June 2007 Archives by thread

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Starting: Fri Jun 1 01:59:55 EDT 2007
Ending: Thu Jun 28 14:06:21 EDT 2007
Messages: 257

• [Bioperl-guts-l] [Bug 2304] Two more methods in Bio/SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2304] Two more methods in Bio/SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Clustalw.pm, 1.51, 1.52   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Clustalw.t,1.35,1.36   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB DBContextI.pm, 1.3, 1.4 SimpleDBContext.pm, 1.8, 1.9   Hilmar Lapp
• [Bioperl-guts-l] bioperl-db/scripts/biosql load_ontology.pl, 1.11, 1.12 load_seqdatabase.pl, 1.24, 1.25   Hilmar Lapp
• [Bioperl-guts-l] bioperl-db/Bio/DB/DBI Pg.pm,1.4,1.5   Hilmar Lapp
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.135,1.136   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph xyplot.pm, 1.33, 1.34   Lincoln Stein
  • [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm, 1.135, 1.136   Sendu Bala
• [Bioperl-guts-l] [Bug 2305] New: Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/Bio/Root RootI.pm,1.77,1.78   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.163,1.164   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.20,1.21   Christopher John Fields
• [Bioperl-guts-l] [Bug 2310] New: nonstandard method docs in Bio::Search::Result::BlastResult   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2312] New: './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2312] './Build test' failures on linux with bioperl-live from cvs now()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2313] New: './Build test' stalls from current cvs bioperl-run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/t Tree.t,1.14,1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t RemoteBlast.t,1.19,1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t BioDBGFF.t,1.45,1.46   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO gbdriver.pm, 1.2, 1.3 genbank.pm, 1.164, 1.165   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/Handler GenericRichSeqHandler.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] [Bug 2314] New: Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2314] Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live INSTALL,1.61,1.62   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2304] Two more methods in Bio/SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.52,1.53   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.53,1.54   Heikki Lehvaslaiho
• [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.134,1.135   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2304] Two more methods in Bio/SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2317] New: Changing parameter MATRIX_NAME in RemoteBlast generates an error   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2317] Changing parameter MATRIX_NAME in RemoteBlast generates an error   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/t PodSyntax.t,NONE,1.1   Nathan Haigh
• [Bioperl-guts-l] [Bug 2203] Signalp extension or new module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/t NetPhos.t,1.14,1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Sopma.t,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t BioGraphics.t,1.22,1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Align DNAStatistics.pm, 1.37, 1.38 ProteinStatistics.pm, 1.9, 1.10 Utilities.pm, 1.26, 1.27   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Cluster ClusterFactory.pm, 1.7, 1.8 SequenceFamily.pm, 1.14, 1.15 UniGene.pm, 1.39, 1.40   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/AlignIO arp.pm, 1.2, 1.3 bl2seq.pm, 1.27, 1.28 clustalw.pm, 1.40, 1.41 emboss.pm, 1.20, 1.21 largemultifasta.pm, 1.12, 1.13 maf.pm, 1.12, 1.13 mega.pm, 1.14, 1.15 meme.pm, 1.16, 1.17 msf.pm, 1.25, 1.26 nexus.pm, 1.30, 1.31 pfam.pm, 1.15, 1.16 phylip.pm, 1.39, 1.40 po.pm, 1.8, 1.9 proda.pm, 1.2, 1.3 prodom.pm, 1.13, 1.14 psi.pm, 1.13, 1.14 selex.pm, 1.16, 1.17 xmfa.pm, 1.2, 1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.16, 1.17 ContigAnalysis.pm, 1.7, 1.8 Scaffold.pm, 1.14, 1.15 Singlet.