TOC for all levels
ensembl-analysis
ensembl-analysis::modules
ensembl-analysis::modules::Bio
ensembl-analysis::modules::Bio::EnsEMBL
ensembl-analysis::modules::Bio::EnsEMBL::Analysis
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Config
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Config::Funcgen
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Config::GeneBuild
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable::Finished
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable::Funcgen
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB::Funcgen
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB::Finished
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Algorithms
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::BPlite
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Filter
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Finished
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ConfigDependent
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::IMGT
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::IMGT::Seq
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::IMGT::SeqIO
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Otter
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Pmatch
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::WGA2Genes
ensembl-analysis::scripts
ensembl-analysis::scripts::Funcgen
ensembl-analysis::scripts::Pseudogenes
ensembl-analysis::scripts::buildchecks
ensembl-analysis::scripts::genebuild
ensembl-analysis::scripts::ig
ensembl-analysis::scripts::imgt
ensembl-analysis::scripts::markers
ensembl-analysis::scripts::protein
ensembl-analysis::scripts::transfer_annotations
ensembl-analysis::scripts::viral_pseudogenes
ensembl-analysis::scripts::wga2genes
ensembl-analysis::sql
ensembl-analysisTop
Nothing here
ensembl-analysis::modulesTop
Nothing here
ensembl-analysis::modules::BioTop
Nothing here
ensembl-analysis::modules::Bio::EnsEMBLTop
Nothing here
ensembl-analysis::modules::Bio::EnsEMBL::AnalysisTop
RunnableBio::EnsEMBL::Analysis::Runnable
RunnableDBBio::EnsEMBL::Analysis::RunnableDB
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::ConfigTop
ImportArrays(1)Bio::EnsEMBL::Analysis::Config::ImportArrays
ProbeAlign(1)Bio::EnsEMBL::Analysis::Config::Funcgen::ProbeAlign?
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Config::FuncgenTop
Nothing here
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Config::GeneBuildTop
ExamineGeneSetsBio::EnsEMBL::Analysis::Config::GeneBuild::OrthologueEvaluator
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableTop
AlignmentChains(1)Bio::EnsEMBL::Pipeline::Runnable::AlignmentChains
AlignmentNets(1)Bio::EnsEMBL::Pipeline::Runnable::AlignmentNets
BaseAbInitio
BaseExonerateBio::EnsEMBL::Analysis::Runnable::ExonerateTranscript
BestPmatch(1)
BestTargetted(1)
BestTargettedExonerate
Blast(1)Bio::EnsEMBL::Analysis::Runnable::Blast
BlastMiniBuilderBio::EnsEMBL::Analysis::Runnable::BlastMiniBuilder;
BlastMiniGenewise(1)Bio::EnsEMBL::Analysis::Runnable::BlastMiniGenewise
BlastRfam(1)Bio::EnsEMBL::Analysis::Runnable::BlastRfam
BlastTranscriptDNA(1)Bio::EnsEMBL::Analysis::Runnable::BlastTranscriptDNA
BlastTranscriptPep(1)Bio::EnsEMBL::Analysis::Runnable::BlastTranscriptPep
BlastmiRNA(1)Bio::EnsEMBL::Analysis::Runnable::BlastmiRNA
Blastz(1)Bio::EnsEMBL::Analysis::Runnable::Blastz
BlatBio::EnsEMBL::Analysis::Runnable::Blat
CPG(1)Bio::EnsEMBL::Analysis::Runnable::CPG
CrossMatch
Dust(1)Bio::EnsEMBL::Analysis::Runnable::Dust
EPCR(1)Bio::EnsEMBL::Analysis::Runnable::EPCR
EponineTSS(1)Bio::EnsEMBL::Analysis::Runnable::EponineTSS
ExonerateAffyBio::EnsEMBL::Analysis::Runnable::ExonerateAffy
