bin/AED_cdf_generator.pl
bin/cegma2zff
bin/chado2gff3
bin/compare_gff3_to_chado
bin/cufflinks2gff3
bin/evaluator
bin/fasta_merge
bin/fasta_tool
bin/genemark_gtf2gff3
bin/gff3_merge
bin/ipr_update_gff
bin/iprscan2gff3
bin/maker
bin/maker2chado
bin/maker2eval_gtf
bin/maker2jbrowse
bin/maker2wap
bin/maker2zff
bin/maker_functional_fasta
bin/maker_functional_gff
bin/maker_map_ids
bin/map2assembly
bin/map_data_ids
bin/map_fasta_ids
bin/map_gff_ids
bin/match2gene.pl
bin/quality_filter.pl
bin/split_gff3
bin/tophat2gff3
bin/train_augustus.pl
bin/zff2genbank.pl
lib/Bio/Search/HSP/PhatHSP.pod
lib/Bio/Search/HSP/PhatHSP/Base.pm
lib/Bio/Search/HSP/PhatHSP/augustus.pm
lib/Bio/Search/HSP/PhatHSP/blastn.pm
lib/Bio/Search/HSP/PhatHSP/blastx.pm
lib/Bio/Search/HSP/PhatHSP/cdna2genome.pm
lib/Bio/Search/HSP/PhatHSP/est2genome.pm
lib/Bio/Search/HSP/PhatHSP/evm.pm
lib/Bio/Search/HSP/PhatHSP/fgenesh.pm
lib/Bio/Search/HSP/PhatHSP/genemark.pm
lib/Bio/Search/HSP/PhatHSP/gff3.pm
lib/Bio/Search/HSP/PhatHSP/protein2genome.pm
lib/Bio/Search/HSP/PhatHSP/qrna.pm
lib/Bio/Search/HSP/PhatHSP/rapsearch.pm
lib/Bio/Search/HSP/PhatHSP/repeatmasker.pm
lib/Bio/Search/HSP/PhatHSP/snap.pm
lib/Bio/Search/HSP/PhatHSP/snoscan.pm
lib/Bio/Search/HSP/PhatHSP/tblastx.pm
lib/Bio/Search/HSP/PhatHSP/trnascan.pm
lib/Bio/Search/Hit/PhatHit.pod
lib/Bio/Search/Hit/PhatHit/Base.pm
lib/Bio/Search/Hit/PhatHit/augustus.pm
lib/Bio/Search/Hit/PhatHit/blastn.pm
lib/Bio/Search/Hit/PhatHit/blastx.pm
lib/Bio/Search/Hit/PhatHit/cdna2genome.pm
lib/Bio/Search/Hit/PhatHit/est2genome.pm
lib/Bio/Search/Hit/PhatHit/evm.pm
lib/Bio/Search/Hit/PhatHit/fgenesh.pm
lib/Bio/Search/Hit/PhatHit/genemark.pm
lib/Bio/Search/Hit/PhatHit/gff3.pm
lib/Bio/Search/Hit/PhatHit/protein2genome.pm
lib/Bio/Search/Hit/PhatHit/qrna.pm
lib/Bio/Search/Hit/PhatHit/rapsearch.pm
lib/Bio/Search/Hit/PhatHit/repeatmasker.pm
lib/Bio/Search/Hit/PhatHit/snap.pm
lib/Bio/Search/Hit/PhatHit/snoscan.pm
lib/Bio/Search/Hit/PhatHit/tblastx.pm
lib/Bio/Search/Hit/PhatHit/trnascan.pm
lib/Bio/SearchIO/wublasttable.pm
lib/CGL/Annotation.pm
lib/CGL/Annotation/Feature.pm
lib/CGL/Annotation/Feature/Contig.pm
lib/CGL/Annotation/Feature/Exon.pm
lib/CGL/Annotation/Feature/Gene.pm
lib/CGL/Annotation/Feature/Intron.pm
lib/CGL/Annotation/Feature/Protein.pm
lib/CGL/Annotation/Feature/Sequence_variant.pm
lib/CGL/Annotation/Feature/Transcript.pm
lib/CGL/Annotation/FeatureLocation.pm
lib/CGL/Annotation/FeatureRelationship.pm
lib/CGL/Annotation/GFF3/DictyBase.pm
lib/CGL/Annotation/GFF3/FlyBase.pm
lib/CGL/Annotation/GFF3/Maker.pm
lib/CGL/Annotation/GFF3/Maker_snap.pm
lib/CGL/Annotation/GFF3/WormBase.pm
lib/CGL/Annotation/GFF3/nGASP.pm
lib/CGL/Annotation/GFF3/nGASP2.pm
lib/CGL/Annotation/Iterator.pm
lib/CGL/Annotation/Trace.pm
lib/CGL/Clone.pm
lib/CGL/Ontology/GO.pm
lib/CGL/Ontology/Node.pm
lib/CGL/Ontology/NodeRelationship.pm
lib/CGL/Ontology/Ontology.pm
lib/CGL/Ontology/Parser/OBO.pm
lib/CGL/Ontology/SO.pm
lib/CGL/Ontology/Trace.pm
lib/CGL/Revcomp.pm