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio AnalysisI.pm, 1.13, 1.14 Biblio.pm, 1.19, 1.20 FeatureIO.pm, 1.21, 1.22 LocatableSeq.pm, 1.42, 1.43 MapIO.pm, 1.11, 1.12 PullParserI.pm, 1.12, 1.13 Range.pm, 1.28, 1.29 SearchIO.pm, 1.42, 1.43 Seq.pm, 1.93, 1.94 SeqFeatureI.pm, 1.70, 1.71 SeqIO.pm, 1.96, 1.97 SeqUtils.pm, 1.37, 1.38 SimpleAlign.pm, 1.135, 1.136 Species.pm, 1.49, 1.50 Taxon.pm, 1.6, 1.7 Taxonomy.pm, 1.12, 1.13 TreeIO.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm, 1.16, 1.17 phrap.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Annotation AnnotationFactory.pm, 1.7, 1.8 DBLink.pm, 1.21, 1.22 OntologyTerm.pm, 1.17, 1.18 SimpleValue.pm, 1.22, 1.23 StructuredValue.pm, 1.10, 1.11 Target.pm, 1.10, 1.11 Tree.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate/Result Gap.pm, 1.11, 1.12 Match.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Biblio/IO medline2ref.pm, 1.17, 1.18 medlinexml.pm, 1.11, 1.12 pubmedxml.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.16, 1.17 Book.pm, 1.16, 1.17 BookArticle.pm, 1.15, 1.16 IO.pm, 1.19, 1.20 Journal.pm, 1.15, 1.16 JournalArticle.pm, 1.16, 1.17 MedlineArticle.pm, 1.13, 1.14 MedlineBook.pm, 1.12, 1.13 MedlineBookArticle.pm, 1.12, 1.13 MedlineJournal.pm, 1.11, 1.12 MedlineJournalArticle.pm, 1.12, 1.13 Organisation.pm, 1.15, 1.16 Patent.pm, 1.15, 1.16 Person.pm, 1.17, 1.18 Proceeding.pm, 1.14, 1.15 Provider.pm, 1.12, 1.13 PubmedArticle.pm, 1.11, 1.12 PubmedBookArticle.pm, 1.11, 1.12 PubmedJournalArticle.pm, 1.12, 1.13 Ref.pm, 1.14, 1.15 Service.pm, 1.14, 1.15 TechReport.pm, 1.14, 1.15 Thesis.pm, 1.13, 1.14 WebResource.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Coordinate Chain.pm, 1.8, 1.9 Collection.pm, 1.25, 1.26 GeneMapper.pm, 1.28, 1.29 Pair.pm, 1.21, 1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graph/IO dip.pm,1.15,1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graph/SimpleGraph Traversal.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Index Blast.pm, 1.28, 1.29 GenBank.pm, 1.25, 1.26 Hmmer.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio biofetch.pm, 1.15, 1.16 eutils.pm, 1.13, 1.14 soap.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Factory AnalysisI.pm, 1.9, 1.10 FTLocationFactory.pm, 1.26, 1.27 ObjectFactory.pm, 1.6, 1.7 SequenceFactoryI.pm, 1.11, 1.12 SequenceStreamI.pm, 1.8, 1.9 TreeFactoryI.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graph SimpleGraph.pm,1.14,1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Query GenBank.pm,1.21,1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Flat BinarySearch.pm, 1.28, 1.29   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB BiblioI.pm, 1.12, 1.13 BioFetch.pm, 1.33, 1.34 EMBL.pm, 1.22, 1.23 Expression.pm, 1.5, 1.6 Fasta.pm, 1.49, 1.50 GDB.pm, 1.22, 1.23 GFF.pm, 1.150, 1.151 GenBank.pm, 1.60, 1.61 GenPept.pm, 1.32, 1.33 MeSH.pm, 1.10, 1.11 NCBIHelper.pm, 1.56, 1.57 QueryI.pm, 1.6, 1.7 RefSeq.pm, 1.14, 1.15 Registry.pm, 1.41, 1.42 SeqHound.pm, 1.8, 1.9 SeqVersion.pm, 1.13, 1.14 SwissProt.pm, 1.31, 1.32 Taxonomy.pm, 1.17, 1.18 XEMBL.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.30, 1.31   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy entrez.pm, 1.23, 1.24 flatfile.pm, 1.20, 1.21 list.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Expression Contact.pm, 1.6, 1.7 DataSet.pm, 1.5, 1.6 Platform.pm, 1.6, 1.7 Sample.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF Segment.pm,1.31,1.32   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix Generic.pm, 1.16, 1.17 IO.pm, 1.7, 1.8 Mlagan.pm, 1.1, 1.2 Scoring.