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A list of all files with their relative paths.
Analysis/Runnable.pm [code]
Analysis/RunnableDB.pm [code]
Analysis/Config/ImportArrays.pm [code]
Analysis/Config/ProbeAlign.pm [code]
Analysis/Config/SelenoBuild.pm [code]
Analysis/Config/GeneBuild/BlastMiniGenewise.pm [code]
Analysis/Config/GeneBuild/ExamineGeneSets.pm [code]
Analysis/Config/GeneBuild/Pmatch.pm [code]
Analysis/Runnable/AlignmentChains.pm [code]
Analysis/Runnable/AlignmentNets.pm [code]
Analysis/Runnable/Bam2Introns.pm [code]
Analysis/Runnable/BaseAbInitio.pm [code]
Analysis/Runnable/BaseExonerate.pm [code]
Analysis/Runnable/BestPmatch.pm [code]
Analysis/Runnable/BestTargetted.pm [code]
Analysis/Runnable/Blast.pm [code]
Analysis/Runnable/BlastMiniBuilder.pm [code]
Analysis/Runnable/BlastMiniGenewise.pm [code]
Analysis/Runnable/BlastmiRNA.pm [code]
Analysis/Runnable/BlastPep.pm [code]
Analysis/Runnable/BlastRfam.pm [code]
Analysis/Runnable/BlastTranscriptDNA.pm [code]
Analysis/Runnable/BlastTranscriptPep.pm [code]
Analysis/Runnable/Blastz.pm [code]
Analysis/Runnable/Blat.pm [code]
Analysis/Runnable/BWA.pm [code]
Analysis/Runnable/BWA2BAM.pm [code]
Analysis/Runnable/CPG.pm [code]
Analysis/Runnable/CrossMatch.pm [code]
Analysis/Runnable/Dust.pm [code]
Analysis/Runnable/EPCR.pm [code]
Analysis/Runnable/EponineTSS.pm [code]
Analysis/Runnable/ExonerateAffy.pm [code]
Analysis/Runnable/ExonerateAlignFeature.pm [code]
Analysis/Runnable/ExonerateArray.pm [code]
Analysis/Runnable/ExonerateCloneEnds.pm [code]
Analysis/Runnable/ExonerateProbe.pm [code]
Analysis/Runnable/ExonerateSolexaLocalAlignment.pm [code]
Analysis/Runnable/ExonerateTags.pm [code]
Analysis/Runnable/ExonerateTranscript.pm [code]
Analysis/Runnable/Fgenesh.pm [code]
Analysis/Runnable/FirstEF.pm [code]
Analysis/Runnable/Funcgen.pm [code]
Analysis/Runnable/GenBlast.pm [code]
Analysis/Runnable/GeneBuilder.pm [code]
Analysis/Runnable/Genefinder.pm [code]
Analysis/Runnable/Genewise.pm [code]
Analysis/Runnable/Genscan.pm [code]
Analysis/Runnable/HaplotypeMapper.pm [code]
Analysis/Runnable/HaplotypeProjection.pm [code]
Analysis/Runnable/HavanaAdder.pm [code]
Analysis/Runnable/Infernal.pm [code]
Analysis/Runnable/Lagan.pm [code]
Analysis/Runnable/Lastz.pm [code]
Analysis/Runnable/lincRNAEvaluator.pm [code]
Analysis/Runnable/lincRNAFinder.pm [code]
Analysis/Runnable/LowCoverageGenomeAlignment.pm [code]
Analysis/Runnable/Mavid.pm [code]
Analysis/Runnable/Mercator.pm [code]
Analysis/Runnable/MiniGenewise.pm [code]
Analysis/Runnable/miRNA.pm [code]
Analysis/Runnable/Mlagan.pm [code]
Analysis/Runnable/MultiMiniGenewise.pm [code]
Analysis/Runnable/Ortheus.pm [code]
Analysis/Runnable/Pecan.pm [code]
Analysis/Runnable/Pmatch.pm [code]
Analysis/Runnable/ProteinAnnotation.pm [code]
Analysis/Runnable/Pseudogene.pm [code]
Analysis/Runnable/Pseudogene2x.pm [code]
Analysis/Runnable/PSILC.pm [code]
Analysis/Runnable/PSILC_BlastP.pm [code]
Analysis/Runnable/RepeatMasker.pm [code]
Analysis/Runnable/RNAFold.pm [code]
