[Bioperl-guts-l] [bioperl/bioperl-live] b4d329: match SSEARCH

noreply at github.com noreply at github.com
Thu Feb 10 18:38:59 EST 2011


Branch: refs/heads/topic/tree_api_refresh
Home:   https://github.com/bioperl/bioperl-live

Commit: b4d32932767ee98376a0fa9633b203e009742d30
    https://github.com/bioperl/bioperl-live/commit/b4d32932767ee98376a0fa9633b203e009742d30
Author: hyphaltip <jason at bioperl.org>
Date:   2010-12-15 (Wed, 15 Dec 2010)

Changed paths:
  M Bio/Search/HSP/GenericHSP.pm

Log Message:
-----------
match SSEARCH


Commit: 30ce2c346fb6e8cf0a1082e8c9eaa13d6dd8918e
    https://github.com/bioperl/bioperl-live/commit/30ce2c346fb6e8cf0a1082e8c9eaa13d6dd8918e
Author: hyphaltip <jason at bioperl.org>
Date:   2010-12-15 (Wed, 15 Dec 2010)

Changed paths:
  M Bio/SearchIO/fasta.pm

Log Message:
-----------
when processing SSEARCH get the strand info from the rev-comp line


Commit: 1142657b105f5c110320256573513932f17747e7
    https://github.com/bioperl/bioperl-live/commit/1142657b105f5c110320256573513932f17747e7
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-12-19 (Sun, 19 Dec 2010)

Changed paths:
  M Bio/Assembly/IO/ace.pm
  M t/data/assembly_with_singlets.ace

Log Message:
-----------
Bug fix for contig IDs that contain special characters (Lee Katz: http://article.gmane.org/gmane.comp.lang.perl.bio.general/23732/match=contig)


Commit: e8c205cfcdca084a96765112ae0832f04b52b4fe
    https://github.com/bioperl/bioperl-live/commit/e8c205cfcdca084a96765112ae0832f04b52b4fe
Author: hyphaltip <jason at bioperl.org>
Date:   2010-12-21 (Tue, 21 Dec 2010)

Changed paths:
  M Bio/Tools/GFF.pm

Log Message:
-----------
use the proper method names - get_XXX instead of _each_XXX


Commit: 8b00b61d8641c636ad33e420197b9b7fc452ef42
    https://github.com/bioperl/bioperl-live/commit/8b00b61d8641c636ad33e420197b9b7fc452ef42
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-12-22 (Wed, 22 Dec 2010)

Changed paths:
  M Bio/SeqIO/embl.pm
  M t/SeqIO/embl.t

Log Message:
-----------
deal with OX lines and TaxIDs (patch courtesy Jacob Bunk Nielsen)


Commit: 7a1dc960f9155396579a907ddcc03c5c37a35421
    https://github.com/bioperl/bioperl-live/commit/7a1dc960f9155396579a907ddcc03c5c37a35421
Author: hyphaltip <jason at bioperl.org>
Date:   2010-12-27 (Mon, 27 Dec 2010)

Changed paths:
  M Bio/DB/Taxonomy/flatfile.pm

Log Message:
-----------
missing comma in SYNPOSIS pdoc


Commit: 67d8f4b5a4158c58242dcbb0303c035425f4ea63
    https://github.com/bioperl/bioperl-live/commit/67d8f4b5a4158c58242dcbb0303c035425f4ea63
Author: hyphaltip <jason at bioperl.org>
Date:   2010-12-27 (Mon, 27 Dec 2010)

Changed paths:
  M Bio/SeqIO/embl.pm
  M t/SeqIO/embl.t

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: 0e04486ca4cc2e61fd72b8939f444aec6100aba1
    https://github.com/bioperl/bioperl-live/commit/0e04486ca4cc2e61fd72b8939f444aec6100aba1
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-03 (Mon, 03 Jan 2011)

Changed paths:
  M Bio/SeqIO.pm
  A t/SeqIO/SeqIO.t

Log Message:
-----------
tweak SeqIO to catch odd file types, add generic SeqIO-specific tests (just exception checking for now)


Commit: 53a0361e42fa6cad0afe2ecbbe404a84b5ecb657
    https://github.com/bioperl/bioperl-live/commit/53a0361e42fa6cad0afe2ecbbe404a84b5ecb657
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-11 (Tue, 11 Jan 2011)

Log Message:
-----------
Merge branch 'master', remote branch 'origin'


Commit: 1ef6600ac4fef830844a86ea44afe8aa18d465ec
    https://github.com/bioperl/bioperl-live/commit/1ef6600ac4fef830844a86ea44afe8aa18d465ec
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-18 (Tue, 18 Jan 2011)

Changed paths:
  M Bio/PrimarySeqI.pm
  M Bio/Tools/CodonTable.pm
  M t/Seq/Seq.t

Log Message:
-----------
rectify a conflict in behavior between PrimarySeq::translate and CodonTable::translate(); sequences to be translated are not automatically assumed to be codons, add a flag (-complete_codons) that allows partial codons to be translated, but off by default (thanks to Amir Karger for pointing this out)


Commit: 68979de93da4b0559c80860d77e2f8ff5d87ed49
    https://github.com/bioperl/bioperl-live/commit/68979de93da4b0559c80860d77e2f8ff5d87ed49
Author: Johan Viklund <johan.viklund at gmail.com>
Date:   2011-01-25 (Tue, 25 Jan 2011)