ExonerateAlignFeature(1)Bio::EnsEMBL::Analysis::Runnable::ExonerateAlignFeature
ExonerateArrayBio::EnsEMBL::Pipeline::Runnable::ExonerateArray
ExonerateCloneEnds(1)Bio::EnsEMBL::Analysis::Runnable::ExonerateCloneEnds
ExonerateProbeBio::EnsEMBL::Analysis::Runnable::ExonerateProbe
ExonerateTags(1)Bio::EnsEMBL::Analysis::Runnable::ExonerateTags
ExonerateTranscriptBio::EnsEMBL::Analysis::Runnable::ExonerateTranscript
Fgenesh(1)Bio::EnsEMBL::Analysis::Runnable::Fgenes
FirstEF(1)Bio::EnsEMBL::Analysis::Runnable::FirstEF
Funcgen(1)Bio::EnsEMBL::Analysis::Runnable::Fungen
GeneBuilder(1)
Genefinder(1)Bio::EnsEMBL::Analysis::Runnable::Genefinder
Genewisealigns protein hits to genomic sequence
Genscan(1)Bio::EnsEMBL::Analysis::Runnable::Genscan
HaplotypeMapper(1)Bio::EnsEMBL::Analysis::Runnable::HaplotypeProjection
HaplotypeProjection(1)Bio::EnsEMBL::Analysis::Runnable::HaplotypeProjection
HavanaAdder(1)Bio::EnsEMBL::Analysis::Runnable::HavanaAdder
Infernal(1)Bio::EnsEMBL::Analysis::Runnable::Infernal
LaganBio::EnsEMBL::Analysis::Runnable::Mlagan
LowCoverageGenomeAlignmentBio::EnsEMBL::Analysis::Runnable::LowCoverageGenomeAlignment
MavidBio::EnsEMBL::Analysis::Runnable::Mavid
MercatorBio::EnsEMBL::Analysis::Runnable::Mercator
MiniGenewiseBio::EnsEMBL::Analysis::Runnable::MiniGenewise
MlaganBio::EnsEMBL::Analysis::Runnable::Mlagan
MultiMiniGenewiseBio::EnsEMBL::Analysis::Runnable::MultiMiniGenewise
OrtheusBio::EnsEMBL::Analysis::Runnable::Ortheus
PSILC(1)Bio::EnsEMBL::Analysis::Runnable::PSILC;
PSILC_BlastPBio::EnsEMBL::Analysis::Runnable::PSILC;
PecanBio::EnsEMBL::Analysis::Runnable::Mlagan
Pmatch(1)
ProteinAnnotation(1)
PseudogeneBio::EnsEMBL::Analysis::Runnable::Pseudogene
Pseudogene2x(1)of Pseudogene calling code for 2x genomes
RNAFoldBio::EnsEMBL::Analysis::Runnable::RNAfold
RepeatMasker(1)Bio::EnsEMBL::Analysis::Runnable::RepeatMasker
Snap(1)Bio::EnsEMBL::Analysis::Runnable::Snap
Spliced_elsewhere(1)Bio::EnsEMBL::Analysis::Runnable::Spliced_elsewhere;
TRF(1)Bio::EnsEMBL::Analysis::Runnable::TRF
TranscriptCoalescer(1)
TranscriptConsensus(1)
miRNA(1)Bio::EnsEMBL::Analysis::Runnable:miRNA
tRNAscan_SE(1)Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable::FinishedTop
Augustus(1)Bio::EnsEMBL::Analysis::Runnable::Finished::Augustus
Blast(2)
BlastExonerate(1)
EPCR(2)EPCR.pm
EST(1)
Est2GenomeBio::EnsEMBL::Analysis::Runnable::Finished::Est2Genome
Exonerate(1)
GenewiseHmmHmms to genomic sequence
HalfwiseHMM(1)Bio::EnsEMBL::Analysis::Runnable::Finished::HalfwiseHMM
MiniEst2GenomeBio::EnsEMBL::Analysis::Runnable::Finished::MiniEst2Genome
RepeatMasker(2)Bio::EnsEMBL::Analysis::Runnable::Finished::RepeatMasker
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable::FuncgenTop
ACME(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::ACME
Chipotle(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::Chipotle
MAT(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::MAT
Nessie(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie
SWEmbl(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl
Splitter(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::Splitter
TileMap(1)Bio::EnsEMBL::Analysis::Runnable::Funcgen::TileMap
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotationTop
Coil(1)Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Coil
Gene3d(1)Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Genes3d
Hmmpfam(1)Bio::EnsEMBL::Analysis::Runnable::Protein::Hmmpfam
IPRScan(1)
PIRSF(1)Bio::EnsEMBL::Pipeline::Runnable::ProteinAnnotation::PIRSF
PIRSF_wormbase
Panther(1)Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Panther
Pfam(1)Bio::EnsEMBL::Analysis::Runnable::Protein::Hmmpfam
Pfam_wormbase
Prints(1)DESCRIPTION of Object