Analysis/Runnable/Sam2Bam.pm [code]
Analysis/Runnable/Snap.pm [code]
Analysis/Runnable/Spliced_elsewhere.pm [code]
Analysis/Runnable/TranscriptCoalescer.pm [code]
Analysis/Runnable/TranscriptConsensus.pm [code]
Analysis/Runnable/TRF.pm [code]
Analysis/Runnable/tRNAscan_SE.pm [code]
Analysis/Runnable/Finished/Augustus.pm [code]
Analysis/Runnable/Finished/Blast.pm [code]
Analysis/Runnable/Finished/BlastExonerate.pm [code]
Analysis/Runnable/Finished/EPCR.pm [code]
Analysis/Runnable/Finished/EST.pm [code]
Analysis/Runnable/Finished/Est2Genome.pm [code]
Analysis/Runnable/Finished/Exonerate.pm [code]
Analysis/Runnable/Finished/GenewiseHmm.pm [code]
Analysis/Runnable/Finished/HalfwiseHMM.pm [code]
Analysis/Runnable/Finished/MiniEst2Genome.pm [code]
Analysis/Runnable/Finished/RepeatMasker.pm [code]
Analysis/Runnable/Funcgen/ACME.pm [code]
Analysis/Runnable/Funcgen/Chipotle.pm [code]
Analysis/Runnable/Funcgen/MAT.pm [code]
Analysis/Runnable/Funcgen/Nessie.pm [code]
Analysis/Runnable/Funcgen/Splitter.pm [code]
Analysis/Runnable/Funcgen/SWEmbl.pm [code]
Analysis/Runnable/Funcgen/TileMap.pm [code]
Analysis/Runnable/ProteinAnnotation/Coil.pm [code]
Analysis/Runnable/ProteinAnnotation/Gene3d.pm [code]
Analysis/Runnable/ProteinAnnotation/Hamap_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Hmmpfam.pm [code]
Analysis/Runnable/ProteinAnnotation/IPRScan.pm [code]
Analysis/Runnable/ProteinAnnotation/Panther.pm [code]
Analysis/Runnable/ProteinAnnotation/Pfam_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/PIRSF.pm [code]
Analysis/Runnable/ProteinAnnotation/PIRSF_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Prints.pm [code]
Analysis/Runnable/ProteinAnnotation/Prints_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Prodom.pm [code]
Analysis/Runnable/ProteinAnnotation/PrositePattern.pm [code]
Analysis/Runnable/ProteinAnnotation/PrositePattern_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/PrositeProfile.pm [code]
Analysis/Runnable/ProteinAnnotation/PrositeProfile_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Seg.pm [code]
Analysis/Runnable/ProteinAnnotation/Signalp.pm [code]
Analysis/Runnable/ProteinAnnotation/Smart_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Superfamily.pm [code]
Analysis/Runnable/ProteinAnnotation/Superfamily_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Tigrfam_wormbase.pm [code]
Analysis/Runnable/ProteinAnnotation/Tmhmm.pm [code]
Analysis/RunnableDB/Accumulator.pm [code]
Analysis/RunnableDB/AlignAffyProbes.pm [code]
Analysis/RunnableDB/AlignmentChains.pm [code]
Analysis/RunnableDB/AlignmentFilter.pm [code]
Analysis/RunnableDB/AlignmentNets.pm [code]
Analysis/RunnableDB/Bam2Genes.pm [code]
Analysis/RunnableDB/Bam2Introns.pm [code]
Analysis/RunnableDB/BaseGeneBuild.pm [code]
Analysis/RunnableDB/BestPmatch.pm [code]
Analysis/RunnableDB/BestTargetted.pm [code]
Analysis/RunnableDB/Blast.pm [code]
Analysis/RunnableDB/BlastGenscanDNA.pm [code]
Analysis/RunnableDB/BlastGenscanPep.pm [code]
