├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── modules ├── Bio │ └── EnsEMBL │ │ └── Pipeline │ │ ├── Alignment.pm │ │ ├── Alignment │ │ ├── AlignmentSeq.pm │ │ ├── AlignmentSquiz.pm │ │ ├── AlignmentStats.pm │ │ ├── EvidenceAlignment.pm │ │ └── InformativeSites.pm │ │ ├── Analysis.pm │ │ ├── AnalysisCreation.pm │ │ ├── BatchSubmission.pm │ │ ├── BatchSubmission │ │ ├── Dummy.pm │ │ ├── GridEngine.pm │ │ ├── LSF.pm │ │ ├── Local.pm │ │ └── SGE_GridEngine_v6.pm │ │ ├── Config │ │ ├── BatchQueue.pm.efg_arrays │ │ ├── BatchQueue.pm.example │ │ ├── General.pm.example │ │ ├── PseudoGenes │ │ │ └── PseudoGenes.pm.example │ │ └── README.config.pod │ │ ├── DBSQL │ │ ├── AnalysisAdaptor.pm │ │ ├── CompressedDnaAlignFeatureAdaptor.pm │ │ ├── DBAdaptor.pm │ │ ├── Finished │ │ │ ├── DBAdaptor.pm │ │ │ ├── DnaAlignFeatureAdaptor.pm │ │ │ ├── HitDescriptionAdaptor.pm │ │ │ ├── JobAdaptor.pm │ │ │ ├── ProteinAlignFeatureAdaptor.pm │ │ │ └── StateInfoContainer.pm │ │ ├── FlagAdaptor.pm │ │ ├── JobAdaptor.pm │ │ ├── RuleAdaptor.pm │ │ └── StateInfoContainer.pm │ │ ├── Finished │ │ ├── HitDescription.pm │ │ ├── Job.pm │ │ ├── PipeQueue.pm │ │ ├── RuleManager.pm │ │ └── runner.pl │ │ ├── Finished_RuleManager.pl │ │ ├── Flag.pm │ │ ├── GeneDuplication │ │ ├── CodonBasedAlignment.pm │ │ ├── Finder.pm │ │ ├── PAML.pm │ │ └── Result.pm │ │ ├── Hive │ │ └── HiveInputIDFactory.pm │ │ ├── Job.pm │ │ ├── Monitor.pm │ │ ├── Rule.pm │ │ ├── RuleCreation.pm │ │ ├── RuleManager.pm │ │ ├── Runnable │ │ └── WHERE_HAVE_MY_RUNNABLES_GONE │ │ ├── RunnableDB │ │ └── WHERE_HAVE_MY_RUNNABLEDBS_GONE │ │ ├── SeqFetcher.pm │ │ ├── SeqFetcher │ │ ├── BPIndex.pm │ │ ├── BioIndex.pm │ │ ├── DBIndex.pm │ │ ├── Efetch.pm │ │ ├── FetchFromBlastDB.pm │ │ ├── FileIndex.pm │ │ ├── Finished_Dfetch.pm │ │ ├── Finished_Pfetch.pm │ │ ├── Finished_xdget.pm │ │ ├── Getseqs.pm │ │ ├── Getz.pm │ │ ├── Mfetch.pm │ │ ├── OBDAIndexSeqFetcher.pm │ │ ├── Pfetch.pm │ │ ├── UniProtKB.pm │ │ └── xdget.pm │ │ ├── Status.pm │ │ ├── Tools │ │ ├── Embl.pm │ │ ├── GeneBankParser.pm │ │ └── MM_Taxonomy.pm │ │ ├── Utils │ │ ├── InputIDFactory.pm │ │ ├── Node.pm │ │ ├── PipelineSanityChecks.pm │ │ └── SliceDump.pm │ │ └── runner.pl ├── Makefile.PL └── t │ ├── Blast.t │ ├── BlastDB.t │ ├── BlastMiniGenewise.t │ ├── Blast_DB.t │ ├── Blast_conf.pl │ ├── Chooser.t │ ├── CodonBasedAlignment.t │ ├── EnsTestDB.conf.example │ ├── EnsTestDB.pm │ ├── EponineTSS.t │ ├── EponineTSSDB.t │ ├── Est2Genome.t │ ├── ExonPair.t │ ├── Exonerate.t │ ├── ExonerateArray.t │ ├── ExonerateESTs.t │ ├── FPC_BlastMiniEst2Genome.t │ ├── FPC_BlastMiniGenewise.t │ ├── FeatureFilter.t │ ├── FetchFromBlastDB.t │ ├── FileIndex.t │ ├── FilterESTs_and_E2G_db.t │ ├── GeneConf.pm.test │ ├── GeneDuplication.t │ ├── GeneUtils.t │ ├── Genewise.t │ ├── Genscan.t │ ├── GenscanDB.t │ ├── MiniEst2Genome.t │ ├── MiniGenewise.t │ ├── MinimalBlast.t │ ├── MultiMiniGenewise.t │ ├── Paml.t │ ├── RepeatMasker.t │ ├── RepeatMaskerDB.t │ ├── Riken_BlastMiniGenewise.t │ ├── Runnable_bl2seq.t │ ├── SSAHA.t │ ├── Slice_EPCRDB.t │ ├── Slice_EponineTSSDB.t │ ├── TargettedGeneE2G.t │ ├── TargettedGeneWise.t │ ├── Tools_bl2seq.t │ ├── alignfeature.t │ ├── blastgenscandna.t │ ├── blastgenscandnaDB.t │ ├── blastgenscanpep.t │ ├── blastgenscanpepDB.t │ ├── blastminiest2genome.t │ ├── cpg.t │ ├── cpgDB.t │ ├── crossmatch.t │ ├── data │ ├── AC099340.fa │ ├── AC099340.fa.masked │ ├── AI053588.fa │ ├── AI053588.fa.csq │ ├── AI053588.fa.nhd │ ├── AI053588.fa.ntb │ ├── AP000074.fa │ ├── AP000074.fa.csq │ ├── AP000074.fa.nhd │ ├── AP000074.fa.ntb │ ├── AP000074.pep │ ├── AP000074.pep.ahd │ ├── AP000074.pep.atb │ ├── AP000074.pep.bsq │ ├── PKD_testdata.fa │ ├── array_db.fa │ ├── array_test.fa │ ├── bl2seq.out │ ├── emotif.dat │ ├── ests │ │ ├── config.dat │ │ ├── key_ACC.key │ │ └── test_ests.fa │ ├── genomewise2.seq │ ├── human.genomic │ ├── mini_mrna.fa │ ├── mini_mrna.fa.csq │ ├── mini_mrna.fa.nhd │ ├── mini_mrna.fa.ntb │ ├── mini_protein.fa │ ├── mini_protein.fa.ahd │ ├── mini_protein.fa.atb │ ├── mini_protein.fa.bsq │ ├── paml_test.fa │ ├── prints.dat │ ├── profile.dat │ ├── relaxins.fa │ ├── seq_test.pep │ ├── testest.fa │ └── testpep.fa │ ├── dumps │ ├── BlastMiniGenewise.dump │ ├── FilterESTs_and_E2G_db.dump │ ├── TargettedGene.dump │ ├── analysis.dump │ ├── blastgenscanpepDB.dump │ ├── chr12_snippet.dump │ ├── dna.dump │ ├── dna_align_feature.dump │ ├── epcrdb.dump │ ├── prediction_transcript.dump │ ├── protein_align_feature.dump │ ├── repeat.dump │ ├── runnabledb.dump │ ├── slice_epcr.dump │ └── slice_eponine.dump │ ├── epcr.t │ ├── epcrDB.t │ ├── gc.t │ ├── gcDB.t │ ├── genomewise.t │ ├── minigenomewise.t │ ├── motifwise.t │ ├── motifwiseDB.t │ ├── orf.t │ ├── prints.t │ ├── scanprosite.t │ ├── searchfilter.t │ ├── signalp.t │ ├── sptr │ ├── README │ ├── config.dat │ └── key_ACC.key │ ├── tRNA.t │ ├── tRNADB.t │ ├── trf.t │ └── trfDB.t ├── scripts ├── AlignWise │ ├── dumpgff_compara_alignments.pl │ └── run_alignwise.pl ├── DataConversion │ ├── flybase │ │ ├── FlyBaseConf.pm.example │ │ ├── FlyBaseGff.pm │ │ ├── FlyBaseToolbox.pm │ │ └── flybase_to_ensembl.pl │ ├── medaka │ │ ├── MedakaConf.pm │ │ ├── fix_gff.pl │ │ └── load_medaka.pl │ ├── mitochondria │ │ ├── MitConf.pm │ │ └── load_mitochondria.pl │ ├── tetraodon │ │ ├── annotation │ │ │ ├── README │ │ │ ├── genoscope2alignGFF.pl │ │ │ ├── genoscope2cDNAalign.pl │ │ │ ├── genoscope2geneGFF.pl │ │ │ ├── genoscope2repeatGFF.pl │ │ │ ├── genoscope2simpleGFF.pl │ │ │ ├── load_align_features.pl │ │ │ ├── load_genes.pl │ │ │ ├── load_prediction_transcripts.pl │ │ │ ├── load_repeats.pl │ │ │ └── load_simple_features.pl │ │ └── assembly │ │ │ ├── README │ │ │ ├── convert_to_agp.pl │ │ │ └── extract_ultracontigs.pl │ └── wormbase │ │ ├── Clone2Acc.pm │ │ ├── WormBase.pm │ │ ├── WormBaseConf.pm.example │ │ ├── converting_wormbase_to_ensembl.txt │ │ ├── expr_store.pl │ │ ├── feature_store.pl │ │ ├── gene_store.pl │ │ ├── operon_store.pl │ │ ├── pseudo_store.pl │ │ ├── raw_compute_transfer.pl │ │ ├── rnai_store.pl │ │ ├── sequence_store.pl │ │ ├── sl1_store.pl │ │ ├── sl2_store.pl │ │ ├── translation_check.pl │ │ └── wormbase_to_ensembl.pl ├── EST │ ├── check_estgenebuilder_jobs.pl │ ├── check_node.pl │ ├── clip_cdnas.pl │ ├── cluster_merge.pl │ ├── dump_estgene_evidence.pl │ ├── dump_golden_contigs.pl │ ├── dust │ │ ├── check_node.sh │ │ ├── config.txt │ │ ├── fam.sh │ │ ├── fam_config.sh │ │ ├── is_complete.sh │ │ ├── process_job.sh │ │ └── run_job.sh │ ├── exon2feature.pl │ ├── filter_and_e2g_byAcc.pl │ ├── get_estgenebuilder_score_lines.pl │ ├── get_estlengths.pl │ ├── get_human_ests.pl │ ├── human_EST_kill_list.txt │ ├── look_for_errors.pl │ ├── make_blat_bsubs.pl │ ├── make_estgenebuilder_bsubs.pl │ ├── make_exonerate_bsubs.pl │ ├── make_gene2expression_bsubs.pl │ ├── map_ExpressionData.pl │ ├── new_polyA_clipping.pl │ ├── prepare_ests.pl │ ├── recover_estgenebuilder_bsub_lines_from_input_ids.pl │ ├── run_EST_GeneBuilder.pl │ ├── run_blat.pl │ ├── run_exonerate.pl │ ├── submit.pl │ ├── submit_jobs.pl │ ├── test_ClusterMerge.pl │ └── test_ESTTranscriptFilter.pl ├── ExonerateArray.pl ├── Features │ ├── calculate_slices.pl │ └── make_bsubs_for_calculate_slices.pl ├── Finished │ ├── assembly │ │ ├── AssemblyMapper │ │ │ ├── AlignSession.pm │ │ │ ├── AlignStage.pm │ │ │ ├── BlastzAligner.pm │ │ │ ├── ClassUtils.pm │ │ │ ├── SlicePair.pm │ │ │ └── Support.pm │ │ ├── README │ │ ├── add_extra_mappings.pl │ │ ├── align_by_component_identity.pl │ │ ├── align_by_component_identity_zfish.pl │ │ ├── align_nonident.pl │ │ ├── align_nonident_zfish.pl │ │ ├── check_repeat_masked.pl │ │ ├── fix_overlaps.pl │ │ ├── fix_overlaps_zfish.pl │ │ ├── lastz_matrix.txt │ │ ├── new_align_session.pl │ │ ├── reverse_existing_mapping.pl │ │ ├── transfer_annotation.pl │ │ ├── transfer_annotation_across.pl │ │ ├── transfer_annotation_logfilter.pl │ │ └── transfer_annotation_zfish.pl │ ├── create_agp_from_scaffold.pl │ ├── create_agp_from_scaffold_xtrop.pl │ ├── delete_duplicates_from_protfeat_table.pl │ ├── delete_sequence_set.pl │ ├── dequeuer.pl │ ├── fill_hit_desc.pl │ ├── fillin_ids.pl │ ├── job_output_files │ ├── list_input_ids.pl │ ├── list_new_clones.pl │ ├── load_clone_features.pl │ ├── load_from_loutre_or_pipe.pl │ ├── load_from_otter.pl │ ├── load_loutre_pipeline.pl │ ├── make_input_ids.pl │ ├── make_subregion_agp.pl │ ├── pipe_error_summary.pl │ ├── pipeline_zap.pl │ ├── postqc_logfilter.pl │ ├── rulemanager.pl │ ├── run_prot_pipeline.pl │ ├── set_job_status │ └── test_RunnableDB ├── GeneBuild │ ├── SimilarityInputIdConfig.pm │ ├── cDNA_kill_list.txt │ ├── kill_list.txt │ ├── make_TranscriptCoalescer_inputIDS.pl │ ├── make_TranscriptConsensus_inputIDS.pl │ ├── make_input_ids_for_similarity_build.pl │ ├── refseq_NM_NP_Pairs.pl │ └── setup_clones_pipeline.pl ├── GeneComparison │ ├── bsubs_for_comparing_whole_genomes.pl │ ├── check_node.pl │ ├── collect_isoform_comparison_output.pl │ ├── compare_CDS.pl │ ├── compare_Exons.pl │ ├── compare_HomoloGene_pair.pl │ ├── compare_Translations.pl │ ├── compare_cDNA_exonerate.pl │ ├── compare_isoforms.pl │ ├── compute_syntenic_gene.pl │ ├── exon_Coverage.pl │ ├── exon_length_Coverage.pl │ ├── find_isoform_pairs.pl │ ├── find_pairs_cDNA_exonerate.pl │ ├── make_bsubs_compare_Exons.pl │ ├── make_bsubs_compare_HomoloGene_pairs.pl │ ├── make_bsubs_compare_isoforms.pl │ ├── make_bsubs_compute_syntenic_genes.pl │ ├── make_cDNA_exonerate_bsub.pl │ └── test_genes_for_orthology.pl ├── HMMs │ ├── make_genewiseHMM_bsubs.pl │ ├── make_genewisedb_bsubs.pl │ ├── run_genewiseHMM.pl │ ├── run_genewisedb.pl │ └── split_hmm.pl ├── InputIdManager.pl ├── LowCoverage │ ├── LowCoverageGeneBuild.pl │ ├── LowCoverageGeneBuildConf.pm │ └── generic_config │ │ ├── Bio │ │ └── EnsEMBL │ │ │ ├── Analysis │ │ │ └── Config │ │ │ │ ├── Blast.pm │ │ │ │ ├── Blast.pm.example │ │ │ │ ├── General.pm │ │ │ │ └── General.pm.example │ │ │ └── Pipeline │ │ │ └── Config │ │ │ ├── BatchQueue.pm │ │ │ ├── BatchQueue.pm.example │ │ │ ├── General.pm │ │ │ └── General.pm.example │ │ └── pipe_conf │ │ ├── analysis.conf │ │ └── rule.conf ├── ModelTraining │ └── genewise_splice_site.pl ├── Pre-release-site │ └── set_stable_ids.pl ├── Pseudogenes │ ├── collect_PseudoGeneLabelling_output.pl │ ├── find_processed_pseudogenes.pl │ ├── label_pseudogenes.pl │ ├── make_PseudoGeneFinder_bsubs.pl │ ├── make_PseudoGeneLabelling_bsubs.pl │ ├── prepare_PSILC.pl │ ├── pseudogene_finder.pl │ ├── test_genewises.pl │ ├── test_this_genewise.pl │ └── update_pseudogenes.pl ├── RuleHandler.pl ├── Sequence │ ├── bsub_for_getting_chr_sequence.pl │ ├── dump_chromosomes.pl │ ├── dump_seq_into_fastA.pl │ ├── fetch_cdna_sequence.pl │ └── get_sequence_for_chr.pl ├── add_Analysis ├── add_to_Pipeline ├── alfanumeric_id_increment.pl ├── alignment_squiz.pl ├── analysis_setup.pl ├── awol_check.pl ├── bsub_ssaha.pl ├── cDNA_update │ ├── cDNAUpdate.pm.example │ ├── cDNA_update.pl │ ├── comparison.pl │ ├── config_files.txt │ ├── find_N.pl │ ├── record_unmapped_cdnas.pl │ ├── store_unmapped_cdnas.pl │ └── why_cdnas_didnt_hit.pl ├── chr_splitter ├── chr_subseq │ ├── INSTALL │ ├── Makefile │ └── chr_subseq.c ├── compara │ ├── run_compara.pl │ └── run_test_compara.pl ├── display_alignment.pl ├── dump_genes_from_core.pl ├── est_discriminator.pl ├── example_analysis.conf ├── example_rule.conf ├── examples │ ├── dump_transcripts.pl │ ├── get_rnaseq_data_by_gene.pl │ ├── get_rnaseq_genes_reads_info.pl │ ├── print_alternate_loci.pl │ └── print_refseq_transcripts.pl ├── extra_database_setup.pl ├── extract_gene_ids_for_hive.pl ├── fasta2otter ├── find_big_clusters.pl ├── flush_Pipeline ├── ge_wrapper.pl ├── id_increment.pl ├── init_Pipeline ├── job_submission.pl ├── load_agp.pl ├── load_seq_region.pl ├── load_taxonomy.pl ├── lsf_submission.pl ├── mRNA │ └── get_cdnas_from_EMBL.pl ├── make_assembly_patch_input_ids.pl ├── make_clone_sgp ├── make_compara_pipeline ├── make_firstef_bsubs.pl ├── make_input_ids ├── monitor ├── ncRNA │ ├── README │ ├── config_files.txt │ ├── make_tRNA_into_Genes.pl │ ├── ncRNA_update.pl │ ├── ncRNA_update_config.pm.example │ ├── predict_ncRNA.pl │ └── transfer_ncRNAs.pl ├── pipeline_from_scratch ├── pipeline_sanity.pl ├── post_GeneBuild │ ├── check_CDSs.pl │ ├── check_cDNA.pl │ ├── check_evidence.pl │ ├── check_feature_density.pl │ ├── check_splice_sites.pl │ ├── check_transcript.pl │ ├── check_translation.pl │ ├── classify_transcripts_by_evidence.pl │ ├── cluster_Genes.pl │ ├── count_intron_sizes.pl │ ├── count_single_exons_transcripts.pl │ ├── count_transcripts_with_UTRs.pl │ ├── create_stable_ids.pl │ ├── dump_CDSs.pl │ ├── dump_ensembl_cdnas.pl │ ├── dump_ensembl_transcript_structures.pl │ ├── dump_translations.pl │ ├── find_nearby_splice_sites.pl │ ├── get_transcripts_with_this_evidence.pl │ ├── post_GeneBuild_checks_denormalised.pl │ └── produce_training_set.pl ├── refseq_import │ ├── load_refseq_synonyms.pl │ └── parse_ncbi_gff3.pl ├── rework_minus_big_clust.pl ├── rework_paralogues_data.pl ├── rule_checker.pl ├── rule_setup.pl ├── rulemanager.pl ├── run_EST_RunnableDB ├── run_GeneBuild_RunnableDB ├── set_PERL5LIB_SGE.sh ├── set_toplevel.pl ├── setup ├── setup_batchqueue_outputdir.pl ├── setup_orthologue_evaluator.pl ├── slice_groups.pl ├── sql │ ├── delete_features │ ├── delete_genes │ ├── delete_jobs │ └── delete_pipeline └── wga2genes │ ├── make_alignment_filter_iids.pl │ └── make_wga2genes_iids.pl ├── sql ├── clones.sql ├── drop_tables.sql ├── efg.sql ├── flag.sql ├── hit_description.sql ├── patch_01_2007.sql ├── patch_08_2012.sql └── table.sql ├── test_system ├── RefDB.conf.example ├── TestDB.conf.example ├── cleanup_output.pl ├── config │ └── Bio │ │ └── EnsEMBL │ │ ├── Analysis │ │ └── Config │ │ │ ├── Blast.pm │ │ │ ├── Databases.pm │ │ │ ├── GeneBuild │ │ │ └── Pmatch.pm │ │ │ └── General.pm │ │ └── Pipeline │ │ └── Config │ │ ├── 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