@comment $NetBSD$
maker/bin/AED_cdf_generator.pl
maker/bin/cegma2zff
maker/bin/chado2gff3
maker/bin/compare_gff3_to_chado
maker/bin/cufflinks2gff3
maker/bin/fasta_merge
maker/bin/fasta_tool
maker/bin/genemark_gtf2gff3
maker/bin/gff3_merge
maker/bin/ipr_update_gff
maker/bin/iprscan2gff3
maker/bin/maker
maker/bin/maker2chado
maker/bin/maker2eval_gtf
maker/bin/maker2jbrowse
maker/bin/maker2wap
maker/bin/maker2zff
maker/bin/maker_functional_fasta
maker/bin/maker_functional_gff
maker/bin/maker_map_ids
maker/bin/map2assembly
maker/bin/map_data_ids
maker/bin/map_fasta_ids
maker/bin/map_gff_ids
maker/bin/match2gene.pl
maker/bin/quality_filter.pl
maker/bin/split_gff3
maker/bin/tophat2gff3
maker/bin/train_augustus.pl
maker/bin/zff2genbank.pl
maker/data/dpp_contig.fasta
maker/data/dpp_est.fasta
maker/data/dpp_protein.fasta
maker/data/evm_weights.txt
maker/data/hsap_contig.fasta
maker/data/hsap_est.fasta
maker/data/hsap_protein.fasta
maker/data/te_proteins.fasta
maker/lib/Bio/Search/HSP/PhatHSP.pod
maker/lib/Bio/Search/HSP/PhatHSP/Base.pm
maker/lib/Bio/Search/HSP/PhatHSP/augustus.pm
maker/lib/Bio/Search/HSP/PhatHSP/blastn.pm
maker/lib/Bio/Search/HSP/PhatHSP/blastx.pm
maker/lib/Bio/Search/HSP/PhatHSP/cdna2genome.pm
maker/lib/Bio/Search/HSP/PhatHSP/est2genome.pm
maker/lib/Bio/Search/HSP/PhatHSP/evm.pm
maker/lib/Bio/Search/HSP/PhatHSP/fgenesh.pm
maker/lib/Bio/Search/HSP/PhatHSP/genemark.pm
maker/lib/Bio/Search/HSP/PhatHSP/gff3.pm
maker/lib/Bio/Search/HSP/PhatHSP/protein2genome.pm
maker/lib/Bio/Search/HSP/PhatHSP/qrna.pm
maker/lib/Bio/Search/HSP/PhatHSP/rapsearch.pm
maker/lib/Bio/Search/HSP/PhatHSP/repeatmasker.pm
maker/lib/Bio/Search/HSP/PhatHSP/snap.pm
maker/lib/Bio/Search/HSP/PhatHSP/snoscan.pm
maker/lib/Bio/Search/HSP/PhatHSP/tblastx.pm
maker/lib/Bio/Search/HSP/PhatHSP/trnascan.pm
maker/lib/Bio/Search/Hit/PhatHit.pod
maker/lib/Bio/Search/Hit/PhatHit/Base.pm
maker/lib/Bio/Search/Hit/PhatHit/augustus.pm
maker/lib/Bio/Search/Hit/PhatHit/blastn.pm
maker/lib/Bio/Search/Hit/PhatHit/blastx.pm
maker/lib/Bio/Search/Hit/PhatHit/cdna2genome.pm
maker/lib/Bio/Search/Hit/PhatHit/est2genome.pm
maker/lib/Bio/Search/Hit/PhatHit/evm.pm
maker/lib/Bio/Search/Hit/PhatHit/fgenesh.pm
maker/lib/Bio/Search/Hit/PhatHit/genemark.pm
maker/lib/Bio/Search/Hit/PhatHit/gff3.pm
maker/lib/Bio/Search/Hit/PhatHit/protein2genome.pm
maker/lib/Bio/Search/Hit/PhatHit/qrna.pm
maker/lib/Bio/Search/Hit/PhatHit/rapsearch.pm
maker/lib/Bio/Search/Hit/PhatHit/repeatmasker.pm
maker/lib/Bio/Search/Hit/PhatHit/snap.pm
