September 2006 Archives by author

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Starting: Fri Sep 1 08:17:43 EDT 2006
Ending: Fri Sep 29 17:31:04 EDT 2006
Messages: 940

• [Bioperl-guts-l] bioperl-live/t psm.t,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.33, 1.34   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO embl.pm,1.99,1.100   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.34, 1.35   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t SeqFeature.t, 1.41, 1.42 DB.t, 1.67, 1.68   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO embl.pm,1.100,1.101   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t NetPhos.t,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Align Utilities.pm, 1.20, 1.20.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm, 1.23, 1.23.4.1 clustalw.pm, 1.37, 1.37.4.1 emboss.pm, 1.17, 1.17.4.1 largemultifasta.pm, 1.9, 1.9.4.1 mase.pm, 1.11, 1.11.4.1 mega.pm, 1.11, 1.11.4.1 meme.pm, 1.10, 1.10.4.1 msf.pm, 1.22, 1.22.4.1 pfam.pm, 1.12, 1.12.4.1 phylip.pm, 1.36, 1.36.4.1 po.pm, 1.6, 1.6.4.1 prodom.pm, 1.10, 1.10.4.1 selex.pm, 1.14, 1.14.4.1 stockholm.pm, 1.15, 1.15.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live INSTALL, 1.47, 1.47.4.1 Makefile.PL, 1.94, 1.94.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm, 1.46.4.1, 1.46.4.2 AnnotationCollectionI.pm, 1.17.4.1, 1.17.4.2 AnnotationI.pm, 1.10.4.1, 1.10.4.2 DasI.pm, 1.18.4.1, 1.18.4.2 IdentifiableI.pm, 1.11.4.1, 1.11.4.2 LocatableSeq.pm, 1.39.4.1, 1.39.4.2 Perl.pm, 1.26.4.1, 1.26.4.2 PrimarySeq.pm, 1.95.4.1, 1.95.4.2 PrimarySeqI.pm, 1.65.4.1, 1.65.4.2 PullParserI.pm, 1.1.2.1, 1.1.2.2 SearchDist.pm, 1.20.4.1, 1.20.4.2 SeqFeatureI.pm, 1.66.4.1, 1.66.4.2 SeqI.pm, 1.29.4.1, 1.29.4.2 SeqIO.pm, 1.92.4.1, 1.92.4.2 SimpleAlign.pm, 1.108.2.1, 1.108.2.2 Species.pm, 1.35, 1.35.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Annotation OntologyTerm.pm, 1.15, 1.15.4.1 Reference.pm, 1.24, 1.24.4.1 SimpleValue.pm, 1.18, 1.18.4.1 StructuredValue.pm, 1.7, 1.7.4.1 Target.pm, 1.7, 1.7.4.1 TypeManager.pm, 1.6, 1.6.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy list.pm,1.1,1.1.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq Mutator.pm, 1.33, 1.33.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.20, 1.20.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.13, 1.13.4.1 Store.pm, 1.21, 1.21.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.11, 1.11.4.1 IO.pm, 1.6, 1.6.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.14, 1.14.4.1 Book.pm, 1.14, 1.14.4.1 BookArticle.pm, 1.13, 1.13.4.1 IO.pm, 1.17, 1.17.4.1 Journal.pm, 1.13, 1.13.4.1 JournalArticle.pm, 1.14, 1.14.4.1 MedlineBook.pm, 1.10, 1.10.4.1 MedlineBookArticle.pm, 1.10, 1.10.4.1 MedlineJournalArticle.pm, 1.10, 1.10.4.1 Person.pm, 1.15, 1.15.4.1 PubmedArticle.pm, 1.9, 1.9.4.1 PubmedBookArticle.pm, 1.9, 1.9.4.1 PubmedJournalArticle.pm, 1.10, 1.10.4.1 Ref.pm, 1.12, 1.12.4.1 TechReport.pm, 1.12, 1.12.4.1 WebResource.pm, 1.13, 1.13.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph primers.pm, 1.7, 1.7.4.1 translation.pm, 1.36, 1.36.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.15, 1.15.4.1 berkeleydb.pm, 1.5, 1.5.4.1 memory.pm, 1.5, 1.5.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Fasta.pm,1.44,1.44.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureFile.pm, 1.78, 1.78.4.1 Glyph.pm, 1.113, 1.113.4.1 Panel.pm, 1.119, 1.119.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm,1.43,1.43.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastResult.pm, 1.22, 1.22.4.1 GenericResult.pm, 1.23.2.1, 1.23.2.2 HmmpfamResult.pm, 1.1.2.1, 1.1.2.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Ontology OBOEngine.pm, 1.6, 1.6.4.1 Ontology.pm, 1.18, 1.18.4.1 SimpleOntologyEngine.pm, 1.17, 1.17.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map FPCMarker.pm, 1.7, 1.7.4.1 Physical.pm, 1.8, 1.8.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root RootI.pm,1.69.4.1,1.69.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/MapIO fpc.pm,1.6,1.6.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP GenericHSP.pm, 1.68, 1.68.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO obo.pm, 1.8.4.1, 1.8.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO masta.pm, 1.10, 1.10.4.1 transfac.pm, 1.14, 1.14.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search SearchUtils.pm, 1.17, 1.17.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.31, 1.31.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data biofpc.cor, NONE, 1.1.2.1 biofpc.fpc, NONE, 1.1.2.1 ctgdemo.fpc, NONE, 1.1.2.1 ssp160.embl.1, NONE, 1.1.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO embl.pm, 1.92, 1.92.4.1 genbank.pm, 1.140, 1.140.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.12, 1.12.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree Compatible.pm,1.5,1.5.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.10, 1.10.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data/seqfeaturedb test.gff3, NONE, 1.1.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm, 1.99, 1.99.4.1 blastxml.pm, 1.36, 1.36.4.1 hmmer_pull.pm, 1.1.2.1, 1.1.2.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t BioDBSeqFeature.t, NONE, 1.1.2.1 DB.t, 1.67, 1.67.2.1 Index.t, 1.44, 1.44.2.1 MapIO.t, 1.4, 1.4.4.1 Mutator.t, 1.9, 1.9.14.1 NetPhos.t, 1.8, 1.8.4.1 PhysicalMap.t, 1.2, 1.2.4.1 SeqFeature.t, 1.41, 1.41.4.1 SiteMatrix.t, 1.4, 1.4.6.1 genbank.t, 1.11, 1.11.2.1 masta.t, 1.3, 1.3.6.1 psm.t, 1.12, 1.12.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools RNAMotif.pm, 1.10.4.1, 1.10.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO clustalw.pm,1.38,1.39   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Taxonomy.pm,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Taxonomy.t,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree Node.pm,1.49,1.50   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio Species.pm, 1.36, 1.37 Taxon.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Species.t,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio Species.pm,1.37,1.38   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO swiss.pm, 1.92, 1.93 embl.pm, 1.101, 1.102 genbank.pm, 1.144, 1.145   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO swiss.pm, 1.93, 1.94 embl.pm, 1.102, 1.103 genbank.pm, 1.145, 1.146   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t psm.t,1.15,1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.35, 1.36   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO meme.pm,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO meme.pm,1.12,1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.36, 1.37   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t SiteMatrix.t,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP HSPI.pm,1.36,1.37   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search SearchUtils.pm,1.18,1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data frac_problems.blast,NONE,1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t SearchIO.t,1.96,1.97   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP HSPI.pm,1.37,1.38   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search SearchUtils.pm,1.19,1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search SearchUtils.pm,1.20,1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO meme.pm,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map MapI.pm, 1.15, 1.16 Mappable.pm, 1.6, 1.7 MappableI.pm, 1.17, 1.18 Marker.pm, 1.22, 1.23 MarkerI.pm, 1.16, 1.17 Relative.pm, 1.1, 1.2 RelativeI.pm, 1.1, 1.2 SimpleMap.pm, 1.17, 1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PullParserI.pm,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB GDB.pm,1.20,1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t DBCUTG.t,1.20,1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB CUTG.pm,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t DBCUTG.t,1.21,1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t ESEfinder.t,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.11.4.1, 1.11.4.2 IO.pm, 1.6.4.1, 1.6.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm, 1.23.4.1, 1.23.4.2 clustalw.pm, 1.37.4.1, 1.37.4.2 emboss.pm, 1.17.4.1, 1.17.4.2 largemultifasta.pm, 1.9.4.1, 1.9.4.2 mase.pm, 1.11.4.1, 1.11.4.2 mega.pm, 1.11.4.1, 1.11.4.2 meme.pm, 1.10.4.1, 1.10.4.2 msf.pm, 1.22.4.1, 1.22.4.2 pfam.pm, 1.12.4.1, 1.12.4.2 phylip.pm, 1.36.4.1, 1.36.4.2 prodom.pm, 1.10.4.1, 1.10.4.2 selex.pm, 1.14.4.1, 1.14.4.2 stockholm.pm, 1.15.4.1, 1.15.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm, 1.46.4.2, 1.46.4.3 AnnotationCollectionI.pm, 1.17.4.2, 1.17.4.3 AnnotationI.pm, 1.10.4.2, 1.10.4.3 DasI.pm, 1.18.4.2, 1.18.4.3 FeatureIO.pm, 1.15, 1.15.4.1 IdentifiableI.pm, 1.11.4.2, 1.11.4.3 LocatableSeq.pm, 1.39.4.2, 1.39.4.3 Perl.pm, 1.26.4.2, 1.26.4.3 PrimarySeq.pm, 1.95.4.2, 1.95.4.3 PrimarySeqI.pm, 1.65.4.2, 1.65.4.3 PullParserI.pm, 1.1.2.2, 1.1.2.3 SearchDist.pm, 1.20.4.2, 1.20.4.3 SeqFeatureI.pm, 1.66.4.2, 1.66.4.3 SeqI.pm, 1.29.4.2, 1.29.4.3 SeqIO.pm, 1.92.4.2, 1.92.4.3 SimpleAlign.pm, 1.108.2.2, 1.108.2.3 Species.pm, 1.35.4.1, 1.35.4.2 Taxon.pm, 1.1, 1.1.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live INSTALL, 1.47.4.1, 1.47.4.2 Makefile.PL, 1.94.4.1, 1.94.4.2 bptutorial.pl, 1.169, 1.169.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Align DNAStatistics.pm, 1.32, 1.32.4.1 Utilities.pm, 1.20.4.1, 1.20.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Annotation OntologyTerm.pm, 1.15.4.1, 1.15.4.2 Reference.pm, 1.24.4.1, 1.24.4.2 SimpleValue.pm, 1.18.4.1, 1.18.4.2 StructuredValue.pm, 1.7.4.1, 1.7.4.2 Target.pm, 1.7.4.1, 1.7.4.2 TypeManager.pm, 1.6.4.1, 1.6.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.14.4.1, 1.14.4.2 Book.pm, 1.14.4.1, 1.14.4.2 BookArticle.pm, 1.13.4.1, 1.13.4.2 IO.pm, 1.17.4.1, 1.17.4.2 Journal.pm, 1.13.4.1, 1.13.4.2 JournalArticle.pm, 1.14.4.1, 1.14.4.2 MedlineBook.pm, 1.10.4.1, 1.10.4.2 MedlineBookArticle.pm, 1.10.4.1, 1.10.4.2 MedlineJournalArticle.pm, 1.10.4.1, 1.10.4.2 Person.pm, 1.15.4.1, 1.15.4.2 PubmedArticle.pm, 1.9.4.1, 1.9.4.2 PubmedBookArticle.pm, 1.9.4.1, 1.9.4.2 PubmedJournalArticle.pm, 1.10.4.1, 1.10.4.2 Ref.pm, 1.12.4.1, 1.12.4.2 TechReport.pm, 1.12.4.1, 1.12.4.2 WebResource.pm, 1.13.4.1, 1.13.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph generic.pm, 1.40, 1.40.2.1 primers.pm, 1.7.4.1, 1.7.4.2 segments.pm, 1.44, 1.44.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy list.pm, 1.1.4.1, 1.1.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm,1.4,1.4.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.3, 1.3.4.1 ElinkData.pm, 1.12, 1.12.4.1 einfo.pm, 1.8, 1.8.4.1 elink.pm, 1.24, 1.24.4.1 esearch.pm, 1.11, 1.11.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm, 1.10, 1.10.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Factory FTLocationFactory.pm, 1.21, 1.21.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.15.4.1, 1.15.4.2 berkeleydb.pm, 1.5.4.1, 1.5.4.2 memory.pm, 1.5.4.1, 1.5.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.13.4.1, 1.13.4.2 Store.pm, 1.21.4.1, 1.21.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureFile.pm, 1.78.4.1, 1.78.4.2 Glyph.pm, 1.113.4.1, 1.113.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.20.4.1, 1.20.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB LocationI.pm, NONE, 1.1.2.1 ReferenceI.pm, NONE, 1.1.2.1 Ace.pm, 1.15, 1.15.4.1 CUTG.pm, 1.11, 1.11.4.1 DBFetch.pm, 1.13, 1.13.4.1 EUtilities.pm, 1.24, 1.24.4.1 Failover.pm, 1.10, 1.10.4.1 Fasta.pm, 1.44.4.1, 1.44.4.2 FileCache.pm, 1.11, 1.11.4.1 GDB.pm, 1.20, 1.20.4.1 InMemoryCache.pm, 1.7, 1.7.4.1 RandomAccessI.pm, 1.14, 1.14.4.1 Registry.pm, 1.32, 1.32.4.1 SeqFeature.pm, 1.7, 1.7.4.1 Taxonomy.pm, 1.11, 1.11.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.21, 1.21.4.1 masta.pm, 1.10.4.1, 1.10.4.2 transfac.pm, 1.14.4.1, 1.14.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root RootI.pm,1.69.4.2,1.69.4.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM InstanceSite.pm, 1.14, 1.14.4.1 SiteMatrix.pm, 1.31.4.1, 1.31.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search SearchUtils.pm, 1.17.4.1, 1.17.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP GenericHSP.pm, 1.68.4.1, 1.68.4.2 HSPI.pm, 1.36, 1.36.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Location Fuzzy.pm,1.33,1.33.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map FPCMarker.pm, 1.7.4.1, 1.7.4.2 MapI.pm, 1.15, 1.15.4.1 Mappable.pm, 1.6, 1.6.4.1 MappableI.pm, 1.17, 1.17.4.1 Marker.pm, 1.22, 1.22.4.1 MarkerI.pm, 1.16, 1.16.4.1 Physical.pm, 1.8.4.1, 1.8.4.2 Relative.pm, 1.1, 1.1.4.1 RelativeI.pm, 1.1, 1.1.4.1 SimpleMap.pm, 1.17, 1.17.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO obo.pm, 1.8.4.2, 1.8.4.