Changeset 1

Timestamp:

11/03/07 12:08:26 (2 years ago)

Author:

svn

Message:

initial import

Files:

• README (added)
• bin (added)
• bin/add_utr_gff.pl (added)
• bin/maker (added)
• bin/maker2zff.pl (added)
• bin/multifasta_maker (added)
• bin/special_apps (added)
• bin/special_apps/convert-hmm.pl (added)
• bin/special_apps/exonerate_debugger (added)
• bin/special_apps/maker_ngasp (added)
• bin/special_apps/transposon_masker (added)
• config (added)
• config/maker_bopts.ctl (added)
• config/maker_exe.ctl (added)
• config/maker_opts.ctl (added)
• data (added)
• data/dpp_contig.fasta (added)
• data/dpp_proteins.fasta (added)
• data/dpp_transcripts.fasta (added)
• data/te_proteins.fasta (added)
• lib (added)
• lib/Bio (added)
• lib/Bio/Search (added)
• lib/Bio/Search/HSP (added)
• lib/Bio/Search/HSP/PhatHSP (added)
• lib/Bio/Search/HSP/PhatHSP.pod (added)
• lib/Bio/Search/HSP/PhatHSP/Base.pm (added)
• lib/Bio/Search/HSP/PhatHSP/blastn.pm (added)
• lib/Bio/Search/HSP/PhatHSP/blastp.pm (added)
• lib/Bio/Search/HSP/PhatHSP/blastx.pm (added)
• lib/Bio/Search/HSP/PhatHSP/tblastn.pm (added)
• lib/Bio/Search/HSP/PhatHSP/tblastx.pm (added)
• lib/Bio/Search/Hit (added)
• lib/Bio/Search/Hit/PhatHit (added)
• lib/Bio/Search/Hit/PhatHit.pod (added)
• lib/Bio/Search/Hit/PhatHit/Base.pm (added)
• lib/Bio/Search/Hit/PhatHit/blastn.pm (added)
• lib/Bio/Search/Hit/PhatHit/blastp.pm (added)
• lib/Bio/Search/Hit/PhatHit/blastx.pm (added)
• lib/Bio/Search/Hit/PhatHit/tblastn.pm (added)
• lib/Bio/Search/Hit/PhatHit/tblastx.pm (added)
• lib/CGL (added)
• lib/CGL/Annotation (added)
• lib/CGL/Annotation.pm (added)
• lib/CGL/Annotation/Feature (added)
• lib/CGL/Annotation/Feature.pm (added)
• lib/CGL/Annotation/Feature/Contig.pm (added)
• lib/CGL/Annotation/Feature/Exon.pm (added)
• lib/CGL/Annotation/Feature/Gene.pm (added)
• lib/CGL/Annotation/Feature/Intron.pm (added)
• lib/CGL/Annotation/Feature/Protein.pm (added)
• lib/CGL/Annotation/Feature/Sequence_variant.pm (added)
• lib/CGL/Annotation/Feature/Transcript.pm (added)
• lib/CGL/Annotation/FeatureLocation.pm (added)
• lib/CGL/Annotation/FeatureRelationship.pm (added)
• lib/CGL/Annotation/GFF3 (added)
• lib/CGL/Annotation/GFF3/DictyBase.pm (added)
• lib/CGL/Annotation/GFF3/FlyBase.pm (added)
• lib/CGL/Annotation/GFF3/Maker.pm (added)
• lib/CGL/Annotation/GFF3/Maker_snap.pm (added)
• lib/CGL/Annotation/GFF3/WormBase.pm (added)
• lib/CGL/Annotation/GFF3/nGASP.pm (added)
• lib/CGL/Annotation/GFF3/nGASP2.pm (added)
• lib/CGL/Annotation/Iterator.pm (added)
• lib/CGL/Annotation/Trace.pm (added)
• lib/CGL/Clone.pm (added)
• lib/CGL/Ontology (added)
• lib/CGL/Ontology/GO.pm (added)
• lib/CGL/Ontology/Node.pm (added)
• lib/CGL/Ontology/NodeRelationship.pm (added)
• lib/CGL/Ontology/Ontology.pm (added)
• lib/CGL/Ontology/Parser (added)