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq/IO BioPerl.pm,1.21,1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.23, 1.24 meme.pm, 1.22, 1.23 psiblast.pm, 1.13, 1.14 transfac.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/OntologyIO obo.pm,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Ontology Ontology.pm, 1.23, 1.24 OntologyStore.pm, 1.14, 1.15 RelationshipFactory.pm, 1.6, 1.7 TermFactory.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/IO mlagan.pm, 1.1, 1.2 phylip.pm, 1.5, 1.6 scoring.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map CytoMap.pm, 1.11, 1.12 CytoMarker.pm, 1.13, 1.14 CytoPosition.pm, 1.18, 1.19 LinkageMap.pm, 1.18, 1.19 LinkagePosition.pm, 1.17, 1.18 Mappable.pm, 1.12, 1.13 Marker.pm, 1.25, 1.26 Microsatellite.pm, 1.15, 1.16 OrderedPosition.pm, 1.13, 1.14 OrderedPositionWithDistance.pm, 1.11, 1.12 Physical.pm, 1.10, 1.11 Position.pm, 1.22, 1.23 PositionHandler.pm, 1.6, 1.7 Relative.pm, 1.7, 1.8 SimpleMap.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Location Atomic.pm, 1.19, 1.20 Fuzzy.pm, 1.36, 1.37 Simple.pm, 1.43, 1.44 Split.pm, 1.53, 1.54   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq Mutator.pm, 1.35, 1.36 Translation.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/MapIO fpc.pm, 1.10, 1.11 mapmaker.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM IO.pm, 1.16, 1.17 InstanceSite.pm, 1.16, 1.17 ProtMatrix.pm, 1.18, 1.19 ProtPsm.pm, 1.10, 1.11 Psm.pm, 1.15, 1.16 PsmHeader.pm, 1.12, 1.13 PsmHeaderI.pm, 1.11, 1.12 PsmI.pm, 1.9, 1.10 SiteMatrix.pm, 1.39, 1.40   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Analysis.pm, 1.20, 1.21 Enzyme.pm, 1.19, 1.20 EnzymeCollection.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM OMIMparser.pm, 1.23, 1.24   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction/IO base.pm, 1.12, 1.13 itype2.pm, 1.7, 1.8 withrefm.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root HTTPget.pm, 1.17, 1.18 Utilities.pm, 1.40, 1.41   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/HSP BlastHSP.pm, 1.34, 1.35 BlastPullHSP.pm, 1.3, 1.4 FastaHSP.pm, 1.11, 1.12 GenericHSP.pm, 1.77, 1.78 HMMERHSP.pm, 1.9, 1.10 HSPFactory.pm, 1.9, 1.10 HSPI.pm, 1.41, 1.42 HmmpfamHSP.pm, 1.5, 1.6 ModelHSP.pm, 1.2, 1.3 PSLHSP.pm, 1.6, 1.7 PsiBlastHSP.pm, 1.13, 1.14 PullHSPI.pm, 1.5, 1.6 WABAHSP.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search Processor.pm,1.13,1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/PopGen Genotype.pm, 1.11, 1.12 IO.pm, 1.8, 1.9 Individual.pm, 1.16, 1.17 Marker.pm, 1.9, 1.10 PopStats.pm, 1.11, 1.12 Population.pm, 1.20, 1.21 Statistics.pm, 1.36, 1.37 Utilities.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/Simulation Coalescent.pm, 1.13, 1.14 GeneticDrift.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/PopGen/IO csv.pm, 1.9, 1.10 hapmap.pm, 1.11, 1.12 phase.pm, 1.8, 1.9 prettybase.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastPullResult.pm, 1.5, 1.6 BlastResult.pm, 1.26, 1.27 CrossMatchResult.pm, 1.1, 1.2 GenericResult.pm, 1.28, 1.29 HMMERResult.pm, 1.8, 1.9 HmmpfamResult.pm, 1.5, 1.6 PullResultI.pm, 1.5, 1.6 ResultFactory.pm, 1.8, 1.9 ResultI.pm, 1.24, 1.25 WABAResult.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqEvolution DNAPoint.pm, 1.1, 1.2 Factory.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Hit BlastHit.pm, 1.20, 1.21 BlastPullHit.pm, 1.2, 1.3 GenericHit.pm, 1.43, 1.44 HMMERHit.pm, 1.8, 1.9 HitFactory.pm, 1.8, 1.9 HitI.pm, 1.25, 1.26 HmmpfamHit.pm, 1.5, 1.6 ModelHit.pm, 1.1, 1.2 PullHitI.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer BSMLResultWriter.pm, 1.6, 1.7 GbrowseGFF.pm, 1.16, 1.17 HTMLResultWriter.pm, 1.41, 1.42 TextResultWriter.pm, 1.20, 1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Seq BaseSeqProcessor.pm, 1.9, 1.10 EncodedSeq.pm, 1.13, 1.14 LargeLocatableSeq.pm, 1.7, 1.8 LargeSeq.pm, 1.17, 1.18 PrimedSeq.pm, 1.24, 1.25 SeqBuilder.pm, 1.11, 1.12 SeqFactory.pm, 1.13, 1.14 SeqFastaSpeedFactory.pm, 1.10, 1.11 SequenceTrace.