Changed paths:
  R .shipit
  M Bio/Align/AlignI.pm
  M Bio/Align/DNAStatistics.pm
  M Bio/Align/PairwiseStatistics.pm
  M Bio/Align/ProteinStatistics.pm
  M Bio/Align/StatisticsI.pm
  M Bio/Align/Utilities.pm
  M Bio/AlignIO.pm
  M Bio/AlignIO/arp.pm
  M Bio/AlignIO/bl2seq.pm
  M Bio/AlignIO/clustalw.pm
  M Bio/AlignIO/emboss.pm
  M Bio/AlignIO/fasta.pm
  M Bio/AlignIO/maf.pm
  M Bio/AlignIO/mase.pm
  M Bio/AlignIO/mega.pm
  M Bio/AlignIO/meme.pm
  M Bio/AlignIO/metafasta.pm
  M Bio/AlignIO/msf.pm
  M Bio/AlignIO/nexml.pm
  M Bio/AlignIO/nexus.pm
  M Bio/AlignIO/pfam.pm
  M Bio/AlignIO/phylip.pm
  M Bio/AlignIO/proda.pm
  M Bio/AlignIO/prodom.pm
  M Bio/AlignIO/psi.pm
  M Bio/AlignIO/selex.pm
  M Bio/AlignIO/stockholm.pm
  M Bio/AlignIO/xmfa.pm
  M Bio/AnalysisI.pm
  M Bio/AnalysisParserI.pm
  M Bio/AnalysisResultI.pm
  M Bio/AnnotatableI.pm
  M Bio/Annotation/AnnotationFactory.pm
  M Bio/Annotation/Collection.pm
  M Bio/Annotation/Comment.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Annotation/OntologyTerm.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/SimpleValue.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Annotation/Target.pm
  M Bio/Annotation/TypeManager.pm
  M Bio/AnnotationCollectionI.pm
  M Bio/AnnotationI.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/ContigAnalysis.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/bowtie.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Scaffold.pm
  M Bio/Assembly/ScaffoldI.pm
  M Bio/Assembly/Singlet.pm
  M Bio/Assembly/Tools/ContigSpectrum.pm
  M Bio/Biblio.pm
  M Bio/Biblio/Article.pm
  M Bio/Biblio/BiblioBase.pm
  M Bio/Biblio/Book.pm
  M Bio/Biblio/BookArticle.pm
  M Bio/Biblio/IO.pm
  M Bio/Biblio/IO/medline2ref.pm
  M Bio/Biblio/IO/medlinexml.pm
  M Bio/Biblio/IO/pubmed2ref.pm
  M Bio/Biblio/IO/pubmedxml.pm
  M Bio/Biblio/Journal.pm
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  M Bio/Biblio/MedlineArticle.pm
  M Bio/Biblio/MedlineBook.pm
  M Bio/Biblio/MedlineBookArticle.pm
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  M Bio/Biblio/Organisation.pm
  M Bio/Biblio/Patent.pm
  M Bio/Biblio/Person.pm
  M Bio/Biblio/Proceeding.pm
  M Bio/Biblio/Provider.pm
  M Bio/Biblio/PubmedArticle.pm
  M Bio/Biblio/PubmedBookArticle.pm
  M Bio/Biblio/PubmedJournalArticle.pm
  M Bio/Biblio/Ref.pm
  M Bio/Biblio/Service.pm
  M Bio/Biblio/TechReport.pm
  M Bio/Biblio/Thesis.pm
  M Bio/Biblio/WebResource.pm
  M Bio/Cluster/ClusterFactory.pm
  M Bio/Cluster/SequenceFamily.pm
  M Bio/Cluster/UniGene.pm
  M Bio/Cluster/UniGeneI.pm
  M Bio/ClusterI.pm
  M Bio/ClusterIO.pm
  M Bio/ClusterIO/dbsnp.pm
  M Bio/ClusterIO/unigene.pm
  M Bio/CodonUsage/IO.pm
  M Bio/CodonUsage/Table.pm
  M Bio/Coordinate/Chain.pm
  M Bio/Coordinate/Collection.pm
  M Bio/Coordinate/ExtrapolatingPair.pm
  M Bio/Coordinate/GeneMapper.pm
  M Bio/Coordinate/Graph.pm
  M Bio/Coordinate/MapperI.pm
  M Bio/Coordinate/Pair.pm
  M Bio/Coordinate/Result.pm
  M Bio/Coordinate/Result/Gap.pm
  M Bio/Coordinate/Result/Match.pm
  M Bio/Coordinate/ResultI.pm
  M Bio/Coordinate/Utils.pm
  M Bio/DB/Ace.pm
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/Biblio/eutils.pm
  M Bio/DB/Biblio/soap.pm
  M Bio/DB/BiblioI.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/CUTG.pm
  M Bio/DB/DBFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/EUtilities.pm
  M Bio/DB/EntrezGene.pm
  M Bio/DB/Expression.pm
  M Bio/DB/Failover.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/FileCache.pm
  M Bio/DB/Flat.pm
  M Bio/DB/Flat/BDB.pm
  M Bio/DB/Flat/BDB/embl.pm
  M Bio/DB/Flat/BDB/fasta.pm
  M Bio/DB/Flat/BDB/genbank.pm
  M Bio/DB/Flat/BDB/swiss.pm
  M Bio/DB/Flat/BinarySearch.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/berkeleydb.pm
  M Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/mysql.pm
  M Bio/DB/GFF/Adaptor/dbi/oracle.pm
  M Bio/DB/GFF/Adaptor/dbi/pg.pm
  M Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
  M Bio/DB/GFF/Adaptor/memory.pm
  M Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
  M Bio/DB/GFF/Adaptor/memory/iterator.pm
  M Bio/DB/GenBank.pm
  M Bio/DB/GenPept.pm
  M Bio/DB/GenericWebAgent.pm
  M Bio/DB/InMemoryCache.pm
  M Bio/DB/LocationI.pm
  M Bio/DB/MeSH.pm
  M Bio/DB/NCBIHelper.pm
  M Bio/DB/Qual.pm
  M Bio/DB/Query/GenBank.pm
  M Bio/DB/Query/WebQuery.pm
  M Bio/DB/QueryI.pm
  M Bio/DB/RandomAccessI.pm
  M Bio/DB/RefSeq.pm
  M Bio/DB/ReferenceI.pm
  M Bio/DB/Registry.pm
