changes all issue tracking in preparation for switch to github issues
commit7814d898d40bc874743e7cac623d4d0eee4e1b4f
authorChris Fields <cjfields@bioperl.org>
Mon, 21 Apr 2014 04:14:51 +0000 (20 23:14 -0500)
committerChris Fields <cjfields@bioperl.org>
Mon, 21 Apr 2014 04:14:51 +0000 (20 23:14 -0500)
tree51c4181c53c42fb8eb9e880dfc43b7cb482b1e56
parentc682abd1a61cc73f7a15c8015f06f942d4e16a79
changes all issue tracking in preparation for switch to github issues
718 files changed:
BUGS
Bio/Align/AlignI.pm
Bio/Align/DNAStatistics.pm
Bio/Align/PairwiseStatistics.pm
Bio/Align/ProteinStatistics.pm
Bio/Align/StatisticsI.pm
Bio/Align/Utilities.pm
Bio/AlignIO.pm
Bio/AlignIO/Handler/GenericAlignHandler.pm
Bio/AlignIO/arp.pm
Bio/AlignIO/bl2seq.pm
Bio/AlignIO/clustalw.pm
Bio/AlignIO/emboss.pm
Bio/AlignIO/fasta.pm
Bio/AlignIO/largemultifasta.pm
Bio/AlignIO/maf.pm
Bio/AlignIO/mase.pm
Bio/AlignIO/mega.pm
Bio/AlignIO/meme.pm
Bio/AlignIO/metafasta.pm
Bio/AlignIO/msf.pm
Bio/AlignIO/nexml.pm
Bio/AlignIO/nexus.pm
Bio/AlignIO/pfam.pm
Bio/AlignIO/phylip.pm
Bio/AlignIO/po.pm
Bio/AlignIO/proda.pm
Bio/AlignIO/prodom.pm
Bio/AlignIO/psi.pm
Bio/AlignIO/selex.pm
Bio/AlignIO/stockholm.pm
Bio/AlignIO/xmfa.pm
Bio/AnalysisI.pm
Bio/AnalysisParserI.pm
Bio/AnalysisResultI.pm
Bio/AnnotatableI.pm
Bio/Annotation/AnnotationFactory.pm
Bio/Annotation/Collection.pm
Bio/Annotation/OntologyTerm.pm
Bio/Annotation/Relation.pm
Bio/Annotation/SimpleValue.pm
Bio/Annotation/StructuredValue.pm
Bio/Annotation/TagTree.pm
Bio/Annotation/TypeManager.pm
Bio/AnnotationCollectionI.pm
Bio/AnnotationI.pm
Bio/Assembly/Contig.pm
Bio/Assembly/ContigAnalysis.pm
Bio/Assembly/IO.pm
Bio/Assembly/IO/ace.pm
Bio/Assembly/IO/bowtie.pm
Bio/Assembly/IO/maq.pm
Bio/Assembly/IO/phrap.pm
Bio/Assembly/IO/sam.pm
Bio/Assembly/IO/tigr.pm
Bio/Assembly/Scaffold.pm
Bio/Assembly/ScaffoldI.pm
Bio/Assembly/Singlet.pm
Bio/Assembly/Tools/ContigSpectrum.pm
Bio/Cluster/ClusterFactory.pm
Bio/Cluster/FamilyI.pm
Bio/Cluster/SequenceFamily.pm
Bio/Cluster/UniGene.pm
Bio/Cluster/UniGeneI.pm
Bio/ClusterI.pm
Bio/ClusterIO.pm
Bio/ClusterIO/dbsnp.pm
Bio/ClusterIO/unigene.pm
Bio/CodonUsage/IO.pm
Bio/CodonUsage/Table.pm
Bio/DB/Ace.pm
Bio/DB/BioFetch.pm
Bio/DB/CUTG.pm
Bio/DB/DBFetch.pm
Bio/DB/EMBL.pm
Bio/DB/EntrezGene.pm
Bio/DB/Expression.pm
Bio/DB/Expression/geo.pm