Prints_wormbase
Prodom(1)Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom
PrositePattern(1)
PrositePattern_wormbase
PrositeProfile(1)PrositeProfile
PrositeProfile_wormbase
Seg(1)Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg
Signalp(1)Bio::EnsEMBL::Analysis::Runnable::Protein::Signalp
Smart_wormbase
Superfamily(1)Bio::EnsEMBL::Analysis::Runnable::Protein::Hmmpfam
Superfamily_wormbase
Tigrfam_wormbase
Tmhmm(1)Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Tmhmm
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDBTop
AccumulatorBio::EnsEMBL::Analysis::RunnableDB::Accumulator
AlignAffyProbesBio::EnsEMBL::Analysis::RunnableDB::Exonerate2Genes;
AlignmentChains(2)Bio::EnsEMBL::Analysis::RunnableDB::AlignmentChains
AlignmentFilterBio::EnsEMBL::Analysis::RunnableDB::AlignmentFilter
AlignmentNets(2)Bio::EnsEMBL::Analysis::RunnableDB::AlignmentNets
BaseGeneBuild
BestPmatch(2)
BestTargetted(2)Bio::EnsEMBL::Analysis::RunnableDB::BestTargetted
Blast(3)Bio::EnsEMBL::Analysis::RunnableDB::Blast
BlastGenscanDNABio::EnsEMBL::Analysis::RunnableDB::Blast
BlastGenscanPepBio::EnsEMBL::Analysis::RunnableDB::Blast
BlastMiniGenewise(2)Bio::EnsEMBL::Analysis::RunnableDB::BlastMiniGenewise
BlastRfam(2)Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam
BlastTranscriptDNA(2)Bio::EnsEMBL::Analysis::RunnableDB::BlastTranscriptDNA
BlastTranscriptPep(2)Bio::EnsEMBL::Analysis::RunnableDB::BlastTranscriptPep
BlastmiRNA(2)Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam
CPG(2)Bio::EnsEMBL::Analysis::RunnableDB::CPG
CollapseAffyProbesBio::EnsEMBL::Analysis::RunnableDB::Exonerate2Genes;
CopyGenesDESCRIPTION of Object
Dust(2)Bio::EnsEMBL::Analysis::RunnableDB::Dust
EPCR(3)
EponineTSS(2)Bio::EnsEMBL::Analysis::RunnableDB::EponineTSS
Exonerate2ArrayBio::EnsEMBL::Pipeline::RunnableDB::Exonerate2Array
Exonerate2GenesBio::EnsEMBL::Analysis::RunnableDB::Exonerate2Genes;
ExonerateAlignFeature(2)Bio::EnsEMBL::Analysis::RunnableDB::ExonerateAlignFeature
ExonerateCloneEnds(2)Bio::EnsEMBL::Analysis::RunnableDB::Exonerate2Genes;
ExonerateClonesBio::EnsEMBL::Analysis::RunnableDB::Exonerate2Genes;
ExonerateForGenewiseBio::EnsEMBL::Analysis::RunnableDB::ExonerateForGenewise
ExonerateOrthologueEvaluatorBio::EnsEMBL::Analysis::RunnableDB::ExonerateOrthologueEvaluator;
ExonerateRefineCloneEndsBio::EnsEMBL::Analysis::RunnableDB::Exonerate2Genes;
ExonerateSolexaBio::EnsEMBL::Analysis::RunnableDB::ExonerateSolexa
ExonerateSolexaTranscriptBio::EnsEMBL::Analysis::RunnableDB::ExonerateSolexaTranscript
ExonerateTags(2)Bio::EnsEMBL::Analysis::RunnableDB::ExonerateTags
Fgenesh(2)
FilterGenesBio::EnsEMBL::Analysis::RunnableDB::FilterGenes;
FindFalseIntronsBio::EnsEMBL::Analysis::RunnableDB::FindFalseIntrons
FindMissingOrthologuesBio::EnsEMBL::Analysis::RunnableDB::FindMissingOrthologues;
FindPartialGenes;
FindSplitGenes
Finished
FirstEF(2)Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
Funcgen(2)Bio::EnsEMBL::Analysis::RunnableDB::Fungen
GeneBuilder(2)
GeneRecord
Genefinder(2)
Genscan(2)
HaplotypeMapper(2)Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection
HaplotypeProjection(2)Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection
HavanaAdder(2)Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder
IgSegBuilderBio::EnsEMBL::Analysis::RunnableDB::IgSegBuilder
ImportArrays(2)Bio::EnsEMBL::Analysis::RunnableDB::ImportArrays;
IncrementalBuild
Infernal(2)Bio::EnsEMBL::Analysis::RunnableDB::Infernal;
Layer
LayerAnnotationDESCRIPTION of Object
MakeSimilarityInputIDs
MapCloneEndsBio::EnsEMBL::Analysis::RunnableDB::MapCloneEnds;
MissingOrthologuesBio::EnsEMBL::Analysis::RunnableDB::MissingOrthologues;
OrthologueEvaluatorBio::EnsEMBL::Analysis::RunnableDB::OrthologueEvaluator;