  M Bio/DB/SeqFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeatureI.pm
  M Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
  M Bio/DB/SeqFeature/Segment.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Iterator.pm
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/LoadHelper.pm
  M Bio/DB/SeqFeature/Store/Loader.pm
  M Bio/DB/SeqFeature/Store/bdb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M Bio/DB/SeqI.pm
  M Bio/DB/SeqVersion.pm
  M Bio/DB/SeqVersion/gi.pm
  M Bio/DB/SwissProt.pm
  M Bio/DB/Taxonomy.pm
  M Bio/DB/Taxonomy/entrez.pm
  M Bio/DB/Taxonomy/flatfile.pm
  M Bio/DB/Taxonomy/list.pm
  M Bio/DB/UpdateableSeqI.pm
  M Bio/DB/WebDBSeqI.pm
  M Bio/DBLinkContainerI.pm
  M Bio/Das/FeatureTypeI.pm
  M Bio/Das/SegmentI.pm
  M Bio/DasI.pm
  M Bio/DescribableI.pm
  M Bio/Event/EventGeneratorI.pm
  M Bio/Event/EventHandlerI.pm
  R Bio/Expression/Contact.pm
  R Bio/Expression/DataSet.pm
  R Bio/Expression/FeatureGroup.pm
  R Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
  R Bio/Expression/FeatureI.pm
  R Bio/Expression/FeatureSet/FeatureSetMas50.pm
  R Bio/Expression/Platform.pm
  R Bio/Expression/ProbeI.pm
  R Bio/Expression/Sample.pm
  M Bio/Factory/AnalysisI.pm
  M Bio/Factory/ApplicationFactoryI.pm
  M Bio/Factory/DriverFactory.pm
  M Bio/Factory/FTLocationFactory.pm
  M Bio/Factory/LocationFactoryI.pm
  M Bio/Factory/MapFactoryI.pm
  M Bio/Factory/ObjectBuilderI.pm
  M Bio/Factory/ObjectFactory.pm
  M Bio/Factory/ObjectFactoryI.pm
  M Bio/Factory/SeqAnalysisParserFactory.pm
  M Bio/Factory/SeqAnalysisParserFactoryI.pm
  M Bio/Factory/SequenceFactoryI.pm
  M Bio/Factory/SequenceProcessorI.pm
  M Bio/Factory/SequenceStreamI.pm
  M Bio/Factory/TreeFactoryI.pm
  M Bio/FeatureHolderI.pm
  M Bio/FeatureIO.pm
  M Bio/FeatureIO/gff.pm
  M Bio/FeatureIO/gtf.pm
  M Bio/HandlerBaseI.pm
  M Bio/IdCollectionI.pm
  M Bio/IdentifiableI.pm
  M Bio/Index/Abstract.pm
  M Bio/Index/AbstractSeq.pm
  M Bio/Index/Blast.pm
  M Bio/Index/BlastTable.pm
  M Bio/Index/EMBL.pm
  M Bio/Index/Fasta.pm
  M Bio/Index/GenBank.pm
  M Bio/Index/Qual.pm
  M Bio/Index/Stockholm.pm
  M Bio/Index/SwissPfam.pm
  M Bio/Index/Swissprot.pm
  M Bio/LiveSeq/AARange.pm
  M Bio/LiveSeq/Chain.pm
  M Bio/LiveSeq/ChainI.pm
  M Bio/LiveSeq/DNA.pm
  M Bio/LiveSeq/Exon.pm
  M Bio/LiveSeq/Gene.pm
  M Bio/LiveSeq/IO/BioPerl.pm
  M Bio/LiveSeq/IO/Loader.pm
  M Bio/LiveSeq/Intron.pm
  M Bio/LiveSeq/Mutation.pm
  M Bio/LiveSeq/Mutator.pm
  M Bio/LiveSeq/Prim_Transcript.pm
  M Bio/LiveSeq/Range.pm
  M Bio/LiveSeq/Repeat_Region.pm
  M Bio/LiveSeq/Repeat_Unit.pm
  M Bio/LiveSeq/SeqI.pm
  M Bio/LiveSeq/Transcript.pm
  M Bio/LiveSeq/Translation.pm
  M Bio/LocatableSeq.pm
  M Bio/Location/Atomic.pm
  M Bio/Location/AvWithinCoordPolicy.pm
  M Bio/Location/CoordinatePolicyI.pm
  M Bio/Location/Fuzzy.pm
  M Bio/Location/FuzzyLocationI.pm
  M Bio/Location/NarrowestCoordPolicy.pm
  M Bio/Location/Simple.pm
  M Bio/Location/Split.pm
  M Bio/Location/SplitLocationI.pm
  M Bio/Location/WidestCoordPolicy.pm
  M Bio/LocationI.pm
  M Bio/Map/Clone.pm
  M Bio/Map/Contig.pm
  M Bio/Map/CytoMap.pm
  M Bio/Map/CytoMarker.pm
  M Bio/Map/CytoPosition.pm
  M Bio/Map/EntityI.pm
  M Bio/Map/FPCMarker.pm
  M Bio/Map/MapI.pm
  M Bio/Map/Mappable.pm
  M Bio/Map/MappableI.pm
  M Bio/Map/Marker.pm
  M Bio/Map/MarkerI.pm
  M Bio/Map/Physical.pm
  M Bio/Map/Position.pm
  M Bio/Map/PositionHandler.pm
  M Bio/Map/PositionHandlerI.pm
  M Bio/Map/PositionI.pm
  M Bio/Map/Relative.pm
  M Bio/Map/RelativeI.pm
  M Bio/Map/SimpleMap.pm
  M Bio/MapIO.pm
  M Bio/MapIO/mapmaker.pm
  M Bio/Matrix/Generic.pm
  M Bio/Matrix/IO.pm
  M Bio/Matrix/IO/mlagan.pm
  M Bio/Matrix/IO/phylip.pm
  M Bio/Matrix/IO/scoring.pm
  M Bio/Matrix/Mlagan.pm
  M Bio/Matrix/PSM/IO.pm
  M Bio/Matrix/PSM/IO/mast.pm
  M Bio/Matrix/PSM/IO/masta.pm
  M Bio/Matrix/PSM/IO/meme.pm
  M Bio/Matrix/PSM/IO/psiblast.pm
  M Bio/Matrix/PSM/IO/transfac.pm
  M Bio/Matrix/PSM/InstanceSite.pm
  M Bio/Matrix/PSM/InstanceSiteI.pm
  M Bio/Matrix/PSM/ProtMatrix.pm
  M Bio/Matrix/PSM/ProtPsm.pm
  M Bio/Matrix/PSM/Psm.pm
  M Bio/Matrix/PSM/PsmHeader.pm
  M Bio/Matrix/PSM/PsmHeaderI.pm
  M Bio/Matrix/PSM/PsmI.pm
  M Bio/Matrix/PSM/SiteMatrix.pm
  M Bio/Matrix/PSM/SiteMatrixI.pm
  M Bio/Matrix/PhylipDist.pm
  M Bio/Matrix/Scoring.pm
  R Bio/Microarray/Tools/MitoChipV2Parser.pm
  R Bio/Microarray/Tools/ReseqChip.pm
  M Bio/MolEvol/CodonModel.pm
  M Bio/Ontology/DocumentRegistry.pm
  M Bio/Ontology/GOterm.pm
  M Bio/Ontology/InterProTerm.pm