Bio/DB/Failover.pm
Bio/DB/FileCache.pm
Bio/DB/Flat.pm
Bio/DB/Flat/BDB.pm
Bio/DB/Flat/BDB/embl.pm
Bio/DB/Flat/BDB/fasta.pm
Bio/DB/Flat/BDB/genbank.pm
Bio/DB/Flat/BDB/swiss.pm
Bio/DB/Flat/BinarySearch.pm
Bio/DB/GenBank.pm
Bio/DB/GenPept.pm
Bio/DB/GenericWebAgent.pm
Bio/DB/HIV.pm
Bio/DB/HIV/HIVAnnotProcessor.pm
Bio/DB/HIV/HIVQueryHelper.pm
Bio/DB/InMemoryCache.pm
Bio/DB/LocationI.pm
Bio/DB/MeSH.pm
Bio/DB/NCBIHelper.pm
Bio/DB/Query/GenBank.pm
Bio/DB/Query/HIVQuery.pm
Bio/DB/Query/WebQuery.pm
Bio/DB/QueryI.pm
Bio/DB/RandomAccessI.pm
Bio/DB/RefSeq.pm
Bio/DB/ReferenceI.pm
Bio/DB/Registry.pm
Bio/DB/SeqI.pm
Bio/DB/SeqVersion.pm
Bio/DB/SeqVersion/gi.pm
Bio/DB/SwissProt.pm
Bio/DB/TFBS.pm
Bio/DB/TFBS/transfac_pro.pm
Bio/DB/Taxonomy.pm
Bio/DB/Taxonomy/entrez.pm
Bio/DB/Taxonomy/flatfile.pm
Bio/DB/Taxonomy/greengenes.pm
Bio/DB/Taxonomy/list.pm
Bio/DB/Taxonomy/silva.pm
Bio/DB/Universal.pm
Bio/DB/UpdateableSeqI.pm
Bio/DB/WebDBSeqI.pm
Bio/DBLinkContainerI.pm
Bio/Das/FeatureTypeI.pm
Bio/Das/SegmentI.pm
Bio/DasI.pm
Bio/DescribableI.pm
Bio/Draw/Pictogram.pm
Bio/Event/EventGeneratorI.pm
Bio/Event/EventHandlerI.pm
Bio/Factory/AnalysisI.pm
Bio/Factory/ApplicationFactoryI.pm
Bio/Factory/DriverFactory.pm
Bio/Factory/FTLocationFactory.pm
Bio/Factory/LocationFactoryI.pm
Bio/Factory/MapFactoryI.pm
Bio/Factory/ObjectBuilderI.pm
Bio/Factory/ObjectFactory.pm
Bio/Factory/ObjectFactoryI.pm
Bio/Factory/SeqAnalysisParserFactory.pm
Bio/Factory/SeqAnalysisParserFactoryI.pm
Bio/Factory/SequenceFactoryI.pm
Bio/Factory/SequenceProcessorI.pm
Bio/Factory/SequenceStreamI.pm
Bio/Factory/TreeFactoryI.pm
Bio/FeatureHolderI.pm
Bio/HandlerBaseI.pm
Bio/IdCollectionI.pm
Bio/IdentifiableI.pm
Bio/Index/Abstract.pm
Bio/Index/AbstractSeq.pm
Bio/Index/Blast.pm
Bio/Index/BlastTable.pm
Bio/Index/EMBL.pm
Bio/Index/Fasta.pm
Bio/Index/Fastq.pm
Bio/Index/GenBank.pm
Bio/Index/Hmmer.pm
Bio/Index/Qual.pm
Bio/Index/Stockholm.pm
Bio/Index/SwissPfam.pm
Bio/Index/Swissprot.pm
Bio/LiveSeq/ChainI.pm
Bio/LiveSeq/Mutation.pm
Bio/LiveSeq/Mutator.pm
Bio/LiveSeq/SeqI.pm
Bio/LocatableSeq.pm
Bio/Location/Atomic.pm
Bio/Location/AvWithinCoordPolicy.pm
Bio/Location/CoordinatePolicyI.pm
Bio/Location/Fuzzy.pm
Bio/Location/FuzzyLocationI.pm
Bio/Location/NarrowestCoordPolicy.pm
Bio/Location/Simple.pm
Bio/Location/Split.pm
Bio/Location/SplitLocationI.pm
