TOC for all levels

AnophelesGambiae
ApisMellifera
BasicConverter
CaenorhabditisBriggsae
CaenorhabditisElegans
CanisFamiliaris(1)
DanioRerio(1)
DrosophilaMelanogaster
FuguRubripes
GallusGallus
HomoSapiens(1)
MusMusculus(1)
PanTroglodytes
RattusNorvegicus

ensembl::misc-scripts::surgery::SeqStoreConverter::vega

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CanisFamiliaris(2)
DanioRerio(2)
HomoSapiens(2)
MusMusculus(2)
VBasicConverter

ensembl::misc-scripts::unmapped_reason

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Nothing here

ensembl::misc-scripts::utilities

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Nothing here

ensembl::misc-scripts::xref_mapping

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Nothing here

ensembl::misc-scripts::xref_mapping::XrefMapper

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ensembl::misc-scripts::xref_mapping::XrefMapper::Methods

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ExonerateBasic
ExonerateBest1
ExonerateGappedBest1
ExonerateGappedBest1_agam
ExonerateGappedBest_90_perc_id
ExonerateUngappedBest1
LocalExonerateGappedBest1
PBSExonerateGappedBest1

ensembl::misc-scripts::xref_mapping::XrefParser

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AedesGenBankParser
AgilentParser
AnophelesSymbolParser
BaseParser(2)
CCDSParser
CeleraParser
CeleraProteinParser
CeleraTranscriptParser
CodelinkParser
CoordinateParser
DBASSParser
DatabaseParser
DirectParser
EntrezGeneParser
FastaParser
FlybaseParser
Flybase_dmel_GFFv3_Parser
GOParser
HGNCParser
HGNC_CCDSParser
HGNC_ENSGParser
HGNC_ENSTParser
HGNC_curated_transcriptParser
HPAParser
IPIParser
IlluminaParser
IlluminaWGParser
InterproGoParser
InterproParser
JGI_Parser
JGI_ProteinParser
MGDParser
MGI_CCDS_Parser
MGI_Desc_Parser
MGI_Vega_Parser
MGI_curated_transcriptParser
MIMParser
OTTTParser
RGDParser
RefSeqGPFFParser
RefSeqParser
RefSeq_CCDSParser
SGDParser
SegmentParser
UCSCParser
UniGeneParser
UniProtParser
UniProtParser_descriptions_only
UniProtVarSplicParser
VbDirectParser
VbGFF3Parser
VegaParser
Vega_TranParser
WilsonAffyParser
WormPepParser
WormbaseDatabaseStableIDParser
XenopusJamboreeParser
ZFINParser
ncRNAParser
ncRNA_DBParser