Analysis/RunnableDB/BlastMiniGenewise.pm [code]
Analysis/RunnableDB/BlastmiRNA.pm [code]
Analysis/RunnableDB/BlastPep.pm [code]
Analysis/RunnableDB/BlastRfam.pm [code]
Analysis/RunnableDB/BlastRNASeqPep.pm [code]
Analysis/RunnableDB/BlastTranscriptDNA.pm [code]
Analysis/RunnableDB/BlastTranscriptPep.pm [code]
Analysis/RunnableDB/BWA.pm [code]
Analysis/RunnableDB/BWA2BAM.pm [code]
Analysis/RunnableDB/CollapseAffyProbes.pm [code]
Analysis/RunnableDB/CopyGenes.pm [code]
Analysis/RunnableDB/CPG.pm [code]
Analysis/RunnableDB/Dust.pm [code]
Analysis/RunnableDB/EnsemblDisableKeys.pm [code]
Analysis/RunnableDB/EPCR.pm [code]
Analysis/RunnableDB/EponineTSS.pm [code]
Analysis/RunnableDB/Exonerate2Array.pm [code]
Analysis/RunnableDB/Exonerate2Genes.pm [code]
Analysis/RunnableDB/Exonerate2GenesRegion.pm [code]
Analysis/RunnableDB/ExonerateAlignFeature.pm [code]
Analysis/RunnableDB/ExonerateCloneEnds.pm [code]
Analysis/RunnableDB/ExonerateClones.pm [code]
Analysis/RunnableDB/ExonerateForGenewise.pm [code]
Analysis/RunnableDB/ExonerateForSeleno.pm [code]
Analysis/RunnableDB/ExonerateOrthologueEvaluator.pm [code]
Analysis/RunnableDB/ExonerateRefinedCloneEnds.pm [code]
Analysis/RunnableDB/ExonerateSolexa.pm [code]
Analysis/RunnableDB/ExonerateSolexaCloud.pm [code]
Analysis/RunnableDB/ExonerateSolexaLocalAlignment.pm [code]
Analysis/RunnableDB/ExonerateSolexaTranscript.pm [code]
Analysis/RunnableDB/ExonerateTags.pm [code]
Analysis/RunnableDB/Fgenesh.pm [code]
Analysis/RunnableDB/FilterGenes.pm [code]
Analysis/RunnableDB/FindFalseIntrons.pm [code]
Analysis/RunnableDB/FindMissingOrthologues.pm [code]
Analysis/RunnableDB/FindPartialGenes.pm [code]
Analysis/RunnableDB/FindSplitGenes.pm [code]
Analysis/RunnableDB/Finished.pm [code]
Analysis/RunnableDB/FirstEF.pm [code]
Analysis/RunnableDB/Funcgen.pm [code]
Analysis/RunnableDB/GenBlast.pm [code]
Analysis/RunnableDB/GeneBuilder.pm [code]
Analysis/RunnableDB/Genefinder.pm [code]
Analysis/RunnableDB/Genscan.pm [code]
Analysis/RunnableDB/HaplotypeMapper.pm [code]
Analysis/RunnableDB/HaplotypeProjection.pm [code]
Analysis/RunnableDB/HavanaAdder.pm [code]
Analysis/RunnableDB/IgSegBuilder.pm [code]
Analysis/RunnableDB/ImportArrays.pm [code]
Analysis/RunnableDB/IncrementalBuild.pm [code]
Analysis/RunnableDB/Infernal.pm [code]
Analysis/RunnableDB/LayerAnnotation.pm [code]
Analysis/RunnableDB/lincRNAEvaluator.pm [code]
Analysis/RunnableDB/lincRNAFinder.pm [code]
Analysis/RunnableDB/MakeCdna2GenomeRegionInputIDs.pm [code]
Analysis/RunnableDB/MakeSimilarityInputIDs.pm [code]
Analysis/RunnableDB/MapCloneEnds.pm [code]
Analysis/RunnableDB/miRNA.pm [code]
Analysis/RunnableDB/MissingOrthologues.pm [code]
Analysis/RunnableDB/OrthologueEvaluator.pm [code]
Analysis/RunnableDB/Pmatch.pm [code]
Analysis/RunnableDB/ProbeAlign.pm [code]
Analysis/RunnableDB/ProjectedTranscriptEvidence.pm [code]
Analysis/RunnableDB/ProteinAnnotation.pm [code]
Analysis/RunnableDB/Pseudogene2x.pm [code]
Analysis/RunnableDB/Pseudogene_DB.pm [code]
Analysis/RunnableDB/PSILC.pm [code]
