July 2006 Archives by author

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Starting: Sat Jul 1 01:41:11 EDT 2006
Ending: Sat Jul 29 15:31:26 EDT 2006
Messages: 719

• [Bioperl-guts-l] bioperl-live/t Map.t,1.6,1.7 CytoMap.t,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t CytoMap.t,1.4,1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map PositionHandler.pm, NONE, 1.1 PositionHandlerI.pm, NONE, 1.1 Clone.pm, 1.5, 1.6 Contig.pm, 1.5, 1.6 CytoMap.pm, 1.9, 1.10 CytoMarker.pm, 1.11, 1.12 CytoPosition.pm, 1.15, 1.16 FPCMarker.pm, 1.6, 1.7 LinkageMap.pm, 1.16, 1.17 LinkagePosition.pm, 1.14, 1.15 MapI.pm, 1.12, 1.13 Mappable.pm, 1.3, 1.4 MappableI.pm, 1.14, 1.15 Marker.pm, 1.20, 1.21 MarkerI.pm, 1.14, 1.15 Microsatellite.pm, 1.12, 1.13 OrderedPosition.pm, 1.9, 1.10 OrderedPositionWithDistance.pm, 1.9, 1.10 Physical.pm, 1.7, 1.8 Position.pm, 1.16, 1.17 PositionI.pm, 1.14, 1.15 SimpleMap.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map EntityI.pm,NONE,1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map EntityI.pm, 1.1, 1.2 MapI.pm, 1.13, 1.14 Mappable.pm, 1.4, 1.5 MappableI.pm, 1.15, 1.16 OrderedPosition.pm, 1.10, 1.11 PositionHandler.pm, 1.1, 1.2 PositionI.pm, 1.15, 1.16 SimpleMap.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio RangeI.pm,1.48,1.49   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Fasta.pm,1.43,1.44   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Exception.t,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Relative.pm, NONE, 1.1 RelativeI.pm, NONE, 1.1 EntityI.pm, 1.2, 1.3 MapI.pm, 1.14, 1.15 Mappable.pm, 1.5, 1.6 MappableI.pm, 1.16, 1.17 Marker.pm, 1.21, 1.22 MarkerI.pm, 1.15, 1.16 OrderedPosition.pm, 1.11, 1.12 Position.pm, 1.17, 1.18 PositionHandler.pm, 1.2, 1.3 PositionHandlerI.pm, 1.1, 1.2 PositionI.pm, 1.16, 1.17 SimpleMap.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Map.t,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live AUTHORS,1.47,1.48   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Taxonomy.t,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy flatfile.pm, 1.11, 1.12 entrez.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Node.pm,1.14,1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data/taxdump - New directory   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data/taxdump names.dmp, NONE, 1.1 nodes.dmp, NONE, 1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Taxonomy.pm,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Taxonomy.t,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy entrez.pm, 1.15, 1.16 flatfile.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Node.pm,1.15,1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Taxon.pm,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t TaxonTree.t,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy flatfile.pm, 1.13, 1.14 entrez.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Taxonomy.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.136,1.137   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data ay149291.gb, NONE, 1.1 ay116458.gb, NONE, 1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t SeqUtils.t,1.18,1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.6,1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.137,1.138   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data ay007676.gb, NONE, 1.1 dq519393.gb, NONE, 1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Species.t,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Species.t,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] Mauricio Herrera Cuadra   Korn Bernhard
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi pg.pm, 1.18, 1.19   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi pg.pm, 1.19, 1.20   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/Tools GFF.pm,1.57,1.58   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm,1.41,1.42   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm,1.42,1.43   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.118,1.119   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph translation.pm, 1.35, 1.36   Scott Cain
• [Bioperl-guts-l] bioperl-live/Bio/Root RootI.pm,1.68,1.69   Steve Chervitz
• [Bioperl-guts-l] bioperl-live/t RootI.t,1.7,1.8   Steve Chervitz
• [Bioperl-guts-l] bioperl-live/Bio/Tools Fgenesh.pm,1.8,1.9   Malcom Cook
• [Bioperl-guts-l] bioperl-live/scripts/searchio filter_search.PLS, 1.1, 1.2 parse_hmmsearch.PLS, 1.1, 1.2 search2table.PLS, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/biblio biblio.PLS,1.3,1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/seqstats aacomp.PLS, 1.3, 1.4 chaos_plot.PLS, 1.4, 1.5 gccalc.PLS, 1.3, 1.4 oligo_count.PLS, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/seq extract_feature_seq.PLS, 1.3, 1.4 seqconvert.PLS, 1.6, 1.7 split_seq.PLS, 1.5, 1.6 translate_seq.PLS, 1.5, 1.6 unflatten_seq.PLS, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/utilities dbsplit.PLS, 1.6, 1.7 mutate.PLS, 1.9, 1.10 pairwise_kaks.PLS, 1.10, 1.11 remote_blast.PLS, 1.5, 1.6 seq_length.PLS, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/index bp_fetch.PLS, 1.3, 1.4 bp_index.PLS, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO emboss.pm, 1.15, 1.16 mega.pm, 1.9, 1.10 psi.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Align AlignI.pm, 1.14, 1.15 DNAStatistics.pm, 1.30, 1.31 PairwiseStatistics.pm, 1.8, 1.9 ProteinStatistics.pm, 1.5, 1.6 StatisticsI.pm, 1.5, 1.6 Utilities.pm, 1.18, 1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio AnalysisI.pm, 1.8, 1.9 AnnotatableI.pm, 1.10, 1.11 Biblio.pm, 1.14, 1.15 ClusterI.pm, 1.4, 1.5 ClusterIO.pm, 1.14, 1.15 DBLinkContainerI.pm, 1.10, 1.11 FeatureHolderI.pm, 1.8, 1.9 FeatureIO.pm, 1.11, 1.12 Graphics.pm, 1.15, 1.16 MapIO.pm, 1.7, 1.8 OntologyIO.pm, 1.10, 1.11 SearchIO.pm, 1.37, 1.38 Seq.pm, 1.88, 1.89 SeqIO.pm, 1.88, 1.89 SimpleAlign.pm, 1.103, 1.104 SimpleAnalysisI.pm, 1.7, 1.8 Species.pm, 1.32, 1.33 Taxonomy.pm, 1.6, 1.7 TreeIO.pm, 1.18, 1.19 UpdateableSeqI.pm, 1.5, 1.6 WebAgent.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live bioperl.lisp,1.28,1.29   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm, 1.8, 1.9 eutils.pm, 1.9, 1.10 pdf.pm, 1.4, 1.5 soap.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat/BDB embl.pm, 1.9, 1.10 fasta.pm, 1.5, 1.6 genbank.pm, 1.4, 1.5 swiss.pm, 1.3, 1.4 swissprot.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.12, 1.13 BiblioBase.pm, 1.11, 1.12 Book.pm, 1.12, 1.13 BookArticle.pm, 1.11, 1.12 IO.pm, 1.13, 1.14 Journal.pm, 1.11, 1.12 JournalArticle.pm, 1.12, 1.13 MedlineArticle.pm, 1.10, 1.11 MedlineBook.pm, 1.8, 1.9 MedlineBookArticle.pm, 1.8, 1.9 MedlineJournal.pm, 1.8, 1.9 MedlineJournalArticle.pm, 1.8, 1.9 Organisation.pm, 1.12, 1.13 Patent.pm, 1.12, 1.13 Person.pm, 1.13, 1.14 Proceeding.pm, 1.11, 1.12 Provider.pm, 1.9, 1.10 PubmedArticle.pm, 1.7, 1.8 PubmedBookArticle.pm, 1.7, 1.8 PubmedJournalArticle.pm, 1.8, 1.9 Ref.pm, 1.10, 1.11 Service.pm, 1.11, 1.12 TechReport.pm, 1.10, 1.11 Thesis.pm, 1.10, 1.11 WebResource.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Annotation AnnotationFactory.pm, 1.4, 1.5 Collection.pm, 1.20, 1.21 OntologyTerm.pm, 1.12, 1.13 SimpleValue.pm, 1.15, 1.16 StructuredValue.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Query GenBank.pm, 1.15, 1.16 WebQuery.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BDB.pm, 1.13, 1.14 BinarySearch.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities esearch.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Cluster ClusterFactory.pm, 1.4, 1.5 FamilyI.pm, 1.4, 1.5 SequenceFamily.pm, 1.7, 1.8 UniGene.pm, 1.35, 1.36 UniGeneI.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/ClusterIO dbsnp.pm, 1.12, 1.13 unigene.pm, 1.25, 1.26   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB Ace.pm, 1.13, 1.14 BiblioI.pm, 1.8, 1.9 EMBL.pm, 1.18, 1.19 EntrezGene.pm, 1.5, 1.6 Expression.pm, 1.2, 1.3 Flat.pm, 1.20, 1.21 GDB.pm, 1.18, 1.19 GenBank.pm, 1.57, 1.58 GenPept.pm, 1.29, 1.30 NCBIHelper.pm, 1.51, 1.52 QueryI.pm, 1.3, 1.4 SeqI.pm, 1.8, 1.9 SeqVersion.pm, 1.2, 1.3 Taxonomy.pm, 1.6, 1.7 WebDBSeqI.pm, 1.54, 1.55   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqVersion gi.pm,1.1,1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Biblio/IO medline2ref.pm, 1.13, 1.14 medlinexml.pm, 1.7, 1.8 pubmed2ref.pm, 1.4, 1.5 pubmedxml.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics ConfiguratorI.pm, 1.5, 1.6 Pictogram.pm, 1.11, 1.12 RendererI.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph/SimpleGraph Traversal.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy entrez.pm, 1.12, 1.13 flatfile.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Event EventGeneratorI.pm, 1.9, 1.10 EventHandlerI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm, 1.2, 1.3 gff.pm, 1.39, 1.40 gtf.pm, 1.2, 1.3 interpro.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm, 1.45, 1.46 AbstractSeq.pm, 1.19, 1.20 Blast.pm, 1.19, 1.20 EMBL.pm, 1.28, 1.29 Fasta.pm, 1.31, 1.32 Fastq.pm, 1.8, 1.9 GenBank.pm, 1.19, 1.20 Hmmer.pm, 1.7, 1.8 Qual.pm, 1.5, 1.6 SwissPfam.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph Edge.pm, 1.8, 1.9 IO.pm, 1.13, 1.14 ProteinGraph.pm, 1.32, 1.33   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.22, 1.23   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Expression Contact.pm, 1.2, 1.3 DataSet.pm, 1.1, 1.2 FeatureGroup.pm, 1.4, 1.5 FeatureI.pm, 1.5, 1.6 Platform.pm, 1.2, 1.3 Sample.pm, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Factory AnalysisI.pm, 1.5, 1.6 FTLocationFactory.pm, 1.19, 1.20 LocationFactoryI.pm, 1.5, 1.6 MapFactoryI.pm, 1.6, 1.7 ObjectBuilderI.pm, 1.3, 1.4 ObjectFactory.pm, 1.3, 1.4 ObjectFactoryI.pm, 1.4, 1.5 SequenceFactoryI.pm, 1.8, 1.9 SequenceProcessorI.pm, 1.2, 1.3 SequenceStreamI.pm, 1.4, 1.5 TreeFactoryI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/IO csv.pm, 1.6, 1.7 hapmap.pm, 1.6, 1.7 phase.pm, 1.5, 1.6 prettybase.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Map Clone.pm, 1.3, 1.4 Contig.pm, 1.3, 1.4 CytoMap.pm, 1.7, 1.8 CytoMarker.pm, 1.9, 1.10 FPCMarker.pm, 1.4, 1.5 LinkageMap.pm, 1.13, 1.14 LinkagePosition.pm, 1.12, 1.13 MapI.pm, 1.9, 1.10 Mappable.pm, 1.1, 1.2 MappableI.pm, 1.12, 1.13 Marker.pm, 1.18, 1.19 MarkerI.pm, 1.12, 1.13 Microsatellite.pm, 1.10, 1.11 OrderedPosition.pm, 1.7, 1.8 OrderedPositionWithDistance.pm, 1.7, 1.8 Physical.pm, 1.5, 1.6 Position.pm, 1.14, 1.15 PositionI.pm, 1.12, 1.13 SimpleMap.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix Generic.pm, 1.12, 1.13 IO.pm, 1.3, 1.4 MatrixI.pm, 1.2, 1.3 PhylipDist.pm, 1.13, 1.14 Scoring.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO/Handlers InterProHandler.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/MapIO fpc.pm, 1.4, 1.5 mapmaker.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/Simulation Coalescent.pm, 1.9, 1.10 GeneticDrift.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology DocumentRegistry.pm, 1.9, 1.10 InterProTerm.pm, 1.8, 1.9 Ontology.pm, 1.16, 1.17 OntologyEngineI.pm, 1.13, 1.14 OntologyI.pm, 1.7, 1.8 OntologyStore.pm, 1.11, 1.12 PathI.pm, 1.4, 1.5 RelationshipFactory.pm, 1.3, 1.4 RelationshipI.pm, 1.7, 1.8 SimpleOntologyEngine.pm, 1.15, 1.16 TermFactory.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO InterProParser.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/PopGen Genotype.pm, 1.8, 1.9 GenotypeI.pm, 1.1, 1.2 HtSNP.pm, 1.4, 1.5 IO.pm, 1.4, 1.5 Individual.pm, 1.13, 1.14 IndividualI.pm, 1.5, 1.6 Marker.pm, 1.5, 1.6 MarkerI.pm, 1.4, 1.5 PopStats.pm, 1.8, 1.9 Population.pm, 1.17, 1.18 PopulationI.pm, 1.7, 1.8 Statistics.pm, 1.32, 1.33 TagHaplotype.pm, 1.3, 1.4 Utilities.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/IO phylip.pm, 1.1, 1.2 scoring.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO EventHandlerI.pm, 1.11, 1.12 FastHitEventBuilder.pm, 1.10, 1.11 IteratedSearchResultEventBuilder.pm, 1.8, 1.9 SearchResultEventBuilder.pm, 1.39, 1.40 axt.pm, 1.6, 1.7 blast.pm, 1.97, 1.98 blasttable.pm, 1.5, 1.6 blastxml.pm, 1.32, 1.33 exonerate.pm, 1.15, 1.16 fasta.pm, 1.48, 1.49 hmmer.pm, 1.30, 1.31 megablast.pm, 1.5, 1.6 psl.pm, 1.11, 1.12 sim4.pm, 1.11, 1.12 waba.pm, 1.14, 1.15 wise.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit BlastHit.pm, 1.15, 1.16 GenericHit.pm, 1.35, 1.36 HMMERHit.pm, 1.4, 1.5 HitFactory.pm, 1.4, 1.5 PsiBlastHit.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.4, 1.5 IterationI.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.13, 1.14 Enzyme.pm, 1.11, 1.12 EnzymeCollection.pm, 1.6, 1.7 EnzymeI.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Root Err.pm, 1.17, 1.18 IOManager.pm, 1.15, 1.16 Object.pm, 1.27, 1.28 Utilities.pm, 1.27, 1.28 Vector.pm, 1.13, 1.14 Xref.