  M Bio/Ontology/OBOEngine.pm
  M Bio/Ontology/OBOterm.pm
  M Bio/Ontology/Ontology.pm
  M Bio/Ontology/OntologyEngineI.pm
  M Bio/Ontology/OntologyI.pm
  M Bio/Ontology/OntologyStore.pm
  M Bio/Ontology/Path.pm
  M Bio/Ontology/PathI.pm
  M Bio/Ontology/Relationship.pm
  M Bio/Ontology/RelationshipFactory.pm
  M Bio/Ontology/RelationshipI.pm
  M Bio/Ontology/RelationshipType.pm
  M Bio/Ontology/SimpleOntologyEngine.pm
  M Bio/Ontology/Term.pm
  M Bio/Ontology/TermFactory.pm
  M Bio/Ontology/TermI.pm
  M Bio/OntologyIO.pm
  M Bio/OntologyIO/Handlers/BaseSAXHandler.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
  M Bio/OntologyIO/InterProParser.pm
  M Bio/OntologyIO/dagflat.pm
  M Bio/OntologyIO/goflat.pm
  M Bio/OntologyIO/obo.pm
  M Bio/OntologyIO/simplehierarchy.pm
  M Bio/OntologyIO/soflat.pm
  M Bio/ParameterBaseI.pm
  M Bio/Perl.pm
  M Bio/Phenotype/Correlate.pm
  M Bio/Phenotype/MeSH/Term.pm
  M Bio/Phenotype/MeSH/Twig.pm
  M Bio/Phenotype/Measure.pm
  M Bio/Phenotype/OMIM/MiniMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
  M Bio/Phenotype/OMIM/OMIMparser.pm
  M Bio/Phenotype/Phenotype.pm
  M Bio/Phenotype/PhenotypeI.pm
  M Bio/PhyloNetwork.pm
  M Bio/PhyloNetwork/Factory.pm
  M Bio/PhyloNetwork/FactoryX.pm
  M Bio/PhyloNetwork/GraphViz.pm
  M Bio/PhyloNetwork/RandomFactory.pm
  M Bio/PhyloNetwork/TreeFactory.pm
  M Bio/PhyloNetwork/TreeFactoryMulti.pm
  M Bio/PhyloNetwork/TreeFactoryX.pm
  M Bio/PhyloNetwork/muVector.pm
  M Bio/PopGen/Genotype.pm
  M Bio/PopGen/IO.pm
  M Bio/PopGen/IO/csv.pm
  M Bio/PopGen/IO/hapmap.pm
  M Bio/PopGen/IO/phase.pm
  M Bio/PopGen/IO/prettybase.pm
  M Bio/PopGen/Individual.pm
  M Bio/PopGen/Marker.pm
  M Bio/PopGen/PopStats.pm
  M Bio/PopGen/Population.pm
  M Bio/PopGen/PopulationI.pm
  M Bio/PopGen/Simulation/Coalescent.pm
  M Bio/PopGen/Simulation/GeneticDrift.pm
  M Bio/PopGen/Statistics.pm
  M Bio/PopGen/Utilities.pm
  M Bio/PrimarySeq.pm
  M Bio/PrimarySeqI.pm
  M Bio/PullParserI.pm
  M Bio/Range.pm
  M Bio/RangeI.pm
  M Bio/Restriction/Analysis.pm
  M Bio/Restriction/Enzyme.pm
  M Bio/Restriction/Enzyme/MultiCut.pm
  M Bio/Restriction/Enzyme/MultiSite.pm
  M Bio/Restriction/EnzymeCollection.pm
  M Bio/Restriction/EnzymeI.pm
  M Bio/Restriction/IO.pm
  M Bio/Restriction/IO/bairoch.pm
  M Bio/Restriction/IO/base.pm
  M Bio/Restriction/IO/itype2.pm
  M Bio/Restriction/IO/prototype.pm
  M Bio/Restriction/IO/withrefm.pm
  M Bio/Root/Build.pm
  M Bio/Root/Exception.pm
  M Bio/Root/HTTPget.pm
  M Bio/Root/IO.pm
  M Bio/Root/Root.pm
  M Bio/Root/RootI.pm
  M Bio/Root/Storable.pm
  M Bio/Root/Test.pm
  M Bio/Root/Test/Warn.pm
  M Bio/Root/Utilities.pm
  M Bio/Root/Version.pm
  M Bio/Search/DatabaseI.pm
  M Bio/Search/GenericDatabase.pm
  M Bio/Search/HSP/BlastHSP.pm
  M Bio/Search/HSP/BlastPullHSP.pm
  M Bio/Search/HSP/FastaHSP.pm
  M Bio/Search/HSP/GenericHSP.pm
  M Bio/Search/HSP/HMMERHSP.pm
  M Bio/Search/HSP/HSPFactory.pm
  M Bio/Search/HSP/HSPI.pm
  M Bio/Search/HSP/HmmpfamHSP.pm
  M Bio/Search/HSP/ModelHSP.pm
  M Bio/Search/HSP/PSLHSP.pm
  M Bio/Search/HSP/PsiBlastHSP.pm
  M Bio/Search/HSP/PullHSPI.pm
  M Bio/Search/HSP/WABAHSP.pm
  A Bio/Search/HSP/hmmer3HSP.pm
  M Bio/Search/Hit/BlastHit.pm
  M Bio/Search/Hit/BlastPullHit.pm
  M Bio/Search/Hit/Fasta.pm
  M Bio/Search/Hit/GenericHit.pm
  M Bio/Search/Hit/HMMERHit.pm
  M Bio/Search/Hit/HitFactory.pm
  M Bio/Search/Hit/HitI.pm
  M Bio/Search/Hit/HmmpfamHit.pm
  M Bio/Search/Hit/ModelHit.pm
  M Bio/Search/Hit/PsiBlastHit.pm
  M Bio/Search/Hit/PullHitI.pm
  A Bio/Search/Hit/hmmer3Hit.pm
  M Bio/Search/Iteration/GenericIteration.pm
  M Bio/Search/Iteration/IterationI.pm
  M Bio/Search/Result/BlastPullResult.pm
  M Bio/Search/Result/BlastResult.pm
  M Bio/Search/Result/CrossMatchResult.pm
  M Bio/Search/Result/GenericResult.pm
  M Bio/Search/Result/HMMERResult.pm
  M Bio/Search/Result/HmmpfamResult.pm
  M Bio/Search/Result/PullResultI.pm
  M Bio/Search/Result/ResultFactory.pm
  M Bio/Search/Result/ResultI.pm
  M Bio/Search/Result/WABAResult.pm
  A Bio/Search/Result/hmmer3Result.pm
  M Bio/Search/Tiling/MapTiling.pm
  M Bio/Search/Tiling/TilingI.pm
  M Bio/SearchDist.pm
  M Bio/SearchIO.pm
  M Bio/SearchIO/EventHandlerI.pm
  M Bio/SearchIO/FastHitEventBuilder.pm
  M Bio/SearchIO/IteratedSearchResultEventBuilder.pm
  M Bio/SearchIO/SearchResultEventBuilder.pm
  M Bio/SearchIO/SearchWriterI.pm
  M Bio/SearchIO/Writer/BSMLResultWriter.pm
  M Bio/SearchIO/Writer/GbrowseGFF.pm
  M Bio/SearchIO/Writer/HSPTableWriter.pm