ensembl::misc-scripts::xref_mapping::sql

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Nothing here

ensembl::misc-scripts::xref_projection

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Nothing here

ensembl::modules

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Nothing here

ensembl::modules::Bio

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Nothing here

ensembl::modules::Bio::EnsEMBL

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AffyArray	A module to represent an Affymetrix array.
AffyFeature	A module to represent an Affy probe's genomic mapping.
AffyProbe	A module to represent an Affymetrix probe.
AlignStrainSlice	Represents the slice of the genome aligned with certain strains (applying the variations/indels)
Analysis	Stores details of an analysis run
ArchiveStableId	Bio::EnsEMBL::ArchiveStableId
AssemblyExceptionFeature	A feature that represents an assembly exception
AssemblyMapper	Handles mapping between two coordinate systems using the information stored in the assembly table.
Attribute	A generic Attribute class.
BaseAlignFeature	Baseclass providing a common abstract implmentation for alignment features
ChainedAssemblyMapper	Handles mapping between two coordinate systems using the information stored in the assembly table
Collection	Abstract base class for feature collection classes.
CoordSystem	Bio::EnsEMBL::CoordSystem
DBEntry	Object representing an external reference (xref)
DBLoader	Run time database loader
DensityFeature	A feature representing a density, or precentage coverage etc. in a given region.
DensityFeatureSet	A feature representing a set of density features
DensityType	A type representing a density, or percentage coverage etc. in a given region.
DnaDnaAlignFeature	Ensembl specific dna-dna pairwise alignment feature
DnaPepAlignFeature	Ensembl specific dna-pep pairwise alignment feature
Exon(1)	A class representing an Exon
Feature	Ensembl specific sequence feature.
FeaturePair	Stores sequence Features which are themselves hits to other sequence features.
Gene(2)	Object representing a genes
GoXref	Bio::EnsEMBL::GoXref
IdentityXref	Bio::EnsEMBL::IdentityXref
IndividualSlice	SubClass of the Slice. Represents the slice of the genome for a certain individual (applying the alleles for this individual)
IndividualSliceFactory
Intron
KaryotypeBand	Bio::EnsEMBL::DBSQL::KaryotypeBand
MappedSlice	an object representing a mapped slice
MappedSliceContainer	container for mapped slices
Mapper	Bio::EnsEMBL::Mapper
MiscFeature	A miscelaneous feature with arbitrary features and associations.
MiscSet	This is a set representing a classification of a group of miscellaneuos features.
OligoArray	A module to represent an oligonucleotide microarray.
OligoFeature	A module to represent an oligonucleotide probe's genomic mapping.
OligoProbe	A module to represent an oligonucleotide probe.
OntologyTerm	Bio::EnsEMBL::OntologyTerm
PepDnaAlignFeature	Ensembl specific pep-dna pairwise alignment feature
PredictionExon	A class representing an Exon from an ab initio prediction method
PredictionTranscript	PredictionTranscript
ProjectionSegment	part of the list that is returned from project function calls
ProteinFeature	Bio::EnsEMBL::ProteinFeature
Registry	Bio::EnsEMBL::Registry
RepeatConsensus
RepeatFeature(1)	A feature representing a repeat on a piece of sequence.
RepeatMaskedSlice	Arbitary Slice of a genome
Root	Bio::EnsEMBL::Root
SNP	Bio::EnsEMBL::SNP
SeqEdit	A class representing a post transcriptional edit to a sequence.
SeqFeature	Ensembl specific sequence feature.
SeqFeatureI	Bio::EnsEMBL::SeqFeatureI
SimpleFeature	A simple feature with a location and label
Slice(1)	Arbitary Slice of a genome
StableIdEvent	object representing a stable ID mapping event
StableIdHistoryTree	object representing a stable ID history tree
Storable	Bio::EnsEMBL::Storable
StrainSlice	SubClass of the Slice. Represents the slice of the genome for a certain strain (applying the variations)
TopLevelAssemblyMapper	Handles mapping between a given coordinate system and the toplevel pseudo coordinate system.
Transcript(2)	object representing an Ensembl transcript
TranscriptFactory	Module having the fset2transcript* subroutines
TranscriptMapper	A utility class used to perform coordinate conversions between a number of coordinate systems relating to transcripts
Translation(1)	A class representing the translation of a transcript
UnconventionalTranscriptAssociation	A class representing an some sort of unconventional association between a gene and a transcript.
UnmappedObject	A object representing why a particular entity was NOT mapped to the ensembl.
Upstream	Object that defines an upstream region

ensembl::modules::Bio::EnsEMBL::Analysis

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PairAlign	Dna pairwise alignment module
Programs

ensembl::modules::Bio::EnsEMBL::Collection

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Exon(2)	Feature collection implementation for exon features.
Gene(3)	Feature collection implementation for gene features.
RepeatFeature(2)	Feature collection implementation for repeat features.
Transcript(3)	Feature collection implementation for transcript features.

ensembl::modules::Bio::EnsEMBL::DB

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ExternalFeatureFactoryI

Legacy Abstract interface for External Feature Factories. Bio::EnsEMBL::External::ExternalFeatureAdaptor should be used instead if possible.