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP FastaHSP.pm, 1.8, 1.9 GenericHSP.pm, 1.66, 1.67 HMMERHSP.pm, 1.6, 1.7 HSPFactory.pm, 1.6, 1.7 HSPI.pm, 1.34, 1.35 PSLHSP.pm, 1.2, 1.3 WABAHSP.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search BlastStatistics.pm, 1.3, 1.4 GenericStatistics.pm, 1.3, 1.4 Processor.pm, 1.9, 1.10 StatisticsI.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastResult.pm, 1.20, 1.21 GenericResult.pm, 1.20, 1.21 HMMERResult.pm, 1.4, 1.5 ResultFactory.pm, 1.4, 1.5 ResultI.pm, 1.20, 1.21 WABAResult.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/Enzyme MultiCut.pm, 1.4, 1.5 MultiSite.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO abi.pm, 1.10, 1.11 agave.pm, 1.11, 1.12 alf.pm, 1.8, 1.9 ctf.pm, 1.11, 1.12 entrezgene.pm, 1.20, 1.21 exp.pm, 1.11, 1.12 fasta.pm, 1.53, 1.54 fastq.pm, 1.11, 1.12 game.pm, 1.35, 1.36 interpro.pm, 1.7, 1.8 largefasta.pm, 1.20, 1.21 locuslink.pm, 1.10, 1.11 metafasta.pm, 1.5, 1.6 pln.pm, 1.8, 1.9 strider.pm, 1.2, 1.3 tigr.pm, 1.9, 1.10 tigrxml.pm, 1.7, 1.8 tinyseq.pm, 1.6, 1.7 ztr.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer BSMLResultWriter.pm, 1.2, 1.3 GbrowseGFF.pm, 1.13, 1.14 HSPTableWriter.pm, 1.13, 1.14 HTMLResultWriter.pm, 1.36, 1.37 HitTableWriter.pm, 1.16, 1.17 ResultTableWriter.pm, 1.15, 1.16 TextResultWriter.pm, 1.16, 1.17   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature AnnotationAdaptor.pm, 1.8, 1.9 Collection.pm, 1.16, 1.17 CollectionI.pm, 1.3, 1.4 SimilarityPair.pm, 1.27, 1.28 TypedSeqFeatureI.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/SiRNA Oligo.pm, 1.4, 1.5 Pair.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq BaseSeqProcessor.pm, 1.5, 1.6 LargeLocatableSeq.pm, 1.3, 1.4 LargeSeqI.pm, 1.4, 1.5 SeqBuilder.pm, 1.7, 1.8 SeqFactory.pm, 1.9, 1.10 SeqFastaSpeedFactory.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene GeneStructure.pm, 1.18, 1.19 Intron.pm, 1.8, 1.9 NC_Feature.pm, 1.9, 1.10 Poly_A_site.pm, 1.5, 1.6 Promoter.pm, 1.6, 1.7 Transcript.pm, 1.35, 1.36 UTR.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EMBOSS Palindrome.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Molphy Result.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Symbol Alphabet.pm, 1.8, 1.9 AlphabetI.pm, 1.6, 1.7 DNAAlphabet.pm, 1.4, 1.5 ProteinAlphabet.pm, 1.4, 1.5 Symbol.pm, 1.7, 1.8 SymbolI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/BPlite HSP.pm, 1.28, 1.29 Sbjct.pm, 1.30, 1.31   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools BPpsilite.pm, 1.23, 1.24 Blat.pm, 1.4, 1.5 Coil.pm, 1.3, 1.4 EPCR.pm, 1.15, 1.16 ERPIN.pm, 1.2, 1.3 Est2Genome.pm, 1.15, 1.16 FootPrinter.pm, 1.6, 1.7 Gel.pm, 1.8, 1.9 Glimmer.pm, 1.2, 1.3 GuessSeqFormat.pm, 1.12, 1.13 HMM.pm, 1.5, 1.6 Hmmpfam.pm, 1.5, 1.6 Prints.pm, 1.10, 1.11 Profile.pm, 1.5, 1.6 Promoterwise.pm, 1.6, 1.7 QRNA.pm, 1.3, 1.4 RNAMotif.pm, 1.7, 1.8 RandomDistFunctions.pm, 1.5, 1.6 RepeatMasker.pm, 1.8, 1.9 RestrictionEnzyme.pm, 1.31, 1.32 Seg.pm, 1.8, 1.9 SeqPattern.pm, 1.17, 1.18 SiRNA.pm, 1.11, 1.12 Signalp.pm, 1.5, 1.6 Tmhmm.pm, 1.8, 1.9 dpAlign.pm, 1.15, 1.16 ipcress.pm, 1.5, 1.6 isPcr.pm, 1.6, 1.7 pSW.pm, 1.24, 1.25 tRNAscanSE.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Node.pm,1.12,1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Molphy.pm, 1.7, 1.8 PAML.pm, 1.42, 1.43   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/tinyseq tinyseqHandler.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure IO.pm, 1.8, 1.9 StructureI.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/game featHandler.pm, 1.12, 1.13 gameHandler.pm, 1.5, 1.6 gameSubs.pm, 1.6, 1.7 gameWriter.pm, 1.10, 1.11 seqHandler.pm, 1.24, 1.25   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO TreeEventBuilder.pm, 1.21, 1.22 cluster.pm, 1.2, 1.3 lintree.pm, 1.6, 1.7 newick.pm, 1.34, 1.35 nexus.pm, 1.11, 1.12 nhx.pm, 1.16, 1.17 pag.pm, 1.7, 1.8 svggraph.pm, 1.3, 1.4 tabtree.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/SiRNA/Ruleset saigo.pm, 1.2, 1.3 tuschl.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tree AlleleNode.pm, 1.11, 1.12 Compatible.pm, 1.3, 1.4 DistanceFactory.pm, 1.6, 1.7 Node.pm, 1.46, 1.47 NodeI.pm, 1.33, 1.34 NodeNHX.pm, 1.8, 1.9 RandomFactory.pm, 1.16, 1.17 Statistics.pm, 1.10, 1.11 Tree.pm, 1.18, 1.19 TreeFunctionsI.pm, 1.24, 1.25 TreeI.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Primer/Assessor Base.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML ModelResult.pm, 1.5, 1.6 Result.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Primer AssessorI.pm, 1.3, 1.4 Feature.pm, 1.3, 1.4 Pair.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run GenericParameters.pm, 1.3, 1.4 ParametersI.pm, 1.3, 1.4 WrapperBase.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/examples/tools run_primer3.pl, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Phylip ProtDist.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio Seq.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/maintenance authors.pl, 1.4, 1.5 check_URLs.pl, 1.3, 1.4 modules.pl, 1.20, 1.21 pod.pl, 1.7, 1.8 symlink_scripts.PLS, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-corba-server/Bio/CorbaServer Alphabet.pm, 1.1, 1.2 Annotation.pm, 1.4, 1.5 AnnotationCollection.pm, 1.5, 1.6 SeqIterator.pm, 1.3, 1.4 Symbol.pm, 1.2, 1.3 Utils.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB DBAdaptorI.pm, 1.1, 1.2 DBD.pm, 1.1, 1.2 DBI.pm, 1.4, 1.5 PersistenceAdaptorI.pm, 1.2, 1.3 PersistentObjectI.pm, 1.3, 1.4 SimpleDBContext.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio BioEntry.pm,1.1,1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL BaseDriver.pm, 1.28, 1.29 BasePersistenceAdaptor.pm, 1.38, 1.39   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/Persistent BioNamespace.pm, 1.2, 1.3 ObjectRelMapperI.pm, 1.1, 1.2 PersistentObject.pm, 1.6, 1.7 PersistentObjectFactory.pm, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Pg AnnotationCollectionAdaptorDriver.pm, 1.1, 1.2 BasePersistenceAdaptorDriver.pm, 1.7, 1.8 BiosequenceAdaptorDriver.pm, 1.4, 1.5 PathAdaptorDriver.pm, 1.3, 1.4 SpeciesAdaptorDriver.pm, 1.3, 1.4 TermAdaptorDriver.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/DBI Oracle.pm, 1.6, 1.7 Pg.pm, 1.2, 1.3 Transaction.pm, 1.1, 1.2 TransactionListener.pm, 1.1, 1.2 base.pm, 1.8, 1.9 mysql.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/Query DBQueryResult.pm, 1.2, 1.3 PrebuiltResult.pm, 1.1, 1.2 QueryResultI.pm, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/mysql AnnotationCollectionAdaptorDriver.pm, 1.2, 1.3 BasePersistenceAdaptorDriver.pm, 1.16, 1.17 BiosequenceAdaptorDriver.pm, 1.4, 1.5 PathAdaptorDriver.pm, 1.3, 1.4 SpeciesAdaptorDriver.pm, 1.6, 1.7 TermAdaptorDriver.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Oracle AnnotationCollectionAdaptorDriver.pm, 1.1, 1.2 BasePersistenceAdaptorDriver.pm, 1.14, 1.15 BiosequenceAdaptorDriver.pm, 1.9, 1.10 PathAdaptorDriver.pm, 1.3, 1.4 SpeciesAdaptorDriver.pm, 1.2, 1.3 TermAdaptorDriver.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-ext/Bio/SeqIO/staden read.pm,1.9,1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression MicroarrayIO.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/Microarray/Affymetrix Array.pm, 1.10, 1.11 ArrayDesign.pm, 1.7, 1.8 CelArray.pm, 1.2, 1.3 Data.pm, 1.10, 1.11 Feature.pm, 1.5, 1.6 Mas50TxtArray.pm, 1.4, 1.5 dChipArray.pm, 1.2, 1.3 dChipXLS.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/Microarray FeatureI.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/MicroarrayIO affymetrix.pm, 1.14, 1.15 dchipxls.pm, 1.5, 1.6 mas50txt.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network IO.pm,1.4,1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree/PedIO lapis.pm, 1.13, 1.14 linkage.pm, 1.8, 1.9 ped.pm, 1.13, 1.14 xml.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree Draw.pm, 1.11, 1.12 Group.pm, 1.16, 1.17 GroupI.pm, 1.8, 1.9 MarkerI.pm, 1.7, 1.8 PedIO.pm, 1.11, 1.12 Pedigree.pm, 1.12, 1.13 Person.pm, 1.13, 1.14 PersonI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree/Draw Command.pm, 1.5, 1.6 GD.pm, 1.9, 1.10 GraphicsI.pm, 1.5, 1.6 PedPlot.pm, 1.10, 1.11 PedRenderI.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/scripts validate_xml.pl,1.2,1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline Node.pm, 1.2, 1.3 NodeGroup.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/SQL DataMongerAdaptor.pm, 1.5, 1.6 NodeAdaptor.pm, 1.4, 1.5 NodeGroupAdaptor.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Installer Clustalw.pm, 1.1, 1.2 EMBOSS.pm, 1.5, 1.6 Generic.pm, 1.2, 1.3 PAML.pm, 1.4, 1.5 Probcons.pm, 1.2, 1.3 TCoffee.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/PAML Baseml.pm, 1.4, 1.5 Codeml.pm, 1.41, 1.42 Evolver.pm, 1.9, 1.10 Yn00.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Analysis soap.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip Base.pm, 1.9, 1.10 DrawGram.pm, 1.11, 1.12 DrawTree.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Analysis.pm, 1.9, 1.10 AnalysisFactory.pm, 1.8, 1.9 Cap3.pm, 1.1, 1.2 Coil.pm, 1.7, 1.8 FootPrinter.pm, 1.11, 1.12 Mdust.pm, 1.7, 1.8 PiseApplication.pm, 1.7, 1.8 PiseJob.pm, 1.12, 1.13 PiseJobParser.pm, 1.7, 1.8 RepeatMasker.pm, 1.22, 1.23 TribeMCL.pm, 1.18, 1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Molphy ProtML.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Blat.pm, 1.10, 1.11 Lagan.pm, 1.10, 1.11 TCoffee.pm, 1.40, 1.41   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/AnalysisFactory Pise.pm, 1.7, 1.8 soap.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/scripts multi_hmmsearch.PLS, 1.1, 1.2 panalysis.PLS, 1.8, 1.9 papplmaker.PLS, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/PiseApplication Puzzle.pm, 1.4, 1.5 abiview.pm, 1.4, 1.5 addquart.pm, 1.4, 1.5 align2model.pm, 1.4, 1.5 alistat.pm, 1.4, 1.5 antigenic.pm, 1.4, 1.5 assp.pm, 1.4, 1.5 backtranseq.pm, 1.4, 1.5 bambe.pm, 1.4, 1.5 banana.pm, 1.4, 1.5 bionj.pm, 1.4, 1.5 biosed.pm, 1.4, 1.5 bl2seq.pm, 1.4, 1.5 blast2.pm, 1.4, 1.5 blimps.pm, 1.4, 1.5 blimps_block.pm, 1.4, 1.5 blimps_matrix.pm, 1.4, 1.5 boxshade.pm, 1.4, 1.5 btwisted.pm, 1.4, 1.5 cai.pm, 1.4, 1.5 cap.pm, 1.4, 1.5 cds.pm, 1.4, 1.5 chaos.pm, 1.4, 1.5 charge.pm, 1.4, 1.5 checktrans.pm, 1.4, 1.5 chips.pm, 1.4, 1.5 cirdna.pm, 1.4, 1.5 clique.pm, 1.4, 1.5 clustalw.pm, 1.4, 1.5 clustalw_convert.pm, 1.6, 1.7 codcmp.pm, 1.4, 1.5 coderet.pm, 1.4, 1.5 codnocod.pm, 1.4, 1.5 codontree.pm, 1.4, 1.5 codonw.pm, 1.4, 1.5 comalign.pm, 1.4, 1.5 combat.pm, 1.4, 1.5 compseq.pm, 1.4, 1.5 con_filter.pm, 1.4, 1.5 confmat.pm, 1.4, 1.5 cons.pm, 1.4, 1.5 consense.pm, 1.4, 1.5 consensus.pm, 1.4, 1.5 cpgplot.pm, 1.4, 1.5 cpgreport.pm, 1.4, 1.5 cusp.pm, 1.4, 1.5 cutseq.pm, 1.4, 1.5 dan.pm, 1.4, 1.5 dca.pm, 1.4, 1.5 decorate! .pm, 1.4, 1.5 degapseq.pm, 1.4, 1.5 descseq.pm, 1.4, 1.5 dialign2.pm, 1.6, 1.7 diffseq.pm, 1.4, 1.5 digest.pm, 1.4, 1.5 distmat.pm, 1.4, 1.5 distquart.pm, 1.4, 1.5 dnadist.pm, 1.4, 1.5 dnapars.pm, 1.4, 1.5 dollop.pm, 1.4, 1.5 domainer.pm, 1.4, 1.5 dotmatcher.pm, 1.4, 1.5 dotpath.pm, 1.4, 1.5 dottup.pm, 1.4, 1.5 drawgram.pm, 1.4, 1.5 drawpyr.pm, 1.4, 1.5 drawtree.pm, 1.4, 1.5 dreg.pm, 1.4, 1.5 druid.pm, 1.4, 1.5 dsc.pm, 1.4, 1.5 dssp.pm, 1.4, 1.5 einverted.pm, 1.4, 1.5 emma.pm, 1.4, 1.5 emowse.pm, 1.4, 1.5 environ.pm, 1.4, 1.5 eprimer3.pm, 1.4, 1.5 equicktandem.pm, 1.4, 1.5 est2genome.pm, 1.4, 1.5 etandem.pm, 1.4, 1.5 extractfeat.pm, 1.4, 1.5 extractseq.pm, 1.4, 1.5 fasta.pm, 1.4, 1.5 fastdnaml.pm, 1.4, 1.5 fastrna.pm, 1.4, 1.5 filtersites.pm, 1.4, 1.5 findkm.pm, 1.4, 1.5 fitch.pm, 1.4, 1.5 fmtseq.pm, 1.4, 1.5 freak.pm, 1.4, 1.5 fuzznuc.pm, 1.4, 1.5 fuzzpro.pm, 1.4, 1.5 fuzztran.pm, 1.4, 1.5 gb2xml.pm, 1.4, 1.5 geecee.pm, 1.4, 1.5 genscan.pm, 1.5, 1.6 getblock.pm, 1.4, 1.5 getorf.pm, 1.4, 1.5 gff2ps.pm, 1.4, 1.5 gibbs.pm, 1.4, 1.5 gibbs_scan.pm, 1.4, 1.5 golden.pm, 1.4, 1.5 gr! ailclnt.pm, 1.6, 1.7 gruppi.pm, 1.4, 1.5 helixturnhelix.pm, 1.4, 1.5 hmmalig   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Annotation Collection.pm, 1.21, 1.22 OntologyTerm.pm, 1.13, 1.14 SimpleValue.pm, 1.16, 1.17 StructuredValue.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm, 1.10, 1.11 phrap.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm, 1.20, 1.21 clustalw.pm, 1.31, 1.32   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm, 1.43, 1.44 AnalysisParserI.pm, 1.9, 1.10 AnalysisResultI.pm, 1.7, 1.8 ClusterIO.pm, 1.15, 1.16 DescribableI.pm, 1.7, 1.8 FeatureIO.pm, 1.12, 1.13 IdCollectionI.pm, 1.3, 1.4 IdentifiableI.pm, 1.8, 1.9 LocatableSeq.pm, 1.36, 1.37 LocationI.pm, 1.22, 1.23 PrimarySeq.pm, 1.92, 1.93 PrimarySeqI.pm, 1.62, 1.63 Range.pm, 1.24, 1.25 RangeI.pm, 1.45, 1.46 SearchDist.pm, 1.17, 1.18 Seq.pm, 1.89, 1.90 SeqAnalysisParserI.pm, 1.13, 1.14 SeqFeatureI.pm, 1.62, 1.63 SeqI.pm, 1.26, 1.27 SeqIO.pm, 1.89, 1.90 SeqUtils.pm, 1.27, 1.28 SimpleAlign.pm, 1.104, 1.105   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.7, 1.8 ContigAnalysis.pm, 1.3, 1.4 IO.pm, 1.3, 1.4 Scaffold.pm, 1.8, 1.9 ScaffoldI.pm, 1.3, 1.4 Singlet.