# # ChangeLog for /Apollo # # Generated by Trac 0.10.4 # 11/24/09 03:15:46 # 09/15/09 16:30:27 cholt [264] * Apollo/fly.tiers (deleted) remove old fly.tiers 07/12/09 21:03:39 cholt [230] * Apollo/gff3.tiers (modified) updated gff3.tiers 03/31/09 16:14:50 cholt [185] * Apollo/gff3.tiers (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) fix auto_annotator error and control files error and updarte gff3.tiers 03/26/09 22:50:47 cholt [182] * Apollo/gff3.tiers (modified) * lib/Widget/augustus.pm (modified) * lib/runlog.pm (modified) augustus bug fix and gff3.tiers edit 02/20/09 12:38:14 cholt [151] * Apollo/gff3.tiers (modified) * MPI/mpi_maker (modified) * bin/gff3_merge (modified) * bin/maker (modified) * lib/Bio/Search/Hit/PhatHit/Base.pm (modified) * lib/CGL/TranslationMachine.pm (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/Fasta.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/augustus.pm (modified) * lib/clean.pm (modified) * lib/cluster.pm (modified) * lib/evaluator/funs.pm (modified) * lib/evaluator/quality_index.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/shadow_AED.pm (modified) maker update CDS has stop codon and other opts 08/26/08 17:15:30 cholt [89] * Apollo (added) * Apollo/fly.tiers (added) * Apollo/gff3.tiers (added) * INSTALL (added) * MPI (added) * MPI/MANIFEST (added) * MPI/MANIFEST.SKIP (added) * MPI/MPIcar.pm (added) * MPI/MPIcar.xs (added) * MPI/Makefile.PL (added) * MPI/contrib (added) * MPI/contrib/cpi (added) * MPI/contrib/cpi/Makefile (added) * MPI/contrib/cpi/cpi.PL (added) * MPI/contrib/cpi/cpi.c (added) * MPI/contrib/heat (added) * MPI/contrib/heat/Makefile (added) * MPI/contrib/heat/heat_plate_mpi.PL (added) * MPI/contrib/heat/heat_plate_mpi.f (added) * MPI/contrib/perf (added) * MPI/contrib/perf/Makefile (added) * MPI/contrib/perf/mpi_timing.PL (added) * MPI/contrib/perf/mpi_timing.c (added) * MPI/contrib/perf/runtiming.pl (added) * MPI/docs (added) * MPI/docs/MPI-C-Bindings.txt (added) * MPI/docs/README (added) * MPI/docs/TODO (added) * MPI/docs/paper.tex (added) * MPI/mpi_maker (added) * MPI/t (added) * MPI/t/00_use_mpi.t (added) * MPI/t/01_mpi_init.PL (added) * MPI/t/01_mpi_init.t (added) * MPI/t/02_mpi_finalize.PL (added) * MPI/t/02_mpi_finalize.t (added) * MPI/t/03_mpi_comm_rank.PL (added) * MPI/t/03_mpi_comm_rank.t (added) * MPI/t/04_mpi_comm_size.PL (added) * MPI/t/04_mpi_comm_size.t (added) * MPI/t/05_mpi_initialized.PL (added) * MPI/t/05_mpi_initialized.t (added) * MPI/t/06_mpi_sendrecv.PL (added) * MPI/t/06_mpi_sendrecv.t (added) * MPI/t/06_sendrecv_dbl.PL (added) * MPI/t/06_sendrecv_dbl.t (added) * MPI/t/06_sendrecv_dblarray.PL (added) * MPI/t/06_sendrecv_dblarray.t (added) * MPI/t/06_sendrecv_flt.PL (added) * MPI/t/06_sendrecv_flt.t (added) * MPI/t/06_sendrecv_fltarray.PL (added) * MPI/t/06_sendrecv_fltarray.t (added) * MPI/t/06_sendrecv_int.PL (added) * MPI/t/06_sendrecv_int.t (added) * MPI/t/06_sendrecv_intarray.PL (added) * MPI/t/06_sendrecv_intarray.t (added) * MPI/t/07_mpi_bcast.PL (added) * MPI/t/07_mpi_bcast.t (added) * MPI/t/07_mpi_bcastarray.PL (added) * MPI/t/07_mpi_bcastarray.t (added) * MPI/t/08_mpi_reduce.PL (added) * MPI/t/08_mpi_reduce.t (added) * MPI/t/09_mpi_barrier.PL (added) * MPI/t/09_mpi_barrier.t (added) * MPI/t/10_mpi_wtime.PL (added) * MPI/t/10_mpi_wtime.t (added) * MPI/t/11_mpi_scattergather.PL (added) * MPI/t/11_mpi_scattergather.t (added) * MPI/t/11_mpi_scattergatherarray.PL (added) * MPI/t/11_mpi_scattergatherarray.t (added) * MPI/t/12_mpi_allreduce.PL (added) * MPI/t/12_mpi_allreduce.t (added) * MPI/t/13_mpi_sendrecv.PL (added) * MPI/t/13_mpi_sendrecv.t (added) * MPI/t/greetings.c (added) * MPI/t/machinefile (added) * MPI/typemap (added) * MPI/utils.c (added) * README (added) * bin (added) * bin/add_utr_gff.pl (added) * bin/maker (added) * bin/maker2zff.pl (added) * bin/maker_manager (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) * 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/Bio/SearchIO (added) * lib/Bio/SearchIO/wublasttable.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/Datastore (added) * lib/Datastore/Base.pm (added) * lib/Datastore/CG.pm (added) * lib/Datastore/MD5.pm (added) * lib/Datastore/bin (added) * lib/Datastore/bin/ds_dir (added) * lib/Datastore/bin/ds_do (added) * lib/Datastore/docs (added) * lib/Datastore/docs/Datastore::Base.3pm (added) * lib/Datastore/docs/Datastore::CG.3pm (added) * lib/Datastore/docs/Datastore::MD5.3pm (added) * lib/Datastore/docs/ds_dir.1 (added) * lib/Datastore/docs/ds_do.1 (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/Error (added) * lib/Error.pm (added) * lib/Error/Simple.pm (added) * lib/Error/docs (added) * lib/Error/docs/Error.3pm (added) * lib/Error/docs/Error::Simple.3pm (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/Process (added) * lib/Process/MakerChunk.pm (added) * lib/Process/MakerTiers.pm (added) * lib/Shadower.pm (added) * lib/Shared_Functions.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/augustus.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/Widget/xdformat.pm (added) * lib/augustus (added) * lib/augustus/PhatHit.pm (added) * lib/augustus/PhatHsp.pm (added) * lib/auto (added) * lib/auto/Datastore (added) * lib/auto/Datastore/.packlist (added) * lib/auto/Datastore/Base (added) * lib/auto/Datastore/Base/autosplit.ix (added) * lib/auto/Datastore/CG (added) * lib/auto/Datastore/CG/autosplit.ix (added) * lib/auto/Datastore/MD5 (added) * lib/auto/Datastore/MD5/autosplit.ix (added) * lib/auto/Error (added) * lib/auto/Error/.packlist (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/perllocal.pod (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/runlog.pm (added) * lib/snap (added) * lib/snap/PhatHit.pm (added) * lib/snap/PhatHsp.pm (added) * lib/verifier (added) error