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search/Iteration GenericIteration.pm, 1.10, 1.11 IterationI.pm, 1.9, 1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SearchIO EventHandlerI.pm, 1.14, 1.15 FastHitEventBuilder.pm, 1.14, 1.15 IteratedSearchResultEventBuilder.pm, 1.13, 1.14 SearchResultEventBuilder.pm, 1.46, 1.47 axt.pm, 1.11, 1.12 blast.pm, 1.114, 1.115 blast_pull.pm, 1.2, 1.3 blasttable.pm, 1.9, 1.10 blastxml.pm, 1.48, 1.49 cross_match.pm, 1.1, 1.2 erpin.pm, 1.5, 1.6 exonerate.pm, 1.19, 1.20 fasta.pm, 1.54, 1.55 hmmer.pm, 1.37, 1.38 hmmer_pull.pm, 1.6, 1.7 infernal.pm, 1.6, 1.7 megablast.pm, 1.11, 1.12 psl.pm, 1.14, 1.15 rnamotif.pm, 1.6, 1.7 sim4.pm, 1.14, 1.15 waba.pm, 1.17, 1.18 wise.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.37, 1.38 AnnotationAdaptor.pm, 1.12, 1.13 Collection.pm, 1.20, 1.21 CollectionI.pm, 1.7, 1.8 Computation.pm, 1.18, 1.19 FeaturePair.pm, 1.23, 1.24 Generic.pm, 1.104, 1.105 PositionProxy.pm, 1.10, 1.11 Primer.pm, 1.22, 1.23 SimilarityPair.pm, 1.32, 1.33   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools BPbl2seq.pm, 1.32, 1.33 BPlite.pm, 1.46, 1.47 Blat.pm, 1.9, 1.10 Coil.pm, 1.8, 1.9 EPCR.pm, 1.19, 1.20 ERPIN.pm, 1.9, 1.10 Est2Genome.pm, 1.19, 1.20 FootPrinter.pm, 1.12, 1.13 GFF.pm, 1.65, 1.66 Gel.pm, 1.12, 1.13 Genemark.pm, 1.21, 1.22 Genewise.pm, 1.27, 1.28 Genomewise.pm, 1.10, 1.11 Glimmer.pm, 1.8, 1.9 GuessSeqFormat.pm, 1.19, 1.20 HMM.pm, 1.10, 1.11 Hmmpfam.pm, 1.10, 1.11 IUPAC.pm, 1.31, 1.32 Infernal.pm, 1.4, 1.5 Prints.pm, 1.14, 1.15 Profile.pm, 1.9, 1.10 Promoterwise.pm, 1.10, 1.11 QRNA.pm, 1.7, 1.8 RNAMotif.pm, 1.15, 1.16 RepeatMasker.pm, 1.13, 1.14 RestrictionEnzyme.pm, 1.41, 1.42 SeqPattern.pm, 1.25, 1.26 Sigcleave.pm, 1.23, 1.24 Signalp.pm, 1.13, 1.14 TandemRepeatsFinder.pm, 1.1, 1.2 WebBlat.pm, 1.6, 1.7 dpAlign.pm, 1.20, 1.21 ipcress.pm, 1.10, 1.11 isPcr.pm, 1.10, 1.11 pSW.pm, 1.28, 1.29 tRNAscanSE.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Symbol Alphabet.pm, 1.12, 1.13 DNAAlphabet.pm, 1.8, 1.9 ProteinAlphabet.pm, 1.9, 1.10 Symbol.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/STRIDE Res.pm, 1.10, 1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/DNA ESEfinder.pm, 1.17, 1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO abi.pm, 1.15, 1.16 ace.pm, 1.19, 1.20 alf.pm, 1.13, 1.14 bsml.pm, 1.26, 1.27 bsml_sax.pm, 1.6, 1.7 chadoxml.pm, 1.32, 1.33 chaos.pm, 1.13, 1.14 ctf.pm, 1.16, 1.17 embl.pm, 1.111, 1.112 entrezgene.pm, 1.29, 1.30 exp.pm, 1.16, 1.17 fastq.pm, 1.17, 1.18 gcg.pm, 1.29, 1.30 genbank.pm, 1.165, 1.166 interpro.pm, 1.13, 1.14 kegg.pm, 1.21, 1.22 largefasta.pm, 1.26, 1.27 phd.pm, 1.25, 1.26 pir.pm, 1.25, 1.26 pln.pm, 1.13, 1.14 qual.pm, 1.33, 1.34 raw.pm, 1.23, 1.24 scf.pm, 1.41, 1.42 swiss.pm, 1.106, 1.107 tigr.pm, 1.13, 1.14 tigrxml.pm, 1.9, 1.10 ztr.pm, 1.15, 1.16   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Alignment Consed.pm, 1.48, 1.49 Trim.pm, 1.22, 1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Taxonomy Taxon.pm, 1.9, 1.10 Tree.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.32, 1.33   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree AlleleNode.pm, 1.16, 1.17 Compatible.pm, 1.7, 1.8 DistanceFactory.pm, 1.10, 1.11 Node.pm, 1.54, 1.55 NodeI.pm, 1.37, 1.38 NodeNHX.pm, 1.11, 1.12 RandomFactory.pm, 1.19, 1.20 Statistics.pm, 1.13, 1.14 Tree.pm, 1.23, 1.24 TreeFunctionsI.pm, 1.36, 1.37 TreeI.pm, 1.18, 1.19   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.43, 1.44 WrapperBase.pm, 1.35, 1.36   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EMBOSS Palindrome.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Domcut.pm, 1.15, 1.16 GOR4.pm, 1.14, 1.15 HNN.pm, 1.14, 1.15 Mitoprot.pm, 1.10, 1.11 NetPhos.