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Biblio IO.pm,1.14,1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Factory ApplicationFactoryI.pm, 1.7, 1.8 DriverFactory.pm, 1.12, 1.13 HitFactoryI.pm, 1.8, 1.9 ResultFactoryI.pm, 1.7, 1.8 SeqAnalysisParserFactory.pm, 1.12, 1.13 SeqAnalysisParserFactoryI.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat/BDB embl.pm, 1.10, 1.11 fasta.pm, 1.6, 1.7 genbank.pm, 1.5, 1.6 swiss.pm, 1.4, 1.5 swissprot.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqVersion gi.pm,1.2,1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB BioFetch.pm, 1.26, 1.27 CUTG.pm, 1.8, 1.9 DBFetch.pm, 1.10, 1.11 EMBL.pm, 1.19, 1.20 EntrezGene.pm, 1.6, 1.7 Flat.pm, 1.21, 1.22 MeSH.pm, 1.5, 1.6 RefSeq.pm, 1.10, 1.11 SeqVersion.pm, 1.3, 1.4 SwissProt.pm, 1.27, 1.28 XEMBL.pm, 1.7, 1.8 XEMBLService.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate Chain.pm, 1.4, 1.5 Collection.pm, 1.21, 1.22 ExtrapolatingPair.pm, 1.13, 1.14 GeneMapper.pm, 1.24, 1.25 Graph.pm, 1.7, 1.8 MapperI.pm, 1.7, 1.8 Pair.pm, 1.16, 1.17 Result.pm, 1.12, 1.13 ResultI.pm, 1.3, 1.4 Utils.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/ClusterIO dbsnp.pm, 1.13, 1.14 unigene.pm, 1.26, 1.27   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Expression FeatureGroup.pm, 1.5, 1.6 FeatureI.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/CodonUsage IO.pm, 1.8, 1.9 Table.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BDB.pm, 1.14, 1.15 BinarySearch.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Cluster SequenceFamily.pm, 1.8, 1.9 UniGene.pm, 1.36, 1.37 UniGeneI.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate/Result Gap.pm, 1.6, 1.7 Match.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix PhylipDist.pm,1.14,1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.23, 1.24   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm, 1.46, 1.47 AbstractSeq.pm, 1.20, 1.21 EMBL.pm, 1.29, 1.30 Fasta.pm, 1.32, 1.33 Fastq.pm, 1.9, 1.10 GenBank.pm, 1.20, 1.21 Hmmer.pm, 1.8, 1.9 Qual.pm, 1.6, 1.7 SwissPfam.pm, 1.21, 1.22 Swissprot.pm, 1.23, 1.24   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Map CytoPosition.pm, 1.12, 1.13 LinkageMap.pm, 1.14, 1.15 MapI.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq ChainI.pm, 1.13, 1.14 Mutation.pm, 1.10, 1.11 Mutator.pm, 1.30, 1.31 SeqI.pm, 1.28, 1.29   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics ConfiguratorI.pm, 1.6, 1.7 Pictogram.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph Edge.pm, 1.9, 1.10 IO.pm, 1.14, 1.15 ProteinGraph.pm, 1.33, 1.34   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph/SimpleGraph Traversal.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Location Atomic.pm, 1.13, 1.14 AvWithinCoordPolicy.pm, 1.5, 1.6 CoordinatePolicyI.pm, 1.5, 1.6 Fuzzy.pm, 1.30, 1.31 FuzzyLocationI.pm, 1.18, 1.19 NarrowestCoordPolicy.pm, 1.8, 1.9 Simple.pm, 1.38, 1.39 Split.pm, 1.43, 1.44 SplitLocationI.pm, 1.15, 1.16 WidestCoordPolicy.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO dagflat.pm, 1.26, 1.27 goflat.pm, 1.4, 1.5 obo.pm, 1.4, 1.5 simplehierarchy.pm, 1.14, 1.15 soflat.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM IO.pm, 1.12, 1.13 InstanceSite.pm, 1.11, 1.12 InstanceSiteI.pm, 1.7, 1.8 ProtMatrix.pm, 1.13, 1.14 ProtPsm.pm, 1.5, 1.6 Psm.pm, 1.11, 1.12 PsmHeader.pm, 1.8, 1.9 PsmHeaderI.pm, 1.7, 1.8 PsmI.pm, 1.5, 1.6 SiteMatrix.pm, 1.28, 1.29 SiteMatrixI.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.18, 1.19 masta.pm, 1.7, 1.8 meme.pm, 1.17, 1.18 psiblast.pm, 1.8, 1.9 transfac.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Correlate.pm, 1.6, 1.7 Measure.pm, 1.6, 1.7 Phenotype.pm, 1.9, 1.10 PhenotypeI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology/SimpleGOEngine GraphAdaptor.pm, 1.3, 1.4 GraphAdaptor02.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/MeSH Term.pm, 1.4, 1.5 Twig.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology GOterm.pm, 1.19, 1.20 OBOEngine.pm, 1.3, 1.4 OBOterm.pm, 1.2, 1.3 Path.pm, 1.4, 1.5 Relationship.pm, 1.11, 1.12 RelationshipType.pm, 1.14, 1.15 SimpleGOEngine.pm, 1.33, 1.34 Term.pm, 1.28, 1.29 TermI.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.14, 1.15 EnzymeCollection.pm, 1.7, 1.8 IO.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/IO bairoch.pm, 1.5, 1.6 base.pm, 1.8, 1.9 itype2.pm, 1.3, 1.4 withrefm.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.25, 1.26 PsiBlastHSP.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM MiniMIMentry.pm, 1.6, 1.7 OMIMentry.pm, 1.13, 1.14 OMIMentryAllelicVariant.pm, 1.6, 1.7 OMIMparser.pm, 1.17, 1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit Fasta.pm, 1.7, 1.8 HitI.pm, 1.21, 1.22 PsiBlastHit.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search DatabaseI.pm, 1.7, 1.8 GenericDatabase.pm, 1.6, 1.7 Processor.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration IterationI.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Root Err.pm, 1.18, 1.19 HTTPget.pm, 1.11, 1.12 IO.pm, 1.58, 1.59 IOManager.pm, 1.16, 1.17 Object.pm, 1.28, 1.29 Utilities.pm, 1.28, 1.29 Vector.pm, 1.14, 1.15 Version.pm, 1.6, 1.7 Xref.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result ResultI.pm, 1.21, 1.22   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq/Meta Array.pm,1.10,1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer HSPTableWriter.pm, 1.14, 1.15 HitTableWriter.pm, 1.17, 1.18 ResultTableWriter.pm, 1.16, 1.17   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq LargePrimarySeq.pm, 1.29, 1.30 Meta.pm, 1.9, 1.10 MetaI.pm, 1.7, 1.8 PrimaryQual.pm, 1.21, 1.22 PrimedSeq.pm, 1.20, 1.21 QualI.pm, 1.8, 1.9 Quality.pm, 1.7, 1.8 RichSeq.pm, 1.16, 1.17 RichSeqI.pm, 1.11, 1.12 SeqWithQuality.pm, 1.24, 1.25 SequenceTrace.pm, 1.11, 1.12 TraceI.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene Exon.pm, 1.12, 1.13 ExonI.pm, 1.8, 1.9 GeneStructure.pm, 1.19, 1.20 GeneStructureI.pm, 1.9, 1.10 Transcript.pm, 1.36, 1.37 TranscriptI.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.30, 1.31 Computation.pm, 1.13, 1.14 Generic.pm, 1.100, 1.101 PositionProxy.pm, 1.6, 1.7 Primer.pm, 1.18, 1.19 Similarity.pm, 1.13, 1.14 SimilarityPair.pm, 1.28, 1.29   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools FeatureNamer.pm, 1.3, 1.4 IDHandler.pm, 1.7, 1.8 TypeMapper.pm, 1.11, 1.12 Unflattener.pm, 1.34, 1.35   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/game featHandler.pm, 1.13, 1.14 gameHandler.pm, 1.6, 1.7 gameSubs.pm, 1.7, 1.8 gameWriter.pm, 1.11, 1.12 seqHandler.pm, 1.25, 1.26   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/STRIDE Res.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO abi.pm, 1.11, 1.12 agave.pm, 1.12, 1.13 alf.pm, 1.9, 1.10 ctf.pm, 1.12, 1.13 exp.pm, 1.12, 1.13 fasta.pm, 1.54, 1.55 fastq.pm, 1.12, 1.13 game.pm, 1.36, 1.37 largefasta.pm, 1.21, 1.22 metafasta.pm, 1.6, 1.7 pln.pm, 1.9, 1.10 strider.pm, 1.3, 1.4 swiss.pm, 1.89, 1.90 tigr.pm, 1.10, 1.11 ztr.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure Atom.pm, 1.9, 1.10 Chain.pm, 1.7, 1.8 Entry.pm, 1.22, 1.23 IO.pm, 1.9, 1.10 Model.pm, 1.7, 1.8 Residue.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools BPbl2seq.pm, 1.26, 1.27 BPpsilite.pm, 1.24, 1.25 Blast.pm, 1.34, 1.35 CodonTable.pm, 1.33, 1.34 ECnumber.pm, 1.8, 1.9 EPCR.pm, 1.16, 1.17 ESTScan.pm, 1.11, 1.12 Eponine.pm, 1.10, 1.11 Fgenesh.pm, 1.5, 1.6 GFF.pm, 1.54, 1.55 Gel.pm, 1.9, 1.10 Geneid.pm, 1.2, 1.3 Genemark.pm, 1.14, 1.15 Genewise.pm, 1.22, 1.23 Genomewise.pm, 1.3, 1.4 Genscan.pm, 1.26, 1.27 Grail.pm, 1.8, 1.9 Lucy.pm, 1.12, 1.13 MZEF.pm, 1.11, 1.12 Pseudowise.pm, 1.7, 1.8 RestrictionEnzyme.pm, 1.32, 1.33 SeqAnal.pm, 1.15, 1.16 SeqPattern.pm, 1.18, 1.19 SeqStats.pm, 1.27, 1.28 SeqWords.pm, 1.14, 1.15 ipcress.pm, 1.6, 1.7 isPcr.pm, 1.7, 1.8 pICalculator.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.38, 1.39 Trim.pm, 1.18, 1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Domcut.pm, 1.11, 1.12 ELM.pm, 1.9, 1.10 GOR4.pm, 1.9, 1.10 HNN.pm, 1.9, 1.10 Mitoprot.pm, 1.5, 1.6 NetPhos.pm, 1.10, 1.11 Scansite.pm, 1.13, 1.14 Sopma.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.20, 1.21 HTML.pm, 1.16, 1.17 Sbjct.pm, 1.22, 1.23   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.33, 1.34 StandAloneBlast.pm, 1.60, 1.61   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis SimpleAnalysisBase.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/BPlite HSP.pm, 1.29, 1.30 Sbjct.pm, 1.31, 1.32   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Prediction Exon.pm, 1.13, 1.14 Gene.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Sim4 Exon.pm, 1.13, 1.14 Results.pm, 1.22, 1.23   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio PrimarySeq.pm, 1.3, 1.4 PrimarySeqI.pm, 1.3, 1.4 Seq.pm, 1.4, 1.5 SeqI.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Spidey Exon.pm, 1.3, 1.4 Results.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/utilities remote_blast.PLS, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation/IO flat.pm, 1.16, 1.17 xml.pm, 1.16, 1.17   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/DB flanks.PLS,1.4,1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation AAChange.pm, 1.17, 1.18 AAReverseMutate.pm, 1.9, 1.10 Allele.pm, 1.12, 1.13 DNAMutation.pm, 1.15, 1.16 IO.pm, 1.19, 1.20 RNAChange.pm, 1.14, 1.15 SNP.pm, 1.13, 1.14 SeqDiff.pm, 1.20, 1.21 VariantI.pm, 1.17, 1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-corba-server/Bio/CorbaServer Utils.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-ext/Bio/SeqIO/staden read.pm,1.10,1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression MicroarrayIO.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/Microarray FeatureI.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/MicroarrayIO affymetrix.pm, 1.15, 1.16 dchipxls.pm, 1.6, 1.7 mas50txt.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/Microarray/Affymetrix Array.pm, 1.11, 1.12 ArrayDesign.pm, 1.8, 1.9 CelArray.pm, 1.3, 1.4 Data.pm, 1.11, 1.12 Feature.pm, 1.6, 1.7 Mas50TxtArray.pm, 1.5, 1.6 dChipArray.pm, 1.3, 1.4 dChipXLS.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO dip_tab.pm, 1.2, 1.3 psi.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO/psi intact.pm, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network Edge.pm, 1.2, 1.3 IO.pm, 1.5, 1.6 Interaction.pm, 1.2, 1.3 Node.pm, 1.1, 1.2 ProteinNet.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree Draw.pm, 1.12, 1.13 Group.pm, 1.17, 1.18 GroupI.pm, 1.9, 1.10 MarkerI.pm, 1.8, 1.9 PedIO.pm, 1.12, 1.13 Pedigree.pm, 1.13, 1.14 Person.pm, 1.14, 1.15 PersonI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree/Draw Command.pm, 1.6, 1.7 GD.pm, 1.10, 1.11 GraphicsI.pm, 1.6, 1.7 PedPlot.pm, 1.11, 1.12 PedRenderI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree/PedIO lapis.pm, 1.14, 1.15 linkage.pm, 1.9, 1.10 ped.pm, 1.14, 1.15 xml.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline Analysis.pm, 1.31, 1.32 Argument.pm, 1.8, 1.9 DataHandler.pm, 1.4, 1.5 DataType.pm, 1.6, 1.7 IOHandler.pm, 1.37, 1.38 Input.pm, 1.10, 1.11 InputCreate.pm, 1.9, 1.10 Job.pm, 1.46, 1.47 Manager.pm, 1.11, 1.12 Method.pm, 1.5, 1.6 Node.pm, 1.3, 1.4 NodeGroup.pm, 1.4, 1.5 Rule.pm, 1.9, 1.10 RunnableDB.pm, 1.37, 1.38 RunnableI.pm, 1.15, 1.16 Transformer.pm, 1.13, 1.14 XMLImporter.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Runnable Blat.pm, 1.3, 1.4 Coil.pm, 1.2, 1.3 EnsemblRunnable.pm, 1.3, 1.4 Hmmpfam.pm, 1.9, 1.10 Prints.pm, 1.2, 1.3 Profile.pm, 1.2, 1.3 ProteinAnnotation.pm, 1.3, 1.4 Seg.pm, 1.2, 1.3 Signalp.pm, 1.2, 1.3 Tmhmm.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/BatchSubmission LSF.pm, 1.15, 1.16 PBS.pm, 1.10, 1.11 SunGrid.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/InputCreate setup_cdna2genome.pm, 1.1, 1.2 setup_family.pm, 1.1, 1.2 setup_file.pm, 1.6, 1.7 setup_file_blast.pm, 1.2, 1.3 setup_genewise.pm, 1.11, 1.12 setup_initial.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/SQL DataMongerAdaptor.pm, 1.6, 1.7 IOHandlerAdaptor.pm, 1.20, 1.21 InputAdaptor.pm, 1.27, 1.28 JobAdaptor.pm, 1.34, 1.35 NodeAdaptor.pm, 1.5, 1.6 NodeGroupAdaptor.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/scripts validate_xml.pl,1.3,1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils Dumper.pm, 1.8, 1.9 Filter.pm, 1.8, 1.9 Iterator.pm, 1.2, 1.3 SaxHandler.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils/Filter feature_coverage.pm, 1.9, 1.10 feature_filter.pm, 1.5, 1.6 simple_align.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils/Dumper blastscore.pm, 1.7, 1.8 generic.