PSILC(2)Bio::EnsEMBL::Analysis::RunnableDB::PSILC;
Pmatch(2)aligns protein sequence to genomic sequence
ProbeAlign(2)Bio::EnsEMBL::Analysis::RunnableDB::ProbeAlign;
ProteinAnnotation(2)DESCRIPTION of Object
Pseudogene2x(2)Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene2x.pm
Pseudogene_DBBio::EnsEMBL::Analysis::RunnableDB::Pseudogene_DB.pm
RecoverFalseIntronsBio::EnsEMBL::Analysis::RunnableDB::RecoverFalseIntrons;
RefineSolexaGenesBio::EnsEMBL::Analysis::RunnableDB::RefineSolexaGenes
RepeatMasker(3)Bio::EnsEMBL::Analysis::RunnableDB::RepeatMasker
Snap(2)
Solexa2GenesBio::EnsEMBL::Analysis::RunnableDB::Solexa2Genes
Spliced_elsewhere(2)Bio::EnsEMBL::Analysis::RunnableDB::Spliced_elsewhere;
TRF(2)Bio::EnsEMBL::Analysis::RunnableDB::TRF
TranscriptCoalescer(2)Bio::EnsEMBL::Analysis::RunnableDB::TranscriptCoalescer
TranscriptConsensus(2)
UTR_BuilderBio::EnsEMBL::Analysis::RunnableDB::UTR_Builder
WGA2GenesBio::EnsEMBL::Analysis::RunnableDB::WGA2Genes
WGA2GenesDirectBio::EnsEMBL::Analysis::RunnableDB::WGA2GenesDirect
miRNA(2)Bio::EnsEMBL::Analysis::RunnableDB::miRNA
tRNAscan_SE(2)Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB::FuncgenTop
ACME(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME
Chipotle(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle
MAT(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT
Nessie(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie
SWEmbl(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::SWEmbl
Splitter(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Splitter
TileMap(2)Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotationTop
Coil(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Coil
Gene3d(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Gene3d
Hmmpfam(2)Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::Hmmpfam
IPRScan(2)Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::IPRScan
PIRSF(2)Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::PIRSF
Panther(2)Bio::EnsEMBL::Analysis::RunnableDB::Protein::Panther
Pfam(2)Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::Pfam
Prints(2)DESCRIPTION of Object
Prodom(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Prodom
PrositePattern(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::PrositePattern
PrositeProfile(2)
Seg(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg
Signalp(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Signalp
Superfamily(2)Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::Superfamily
Tmhmm(2)Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Tmhmm
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::RunnableDB::FinishedTop
Augustus(2)
Blast(4)Bio::EnsEMBL::Analysis::RunnableDB::Finished::Blast
BlastExonerate(2)
ClusterDepthFilter
DepthFilter
EPCR(4)EPCR.pm
EST(2)
Exonerate(2)
HalfwiseHMM(2)Bio::EnsEMBL::Analysis::RunnableDB::Finished::HalfwiseHMM
RepeatMasker(4)Bio::EnsEMBL::Analysis::RunnableDB::Finished::RepeatMasker
TRF(3)Bio::EnsEMBL::Analysis::RunnableDB::Finished::TRF
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::ToolsTop
BPliteLightweight BLAST parser
BPliteWrapper(1)Bio::EnsEMBL::Analysis::Tools::BPliteWrapper
BasicFilterBio::EnsEMBL::Analysis::Tools::BasicFilter
BlastDB
Blastz(2)Ensembl specific blastz output parser
CdnaUpdateTranscriptFilterBio::EnsEMBL::Analysis::Tools::CdnaUpdateTranscriptFilter
ClusterFilterBio::EnsEMBL::Analysis::Tools::ClusterFilter
ConfigUtils
ExonerateTranscriptFilterBio::EnsEMBL::Analysis::Tools::ExonerateTranscriptFilter
FeatureFactoryBio::EnsEMBL::Analysis::Tools::FeatureFactory
FeatureFilterBio::EnsEMBL::Analysis::Tools::FeatureFilter
FilterBPliteBio::EnsEMBL::Analysis::Tools::FilterBPlite