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Phylip ProtDist.pm, 1.11, 1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/Molphy Result.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Signalp ExtendedSignalp.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.17, 1.18   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Molphy.pm, 1.11, 1.12 PAML.pm, 1.53, 1.54   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML ModelResult.pm, 1.13, 1.14 Result.pm, 1.26, 1.27   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/BPlite HSP.pm, 1.32, 1.33 Iteration.pm, 1.21, 1.22 Sbjct.pm, 1.34, 1.35   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Variation/IO xml.pm,1.21,1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO TreeEventBuilder.pm, 1.25, 1.26 cluster.pm, 1.8, 1.9 lintree.pm, 1.10, 1.11 newick.pm, 1.41, 1.42 nexus.pm, 1.20, 1.21 nhx.pm, 1.19, 1.20 pag.pm, 1.12, 1.13 svggraph.pm, 1.6, 1.7 tabtree.pm, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Variation AAReverseMutate.pm, 1.13, 1.14 SeqDiff.pm, 1.24, 1.25   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio Seq.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t AAReverseMutate.t, 1.6, 1.7 AlignIO.t, 1.74, 1.75 AlignStats.t, 1.14, 1.15 AlignUtil.t, 1.4, 1.5 Alphabet.t, 1.6, 1.7 Annotation.t, 1.23, 1.24 AnnotationAdaptor.t, 1.4, 1.5 Biblio.t, 1.12, 1.13 BiblioReferences.t, 1.11, 1.12 Biblio_biofetch.t, 1.15, 1.16 Biblio_eutils.t, 1.4, 1.5 BioFetch_DB.t, 1.15, 1.16 BlastIndex.t, 1.8, 1.9 ClusterIO.t, 1.7, 1.8 Coalescent.t, 1.7, 1.8 Compatible.t, 1.6, 1.7 CoordinateGraph.t, 1.3, 1.4 CoordinateMapper.t, 1.15, 1.16 CytoMap.t, 1.7, 1.8 DB.t, 1.78, 1.79 Domcut.t, 1.15, 1.16 ELM.t, 1.7, 1.8 EMBL_DB.t, 1.18, 1.19 EMBOSS_Tools.t, 1.4, 1.5 EncodedSeq.t, 1.5, 1.6 Exonerate.t, 1.7, 1.8 GDB.t, 1.15, 1.16 GFF.t, 1.11, 1.12 GbrowseGFF.t, 1.4, 1.5 GeneCoordinateMapper.t, 1.17, 1.18 Genewise.t, 1.8, 1.9 Genpred.t, 1.23, 1.24 GraphAdaptor.t, 1.4, 1.5 GuessSeqFormat.t, 1.11, 1.12 Handler.t, 1.1, 1.2 IUPAC.t, 1.4, 1.5 LinkageMap.t, 1.4, 1.5 LocatableSeq.t, 1.12, 1.13 Location.t, 1.34, 1.35 Map.t, 1.11, 1.12 MapIO.t, 1.7, 1.8 Matrix.t, 1.11, 1.12 MicrosatelliteMarker.t, 1.3, 1.4 Molphy.t, 1.4, 1.5 Mutator.t, 1.14, 1.15! Node.t, 1.9, 1.10 PAML.t, 1.28, 1.29 PhysicalMap.t, 1.5, 1.6 Pictogram.t, 1.7, 1.8 PopGen.t, 1.28, 1.29 PopGenSims.t, 1.5, 1.6 PrimarySeq.t, 1.24, 1.25 ProtMatrix.t, 1.5, 1.6 ProtPsm.t, 1.5, 1.6 QRNA.t, 1.2, 1.3 RandomTreeFactory.t, 1.8, 1.9 RangeI.t, 1.8, 1.9 RefSeq.t, 1.12, 1.13 RestrictionAnalysis.t, 1.9, 1.10 RootI.t, 1.9, 1.10 SNP.t, 1.2, 1.3 Scansite.t, 1.4, 1.5 SearchDist.t, 1.14, 1.15 SearchIO.t, 1.114, 1.115 Seq.t, 1.29, 1.30 SeqAnalysisParser.t, 1.5, 1.6 SeqEvolution.t, 1.1, 1.2 SeqFeatCollection.t, 1.11, 1.12 SeqFeature.t, 1.48, 1.49 SeqHound_DB.t, 1.6, 1.7 SeqPattern.t, 1.3, 1.4 SeqUtils.t, 1.20, 1.21 SequenceFamily.t, 1.1, 1.2 Sigcleave.t, 1.10, 1.11 Sim4.t, 1.14, 1.15 SimilarityPair.t, 1.5, 1.6 SimpleAlign.t, 1.54, 1.55 SiteMatrix.t, 1.6, 1.7 Species.t, 1.15, 1.16 Spidey.t, 1.2, 1.3 Symbol.t, 1.1, 1.2 TandemRepeatsFinder.t, 1.2, 1.3 TaxonTree.t, 1.5, 1.6 Tree.t, 1.15, 1.16 TreeBuild.t, 1.2, 1.3 TreeIO.t, 1.39, 1.40 UCSCParsers.t, 1.5, 1.6 WABA.t, 1.5, 1.6 alignUtilities.t, 1.5, 1.6 blast_pull.t, 1.2, 1.3 cigarstring.t, 1.5, 1.6 ePCR.t, 1.4, 1.5 embl.t! , 1.8, 1.9 entrezgene.t, 1.6, 1.7 est2genome.t, 1.5, 1.6 game.t, 1.22, 1.23 ge   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Genemark.hmm.prokaryotic.t,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Glimmer2.t,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Glimmer3.t,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t tRNAscanSE.t,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Njtree.t,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Njtree.t,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t ProtPars.t, 1.9, 1.10 ProtDist.t, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Simprot.t,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Hyphy.t,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Factory EMBOSS.