Bio/Location/WidestCoordPolicy.pm
Bio/LocationI.pm
Bio/Map/Clone.pm
Bio/Map/Contig.pm
Bio/Map/CytoMap.pm
Bio/Map/CytoMarker.pm
Bio/Map/CytoPosition.pm
Bio/Map/EntityI.pm
Bio/Map/FPCMarker.pm
Bio/Map/Gene.pm
Bio/Map/GeneMap.pm
Bio/Map/GenePosition.pm
Bio/Map/GeneRelative.pm
Bio/Map/LinkageMap.pm
Bio/Map/LinkagePosition.pm
Bio/Map/MapI.pm
Bio/Map/Mappable.pm
Bio/Map/MappableI.pm
Bio/Map/Marker.pm
Bio/Map/MarkerI.pm
Bio/Map/Microsatellite.pm
Bio/Map/OrderedPosition.pm
Bio/Map/OrderedPositionWithDistance.pm
Bio/Map/Physical.pm
Bio/Map/Position.pm
Bio/Map/PositionHandler.pm
Bio/Map/PositionHandlerI.pm
Bio/Map/PositionI.pm
Bio/Map/PositionWithSequence.pm
Bio/Map/Prediction.pm
Bio/Map/Relative.pm
Bio/Map/RelativeI.pm
Bio/Map/SimpleMap.pm
Bio/Map/TranscriptionFactor.pm
Bio/MapIO.pm
Bio/MapIO/fpc.pm
Bio/MapIO/mapmaker.pm
Bio/Matrix/Generic.pm
Bio/Matrix/IO.pm
Bio/Matrix/IO/mlagan.pm
Bio/Matrix/IO/phylip.pm
Bio/Matrix/IO/scoring.pm
Bio/Matrix/MatrixI.pm
Bio/Matrix/Mlagan.pm
Bio/Matrix/PSM/IO.pm
Bio/Matrix/PSM/IO/mast.pm
Bio/Matrix/PSM/IO/masta.pm
Bio/Matrix/PSM/IO/meme.pm
Bio/Matrix/PSM/IO/psiblast.pm
Bio/Matrix/PSM/IO/transfac.pm
Bio/Matrix/PSM/InstanceSite.pm
Bio/Matrix/PSM/InstanceSiteI.pm
Bio/Matrix/PSM/ProtMatrix.pm
Bio/Matrix/PSM/ProtPsm.pm
Bio/Matrix/PSM/Psm.pm
Bio/Matrix/PSM/PsmHeader.pm
Bio/Matrix/PSM/PsmHeaderI.pm
Bio/Matrix/PSM/PsmI.pm
Bio/Matrix/PSM/SiteMatrix.pm
Bio/Matrix/PSM/SiteMatrixI.pm
Bio/Matrix/PhylipDist.pm
Bio/Matrix/Scoring.pm
Bio/MolEvol/CodonModel.pm
Bio/Nexml/Factory.pm
Bio/NexmlIO.pm
Bio/Ontology/DocumentRegistry.pm
Bio/Ontology/GOterm.pm
Bio/Ontology/InterProTerm.pm
Bio/Ontology/OBOEngine.pm
Bio/Ontology/OBOterm.pm
Bio/Ontology/Ontology.pm
Bio/Ontology/OntologyEngineI.pm
Bio/Ontology/OntologyI.pm
Bio/Ontology/OntologyStore.pm
Bio/Ontology/Path.pm
Bio/Ontology/PathI.pm
Bio/Ontology/Relationship.pm
Bio/Ontology/RelationshipFactory.pm
Bio/Ontology/RelationshipI.pm
Bio/Ontology/RelationshipType.pm
Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
Bio/Ontology/SimpleOntologyEngine.pm
Bio/Ontology/Term.pm
Bio/Ontology/TermFactory.pm
Bio/Ontology/TermI.pm
Bio/OntologyIO.pm
Bio/OntologyIO/Handlers/BaseSAXHandler.pm
Bio/OntologyIO/Handlers/InterProHandler.pm
Bio/OntologyIO/InterProParser.pm
Bio/OntologyIO/dagflat.pm
Bio/OntologyIO/goflat.pm