ensembl::modules::Bio::EnsEMBL::DBSQL

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AffyArrayAdaptor	A database adaptor for fetching and storing AffyArray objects.
AffyFeatureAdaptor	A database adaptor for fetching and storing AffyFeature objects.
AffyProbeAdaptor	A database adaptor for fetching and storing AffyProbe objects.
AnalysisAdaptor	Bio::EnsEMBL::DBSQL::AnalysisAdaptor
ArchiveStableIdAdaptor	Bio::EnsEMBL::ArchiveStableIdAdaptor
AssemblyExceptionFeatureAdaptor	Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor
AssemblyMapperAdaptor	Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
AssemblySliceAdaptor	adaptor/factory for MappedSlices representing alternative assemblies
AttributeAdaptor	Provides database interaction for Bio::EnsEMBL::Attribute objects.
BaseAdaptor	Base Adaptor for DBSQL adaptors
BaseAlignFeatureAdaptor	Abstract Base class for AlignFeatureAdaptors
BaseFeatureAdaptor	An Abstract Base class for all FeatureAdaptors
BaseMetaContainer	Encapsulates all generic access to database meta information
CompressedSequenceAdaptor	Facilitates DB storage and retrieval of compressed sequence
CoordSystemAdaptor	Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
DBAdaptor(1)	Bio::EnsEMBL::DBSQL::DBAdaptor
DBConnection	Bio::EnsEMBL::DBSQL::DBConnection
DBEntryAdaptor	MySQL Database queries to load and store external object references.
DensityFeatureAdaptor	Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor
DensityTypeAdaptor	Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
DnaAlignFeatureAdaptor	Adaptor for DnaAlignFeatures
ExonAdaptor	An adaptor responsible for the retrieval and storage of exon objects
GOTermAdaptor	Bio::EnsEMBL::DBSQL::GOTermAdaptor
GeneAdaptor	Database adaptor for the retrieval and storage of Gene objects
KaryotypeBandAdaptor	Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor
MergedAdaptor	Bio::EnsEMBL::DBSQL::MergedAdaptor
MetaContainer	Encapsulates all access to core database meta information
MetaCoordContainer
MiscFeatureAdaptor	Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor
MiscSetAdaptor	Provides database interaction for Bio::EnsEMBL::MiscSet objects.
OligoArrayAdaptor	A database adaptor for fetching and storing OligoArray objects.
OligoFeatureAdaptor	A database adaptor for fetching and storing OligoFeature objects.
OligoProbeAdaptor	A database adaptor for fetching and storing OligoProbe objects.
OntologyDBAdaptor	Bio::EnsEMBL::DBSQL::OntologyDBAdaptor
OntologyTermAdaptor	Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
PredictionExonAdaptor	Performs database interaction for PredictionExons.
PredictionTranscriptAdaptor	Performs database interaction related to PredictionTranscripts
ProteinAlignFeatureAdaptor	Adaptor for ProteinAlignFeatures
ProteinFeatureAdaptor	Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor
ProxySNPAdaptor	Bio::EnsEMBL::DBSQL::ProxySNPAdaptor
RepeatConsensusAdaptor	Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor
RepeatFeatureAdaptor	Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor
SequenceAdaptor	produce sequence strings from locations
SimpleFeatureAdaptor	Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
SliceAdaptor	A database aware adaptor responsible for the creation of Slice objects.
StatementHandle	Bio::EnsEMBL::DBSQL::StatementHandle
SupportingFeatureAdaptor	Retrieves supporting features from the database.
TranscriptAdaptor	An adaptor which performs database interaction relating to the storage and retrieval of Transcripts
TranscriptSupportingFeatureAdaptor	Retrieves supporting features from the database.
TranslationAdaptor	Provides a means to fetch and store Translation objects from a database.
UnconventionalTranscriptAssociationAdaptor	Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor
UnmappedObjectAdaptor	Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor

ensembl::modules::Bio::EnsEMBL::DensityPlot

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BinValue	Bio::EnsEMBL::DensityPlot::BinValue
BinValueSet	Bio::EnsEMBL::DensityPlot::BinValueSet

ensembl::modules::Bio::EnsEMBL::External

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BlastAdaptor
ExternalFeatureAdaptor	Bio::EnsEMBL::External::ExternalFeatureAdaptor

ensembl::modules::Bio::EnsEMBL::IdMapping

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Archiver	create gene_archive and peptide_archive
BaseObject	base object for IdMapping objects
Cache(1)	a cache to hold data objects used by the IdMapping application
Entry	object representing a ScoredMappingMatrix entry
ExonScoreBuilder
GeneScoreBuilder
InternalIdMapper
MappingList	object holding a list of Entries
ResultAnalyser	analyse stable Id mapping results
ScoreBuilder	score builder base class
ScoredMappingMatrix	object holding a list of scored Entries
Serialisable	base class for serialisable objects
StableIdMapper
SyntenyFramework	framework representing syntenic regions across the genome
SyntenyRegion	object representing syntenic regions
TinyExon	lightweight exon object
TinyFeature	lightweight feature object
TinyGene	lightweight gene object
TinyTranscript	lightweight transcript object
TinyTranslation	lightweight translation object
TranscriptScoreBuilder

ensembl::modules::Bio::EnsEMBL::IdMapping::InternalIdMapper

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BaseMapper
EnsemblExonGeneric
EnsemblGeneGeneric	default Ensembl InternalIdMapper implementation for genes
EnsemblTranscriptGeneric

ensembl::modules::Bio::EnsEMBL::IdMapping::StableIdGenerator

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AedesAegypti(1)
AedesAegypti(2)
EnsemblGeneric	default Ensembl StableIdGenerator implementation

ensembl::modules::Bio::EnsEMBL::Lite

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DBAdaptor(2)	Bio::EnsEMBL::Lite::DBAdaptor
SNPAdaptor	MySQL Database queries to retrieve genes quickly from denormalized tables.