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq Mutator.pm, 1.33.4.1, 1.33.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Ontology OBOEngine.pm, 1.6.4.1, 1.6.4.2 Ontology.pm, 1.18.4.1, 1.18.4.2 SimpleOntologyEngine.pm, 1.17.4.1, 1.17.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.12, 1.12.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO axt.pm, 1.8, 1.8.4.1 blast.pm, 1.99.4.1, 1.99.4.2 blastxml.pm, 1.36.4.1, 1.36.4.2 hmmer_pull.pm, 1.1.2.2, 1.1.2.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools Unflattener.pm, 1.37, 1.37.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.10.4.1, 1.10.4.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO embl.pm, 1.92.4.1, 1.92.4.2 entrezgene.pm, 1.22, 1.22.4.1 genbank.pm, 1.140.2.1, 1.140.2.2 strider.pm, 1.6, 1.6.4.1 swiss.pm, 1.92, 1.92.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree Compatible.pm, 1.5.4.1, 1.5.4.2 Node.pm, 1.49, 1.49.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools Fgenesh.pm, 1.10, 1.10.4.1 RNAMotif.pm, 1.10.4.2, 1.10.4.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastResult.pm, 1.22.4.1, 1.22.4.2 GenericResult.pm, 1.23.2.2, 1.23.2.3 HmmpfamResult.pm, 1.1.2.2, 1.1.2.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t EUtilities.t, NONE, 1.10.2.1 Biblio_biofetch.t, 1.11, 1.11.6.1 BioDBSeqFeature.t, 1.1.2.1, 1.1.2.2 DB.t, 1.67.2.1, 1.67.2.2 DBCUTG.t, 1.20, 1.20.4.1 ESEfinder.t, 1.13, 1.13.6.1 Index.t, 1.44.2.1, 1.44.2.2 Location.t, 1.29, 1.29.4.1 LocationFactory.t, 1.12, 1.12.4.1 MapIO.t, 1.4.4.1, 1.4.4.2 Mutator.t, 1.9.14.1, 1.9.14.2 NetPhos.t, 1.8.4.1, 1.8.4.2 PhysicalMap.t, 1.2.4.1, 1.2.4.2 SearchIO.t, 1.96, 1.96.4.1 SeqFeature.t, 1.41.4.1, 1.41.4.2 SiteMatrix.t, 1.4.6.1, 1.4.6.2 Species.t, 1.11, 1.11.4.1 StructIO.t, 1.8, 1.8.4.1 Taxonomy.t, 1.11, 1.11.4.1 TreeIO.t, 1.32, 1.32.6.1 Unflattener.t, 1.8, 1.8.4.1 genbank.t, 1.11.2.1, 1.11.2.2 psm.t, 1.12.4.1, 1.12.4.2 swiss.t, 1.3, 1.3.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib/Test Builder.pm, NONE, 1.1.2.1 More.pm, NONE, 1.1.2.1 Simple.pm, NONE, 1.1.2.1 Tutorial.pod, NONE, 1.1.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data/seqfeaturedb test.gff3, 1.1.2.1, 1.1.2.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO newick.pm,1.36,1.36.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data 1A11.pdb, NONE, 1.1.2.1 1BPT.pdb, NONE, 1.1.2.1 8HVP.pdb, NONE, 1.1.2.1 frac_problems.blast, NONE, 1.1.2.1 mixedmast.dat, NONE, 1.1.2.1 no_cds_example.gb, NONE, 1.1.2.1 puzzle.tre, NONE, 1.1.2.1 newformat.swiss, 1.1, 1.1.4.1 pdb1bpt.ent, 1.1, NONE   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder Module.pm, NONE, 1.1.2.1 Tester.pm, NONE, 1.1.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder/Tester Color.pm, NONE, 1.1.2.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP GenericHSP.pm, 1.68.4.2, 1.68.4.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit GenericHit.pm, 1.37, 1.37.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO IteratedSearchResultEventBuilder.pm, 1.10, 1.10.4.1 SearchResultEventBuilder.pm, 1.41, 1.41.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result GenericResult.pm, 1.23.2.3, 1.23.2.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.6, 1.6.4.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Assembly.t,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP GenericHSP.pm, 1.70, 1.71   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO SearchResultEventBuilder.pm, 1.41, 1.42 IteratedSearchResultEventBuilder.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result GenericResult.pm, 1.24, 1.25   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit GenericHit.pm, 1.37, 1.38   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrixI.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy flatfile.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy flatfile.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio eutils.pm, 1.11, 1.12 pdf.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm,1.46,1.47   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB WebDBSeqI.pm,1.57,1.58   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.38, 1.39   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root IOManager.pm, 1.19, 1.20 Object.pm, 1.31, 1.32   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM OMIMparser.pm, 1.20, 1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy entrez.pm, 1.18, 1.19 list.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP GenericHSP.pm, 1.71, 1.72 HmmpfamHSP.pm, 1.1, 1.2 PullHSPI.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit HmmpfamHit.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Clone.pm, 1.6, 1.7 Contig.pm, 1.6, 1.7 FPCMarker.pm, 1.8, 1.9 LinkagePosition.pm, 1.15, 1.16 Marker.pm, 1.23, 1.24 Position.pm, 1.18, 1.19 PositionHandler.pm, 1.3, 1.4 PositionI.pm, 1.18, 1.19 Relative.pm, 1.2, 1.3 RelativeI.pm, 1.2, 1.3 SimpleMap.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.5, 1.6 ElinkData.pm, 1.16, 1.17 efetch.pm, 1.8, 1.9 egquery.pm, 1.6, 1.7 elink.pm, 1.25, 1.26 epost.pm, 1.7, 1.8 esummary.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm, 1.28, 1.29 GenericWebDBI.pm, 1.3, 1.4 SeqVersion.pm, 1.5, 1.6 Taxonomy.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PullParserI.pm, 1.3, 1.4 Species.pm, 1.39, 1.40 Taxon.pm, 1.2, 1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO ptt.pm,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.37, 1.38   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools ERPIN.pm,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree Tree.pm, 1.21, 1.22 TreeFunctionsI.pm, 1.28, 1.29   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result HmmpfamResult.pm, 1.2, 1.3 PullResultI.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO hmmer_pull.pm,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PrimarySeqI.pm,1.67,1.68   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Relative.pm,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.14, 1.15 Segment.pm, 1.13, 1.14 Store.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio FeatureIO.pm, 1.18, 1.19 PullParserI.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.17, 1.18 berkeleydb.pm, 1.6, 1.7 memory.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph dna.pm,1.25,1.26   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm, 1.121, 1.122 Panel.pm, 1.122, 1.123   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities efetch.pm, 1.9, 1.10 egquery.pm, 1.7, 1.8 einfo.pm, 1.10, 1.11 elink.pm, 1.26, 1.27 epost.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Failover.pm, 1.13, 1.14 FileCache.pm, 1.12, 1.13 InMemoryCache.pm, 1.8, 1.9 RandomAccessI.pm, 1.15, 1.16 SeqFeature.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm, 1.7, 1.8 interpro.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map FPCMarker.pm, 1.9, 1.10 Relative.pm, 1.4, 1.5 RelativeI.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO strider.pm,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools Fgenesh.pm, 1.12, 1.13 RNAMotif.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML ModelResult.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Relative.pm, 1.5, 1.6 RelativeI.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Variation IO.pm,1.23,1.24   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Mappable.pm,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi pg_fts.pm, 1.2, 1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities epost.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Expression geo.pm,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Align DNAStatistics.pm, 1.34, 1.35   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi pg.pm, 1.20, 1.21 mysqlcmap.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.123,1.124   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run StandAloneBlast.pm, 1.63, 1.64   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Ontology DocumentRegistry.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio AnnotatableI.pm,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Expression geo.pm,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.17, 1.18 esearch.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Cap3.pm, 1.5, 1.6 Coil.pm, 1.11, 1.12 AbstractRunner.pm, 1.2, 1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t DB.t,1.68,1.69   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t NetPhos.t,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t NetPhos.t,1.10,1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root Root.pm, 1.35, 1.36 RootI.pm, 1.70, 1.71   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root IO.pm,1.62,1.63   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-network/t IO_psi.t,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO psi.pm,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio Species.pm,1.40,1.41   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PullParserI.pm,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PullParserI.pm,1.6,1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP HmmpfamHSP.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Annotation AnnotationFactory.pm, 1.6, 1.7 Collection.pm, 1.23, 1.24 Comment.pm, 1.13, 1.14 DBLink.pm, 1.19, 1.20 OntologyTerm.pm, 1.16, 1.17 Reference.pm, 1.27, 1.28 SimpleValue.pm, 1.20, 1.21 StructuredValue.pm, 1.9, 1.10 Target.pm, 1.9, 1.10 TypeManager.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/CodonUsage IO.pm, 1.11, 1.12 Table.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm, 1.47, 1.48 AnalysisI.pm, 1.11, 1.12 AnalysisParserI.pm, 1.12, 1.13 AnalysisResultI.pm, 1.10, 1.11 AnnotatableI.pm, 1.14, 1.15 AnnotationCollectionI.pm, 1.19, 1.20 AnnotationI.pm, 1.12, 1.13 Biblio.pm, 1.16, 1.17 ClusterI.pm, 1.6, 1.7 ClusterIO.pm, 1.18, 1.19 DBLinkContainerI.pm, 1.12, 1.13 DasI.pm, 1.19, 1.20 DescribableI.pm, 1.10, 1.11 FeatureHolderI.pm, 1.11, 1.12 FeatureIO.pm, 1.19, 1.20 IdCollectionI.pm, 1.7, 1.8 IdentifiableI.pm, 1.12, 1.13 LocatableSeq.pm, 1.40, 1.41 LocationI.pm, 1.25, 1.26 MapIO.pm, 1.10, 1.11 OntologyIO.pm, 1.13, 1.14 Perl.pm, 1.27, 1.28 PrimarySeq.pm, 1.96, 1.97 PrimarySeqI.pm, 1.68, 1.69 PullParserI.pm, 1.7, 1.8 Range.pm, 1.27, 1.28 RangeI.pm, 1.50, 1.51 SearchDist.pm, 1.21, 1.22 SearchIO.pm, 1.39, 1.40 Seq.pm, 1.91, 1.92 SeqAnalysisParserI.pm, 1.16, 1.17 SeqFeatureI.pm, 1.68, 1.69 SeqI.pm, 1.30, 1.31 SeqIO.pm, 1.94, 1.95 SeqUtils.pm, 1.35, 1.36 SimpleAlign.pm, 1.111, 1.112 SimpleAnalysisI.pm, 1.9, 1.10 Species.pm, 1.41, 1.42 Taxon.pm, 1.3, 1.4 Taxonomy.pm, 1.9, 1.10 TreeIO.pm, 1.20, 1.21 U! pdateableSeqI.pm, 1.7, 1.8 WebAgent.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Cluster ClusterFactory.pm, 1.6, 1.7 FamilyI.pm, 1.6, 1.7 SequenceFamily.pm, 1.10, 1.11 UniGene.pm, 1.38, 1.39 UniGeneI.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Biblio/IO medline2ref.pm, 1.15, 1.16 medlinexml.pm, 1.9, 1.10 pubmed2ref.pm, 1.6, 1.7 pubmedxml.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.15, 1.16 BiblioBase.pm, 1.13, 1.14 Book.pm, 1.15, 1.16 BookArticle.pm, 1.14, 1.15 IO.pm, 1.18, 1.19 Journal.pm, 1.14, 1.15 JournalArticle.pm, 1.15, 1.16 MedlineArticle.pm, 1.12, 1.13 MedlineBook.pm, 1.11, 1.12 MedlineBookArticle.pm, 1.11, 1.12 MedlineJournal.pm, 1.10, 1.11 MedlineJournalArticle.pm, 1.11, 1.12 Organisation.pm, 1.14, 1.15 Patent.pm, 1.14, 1.15 Person.pm, 1.16, 1.17 Proceeding.pm, 1.13, 1.14 Provider.pm, 1.11, 1.12 PubmedArticle.pm, 1.10, 1.11 PubmedBookArticle.pm, 1.10, 1.11 PubmedJournalArticle.pm, 1.11, 1.12 Ref.pm, 1.13, 1.14 Service.pm, 1.13, 1.14 TechReport.pm, 1.13, 1.14 Thesis.pm, 1.12, 1.13 WebResource.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/ClusterIO dbsnp.pm, 1.16, 1.17 unigene.pm, 1.29, 1.30   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm, 1.15, 1.16 phrap.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Align AlignI.pm, 1.16, 1.17 DNAStatistics.pm, 1.36, 1.37 PairwiseStatistics.pm, 1.10, 1.11 ProteinStatistics.pm, 1.8, 1.9 StatisticsI.pm, 1.8, 1.9 Utilities.pm, 1.21, 1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.14, 1.15 ContigAnalysis.pm, 1.6, 1.7 IO.pm, 1.7, 1.8 Scaffold.pm, 1.13, 1.14 ScaffoldI.pm, 1.7, 1.8 Singlet.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm, 1.25, 1.26 clustalw.pm, 1.39, 1.40 emboss.pm, 1.19, 1.20 fasta.pm, 1.27, 1.28 largemultifasta.pm, 1.11, 1.12 maf.pm, 1.10, 1.11 mase.pm, 1.13, 1.14 mega.pm, 1.12, 1.13 meme.pm, 1.15, 1.16 metafasta.pm, 1.6, 1.7 msf.pm, 1.23, 1.24 nexus.pm, 1.27, 1.28 pfam.pm, 1.13, 1.14 phylip.pm, 1.37, 1.38 po.pm, 1.7, 1.8 prodom.pm, 1.12, 1.13 psi.pm, 1.12, 1.13 selex.pm, 1.15, 1.16 stockholm.pm, 1.17, 1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF Aggregator.pm, 1.30, 1.31 Featname.pm, 1.9, 1.10 Feature.pm, 1.75, 1.76 Homol.pm, 1.5, 1.6 RelSegment.pm, 1.51, 1.52 Segment.pm, 1.30, 1.31 Typename.