Bio/OntologyIO/obo.pm
Bio/OntologyIO/simplehierarchy.pm
Bio/OntologyIO/soflat.pm
Bio/ParameterBaseI.pm
Bio/Perl.pm
Bio/Phenotype/Correlate.pm
Bio/Phenotype/MeSH/Term.pm
Bio/Phenotype/MeSH/Twig.pm
Bio/Phenotype/Measure.pm
Bio/Phenotype/OMIM/MiniMIMentry.pm
Bio/Phenotype/OMIM/OMIMentry.pm
Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
Bio/Phenotype/OMIM/OMIMparser.pm
Bio/Phenotype/Phenotype.pm
Bio/Phenotype/PhenotypeI.pm
Bio/PopGen/Genotype.pm
Bio/PopGen/GenotypeI.pm
Bio/PopGen/HtSNP.pm
Bio/PopGen/IO.pm
Bio/PopGen/IO/csv.pm
Bio/PopGen/IO/hapmap.pm
Bio/PopGen/IO/phase.pm
Bio/PopGen/IO/prettybase.pm
Bio/PopGen/Individual.pm
Bio/PopGen/IndividualI.pm
Bio/PopGen/Marker.pm
Bio/PopGen/MarkerI.pm
Bio/PopGen/PopStats.pm
Bio/PopGen/Population.pm
Bio/PopGen/PopulationI.pm
Bio/PopGen/Simulation/Coalescent.pm
Bio/PopGen/Simulation/GeneticDrift.pm
Bio/PopGen/Statistics.pm
Bio/PopGen/TagHaplotype.pm
Bio/PopGen/Utilities.pm
Bio/PrimarySeq.pm
Bio/PrimarySeqI.pm
Bio/PullParserI.pm
Bio/Range.pm
Bio/RangeI.pm
Bio/Restriction/Analysis.pm
Bio/Restriction/Enzyme.pm
Bio/Restriction/Enzyme/MultiCut.pm
Bio/Restriction/Enzyme/MultiSite.pm
Bio/Restriction/EnzymeCollection.pm
Bio/Restriction/EnzymeI.pm
Bio/Restriction/IO.pm
Bio/Restriction/IO/bairoch.pm
Bio/Restriction/IO/base.pm
Bio/Restriction/IO/itype2.pm
Bio/Restriction/IO/prototype.pm
Bio/Restriction/IO/withrefm.pm
Bio/Root/HTTPget.pm
Bio/Search/BlastStatistics.pm
Bio/Search/DatabaseI.pm
Bio/Search/GenericDatabase.pm
Bio/Search/GenericStatistics.pm
Bio/Search/HSP/BlastHSP.pm
Bio/Search/HSP/BlastPullHSP.pm
Bio/Search/HSP/FastaHSP.pm
Bio/Search/HSP/GenericHSP.pm
Bio/Search/HSP/HMMERHSP.pm
Bio/Search/HSP/HSPFactory.pm
Bio/Search/HSP/HSPI.pm
Bio/Search/HSP/HmmpfamHSP.pm
Bio/Search/HSP/ModelHSP.pm
Bio/Search/HSP/PSLHSP.pm
Bio/Search/HSP/PsiBlastHSP.pm
Bio/Search/HSP/PullHSPI.pm
Bio/Search/HSP/WABAHSP.pm
Bio/Search/Hit/BlastHit.pm
Bio/Search/Hit/BlastPullHit.pm
Bio/Search/Hit/Fasta.pm
Bio/Search/Hit/GenericHit.pm
Bio/Search/Hit/HMMERHit.pm
Bio/Search/Hit/HitFactory.pm
Bio/Search/Hit/HitI.pm
Bio/Search/Hit/HmmpfamHit.pm
Bio/Search/Hit/ModelHit.pm
Bio/Search/Hit/PsiBlastHit.pm
Bio/Search/Hit/PullHitI.pm
Bio/Search/Hit/hmmer3Hit.pm
Bio/Search/Iteration/GenericIteration.pm
Bio/Search/Iteration/IterationI.pm
Bio/Search/Processor.pm