  M Bio/SearchIO/Writer/HTMLResultWriter.pm
  M Bio/SearchIO/Writer/HitTableWriter.pm
  M Bio/SearchIO/Writer/ResultTableWriter.pm
  M Bio/SearchIO/Writer/TextResultWriter.pm
  M Bio/SearchIO/XML/BlastHandler.pm
  M Bio/SearchIO/XML/PsiBlastHandler.pm
  M Bio/SearchIO/axt.pm
  M Bio/SearchIO/blast.pm
  M Bio/SearchIO/blast_pull.pm
  M Bio/SearchIO/blasttable.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SearchIO/cross_match.pm
  M Bio/SearchIO/erpin.pm
  M Bio/SearchIO/exonerate.pm
  M Bio/SearchIO/fasta.pm
  M Bio/SearchIO/hmmer.pm
  A Bio/SearchIO/hmmer2.pm
  A Bio/SearchIO/hmmer3.pm
  M Bio/SearchIO/hmmer_pull.pm
  M Bio/SearchIO/infernal.pm
  M Bio/SearchIO/megablast.pm
  M Bio/SearchIO/psl.pm
  M Bio/SearchIO/rnamotif.pm
  M Bio/SearchIO/sim4.pm
  M Bio/SearchIO/waba.pm
  M Bio/SearchIO/wise.pm
  M Bio/Seq.pm
  M Bio/Seq/BaseSeqProcessor.pm
  M Bio/Seq/EncodedSeq.pm
  M Bio/Seq/LargePrimarySeq.pm
  M Bio/Seq/LargeSeq.pm
  M Bio/Seq/LargeSeqI.pm
  M Bio/Seq/Meta.pm
  M Bio/Seq/Meta/Array.pm
  M Bio/Seq/MetaI.pm
  M Bio/Seq/PrimaryQual.pm
  M Bio/Seq/PrimedSeq.pm
  M Bio/Seq/QualI.pm
  M Bio/Seq/Quality.pm
  M Bio/Seq/RichSeq.pm
  M Bio/Seq/RichSeqI.pm
  M Bio/Seq/SeqBuilder.pm
  M Bio/Seq/SeqFactory.pm
  M Bio/Seq/SeqFastaSpeedFactory.pm
  M Bio/Seq/SeqWithQuality.pm
  M Bio/Seq/SequenceTrace.pm
  M Bio/SeqAnalysisParserI.pm
  M Bio/SeqEvolution/DNAPoint.pm
  M Bio/SeqEvolution/EvolutionI.pm
  M Bio/SeqEvolution/Factory.pm
  M Bio/SeqFeature/Annotated.pm
  M Bio/SeqFeature/AnnotationAdaptor.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/CollectionI.pm
  M Bio/SeqFeature/Computation.pm
  M Bio/SeqFeature/FeaturePair.pm
  M Bio/SeqFeature/Gene/Exon.pm
  M Bio/SeqFeature/Gene/ExonI.pm
  M Bio/SeqFeature/Gene/GeneStructure.pm
  M Bio/SeqFeature/Gene/GeneStructureI.pm
  M Bio/SeqFeature/Gene/Intron.pm
  M Bio/SeqFeature/Gene/NC_Feature.pm
  M Bio/SeqFeature/Gene/Poly_A_site.pm
  M Bio/SeqFeature/Gene/Promoter.pm
  M Bio/SeqFeature/Gene/Transcript.pm
  M Bio/SeqFeature/Gene/TranscriptI.pm
  M Bio/SeqFeature/Gene/UTR.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeature/Lite.pm
  M Bio/SeqFeature/PositionProxy.pm
  M Bio/SeqFeature/Primer.pm
  M Bio/SeqFeature/SiRNA/Oligo.pm
  M Bio/SeqFeature/SiRNA/Pair.pm
  M Bio/SeqFeature/Similarity.pm
  M Bio/SeqFeature/SimilarityPair.pm
  M Bio/SeqFeature/Tools/FeatureNamer.pm
  M Bio/SeqFeature/Tools/IDHandler.pm
  M Bio/SeqFeature/Tools/TypeMapper.pm
  M Bio/SeqFeature/Tools/Unflattener.pm
  M Bio/SeqFeature/TypedSeqFeatureI.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/FTHelper.pm
  M Bio/SeqIO/Handler/GenericRichSeqHandler.pm
  M Bio/SeqIO/MultiFile.pm
  M Bio/SeqIO/abi.pm
  M Bio/SeqIO/ace.pm
  M Bio/SeqIO/alf.pm
  M Bio/SeqIO/asciitree.pm
  M Bio/SeqIO/bsml_sax.pm
  M Bio/SeqIO/chadoxml.pm
  M Bio/SeqIO/chaos.pm
  M Bio/SeqIO/chaosxml.pm
  M Bio/SeqIO/ctf.pm
  M Bio/SeqIO/embl.pm
  M Bio/SeqIO/embldriver.pm
  M Bio/SeqIO/entrezgene.pm
  M Bio/SeqIO/excel.pm
  M Bio/SeqIO/exp.pm
  M Bio/SeqIO/fasta.pm
  M Bio/SeqIO/fastq.pm
  M Bio/SeqIO/flybase_chadoxml.pm
  M Bio/SeqIO/game.pm
  M Bio/SeqIO/game/featHandler.pm
  M Bio/SeqIO/game/gameSubs.pm
  M Bio/SeqIO/game/gameWriter.pm
  M Bio/SeqIO/game/seqHandler.pm
  M Bio/SeqIO/gbdriver.pm
  M Bio/SeqIO/gcg.pm
  M Bio/SeqIO/genbank.pm
  M Bio/SeqIO/interpro.pm
  M Bio/SeqIO/kegg.pm
  M Bio/SeqIO/largefasta.pm
  M Bio/SeqIO/lasergene.pm
  M Bio/SeqIO/locuslink.pm
  A Bio/SeqIO/mbsout.pm
  M Bio/SeqIO/metafasta.pm
  A Bio/SeqIO/msout.pm
  M Bio/SeqIO/nexml.pm
  M Bio/SeqIO/phd.pm
  M Bio/SeqIO/pir.pm
  M Bio/SeqIO/pln.pm
  M Bio/SeqIO/qual.pm
  M Bio/SeqIO/raw.pm
  M Bio/SeqIO/scf.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/SeqIO/strider.pm
  M Bio/SeqIO/swiss.pm
  M Bio/SeqIO/swissdriver.pm
  M Bio/SeqIO/tab.pm
  M Bio/SeqIO/table.pm
  M Bio/SeqIO/tigr.pm
  M Bio/SeqIO/tigrxml.pm
  M Bio/SeqIO/ztr.pm
  M Bio/SeqUtils.pm
  M Bio/SimpleAlign.pm
  M Bio/SimpleAnalysisI.pm
  M Bio/Species.pm
  M Bio/Structure/Atom.pm
  M Bio/Structure/Chain.pm
  M Bio/Structure/Entry.pm
  M Bio/Structure/IO.pm
  M Bio/Structure/IO/pdb.pm
  M Bio/Structure/Model.pm
  M Bio/Structure/Residue.pm
  M Bio/Structure/StructureI.pm
  M Bio/Symbol/Alphabet.pm
  M Bio/Symbol/AlphabetI.pm
  M Bio/Symbol/DNAAlphabet.pm
  M Bio/Symbol/ProteinAlphabet.pm
  M Bio/Symbol/Symbol.pm
  M Bio/Symbol/SymbolI.pm
  M Bio/Taxon.pm
  M Bio/Taxonomy.pm
  M Bio/Taxonomy/Node.pm
  M Bio/Taxonomy/Taxon.pm
  M Bio/Taxonomy/Tree.pm