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB Ace.pm, 1.16, 1.17 BiblioI.pm, 1.10, 1.11 BioFetch.pm, 1.29, 1.30 CUTG.pm, 1.12, 1.13 DBFetch.pm, 1.14, 1.15 EMBL.pm, 1.21, 1.22 EUtilities.pm, 1.29, 1.30 EntrezGene.pm, 1.8, 1.9 Failover.pm, 1.14, 1.15 Fasta.pm, 1.45, 1.46 FileCache.pm, 1.13, 1.14 Flat.pm, 1.24, 1.25 GDB.pm, 1.21, 1.22 GFF.pm, 1.139, 1.140 GenBank.pm, 1.59, 1.60 GenPept.pm, 1.31, 1.32 GenericWebDBI.pm, 1.5, 1.6 InMemoryCache.pm, 1.9, 1.10 LocationI.pm, 1.1, 1.2 MeSH.pm, 1.8, 1.9 NCBIHelper.pm, 1.54, 1.55 QueryI.pm, 1.5, 1.6 RandomAccessI.pm, 1.16, 1.17 RefSeq.pm, 1.13, 1.14 ReferenceI.pm, 1.1, 1.2 Registry.pm, 1.37, 1.38 SeqHound.pm, 1.4, 1.5 SeqI.pm, 1.11, 1.12 SeqVersion.pm, 1.6, 1.7 SwissProt.pm, 1.30, 1.31 Taxonomy.pm, 1.14, 1.15 Universal.pm, 1.6, 1.7 UpdateableSeqI.pm, 1.8, 1.9 WebDBSeqI.pm, 1.59, 1.60 XEMBL.pm, 1.10, 1.11 XEMBLService.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BDB.pm, 1.17, 1.18 BinarySearch.pm, 1.24, 1.25   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi caching_handle.pm, 1.12, 1.13 mysql.pm, 1.66, 1.67 mysqlace.pm, 1.2, 1.3 mysqlcmap.pm, 1.7, 1.8 mysqlopt.pm, 1.34, 1.35 oracle.pm, 1.9, 1.10 oracleace.pm, 1.1, 1.2 pg.pm, 1.21, 1.22 pg_fts.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor biofetch.pm, 1.17, 1.18 biofetch_oracle.pm, 1.5, 1.6 dbi.pm, 1.60, 1.61 memory.pm, 1.46, 1.47   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.8, 1.9 ElinkData.pm, 1.18, 1.19 efetch.pm, 1.10, 1.11 egquery.pm, 1.8, 1.9 einfo.pm, 1.11, 1.12 elink.pm, 1.27, 1.28 epost.pm, 1.10, 1.11 esearch.pm, 1.15, 1.16 esummary.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/memory feature_serializer.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm, 1.11, 1.12 soap.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate/Result Gap.pm, 1.9, 1.10 Match.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate Chain.pm, 1.7, 1.8 Collection.pm, 1.24, 1.25 ExtrapolatingPair.pm, 1.16, 1.17 GeneMapper.pm, 1.27, 1.28 Graph.pm, 1.10, 1.11 MapperI.pm, 1.10, 1.11 Pair.pm, 1.19, 1.20 Result.pm, 1.15, 1.16 ResultI.pm, 1.6, 1.7 Utils.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat/BDB embl.pm, 1.13, 1.14 fasta.pm, 1.9, 1.10 genbank.pm, 1.8, 1.9 swiss.pm, 1.7, 1.8 swissprot.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy entrez.pm, 1.19, 1.20 flatfile.pm, 1.17, 1.18 list.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Aggregator alignment.pm, 1.12, 1.13 clone.pm, 1.11, 1.12 coding.pm, 1.2, 1.3 match.pm, 1.1, 1.2 none.pm, 1.4, 1.5 processed_transcript.pm, 1.6, 1.7 so_transcript.pm, 1.1, 1.2 transcript.pm, 1.9, 1.10 ucsc_acembly.pm, 1.3, 1.4 ucsc_ensgene.pm, 1.3, 1.4 ucsc_genscan.pm, 1.3, 1.4 ucsc_refgene.pm, 1.3, 1.4 ucsc_sanger22.pm, 1.3, 1.4 ucsc_sanger22pseudo.pm, 1.3, 1.4 ucsc_softberry.pm, 1.3, 1.4 ucsc_twinscan.pm, 1.3, 1.4 ucsc_unigene.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graph Edge.pm, 1.11, 1.12 IO.pm, 1.17, 1.18 ProteinGraph.pm, 1.35, 1.36 SimpleGraph.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graph/IO dip.pm, 1.14, 1.15 psi_xml.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Event EventGeneratorI.pm, 1.12, 1.13 EventHandlerI.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Factory AnalysisI.pm, 1.7, 1.8 ApplicationFactoryI.pm, 1.10, 1.11 DriverFactory.pm, 1.15, 1.16 FTLocationFactory.pm, 1.25, 1.26 HitFactoryI.pm, 1.11, 1.12 LocationFactoryI.pm, 1.7, 1.8 MapFactoryI.pm, 1.9, 1.10 ObjectBuilderI.pm, 1.6, 1.7 ObjectFactory.pm, 1.5, 1.6 ObjectFactoryI.pm, 1.7, 1.8 ResultFactoryI.pm, 1.10, 1.11 SeqAnalysisParserFactory.pm, 1.15, 1.16 SeqAnalysisParserFactoryI.pm, 1.12, 1.13 SequenceFactoryI.pm, 1.10, 1.11 SequenceProcessorI.pm, 1.5, 1.6 SequenceStreamI.pm, 1.7, 1.8 TreeFactoryI.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Das FeatureTypeI.pm, 1.6, 1.7 SegmentI.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Util Binning.pm, 1.7, 1.8 Rearrange.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Query GenBank.pm, 1.18, 1.19 WebQuery.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqVersion gi.pm,1.4,1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq AARange.pm, 1.12, 1.13 DNA.pm, 1.11, 1.12 Exon.pm, 1.10, 1.11 Gene.pm, 1.15, 1.16 Intron.pm, 1.9, 1.10 Mutation.pm, 1.13, 1.14 Mutator.pm, 1.34, 1.35 Prim_Transcript.pm, 1.9, 1.10 Range.pm, 1.9, 1.10 Repeat_Region.pm, 1.9, 1.10 Repeat_Unit.pm, 1.9, 1.10 SeqI.pm, 1.31, 1.32 Transcript.pm, 1.21, 1.22 Translation.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.27, 1.28 alignment.pm, 1.4, 1.5 anchored_arrow.pm, 1.10, 1.11 arrow.pm, 1.31, 1.32 box.pm, 1.6, 1.7 broken_line.pm, 1.2, 1.3 cds.pm, 1.35, 1.36 christmas_arrow.pm, 1.2, 1.3 crossbox.pm, 1.6, 1.7 dashed_line.pm, 1.3, 1.4 diamond.pm, 1.13, 1.14 dna.pm, 1.26, 1.27 dot.pm, 1.7, 1.8 dumbbell.pm, 1.4, 1.5 ellipse.pm, 1.5, 1.6 extending_arrow.pm, 1.3, 1.4 flag.pm, 1.4, 1.5 generic.pm, 1.42, 1.43 graded_segments.pm, 1.18, 1.19 group.pm, 1.10, 1.11 heterogeneous_segments.pm, 1.9, 1.10 lightning.pm, 1.2, 1.3 line.pm, 1.6, 1.7 merge_parts.pm, 1.3, 1.4 merged_alignment.pm, 1.4, 1.5 minmax.pm, 1.2, 1.3 oval.pm, 1.4, 1.5 pentagram.pm, 1.2, 1.3 pinsertion.pm, 1.7, 1.8 primers.pm, 1.8, 1.9 processed_transcript.pm, 1.12, 1.13 protein.pm, 1.2, 1.3 ragged_ends.pm, 1.1, 1.2 redgreen_box.pm, 1.5, 1.6 redgreen_segment.pm, 1.3, 1.4 repeating_shape.pm, 1.2, 1.3 ruler_arrow.pm, 1.7, 1.8 saw_teeth.pm, 1.3, 1.4 segmented_keyglyph.pm, 1.6, 1.7 segments.pm, 1.47, 1.48 so_transcript.pm, 1.2, 1.3 span.pm, 1.6, 1.7 splice_site.pm, 1.3, ! 1.4 text_in_box.pm, 1.2, 1.3 three_letters.pm, 1.4, 1.5 tic_tac_toe.pm, 1.2, 1.3 toomany.pm, 1.5, 1.6 track.pm, 1.10, 1.11 transcript.pm, 1.23, 1.24 transcript2.pm, 1.28, 1.29 translation.pm, 1.37, 1.38 triangle.pm, 1.11, 1.12 two_bolts.pm, 1.2, 1.3 wave.pm, 1.2, 1.3 weighted_arrow.pm, 1.2, 1.3 whiskerplot.pm, 1.2, 1.3 xyplot.pm, 1.26, 1.27   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm, 1.49, 1.50 AbstractSeq.pm, 1.25, 1.26 Blast.pm, 1.22, 1.23 EMBL.pm, 1.32, 1.33 Fasta.pm, 1.35, 1.36 Fastq.pm, 1.12, 1.13 GenBank.pm, 1.23, 1.24 Hmmer.pm, 1.10, 1.11 Qual.pm, 1.9, 1.10 SwissPfam.pm, 1.24, 1.25 Swissprot.pm, 1.26, 1.27   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq/IO BioPerl.pm, 1.20, 1.21 Loader.pm, 1.19, 1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Location Atomic.pm, 1.16, 1.17 AvWithinCoordPolicy.pm, 1.8, 1.9 CoordinatePolicyI.pm, 1.8, 1.9 Fuzzy.pm, 1.34, 1.35 FuzzyLocationI.pm, 1.21, 1.22 NarrowestCoordPolicy.pm, 1.11, 1.12 Simple.pm, 1.41, 1.42 Split.pm, 1.47, 1.48 SplitLocationI.pm, 1.19, 1.20 WidestCoordPolicy.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics ConfiguratorI.pm, 1.8, 1.9 FeatureBase.pm, 1.12, 1.13 Glyph.pm, 1.123, 1.124 Panel.pm, 1.125, 1.126 Pictogram.pm, 1.16, 1.17 RendererI.pm, 1.6, 1.7 Util.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graph/SimpleGraph Traversal.pm, 1.17, 1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/IO phylip.pm, 1.4, 1.5 scoring.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Clone.pm, 1.7, 1.8 Contig.pm, 1.7, 1.8 CytoMap.pm, 1.10, 1.11 CytoMarker.pm, 1.12, 1.13 CytoPosition.pm, 1.16, 1.17 EntityI.pm, 1.3, 1.4 FPCMarker.pm, 1.10, 1.11 LinkageMap.pm, 1.17, 1.18 LinkagePosition.pm, 1.16, 1.17 MapI.pm, 1.16, 1.17 Mappable.pm, 1.8, 1.9 MappableI.pm, 1.18, 1.19 Marker.pm, 1.24, 1.25 MarkerI.pm, 1.18, 1.19 Microsatellite.pm, 1.14, 1.15 OrderedPosition.pm, 1.12, 1.13 OrderedPositionWithDistance.pm, 1.10, 1.11 Physical.pm, 1.9, 1.10 Position.pm, 1.19, 1.20 PositionHandler.pm, 1.4, 1.5 PositionHandlerI.pm, 1.2, 1.3 PositionI.pm, 1.19, 1.20 Relative.pm, 1.6, 1.7 RelativeI.pm, 1.5, 1.6 SimpleMap.pm, 1.19, 1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.22, 1.23 masta.pm, 1.11, 1.12 meme.pm, 1.21, 1.22 psiblast.pm, 1.12, 1.13 transfac.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/MapIO fpc.pm, 1.7, 1.8 mapmaker.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM IO.pm, 1.15, 1.16 InstanceSite.pm, 1.15, 1.16 InstanceSiteI.pm, 1.10, 1.11 ProtMatrix.pm, 1.16, 1.17 ProtPsm.pm, 1.9, 1.10 Psm.pm, 1.14, 1.15 PsmHeader.pm, 1.11, 1.12 PsmHeaderI.pm, 1.10, 1.11 PsmI.pm, 1.8, 1.9 SiteMatrix.pm, 1.38, 1.39 SiteMatrixI.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix Generic.pm, 1.15, 1.16 IO.pm, 1.6, 1.7 MatrixI.pm, 1.4, 1.5 PhylipDist.pm, 1.16, 1.17 Scoring.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Ontology/SimpleGOEngine GraphAdaptor.pm, 1.7, 1.8 GraphAdaptor02.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Ontology GOterm.pm, 1.23, 1.24 InterProTerm.pm, 1.11, 1.12 OBOEngine.pm, 1.9, 1.10 OBOterm.pm, 1.6, 1.7 Ontology.pm, 1.20, 1.21 OntologyEngineI.pm, 1.17, 1.18 OntologyI.pm, 1.9, 1.10 OntologyStore.pm, 1.13, 1.14 Path.pm, 1.8, 1.9 PathI.pm, 1.7, 1.8 Relationship.pm, 1.15, 1.16 RelationshipFactory.pm, 1.5, 1.6 RelationshipI.pm, 1.10, 1.11 RelationshipType.pm, 1.18, 1.19 SimpleGOEngine.pm, 1.37, 1.38 SimpleOntologyEngine.pm, 1.18, 1.19 Term.pm, 1.32, 1.33 TermFactory.pm, 1.7, 1.8 TermI.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO InterProParser.pm, 1.12, 1.13 dagflat.pm, 1.30, 1.31 goflat.pm, 1.8, 1.9 obo.pm, 1.10, 1.11 simplehierarchy.pm, 1.18, 1.19 soflat.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/Simulation Coalescent.pm, 1.11, 1.12 GeneticDrift.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO/Handlers BaseSAXHandler.pm, 1.4, 1.5 InterProHandler.pm, 1.16, 1.17 InterPro_BioSQL_Handler.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Correlate.pm, 1.10, 1.11 Measure.pm, 1.10, 1.11 Phenotype.pm, 1.13, 1.14 PhenotypeI.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM MiniMIMentry.pm, 1.10, 1.11 OMIMentry.pm, 1.17, 1.18 OMIMentryAllelicVariant.pm, 1.10, 1.11 OMIMparser.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/MeSH Term.pm, 1.7, 1.8 Twig.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.19, 1.20 Enzyme.pm, 1.16, 1.17 EnzymeCollection.pm, 1.10, 1.11 EnzymeI.pm, 1.6, 1.7 IO.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/Enzyme MultiCut.pm, 1.7, 1.8 MultiSite.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/IO csv.pm, 1.8, 1.9 hapmap.pm, 1.10, 1.11 phase.pm, 1.7, 1.8 prettybase.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/PopGen Genotype.pm, 1.10, 1.11 GenotypeI.pm, 1.4, 1.5 HtSNP.pm, 1.6, 1.7 IO.pm, 1.7, 1.8 Individual.pm, 1.15, 1.16 IndividualI.pm, 1.8, 1.9 Marker.pm, 1.7, 1.8 MarkerI.pm, 1.6, 1.7 PopStats.pm, 1.10, 1.11 Population.pm, 1.19, 1.20 PopulationI.pm, 1.9, 1.10 Statistics.pm, 1.34, 1.35 TagHaplotype.pm, 1.5, 1.6 Utilities.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root Err.pm, 1.22, 1.23 Global.pm, 1.9, 1.10 HTTPget.pm, 1.14, 1.15 IO.pm, 1.63, 1.64 IOManager.pm, 1.21, 1.22 Object.pm, 1.33, 1.34 Root.pm, 1.37, 1.38 RootI.pm, 1.71, 1.72 Storable.pm, 1.8, 1.9 Utilities.pm, 1.32, 1.33 Vector.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.8, 1.9 IterationI.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit BlastHit.pm, 1.17, 1.18 Fasta.pm, 1.10, 1.11 GenericHit.pm, 1.38, 1.39 HMMERHit.pm, 1.7, 1.8 HitFactory.pm, 1.7, 1.8 HitI.pm, 1.24, 1.25 HmmpfamHit.pm, 1.3, 1.4 PsiBlastHit.pm, 1.7, 1.8 PullHitI.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/IO bairoch.pm, 1.8, 1.9 base.pm, 1.11, 1.12 itype2.pm, 1.6, 1.7 withrefm.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastResult.pm, 1.24, 1.25 GenericResult.pm, 1.25, 1.26 HMMERResult.pm, 1.7, 1.8 HmmpfamResult.pm, 1.3, 1.4 PullResultI.pm, 1.3, 1.4 ResultFactory.pm, 1.7, 1.8 ResultI.pm, 1.23, 1.24 WABAResult.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.29, 1.30 FastaHSP.pm, 1.10, 1.11 GenericHSP.pm, 1.72, 1.73 HMMERHSP.pm, 1.8, 1.9 HSPFactory.pm, 1.8, 1.9 HSPI.pm, 1.38, 1.39 PSLHSP.pm, 1.5, 1.6 PsiBlastHSP.pm, 1.8, 1.9 PullHSPI.pm, 1.2, 1.3 WABAHSP.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO EventHandlerI.pm, 1.13, 1.14 FastHitEventBuilder.pm, 1.13, 1.14 IteratedSearchResultEventBuilder.pm, 1.11, 1.12 SearchResultEventBuilder.pm, 1.42, 1.43 SearchWriterI.pm, 1.10, 1.11 axt.pm, 1.10, 1.11 blast.pm, 1.105, 1.106 blasttable.pm, 1.8, 1.9 blastxml.pm, 1.37, 1.38 exonerate.pm, 1.17, 1.18 fasta.pm, 1.50, 1.51 hmmer.pm, 1.35, 1.36 hmmer_pull.pm, 1.4, 1.5 megablast.pm, 1.8, 1.9 psl.pm, 1.13, 1.14 sim4.pm, 1.13, 1.14 waba.pm, 1.16, 1.17 wise.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search BlastStatistics.pm, 1.5, 1.6 DatabaseI.pm, 1.10, 1.11 GenericDatabase.pm, 1.9, 1.10 GenericStatistics.pm, 1.6, 1.7 Processor.pm, 1.12, 1.13 StatisticsI.