• lib/CGL/Ontology/Parser/OBO.pm (added)
• lib/CGL/Ontology/SO.pm (added)
• lib/CGL/Ontology/Trace.pm (added)
• lib/CGL/Revcomp.pm (added)
• lib/CGL/TranslationMachine.pm (added)
• lib/CGL/Version.pm (added)
• lib/CGL/gene_ontology.obo (added)
• lib/CGL/so.new.obo (added)
• lib/CGL/so.obo (added)
• lib/CGL/sofa.obo (added)
• lib/Dumper (added)
• lib/Dumper/GFF (added)
• lib/Dumper/GFF/GFF3.pm (added)
• lib/Dumper/GFF/GFF3_DEF.pm (added)
• lib/Dumper/GFF/GFFV3.pm (added)
• lib/Dumper/SpaceBase.pm (added)
• lib/Dumper/XML (added)
• lib/Dumper/XML/Game.pm (added)
• lib/Dumper/XML/Game_Xml.pm (added)
• lib/Fasta.pm (added)
• lib/FastaChunk.pm (added)
• lib/FastaChunker.pm (added)
• lib/FastaFile.pm (added)
• lib/Iterator (added)
• lib/Iterator.pm (added)
• lib/Iterator/Fasta.pm (added)
• lib/PhatHit.pm (added)
• lib/PhatHit_utils.pm (added)
• lib/PhatHsp.pm (added)
• lib/PostData.pm (added)
• lib/Shadower.pm (added)
• lib/SimpleCluster.pm (added)
• lib/SpaceBase.pm (added)
• lib/Widget (added)
• lib/Widget.pm (added)
• lib/Widget/.snap.pm.swp (added)
• lib/Widget/PolyBayes.pm (added)
• lib/Widget/RepeatMasker.pm (added)
• lib/Widget/TblastN.pm (added)
• lib/Widget/blastn.pm (added)
• lib/Widget/blastp.pm (added)
• lib/Widget/blastx.pm (added)
• lib/Widget/exonerate (added)
• lib/Widget/exonerate.pm (added)
• lib/Widget/exonerate/est2genome.pm (added)
• lib/Widget/exonerate/est2genome.pm_orig (added)
• lib/Widget/exonerate/est2genome.pm_rev (added)
• lib/Widget/exonerate/protein2genome.pm (added)
• lib/Widget/exonerate/protein2genome.pm_orig (added)
• lib/Widget/exonerate/protein2genome.pm_rev (added)
• lib/Widget/geneid.pm (added)
• lib/Widget/genscan.pm (added)
• lib/Widget/primer3.pm (added)
• lib/Widget/qrna.pm (added)
• lib/Widget/snap.pm (added)
• lib/Widget/tblastx.pm (added)
• lib/clean.pm (added)
• lib/cluster.pm (added)
• lib/compare.pm (added)
• lib/evaluator (added)
• lib/exonerate (added)
• lib/exonerate/PhatHSP (added)
• lib/exonerate/PhatHSP/est2genome.pm (added)
• lib/exonerate/PhatHSP/protein2genome.pm (added)
• lib/exonerate/PhatHit (added)
• lib/exonerate/PhatHit/est2genome.pm (added)
• lib/exonerate/PhatHit/protein2genome.pm (added)
• lib/exonerate/splice_info.pm (added)
• lib/maker (added)
• lib/maker/auto_annotator.pm (added)
• lib/maker/join.pm (added)
• lib/maker/quality_index.pm (added)
• lib/maker/sens_spec.pm (added)
• lib/polisher (added)
• lib/polisher.pm (added)
• lib/polisher/exonerate (added)
• lib/polisher/exonerate.pm (added)
• lib/polisher/exonerate/est.pm (added)
• lib/polisher/exonerate/protein.pm (added)
• lib/repeat_mask_seq.pm (added)
• lib/repeatmasker (added)
• lib/repeatmasker/PhatHit.pm (added)
• lib/repeatmasker/PhatHsp.pm (added)
• lib/snap (added)
• lib/snap/PhatHit.pm (added)
• lib/snap/PhatHsp.pm (added)
• lib/verifier (added)