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Analysis.pm, 1.11, 1.12 AnalysisFactory.pm, 1.10, 1.11 EMBOSSApplication.pm, 1.28, 1.29 EMBOSSacd.pm, 1.9, 1.10 PiseApplication.pm, 1.9, 1.10 PiseJob.pm, 1.18, 1.19 PiseWorkflow.pm, 1.2, 1.3 Primate.pm, 1.16, 1.17 Simprot.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Analysis soap.pm, 1.13, 1.14   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Hyphy Base.pm, 1.1, 1.2 FEL.pm, 1.3, 1.4 Modeltest.pm, 1.3, 1.4 REL.pm, 1.3, 1.4 SLAC.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/AnalysisFactory Pise.pm, 1.9, 1.10 soap.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Molphy ProtML.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Amap.pm, 1.6, 1.7 Clustalw.pm, 1.52, 1.53 Kalign.pm, 1.1, 1.2 Lagan.pm, 1.21, 1.22 Muscle.pm, 1.13, 1.14 Probalign.pm, 1.3, 1.4 Probcons.pm, 1.10, 1.11 Proda.pm, 1.3, 1.4 StandAloneFasta.pm, 1.14, 1.15 TCoffee.pm, 1.44, 1.45   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/PAML Baseml.pm, 1.6, 1.7 Codeml.pm, 1.44, 1.45 Evolver.pm, 1.13, 1.14 Yn00.pm, 1.21, 1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo QuickTree.pm, 1.1, 1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Njtree Best.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip Base.pm, 1.11, 1.12 DrawGram.pm, 1.13, 1.14 DrawTree.pm, 1.14, 1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-run/t Consense.t, 1.5, 1.6 DrawGram.t, 1.2, 1.3 DrawTree.t, 1.2, 1.3 EMBOSS.t, 1.16, 1.17 Molphy.t, 1.7, 1.8 PAML.t, 1.14, 1.15 Probcons.t, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/mysql BasePersistenceAdaptorDriver.pm, 1.18, 1.19 SpeciesAdaptorDriver.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/Query DBQueryResult.pm, 1.4, 1.5 PrebuiltResult.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/DBI Oracle.pm, 1.8, 1.9 Pg.pm, 1.5, 1.6 Transaction.pm, 1.3, 1.4 TransactionListener.pm, 1.3, 1.4 mysql.pm, 1.8, 1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL AnnotationCollectionAdaptor.pm, 1.14, 1.15 BaseDriver.pm, 1.31, 1.32 BasePersistenceAdaptor.pm, 1.41, 1.42   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Oracle BasePersistenceAdaptorDriver.pm, 1.16, 1.17 SpeciesAdaptorDriver.pm, 1.4, 1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/BioSQL/Pg BasePersistenceAdaptorDriver.pm, 1.9, 1.10 SpeciesAdaptorDriver.pm, 1.5, 1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB/Persistent BioNamespace.pm, 1.4, 1.5 PersistentObject.pm, 1.8, 1.9 PersistentObjectFactory.pm, 1.3, 1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio BioEntry.pm,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-db/Bio/DB SimpleDBContext.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-network/t Interaction.t,1.4,1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-network/Bio/Network Interaction.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Restriction Enzyme.pm,1.20,1.21   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Gumby.pm,1.1,1.2   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph stackedplot.pm, 1.5, 1.6   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/Bio/FeatureIO ptt.pm,1.4,1.5   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/scripts/Bio-DB-GFF genbank2gff3.PLS, 1.12, 1.13   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.22,1.23   Christopher John Fields
• [Bioperl-guts-l] biosql-schema/sql biosql-phylodb-mysql.sql, NONE, 1.1   James C. Estill
• [Bioperl-guts-l] bioperl-live/examples/tools seq_pattern.pl, 1.1, 1.2   Steve Chervitz