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene Exon.pm, 1.16, 1.17 ExonI.pm, 1.12, 1.13 GeneStructure.pm, 1.21, 1.22 GeneStructureI.pm, 1.14, 1.15 Intron.pm, 1.11, 1.12 NC_Feature.pm, 1.13, 1.14 Poly_A_site.pm, 1.10, 1.11 Promoter.pm, 1.8, 1.9 Transcript.pm, 1.39, 1.40 TranscriptI.pm, 1.14, 1.15 UTR.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer BSMLResultWriter.pm, 1.5, 1.6 GbrowseGFF.pm, 1.15, 1.16 HSPTableWriter.pm, 1.17, 1.18 HTMLResultWriter.pm, 1.38, 1.39 HitTableWriter.pm, 1.20, 1.21 ResultTableWriter.pm, 1.19, 1.20 TextResultWriter.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Seq BaseSeqProcessor.pm, 1.8, 1.9 EncodedSeq.pm, 1.12, 1.13 LargeLocatableSeq.pm, 1.6, 1.7 LargePrimarySeq.pm, 1.32, 1.33 LargeSeq.pm, 1.16, 1.17 LargeSeqI.pm, 1.6, 1.7 Meta.pm, 1.13, 1.14 MetaI.pm, 1.10, 1.11 PrimaryQual.pm, 1.24, 1.25 PrimedSeq.pm, 1.23, 1.24 QualI.pm, 1.11, 1.12 Quality.pm, 1.10, 1.11 RichSeq.pm, 1.20, 1.21 RichSeqI.pm, 1.15, 1.16 SeqBuilder.pm, 1.9, 1.10 SeqFactory.pm, 1.12, 1.13 SeqFastaSpeedFactory.pm, 1.9, 1.10 SeqWithQuality.pm, 1.27, 1.28 SequenceTrace.pm, 1.14, 1.15 TraceI.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/SiRNA Oligo.pm, 1.6, 1.7 Pair.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.34, 1.35 AnnotationAdaptor.pm, 1.11, 1.12 Collection.pm, 1.18, 1.19 CollectionI.pm, 1.6, 1.7 Computation.pm, 1.16, 1.17 FeaturePair.pm, 1.22, 1.23 Generic.pm, 1.103, 1.104 PositionProxy.pm, 1.9, 1.10 Primer.pm, 1.21, 1.22 Similarity.pm, 1.17, 1.18 SimilarityPair.pm, 1.31, 1.32 TypedSeqFeatureI.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Seq/Meta Array.pm,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO FTHelper.pm, 1.63, 1.64 MultiFile.pm, 1.14, 1.15 ace.pm, 1.18, 1.19 agave.pm, 1.15, 1.16 asciitree.pm, 1.5, 1.6 bsml.pm, 1.25, 1.26 bsml_sax.pm, 1.5, 1.6 chadoxml.pm, 1.20, 1.21 chaos.pm, 1.11, 1.12 chaosxml.pm, 1.4, 1.5 embl.pm, 1.106, 1.107 entrezgene.pm, 1.24, 1.25 excel.pm, 1.5, 1.6 fasta.pm, 1.58, 1.59 fastq.pm, 1.15, 1.16 game.pm, 1.38, 1.39 gcg.pm, 1.27, 1.28 genbank.pm, 1.149, 1.150 interpro.pm, 1.10, 1.11 kegg.pm, 1.19, 1.20 largefasta.pm, 1.24, 1.25 lasergene.pm, 1.7, 1.8 locuslink.pm, 1.14, 1.15 metafasta.pm, 1.9, 1.10 phd.pm, 1.22, 1.23 pir.pm, 1.24, 1.25 qual.pm, 1.32, 1.33 raw.pm, 1.22, 1.23 scf.pm, 1.37, 1.38 strider.pm, 1.8, 1.9 swiss.pm, 1.97, 1.98 tab.pm, 1.7, 1.8 table.pm, 1.5, 1.6 tigr.pm, 1.12, 1.13 tigrxml.pm, 1.8, 1.9 tinyseq.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools FeatureNamer.pm, 1.6, 1.7 IDHandler.pm, 1.10, 1.11 TypeMapper.pm, 1.14, 1.15 Unflattener.pm, 1.38, 1.39   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/game featHandler.pm, 1.15, 1.16 gameHandler.pm, 1.8, 1.9 gameSubs.pm, 1.9, 1.10 gameWriter.pm, 1.14, 1.15 seqHandler.pm, 1.27, 1.28   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure Atom.pm, 1.12, 1.13 Chain.pm, 1.11, 1.12 Entry.pm, 1.27, 1.28 IO.pm, 1.14, 1.15 Model.pm, 1.10, 1.11 Residue.pm, 1.11, 1.12 StructureI.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/IO pdb.pm,1.18,1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/tinyseq tinyseqHandler.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy FactoryI.pm, 1.4, 1.5 Node.pm, 1.17, 1.18 Taxon.pm, 1.5, 1.6 Tree.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/STRIDE Res.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Symbol Alphabet.pm, 1.11, 1.12 DNAAlphabet.pm, 1.7, 1.8 ProteinAlphabet.pm, 1.8, 1.9 Symbol.pm, 1.10, 1.11 SymbolI.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools AlignFactory.pm, 1.8, 1.9 AnalysisResult.pm, 1.18, 1.19 BPbl2seq.pm, 1.29, 1.30 BPlite.pm, 1.42, 1.43 BPpsilite.pm, 1.26, 1.27 Blast.pm, 1.38, 1.39 Blat.pm, 1.8, 1.9 CodonTable.pm, 1.37, 1.38 Coil.pm, 1.7, 1.8 ECnumber.pm, 1.12, 1.13 EPCR.pm, 1.18, 1.19 ERPIN.pm, 1.6, 1.7 ESTScan.pm, 1.14, 1.15 Eponine.pm, 1.13, 1.14 Est2Genome.pm, 1.17, 1.18 Fgenesh.pm, 1.14, 1.15 FootPrinter.pm, 1.9, 1.10 GFF.pm, 1.58, 1.59 Gel.pm, 1.11, 1.12 Geneid.pm, 1.5, 1.6 Genemark.pm, 1.17, 1.18 Genewise.pm, 1.25, 1.26 Genomewise.pm, 1.6, 1.7 Genscan.pm, 1.30, 1.31 Glimmer.pm, 1.5, 1.6 Grail.pm, 1.11, 1.12 GuessSeqFormat.pm, 1.15, 1.16 HMM.pm, 1.8, 1.9 Hmmpfam.pm, 1.9, 1.10 IUPAC.pm, 1.30, 1.31 Lucy.pm, 1.15, 1.16 MZEF.pm, 1.14, 1.15 OddCodes.pm, 1.20, 1.21 Primer3.pm, 1.21, 1.22 Prints.pm, 1.13, 1.14 Profile.pm, 1.8, 1.9 Promoterwise.pm, 1.9, 1.10 PrositeScan.pm, 1.2, 1.3 Pseudowise.pm, 1.10, 1.11 QRNA.pm, 1.5, 1.6 RNAMotif.pm, 1.12, 1.13 RandomDistFunctions.pm, 1.7, 1.8 RepeatMasker.pm, 1.11, 1.12 RestrictionEnzyme.pm, 1.35, 1.36 Seg.pm, 1.10, 1.11 SeqAn! al.pm, 1.19, 1.20 SeqPattern.pm, 1.23, 1.24 SeqStats.pm, 1.31, 1.32 SeqWords.pm, 1.17, 1.18 SiRNA.pm, 1.13, 1.14 Sigcleave.pm, 1.22, 1.23 Signalp.pm, 1.9, 1.10 WWW.pm, 1.18, 1.19 dpAlign.pm, 1.18, 1.19 ipcress.pm, 1.9, 1.10 isPcr.pm, 1.9, 1.10 pICalculator.pm, 1.11, 1.12 pSW.pm, 1.27, 1.28 tRNAscanSE.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Molphy.pm, 1.10, 1.11 PAML.pm, 1.49, 1.50   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.24, 1.25 HTML.pm, 1.20, 1.21 Sbjct.pm, 1.25, 1.26   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EMBOSS Palindrome.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/BPlite HSP.pm, 1.31, 1.32 Iteration.pm, 1.18, 1.19 Sbjct.pm, 1.33, 1.34   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Domain.pm, 1.12, 1.13 Results.pm, 1.30, 1.31 Set.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis SimpleAnalysisBase.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.41, 1.42 Trim.pm, 1.21, 1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Domcut.pm, 1.14, 1.15 ELM.pm, 1.13, 1.14 GOR4.pm, 1.12, 1.13 HNN.pm, 1.12, 1.13 Mitoprot.pm, 1.8, 1.9 NetPhos.pm, 1.13, 1.14 Scansite.pm, 1.16, 1.17 Sopma.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Phylip ProtDist.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML ModelResult.pm, 1.9, 1.10 Result.pm, 1.23, 1.24   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run GenericParameters.pm, 1.6, 1.7 ParametersI.pm, 1.5, 1.6 RemoteBlast.pm, 1.39, 1.40 StandAloneBlast.pm, 1.64, 1.65 WrapperBase.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Primer/Assessor Base.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Molphy Result.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Prediction Exon.pm, 1.17, 1.18 Gene.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Primer AssessorI.pm, 1.5, 1.6 Feature.pm, 1.5, 1.6 Pair.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Sim4 Exon.pm, 1.16, 1.17 Results.pm, 1.25, 1.26   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Spidey Exon.pm, 1.7, 1.8 Results.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/SiRNA/Ruleset saigo.pm, 1.4, 1.5 tuschl.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree AlleleNode.pm, 1.13, 1.14 Compatible.pm, 1.6, 1.7 DistanceFactory.pm, 1.8, 1.9 Node.pm, 1.50, 1.51 NodeI.pm, 1.35, 1.36 NodeNHX.pm, 1.10, 1.11 RandomFactory.pm, 1.18, 1.19 Statistics.pm, 1.12, 1.13 Tree.pm, 1.22, 1.23 TreeFunctionsI.pm, 1.29, 1.30 TreeI.pm, 1.17, 1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO TreeEventBuilder.pm, 1.23, 1.24 cluster.pm, 1.5, 1.6 lintree.pm, 1.8, 1.9 newick.pm, 1.38, 1.39 nexus.pm, 1.14, 1.15 nhx.pm, 1.18, 1.19 pag.pm, 1.11, 1.12 svggraph.pm, 1.5, 1.6 tabtree.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib/Test Simple.pm,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Test.pm,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Variation AAChange.pm, 1.20, 1.21 AAReverseMutate.pm, 1.12, 1.13 Allele.pm, 1.15, 1.16 DNAMutation.pm, 1.18, 1.19 IO.pm, 1.24, 1.25 RNAChange.pm, 1.17, 1.18 SNP.pm, 1.16, 1.17 SeqDiff.pm, 1.23, 1.24 VariantI.pm, 1.21, 1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Variation/IO flat.pm, 1.19, 1.20 xml.pm, 1.19, 1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio PrimarySeq.pm, 1.6, 1.7 PrimarySeqI.pm, 1.6, 1.7 Seq.pm, 1.6, 1.7 SeqI.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/root/lib TestInterface.pm, 1.1, 1.2 TestObject.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder Module.pm, 1.1, 1.2 Tester.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PrimarySeq.pm,1.97,1.98   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PrimarySeq.pm,1.98,1.99   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map SimpleMap.pm,1.20,1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map MappableI.pm,1.19,1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map MapI.pm,1.17,1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map Position.pm,1.20,1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map PositionHandler.pm,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor memory.pm, 1.47, 1.48 berkeleydb.pm, 1.25, 1.26   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.24, 1.25   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Taxon.pm,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree Node.pm,1.51,1.52   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.44, 1.45   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction EnzymeCollection.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.124,1.125   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map MapI.pm, 1.18, 1.19 Mappable.pm, 1.9, 1.10 MappableI.pm, 1.20, 1.21 PositionI.pm, 1.20, 1.21 SimpleMap.pm, 1.21, 1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio PullParserI.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map CytoPosition.pm,1.17,1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Taxonomy.t,1.12,1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Species.t,1.12,1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root HTTPget.pm,1.15,1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm,1.4,1.5   Malcom Cook
• [Bioperl-guts-l] bioperl-live/Bio FeatureIO.pm,1.15,1.16   Malcom Cook
• [Bioperl-guts-l] bioperl-live/Bio SeqIO.pm,1.93,1.94   Malcom Cook
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO strider.pm,1.6,1.7   Malcom Cook
• [Bioperl-guts-l] bioperl-live/Bio/Tools Fgenesh.pm,1.10,1.11   Malcom Cook
• [Bioperl-guts-l] bioperl-live/Bio/DB Ace.pm, 1.15, 1.16 Failover.pm, 1.12, 1.13 FileCache.pm, 1.11, 1.12 InMemoryCache.pm, 1.7, 1.8 RandomAccessI.pm, 1.14, 1.15   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Seq EncodedSeq.pm, 1.11, 1.12 LargeSeq.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure/IO pdb.pm,1.17,1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio RangeI.pm,1.49,1.50   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO FTHelper.pm, 1.61, 1.62 MultiFile.pm, 1.12, 1.13 ace.pm, 1.17, 1.18 asciitree.pm, 1.4, 1.5 bsml.pm, 1.24, 1.25 bsml_sax.pm, 1.4, 1.5 chadoxml.pm, 1.19, 1.20 chaos.pm, 1.10, 1.11 chaosxml.pm, 1.3, 1.4 embl.pm, 1.104, 1.105 excel.pm, 1.4, 1.5 gcg.pm, 1.26, 1.27 genbank.pm, 1.146, 1.147 kegg.pm, 1.18, 1.19 lasergene.pm, 1.5, 1.6 phd.pm, 1.21, 1.22 pir.pm, 1.23, 1.24 qual.pm, 1.30, 1.31 raw.pm, 1.21, 1.22 scf.pm, 1.36, 1.37 tab.pm, 1.6, 1.7 table.pm, 1.4, 1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Structure IO.pm,1.12,1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools AnalysisResult.pm, 1.17, 1.18 IUPAC.pm, 1.29, 1.30 OddCodes.pm, 1.19, 1.20 Primer3.pm, 1.20, 1.21 WWW.pm, 1.16, 1.17   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.28, 1.29 Set.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.23, 1.24 HTML.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools Blast.pm, 1.37, 1.38 SeqAnal.pm, 1.18, 1.19 SeqPattern.pm, 1.22, 1.23 WWW.pm, 1.17, 1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB GenericWebDBI.pm,1.4,1.5   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.28, 1.29 PsiBlastHSP.pm, 1.7, 1.8   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Root Err.pm, 1.21, 1.22 IOManager.pm, 1.20, 1.21 Object.pm, 1.32, 1.33 Utilities.pm, 1.31, 1.32 Vector.pm, 1.17, 1.18 Xref.pm, 1.15, 1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit PsiBlastHit.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Pictogram.pm,1.15,1.16   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/maintenance symlink_scripts.PLS, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio Taxonomy.pm,1.10,1.11   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.34,1.35   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.30, 1.31 GenericHSP.pm, 1.73, 1.74 PsiBlastHSP.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO chadoxml.pm, 1.21, 1.22 lasergene.pm, 1.8, 1.9 tinyseq.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit PsiBlastHit.pm, 1.8, 1.9   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/tinyseq tinyseqHandler.pm, 1.6, 1.7   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO exonerate.pm,1.18,1.19   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Mitoprot.pm, 1.9, 1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.25, 1.26 HTML.pm, 1.21, 1.22   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools Blast.pm,1.39,1.40   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/maintenance README,1.1,1.2   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Set.pm,1.17,1.18   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Tools GuessSeqFormat.pm, 1.17, 1.18 pICalculator.pm, 1.12, 1.13   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/Variation AAChange.pm, 1.21, 1.22 DNAMutation.pm, 1.19, 1.20   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO lintree.pm,1.9,1.10   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/scripts/Bio-DB-GFF process_sgd.PLS, 1.2, 1.3   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB DBFetch.pm,1.16,1.17   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live Makefile.PL,1.101,1.102   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm,1.13,1.14   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/t tutorial.t,1.2,NONE   Mauricio Herrera Cuadra