Analysis/RunnableDB/RecoverFalseIntrons.pm [code]
Analysis/RunnableDB/RefineSolexaGenes.pm [code]
Analysis/RunnableDB/RepeatMasker.pm [code]
Analysis/RunnableDB/Sam2Bam.pm [code]
Analysis/RunnableDB/SelenoBuilder.pm [code]
Analysis/RunnableDB/Snap.pm [code]
Analysis/RunnableDB/Solexa2Genes.pm [code]
Analysis/RunnableDB/Solexa2GenesLiteNew.pm [code]
Analysis/RunnableDB/Solexa2GenesLiteNewCloud.pm [code]
Analysis/RunnableDB/Spliced_elsewhere.pm [code]
Analysis/RunnableDB/TranscriptCoalescer.pm [code]
Analysis/RunnableDB/TranscriptConsensus.pm [code]
Analysis/RunnableDB/TRF.pm [code]
Analysis/RunnableDB/tRNAscan_SE.pm [code]
Analysis/RunnableDB/UTR_Builder.pm [code]
Analysis/RunnableDB/WGA2Genes.pm [code]
Analysis/RunnableDB/WGA2GenesDirect.pm [code]
Analysis/RunnableDB/Finished/Augustus.pm [code]
Analysis/RunnableDB/Finished/Blast.pm [code]
Analysis/RunnableDB/Finished/BlastExonerate.pm [code]
Analysis/RunnableDB/Finished/ClusterDepthFilter.pm [code]
Analysis/RunnableDB/Finished/DepthFilter.pm [code]
Analysis/RunnableDB/Finished/EPCR.pm [code]
Analysis/RunnableDB/Finished/EST.pm [code]
Analysis/RunnableDB/Finished/Exonerate.pm [code]
Analysis/RunnableDB/Finished/HalfwiseHMM.pm [code]
Analysis/RunnableDB/Finished/RepeatMasker.pm [code]
Analysis/RunnableDB/Finished/TRF.pm [code]
Analysis/RunnableDB/Funcgen/ACME.pm [code]
Analysis/RunnableDB/Funcgen/Chipotle.pm [code]
Analysis/RunnableDB/Funcgen/MAT.pm [code]
Analysis/RunnableDB/Funcgen/Nessie.pm [code]
Analysis/RunnableDB/Funcgen/Splitter.pm [code]
Analysis/RunnableDB/Funcgen/SWEmbl.pm [code]
Analysis/RunnableDB/Funcgen/TileMap.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Coil.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Gene3d.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Hamap_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Hmmpfam.pm [code]
Analysis/RunnableDB/ProteinAnnotation/IPRScan.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Panther.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Pfam.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Pfam_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/PIRSF.pm [code]
Analysis/RunnableDB/ProteinAnnotation/PIRSF_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Prints.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Prints_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Prodom.pm [code]
Analysis/RunnableDB/ProteinAnnotation/PrositePattern.pm [code]
Analysis/RunnableDB/ProteinAnnotation/PrositePattern_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/PrositeProfile.pm [code]
Analysis/RunnableDB/ProteinAnnotation/PrositeProfile_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Seg.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Signalp.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Smart_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Superfamily.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Superfamily_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Tigrfam_wormbase.pm [code]