Bio/Search/Result/BlastPullResult.pm
Bio/Search/Result/BlastResult.pm
Bio/Search/Result/CrossMatchResult.pm
Bio/Search/Result/GenericResult.pm
Bio/Search/Result/HMMERResult.pm
Bio/Search/Result/HmmpfamResult.pm
Bio/Search/Result/PullResultI.pm
Bio/Search/Result/ResultFactory.pm
Bio/Search/Result/ResultI.pm
Bio/Search/Result/WABAResult.pm
Bio/Search/Result/hmmer3Result.pm
Bio/Search/StatisticsI.pm
Bio/Search/Tiling/MapTiling.pm
Bio/Search/Tiling/TilingI.pm
Bio/SearchDist.pm
Bio/SearchIO.pm
Bio/SearchIO/EventHandlerI.pm
Bio/SearchIO/FastHitEventBuilder.pm
Bio/SearchIO/IteratedSearchResultEventBuilder.pm
Bio/SearchIO/SearchResultEventBuilder.pm
Bio/SearchIO/Writer/GbrowseGFF.pm
Bio/SearchIO/Writer/HSPTableWriter.pm
Bio/SearchIO/Writer/HTMLResultWriter.pm
Bio/SearchIO/Writer/HitTableWriter.pm
Bio/SearchIO/Writer/ResultTableWriter.pm
Bio/SearchIO/Writer/TextResultWriter.pm
Bio/SearchIO/axt.pm
Bio/SearchIO/blast.pm
Bio/SearchIO/blast_pull.pm
Bio/SearchIO/blasttable.pm
Bio/SearchIO/cross_match.pm
Bio/SearchIO/erpin.pm
Bio/SearchIO/exonerate.pm
Bio/SearchIO/fasta.pm
Bio/SearchIO/gmap_f9.pm
Bio/SearchIO/hmmer.pm
Bio/SearchIO/hmmer2.pm
Bio/SearchIO/hmmer3.pm
Bio/SearchIO/hmmer_pull.pm
Bio/SearchIO/infernal.pm
Bio/SearchIO/megablast.pm
Bio/SearchIO/psl.pm
Bio/SearchIO/rnamotif.pm
Bio/SearchIO/sim4.pm
Bio/SearchIO/waba.pm
Bio/SearchIO/wise.pm
Bio/Seq.pm
Bio/Seq/BaseSeqProcessor.pm
Bio/Seq/EncodedSeq.pm
Bio/Seq/LargeLocatableSeq.pm
Bio/Seq/LargePrimarySeq.pm
Bio/Seq/LargeSeq.pm
Bio/Seq/LargeSeqI.pm
Bio/Seq/Meta.pm
Bio/Seq/Meta/Array.pm
Bio/Seq/MetaI.pm
Bio/Seq/PrimaryQual.pm
Bio/Seq/PrimedSeq.pm
Bio/Seq/QualI.pm
Bio/Seq/Quality.pm
Bio/Seq/RichSeq.pm
Bio/Seq/RichSeqI.pm
Bio/Seq/SeqBuilder.pm
Bio/Seq/SeqFactory.pm
Bio/Seq/SeqFastaSpeedFactory.pm
Bio/Seq/SeqWithQuality.pm
Bio/Seq/SequenceTrace.pm
Bio/Seq/TraceI.pm
Bio/SeqAnalysisParserI.pm
Bio/SeqEvolution/DNAPoint.pm
Bio/SeqEvolution/EvolutionI.pm
Bio/SeqEvolution/Factory.pm
Bio/SeqFeature/Amplicon.pm
Bio/SeqFeature/AnnotationAdaptor.pm
Bio/SeqFeature/Collection.pm
Bio/SeqFeature/CollectionI.pm
Bio/SeqFeature/Computation.pm
Bio/SeqFeature/Gene/Exon.pm
Bio/SeqFeature/Gene/ExonI.pm
Bio/SeqFeature/Gene/GeneStructure.pm
Bio/SeqFeature/Gene/GeneStructureI.pm
Bio/SeqFeature/Gene/Intron.pm
Bio/SeqFeature/Gene/NC_Feature.pm
Bio/SeqFeature/Gene/Poly_A_site.pm