• [Bioperl-guts-l] bioperl-live/Bio/DB LocationI.pm, NONE, 1.1 ReferenceI.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.24,1.25   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.3, 1.4 ElinkData.pm, 1.12, 1.13 einfo.pm, 1.8, 1.9 esearch.pm, 1.11, 1.12   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,NONE,1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.1,1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.2,1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.25,1.26   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities esearch.pm, 1.12, 1.13   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities esearch.pm, 1.13, 1.14   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.3,1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.26,1.27   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.13, 1.14 einfo.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.4,1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO swiss.pm,1.95,1.96   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/data newformat.swiss,1.1,1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t swiss.t,1.3,1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.4, 1.5 ElinkData.pm, 1.14, 1.15 elink.pm, 1.24, 1.25   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.5,1.6   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.27,1.28   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.15, 1.16   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.6,1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Location Fuzzy.pm,1.33,1.34   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t Location.t, 1.29, 1.30 LocationFactory.t, 1.12, 1.13   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test/Builder - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test/Builder/Tester - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test Builder.pm, NONE, 1.1 More.pm, NONE, 1.1 Simple.pm, NONE, 1.1 Tutorial.pod, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test/Builder/Tester Color.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test/Builder Module.pm, NONE, 1.1 Tester.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO embl.pm,1.103,1.104   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Factory FTLocationFactory.pm, 1.21, 1.22   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test/Builder/Tester Color.pm, 1.1, NONE   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test/Builder Module.pm, 1.1, NONE Tester.pm, 1.1, NONE   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/Test Builder.pm, 1.1, NONE More.pm, 1.1, NONE Simple.pm, 1.1, NONE Tutorial.pod, 1.1, NONE   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib/Test - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder/Tester - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder/Tester Color.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib/Test Builder.pm, NONE, 1.1 More.pm, NONE, 1.1 Simple.pm, NONE, 1.1 Tutorial.pod, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib/Test/Builder Module.pm, NONE, 1.1 Tester.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.7,1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.8,1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t Location.t,1.30,1.31   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Factory FTLocationFactory.pm, 1.22, 1.23   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Factory FTLocationFactory.pm, 1.23, 1.24   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Factory FTLocationFactory.pm, 1.24, 1.25   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.9,1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/data no_cds_example.gb,NONE,1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t Unflattener.t,1.8,1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools Unflattener.pm, 1.37, 1.38   Christopher John Fields
• [Bioperl-guts-l] bioperl-live bptutorial.pl,1.169,1.170   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.102,1.103   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO axt.pm,1.8,1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO axt.pm,1.9,1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP GenericHSP.pm, 1.68.4.3, 1.68.4.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Location Split.pm,1.46,1.47   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.103,1.104   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Root Storable.pm,1.7,1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools SeqPattern.pm,1.21,1.22   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/SiRNA/Ruleset tuschl.pm, 1.4, 1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/game gameWriter.pm, 1.13, 1.14   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.147,1.148   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO qual.pm,1.31,1.32   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP HmmpfamHSP.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result PullResultI.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit HmmpfamHit.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Location SplitLocationI.pm, 1.18, 1.19   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm,1.6,1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Expression/FeatureGroup FeatureGroupMas50.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Expression/FeatureSet FeatureSetMas50.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/memory feature_serializer.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi pg_fts.pm, 1.3, 1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor berkeleydb.pm, 1.24, 1.25 biofetch_oracle.pm, 1.4, 1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store bdb.pm, 1.3, 1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI Iterator.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM ProtPsm.pm, 1.8, 1.9 SiteMatrixI.pm, 1.17, 1.18   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO meme.pm, 1.20, 1.21 psiblast.pm, 1.11, 1.12 transfac.pm, 1.15, 1.16   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph arrow.pm, 1.29, 1.30 ex.pm, 1.5, 1.6 flag.pm, 1.2, 1.3 ruler_arrow.pm, 1.5, 1.6 three_letters.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Util.pm,1.4,1.5   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.148,1.149   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio IdCollectionI.pm,1.6,1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Seq SeqFastaSpeedFactory.pm, 1.8, 1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools ECnumber.pm, 1.11, 1.12 pICalculator.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene GeneStructureI.pm, 1.13, 1.14 Poly_A_site.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Correlate.pm, 1.9, 1.10 Measure.pm, 1.9, 1.10 Phenotype.pm, 1.12, 1.13 PhenotypeI.pm, 1.11, 1.12   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM MiniMIMentry.pm, 1.9, 1.10 OMIMentry.pm, 1.16, 1.17 OMIMentryAllelicVariant.pm, 1.9, 1.10 OMIMparser.pm, 1.21, 1.22   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Ontology GOterm.pm, 1.22, 1.23 InterProTerm.pm, 1.10, 1.11 OBOEngine.pm, 1.8, 1.9 OBOterm.pm, 1.5, 1.6 OntologyEngineI.pm, 1.16, 1.17 Path.pm, 1.7, 1.8 PathI.pm, 1.6, 1.7 Relationship.pm, 1.14, 1.15 RelationshipI.pm, 1.9, 1.10 RelationshipType.pm, 1.17, 1.18 SimpleGOEngine.pm, 1.36, 1.37 Term.pm, 1.31, 1.32 TermI.pm, 1.17, 1.18   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Ontology/SimpleGOEngine GraphAdaptor.pm, 1.6, 1.7 GraphAdaptor02.pm, 1.6, 1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO InterProParser.pm, 1.11, 1.12 dagflat.pm, 1.29, 1.30 goflat.pm, 1.7, 1.8 obo.pm, 1.9, 1.10 simplehierarchy.pm, 1.17, 1.18 soflat.pm, 1.7, 1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO/Handlers InterProHandler.pm, 1.15, 1.16   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.43,1.44   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.44,1.45   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.109,1.110   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB WebDBSeqI.pm,1.58,1.59   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.45,1.46   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.110,1.111   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store berkeleydb.pm, 1.8, 1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store berkeleydb.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.104,1.105   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.10,1.11   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.11,1.12   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Location Atomic.pm, 1.17, 1.18 Fuzzy.pm, 1.35, 1.36 FuzzyLocationI.pm, 1.22, 1.23 Simple.pm, 1.42, 1.43 Split.pm, 1.48, 1.49   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.30,1.31   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities ElinkData.pm, 1.19, 1.20 efetch.pm, 1.11, 1.12 egquery.pm, 1.9, 1.10 einfo.pm, 1.12, 1.13 elink.pm, 1.28, 1.29 epost.pm, 1.11, 1.12 esearch.pm, 1.16, 1.17 esummary.pm, 1.10, 1.11   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/data testfile.erpin,NONE,1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t rnamotif.t,1.2,1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools ERPIN.pm,1.7,1.8   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t rnamotif.t,1.3,1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB GenericWebDBI.pm,1.6,1.7   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.32,1.33   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools ERPIN.pm, 1.8, 1.9 RNAMotif.pm, 1.13, 1.14   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB GFF.pm,1.141,1.142   Christopher John Fields
• [Bioperl-guts-l] bioperl-live INSTALL,1.48,1.49   Christopher John Fields
• [Bioperl-guts-l] bioperl-live INSTALL,1.49,1.50   Christopher John Fields
• [Bioperl-guts-l] bioperl-live Makefile.PL,1.100,1.101   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM InstanceSite.pm, 1.14, 1.15   Stefan Kirov
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm,1.21,1.22   Stefan Kirov
• [Bioperl-guts-l] bioperl-live/t psm.t,1.14,1.15   Stefan Kirov
• [Bioperl-guts-l] bioperl-live/t/data mixedmast.dat,NONE,1.1   Stefan Kirov