lib/CGL/TranslationMachine.pm
lib/CGL/Version.pm
lib/CGL/gene_ontology.obo
lib/CGL/so.new.obo
lib/CGL/so.obo
lib/CGL/sofa.obo
lib/Datastore/Base.pm
lib/Datastore/CG.pm
lib/Datastore/MD5.pm
lib/Datastore/bin/ds_dir
lib/Datastore/bin/ds_do
lib/Dumper/GFF/GFFV3.pm
lib/Dumper/XML/Game.pm
lib/Dumper/XML/Game_Xml.pm
lib/Error.pm
lib/Error/Simple.pm
lib/Fasta.pm
lib/FastaChunk.pm
lib/FastaChunker.pm
lib/FastaDB.pm
lib/FastaFile.pm
lib/FastaSeq.pm
lib/File/NFSLock.pm
lib/File/Which.pm
lib/File/maintain.pl
lib/GFFDB.pm
lib/GI.pm
lib/Gene_obj.pm
lib/IO/Prompt.pm
lib/Iterator.pm
lib/Iterator/Any.pm
lib/Iterator/Fasta.pm
lib/Iterator/GFF3.pm
lib/Longest_orf.pm
lib/MWAS_util.pm
lib/Nuc_translator.pm
lib/Parallel/Application.pm
lib/PhatHit_utils.pm
lib/PostData.pm
lib/Proc/ProcessTable_simple.pm
lib/Proc/Signal.pm
lib/Process/IPRchunk.pm
lib/Process/MpiChunk.pm
lib/Process/MpiTiers.pm
lib/Process/mapChunk.pm
lib/Shadower.pm
lib/SimpleCluster.pm
lib/SpaceBase.pm
lib/Widget.pm
lib/Widget/PolyBayes.pm
lib/Widget/RepeatMasker.pm
lib/Widget/augustus.pm
lib/Widget/blastn.pm
lib/Widget/blastx.pm
lib/Widget/evm.pm
lib/Widget/exonerate.pm
lib/Widget/exonerate/cdna2genome.pm
lib/Widget/exonerate/est2genome.pm
lib/Widget/exonerate/protein2genome.pm
lib/Widget/fgenesh.pm
lib/Widget/fgenesh/fgenesh_wrap
lib/Widget/formatdb.pm
lib/Widget/formater.pm
lib/Widget/genemark.pm
lib/Widget/genemark/gmhmm_wrap
lib/Widget/iprscan.pm
lib/Widget/pressdb.pm
lib/Widget/primer3.pm
lib/Widget/qrna.pm
lib/Widget/rapsearch.pm
lib/Widget/setdb.pm
lib/Widget/snap.pm
lib/Widget/snoscan.pm
lib/Widget/tblastx.pm
lib/Widget/trnascan.pm
lib/Widget/xdformat.pm
lib/auto/Datastore/.packlist
lib/auto/Datastore/Base/autosplit.ix
lib/auto/Datastore/CG/autosplit.ix
lib/auto/Datastore/MD5/autosplit.ix
lib/auto/Error/.packlist
lib/basiclog.pm
lib/clean.pm
lib/cluster.pm
lib/compare.pm
lib/ds_utility.pm
lib/evaluator/AED.pm
lib/evaluator/Widget/blast.pm
lib/evaluator/evaluate.pm
lib/evaluator/fathom_utils.pm
lib/evaluator/funs.pm
lib/evaluator/gff3_to_phatHit/FlyBase.pm
lib/evaluator/gff3_to_phatHit/Maker.pm
lib/evaluator/gff3_to_phatHit/WormBase.pm
lib/evaluator/gff3_to_phatHit/gff3_classifier.pm
lib/evaluator/hey_gff3_to_phatHit.pm
lib/evaluator/maker_gff.pm
lib/evaluator/master_codes
lib/evaluator/pseudo_hit.pm
lib/evaluator/quality_index.pm
lib/evaluator/quality_seq.pm
lib/evaluator/scoring.pm
lib/evaluator/so_classifier.pm
lib/exonerate/splice_info.pm
lib/external_gff/PhatHit.pm
lib/external_gff/PhatHsp.pm
lib/iprscan/runlog.pm
lib/maker/auto_annotator.pm
lib/maker/join.pm
lib/maker/quality_index.pm
lib/maker/sens_spec.pm
lib/polisher.pm
lib/polisher/exonerate.pm
lib/polisher/exonerate/altest.pm
lib/polisher/exonerate/est.pm
lib/polisher/exonerate/protein.pm
lib/repeat_mask_seq.pm
lib/runlog.pm
lib/shadow_AED.pm
perl/lib/MAKER/ConfigData.pm
perl/lib/Parallel/Application/MPI.pm
perl/lib/auto/MAKER/.packlist
perl/lib/auto/Parallel/Application/MPI/MPI.bundle
perl/lib/auto/Parallel/Application/MPI/MPI.inl