Bio/SeqFeature/Gene/Promoter.pm
Bio/SeqFeature/Gene/Transcript.pm
Bio/SeqFeature/Gene/TranscriptI.pm
Bio/SeqFeature/Gene/UTR.pm
Bio/SeqFeature/Generic.pm
Bio/SeqFeature/PositionProxy.pm
Bio/SeqFeature/Primer.pm
Bio/SeqFeature/SiRNA/Oligo.pm
Bio/SeqFeature/SiRNA/Pair.pm
Bio/SeqFeature/Similarity.pm
Bio/SeqFeature/SimilarityPair.pm
Bio/SeqFeature/SubSeq.pm
Bio/SeqFeature/Tools/FeatureNamer.pm
Bio/SeqFeature/Tools/IDHandler.pm
Bio/SeqFeature/Tools/TypeMapper.pm
Bio/SeqFeature/Tools/Unflattener.pm
Bio/SeqFeature/TypedSeqFeatureI.pm
Bio/SeqFeatureI.pm
Bio/SeqI.pm
Bio/SeqIO.pm
Bio/SeqIO/FTHelper.pm
Bio/SeqIO/Handler/GenericRichSeqHandler.pm
Bio/SeqIO/MultiFile.pm
Bio/SeqIO/abi.pm
Bio/SeqIO/ace.pm
Bio/SeqIO/agave.pm
Bio/SeqIO/alf.pm
Bio/SeqIO/asciitree.pm
Bio/SeqIO/bsml.pm
Bio/SeqIO/bsml_sax.pm
Bio/SeqIO/chadoxml.pm
Bio/SeqIO/chaos.pm
Bio/SeqIO/chaosxml.pm
Bio/SeqIO/ctf.pm
Bio/SeqIO/embl.pm
Bio/SeqIO/embldriver.pm
Bio/SeqIO/entrezgene.pm
Bio/SeqIO/excel.pm
Bio/SeqIO/exp.pm
Bio/SeqIO/fasta.pm
Bio/SeqIO/fastq.pm
Bio/SeqIO/flybase_chadoxml.pm
Bio/SeqIO/game.pm
Bio/SeqIO/game/featHandler.pm
Bio/SeqIO/game/gameHandler.pm
Bio/SeqIO/game/gameSubs.pm
Bio/SeqIO/game/gameWriter.pm
Bio/SeqIO/game/seqHandler.pm
Bio/SeqIO/gbdriver.pm
Bio/SeqIO/gbxml.pm
Bio/SeqIO/gcg.pm
Bio/SeqIO/genbank.pm
Bio/SeqIO/interpro.pm
Bio/SeqIO/kegg.pm
Bio/SeqIO/largefasta.pm
Bio/SeqIO/lasergene.pm
Bio/SeqIO/locuslink.pm
Bio/SeqIO/mbsout.pm
Bio/SeqIO/metafasta.pm
Bio/SeqIO/msout.pm
Bio/SeqIO/nexml.pm
Bio/SeqIO/phd.pm
Bio/SeqIO/pir.pm
Bio/SeqIO/pln.pm
Bio/SeqIO/qual.pm
Bio/SeqIO/raw.pm
Bio/SeqIO/scf.pm
Bio/SeqIO/seqxml.pm
Bio/SeqIO/strider.pm
Bio/SeqIO/swiss.pm
Bio/SeqIO/swissdriver.pm
Bio/SeqIO/tab.pm
Bio/SeqIO/table.pm
Bio/SeqIO/tigr.pm
Bio/SeqIO/tigrxml.pm
Bio/SeqIO/tinyseq.pm
Bio/SeqIO/tinyseq/tinyseqHandler.pm
Bio/SeqIO/ztr.pm
Bio/SeqUtils.pm
Bio/SimpleAlign.pm
Bio/SimpleAnalysisI.pm
Bio/Species.pm
Bio/Structure/Atom.pm
Bio/Structure/Chain.pm
Bio/Structure/Entry.pm
Bio/Structure/IO.pm
Bio/Structure/IO/pdb.pm
Bio/Structure/Model.pm
Bio/Structure/Residue.pm
Bio/Structure/SecStr/DSSP/Res.pm
Bio/Structure/SecStr/STRIDE/Res.pm
Bio/Structure/StructureI.pm
Bio/Symbol/Alphabet.pm
Bio/Symbol/AlphabetI.pm
Bio/Symbol/DNAAlphabet.pm
Bio/Symbol/ProteinAlphabet.pm
Bio/Symbol/Symbol.pm
Bio/Symbol/SymbolI.pm