• [Bioperl-guts-l] bioperl-live/Bio/Ontology OBOEngine.pm,1.10,1.11   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Ontology Ontology.pm,1.21,1.22   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/t obo_parser.t,1.1,1.2   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Tools Lucy.pm,1.17,1.18   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Tools BPpsilite.pm,1.27,1.28   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Tools/BPlite Iteration.pm, 1.19, 1.20   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.45, 1.46   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.35,1.36   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio PullParserI.pm,1.8,1.9   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq/IO Loader.pm,1.20,1.21   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.126,1.127   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB WebDBSeqI.pm,1.61,1.62   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB SeqHound.pm,1.5,1.6   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store berkeleydb.pm, 1.10, 1.11   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB Registry.pm,1.38,1.39   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB GFF.pm,1.140,1.141   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor berkeleydb.pm, 1.26, 1.27   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB Flat.pm,1.25,1.26   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BinarySearch.pm, 1.26, 1.27   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB DBFetch.pm,1.15,1.16   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm,1.12,1.13   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.16, 1.17   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.40, 1.41   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB GFF.pm,1.142,1.143   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm,1.7,1.8   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Tools Blat.pm, 1.7, 1.8 Coil.pm, 1.6, 1.7 Hmmpfam.pm, 1.8, 1.9 RepeatMasker.pm, 1.10, 1.11 Signalp.pm, 1.8, 1.9 pICalculator.pm, 1.10, 1.11   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Graph/IO psi_xml.pm,1.13,1.14   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Graph SimpleGraph.pm,1.12,1.13   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein ELM.pm, 1.12, 1.13   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BinarySearch.pm, 1.23, 1.24   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Pictogram.pm, 1.14, 1.15 Util.pm, 1.5, 1.6   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO/Handlers InterPro_BioSQL_Handler.pm, 1.7, 1.8   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store bdb.pm, 1.4, 1.5   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Annotation Target.pm,1.8,1.9   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph arrow.pm, 1.30, 1.31 ex.pm, 1.6, 1.7 flag.pm, 1.3, 1.4 merge_parts.pm, 1.2, 1.3 ruler_arrow.pm, 1.6, 1.7 three_letters.pm, 1.3, 1.4   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Graph/SimpleGraph Traversal.pm, 1.16, 1.17   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.12, 1.13 Scaffold.pm, 1.12, 1.13 ScaffoldI.pm, 1.6, 1.7 Singlet.pm, 1.9, 1.10   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm, 1.13, 1.14 phrap.pm, 1.5, 1.6   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Adaptor/dbi pg_fts.pm, 1.4, 1.5   Dave Messina
• [Bioperl-guts-l] bioperl-live/Bio/DB Registry.pm,1.32,1.33   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO swiss.pm,1.94,1.95   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO entrezgene.pm,1.22,1.23   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB Registry.pm,1.33,1.34   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB Registry.pm,1.34,1.35   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB Registry.pm,1.35,1.36   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB Failover.pm,1.10,1.11   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB BioDatabasePSeqStream.pm, 1.4, NONE BioSeqDatabase.pm, 1.8, NONE   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB BioDB.pm,1.12,1.13   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/Query BioQuery.pm,1.8,1.9   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL AnnotationCollectionAdaptor.pm, 1.13, 1.14   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL BaseDriver.pm,1.30,1.31   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL BasePersistenceAdaptor.pm, 1.40, 1.41   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/CacheServer SeqDB.pm,1.4,1.5   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB Registry.pm,1.36,1.37   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB Failover.pm,1.11,1.12   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL OBDA.pm, NONE, 1.1 DBAdaptor.pm, 1.25, 1.26 PrimarySeqAdaptor.pm, 1.24, 1.25 SeqAdaptor.pm, 1.52, 1.53   Brian Osborne
• [Bioperl-guts-l] bioperl-db/t 16obda.t,NONE,1.1   Brian Osborne
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL OBDA.pm,1.1,1.2   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio Species.pm,1.38,1.39   Brian Osborne
• [Bioperl-guts-l] bioperl-db/t 16obda.t,1.1,1.2   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t Biblio_biofetch.t,1.11,1.12   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm,1.10,1.11   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t Biblio_biofetch.t,1.12,1.13   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB DBFetch.pm,1.13,1.14   Brian Osborne
• [Bioperl-guts-l] bioperl-db/t 16obda.t,1.2,1.3   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t/data 1A11.pdb, NONE, 1.1 8HVP.pdb, NONE, 1.1   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t/data 1BPT.pdb, NONE, 1.1 pdb1bpt.ent, 1.1, NONE   Brian Osborne
• [Bioperl-guts-l] bioperl-live/t StructIO.t,1.8,1.9   Brian Osborne
• [Bioperl-guts-l] bioperl-run/Bio/Factory EMBOSS.pm,1.7,1.8   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Variation IO.pm,1.22,1.23   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.21, 1.22   Brian Osborne
• [Bioperl-guts-l] bioperl-network/Bio/Network/IO/psi intact.pm, 1.4, 1.5   Brian Osborne
• [Bioperl-guts-l] bioperl-network/t ProteinNet.t,1.6,1.7   Brian Osborne
• [Bioperl-guts-l] bioperl-network/t Graph-Articulation.x, NONE, 1.1 Graph-Articulation.t, 1.2, NONE   Brian Osborne
• [Bioperl-guts-l] bioperl-network MANIFEST,1.3,1.4   Brian Osborne
• [Bioperl-guts-l] bioperl-network BUGS,NONE,1.1   Brian Osborne
• [Bioperl-guts-l] bioperl-network BUGS,1.1,1.2   Brian Osborne
• [Bioperl-guts-l] bioperl-network/t Graph-MD5.t,1.2,1.3   Brian Osborne
• [Bioperl-guts-l] bioperl-db/t 16obda.t,1.3,1.4   Brian Osborne
• [Bioperl-guts-l] bioperl-network/Bio/Network ProteinNet.pm, 1.8, 1.9   Brian Osborne
• [Bioperl-guts-l] bioperl-network Makefile.PL,1.2,1.3   Brian Osborne
• [Bioperl-guts-l] bioperl-network INSTALL,1.1,1.2   Brian Osborne
• [Bioperl-guts-l] bioperl-network/Bio/Network ProteinNet.pm, 1.9, 1.10   Brian Osborne
• [Bioperl-guts-l] bioperl-network/t Graph-Seq.t,1.1,1.2   Brian Osborne
• [Bioperl-guts-l] bioperl-network/t IO_psi.t,1.2,1.3   Brian Osborne
• [Bioperl-guts-l] bioperl-network README,NONE,1.1   Brian Osborne
• [Bioperl-guts-l] bioperl-network README,1.1,1.2   Brian Osborne
• [Bioperl-guts-l] bioperl-network MANIFEST,1.4,1.5   Brian Osborne
• [Bioperl-guts-l] bioperl-network/Bio/Network ProteinNet.pm, 1.10, 1.11   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio/Tools BPpsilite.pm,1.28,1.29   Brian Osborne
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Clustalw.pm, 1.47, 1.48   Brian Osborne
• [Bioperl-guts-l] bioperl-live bptutorial.pl,1.170,NONE   Brian Osborne
• [Bioperl-guts-l] bioperl-live/Bio AnnotatableI.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO ptt.pm,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t FeatureIO.t,1.6,1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t/data test.ptt,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio FeatureIO.pm,1.16,1.17   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio FeatureIO.pm,1.17,1.18   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t/data Glimmer2.out, NONE, 1.1 Glimmer3.detail, NONE, 1.1 Glimmer3.predict, NONE, 1.1 GlimmerHMM.out, NONE, 1.1 GlimmerM.out, NONE, 1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Glimmer.pm,1.4,1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t Genpred.t,1.15,1.16   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Expression Platform.pm,1.4,1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Expression Contact.pm, 1.4, 1.5 Sample.pm, 1.3, 1.4 DataSet.pm, 1.3, 1.4   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO interpro.pm, 1.9, 1.10 locuslink.pm, 1.12, 1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Molphy.pm,1.9,1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools FootPrinter.pm, 1.8, 1.9 Promoterwise.pm, 1.8, 1.9   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Phylip ProtDist.pm, 1.9, 1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Molphy Result.pm, 1.9, 1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Annotation DBLink.pm,1.18,1.19   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer BSMLResultWriter.pm, 1.4, 1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Symbol Alphabet.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO interpro.pm, 1.9, 1.10 bed.pm, 1.5, 1.6 gff.pm, 1.45, 1.46   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene Poly_A_site.pm, 1.7, 1.8 NC_Feature.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/maintenance check_NAME.pl,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search SearchUtils.pm, 1.21, 1.22 BlastUtils.pm, 1.10, 1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Expression Platform.pm, 1.5, 1.6 Contact.pm, 1.5, 1.6 Sample.pm, 1.4, 1.5 DataSet.pm, 1.4, 1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/PopGen IO.pm, 1.6, 1.7 Utilities.pm, 1.7, 1.8 GenotypeI.pm, 1.3, 1.4 IndividualI.pm, 1.7, 1.8   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB Expression.pm, 1.4, 1.5 SeqI.pm, 1.10, 1.11 Taxonomy.pm, 1.12, 1.13 Universal.pm, 1.5, 1.6   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result HMMERResult.pm, 1.6, 1.7 WABAResult.pm, 1.5, 1.6 ResultFactory.pm, 1.6, 1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio MapIO.pm, 1.9, 1.10 AnnotationI.pm, 1.11, 1.12 FeatureHolderI.pm, 1.10, 1.11 OntologyIO.pm, 1.12, 1.13 AnnotationCollectionI.pm, 1.18, 1.19   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP WABAHSP.pm, 1.9, 1.10 PSLHSP.pm, 1.4, 1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit HitFactory.pm, 1.6, 1.7 HMMERHit.pm, 1.6, 1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Align DNAStatistics.pm, 1.33, 1.34 StatisticsI.pm, 1.7, 1.8 ProteinStatistics.pm, 1.7, 1.8   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Spidey Exon.pm,1.6,1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO MultiFile.pm, 1.13, 1.14 swiss.pm, 1.96, 1.97 entrezgene.pm, 1.23, 1.24 FTHelper.pm, 1.62, 1.63 locuslink.pm, 1.13, 1.14 embl.pm, 1.105, 1.106   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Structure IO.pm, 1.13, 1.14 StructureI.pm, 1.7, 1.8   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO cluster.pm, 1.4, 1.5 pag.pm, 1.9, 1.10 nexus.pm, 1.13, 1.14 tabtree.pm, 1.10, 1.11 newick.pm, 1.37, 1.38   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Symbol AlphabetI.pm, 1.8, 1.9 Symbol.pm, 1.9, 1.10 DNAAlphabet.pm, 1.6, 1.7 ProteinAlphabet.pm, 1.7, 1.8   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/MapIO mapmaker.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blasttable.pm, 1.7, 1.8 megablast.pm, 1.7, 1.8 hmmer.pm, 1.34, 1.35   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Factory ObjectFactoryI.pm, 1.6, 1.7 MapFactoryI.pm, 1.8, 1.9 SequenceProcessorI.pm, 1.4, 1.5 SequenceStreamI.pm, 1.6, 1.7 ObjectBuilderI.pm, 1.5, 1.6 TreeFactoryI.pm, 1.10, 1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/IO scoring.pm, 1.4, 1.5 phylip.pm, 1.3, 1.4   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO emboss.pm, 1.18, 1.19 psi.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy list.pm,1.4,1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Matrix IO.pm, 1.5, 1.6 Scoring.pm, 1.4, 1.5 Generic.pm, 1.14, 1.15   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Annotation SimpleValue.pm, 1.19, 1.20 StructuredValue.pm, 1.8, 1.9 Comment.pm, 1.12, 1.13 Reference.pm, 1.26, 1.27 TypeManager.pm, 1.7, 1.8   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene ExonI.pm, 1.11, 1.12 GeneStructureI.pm, 1.12, 1.13 Transcript.pm, 1.38, 1.39 Poly_A_site.pm, 1.8, 1.9 NC_Feature.pm, 1.12, 1.13 Exon.pm, 1.15, 1.16 Intron.pm, 1.10, 1.11 TranscriptI.pm, 1.13, 1.14   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Similarity.pm, 1.16, 1.17 CollectionI.pm, 1.5, 1.6 SimilarityPair.pm, 1.30, 1.31 AnnotationAdaptor.pm, 1.10, 1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Seq BaseSeqProcessor.pm, 1.7, 1.8 SeqFastaSpeedFactory.pm, 1.7, 1.8 SeqFactory.pm, 1.11, 1.12 RichSeqI.pm, 1.14, 1.15 RichSeq.pm, 1.19, 1.20 LargeLocatableSeq.pm, 1.5, 1.6   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EMBOSS Palindrome.pm, 1.4, 1.5   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Genscan.pm, 1.29, 1.30 ipcress.pm, 1.8, 1.9 Fgenesh.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Prediction Gene.pm, 1.15, 1.16 Exon.pm, 1.16, 1.17   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML Result.pm, 1.22, 1.23 ModelResult.pm, 1.7, 1.8   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.21, 1.22   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Map MarkerI.pm, 1.17, 1.18 PositionI.pm, 1.17, 1.18   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Event EventGeneratorI.pm, 1.11, 1.12 EventHandlerI.pm, 1.9, 1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Ontology DocumentRegistry.pm, 1.11, 1.12 OntologyEngineI.pm, 1.15, 1.16   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Index AbstractSeq.pm, 1.24, 1.25 Blast.pm, 1.21, 1.22   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gtf.pm, 1.4, 1.5 bed.pm, 1.6, 1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Root IO.pm, 1.61, 1.62 Version.pm, 1.9, 1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/maintenance check_NAME.pl,1.1,1.2   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools SeqStats.pm,1.30,1.31   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO ptt.pm,1.2,1.3   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO lasergene.pm,1.6,1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio AnalysisI.