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Factory EMBOSS.pm,1.4,1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip Consense.pm, 1.11, 1.12 Neighbor.pm, 1.24, 1.25 PhylipConf.pm, 1.12, 1.13 ProtDist.pm, 1.27, 1.28 ProtPars.pm, 1.21, 1.22 SeqBoot.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Blat.pm, 1.11, 1.12 Clustalw.pm, 1.44, 1.45 DBA.pm, 1.11, 1.12 Exonerate.pm, 1.3, 1.4 Muscle.pm, 1.7, 1.8 Probcons.pm, 1.6, 1.7 Sim4.pm, 1.7, 1.8 StandAloneFasta.pm, 1.11, 1.12 TCoffee.pm, 1.41, 1.42   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo LVB.pm,1.5,1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Cap3.pm, 1.2, 1.3 Coil.pm, 1.8, 1.9 EMBOSSApplication.pm, 1.22, 1.23 EMBOSSacd.pm, 1.6, 1.7 Eponine.pm, 1.12, 1.13 FootPrinter.pm, 1.12, 1.13 Genewise.pm, 1.23, 1.24 Genscan.pm, 1.12, 1.13 Hmmer.pm, 1.6, 1.7 Phrap.pm, 1.3, 1.4 Primate.pm, 1.13, 1.14 Prints.pm, 1.8, 1.9 Profile.pm, 1.11, 1.12 Promoterwise.pm, 1.6, 1.7 Pseudowise.pm, 1.15, 1.16 RepeatMasker.pm, 1.23, 1.24 Seg.pm, 1.13, 1.14 Signalp.pm, 1.7, 1.8 Tmhmm.pm, 1.10, 1.11 TribeMCL.pm, 1.19, 1.20 Vista.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-ext/Bio/SeqIO/staden read.pm,1.11,1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm, 1.44, 1.45 AnalysisParserI.pm, 1.10, 1.11 AnalysisResultI.pm, 1.8, 1.9 ClusterIO.pm, 1.16, 1.17 DescribableI.pm, 1.8, 1.9 FeatureIO.pm, 1.13, 1.14 IdCollectionI.pm, 1.4, 1.5 IdentifiableI.pm, 1.9, 1.10 LocatableSeq.pm, 1.37, 1.38 LocationI.pm, 1.23, 1.24 PrimarySeq.pm, 1.93, 1.94 PrimarySeqI.pm, 1.63, 1.64 Range.pm, 1.25, 1.26 RangeI.pm, 1.46, 1.47 SearchDist.pm, 1.18, 1.19 SeqAnalysisParserI.pm, 1.14, 1.15 SeqFeatureI.pm, 1.63, 1.64 SeqI.pm, 1.27, 1.28 SeqIO.pm, 1.90, 1.91 SeqUtils.pm, 1.28, 1.29 SimpleAlign.pm, 1.105, 1.106   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm, 1.11, 1.12 phrap.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.8, 1.9 ContigAnalysis.pm, 1.4, 1.5 IO.pm, 1.4, 1.5 Scaffold.pm, 1.9, 1.10 ScaffoldI.pm, 1.4, 1.5 Singlet.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/CodonUsage IO.pm, 1.9, 1.10 Table.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm, 1.21, 1.22 clustalw.pm, 1.32, 1.33   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Biblio IO.pm,1.15,1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/ClusterIO dbsnp.pm, 1.14, 1.15 unigene.pm, 1.27, 1.28   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate Chain.pm, 1.5, 1.6 Collection.pm, 1.22, 1.23 ExtrapolatingPair.pm, 1.14, 1.15 GeneMapper.pm, 1.25, 1.26 Graph.pm, 1.8, 1.9 MapperI.pm, 1.8, 1.9 Pair.pm, 1.17, 1.18 Result.pm, 1.13, 1.14 ResultI.pm, 1.4, 1.5 Utils.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Factory ApplicationFactoryI.pm, 1.8, 1.9 DriverFactory.pm, 1.13, 1.14 HitFactoryI.pm, 1.9, 1.10 ResultFactoryI.pm, 1.8, 1.9 SeqAnalysisParserFactory.pm, 1.13, 1.14 SeqAnalysisParserFactoryI.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq ChainI.pm, 1.14, 1.15 Mutation.pm, 1.11, 1.12 Mutator.pm, 1.31, 1.32 SeqI.pm, 1.29, 1.30   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph IO.pm,1.15,1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate/Result Gap.pm, 1.7, 1.8 Match.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB BioFetch.pm, 1.27, 1.28 CUTG.pm, 1.9, 1.10 DBFetch.pm, 1.11, 1.12 Flat.pm, 1.22, 1.23 MeSH.pm, 1.6, 1.7 RefSeq.pm, 1.11, 1.12 SwissProt.pm, 1.28, 1.29 XEMBL.pm, 1.8, 1.9 XEMBLService.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.24, 1.25   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Map CytoPosition.pm,1.13,1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat/BDB embl.pm, 1.11, 1.12 fasta.pm, 1.7, 1.8 genbank.pm, 1.6, 1.7 swiss.pm, 1.5, 1.6 swissprot.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BDB.pm, 1.15, 1.16 BinarySearch.pm, 1.21, 1.22   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Expression FeatureGroup.pm, 1.6, 1.7 FeatureI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Location Atomic.pm, 1.14, 1.15 AvWithinCoordPolicy.pm, 1.6, 1.7 CoordinatePolicyI.pm, 1.6, 1.7 Fuzzy.pm, 1.31, 1.32 FuzzyLocationI.pm, 1.19, 1.20 NarrowestCoordPolicy.pm, 1.9, 1.10 Simple.pm, 1.39, 1.40 Split.pm, 1.44, 1.45 SplitLocationI.pm, 1.16, 1.17 WidestCoordPolicy.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm, 1.47, 1.48 AbstractSeq.pm, 1.21, 1.22 EMBL.pm, 1.30, 1.31 Fasta.pm, 1.33, 1.34 Fastq.pm, 1.10, 1.11 GenBank.pm, 1.21, 1.22 Qual.pm, 1.7, 1.8 SwissPfam.pm, 1.22, 1.23 Swissprot.pm, 1.24, 1.25   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/MeSH Term.pm, 1.5, 1.6 Twig.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Correlate.pm, 1.7, 1.8 Measure.pm, 1.7, 1.8 Phenotype.pm, 1.10, 1.11 PhenotypeI.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO/Handlers InterProHandler.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology/SimpleGOEngine GraphAdaptor.pm, 1.4, 1.5 GraphAdaptor02.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM IO.pm, 1.13, 1.14 InstanceSite.pm, 1.12, 1.13 InstanceSiteI.pm, 1.8, 1.9 ProtMatrix.pm, 1.14, 1.15 ProtPsm.pm, 1.6, 1.7 Psm.pm, 1.12, 1.13 PsmHeader.pm, 1.9, 1.10 PsmHeaderI.pm, 1.8, 1.9 PsmI.pm, 1.6, 1.7 SiteMatrix.pm, 1.29, 1.30 SiteMatrixI.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/Enzyme MultiCut.pm, 1.5, 1.6 MultiSite.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.15, 1.16 Enzyme.pm, 1.12, 1.13 EnzymeCollection.pm, 1.8, 1.9 EnzymeI.pm, 1.4, 1.5 IO.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology GOterm.pm, 1.20, 1.21 OBOEngine.pm, 1.4, 1.5 OBOterm.pm, 1.3, 1.4 Path.pm, 1.5, 1.6 Relationship.pm, 1.12, 1.13 RelationshipType.pm, 1.15, 1.16 SimpleGOEngine.pm, 1.34, 1.35 Term.pm, 1.29, 1.30 TermI.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO dagflat.pm, 1.27, 1.28 goflat.pm, 1.5, 1.6 obo.pm, 1.5, 1.6 simplehierarchy.pm, 1.15, 1.16 soflat.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/IO bairoch.pm, 1.6, 1.7 base.pm, 1.9, 1.10 itype2.pm, 1.4, 1.5 withrefm.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.19, 1.20 masta.pm, 1.8, 1.9 meme.pm, 1.18, 1.19 psiblast.pm, 1.9, 1.10 transfac.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM MiniMIMentry.pm, 1.7, 1.8 OMIMentry.pm, 1.14, 1.15 OMIMentryAllelicVariant.pm, 1.7, 1.8 OMIMparser.pm, 1.18, 1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit Fasta.pm, 1.8, 1.9 HitI.pm, 1.22, 1.23 PsiBlastHit.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search DatabaseI.pm, 1.8, 1.9 GenericDatabase.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq/Meta Array.pm,1.11,1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer HSPTableWriter.pm, 1.15, 1.16 HitTableWriter.pm, 1.18, 1.19 ResultTableWriter.pm, 1.17, 1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.31, 1.32 Computation.pm, 1.14, 1.15 Generic.pm, 1.101, 1.102 PositionProxy.pm, 1.7, 1.8 Primer.pm, 1.19, 1.20 Similarity.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.26, 1.27 PsiBlastHSP.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Root Err.pm, 1.19, 1.20 HTTPget.pm, 1.12, 1.13 IO.pm, 1.59, 1.60 IOManager.pm, 1.17, 1.18 Object.pm, 1.29, 1.30 Utilities.pm, 1.29, 1.30 Vector.pm, 1.15, 1.16 Version.pm, 1.7, 1.8 Xref.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq EncodedSeq.pm, 1.9, 1.10 LargePrimarySeq.pm, 1.30, 1.31 LargeSeq.pm, 1.13, 1.14 Meta.pm, 1.10, 1.11 MetaI.pm, 1.8, 1.9 PrimaryQual.pm, 1.22, 1.23 PrimedSeq.pm, 1.21, 1.22 QualI.pm, 1.9, 1.10 Quality.pm, 1.8, 1.9 RichSeq.pm, 1.17, 1.18 RichSeqI.pm, 1.12, 1.13 SeqWithQuality.pm, 1.25, 1.26 SequenceTrace.pm, 1.12, 1.13 TraceI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene Exon.pm, 1.13, 1.14 ExonI.pm, 1.9, 1.10 GeneStructureI.pm, 1.10, 1.11 TranscriptI.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/STRIDE Res.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools AnalysisResult.pm, 1.15, 1.16 BPbl2seq.pm, 1.27, 1.28 Blast.pm, 1.35, 1.36 Blat.pm, 1.5, 1.6 CodonTable.pm, 1.34, 1.35 Coil.pm, 1.4, 1.5 ECnumber.pm, 1.9, 1.10 ESTScan.pm, 1.12, 1.13 Eponine.pm, 1.11, 1.12 Fgenesh.pm, 1.6, 1.7 GFF.pm, 1.55, 1.56 Geneid.pm, 1.3, 1.4 Genemark.pm, 1.15, 1.16 Genewise.pm, 1.23, 1.24 Genomewise.pm, 1.4, 1.5 Genscan.pm, 1.27, 1.28 Grail.pm, 1.9, 1.10 GuessSeqFormat.pm, 1.13, 1.14 HMM.pm, 1.6, 1.7 Hmmpfam.pm, 1.6, 1.7 IUPAC.pm, 1.26, 1.27 Lucy.pm, 1.13, 1.14 MZEF.pm, 1.12, 1.13 OddCodes.pm, 1.17, 1.18 Primer3.pm, 1.18, 1.19 Prints.pm, 1.11, 1.12 Profile.pm, 1.6, 1.7 Pseudowise.pm, 1.8, 1.9 RestrictionEnzyme.pm, 1.33, 1.34 SeqAnal.pm, 1.16, 1.17 SeqPattern.pm, 1.19, 1.20 SeqStats.pm, 1.28, 1.29 SeqWords.pm, 1.15, 1.16 Signalp.pm, 1.6, 1.7 dpAlign.pm, 1.16, 1.17 pICalculator.pm, 1.7, 1.8 pSW.pm, 1.25, 1.26   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure Atom.pm, 1.10, 1.11 Chain.pm, 1.8, 1.9 Entry.pm, 1.23, 1.24 Model.pm, 1.8, 1.9 Residue.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO FTHelper.pm, 1.59, 1.60 MultiFile.pm, 1.10, 1.11 abi.pm, 1.12, 1.13 agave.pm, 1.13, 1.14 alf.pm, 1.10, 1.11 ctf.pm, 1.13, 1.14 embl.pm, 1.88, 1.89 exp.pm, 1.13, 1.14 fasta.pm, 1.55, 1.56 fastq.pm, 1.13, 1.14 gcg.pm, 1.24, 1.25 largefasta.pm, 1.22, 1.23 lasergene.pm, 1.4, 1.5 metafasta.pm, 1.7, 1.8 pir.pm, 1.21, 1.22 pln.pm, 1.10, 1.11 raw.pm, 1.19, 1.20 strider.pm, 1.4, 1.5 swiss.pm, 1.90, 1.91 tab.pm, 1.5, 1.6 tigr.pm, 1.11, 1.12 ztr.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools FeatureNamer.pm, 1.4, 1.5 IDHandler.pm, 1.8, 1.9 TypeMapper.pm, 1.12, 1.13 Unflattener.pm, 1.35, 1.36   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/IO pdb.pm,1.14,1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Sim4 Exon.pm, 1.14, 1.15 Results.pm, 1.23, 1.24   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.34, 1.35 StandAloneBlast.pm, 1.61, 1.62   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Domcut.pm, 1.12, 1.13 ELM.pm, 1.10, 1.11 GOR4.pm, 1.10, 1.11 HNN.pm, 1.10, 1.11 Mitoprot.pm, 1.6, 1.7 NetPhos.pm, 1.11, 1.12 Scansite.pm, 1.14, 1.15 Sopma.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Prediction Exon.pm, 1.14, 1.15 Gene.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.21, 1.22 HTML.pm, 1.17, 1.18 Sbjct.pm, 1.23, 1.24   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.26, 1.27 Set.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis SimpleAnalysisBase.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.39, 1.40 Trim.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/doc/Deobfuscator/cgi-bin deob_detail.cgi, 1.1, 1.2 deob_interface.cgi, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Spidey Exon.pm, 1.4, 1.5 Results.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio PrimarySeq.pm, 1.4, 1.5 PrimarySeqI.pm, 1.4, 1.5 SeqI.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/doc/Deobfuscator/lib Deobfuscator.pm, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/doc/Deobfuscator/bin deob_index.pl, 1.1, 1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation AAChange.pm, 1.18, 1.19 AAReverseMutate.pm, 1.10, 1.11 Allele.pm, 1.13, 1.14 DNAMutation.pm, 1.16, 1.17 IO.pm, 1.20, 1.21 RNAChange.pm, 1.15, 1.16 SNP.pm, 1.14, 1.15 SeqDiff.pm, 1.21, 1.22 VariantI.pm, 1.18, 1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation/IO flat.pm, 1.17, 1.18 xml.pm, 1.17, 1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/utilities remote_blast.PLS, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/DB flanks.PLS,1.5,1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/MicroarrayIO affymetrix.pm, 1.16, 1.17 dchipxls.pm, 1.7, 1.8 mas50txt.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/Microarray FeatureI.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression/Microarray/Affymetrix Array.pm, 1.12, 1.13 ArrayDesign.pm, 1.9, 1.10 CelArray.pm, 1.4, 1.5 Data.pm, 1.12, 1.13 Feature.pm, 1.7, 1.8 Mas50TxtArray.pm, 1.6, 1.7 dChipArray.pm, 1.4, 1.5 dChipXLS.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO/psi intact.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO dip_tab.pm, 1.3, 1.4 psi.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network Edge.pm, 1.3, 1.4 Interaction.pm, 1.3, 1.4 Node.pm, 1.2, 1.3 ProteinNet.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Runnable Blat.pm, 1.4, 1.5 Coil.pm, 1.3, 1.4 EnsemblRunnable.pm, 1.4, 1.5 Hmmpfam.pm, 1.10, 1.11 Prints.pm, 1.3, 1.4 Profile.pm, 1.3, 1.4 ProteinAnnotation.pm, 1.4, 1.5 Seg.pm, 1.3, 1.4 Signalp.pm, 1.3, 1.4 Tmhmm.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline Analysis.pm, 1.32, 1.33 Argument.pm, 1.9, 1.10 DataHandler.pm, 1.5, 1.6 DataType.pm, 1.7, 1.8 IOHandler.pm, 1.38, 1.39 Input.pm, 1.11, 1.12 InputCreate.pm, 1.10, 1.11 Job.pm, 1.47, 1.48 Manager.pm, 1.12, 1.13 Method.pm, 1.6, 1.7 Rule.pm, 1.10, 1.11 RunnableDB.pm, 1.38, 1.39 RunnableI.pm, 1.16, 1.17 Transformer.pm, 1.14, 1.15 XMLImporter.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/BatchSubmission LSF.pm, 1.16, 1.17 PBS.pm, 1.11, 1.12 SunGrid.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/SQL IOHandlerAdaptor.pm, 1.21, 1.22 InputAdaptor.pm, 1.28, 1.29 JobAdaptor.pm, 1.35, 1.36   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/InputCreate setup_cdna2genome.pm, 1.2, 1.3 setup_family.pm, 1.2, 1.3 setup_file.pm, 1.7, 1.8 setup_file_blast.pm, 1.3, 1.4 setup_genewise.pm, 1.12, 1.13 setup_initial.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils Dumper.pm, 1.9, 1.10 Filter.pm, 1.9, 1.10 Iterator.pm, 1.3, 1.4 SaxHandler.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils/Dumper blastscore.pm, 1.8, 1.9 generic.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils/Filter feature_coverage.pm, 1.10, 1.11 feature_filter.pm, 1.6, 1.7 simple_align.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo LVB.pm,1.6,1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Factory EMBOSS.pm,1.5,1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Blat.pm, 1.12, 1.13 Clustalw.pm, 1.45, 1.46 DBA.pm, 1.12, 1.13 Exonerate.pm, 1.4, 1.5 MAFFT.pm, 1.6, 1.7 Muscle.pm, 1.8, 1.9 Probcons.pm, 1.7, 1.8 Sim4.pm, 1.8, 1.9 StandAloneFasta.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip Consense.pm, 1.12, 1.13 Neighbor.pm, 1.25, 1.26 PhylipConf.pm, 1.13, 1.14 ProtDist.pm, 1.28, 1.29 ProtPars.pm, 1.22, 1.23 SeqBoot.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Cap3.pm, 1.3, 1.4 Coil.pm, 1.9, 1.10 EMBOSSApplication.pm, 1.23, 1.24 EMBOSSacd.pm, 1.7, 1.8 Eponine.pm, 1.13, 1.14 Genewise.pm, 1.24, 1.25 Genscan.pm, 1.13, 1.14 Hmmer.pm, 1.7, 1.8 Phrap.pm, 1.4, 1.5 Primate.pm, 1.14, 1.15 Primer3.pm, 1.16, 1.17 Prints.pm, 1.9, 1.10 Profile.pm, 1.12, 1.13 Promoterwise.pm, 1.7, 1.8 Pseudowise.pm, 1.16, 1.17 Seg.pm, 1.14, 1.15 Signalp.pm, 1.8, 1.9 Tmhmm.pm, 1.11, 1.12 Vista.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live AUTHORS,1.46,1.47   Mauricio Herrera Cuadra