ensembl::modules::Bio::EnsEMBL::Map

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Ditag	Bio::EnsEMBL::Map::Ditag
DitagFeature	Bio::EnsEMBL::Map::DitagFeature
MapLocation	Bio::EnsEMBL::Map::MapLocation
Marker	Bio::EnsEMBL::Map::Marker
MarkerFeature	Bio::EnsEMBL::Map::MarkerFeature
MarkerSynonym	Bio::EnsEMBL::Map::MarkerSynonym
Qtl	Bio::EnsEMBL::Map::Qtl
QtlFeature	Bio::EnsEMBL::Map::QtlFeature

ensembl::modules::Bio::EnsEMBL::Map::DBSQL

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DitagAdaptor	Bio::EnsEMBL::Map::DBSQL::DitagAdaptor
DitagFeatureAdaptor	Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor
MarkerAdaptor	Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor
MarkerFeatureAdaptor	Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor
QtlAdaptor	Bio::EnsEMBL::Map::DBSQL::QtlAdaptor
QtlFeatureAdaptor	Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor

ensembl::modules::Bio::EnsEMBL::Mapper

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Coordinate	Bio::EnsEMBL::Mapper::Coordinate
Gap	Bio::EnsEMBL::Mapper::Gap
IndelCoordinate	Bio::EnsEMBL::Mapper::IndelCoordinate
IndelPair	Bio::EnsEMBL::Mapper::IndelPair
Pair	Bio::EnsEMBL::Mapper::Pair
RangeRegistry	Bio::EnsEMBL::Mapper::RangeRegistry
Unit	One side of a map pair

ensembl::modules::Bio::EnsEMBL::Utils

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Argument	Utility functions for argument handling
AssemblyProjector	utility class to post-process projections from one assembly to another
BitString	bitstring object implementation
Cache(2)	LRU Cache in Memory
CigarString	a utilites module to generate cigar strings
ConfParser	configuration parser for perl scripts
ConfigRegistry	Bio::EnsEMBL::Utils::ConfigRegistry;
ConversionSupport	Utility module for Vega release and schema conversion scripts
Converter	a converter factory
EasyArgv	Bio::EnsEMBL::Utils::EasyArgv
Eprof	Bespoke Ensembl profiler
EprofStack	DESCRIPTION of Object
Exception	Utility functions for error handling
Logger	Utility module for Vega release and schema conversion scripts
PolyA	Bio::EnsEMBL::Utils::PolyA
SchemaConversion	Utility module for Vega schema conversion script
ScriptUtils	Bio::EnsEMBL::Utils::ScriptUtils;
SeqDumper	Bio::EnsEMBL::Utils::SeqDumper
SeqRegionCache	A shared LRU cache of information about seq_regions
Sequence	Utility functions for sequences
Slice(2)	Utility functions for slices
TranscriptAlleles	A utility class used to obtain information about the relationships between a transcript and Alleles
TranscriptSNPs	A utility class used to obtain information about the relationships between a transcript and SNPs

ensembl::modules::Bio::EnsEMBL::Utils::Converter

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bio_ens	Bio::EnsEMBL::Utils::Converter::bio_ens
bio_ens_analysis	a converter instance specific for Analysis.
bio_ens_exon	Bio::EnsEMBL::Utils::Converter::bio_ens_exon
bio_ens_featurePair	Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair
bio_ens_gene	Bio::EnsEMBL::Utils::Converter::bio_ens_gene
bio_ens_hit
bio_ens_hsp
bio_ens_predictionExon	Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon
bio_ens_predictionGene	Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene
bio_ens_seqFeature	Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature
bio_ens_transcript	the instance converter
ens_bio	Bio::EnsEMBL::Utils::Converter::ens_bio
ens_bio_featurePair	Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair
ens_bio_seqFeature	Bio::EnsEMBL::Utils::Converter::ens_bio_seqFeature

ensembl::modules::Bio::EnsEMBL::Utils::VegaCuration

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Gene(4)
Transcript(4)
Translation(2)

ensembl::modules::t

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TestUtils

ensembl::modules::t::test-genome-DBs

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Nothing here

ensembl::modules::t::test-genome-DBs::homo_sapiens

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Nothing here

ensembl::modules::t::test-genome-DBs::homo_sapiens::core

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Nothing here

ensembl::sql

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BasicMapper
CoordinateMapper
CoreInfo
DisplayXrefs
Interpro
LoadMapper
ProcessMappings
ProcessPaired
ProcessPrioritys
SubmitMapper
TestMappings
VBCoordinateMapper
XrefLoader
aedes_aegypti
anopheles_gambiae
caenorhabditis_elegans
canis_familiaris
ciona_intestinalis
danio_rerio
db
drosophila_ananassae
drosophila_erecta
drosophila_grimshawi
drosophila_melanogaster
drosophila_mojavensis
drosophila_persimilis
drosophila_pseudoobscura
drosophila_sechellia
drosophila_simulans
drosophila_virilis
drosophila_willistoni
drosophila_yakuba
fugu_rubripes
homo_sapiens
macaca_mulatta
monodelphis_domestica
mus_musculus
ornithorhynchus_anatinus
rattus_norvegicus
tetraodon_nigroviridis
xenopus_tropicalis