maker/lib/Bio/Search/Hit/PhatHit/snoscan.pm
maker/lib/Bio/Search/Hit/PhatHit/tblastx.pm
maker/lib/Bio/Search/Hit/PhatHit/trnascan.pm
maker/lib/Bio/SearchIO/wublasttable.pm
maker/lib/CGL/Annotation.pm
maker/lib/CGL/Annotation/Feature.pm
maker/lib/CGL/Annotation/Feature/Contig.pm
maker/lib/CGL/Annotation/Feature/Exon.pm
maker/lib/CGL/Annotation/Feature/Gene.pm
maker/lib/CGL/Annotation/Feature/Intron.pm
maker/lib/CGL/Annotation/Feature/Protein.pm
maker/lib/CGL/Annotation/Feature/Sequence_variant.pm
maker/lib/CGL/Annotation/Feature/Transcript.pm
maker/lib/CGL/Annotation/FeatureLocation.pm
maker/lib/CGL/Annotation/FeatureRelationship.pm
maker/lib/CGL/Annotation/GFF3/DictyBase.pm
maker/lib/CGL/Annotation/GFF3/FlyBase.pm
maker/lib/CGL/Annotation/GFF3/Maker.pm
maker/lib/CGL/Annotation/GFF3/Maker_snap.pm
maker/lib/CGL/Annotation/GFF3/WormBase.pm
maker/lib/CGL/Annotation/GFF3/nGASP.pm
maker/lib/CGL/Annotation/GFF3/nGASP2.pm
maker/lib/CGL/Annotation/Iterator.pm
maker/lib/CGL/Annotation/Trace.pm
maker/lib/CGL/Clone.pm
maker/lib/CGL/Ontology/GO.pm
maker/lib/CGL/Ontology/Node.pm
maker/lib/CGL/Ontology/NodeRelationship.pm
maker/lib/CGL/Ontology/Ontology.pm
maker/lib/CGL/Ontology/Parser/OBO.pm
maker/lib/CGL/Ontology/SO.pm
maker/lib/CGL/Ontology/Trace.pm
maker/lib/CGL/Revcomp.pm
maker/lib/CGL/TranslationMachine.pm
maker/lib/CGL/Version.pm
maker/lib/CGL/gene_ontology.obo
maker/lib/CGL/so.new.obo
maker/lib/CGL/so.obo
maker/lib/CGL/sofa.obo
maker/lib/Datastore/Base.pm
maker/lib/Datastore/CG.pm
maker/lib/Datastore/MD5.pm
maker/lib/Datastore/bin/ds_dir
maker/lib/Datastore/bin/ds_do
maker/lib/Dumper/GFF/GFFV3.pm
maker/lib/Dumper/XML/Game.pm
maker/lib/Dumper/XML/Game_Xml.pm
maker/lib/Error.pm
maker/lib/Error/Simple.pm
maker/lib/Fasta.pm
maker/lib/FastaChunk.pm
maker/lib/FastaChunker.pm
maker/lib/FastaDB.pm
maker/lib/FastaFile.pm
maker/lib/FastaSeq.pm
maker/lib/File/NFSLock.pm
maker/lib/File/Which.pm
maker/lib/File/maintain.pl
maker/lib/GFFDB.pm
maker/lib/GI.pm
maker/lib/Gene_obj.pm
maker/lib/IO/Prompt.pm
maker/lib/Iterator.pm
maker/lib/Iterator/Any.pm
maker/lib/Iterator/Fasta.pm
maker/lib/Iterator/GFF3.pm
maker/lib/Longest_orf.pm
maker/lib/MWAS_util.pm
maker/lib/Nuc_translator.pm
maker/lib/Parallel/Application.pm
maker/lib/PhatHit_utils.pm
maker/lib/PostData.pm
maker/lib/Proc/ProcessTable_simple.pm
maker/lib/Proc/Signal.pm
maker/lib/Process/IPRchunk.pm
maker/lib/Process/MpiChunk.pm
maker/lib/Process/MpiTiers.pm
maker/lib/Process/mapChunk.pm
maker/lib/Shadower.pm