  M Bio/Tools/AlignFactory.pm
  M Bio/Tools/Alignment/Consed.pm
  M Bio/Tools/Alignment/Trim.pm
  M Bio/Tools/Analysis/DNA/ESEfinder.pm
  M Bio/Tools/Analysis/Protein/ELM.pm
  M Bio/Tools/Analysis/Protein/NetPhos.pm
  M Bio/Tools/Analysis/Protein/Scansite.pm
  M Bio/Tools/Analysis/SimpleAnalysisBase.pm
  M Bio/Tools/AnalysisResult.pm
  M Bio/Tools/Blat.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/Coil.pm
  M Bio/Tools/ECnumber.pm
  M Bio/Tools/EMBOSS/Palindrome.pm
  M Bio/Tools/EPCR.pm
  M Bio/Tools/ERPIN.pm
  M Bio/Tools/ESTScan.pm
  M Bio/Tools/EUtilities.pm
  R Bio/Tools/EUtilities/Cookie.pm
  M Bio/Tools/EUtilities/EUtilDataI.pm
  M Bio/Tools/EUtilities/EUtilParameters.pm
  M Bio/Tools/EUtilities/History.pm
  M Bio/Tools/EUtilities/HistoryI.pm
  M Bio/Tools/EUtilities/Info.pm
  M Bio/Tools/EUtilities/Info/FieldInfo.pm
  M Bio/Tools/EUtilities/Info/LinkInfo.pm
  M Bio/Tools/EUtilities/Link.pm
  M Bio/Tools/EUtilities/Link/LinkSet.pm
  M Bio/Tools/EUtilities/Link/UrlLink.pm
  M Bio/Tools/EUtilities/Query.pm
  M Bio/Tools/EUtilities/Query/GlobalQuery.pm
  M Bio/Tools/EUtilities/Summary.pm
  M Bio/Tools/EUtilities/Summary/DocSum.pm
  M Bio/Tools/EUtilities/Summary/Item.pm
  M Bio/Tools/EUtilities/Summary/ItemContainerI.pm
  M Bio/Tools/Eponine.pm
  M Bio/Tools/Est2Genome.pm
  M Bio/Tools/Fgenesh.pm
  M Bio/Tools/FootPrinter.pm
  M Bio/Tools/GFF.pm
  M Bio/Tools/Gel.pm
  M Bio/Tools/Geneid.pm
  M Bio/Tools/Genemark.pm
  M Bio/Tools/Genewise.pm
  M Bio/Tools/Genomewise.pm
  M Bio/Tools/Genscan.pm
  M Bio/Tools/Glimmer.pm
  M Bio/Tools/Grail.pm
  M Bio/Tools/GuessSeqFormat.pm
  M Bio/Tools/HMMER/Domain.pm
  M Bio/Tools/HMMER/Results.pm
  M Bio/Tools/HMMER/Set.pm
  M Bio/Tools/Hmmpfam.pm
  M Bio/Tools/IUPAC.pm
  M Bio/Tools/Infernal.pm
  M Bio/Tools/Lucy.pm
  M Bio/Tools/MZEF.pm
  M Bio/Tools/Phylo/Gumby.pm
  M Bio/Tools/Phylo/Molphy.pm
  M Bio/Tools/Phylo/Molphy/Result.pm
  M Bio/Tools/Phylo/PAML.pm
  M Bio/Tools/Phylo/PAML/Codeml.pm
  M Bio/Tools/Phylo/PAML/ModelResult.pm
  M Bio/Tools/Phylo/PAML/Result.pm
  M Bio/Tools/Phylo/Phylip/ProtDist.pm
  M Bio/Tools/Prediction/Exon.pm
  M Bio/Tools/Prediction/Gene.pm
  M Bio/Tools/Primer/Assessor/Base.pm
  M Bio/Tools/Primer/AssessorI.pm
  M Bio/Tools/Primer/Feature.pm
  M Bio/Tools/Primer/Pair.pm
  M Bio/Tools/Primer3.pm
  M Bio/Tools/Prints.pm
  M Bio/Tools/Profile.pm
  M Bio/Tools/Promoterwise.pm
  M Bio/Tools/Protparam.pm
  M Bio/Tools/Pseudowise.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RNAMotif.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/RepeatMasker.pm
  M Bio/Tools/Run/GenericParameters.pm
  M Bio/Tools/Run/ParametersI.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/StandAloneWUBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  A Bio/Tools/Run/hmmer3.pm
  M Bio/Tools/Seg.pm
  M Bio/Tools/SeqPattern.pm
  M Bio/Tools/SeqStats.pm
  M Bio/Tools/SeqWords.pm
  M Bio/Tools/SiRNA.pm
  M Bio/Tools/Sigcleave.pm
  M Bio/Tools/Signalp.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/Sim4/Exon.pm
  M Bio/Tools/Sim4/Results.pm
  M Bio/Tools/Spidey/Exon.pm
  M Bio/Tools/Spidey/Results.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/Tmhmm.pm
  M Bio/Tools/dpAlign.pm
  M Bio/Tools/ipcress.pm
  M Bio/Tools/isPcr.pm
  M Bio/Tools/pICalculator.pm
  M Bio/Tools/pSW.pm
  M Bio/Tools/tRNAscanSE.pm
  M Bio/Tree/AlleleNode.pm
  M Bio/Tree/Compatible.pm
  M Bio/Tree/DistanceFactory.pm
  M Bio/Tree/Draw/Cladogram.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/NodeI.pm
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/RandomFactory.pm
  M Bio/Tree/Statistics.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/Tree/TreeI.pm
  M Bio/TreeIO.pm
  A Bio/TreeIO/NewickParser.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/cluster.pm
  M Bio/TreeIO/lintree.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nexml.pm
  M Bio/TreeIO/nexus.pm
  M Bio/TreeIO/nhx.pm
  M Bio/TreeIO/pag.pm
  M Bio/TreeIO/tabtree.pm
  M Bio/UpdateableSeqI.pm
  M Bio/Variation/AAChange.pm
  M Bio/Variation/AAReverseMutate.pm
  M Bio/Variation/Allele.pm
  M Bio/Variation/DNAMutation.pm
  M Bio/Variation/IO.pm
  M Bio/Variation/IO/flat.pm
  M Bio/Variation/IO/xml.pm
  M Bio/Variation/RNAChange.pm
  M Bio/Variation/SNP.pm
  M Bio/Variation/SeqDiff.pm
  M Bio/Variation/VariantI.pm
  M Bio/WebAgent.pm
  M Build.PL
  M Changes
  M DEPRECATED
  M MANIFEST
  M examples/align/aligntutorial.pl
  M examples/align/clustalw.pl