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live DEPRECATED,1.9,1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t/data tmhmm.out,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Tmhmm.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t Tmhmm.t,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t/data prints.out,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm,1.24,1.25   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Restriction IO.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm,1.13,1.14   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO phrap.pm,1.6,1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm,1.14,1.15   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Variation VariantI.pm,1.20,1.21   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/IO hapmap.pm,1.8,1.9   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Map Microsatellite.pm,1.13,1.14   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO pag.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Align DNAStatistics.pm, 1.35, 1.36   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO mase.pm, 1.12, 1.13 prodom.pm, 1.11, 1.12 stockholm.pm, 1.16, 1.17 meme.pm, 1.14, 1.15   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio Taxonomy.pm,1.8,1.9   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio SeqUtils.pm,1.34,1.35   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Root Root.pm,1.36,1.37   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Fgenesh.pm,1.13,1.14   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.29, 1.30   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio soap.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Seq Meta.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio WebAgent.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/IO hapmap.pm,1.9,1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm, 1.50, 1.51 Blast.pm, 1.23, 1.24 EMBL.pm, 1.33, 1.34 Fasta.pm, 1.36, 1.37 Fastq.pm, 1.13, 1.14 GenBank.pm, 1.24, 1.25 Hmmer.pm, 1.11, 1.12 Qual.pm, 1.10, 1.11 SwissPfam.pm, 1.25, 1.26 Swissprot.pm, 1.27, 1.28   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.31, 1.32   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BinarySearch.pm, 1.25, 1.26   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO transfac.pm, 1.17, 1.18   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/MapIO fpc.pm,1.8,1.9   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO embl.pm, 1.107, 1.108 genbank.pm, 1.150, 1.151 swiss.pm, 1.98, 1.99   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO msf.pm, 1.24, 1.25 pfam.pm, 1.14, 1.15 stockholm.pm, 1.18, 1.19   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.33,1.34   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/ClusterIO unigene.pm,1.30,1.31   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools GFF.pm, 1.59, 1.60 Genomewise.pm, 1.7, 1.8 GuessSeqFormat.pm, 1.16, 1.17   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.42, 1.43   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.15, 1.16   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.43, 1.44   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB WebDBSeqI.pm,1.60,1.61   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run StandAloneBlast.pm, 1.65, 1.66   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO chaos.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio AlignIO.pm,1.48,1.49   Torsten Seemann
• [Bioperl-guts-l] bioperl-live DEPRECATED,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Lucy.pm,1.16,1.17   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Root Object.pm,1.34,1.35   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Blast CHANGES, 1.7, NONE HSP.pm, 1.26, NONE HTML.pm, 1.22, NONE README, 1.7, NONE Sbjct.pm, 1.26, NONE   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools SeqAnal.pm, 1.20, NONE WWW.pm, 1.19, NONE Blast.pm, 1.40, NONE   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t SeqFeature.t,1.42,1.43   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilities.pm,1.31,1.32   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.9, 1.10 elink.pm, 1.29, 1.30 esummary.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t Seg.t,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t/data seg.out,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Seg.pm,1.11,1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO bl2seq.pm,1.26,1.27   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/DB SeqI.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit Fasta.pm,1.11,1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Index Abstract.pm,1.51,1.52   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Gene Transcript.pm, 1.40, 1.41   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Sim4 Results.pm,1.26,1.27   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO ctf.pm, 1.15, 1.16 agave.pm, 1.16, 1.17 fastq.pm, 1.16, 1.17 fasta.pm, 1.59, 1.60 ztr.pm, 1.14, 1.15 metafasta.pm, 1.10, 1.11 strider.pm, 1.9, 1.10 abi.pm, 1.14, 1.15 alf.pm, 1.12, 1.13 pln.pm, 1.12, 1.13 largefasta.pm, 1.25, 1.26 exp.pm, 1.15, 1.16   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Spidey Results.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio Taxonomy.pm,1.11,1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Seq RichSeq.pm,1.21,1.22   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Taxon.pm,1.6,1.7   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools Signalp.pm,1.10,1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t/data signalp.negative.out, NONE, 1.1 signalp.positive.out, NONE, 1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/t Signalp.t,NONE,1.1   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Variation/IO xml.pm,1.20,1.21   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit Fasta.pm,1.12,1.13   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.112,1.113   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools SeqPattern.pm,1.24,1.25   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools ECnumber.pm,1.13,1.14   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools ECnumber.pm,1.14,1.15   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Measure.pm,1.11,1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM MiniMIMentry.pm, 1.11, 1.12 OMIMentryAllelicVariant.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype Correlate.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Graph/IO psi_xml.pm,1.15,1.16   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Graph/IO psi_xml.pm,1.16,1.17   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Ontology Term.pm,1.33,1.34   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio Biblio.pm,1.17,1.18   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO SearchWriterI.pm, 1.11, 1.12   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit PsiBlastHit.pm, 1.9, 1.10   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm, 1.36, 1.37 Vector.pm, 1.19, 1.20 Root.pm, 1.38, 1.39 Xref.pm, 1.16, 1.17 IOManager.pm, 1.22, 1.23 Err.pm, 1.23, 1.24 Object.pm, 1.35, 1.36 Exception.pm, 1.15, 1.16 RootI.pm, 1.72, 1.73   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search GenericDatabase.pm, 1.10, 1.11   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP HSPI.pm, 1.39, 1.40 PsiBlastHSP.pm, 1.10, 1.11 BlastHSP.pm, 1.31, 1.32   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/Tools RestrictionEnzyme.pm, 1.36, 1.37   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO entrezgene.pm,1.25,1.26   Torsten Seemann
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO newick.pm,1.36,1.37   Jason Stajich
• [Bioperl-guts-l] bioperl-live/t TreeIO.t,1.32,1.33   Jason Stajich
• [Bioperl-guts-l] bioperl-live/t/data puzzle.tre,NONE,1.1   Jason Stajich
• [Bioperl-guts-l] bioperl-live/scripts/taxa local_taxonomydb_query.PLS, 1.2, 1.3   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.106,1.107   Jason Stajich
• [Bioperl-guts-l] bioperl-live/t/data/seqfeaturedb test.gff3, 1.1, 1.2   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.16, 1.17   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.118,1.119   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/t BioDBSeqFeature.t,1.1,1.2   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/t/data/seqfeaturedb test.gff3, 1.2, 1.3   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph generic.pm, 1.40, 1.41 segments.pm, 1.44, 1.45   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph segments.pm, 1.45, 1.46   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB SeqFeature.pm,1.7,1.8   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.119,1.120   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.120,1.121   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph generic.pm, 1.41, 1.42 segments.pm, 1.46, 1.47   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.23, 1.24   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.18, 1.19 berkeleydb.pm, 1.7, 1.8 memory.pm, 1.7, 1.8   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio Graphics.pm,1.17,1.18   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm, 1.122, 1.123 Panel.pm, 1.124, 1.125   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.26, 1.27 image.pm, 1.3, 1.4   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph segments.pm, 1.48, 1.49   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.15, 1.16   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.19, 1.20   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph segments.pm, 1.49, 1.50   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB SeqFeature.pm,1.9,1.10   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.13, 1.14   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store GFF3Loader.pm, 1.20, 1.21 memory.pm, 1.8, 1.9   Lincoln Stein
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Kalign.pm, NONE, 1.1   Albert Vilella
• [Bioperl-guts-l] bioperl-run/t Kalign.t,NONE,1.1   Albert Vilella
• [Bioperl-guts-l] bioperl-run/Bio/Installer Clustalw.pm,1.3,1.4   Albert Vilella
• [Bioperl-guts-l] bioperl-run/t Probcons.t,1.3,1.4   Albert Vilella
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Probcons.pm, 1.8, 1.9   Albert Vilella
• [Bioperl-guts-l] bioperl-live/Bio/Align DNAStatistics.pm, 1.32, 1.33   Albert Vilella
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO largemultifasta.pm, 1.10, 1.11   Albert Vilella
• [Bioperl-guts-l] bioperl-run AUTHORS,1.5,1.6   Albert Vilella