• [Bioperl-guts-l] Mauricio Herrera Cuadra   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live DEPRECATED, 1.7, 1.8 INSTALL, 1.45, 1.46 INSTALL.WIN, 1.19, 1.20 PLATFORMS, 1.24, 1.25 README, 1.41, 1.42 bptutorial.pl, 1.166, 1.167   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts README,1.1,1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live README,1.42,1.43   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-corba-server/Bio/CorbaServer Alphabet.pm, 1.2, 1.3 Annotation.pm, 1.5, 1.6 AnnotationCollection.pm, 1.6, 1.7 SeqIterator.pm, 1.4, 1.5 Symbol.pm, 1.3, 1.4 Utils.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/DBI Oracle.pm, 1.7, 1.8 Pg.pm, 1.3, 1.4 base.pm, 1.9, 1.10 mysql.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Oracle AnnotationCollectionAdaptorDriver.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/Query DBQueryResult.pm, 1.3, 1.4 PrebuiltResult.pm, 1.2, 1.3 QueryResultI.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio BioEntry.pm,1.2,1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB DBAdaptorI.pm, 1.2, 1.3 DBD.pm, 1.2, 1.3 DBI.pm, 1.5, 1.6 PersistenceAdaptorI.pm, 1.3, 1.4 PersistentObjectI.pm, 1.4, 1.5 SimpleDBContext.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Pg AnnotationCollectionAdaptorDriver.pm, 1.2, 1.3 BiosequenceAdaptorDriver.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/mysql AnnotationCollectionAdaptorDriver.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/Persistent BioNamespace.pm, 1.3, 1.4 ObjectRelMapperI.pm, 1.2, 1.3 PersistentObject.pm, 1.7, 1.8 PersistentObjectFactory.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-microarray/Bio/Expression MicroarrayIO.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree Draw.pm, 1.13, 1.14 Group.pm, 1.18, 1.19 GroupI.pm, 1.10, 1.11 MarkerI.pm, 1.9, 1.10 PedIO.pm, 1.13, 1.14 Person.pm, 1.15, 1.16 PersonI.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree/PedIO lapis.pm, 1.15, 1.16 linkage.pm, 1.10, 1.11 ped.pm, 1.15, 1.16 xml.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree/Draw Command.pm, 1.7, 1.8 GD.pm, 1.11, 1.12 GraphicsI.pm, 1.7, 1.8 PedPlot.pm, 1.12, 1.13 PedRenderI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/scripts validate_xml.pl,1.4,1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/PAML Codeml.pm, 1.42, 1.43 Evolver.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/PiseApplication Puzzle.pm, 1.5, 1.6 phyml.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL AnnotationCollectionAdaptor.pm, 1.12, 1.13 BaseDriver.pm, 1.29, 1.30 BasePersistenceAdaptor.pm, 1.39, 1.40 ClusterAdaptor.pm, 1.13, 1.14 OntologyAdaptor.pm, 1.4, 1.5 PathAdaptor.pm, 1.3, 1.4 ReferenceAdaptor.pm, 1.23, 1.24 RelationshipAdaptor.pm, 1.5, 1.6 SeqAdaptor.pm, 1.51, 1.52 SeqFeatureAdaptor.pm, 1.30, 1.31 SimpleValueAdaptor.pm, 1.12, 1.13 SpeciesAdaptor.pm, 1.22, 1.23 TermAdaptor.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Pg BasePersistenceAdaptorDriver.pm, 1.8, 1.9 PathAdaptorDriver.pm, 1.4, 1.5 SpeciesAdaptorDriver.pm, 1.4, 1.5 TermAdaptorDriver.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/mysql BasePersistenceAdaptorDriver.pm, 1.17, 1.18 BiosequenceAdaptorDriver.pm, 1.5, 1.6 PathAdaptorDriver.pm, 1.4, 1.5 SpeciesAdaptorDriver.pm, 1.7, 1.8 TermAdaptorDriver.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live README, 1.43, 1.44 bioperl.lisp, 1.29, 1.30   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Oracle BasePersistenceAdaptorDriver.pm, 1.15, 1.16 BiosequenceAdaptorDriver.pm, 1.10, 1.11 PathAdaptorDriver.pm, 1.4, 1.5 SpeciesAdaptorDriver.pm, 1.3, 1.4 TermAdaptorDriver.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-ext/Bio/SeqIO/staden read.pm,1.12,1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-db/Bio/DB/DBI Transaction.pm, 1.2, 1.3 TransactionListener.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm, 1.45, 1.46 AnalysisI.pm, 1.9, 1.10 AnalysisParserI.pm, 1.11, 1.12 AnalysisResultI.pm, 1.9, 1.10 AnnotatableI.pm, 1.11, 1.12 AnnotationCollectionI.pm, 1.16, 1.17 AnnotationI.pm, 1.9, 1.10 Biblio.pm, 1.15, 1.16 ClusterI.pm, 1.5, 1.6 ClusterIO.pm, 1.17, 1.18 DBLinkContainerI.pm, 1.11, 1.12 DasI.pm, 1.17, 1.18 DescribableI.pm, 1.9, 1.10 FeatureHolderI.pm, 1.9, 1.10 FeatureIO.pm, 1.14, 1.15 Graphics.pm, 1.16, 1.17 IdCollectionI.pm, 1.5, 1.6 IdentifiableI.pm, 1.10, 1.11 LocatableSeq.pm, 1.38, 1.39 LocationI.pm, 1.24, 1.25 MapIO.pm, 1.8, 1.9 OntologyIO.pm, 1.11, 1.12 Perl.pm, 1.25, 1.26 PrimarySeq.pm, 1.94, 1.95 PrimarySeqI.pm, 1.64, 1.65 Range.pm, 1.26, 1.27 RangeI.pm, 1.47, 1.48 SearchDist.pm, 1.19, 1.20 SearchIO.pm, 1.38, 1.39 Seq.pm, 1.90, 1.91 SeqAnalysisParserI.pm, 1.15, 1.16 SeqFeatureI.pm, 1.64, 1.65 SeqI.pm, 1.28, 1.29 SeqIO.pm, 1.91, 1.92 SeqUtils.pm, 1.29, 1.30 SimpleAlign.pm, 1.106, 1.107 SimpleAnalysisI.pm, 1.8, 1.9 Species.pm, 1.33, 1.34 TreeIO.pm, 1.19, 1.20 UpdateableSeqI.pm, 1.6, 1.7 WebAgent.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm, 1.12, 1.13 phrap.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Align AlignI.pm, 1.15, 1.16 DNAStatistics.pm, 1.31, 1.32 PairwiseStatistics.pm, 1.9, 1.10 ProteinStatistics.pm, 1.6, 1.7 StatisticsI.pm, 1.6, 1.7 Utilities.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.9, 1.10 ContigAnalysis.pm, 1.5, 1.6 IO.pm, 1.5, 1.6 Scaffold.pm, 1.10, 1.11 ScaffoldI.pm, 1.5, 1.6 Singlet.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Annotation AnnotationFactory.pm, 1.5, 1.6 Collection.pm, 1.22, 1.23 OntologyTerm.pm, 1.14, 1.15 SimpleValue.pm, 1.17, 1.18 StructuredValue.pm, 1.6, 1.7 TypeManager.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm, 1.22, 1.23 clustalw.pm, 1.33, 1.34 emboss.pm, 1.16, 1.17 fasta.pm, 1.26, 1.27 largemultifasta.pm, 1.8, 1.9 maf.pm, 1.9, 1.10 mase.pm, 1.10, 1.11 mega.pm, 1.10, 1.11 meme.pm, 1.9, 1.10 metafasta.pm, 1.5, 1.6 msf.pm, 1.21, 1.22 nexus.pm, 1.26, 1.27 pfam.pm, 1.11, 1.12 phylip.pm, 1.35, 1.36 po.pm, 1.5, 1.6 prodom.pm, 1.9, 1.10 psi.pm, 1.10, 1.11 selex.pm, 1.13, 1.14 stockholm.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Biblio/IO medline2ref.pm, 1.14, 1.15 medlinexml.pm, 1.8, 1.9 pubmed2ref.pm, 1.5, 1.6 pubmedxml.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/CodonUsage IO.pm, 1.10, 1.11 Table.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/ClusterIO dbsnp.pm, 1.15, 1.16 unigene.pm, 1.28, 1.29   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate/Result Gap.pm, 1.8, 1.9 Match.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate Chain.pm, 1.6, 1.7 Collection.pm, 1.23, 1.24 ExtrapolatingPair.pm, 1.15, 1.16 GeneMapper.pm, 1.26, 1.27 Graph.pm, 1.9, 1.10 MapperI.pm, 1.9, 1.10 Pair.pm, 1.18, 1.19 Result.pm, 1.14, 1.15 ResultI.pm, 1.5, 1.6 Utils.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Cluster ClusterFactory.pm, 1.5, 1.6 FamilyI.pm, 1.5, 1.6 SequenceFamily.pm, 1.9, 1.10 UniGene.pm, 1.37, 1.38 UniGeneI.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.13, 1.14 BiblioBase.pm, 1.12, 1.13 Book.pm, 1.13, 1.14 BookArticle.pm, 1.12, 1.13 IO.pm, 1.16, 1.17 Journal.pm, 1.12, 1.13 JournalArticle.pm, 1.13, 1.14 MedlineArticle.pm, 1.11, 1.12 MedlineBook.pm, 1.9, 1.10 MedlineBookArticle.pm, 1.9, 1.10 MedlineJournal.pm, 1.9, 1.10 MedlineJournalArticle.pm, 1.9, 1.10 Organisation.pm, 1.13, 1.14 Patent.pm, 1.13, 1.14 Person.pm, 1.14, 1.15 Proceeding.pm, 1.12, 1.13 Provider.pm, 1.10, 1.11 PubmedArticle.pm, 1.8, 1.9 PubmedBookArticle.pm, 1.8, 1.9 PubmedJournalArticle.pm, 1.9, 1.10 Ref.pm, 1.11, 1.12 Service.pm, 1.12, 1.13 TechReport.pm, 1.11, 1.12 Thesis.pm, 1.11, 1.12 WebResource.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqVersion gi.pm,1.3,1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy entrez.pm, 1.13, 1.14 flatfile.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Event EventGeneratorI.pm, 1.10, 1.11 EventHandlerI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat/BDB embl.pm, 1.12, 1.13 fasta.pm, 1.8, 1.9 genbank.pm, 1.7, 1.8 swiss.pm, 1.6, 1.7 swissprot.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Das FeatureTypeI.pm, 1.5, 1.6 SegmentI.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB Ace.pm, 1.14, 1.15 BiblioI.pm, 1.9, 1.10 BioFetch.pm, 1.28, 1.29 CUTG.pm, 1.10, 1.11 DBFetch.pm, 1.12, 1.13 EMBL.pm, 1.20, 1.21 EUtilities.pm, 1.6, 1.7 EntrezGene.pm, 1.7, 1.8 Expression.pm, 1.3, 1.4 Failover.pm, 1.9, 1.10 FileCache.pm, 1.10, 1.11 Flat.pm, 1.23, 1.24 GDB.pm, 1.19, 1.20 GenBank.pm, 1.58, 1.59 GenPept.pm, 1.30, 1.31 InMemoryCache.pm, 1.6, 1.7 MeSH.pm, 1.7, 1.8 NCBIHelper.pm, 1.52, 1.53 QueryI.pm, 1.4, 1.5 RandomAccessI.pm, 1.13, 1.14 RefSeq.pm, 1.12, 1.13 Registry.pm, 1.31, 1.32 SeqI.pm, 1.9, 1.10 SeqVersion.pm, 1.4, 1.5 SwissProt.pm, 1.29, 1.30 Taxonomy.pm, 1.7, 1.8 Universal.pm, 1.4, 1.5 UpdateableSeqI.pm, 1.7, 1.8 WebDBSeqI.pm, 1.55, 1.56 XEMBL.pm, 1.9, 1.10 XEMBLService.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities elink.pm, 1.5, 1.6 esearch.pm, 1.5, 1.6 esummary.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm, 1.9, 1.10 eutils.pm, 1.10, 1.11 pdf.pm, 1.5, 1.6 soap.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Query GenBank.pm, 1.16, 1.17 WebQuery.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BDB.pm, 1.16, 1.17 BinarySearch.pm, 1.22, 1.23   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics ConfiguratorI.pm, 1.7, 1.8 Pictogram.pm, 1.13, 1.14 RendererI.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.25, 1.26   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph Edge.pm, 1.10, 1.11 IO.pm, 1.16, 1.17 ProteinGraph.pm, 1.34, 1.35   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Expression Contact.pm, 1.3, 1.4 DataSet.pm, 1.2, 1.3 FeatureGroup.pm, 1.7, 1.8 FeatureI.pm, 1.8, 1.9 Platform.pm, 1.3, 1.4 Sample.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm, 1.3, 1.4 gff.pm, 1.40, 1.41 gtf.pm, 1.3, 1.4 interpro.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Factory AnalysisI.pm, 1.6, 1.7 ApplicationFactoryI.pm, 1.9, 1.10 DriverFactory.pm, 1.14, 1.15 FTLocationFactory.pm, 1.20, 1.21 HitFactoryI.pm, 1.10, 1.11 LocationFactoryI.pm, 1.6, 1.7 MapFactoryI.pm, 1.7, 1.8 ObjectBuilderI.pm, 1.4, 1.5 ObjectFactory.pm, 1.4, 1.5 ObjectFactoryI.pm, 1.5, 1.6 ResultFactoryI.pm, 1.9, 1.10 SeqAnalysisParserFactory.pm, 1.14, 1.15 SeqAnalysisParserFactoryI.pm, 1.11, 1.12 SequenceFactoryI.pm, 1.9, 1.10 SequenceProcessorI.pm, 1.3, 1.4 SequenceStreamI.pm, 1.5, 1.6 TreeFactoryI.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graph/SimpleGraph Traversal.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm, 1.48, 1.49 AbstractSeq.pm, 1.22, 1.23 Blast.pm, 1.20, 1.21 EMBL.pm, 1.31, 1.32 Fasta.pm, 1.34, 1.35 Fastq.pm, 1.11, 1.12 GenBank.pm, 1.22, 1.23 Hmmer.pm, 1.9, 1.10 Qual.pm, 1.8, 1.9 SwissPfam.pm, 1.23, 1.24 Swissprot.pm, 1.25, 1.26   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq ChainI.pm, 1.15, 1.16 Mutation.pm, 1.12, 1.13 Mutator.pm, 1.32, 1.33 SeqI.pm, 1.30, 1.31   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Location Atomic.pm, 1.15, 1.16 AvWithinCoordPolicy.pm, 1.7, 1.8 CoordinatePolicyI.pm, 1.7, 1.8 Fuzzy.pm, 1.32, 1.33 FuzzyLocationI.pm, 1.20, 1.21 NarrowestCoordPolicy.pm, 1.10, 1.11 Simple.pm, 1.40, 1.41 Split.pm, 1.45, 1.46 SplitLocationI.pm, 1.17, 1.18 WidestCoordPolicy.