  M examples/align/simplealign.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/db/dbfetch
  M examples/liveseq/change_gene.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/rev_and_trans.pl
  M examples/root/exceptions1.pl
  M examples/root/exceptions2.pl
  M examples/root/exceptions3.pl
  M examples/root/exceptions4.pl
  M examples/searchio/custom_writer.pl
  M examples/searchio/hitwriter.pl
  M examples/searchio/hspwriter.pl
  M examples/searchio/htmlwriter.pl
  M examples/searchio/psiblast_features.pl
  M examples/searchio/psiblast_iterations.pl
  M examples/searchio/rawwriter.pl
  M examples/searchio/resultwriter.pl
  M examples/tools/extract_genes.pl
  M examples/tools/psw.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M examples/tools/seq_pattern.pl
  M examples/tools/standaloneblast.pl
  M maintenance/authors.pl
  A maintenance/big_split/file_classification.csv
  A maintenance/big_split/rbuels_notes.txt
  M maintenance/cvs2cl_by_file.pl
  M maintenance/modules.pl
  M maintenance/pod.pl
  M maintenance/symlink_script.pl
  M maintenance/version.pl
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff3.PLS
  M scripts/Bio-DB-GFF/generate_histogram.PLS
  M scripts/Bio-DB-GFF/load_gff.PLS
  M scripts/Bio-DB-GFF/process_sgd.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB/biofetch_genbank_proxy.PLS
  M scripts/DB/biogetseq.PLS
  M scripts/DB/flanks.PLS
  M scripts/biblio/biblio.PLS
  A scripts/bioperl_netinstall.pl
  M scripts/das/das_server.pl
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/composite_LD.PLS
  M scripts/popgen/heterogeneity_test.PLS
  M scripts/searchio/filter_search.PLS
  M scripts/searchio/parse_hmmsearch.PLS
  M scripts/seq/extract_feature_seq.PLS
  M scripts/seq/make_mrna_protein.PLS
  M scripts/seq/seqconvert.PLS
  M scripts/seq/seqretsplit.PLS
  M scripts/seq/split_seq.PLS
  M scripts/seq/translate_seq.PLS
  M scripts/seq/unflatten_seq.PLS
  M scripts/seqstats/aacomp.PLS
  M scripts/seqstats/chaos_plot.PLS
  M scripts/seqstats/gccalc.PLS
  M scripts/seqstats/oligo_count.PLS
  M scripts/taxa/classify_hits_kingdom.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/download_query_genbank.PLS
  M scripts/utilities/mask_by_search.PLS
  M scripts/utilities/pairwise_kaks.PLS
  M scripts/utilities/remote_blast.PLS
  M scripts/utilities/revtrans-motif.PLS
  M scripts/utilities/search2BSML.PLS
  M scripts/utilities/search2alnblocks.PLS
  M scripts/utilities/search2gff.PLS
  M scripts/utilities/search2tribe.PLS
  M t/Align/Graphics.t
  M t/AlignIO/phylip.t
  M t/AlignIO/selex.t
  M t/Annotation/Annotation.t
  R t/Assembly/Assembly.t
  M t/Assembly/ContigSpectrum.t
  A t/Assembly/IO/bowtie.t
  A t/Assembly/IO/sam.t
  A t/Assembly/core.t
  M t/LocalDB/DBFasta.t
  M t/LocalDB/SeqFeature.t
  R t/Microarray/Tools/ReseqChip.t
  M t/Ontology/IO/interpro.t
  M t/Ontology/IO/obo.t
  M t/Ontology/Ontology.t
  M t/Ontology/OntologyEngine.t
  M t/RemoteDB/EMBL.t
  M t/RemoteDB/EUtilities.t
  M t/RemoteDB/GenPept.t
  M t/RemoteDB/SwissProt.t
  M t/RemoteDB/Taxonomy.t
  M t/Root/RootI.t
  M t/Root/RootIO.t
  A t/SearchIO/Writer/TextWriter.t
  A t/SearchIO/axt.t
  M t/SearchIO/hmmer.t
  M t/Seq/Seq.t
  A t/SeqFeature/Clone.t
  M t/SeqFeature/SeqFeature.t
  M t/SeqIO/Handler.t
  A t/SeqIO/SeqIO.t
  M t/SeqIO/embl.t
  M t/SeqIO/genbank.t
  A t/SeqIO/mbsout.t
  A t/SeqIO/msout.t
  M t/SeqIO/seqxml.t
  M t/SeqIO/swiss.t
  M t/Species.t
  M t/Tools/Run/StandAloneBlast.t
  M t/Tree/Node.t
  M t/Tree/TreeIO.t
  M t/Tree/TreeIO/newick.t
  M t/Tree/TreeIO/nhx.t
  A t/data/PX1CG.gb
  R t/data/ReseqChip_ExampleData.fasta
  R t/data/ReseqChip_ParamsNcall.csv
  R t/data/ReseqChip_RefSeq.fasta
  R t/data/ReseqChip_mtDNA_design_annotation_file_FINAL.xls
  M t/data/assembly_with_singlets.ace
  A t/data/biorecipe.nhx
  M t/data/dbfa/1.fa
  A t/data/ex1.nucl.nhx
  A t/data/hmmscan.out
  A t/data/hmmscan_multi_domain.out
  A t/data/hmmscan_sec_struct.out
  A t/data/hmmsearch3.out
  A t/data/interpro.xml
  A t/data/interpro_relationship.xml
  A t/data/interpro_sample.xml
  A t/data/mbsout/mbsout_infile1
  A t/data/mbsout/mbsout_infile2
  A t/data/mbsout/mbsout_infile3
  A t/data/msout_infile1
  A t/data/msout_infile1.gz
  A t/data/msout_infile2
  A t/data/msout_infile2.gz
  A t/data/nhx-bacteria.nhx
  M t/data/seqxml.xml
  A t/data/singlet_w_CT.ace
  A t/data/sp_subset.obo
  A t/data/test_data.axt
  M t/data/testaln.selex
  A t/data/tol-2010-02-18.nhx
  A t/data/wellcome_tol.nhx
  M t/lib/Array/Compare.pm