maker/lib/SimpleCluster.pm
maker/lib/SpaceBase.pm
maker/lib/Widget.pm
maker/lib/Widget/PolyBayes.pm
maker/lib/Widget/RepeatMasker.pm
maker/lib/Widget/augustus.pm
maker/lib/Widget/blastn.pm
maker/lib/Widget/blastx.pm
maker/lib/Widget/evm.pm
maker/lib/Widget/exonerate.pm
maker/lib/Widget/exonerate/cdna2genome.pm
maker/lib/Widget/exonerate/est2genome.pm
maker/lib/Widget/exonerate/protein2genome.pm
maker/lib/Widget/fgenesh.pm
maker/lib/Widget/fgenesh/fgenesh_wrap
maker/lib/Widget/formatdb.pm
maker/lib/Widget/formater.pm
maker/lib/Widget/genemark.pm
maker/lib/Widget/genemark/gmhmm_wrap
maker/lib/Widget/iprscan.pm
maker/lib/Widget/pressdb.pm
maker/lib/Widget/primer3.pm
maker/lib/Widget/qrna.pm
maker/lib/Widget/rapsearch.pm
maker/lib/Widget/setdb.pm
maker/lib/Widget/snap.pm
maker/lib/Widget/snoscan.pm
maker/lib/Widget/tblastx.pm
maker/lib/Widget/trnascan.pm
maker/lib/Widget/xdformat.pm
maker/lib/auto/Datastore/.packlist
maker/lib/auto/Datastore/Base/autosplit.ix
maker/lib/auto/Datastore/CG/autosplit.ix
maker/lib/auto/Datastore/MD5/autosplit.ix
maker/lib/auto/Error/.packlist
maker/lib/basiclog.pm
maker/lib/clean.pm
maker/lib/cluster.pm
maker/lib/compare.pm
maker/lib/ds_utility.pm
maker/lib/evaluator/AED.pm
maker/lib/evaluator/Widget/blast.pm
maker/lib/evaluator/evaluate.pm
maker/lib/evaluator/fathom_utils.pm
maker/lib/evaluator/funs.pm
maker/lib/evaluator/gff3_to_phatHit/FlyBase.pm
maker/lib/evaluator/gff3_to_phatHit/Maker.pm
maker/lib/evaluator/gff3_to_phatHit/WormBase.pm
maker/lib/evaluator/gff3_to_phatHit/gff3_classifier.pm
maker/lib/evaluator/hey_gff3_to_phatHit.pm
maker/lib/evaluator/maker_gff.pm
maker/lib/evaluator/master_codes
maker/lib/evaluator/pseudo_hit.pm
maker/lib/evaluator/quality_index.pm
maker/lib/evaluator/quality_seq.pm
maker/lib/evaluator/scoring.pm
maker/lib/evaluator/so_classifier.pm
maker/lib/exonerate/splice_info.pm
maker/lib/external_gff/PhatHit.pm
maker/lib/external_gff/PhatHsp.pm
maker/lib/iprscan/runlog.pm
maker/lib/maker/auto_annotator.pm
maker/lib/maker/join.pm
maker/lib/maker/quality_index.pm
maker/lib/maker/sens_spec.pm
maker/lib/polisher.pm
maker/lib/polisher/exonerate.pm
maker/lib/polisher/exonerate/altest.pm
maker/lib/polisher/exonerate/est.pm
maker/lib/polisher/exonerate/protein.pm
maker/lib/repeat_mask_seq.pm
maker/lib/runlog.pm
maker/lib/shadow_AED.pm
maker/perl/lib/MAKER/ConfigData.pm
maker/perl/lib/Parallel/Application/MPI.pm
maker/perl/lib/auto/MAKER/.packlist
maker/perl/man/MAKER::ConfigData.3
share/doc/maker/README