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology DocumentRegistry.pm, 1.10, 1.11 GOterm.pm, 1.21, 1.22 InterProTerm.pm, 1.9, 1.10 OBOEngine.pm, 1.5, 1.6 OBOterm.pm, 1.4, 1.5 Ontology.pm, 1.17, 1.18 OntologyEngineI.pm, 1.14, 1.15 OntologyI.pm, 1.8, 1.9 OntologyStore.pm, 1.12, 1.13 Path.pm, 1.6, 1.7 PathI.pm, 1.5, 1.6 Relationship.pm, 1.13, 1.14 RelationshipFactory.pm, 1.4, 1.5 RelationshipI.pm, 1.8, 1.9 RelationshipType.pm, 1.16, 1.17 SimpleGOEngine.pm, 1.35, 1.36 SimpleOntologyEngine.pm, 1.16, 1.17 Term.pm, 1.30, 1.31 TermFactory.pm, 1.6, 1.7 TermI.pm, 1.16, 1.17   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/MapIO fpc.pm, 1.5, 1.6 mapmaker.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Ontology/SimpleGOEngine GraphAdaptor.pm, 1.5, 1.6 GraphAdaptor02.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix Generic.pm, 1.13, 1.14 IO.pm, 1.4, 1.5 MatrixI.pm, 1.3, 1.4 PhylipDist.pm, 1.15, 1.16 Scoring.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/IO phylip.pm, 1.2, 1.3 scoring.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.20, 1.21 masta.pm, 1.9, 1.10 meme.pm, 1.19, 1.20 psiblast.pm, 1.10, 1.11 transfac.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Map Clone.pm, 1.4, 1.5 Contig.pm, 1.4, 1.5 CytoMap.pm, 1.8, 1.9 CytoMarker.pm, 1.10, 1.11 CytoPosition.pm, 1.14, 1.15 FPCMarker.pm, 1.5, 1.6 LinkageMap.pm, 1.15, 1.16 LinkagePosition.pm, 1.13, 1.14 MapI.pm, 1.11, 1.12 Mappable.pm, 1.2, 1.3 MappableI.pm, 1.13, 1.14 Marker.pm, 1.19, 1.20 MarkerI.pm, 1.13, 1.14 Microsatellite.pm, 1.11, 1.12 OrderedPosition.pm, 1.8, 1.9 OrderedPositionWithDistance.pm, 1.8, 1.9 Physical.pm, 1.6, 1.7 Position.pm, 1.15, 1.16 PositionI.pm, 1.13, 1.14 SimpleMap.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM IO.pm, 1.14, 1.15 InstanceSite.pm, 1.13, 1.14 InstanceSiteI.pm, 1.9, 1.10 ProtMatrix.pm, 1.15, 1.16 ProtPsm.pm, 1.7, 1.8 Psm.pm, 1.13, 1.14 PsmHeader.pm, 1.10, 1.11 PsmHeaderI.pm, 1.9, 1.10 PsmI.pm, 1.7, 1.8 SiteMatrix.pm, 1.30, 1.31 SiteMatrixI.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.16, 1.17 Enzyme.pm, 1.13, 1.14 EnzymeCollection.pm, 1.9, 1.10 EnzymeI.pm, 1.5, 1.6 IO.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/IO csv.pm, 1.7, 1.8 hapmap.pm, 1.7, 1.8 phase.pm, 1.6, 1.7 prettybase.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/PopGen Genotype.pm, 1.9, 1.10 GenotypeI.pm, 1.2, 1.3 HtSNP.pm, 1.5, 1.6 IO.pm, 1.5, 1.6 Individual.pm, 1.14, 1.15 IndividualI.pm, 1.6, 1.7 Marker.pm, 1.6, 1.7 MarkerI.pm, 1.5, 1.6 PopStats.pm, 1.9, 1.10 Population.pm, 1.18, 1.19 PopulationI.pm, 1.8, 1.9 Statistics.pm, 1.33, 1.34 TagHaplotype.pm, 1.4, 1.5 Utilities.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM MiniMIMentry.pm, 1.8, 1.9 OMIMentry.pm, 1.15, 1.16 OMIMentryAllelicVariant.pm, 1.8, 1.9 OMIMparser.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/MeSH Term.pm, 1.6, 1.7 Twig.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO/Handlers InterProHandler.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/Simulation Coalescent.pm, 1.10, 1.11 GeneticDrift.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Correlate.pm, 1.8, 1.9 Measure.pm, 1.8, 1.9 Phenotype.pm, 1.11, 1.12 PhenotypeI.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO InterProParser.pm, 1.10, 1.11 dagflat.pm, 1.28, 1.29 goflat.pm, 1.6, 1.7 obo.pm, 1.6, 1.7 simplehierarchy.pm, 1.16, 1.17 soflat.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit BlastHit.pm, 1.16, 1.17 Fasta.pm, 1.9, 1.10 GenericHit.pm, 1.36, 1.37 HMMERHit.pm, 1.5, 1.6 HitFactory.pm, 1.5, 1.6 HitI.pm, 1.23, 1.24   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.5, 1.6 IterationI.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.27, 1.28 FastaHSP.pm, 1.9, 1.10 GenericHSP.pm, 1.67, 1.68 HMMERHSP.pm, 1.7, 1.8 HSPFactory.pm, 1.7, 1.8 HSPI.pm, 1.35, 1.36 PSLHSP.pm, 1.3, 1.4 PsiBlastHSP.pm, 1.6, 1.7 WABAHSP.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/Enzyme MultiCut.pm, 1.6, 1.7 MultiSite.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search BlastStatistics.pm, 1.4, 1.5 DatabaseI.pm, 1.9, 1.10 GenericDatabase.pm, 1.8, 1.9 GenericStatistics.pm, 1.4, 1.5 Processor.pm, 1.11, 1.12 StatisticsI.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastResult.pm, 1.21, 1.22 GenericResult.pm, 1.21, 1.22 HMMERResult.pm, 1.5, 1.6 ResultFactory.pm, 1.5, 1.6 ResultI.pm, 1.22, 1.23 WABAResult.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/IO bairoch.pm, 1.7, 1.8 base.pm, 1.10, 1.11 itype2.pm, 1.5, 1.6 withrefm.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Root Err.pm, 1.20, 1.21 HTTPget.pm, 1.13, 1.14 IO.pm, 1.60, 1.61 IOManager.pm, 1.18, 1.19 Object.pm, 1.30, 1.31 Storable.pm, 1.6, 1.7 Utilities.pm, 1.30, 1.31 Vector.pm, 1.16, 1.17 Version.pm, 1.8, 1.9 Xref.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer BSMLResultWriter.pm, 1.3, 1.4 GbrowseGFF.pm, 1.14, 1.15 HSPTableWriter.pm, 1.16, 1.17 HTMLResultWriter.pm, 1.37, 1.38 HitTableWriter.pm, 1.19, 1.20 ResultTableWriter.pm, 1.18, 1.19 TextResultWriter.pm, 1.17, 1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.32, 1.33 AnnotationAdaptor.pm, 1.9, 1.10 Collection.pm, 1.17, 1.18 CollectionI.pm, 1.4, 1.5 Computation.pm, 1.15, 1.16 Generic.pm, 1.102, 1.103 PositionProxy.pm, 1.8, 1.9 Primer.pm, 1.20, 1.21 Similarity.pm, 1.15, 1.16 SimilarityPair.pm, 1.29, 1.30 TypedSeqFeatureI.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq/Meta Array.pm,1.12,1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO EventHandlerI.pm, 1.12, 1.13 FastHitEventBuilder.pm, 1.11, 1.12 IteratedSearchResultEventBuilder.pm, 1.9, 1.10 SearchResultEventBuilder.pm, 1.40, 1.41 axt.pm, 1.7, 1.8 blast.pm, 1.98, 1.99 blasttable.pm, 1.6, 1.7 blastxml.pm, 1.35, 1.36 exonerate.pm, 1.16, 1.17 fasta.pm, 1.49, 1.50 hmmer.pm, 1.32, 1.33 megablast.pm, 1.6, 1.7 psl.pm, 1.12, 1.13 sim4.pm, 1.12, 1.13 waba.pm, 1.15, 1.16 wise.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq BaseSeqProcessor.pm, 1.6, 1.7 EncodedSeq.pm, 1.10, 1.11 LargeLocatableSeq.pm, 1.4, 1.5 LargePrimarySeq.pm, 1.31, 1.32 LargeSeq.pm, 1.14, 1.15 LargeSeqI.pm, 1.5, 1.6 Meta.pm, 1.11, 1.12 MetaI.pm, 1.9, 1.10 PrimaryQual.pm, 1.23, 1.24 PrimedSeq.pm, 1.22, 1.23 QualI.pm, 1.10, 1.11 Quality.pm, 1.9, 1.10 RichSeq.pm, 1.18, 1.19 RichSeqI.pm, 1.13, 1.14 SeqBuilder.pm, 1.8, 1.9 SeqFactory.pm, 1.10, 1.11 SeqFastaSpeedFactory.pm, 1.6, 1.7 SeqWithQuality.pm, 1.26, 1.27 SequenceTrace.pm, 1.13, 1.14 TraceI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools FeatureNamer.pm, 1.5, 1.6 IDHandler.pm, 1.9, 1.10 TypeMapper.pm, 1.13, 1.14 Unflattener.pm, 1.36, 1.37   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene Exon.pm, 1.14, 1.15 ExonI.pm, 1.10, 1.11 GeneStructure.pm, 1.20, 1.21 GeneStructureI.pm, 1.11, 1.12 Intron.pm, 1.9, 1.10 NC_Feature.pm, 1.10, 1.11 Poly_A_site.pm, 1.6, 1.7 Promoter.pm, 1.7, 1.8 Transcript.pm, 1.37, 1.38 TranscriptI.pm, 1.12, 1.13 UTR.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/SiRNA Oligo.pm, 1.5, 1.6 Pair.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/IO pdb.pm,1.15,1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO FTHelper.pm, 1.60, 1.61 MultiFile.pm, 1.11, 1.12 abi.pm, 1.13, 1.14 ace.pm, 1.16, 1.17 agave.pm, 1.14, 1.15 alf.pm, 1.11, 1.12 asciitree.pm, 1.3, 1.4 bsml.pm, 1.23, 1.24 bsml_sax.pm, 1.2, 1.3 ctf.pm, 1.14, 1.15 embl.pm, 1.89, 1.90 entrezgene.pm, 1.21, 1.22 excel.pm, 1.3, 1.4 exp.pm, 1.14, 1.15 fasta.pm, 1.56, 1.57 fastq.pm, 1.14, 1.15 game.pm, 1.37, 1.38 gcg.pm, 1.25, 1.26 genbank.pm, 1.135, 1.136 interpro.pm, 1.8, 1.9 kegg.pm, 1.17, 1.18 largefasta.pm, 1.23, 1.24 locuslink.pm, 1.11, 1.12 metafasta.pm, 1.8, 1.9 phd.pm, 1.20, 1.21 pir.pm, 1.22, 1.23 pln.pm, 1.11, 1.12 qual.pm, 1.29, 1.30 raw.pm, 1.20, 1.21 scf.pm, 1.35, 1.36 strider.pm, 1.5, 1.6 swiss.pm, 1.91, 1.92 table.pm, 1.3, 1.4 ztr.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/game featHandler.pm, 1.14, 1.15 gameHandler.pm, 1.7, 1.8 gameSubs.pm, 1.8, 1.9 gameWriter.pm, 1.12, 1.13 seqHandler.pm, 1.26, 1.27   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure Atom.pm, 1.11, 1.12 Chain.pm, 1.9, 1.10 Entry.pm, 1.24, 1.25 IO.pm, 1.10, 1.11 Model.pm, 1.9, 1.10 Residue.pm, 1.10, 1.11 StructureI.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/tinyseq tinyseqHandler.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.40, 1.41 Trim.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/STRIDE Res.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Node.pm,1.13,1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis SimpleAnalysisBase.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Symbol Alphabet.pm, 1.9, 1.10 AlphabetI.pm, 1.7, 1.8 DNAAlphabet.pm, 1.5, 1.6 ProteinAlphabet.pm, 1.5, 1.6 Symbol.pm, 1.8, 1.9 SymbolI.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools AnalysisResult.pm, 1.16, 1.17 BPbl2seq.pm, 1.28, 1.29 BPpsilite.pm, 1.25, 1.26 Blast.pm, 1.36, 1.37 Blat.pm, 1.6, 1.7 CodonTable.pm, 1.35, 1.36 Coil.pm, 1.5, 1.6 ECnumber.pm, 1.10, 1.11 EPCR.pm, 1.17, 1.18 ESTScan.pm, 1.13, 1.14 Eponine.pm, 1.12, 1.13 Est2Genome.pm, 1.16, 1.17 Fgenesh.pm, 1.7, 1.8 FootPrinter.pm, 1.7, 1.8 GFF.pm, 1.56, 1.57 Gel.pm, 1.10, 1.11 Geneid.pm, 1.4, 1.5 Genemark.pm, 1.16, 1.17 Genewise.pm, 1.24, 1.25 Genomewise.pm, 1.5, 1.6 Genscan.pm, 1.28, 1.29 Glimmer.pm, 1.3, 1.4 Grail.pm, 1.10, 1.11 GuessSeqFormat.pm, 1.14, 1.15 HMM.pm, 1.7, 1.8 Hmmpfam.pm, 1.7, 1.8 IUPAC.pm, 1.27, 1.28 Lucy.pm, 1.14, 1.15 MZEF.pm, 1.13, 1.14 OddCodes.pm, 1.18, 1.19 Primer3.pm, 1.19, 1.20 Prints.pm, 1.12, 1.13 Profile.pm, 1.7, 1.8 Promoterwise.pm, 1.7, 1.8 Pseudowise.pm, 1.9, 1.10 QRNA.pm, 1.4, 1.5 RandomDistFunctions.pm, 1.6, 1.7 RepeatMasker.pm, 1.9, 1.10 RestrictionEnzyme.pm, 1.34, 1.35 Seg.pm, 1.9, 1.10 SeqAnal.pm, 1.17, 1.18 SeqPattern.pm, 1.20, 1.21 SeqStats.pm, 1.29, 1.30 SeqWords.pm, 1.16, 1.17 SiRNA.pm, 1.12, 1.13 Sigcleave.p! m, 1.21, 1.22 Signalp.pm, 1.7, 1.8 Tmhmm.pm, 1.9, 1.10 WWW.pm, 1.15, 1.16 dpAlign.pm, 1.17, 1.18 ipcress.pm, 1.7, 1.8 isPcr.pm, 1.8, 1.9 pICalculator.pm, 1.8, 1.9 pSW.pm, 1.26, 1.27   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/BPlite HSP.pm, 1.30, 1.31 Sbjct.pm, 1.32, 1.33   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Molphy.pm, 1.8, 1.9 PAML.pm, 1.43, 1.44   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Molphy Result.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EMBOSS Palindrome.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.27, 1.28   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Domcut.pm, 1.13, 1.14 ELM.pm, 1.11, 1.12 GOR4.pm, 1.11, 1.12 HNN.pm, 1.11, 1.12 Mitoprot.pm, 1.7, 1.8 NetPhos.pm, 1.12, 1.13 Scansite.pm, 1.15, 1.16 Sopma.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.22, 1.23 HTML.pm, 1.18, 1.19 README, 1.6, 1.7 Sbjct.pm, 1.24, 1.25   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Primer/Assessor Base.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Sim4 Exon.pm, 1.15, 1.16 Results.pm, 1.24, 1.25   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Phylip ProtDist.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run GenericParameters.pm, 1.4, 1.5 ParametersI.pm, 1.4, 1.5 StandAloneBlast.pm, 1.62, 1.63 WrapperBase.pm, 1.20, 1.21   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Primer AssessorI.pm, 1.4, 1.5 Feature.pm, 1.4, 1.5 Pair.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/SiRNA/Ruleset saigo.pm, 1.3, 1.4 tuschl.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML ModelResult.pm, 1.6, 1.7 Result.pm, 1.21, 1.22   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Prediction Exon.pm, 1.15, 1.16 Gene.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Spidey Exon.pm, 1.5, 1.6 Results.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tree AlleleNode.pm, 1.12, 1.13 Compatible.pm, 1.4, 1.5 DistanceFactory.pm, 1.7, 1.8 Node.pm, 1.47, 1.48 NodeI.pm, 1.34, 1.35 NodeNHX.pm, 1.9, 1.10 RandomFactory.pm, 1.17, 1.18 Statistics.pm, 1.11, 1.12 Tree.pm, 1.19, 1.20 TreeFunctionsI.pm, 1.25, 1.26 TreeI.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/doc/Deobfuscator/lib Deobfuscator.pm, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation/IO flat.pm, 1.18, 1.19 xml.pm, 1.18, 1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO TreeEventBuilder.pm, 1.22, 1.23 cluster.pm, 1.3, 1.4 lintree.pm, 1.7, 1.8 newick.pm, 1.35, 1.36 nexus.pm, 1.12, 1.13 nhx.pm, 1.17, 1.18 pag.pm, 1.8, 1.9 svggraph.pm, 1.4, 1.5 tabtree.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/examples/tools run_primer3.pl, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation AAChange.pm, 1.19, 1.20 AAReverseMutate.pm, 1.11, 1.12 Allele.pm, 1.14, 1.15 DNAMutation.pm, 1.17, 1.18 IO.pm, 1.21, 1.22 README, 1.3, 1.4 RNAChange.pm, 1.16, 1.17 SNP.pm, 1.15, 1.16 SeqDiff.pm, 1.22, 1.23 VariantI.