Apollo Genome Annotation Editor

• Cite Apollo: Dunn, N. A. et al. Apollo: Democratizing genome annotation. PLoS Comput. Biol. 15, e1006790 (2019)
• Latest Documentation
• User's Guide
• Apollo Source
• Request Feature / Report Bug
• User's Group archive and signup. Email user's group directly.

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• Version: 2.7.0
• Grails version: 2.5.5
• Groovy version: 2.4.4
• JVM version: 1.8.0_442
• Servlet Container Version: Apache Tomcat/9.0.31 (Ubuntu)
• JBrowse config: dompurify2
• JBrowse url: https://github.com/cmdcolin/jbrowse
• Web Services

JBrowse Plugins

• WebApollo=[included:true]
• NeatHTMLFeatures=[included:true, linearGradient:0]
• NeatCanvasFeatures=[included:true]
• RegexSequenceSearch=[included:true]
• HideTrackLabels=[included:true]
• ScreenShotPlugin=[git:https://github.com/bhofmei/jbplugin-screenshot.git, branch:master, alwaysRecheck:true, alwaysPull:true]
• ColorByCDS=[git:https://github.com/scottcain/colorbycds.git, branch:master, alwaysRecheck:true, alwaysPull:true]
• MAFViewer=[git:https://github.com/cmdcolin/mafviewer.git, branch:master, alwaysRecheck:true, alwaysPull:true]
• FeatureSequence=[git:https://github.com/twsaari/FeatureSequence.git, branch:master, alwaysRecheck:true, alwaysPull:true]

Apollo Config

• default_minimum_intron_size=1
• history_size=0
• overlapper_class=org.bbop.apollo.sequence.OrfOverlapper
• track_name_comparator=/config/track_name_comparator.js
• use_cds_for_new_transcripts=false
• count_annotations=true
• add_merged_comment=true
• transcript_overlapper=CDS
• feature_has_dbxrefs=true
• feature_has_attributes=true
• feature_has_pubmed_ids=true
• feature_has_go_ids=true
• feature_has_comments=true
• feature_has_status=true
• export_subfeatures_attr=false
• user_pure_memory_store=true
• is_partial_translation_allowed=false
• export_subfeature_attrs=false
• store_orig_id=true
• calculate_non_canonical_splice_sites=true
• common_data_directory=/data/temporary/apollo_data
• chado_export_fasta_for_sequence=false
• chado_export_fasta_for_cds=false
• only_owners_delete=false
• get_translation_code=1
• proxies=[{referenceUrl=http://golr.geneontology.org/select, targetUrl=http://golr.geneontology.org/solr/select, active=true, fallbackOrder=0, replace=true}, {referenceUrl=http://golr.geneontology.org/select, targetUrl=http://golr.berkeleybop.org/solr/select, active=false, fallbackOrder=1, replace=false}]
• fa_to_twobit_exe=/usr/local/bin/faToTwoBit
• sequence_search_tools={blat_nuc={search_exe=/usr/local/bin/blat, search_class=org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide, name=Blat nucleotide, params=}, blat_prot={search_exe=/usr/local/bin/blat, search_class=org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide, name=Blat protein, params=}}
• data_adapters=[{permission=1, key=GFF3, data_adapters=[{permission=1, key=Only GFF3, options=output=file&format=gzip&type=GFF3&exportGff3Fasta=false}, {permission=1, key=GFF3 with FASTA, options=output=file&format=gzip&type=GFF3&exportGff3Fasta=true}]}, {permission=1, key=VCF, data_adapters=[{permission=1, key=VCF, options=output=file&format=gzip&type=VCF}]}, {permission=1, key=FASTA, data_adapters=[{permission=1, key=peptide, options=output=file&format=gzip&type=FASTA&seqType=peptide}, {permission=1, key=cDNA, options=output=file&format=gzip&type=FASTA&seqType=cdna}, {permission=1, key=CDS, options=output=file&format=gzip&type=FASTA&seqType=cds}, {permission=1, key=highlighted region, options=output=file&format=gzip&type=FASTA&seqType=genomic}]}]
• splice_donor_sites=[GT]
• splice_acceptor_sites=[AG]
• gff3=[source:.]
• bootstrap=false
• info_editor=Config$_run_closure6$_closure18@5bdaebb7
• administrativePanel=[{label=Canned Comments, link=/cannedComment/, globalRank=ADMIN}, {label=Canned Key, link=/cannedKey/, globalRank=ADMIN}, {label=Canned Values, link=/cannedValue/, globalRank=ADMIN}, {label=Statuses, link=/availableStatus/, globalRank=ADMIN}, {label=Feature Types, link=/featureType/, globalRank=ADMIN}, {label=Suggested Feature Names, link=/suggestedName/, globalRank=ADMIN}, {label=Gene Product Names, link=/geneProductName/, globalRank=ADMIN}, {label=Proxies, link=/proxy/, globalRank=ADMIN}, {label=Report::Organisms, link=/organism/report/, type=report}, {label=Report::Sequences, link=/sequence/report/, type=report}, {label=Report::Users, link=/annotator/report/, type=report, globalRank=ADMIN}, {label=Report::Instructor, link=/annotator/instructorReport/, type=report}, {label=Report::Changes, link=/featureEvent/report/, type=report}, {label=System Info, link=/home/systemInfo/, type=report, globalRank=ADMIN}, {label=Performance Metrics, link=/home/metrics/, type=report, globalRank=ADMIN}, {label=WebServices, link=/WebServices/, type=report, globalRank=ADMIN}]
• extraTabs=[]
• google_analytics=[UA-62921593-1]
• native_track_selector_default_on=false
• out=[:]
• add_merged_commented=true
• translation_table=/config/translation_tables/ncbi_1_translation_table.txt