Bio/Taxon.pm
Bio/Taxonomy.pm
Bio/Taxonomy/Node.pm
Bio/Tools/Alignment/Consed.pm
Bio/Tools/Alignment/Trim.pm
Bio/Tools/AmpliconSearch.pm
Bio/Tools/Analysis/DNA/ESEfinder.pm
Bio/Tools/Analysis/Protein/Domcut.pm
Bio/Tools/Analysis/Protein/ELM.pm
Bio/Tools/Analysis/Protein/GOR4.pm
Bio/Tools/Analysis/Protein/HNN.pm
Bio/Tools/Analysis/Protein/Mitoprot.pm
Bio/Tools/Analysis/Protein/NetPhos.pm
Bio/Tools/Analysis/Protein/Scansite.pm
Bio/Tools/Analysis/Protein/Sopma.pm
Bio/Tools/Analysis/SimpleAnalysisBase.pm
Bio/Tools/AnalysisResult.pm
Bio/Tools/Blat.pm
Bio/Tools/CodonTable.pm
Bio/Tools/Coil.pm
Bio/Tools/ECnumber.pm
Bio/Tools/EMBOSS/Palindrome.pm
Bio/Tools/EPCR.pm
Bio/Tools/ERPIN.pm
Bio/Tools/ESTScan.pm
Bio/Tools/Eponine.pm
Bio/Tools/Est2Genome.pm
Bio/Tools/Fgenesh.pm
Bio/Tools/FootPrinter.pm
Bio/Tools/GFF.pm
Bio/Tools/Gel.pm
Bio/Tools/Geneid.pm
Bio/Tools/Genemark.pm
Bio/Tools/Genewise.pm
Bio/Tools/Genomewise.pm
Bio/Tools/Genscan.pm
Bio/Tools/Glimmer.pm
Bio/Tools/Grail.pm
Bio/Tools/GuessSeqFormat.pm
Bio/Tools/HMMER/Results.pm
Bio/Tools/HMMER/Set.pm
Bio/Tools/Hmmpfam.pm
Bio/Tools/IUPAC.pm
Bio/Tools/Infernal.pm
Bio/Tools/Lucy.pm
Bio/Tools/MZEF.pm
Bio/Tools/Match.pm
Bio/Tools/OddCodes.pm
Bio/Tools/Phylo/Gerp.pm
Bio/Tools/Phylo/Gumby.pm
Bio/Tools/Phylo/Molphy.pm
Bio/Tools/Phylo/Molphy/Result.pm
Bio/Tools/Phylo/PAML.pm
Bio/Tools/Phylo/PAML/ModelResult.pm
Bio/Tools/Phylo/PAML/Result.pm
Bio/Tools/Phylo/Phylip/ProtDist.pm
Bio/Tools/Prediction/Exon.pm
Bio/Tools/Prediction/Gene.pm
Bio/Tools/Primer/Assessor/Base.pm
Bio/Tools/Primer/AssessorI.pm
Bio/Tools/Primer/Feature.pm
Bio/Tools/Primer/Pair.pm
Bio/Tools/Primer3.pm
Bio/Tools/Prints.pm
Bio/Tools/Profile.pm
Bio/Tools/Promoterwise.pm
Bio/Tools/Pseudowise.pm
Bio/Tools/QRNA.pm
Bio/Tools/RNAMotif.pm
Bio/Tools/RandomDistFunctions.pm
Bio/Tools/RepeatMasker.pm
Bio/Tools/Run/GenericParameters.pm
Bio/Tools/Run/ParametersI.pm
Bio/Tools/Run/RemoteBlast.pm
Bio/Tools/Run/StandAloneBlast.pm
Bio/Tools/Run/StandAloneNCBIBlast.pm
Bio/Tools/Run/StandAloneWUBlast.pm
Bio/Tools/Run/WrapperBase.pm
Bio/Tools/Run/WrapperBase/CommandExts.pm
Bio/Tools/Seg.pm
Bio/Tools/SeqPattern.pm
Bio/Tools/SeqStats.pm
Bio/Tools/SeqWords.pm
Bio/Tools/SiRNA.pm
Bio/Tools/SiRNA/Ruleset/saigo.pm
Bio/Tools/SiRNA/Ruleset/tuschl.pm
Bio/Tools/Sigcleave.pm
Bio/Tools/Signalp.pm
