June 2007 Archives by subject

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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 2203] Signalp extension or new module   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 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 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] [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] [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] [Bug 2310] New: nonstandard method docs in Bio::Search::Result::BlastResult   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 2312] New: './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] [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] [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 2317] Changing parameter MATRIX_NAME in RemoteBlast generates an error   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 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] [Bug 2321] New: AlignIO::next_aln does not return multiple alignments for bl2seq   bugzilla-daemon at portal.open-bio.org
• [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] [Bug 2326] New: bp_fast_load_gff creates mostly empty tables.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-db/Bio BioEntry.pm,1.3,1.4   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/Bio/DB SimpleDBContext.pm,1.9,1.10   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/mysql BasePersistenceAdaptorDriver.pm, 1.18, 1.19 SpeciesAdaptorDriver.pm, 1.8, 1.9   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/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/DBI Pg.pm,1.4,1.5   Hilmar Lapp
• [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/DB/Query DBQueryResult.pm, 1.4, 1.5 PrebuiltResult.pm, 1.3, 1.4   Senduran Balasubramaniam
• [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-live Build.PL,1.22,1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live INSTALL,1.61,1.62   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 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] bioperl-live/Bio SimpleAlign.pm,1.134,1.135   Heikki Lehvaslaiho
• [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/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/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/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/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/Assembly/IO ace.pm, 1.16, 1.17 phrap.pm, 1.8, 1.9   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/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/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/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/Coordinate/Result Gap.pm, 1.11, 1.12 Match.pm, 1.11, 1.12   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/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 EUtilParameters.pm, 1.2, 1.3 EUtilities.pm, 1.38, 1.39 GenericWebDBI.pm, 1.9, 1.10   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/DB WebDBSeqI.pm,1.63,1.64   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/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/Bio/DB/Flat BinarySearch.pm, 1.28, 1.29   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/DB/GFF Segment.pm,1.31,1.32   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/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/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/FeatureIO ptt.pm,1.4,1.5   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/Bio/Graph SimpleGraph.pm,1.14,1.15   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/Graphics FeatureBase.pm, 1.30, 1.31   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm, 1.135, 1.136   Sendu Bala
• [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.135,1.136   Lincoln Stein
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph stackedplot.pm, 1.5, 1.6   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph xyplot.pm, 1.33, 1.34   Lincoln Stein
• [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/LiveSeq Mutator.pm, 1.35, 1.36 Translation.pm, 1.16, 1.17   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/LiveSeq/IO BioPerl.pm,1.21,1.22   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/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/Map CytoPosition.pm,1.19,1.20   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 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/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/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/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/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/OntologyIO obo.pm,1.11,1.12   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Phenotype/OMIM OMIMparser.pm, 1.23, 1.24   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/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/PopGen/Simulation Coalescent.pm, 1.13, 1.14 GeneticDrift.pm, 1.7, 1.8   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/Restriction Enzyme.pm,1.20,1.21   Nathan Haigh
• [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/Root RootI.pm,1.77,1.78   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.41,1.42   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Root Utilities.pm,1.42,1.43   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Search Processor.pm,1.13,1.14   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/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/Iteration GenericIteration.pm, 1.10, 1.11 IterationI.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/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/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/SeqEvolution DNAPoint.pm, 1.1, 1.2 Factory.pm, 1.1, 1.2   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/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/SeqIO gbdriver.pm, 1.2, 1.3 genbank.pm, 1.164, 1.165   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.163,1.164   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO tab.pm,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/SeqIO/Handler GenericRichSeqHandler.pm, 1.1, 1.2   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Structure/SecStr/DSSP Res.pm, 1.13, 1.14   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/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/Taxonomy Taxon.pm, 1.9, 1.10 Tree.pm, 1.4, 1.5   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/Tools EUtilities.pm,1.1,1.2   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/Tools EUtilities.pm,1.3,1.4   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 Protparam.pm,NONE,1.1   Rich Dobson
• [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/Tools/Analysis/DNA ESEfinder.pm, 1.17, 1.18   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/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/Tools/EMBOSS Palindrome.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/EUtilities - New directory   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 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 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 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/Tools/EUtilities/Info FieldInfo.pm, NONE, 1.1 LinkInfo.pm, NONE, 1.1   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/Info LinkInfo.pm, 1.1, 1.2   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/Link LinkSet.pm, 1.1, 1.2 UrlLink.pm, 1.1, 1.2   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/Query GlobalQuery.pm, NONE, 1.1   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/Summary DocSum.pm, 1.1, 1.2 Item.pm, 1.1, 1.2   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/Summary - New directory   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/Bio/Tools/HMMER Results.pm, 1.32, 1.33   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo Gumby.pm,1.1,1.2   Nathan Haigh
• [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/Molphy Result.pm, 1.12, 1.13   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/Phylo/Phylip ProtDist.pm, 1.11, 1.12   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/Signalp ExtendedSignalp.pm, 1.3, 1.4   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/Tree NodeNHX.pm,1.12,1.13   Jason Stajich
• [Bioperl-guts-l] bioperl-live/Bio/Tree/Draw Cladogram.pm, 1.17, 1.18   Senduran Balasubramaniam
• [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] 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/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/Bio/Variation/IO xml.pm,1.21,1.22   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/root/lib TestObject.pm, 1.2, 1.3   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/root/lib/Bio Seq.pm, 1.7, 1.8   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/examples/tools seq_pattern.pl, 1.1, 1.2   Steve Chervitz
• [Bioperl-guts-l] bioperl-live/scripts/Bio-DB-GFF genbank2gff3.PLS, 1.12, 1.13   Nathan Haigh
• [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 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-live/t AlignIO.t,1.77,1.78   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t BioDBGFF.t,1.45,1.46   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t BioGraphics.t,1.22,1.23   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t EUtilities.t,1.19,1.20   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.20,1.21   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t genbank.t,1.22,1.23   Christopher John Fields
• [Bioperl-guts-l] bioperl-live/t NetPhos.t,1.14,1.15   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t PodSyntax.t,NONE,1.1   Nathan Haigh
• [Bioperl-guts-l] bioperl-live/t RemoteBlast.t,1.19,1.20   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 RemoteBlast.t,1.22,1.23   Senduran Balasubramaniam
• [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/t Sopma.t,1.7,1.8   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/t Test.pm,1.3,NONE   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t testformats.pl,1.2,NONE   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t Tree.t,1.14,1.15   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/t/data test.fasta,1.2,1.3   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,1.10,1.11   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/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/t/lib BioperlTest.pm,1.8,1.9   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,1.9,1.10   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-live/t/lib BioperlTest.pm,NONE,1.1   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-network/Bio/Network Interaction.pm, 1.6, 1.7   Senduran Balasubramaniam
• [Bioperl-guts-l] bioperl-network/t Interaction.t,1.4,1.5   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/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/Alignment Clustalw.pm, 1.51, 1.52   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/AnalysisFactory Pise.pm, 1.9, 1.10 soap.pm, 1.8, 1.9   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/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/Phylo/Molphy ProtML.pm, 1.14, 1.15   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/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/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 Clustalw.t,1.35,1.36   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-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 Hyphy.t,1.2,1.3   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 tRNAscanSE.t,1.1,1.2   Senduran Balasubramaniam
• [Bioperl-guts-l] biosql-schema/sql biosql-phylodb-mysql.sql, NONE, 1.1   James C. Estill

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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