Log Message:
-----------
Merge branch 'master' of git://github.com/bioperl/bioperl-live


Commit: ac84449033e94df2d699641a4d071467cd8497ba
    https://github.com/bioperl/bioperl-live/commit/ac84449033e94df2d699641a4d071467cd8497ba
Author: Johan Viklund <johan.viklund at gmail.com>
Date:   2011-01-26 (Wed, 26 Jan 2011)

Changed paths:
  M Bio/SeqIO/swiss.pm
  M t/SeqIO/swiss.t

Log Message:
-----------
[Bio::SeqIO::swiss] Fixed bug where write_seq() were generating non-standard swiss and added tests for this


Commit: 40069eddd4300602b86ce3873f281b66309e9234
    https://github.com/bioperl/bioperl-live/commit/40069eddd4300602b86ce3873f281b66309e9234
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/SeqFeature/Collection.pm

Log Message:
-----------
RT#47704: recursively remove code refs for any SeqFeatureI


Commit: b1c1c6a866d5b30057d893291668dff8136c03ea
    https://github.com/bioperl/bioperl-live/commit/b1c1c6a866d5b30057d893291668dff8136c03ea
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/SearchIO/blastxml.pm

Log Message:
-----------
[bug RT#54590] add some docs on the -blasttype parameter


Commit: aea9ea9eb36ad64ebc9751d58557744708ed20cb
    https://github.com/bioperl/bioperl-live/commit/aea9ea9eb36ad64ebc9751d58557744708ed20cb
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
[bug RT#58492] small synopsis fix, update->store


Commit: ff6997e78098d6b6b175b08e398ac346be594960
    https://github.com/bioperl/bioperl-live/commit/ff6997e78098d6b6b175b08e398ac346be594960
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Build.PL

Log Message:
-----------
squash minor warning


Commit: b45e2d33984cf283b846d7c146ec9e0e9ebae67f
    https://github.com/bioperl/bioperl-live/commit/b45e2d33984cf283b846d7c146ec9e0e9ebae67f
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/Index/Fastq.pm

Log Message:
-----------
[bug 3165] quick fix for fastq indexing, this parser indexes lines starting with @, which could spell trouble down the road


Commit: 0d979f357b8ec089a05eed56c32c68c7039de741
    https://github.com/bioperl/bioperl-live/commit/0d979f357b8ec089a05eed56c32c68c7039de741
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M t/RemoteDB/SeqVersion.t

Log Message:
-----------
future-proof test


Commit: cd418e38de6dab9a4e0dcbea79c6d3cb158c1f08
    https://github.com/bioperl/bioperl-live/commit/cd418e38de6dab9a4e0dcbea79c6d3cb158c1f08
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/SeqIO.pm

Log Message:
-----------
can have a -string option as well


Commit: 6fffd64dbe689bba604089aee83732670e8780d4
    https://github.com/bioperl/bioperl-live/commit/6fffd64dbe689bba604089aee83732670e8780d4
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M t/Seq/Seq.t

Log Message:
-----------
correct test count


Commit: c67722c41a4281dc57f07aca32f08ca23cd58122
    https://github.com/bioperl/bioperl-live/commit/c67722c41a4281dc57f07aca32f08ca23cd58122
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  R t/SeqIO.t
  M t/SeqIO/SeqIO.t

Log Message:
-----------
consolidate tests, fix exception string


Commit: a92f6aa2ee8d9eb81b6a6ee8edd69093ed31f586
    https://github.com/bioperl/bioperl-live/commit/a92f6aa2ee8d9eb81b6a6ee8edd69093ed31f586
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M t/SeqTools/CodonTable.t

Log Message:
-----------
translate() changes


Commit: 8b6723f4bbc46d2d77cc2594b177580861ec4d48
    https://github.com/bioperl/bioperl-live/commit/8b6723f4bbc46d2d77cc2594b177580861ec4d48
Author: gjuggler <greg at ebi.ac.uk>
Date:   2011-02-07 (Mon, 07 Feb 2011)

Changed paths:
  M Bio/Tree/TreeFunctionsI.pm

Log Message:
-----------
Tiny fix to ascii print method.


Commit: 2bee2b58b0df486d03f1e66811adf8d27434725d
    https://github.com/bioperl/bioperl-live/commit/2bee2b58b0df486d03f1e66811adf8d27434725d
Author: gjuggler <greg at ebi.ac.uk>
Date:   2011-02-07 (Mon, 07 Feb 2011)

Changed paths:
  R .shipit
  M Bio/Assembly/IO/ace.pm
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/Biblio/eutils.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GenBank.pm
  M Bio/DB/RefSeq.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SwissProt.pm
  M Bio/DB/Taxonomy/flatfile.pm
  M Bio/Event/EventHandlerI.pm
  M Bio/Index/Fastq.pm
  M Bio/Ontology/SimpleOntologyEngine.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M Bio/PrimarySeqI.pm
  M Bio/Search/HSP/FastaHSP.pm
  M Bio/Search/HSP/GenericHSP.pm
  M Bio/SearchIO.pm
  M Bio/SearchIO/Writer/TextResultWriter.pm
  M Bio/SearchIO/axt.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SearchIO/fasta.pm
  M Bio/SearchIO/hmmer.pm
  A Bio/SearchIO/hmmer2.pm
  M Bio/SearchIO/hmmer3.pm
  M Bio/Seq/PrimaryQual.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/Lite.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/embl.pm
  M Bio/SeqIO/fastq.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/SeqIO/swiss.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/EUtilities.pm
  M Bio/Tools/EUtilities/EUtilParameters.pm
  M Bio/Tools/EUtilities/Summary/ItemContainerI.pm
  M Bio/Tools/GFF.pm
  M Bio/TreeIO/NewickParser.pm
  M Bio/TreeIO/newick.pm
  M Build.PL
  M Changes
  M MANIFEST
  M MANIFEST.SKIP
  M examples/db/dbfetch
  M examples/make_primers.pl
  M scripts/DB/biofetch_genbank_proxy.PLS
  M t/Annotation/Annotation.t
  M t/Ontology/IO/obo.t
  M t/Ontology/Ontology.t
  M t/Ontology/OntologyEngine.t
  M t/RemoteDB/EMBL.t
  M t/RemoteDB/EUtilities.t
  M t/RemoteDB/SeqVersion.t
  A t/SearchIO/Writer/TextWriter.t
  A t/SearchIO/axt.t
  M t/SearchIO/hmmer.t
  R t/SearchIO/hmmer3.t
  M t/Seq/Seq.t
  R t/SeqIO.t
  A t/SeqIO/SeqIO.t
  M t/SeqIO/embl.t
  M t/SeqIO/seqxml.t
  M t/SeqIO/swiss.t
  M t/SeqTools/CodonTable.t
  M t/data/assembly_with_singlets.ace
  A t/data/hmmscan_sec_struct.out
  A t/data/interpro_relationship.xml
  M t/data/seqxml.xml
  A t/data/sp_subset.obo
  A t/data/test_data.axt

Log Message:
-----------
Fix merge conflicts




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