• [Bioperl-guts-l] [Bug 2320] New: problem with high_quality_discrepancies in ContigAnalysis: Can't call method "start" on an undefined value at /home/jayoung/traskdata/perl/lib/Bio/Assembly/ContigAnalysis.pm line 177.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2320] problem with high_quality_discrepancies in ContigAnalysis: Can't call method "start" on an undefined value at /home/jayoung/traskdata/perl/lib/Bio/Assembly/ContigAnalysis.pm line 177.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2320] problem with high_quality_discrepancies in ContigAnalysis: Can't call method "start" on an undefined value at /home/jayoung/traskdata/perl/lib/Bio/Assembly/ContigAnalysis.pm line 177.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2320] problem with high_quality_discrepancies in ContigAnalysis: Can't call method "start" on an undefined value at /home/jayoung/traskdata/perl/lib/Bio/Assembly/ContigAnalysis.pm line 177.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2320] problem with high_quality_discrepancies in ContigAnalysis: Can't call method "start" on an undefined value at /home/jayoung/traskdata/perl/lib/Bio/Assembly/ContigAnalysis.pm line 177.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.18, 1.19   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.19, 1.20   Jason Stajich
• [Bioperl-guts-l] [Bug 2299] Bio::Tools::Glimmer needs workaround to deal with Glimmer 2.X/3.X producing plus strand predictions with start > end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2299] Bio::Tools::Glimmer needs workaround to deal with Glimmer 2.X/3.X producing plus strand predictions with start > end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2299] Bio::Tools::Glimmer needs workaround to deal with Glimmer 2.X/3.X producing plus strand predictions with start > end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2299] Bio::Tools::Glimmer needs workaround to deal with Glimmer 2.X/3.X producing plus strand predictions with start > end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2299] Bio::Tools::Glimmer needs workaround to deal with Glimmer 2.X/3.X producing plus strand predictions with start > end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2299] Bio::Tools::Glimmer needs workaround to deal with Glimmer 2.X/3.X producing plus strand predictions with start > end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2321] New: AlignIO::next_aln does not return multiple alignments for bl2seq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live Build.PL,1.22,1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t RemoteBlast.t,1.20,1.21   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t RemoteBlast.t,1.21,1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Tree.t,1.16,1.17   Jason Stajich
• [Bioperl-guts-l] bioperl-live/t TreeBuild.t,1.3,1.4   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio Taxon.pm,1.7,1.8   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio Taxon.pm,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.19,1.20   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/scripts/Bio-DB-GFF genbank2gff3.PLS, 1.13, 1.14   Scott Cain
• [Bioperl-guts-l] bioperl-live/scripts/Bio-DB-GFF genbank2gff3.PLS, 1.14, 1.15   Scott Cain
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,NONE,1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t RemoteBlast.t,1.22,1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.3,1.4   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.4,1.5   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/root/lib TestObject.pm, 1.2, 1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.5,1.6   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.6,1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.7,1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools Protparam.pm,NONE,1.1   Rich Dobson
