BlastZBio::EnsEMBL::Compara::RunnableDB::BlastZ
BlatBio::EnsEMBL::Compara::RunnableDB::Blat
ChunkAndGroupDnaBio::EnsEMBL::Compara::Production::GenomicAlignBlock::ChunkAndGroupDna
CreateAlignmentChainsJobsBio::EnsEMBL::Compara::RunnableDB::CreateAlignmentChainsJobs
CreateAlignmentNetsJobsBio::EnsEMBL::Compara::RunnableDB::CreateAlignmentNetsJobs
CreateFilterDuplicatesJobsBio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateFilterDuplicatesJobs
CreateLowCoverageJobsBio::EnsEMBL::Compara::RunnableDB::CreateLowCoverageAlignmentJobs
CreatePairAlignerJobsBio::EnsEMBL::Compara::RunnableDB::CreatePairAlignerJobs
CreateRulesBio::EnsEMBL::Compara::RunnableDB::CreateRules
CreateSimpleNetsJobsBio::EnsEMBL::Compara::RunnableDB::CreateSimpleNetsJobs
DumpDnaCollectionBio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpDnaCollection
DumpLargeNibForChainsBio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpLargeNibForChains
FilterDuplicatesBio::EnsEMBL::Compara::Production::GenomicAlignBlock::FilterDuplicates
FilterStackBio::EnsEMBL::Compara::Production::GenomicAlignBlock::FilterStack
GerpBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp
ImportAlignmentBio::EnsEMBL::Compara::Production::GenomicAlignBlock::ImportAlignment
LaganBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Lagan
LowCoverageGenomeAlignmentBio::EnsEMBL::Compara::Production::GenomicAlignBlock::LowCoverageGenomeAlignment
MavidBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mavid
MercatorBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mercator
MlaganBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Mlagan
OrtheusBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Ortheus
PairAlignerBio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner
PecanBio::EnsEMBL::Compara::Production::GenomicAlignBlock::Pecan
PhastConsBio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons
SimpleNetsBio::EnsEMBL::Compara::Production::GenomicAlign::AlignmentSimple
UpdateMaxAlignmentLengthBio::EnsEMBL::Compara::Production::GenomicAlignBlock::FilterDuplicates
ensembl-compara::modules::Bio::EnsEMBL::Compara::RunnableDBTop
BlastComparaPepBio::EnsEMBL::Compara::RunnableDB::BlastComparaPep
BlastComparaPepAcrossBio::EnsEMBL::Compara::RunnableDB::BlastComparaPepAcross
BreakPAFClusterBio::EnsEMBL::Compara::RunnableDB::BreakPAFCluster
BuildHomologyBio::EnsEMBL::Compara::RunnableDB::BuildHomology
ClustalWBio::EnsEMBL::Compara::RunnableDB::ClustalW
CreateBlastRulesBio::EnsEMBL::Compara::RunnableDB::CreateBlastRules
CreateBuildHomologyJobsBio::EnsEMBL::Compara::RunnableDB::CreateBuildHomologyJobs
CreateHclusterPrepareJobsBio::EnsEMBL::Compara::RunnableDB::CreateHclusterPrepareJobs
CreateHomology_dNdSJobsBio::EnsEMBL::Compara::RunnableDB::CreateHomology_dNdSJobs
DummyBio::EnsEMBL::Compara::RunnableDB::Dummy
GenomeCalcStatsBio::EnsEMBL::Compara::RunnableDB::GenomeLoadMembers
GenomeDumpFastaBio::EnsEMBL::Compara::RunnableDB::GenomeDumpFasta
GenomeLoadExonMembersBio::EnsEMBL::Compara::RunnableDB::GenomeLoadExonMembers
GenomeLoadMembersBio::EnsEMBL::Compara::RunnableDB::GenomeLoadMembers
GenomeSubmitPepBio::EnsEMBL::Compara::RunnableDB::GenomeSubmitPep
HclusterPrepareBio::EnsEMBL::Compara::RunnableDB::HclusterPrepare
HclusterRunBio::EnsEMBL::Compara::RunnableDB::HclusterRun
HealthCheckBio::EnsEMBL::Compara::RunnableDB::HealthCheck
HomologyClusterBio::EnsEMBL::Compara::RunnableDB::HomologyCluster
Homology_dNdSBio::EnsEMBL::Compara::RunnableDB::Homology_dNdS
LoadUniProtBio::EnsEMBL::Compara::RunnableDB::LoadUniProt
MCoffeeBio::EnsEMBL::Compara::RunnableDB::MCoffee
MuscleBio::EnsEMBL::Compara::RunnableDB::Muscle
NJTREE_PHYMLBio::EnsEMBL::Compara::RunnableDB::NJTREE_PHYML
OrthoTreeBio::EnsEMBL::Compara::RunnableDB::OrthoTree
PAFClusterBio::EnsEMBL::Compara::RunnableDB::PAFCluster
PHYMLBio::EnsEMBL::Compara::RunnableDB::PHYML
QuickTreeBreakBio::EnsEMBL::Compara::RunnableDB::QuickTreeBreak
RAPBio::EnsEMBL::Compara::RunnableDB::RAP
Sitewise_dNdSBio::EnsEMBL::Compara::RunnableDB::Sitewise_dNdS
Threshold_on_dSBio::EnsEMBL::Compara::RunnableDB::Threshold_on_dS
UpdatePAFIdsBio::EnsEMBL::Compara::RunnableDB::UpdatePAFIds
ensembl-compara::modules::tTop
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ensembl-compara::scriptsTop
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ensembl-compara::scripts::BLATTop
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ensembl-compara::scripts::blastzTop
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ensembl-compara::scripts::compareTop
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ensembl-compara::scripts::dasTop
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ensembl-compara::scripts::domainTop
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ensembl-compara::scripts::dumpsTop
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ensembl-compara::scripts::examplesTop
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ensembl-compara::scripts::examples::exercise_answersTop
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ensembl-compara::scripts::familyTop
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ensembl-compara::scripts::gen_malignTop
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ensembl-compara::scripts::hcrTop
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ensembl-compara::scripts::homologyTop
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ensembl-compara::scripts::initializeTop
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ensembl-compara::scripts::miscTop
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ensembl-compara::scripts::phusionTop
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ensembl-compara::scripts::pipelineTop
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ensembl-compara::scripts::syntenyTop
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ensembl-compara::scripts::taxonomyTop
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ensembl-compara::scripts::treeTop
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ensembl-compara::scripts::view_alignmentTop
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ensembl-compara::sqlTop