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