FragmentTranscriptFilterBio::EnsEMBL::Analysis::Tools::FragmentTranscriptFilter
GeneBuildUtilsbase class for genebuild utility methods
IgTranscriptFilter
KillList
Logger
MiniSeqan artificially constructed cDNA on a genomic sequence
PairAlignDna pairwise alignment module
PolyAClippingpolA-clipping.pl
ProteinAnnotationFilterBio::EnsEMBL::Analysis::Tools::ProteinAnnotationFilter
Stashes
Utilitiesbase class which exports utility methods which don't take Bio::XX objects
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::AlgorithmsTop
ClusterUtils
ExonCluster
GeneClusterGeneCluster
IntronClusterIntronCluster
TranscriptCluster(1)TranscriptCluster
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::BPliteTop
HSP
IterationBPlite::Iteration - object for parsing single iteration of a PSIBLAST report
Sbjct
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::FilterTop
BlastMiniGenewise(3)Bio::EnsEMBL::Analysis::Tools::Filter::BlastMiniGenewise
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::FinishedTop
BPliteWrapper(2)Bio::EnsEMBL::Analysis::Tools::Finished::BPliteWrapper
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::GeneBuildUtilsTop
CollapsedCluster
EvidenceUtils
ExonExtendedBio::EnsEMBL::Analysis:Tools::GeneBuildUtils::ExonExtended;
ExonUtilsutilities for transcript objects
GeneUtilsutilities for gene objects
HomologyUtilsutilities for gene objects
IntronUtilsutilities for transcript objects
TranscriptExtendedBio::EnsEMBL::Analysis:Tools::GeneBuildUtils::TranscriptExtended;
TranscriptUtils(1)utilities for transcript objects
TranslationUtils
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ConfigDependentTop
TranscriptUtils(2)utilities for transcript objects which depend on config files
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::IMGTTop
Nothing here
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::IMGT::SeqTop
RichSeqIMGT
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::IMGT::SeqIOTop
imgt_embl
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::OtterTop
DnaAlignFeatureEnsembl specific dna-dna pairwise alignment feature
DnaAlignFeatureHistoryStores details of an dna_align_feature_history run
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::Otter::DBSQLTop
DBAdaptor
DnaAlignFeatureAdaptorAdaptor for DnaAlignFeatures
DnaAlignFeatureHistoryAdaptorBio::EnsEMBL::Analysis::Tools::Otter::DBSQL::DnaAlignFeatureHistoryAdaptor
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::PmatchTop
ContigHit
CoordPair
First_PMF
MergedHit
PmatchFeatureBio::EnsEMBL::Analysis::PmatchFeature
ProteinHit
Second_PMF
ensembl-analysis::modules::Bio::EnsEMBL::Analysis::Tools::WGA2GenesTop
ChainUtils
CoordUtils
GeneScaffoldBio::EnsEMBL::Analysis::Tools::WGA2Genes::GeneScaffold
ensembl-analysis::scriptsTop
Nothing here
ensembl-analysis::scripts::FuncgenTop
Nothing here
ensembl-analysis::scripts::PseudogenesTop
Nothing here
ensembl-analysis::scripts::buildchecksTop
CheckerBio::EnsEMBL::Test::Checker
ContigGenesCheckerBio::EnsEMBL::Test::ContigGenesChecker
GeneCheckerBio::EnsEMBL::Test::GeneChecker
ScriptUtils
SupportingEvidenceInfoSupportingEvidenceInfo
TranscriptCheckerBio::EnsEMBL::Test::TranscriptChecker
TranscriptCluster(2)TranscriptCluster
ensembl-analysis::scripts::genebuildTop
Nothing here
ensembl-analysis::scripts::igTop
Nothing here
ensembl-analysis::scripts::imgtTop
Nothing here
ensembl-analysis::scripts::markersTop
Nothing here
ensembl-analysis::scripts::proteinTop
Nothing here
ensembl-analysis::scripts::transfer_annotationsTop
Nothing here
ensembl-analysis::scripts::viral_pseudogenesTop
Nothing here
ensembl-analysis::scripts::wga2genesTop
Nothing here
ensembl-analysis::sqlTop