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/doc/Deobfuscator/cgi-bin deob_detail.cgi, 1.2, 1.3 deob_help.html, 1.1, 1.2 deob_interface.cgi, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/doc/Deobfuscator/bin deob_index.pl, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio PrimarySeq.pm, 1.5, 1.6 PrimarySeqI.pm, 1.5, 1.6 Seq.pm, 1.5, 1.6 SeqI.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/searchio filter_search.PLS, 1.2, 1.3 parse_hmmsearch.PLS, 1.2, 1.3 search2table.PLS, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/seq extract_feature_seq.PLS, 1.4, 1.5 seqconvert.PLS, 1.7, 1.8 split_seq.PLS, 1.6, 1.7 translate_seq.PLS, 1.6, 1.7 unflatten_seq.PLS, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/index bp_fetch.PLS, 1.4, 1.5 bp_index.PLS, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/seqstats aacomp.PLS, 1.4, 1.5 chaos_plot.PLS, 1.5, 1.6 gccalc.PLS, 1.4, 1.5 oligo_count.PLS, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network Edge.pm, 1.4, 1.5 IO.pm, 1.6, 1.7 Interaction.pm, 1.4, 1.5 Node.pm, 1.3, 1.4 ProteinNet.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/biblio biblio.PLS,1.4,1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/maintenance authors.pl, 1.5, 1.6 check_URLs.pl, 1.4, 1.5 modules.pl, 1.21, 1.22 pod.pl, 1.8, 1.9 symlink_scripts.PLS, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/utilities dbsplit.PLS, 1.7, 1.8 mutate.PLS, 1.10, 1.11 pairwise_kaks.PLS, 1.11, 1.12 seq_length.PLS, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/DB flanks.PLS,1.6,1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO dip_tab.pm, 1.4, 1.5 psi.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/InputCreate setup_initial.pm, 1.10, 1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline Analysis.pm, 1.33, 1.34 Argument.pm, 1.10, 1.11 DataHandler.pm, 1.6, 1.7 DataType.pm, 1.8, 1.9 IOHandler.pm, 1.39, 1.40 Input.pm, 1.12, 1.13 InputCreate.pm, 1.11, 1.12 Job.pm, 1.48, 1.49 Manager.pm, 1.13, 1.14 Method.pm, 1.7, 1.8 Rule.pm, 1.11, 1.12 RunnableDB.pm, 1.39, 1.40 Transformer.pm, 1.15, 1.16 XMLImporter.pm, 1.21, 1.22   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Runnable Blat.pm, 1.5, 1.6 Coil.pm, 1.4, 1.5 EnsemblRunnable.pm, 1.5, 1.6 Hmmpfam.pm, 1.11, 1.12 Prints.pm, 1.4, 1.5 Profile.pm, 1.4, 1.5 ProteinAnnotation.pm, 1.5, 1.6 Seg.pm, 1.4, 1.5 Signalp.pm, 1.4, 1.5 Tmhmm.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pedigree/Bio/Pedigree Pedigree.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO/psi intact.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils Filter.pm, 1.10, 1.11 Iterator.pm, 1.4, 1.5 SaxHandler.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/BatchSubmission LSF.pm, 1.17, 1.18 PBS.pm, 1.12, 1.13 SunGrid.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/SQL DBAdaptor.pm, 1.25, 1.26   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Factory EMBOSS.pm,1.6,1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils/Filter feature_coverage.pm, 1.11, 1.12 feature_filter.pm, 1.7, 1.8 simple_align.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Installer Clustalw.pm, 1.2, 1.3 EMBOSS.pm, 1.6, 1.7 Generic.pm, 1.3, 1.4 PAML.pm, 1.5, 1.6 Probcons.pm, 1.3, 1.4 TCoffee.pm, 1.3, 1.4   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Blat.pm, 1.13, 1.14 Clustalw.pm, 1.46, 1.47 DBA.pm, 1.13, 1.14 Exonerate.pm, 1.5, 1.6 Lagan.pm, 1.11, 1.12 Sim4.pm, 1.9, 1.10 StandAloneFasta.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Analysis.pm, 1.10, 1.11 AnalysisFactory.pm, 1.9, 1.10 Cap3.pm, 1.4, 1.5 Coil.pm, 1.10, 1.11 EMBOSSApplication.pm, 1.24, 1.25 EMBOSSacd.pm, 1.8, 1.9 Eponine.pm, 1.14, 1.15 FootPrinter.pm, 1.13, 1.14 Genewise.pm, 1.25, 1.26 Genscan.pm, 1.14, 1.15 Hmmer.pm, 1.8, 1.9 Mdust.pm, 1.8, 1.9 Phrap.pm, 1.5, 1.6 PiseApplication.pm, 1.8, 1.9 PiseJob.pm, 1.13, 1.14 PiseJobParser.pm, 1.8, 1.9 Primate.pm, 1.15, 1.16 Primer3.pm, 1.17, 1.18 Prints.pm, 1.10, 1.11 Profile.pm, 1.13, 1.14 Promoterwise.pm, 1.8, 1.9 Pseudowise.pm, 1.17, 1.18 RepeatMasker.pm, 1.24, 1.25 Seg.pm, 1.15, 1.16 Signalp.pm, 1.9, 1.10 Tmhmm.pm, 1.12, 1.13 TribeMCL.pm, 1.20, 1.21 Vista.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Analysis soap.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip Base.pm, 1.10, 1.11 Consense.pm, 1.13, 1.14 DrawGram.pm, 1.12, 1.13 DrawTree.pm, 1.12, 1.13 Neighbor.pm, 1.26, 1.27 PhylipConf.pm, 1.14, 1.15 ProtDist.pm, 1.29, 1.30 ProtPars.pm, 1.23, 1.24 SeqBoot.pm, 1.11, 1.12   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo LVB.pm,1.7,1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/PAML Baseml.pm, 1.5, 1.6   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Molphy ProtML.pm, 1.13, 1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/AnalysisFactory Pise.pm, 1.8, 1.9 soap.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/PiseApplication abiview.pm, 1.5, 1.6 addquart.pm, 1.5, 1.6 align2model.pm, 1.5, 1.6 alistat.pm, 1.5, 1.6 antigenic.pm, 1.5, 1.6 assp.pm, 1.5, 1.6 backtranseq.pm, 1.5, 1.6 bambe.pm, 1.5, 1.6 banana.pm, 1.5, 1.6 bionj.pm, 1.5, 1.6 biosed.pm, 1.5, 1.6 bl2seq.pm, 1.5, 1.6 blast2.pm, 1.5, 1.6 blimps.pm, 1.5, 1.6 blimps_block.pm, 1.5, 1.6 blimps_matrix.pm, 1.5, 1.6 boxshade.pm, 1.5, 1.6 btwisted.pm, 1.5, 1.6 cai.pm, 1.5, 1.6 cap.pm, 1.5, 1.6 cds.pm, 1.5, 1.6 chaos.pm, 1.5, 1.6 charge.pm, 1.5, 1.6 checktrans.pm, 1.5, 1.6 chips.pm, 1.5, 1.6 cirdna.pm, 1.5, 1.6 clique.pm, 1.5, 1.6 clustalw.pm, 1.5, 1.6 clustalw_convert.pm, 1.7, 1.8 codcmp.pm, 1.5, 1.6 coderet.pm, 1.5, 1.6 codnocod.pm, 1.5, 1.6 codontree.pm, 1.5, 1.6 codonw.pm, 1.5, 1.6 comalign.pm, 1.5, 1.6 combat.pm, 1.5, 1.6 compseq.pm, 1.5, 1.6 con_filter.pm, 1.5, 1.6 confmat.pm, 1.5, 1.6 cons.pm, 1.5, 1.6 consense.pm, 1.5, 1.6 consensus.pm, 1.5, 1.6 cpgplot.pm, 1.5, 1.6 cpgreport.pm, 1.5, 1.6 cusp.pm, 1.5, 1.6 cutseq.pm, 1.5, 1.6 dan.pm, 1.5, 1.6 dca.pm, 1.5, 1.6 decorate.pm, 1.5, 1.6 degaps! eq.pm, 1.5, 1.6 descseq.pm, 1.5, 1.6 dialign2.pm, 1.7, 1.8 diffseq.pm, 1.5, 1.6 digest.pm, 1.5, 1.6 distmat.pm, 1.5, 1.6 distquart.pm, 1.5, 1.6 dnadist.pm, 1.5, 1.6 dnapars.pm, 1.5, 1.6 dollop.pm, 1.5, 1.6 domainer.pm, 1.5, 1.6 dotmatcher.pm, 1.5, 1.6 dotpath.pm, 1.5, 1.6 dottup.pm, 1.5, 1.6 drawgram.pm, 1.5, 1.6 drawpyr.pm, 1.5, 1.6 drawtree.pm, 1.5, 1.6 dreg.pm, 1.5, 1.6 druid.pm, 1.5, 1.6 dsc.pm, 1.5, 1.6 dssp.pm, 1.5, 1.6 einverted.pm, 1.5, 1.6 emma.pm, 1.5, 1.6 emowse.pm, 1.5, 1.6 environ.pm, 1.5, 1.6 eprimer3.pm, 1.5, 1.6 equicktandem.pm, 1.5, 1.6 est2genome.pm, 1.5, 1.6 etandem.pm, 1.5, 1.6 extractfeat.pm, 1.5, 1.6 extractseq.pm, 1.5, 1.6 fasta.pm, 1.5, 1.6 fastdnaml.pm, 1.5, 1.6 fastrna.pm, 1.5, 1.6 filtersites.pm, 1.5, 1.6 findkm.pm, 1.5, 1.6 fitch.pm, 1.5, 1.6 fmtseq.pm, 1.5, 1.6 freak.pm, 1.5, 1.6 fuzznuc.pm, 1.5, 1.6 fuzzpro.pm, 1.5, 1.6 fuzztran.pm, 1.5, 1.6 gb2xml.pm, 1.5, 1.6 geecee.pm, 1.5, 1.6 genscan.pm, 1.6, 1.7 getblock.pm, 1.5, 1.6 getorf.pm, 1.5, 1.6 gff2ps.pm, 1.5, 1.6 gibbs.pm, 1.5, 1.6 gibbs_scan.pm, 1.5, 1.6 golden.pm, 1.5, 1.6 grailclnt.pm, 1.7, 1.8! gruppi.pm, 1.5, 1.6 helixturnhelix.pm, 1.5, 1.6 hmmalign.pm, 1.5, 1.6 hmmbu   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-run/scripts multi_hmmsearch.PLS, 1.2, 1.3 panalysis.PLS, 1.9, 1.10 papplmaker.PLS, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live README,1.44,1.45   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live INSTALL,1.46,1.47   Mauricio Herrera Cuadra
• [Bioperl-guts-l] Mauricio Herrera Cuadra   Chris Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities cookie.pm, 1.1, 1.2 efetch.pm, 1.1, 1.2 egquery.pm, 1.1, 1.2 einfo.pm, 1.1, 1.2 elink.pm, 1.1, 1.2 epost.pm, 1.1, 1.2 esearch.pm, 1.1, 1.2 esummary.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.2,1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live AUTHORS,1.45,1.46   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blastxml.pm,1.33,1.34   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blastxml.pm,1.34,1.35   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.3,1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities cookie.pm, 1.2, 1.3 efetch.pm, 1.2, 1.3 egquery.pm, 1.2, 1.3 einfo.pm, 1.2, 1.3 elink.pm, 1.2, 1.3 epost.pm, 1.2, 1.3 esearch.pm, 1.3, 1.4 esummary.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.4,1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.5,1.6   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities cookie.pm, 1.3, 1.4 elink.pm, 1.3, 1.4 esearch.pm, 1.4, 1.5 esummary.pm, 1.3, 1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities elink.pm,1.4,1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO hmmer.pm,1.31,1.32   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO hmmer.pm,1.33,1.34   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities cookie.pm, 1.4, NONE   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkScores.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities egquery.pm, 1.3, 1.4 elink.pm, 1.6, 1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, NONE, 1.1 Cookie.pm, 1.1, 1.2 elink.pm, 1.7, 1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkScores.pm, 1.1, NONE   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.2, 1.3 ElinkData.pm, 1.1, 1.2 elink.pm, 1.8, 1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.7,1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.2, 1.3 elink.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.3, 1.4 elink.pm, 1.10, 1.11   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.4, 1.5 elink.pm, 1.11, 1.12   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities elink.pm, 1.12, 1.13 esearch.pm, 1.6, 1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.8,1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities esearch.pm, 1.7, 1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.9,1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities elink.pm, 1.13, 1.14   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.10,1.11   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.11,1.12   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.5, 1.6 elink.pm, 1.14, 1.15   Christopher John Fields
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip DrawTree.pm, 1.13, 1.14   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO clustalw.pm,1.34,1.35   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio SeqFeatureI.pm,1.65,1.66   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t SeqFeature.t,1.39,1.40   Christopher John Fields
• [Bioperl-guts-l] bioperl-live bptutorial.pl,1.167,1.168   Christopher John Fields
• [Bioperl-guts-l] bioperl-live bptutorial.pl,1.168,1.169   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.35, 1.36   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.12,1.13   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.6, 1.7 efetch.pm, 1.3, 1.4 egquery.pm, 1.4, 1.5 einfo.pm, 1.3, 1.4 elink.pm, 1.15, 1.16 epost.pm, 1.3, 1.4 esearch.pm, 1.8, 1.9 esummary.pm, 1.5, 1.6   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t splicedseq.t,1.5,1.6   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO clustalw.pm,1.35,1.36   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO clustalw.pm,1.36,1.37   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.7, 1.8 einfo.pm, 1.4, 1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.13,1.14   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities elink.pm, 1.16, 1.17 epost.pm, 1.4, 1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.14,1.15   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities efetch.pm, 1.4, 1.5 einfo.pm, 1.5, 1.6 elink.pm, 1.17, 1.18 epost.pm, 1.5, 1.6   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm, 1.15, 1.16 GenericWebDBI.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.16,1.17   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities efetch.pm, 1.5, 1.6 egquery.pm, 1.5, 1.6 einfo.pm, 1.6, 1.7 elink.pm, 1.18, 1.19 esummary.pm, 1.6, 1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities elink.pm, 1.19, 1.20 epost.pm, 1.6, 1.7 esearch.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm, 1.17, 1.18 GenericWebDBI.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.36, 1.37   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.18,1.19   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities efetch.pm,1.6,1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.37, 1.38   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Index AbstractSeq.pm,1.23,1.24   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t Index.t,1.41,1.42   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Scaffold.pm,1.11,1.12   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t Assembly.t,1.4,1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.33, 1.34   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t SeqFeature.t,1.40,1.41   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.8, 1.9 elink.pm, 1.20, 1.21   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.19,1.20   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.20,1.21   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.10, 1.11   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Enzyme.pm,1.14,1.15   Chad Matsalla