• [Bioperl-guts-l] [Bug 1957] Add some tests for fpc.pm to t/MapIO.t   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2086] EMBL parser should not look for FT, DE and other line prefixes when it is ID line   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 843] _readline() in SeqIO.pm   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1363] subseq signature not respected   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1508] SeqIO allows fasta to masquerade as genbank or gcg or ace   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1514] TCoffee parse score_ascii   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1528] Removing sequences from mysql using bioentry-id   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1572] no docs and possible typo in Bio::Location::Simple/Atomic::trunc   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1672] OBDA does not support Biosql protocol   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1683] Makefile arg list too long on OSF1 V5.1   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1732] Unpersistenting a persistent object   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1759] AlignIO reads wrong data from the Clustalw file which has no ClustalW header   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 1873] Bio::AlignIO::xmfa.pm module   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1874] fixedtopo random tree Bio::Tree::RandomFactory   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1875] Slow processing of sequence strings in bioperl 1.5 vs. 1.4   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1877] Bio::PopGen::IO::hapmap.pm write_population method   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1881] implement Bio::PopGen::IO::haploview.pm   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1882] recursive children fetch for Bio::Taxonomy::Node   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1891] Implement a seqgen wrapper in bioperl-run   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1892] Implement an arp (Arlequin/Simcoal2) parser in Bio::AlignIO   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1896] Implement a bioperl-run::Bio::Tools::Run::Phylo::PAML::Evolver module   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1930] Bio::Align::Utilities::bootstrap_replicates() does not work   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1937] Bio::Tree::NodeI - height method produces wrong results after resizing branches   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1953] Inconsistency between Bio::Factory::FTLocationFactory->from_string and Bio::Location::Split->to_FTstring   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2002] Infinite recursive loop in Unflattener.pm   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2011] Bio::Restriction::IO enhancements/code issues   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2069] Bio::Tools:pSW stop codon bug   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2070] mumsa wrapper   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2078] informative codons method for kaks -- Bio/Align/DNAStatistics.pm   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2083] Biblio_biofetch.t tests pass, but they really don't!   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1829] -ve xyplot.pm - gff data must be in order   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2074] bioperl-ext: make test fails using io_lib v. 1.9 or higher   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 1875] Slow processing of sequence strings in bioperl 1.5 vs. 1.4   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1953] Inconsistency between Bio::Factory::FTLocationFactory->from_string and Bio::Location::Split->to_FTstring   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1672] OBDA does not support Biosql protocol   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 992] Fuzzy location object problem (double location)   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 992] Fuzzy location object problem (double location)   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1392] Make install of cvs main trunk of bioperl-ext doesn't install read.so   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1419] Bio::Search::Result::ResultFactory isnota Bio::Factory::ResultFactoryI   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2077] bp_sreformat.pl creates broken GenBank formatted file from EMBL input   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2086] EMBL parser should not look for FT, DE and other line prefixes when it is ID line   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2086] EMBL parser should not look for FT, DE and other line prefixes when it is ID line   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2086] EMBL parser should not look for FT, DE and other line prefixes when it is ID line   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2088] New: Bio::AlignIO::maf is missing write_aln method   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2086] EMBL parser should not look for FT, DE and other line prefixes when it is ID line   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2088] Bio::AlignIO::maf is missing write_aln method   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2089] New: Bio::SeqIO::embl - Only the last parsed OS line is saved   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2089] Bio::SeqIO::embl - Only the last parsed OS line is saved   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2089] Bio::SeqIO::embl - Only the last parsed OS line is saved   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2089] Bio::SeqIO::embl - Only the last parsed OS line is saved   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1953] Inconsistency between Bio::Factory::FTLocationFactory->from_string and Bio::Location::Split->to_FTstring   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2089] Bio::SeqIO::embl - Only the last parsed OS line is saved   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2084] Bio::Matrix::PSM::IO::mast.pm shows wrong positions   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1672] OBDA does not support Biosql protocol   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1732] Unpersistenting a persistent object   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] New: SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] New: Can't store proteins with species using bioperl-db   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   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 2096] New: Bio::Structure::IO PDB default chain always exists   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1953] Inconsistency between Bio::Factory::FTLocationFactory->from_string and Bio::Location::Split->to_FTstring   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2083] Biblio_biofetch.t tests pass, but they really don't!   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2083] Biblio_biofetch.t tests pass, but they really don't!   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2096] Bio::Structure::IO PDB default chain always exists   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2096] Bio::Structure::IO PDB default chain always exists   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] New: Parsing BLAST/SIM4 results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST/SIM4 results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST/SIM4 results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST/SIM4 results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST/SIM4 results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST/SIM4 results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2097] Parsing BLAST results with SearchIO leads to wrong frac_identical values   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2096] Bio::Structure::IO PDB default chain always exists   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1953] Inconsistency between Bio::Factory::FTLocationFactory->from_string and Bio::Location::Split->to_FTstring   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1810] Error in output of unflattener   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2077] bp_sreformat.pl creates broken GenBank formatted file from EMBL input   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2077] bp_sreformat.pl creates broken GenBank formatted file from EMBL input   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1810] Error in output of unflattener   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2091] SearchIO generates incorrect E values when parsing psiblast results   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2002] Infinite recursive loop in Unflattener.pm   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2002] Infinite recursive loop in Unflattener.pm   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2098] New: Bug in Bio::Matrix::PSM SiteMatrixI   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2098] Bug in Bio::Matrix::PSM SiteMatrixI   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2099] New: Bug in Bio::SimpleAlign->slice   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2099] Bug in Bio::SimpleAlign->slice   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2100] New: IO-stringy.ppd not found at www.Bribes.org on Windows XP install   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2101] New: Bio::Location mishandling of join(complement(..), complement(..))   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2100] IO-stringy.ppd not found at www.Bribes.org on Windows XP install   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2100] IO-stringy.ppd not found at www.Bribes.org on Windows XP install   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2102] New: feature location "complement(join" isn't handled correctly   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2102] feature location "complement(join" isn't handled correctly   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2101] Bio::Location mishandling of join(complement(..), complement(..))   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1953] Inconsistency between Bio::Factory::FTLocationFactory->from_string and Bio::Location::Split->to_FTstring   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2101] Bio::Location mishandling of join(complement(..), complement(..))   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2103] New: Blast Parser Error   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2103] Blast Parser Error   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2103] Blast Parser Error   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] New: Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at newportal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2105] New: Bio::Tools::Glimmer parses only "M", not "2", "3" or "HMM"   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2105] Bio::Tools::Glimmer parses only "M", not "2", "3" or "HMM"   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2106] New: SimpleAlign->remove_columns(['all_gap_columns']) does not work   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2106] SimpleAlign->remove_columns(['all_gap_columns']) does not work   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2106] SimpleAlign->remove_columns(['all_gap_columns']) does not work   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2104] Bio::DB::WebDBSeqI does not work under mod_perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] New: SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2002] Infinite recursive loop in Unflattener.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 1875] Slow processing of sequence strings in bioperl 1.5 vs. 1.4   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2011] Bio::Restriction::IO enhancements/code issues   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2021] Abstract method "Bio::Assembly::Contig::slice" is not implemented by package Bio::Assembly::Contig   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2088] Bio::AlignIO::maf is missing write_aln method   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2101] Bio::Location mishandling of join(complement(..), complement(..))   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2108] SearchIO::blast misses frame information for phi/psitblastn reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2109] New: Deep recursion on subroutine Bio::DB::GenericWebDBI::proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2109] Deep recursion on subroutine Bio::DB::GenericWebDBI::proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2109] Deep recursion on subroutine Bio::DB::GenericWebDBI::proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2109] Deep recursion on subroutine Bio::DB::GenericWebDBI::proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2110] New: Species.t fails test when behind authenticated proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2111] New: Taxonomy.t fails tests when behind authenticated proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2112] New: SeqVersion.t often fails when behind authenticated proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2113] New: XEMBL-related URLs in Bio::DB::XEMBL and Bio::DB::XEMBLServices no longer work   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2113] XEMBL-related URLs in Bio::DB::XEMBL and Bio::DB::XEMBLServices no longer work   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2113] XEMBL-related URLs in Bio::DB::XEMBL and Bio::DB::XEMBLServices no longer work   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2111] Taxonomy.t fails tests when behind authenticated proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2110] Species.t fails test when behind authenticated proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2112] SeqVersion.t often fails when behind authenticated proxy   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2114] New: Obfuscator doesn't show "Bio:Matrix:Generic"   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2114] Obfuscator doesn't show "Bio:Matrix:Generic"   bugzilla-daemon at portal.open-bio.org

Last message date: Fri Sep 29 17:31:04 EDT 2006
Archived on: Fri Sep 29 17:31:06 EDT 2006

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