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO nhx.pm,1.20,1.21   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio/TreeIO nhx.pm,1.21,1.22   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio/Tree NodeNHX.pm,1.12,1.13   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Summary - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Info - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Link - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Query - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools EUtilities.pm,NONE,1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Query GlobalQuery.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Summary DocSum.pm, NONE, 1.1 Item.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Link LinkSet.pm, NONE, 1.1 UrlLink.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Info FieldInfo.pm, NONE, 1.1 LinkInfo.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities EUtilDataI.pm, NONE, 1.1 History.pm, NONE, 1.1 HistoryI.pm, NONE, 1.1 Info.pm, NONE, 1.1 Link.pm, NONE, 1.1 Query.pm, NONE, 1.1 Summary.pm, NONE, 1.1   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools EUtilities.pm,1.1,1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Summary DocSum.pm, 1.1, 1.2 Item.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities History.pm, 1.1, 1.2 Info.pm, 1.1, 1.2 Link.pm, 1.1, 1.2 Query.pm, 1.1, 1.2 Summary.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Link LinkSet.pm, 1.1, 1.2 UrlLink.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities/Info LinkInfo.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.41,1.42   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB WebDBSeqI.pm,1.63,1.64   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO tab.pm,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities History.pm, 1.2, 1.3 Info.pm, 1.2, 1.3 Link.pm, 1.2, 1.3 Query.pm, 1.2, 1.3 Summary.pm, 1.2, 1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools EUtilities.pm,1.2,1.3   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio LocatableSeq.pm,1.43,1.44   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio SearchIO.pm,1.43,1.44   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2325] New: Bio::SimpleAlign->remove_columns() fails with all_gaps_columns   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/t testformats.pl,1.2,NONE   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/data test.fasta,1.2,1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilParameters.pm, 1.1, 1.2 EUtilities.pm, 1.37, 1.38 GenericWebDBI.pm, 1.8, 1.9   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities Cookie.pm, 1.10, NONE DocSum.pm, 1.6, NONE ElinkData.pm, 1.21, NONE QueryData.pm, 1.1, NONE efetch.pm, 1.12, NONE egquery.pm, 1.11, NONE einfo.pm, 1.13, NONE elink.pm, 1.31, NONE epost.pm, 1.12, NONE esearch.pm, 1.21, NONE esummary.pm, 1.17, NONE   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Map CytoPosition.pm,1.19,1.20   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Test.pm,1.3,NONE   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.10,1.11   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t AlignIO.t,1.77,1.78   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t StandAloneBlast.t, 1.31, 1.32 qual.t, 1.10, 1.11 Perl.t, 1.12, 1.13   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.42,1.43   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2326] New: bp_fast_load_gff creates mostly empty tables.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-live/Bio/Tools EUtilities.pm,1.3,1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities HistoryI.pm, 1.1, 1.2 Link.pm, 1.3, 1.4 Summary.pm, 1.3, 1.4   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB EUtilParameters.pm, 1.2, 1.3 EUtilities.pm, 1.38, 1.39 GenericWebDBI.pm, 1.9, 1.10   Christopher John Fields

Last message date: Thu Jun 28 14:06:21 EDT 2007
Archived on: Thu Jun 28 14:06:26 EDT 2007

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