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.17, 1.18 Enzyme.pm, 1.15, 1.16   Chad Matsalla
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.18, 1.19   Chad Matsalla
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO obo.pm,1.7,1.8   Sohel Merchant
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO fasta.pm,1.57,1.58   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio SeqUtils.pm,1.30,1.31   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio SeqUtils.pm,1.31,1.32   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t SeqUtils.t,1.17,1.18   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio SeqUtils.pm,1.32,1.33   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Structure Entry.pm,1.25,1.26   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Structure StructureI.pm,1.6,1.7   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Structure Entry.pm,1.26,1.27   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Structure IO.pm,1.11,1.12   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t/data 1A0N.pdb,NONE,1.1   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t/data 1A3I.pdb, NONE, 1.1 1A0N.pdb, 1.1, NONE   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Structure/IO pdb.pm,1.16,1.17   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Structure Chain.pm,1.10,1.11   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t StructIO.t,1.7,1.8   Brian Osborne
• [Bioperl-guts-l] bioperl-live/scripts/taxa taxonomy2tree.PLS, NONE, 1.1   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Tools Fgenesh.pm,1.9,1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.110,1.111   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.14, 1.15   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.17, 1.18   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph gene.pm, 1.9, 1.10 image.pm, 1.2, 1.3 processed_transcript.pm, 1.11, 1.12 transcript.pm, 1.22, 1.23 transcript2.pm, 1.27, 1.28   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/scripts/Bio-SeqFeature-Store bp_seqfeature_load.PLS, 1.6, 1.7   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph cds.pm, 1.34, 1.35 generic.pm, 1.38, 1.39   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB SeqFeature.pm,1.6,1.7   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature Store.pm, 1.19, 1.20   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI broken.pm, NONE, 1.1   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.111,1.112   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature Segment.pm, 1.10, 1.11   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph heterogeneous_segments.pm, 1.7, 1.8   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph heterogeneous_segments.pm, 1.8, 1.9   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature Segment.pm, 1.11, 1.12 Store.pm, 1.20, 1.21   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.18, 1.19   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI broken.pm, 1.1, NONE   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.112,1.113   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature Segment.pm, 1.12, 1.13   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.11, 1.12   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.19, 1.20   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.117,1.118   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/scripts/taxa taxonomy2tree.PLS, 1.1, 1.2   Gabriel Valiente
• [Bioperl-guts-l] bioperl-live/scripts/taxa taxonomy2tree.PLS, 1.2, 1.3   Gabriel Valiente
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline Analysis.pm, 1.34, 1.35 Manager.pm, 1.14, 1.15   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils Dumper.pm, 1.10, 1.11   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Utils/Dumper blastscore.pm, 1.9, 1.10   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline IOHandler.pm, 1.40, 1.41   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Runnable Fasta.pm, 1.2, 1.3   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Runnable Phylip.pm, 1.4, 1.5   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/Runnable TribeMCL.pm, 1.9, 1.10   olivier at dev.open-bio.org
• [Bioperl-guts-l] bioperl-pipeline/Bio/Pipeline/InputCreate setup_initial_seq_region.pm, NONE, 1.1   olivier at dev.open-bio.org
• [Bioperl-guts-l] [Bug 1701] Bio::Variation::SeqDiff does not report trivname   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2039] New: Bug when fetching sequences from circular genomes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2039] Bug when fetching sequences from circular genomes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2039] Bug when fetching sequences from circular genomes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2039] Bug when fetching sequences from circular genomes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2039] Bug when fetching sequences from circular genomes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2040] New: DrawTree.pm tries to use drawgram menu   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2041] New: Bio::AlignIO::needle parser broken for EMBOSS v 3 output   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2041] Bio::AlignIO::needle parser broken for EMBOSS v 3 output   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2041] Bio::AlignIO::needle parser broken for EMBOSS v 3 output   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2041] Bio::AlignIO::needle parser broken for EMBOSS v 3 output   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2041] Bio::AlignIO::needle parser broken for EMBOSS v 3 output   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2040] DrawTree.pm tries to use drawgram menu   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2040] DrawTree.pm tries to use drawgram menu   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] New: AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2039] Bug when fetching sequences from circular genomes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2036] Bio::SearchIO::hmmer hmmpfam parsing misses model/domain pairs   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2026] difficult to convert Bio::SeqFeatureI features into Bio::AnnotationCollectionI features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1945] tblastn reports the wrong frame and hit position   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1779] New install of bioperl-db does not fully function   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1821] Bio::Align::DNAStatistics cannot calculate correct the number of synonymouse site of sequece in alignment   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2026] difficult to convert Bio::SeqFeatureI features into Bio::AnnotationCollectionI features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2024] Bio::Tools::GFF creates invalid LocatableSeq objects from ##sequence-region headers of a GFF3 string   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2044] New: wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] New: wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2044] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2045] wrong sequence length returned from Bio::DB::Fasta   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2042] AlignIO-clustal overwrites sequence w/o warning   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1872] Bio::AlignIO::stockholm.pm write_aln method   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] New: Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2048] New: Bio::Assembly::Scaffold::get_contig_ids doesn't work in scalar context   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2048] Bio::Assembly::Scaffold::get_contig_ids doesn't work in scalar context   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2048] Bio::Assembly::Scaffold::get_contig_ids doesn't work in scalar context   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2049] New: using Bio::Index::Fasta, fetching a nonexistent seq causes a crash   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2049] using Bio::Index::Fasta, fetching a nonexistent seq causes a crash   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2049] using Bio::Index::Fasta, fetching a nonexistent seq causes a crash   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2048] Bio::Assembly::Scaffold::get_contig_ids doesn't work in scalar context   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2026] difficult to convert Bio::SeqFeatureI features into Bio::AnnotationCollectionI features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2026] difficult to convert Bio::SeqFeatureI features into Bio::AnnotationCollectionI features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2047] Bio::*Taxonomy* changes, round 1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1883] Bio::Tools::Phylo::PAML::PAML _parse_NSsitesBatch for only 1 model in mlc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2052] New: Bio::SeqUtils stoip and quotes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2053] New: New Bio::SeqUtils::revcom_with_features method and bugfixes for trunc_with_features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2053] New Bio::SeqUtils::revcom_with_features method and bugfixes for trunc_with_features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2053] New Bio::SeqUtils::revcom_with_features method and bugfixes for trunc_with_features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1883] Bio::Tools::Phylo::PAML::PAML _parse_NSsitesBatch for only 1 model in mlc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2054] New: Bio::Tools::Phylo::PAML.pm can not obtain omega(w) if model is M0.   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2054] Bio::Tools::Phylo::PAML.pm can not obtain omega(w) if model is M0.   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2054] Bio::Tools::Phylo::PAML.pm can not obtain omega(w) if model is M0.   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2055] New: Bio::Tools::Phylo::PAML.pm cannot parse dN/dS for branch site/clade models   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2055] Bio::Tools::Phylo::PAML.pm cannot parse dN/dS for branch site/clade models   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2052] Bio::SeqUtils stoip and quotes   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2053] New Bio::SeqUtils::revcom_with_features method and bugfixes for trunc_with_features   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2056] New: EMBL Parser needs to work with new release 87 format (Patch is attached)   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2056] EMBL Parser needs to work with new release 87 format (Patch is attached)   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2056] EMBL Parser needs to work with new release 87 format (Patch is attached)   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2055] Bio::Tools::Phylo::PAML.pm cannot parse dN/dS for branch site/clade models   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1883] Bio::Tools::Phylo::PAML::PAML _parse_NSsitesBatch for only 1 model in mlc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1883] Bio::Tools::Phylo::PAML::PAML _parse_NSsitesBatch for only 1 model in mlc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1883] Bio::Tools::Phylo::PAML::PAML _parse_NSsitesBatch for only 1 model in mlc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1883] Bio::Tools::Phylo::PAML::PAML _parse_NSsitesBatch for only 1 model in mlc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2054] Bio::Tools::Phylo::PAML.pm can not obtain omega(w) if model is M0.   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2054] Bio::Tools::Phylo::PAML.pm can not obtain omega(w) if model is M0.   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2055] Bio::Tools::Phylo::PAML.pm cannot parse dN/dS for branch site/clade models   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2055] Bio::Tools::Phylo::PAML.pm cannot parse dN/dS for branch site/clade models   bugzilla-daemon at newportal.open-bio.org

Last message date: Sat Jul 29 15:31:26 EDT 2006
Archived on: Sat Jul 29 15:31:40 EDT 2006

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