Analysis/RunnableDB/ProteinAnnotation/Tmhmm.pm [code]
Analysis/Tools/BasicFilter.pm [code]
Analysis/Tools/BlastDB.pm [code]
Analysis/Tools/BlastDBTracking.pm [code]
Analysis/Tools/Blastz.pm [code]
Analysis/Tools/BPlite.pm [code]
Analysis/Tools/BPliteWrapper.pm [code]
Analysis/Tools/CdnaUpdateTranscriptFilter.pm [code]
Analysis/Tools/ClusterFilter.pm [code]
Analysis/Tools/ConfigUtils.pm [code]
Analysis/Tools/ExonerateTranscriptFilter.pm [code]
Analysis/Tools/FeatureFactory.pm [code]
Analysis/Tools/FeatureFilter.pm [code]
Analysis/Tools/FilterBPlite.pm [code]
Analysis/Tools/FragmentTranscriptFilter.pm [code]
Analysis/Tools/GeneBuildUtils.pm [code]
Analysis/Tools/IgTranscriptFilter.pm [code]
Analysis/Tools/KillListUtils.pm [code]
Analysis/Tools/Logger.pm [code]
Analysis/Tools/MiniSeq.pm [code]
Analysis/Tools/PairAlign.pm [code]
Analysis/Tools/PolyAClipping.pm [code]
Analysis/Tools/ProteinAnnotationFilter.pm [code]
Analysis/Tools/ReadBaseDataFromGff.pm [code]
Analysis/Tools/S3Utils.pm [code]
Analysis/Tools/Stashes.pm [code]
Analysis/Tools/Utilities.pm [code]
Analysis/Tools/Algorithms/ClusterUtils.pm [code]
Analysis/Tools/Algorithms/ExonCluster.pm [code]
Analysis/Tools/Algorithms/GeneCluster.pm [code]
Analysis/Tools/Algorithms/IntronCluster.pm [code]
Analysis/Tools/Algorithms/TranscriptCluster.pm [code]
Analysis/Tools/BlastDBTracking/Entry.pm [code]
Analysis/Tools/BPlite/HSP.pm [code]
Analysis/Tools/BPlite/Iteration.pm [code]
Analysis/Tools/BPlite/Sbjct.pm [code]
Analysis/Tools/Filter/BlastMiniGenewise.pm [code]
Analysis/Tools/Finished/BPliteWrapper.pm [code]
Analysis/Tools/GeneBuildUtils/CollapsedCluster.pm [code]
Analysis/Tools/GeneBuildUtils/EvidenceUtils.pm [code]
Analysis/Tools/GeneBuildUtils/ExonExtended.pm [code]
Analysis/Tools/GeneBuildUtils/ExonUtils.pm [code]
Analysis/Tools/GeneBuildUtils/GeneUtils.pm [code]
Analysis/Tools/GeneBuildUtils/HomologyUtils.pm [code]
Analysis/Tools/GeneBuildUtils/IntronUtils.pm [code]
Analysis/Tools/GeneBuildUtils/TranscriptExtended.pm [code]
Analysis/Tools/GeneBuildUtils/TranscriptUtils.pm [code]
Analysis/Tools/GeneBuildUtils/TranslationUtils.pm [code]
Analysis/Tools/GeneBuildUtils/ConfigDependent/TranscriptUtils.pm [code]
Analysis/Tools/IMGT/Seq/RichSeqIMGT.pm [code]
Analysis/Tools/IMGT/SeqIO/imgt_embl.pm [code]
Analysis/Tools/Otter/DnaAlignFeature.pm [code]
Analysis/Tools/Otter/DnaAlignFeatureHistory.pm [code]
Analysis/Tools/Otter/DBSQL/DBAdaptor.pm [code]
Analysis/Tools/Otter/DBSQL/DnaAlignFeatureAdaptor.pm [code]
Analysis/Tools/Otter/DBSQL/DnaAlignFeatureHistoryAdaptor.pm [code]
Analysis/Tools/Pmatch/ContigHit.pm [code]
Analysis/Tools/Pmatch/CoordPair.pm [code]
Analysis/Tools/Pmatch/First_PMF.pm [code]
Analysis/Tools/Pmatch/MergedHit.pm [code]
Analysis/Tools/Pmatch/PmatchFeature.pm [code]
Analysis/Tools/Pmatch/ProteinHit.pm [code]
Analysis/Tools/Pmatch/Second_PMF.pm [code]
Analysis/Tools/WGA2Genes/ChainUtils.pm [code]
Analysis/Tools/WGA2Genes/CoordUtils.pm [code]
Analysis/Tools/WGA2Genes/GeneScaffold.pm [code]