Bio/Tools/Signalp/ExtendedSignalp.pm
Bio/Tools/Sim4/Exon.pm
Bio/Tools/Sim4/Results.pm
Bio/Tools/Spidey/Exon.pm
Bio/Tools/Spidey/Results.pm
Bio/Tools/TandemRepeatsFinder.pm
Bio/Tools/TargetP.pm
Bio/Tools/Tmhmm.pm
Bio/Tools/dpAlign.pm
Bio/Tools/ipcress.pm
Bio/Tools/isPcr.pm
Bio/Tools/pICalculator.pm
Bio/Tools/pSW.pm
Bio/Tools/tRNAscanSE.pm
Bio/Tree/AlleleNode.pm
Bio/Tree/AnnotatableNode.pm
Bio/Tree/Compatible.pm
Bio/Tree/DistanceFactory.pm
Bio/Tree/Draw/Cladogram.pm
Bio/Tree/Node.pm
Bio/Tree/NodeI.pm
Bio/Tree/NodeNHX.pm
Bio/Tree/RandomFactory.pm
Bio/Tree/Statistics.pm
Bio/Tree/Tree.pm
Bio/Tree/TreeFunctionsI.pm
Bio/Tree/TreeI.pm
Bio/TreeIO.pm
Bio/TreeIO/NewickParser.pm
Bio/TreeIO/TreeEventBuilder.pm
Bio/TreeIO/cluster.pm
Bio/TreeIO/lintree.pm
Bio/TreeIO/newick.pm
Bio/TreeIO/nexml.pm
Bio/TreeIO/nexus.pm
Bio/TreeIO/nhx.pm
Bio/TreeIO/pag.pm
Bio/TreeIO/phyloxml.pm
Bio/TreeIO/svggraph.pm
Bio/TreeIO/tabtree.pm
Bio/UpdateableSeqI.pm
Bio/Variation/AAChange.pm
Bio/Variation/AAReverseMutate.pm
Bio/Variation/Allele.pm
Bio/Variation/DNAMutation.pm
Bio/Variation/IO.pm
Bio/Variation/IO/flat.pm
Bio/Variation/IO/xml.pm
Bio/Variation/README
Bio/Variation/RNAChange.pm
Bio/Variation/SNP.pm
Bio/Variation/SeqDiff.pm
Bio/Variation/VariantI.pm
Bio/WebAgent.pm
BioPerl.pm
Changes
README
README.md
doc/Deobfuscator/bin/deob_index.pl
doc/Deobfuscator/cgi-bin/deob_help.html
doc/Deobfuscator/cgi-bin/deob_interface.cgi
examples/tools/run_primer3.pl
ide/bioperl-mode/site-lisp/bioperl-skel.el
ide/bioperl.komodo
ide/bioperl.lisp
maintenance/authors.pl
maintenance/check_NAME.pl
maintenance/check_URLs.pl
maintenance/dependencies.pl
maintenance/deprecated.pl
maintenance/modules.pl
maintenance/pod.pl
maintenance/symlink_script.pl
scripts/DB-HIV/bp_hivq.pl
scripts/DB/bp_flanks.pl
scripts/index/bp_fetch.pl
scripts/index/bp_index.pl
scripts/searchio/bp_filter_search.pl
scripts/searchio/bp_parse_hmmsearch.pl
scripts/searchio/bp_search2table.pl
scripts/seq/bp_extract_feature_seq.pl
scripts/seq/bp_seqconvert.pl
scripts/seq/bp_seqcut.pl
scripts/seq/bp_seqpart.pl
scripts/seq/bp_seqretsplit.pl
scripts/seq/bp_split_seq.pl
scripts/seq/bp_translate_seq.pl
scripts/seq/bp_unflatten_seq.pl
scripts/seqstats/bp_aacomp.pl
scripts/seqstats/bp_chaos_plot.pl
scripts/seqstats/bp_gccalc.pl
scripts/seqstats/bp_oligo_count.pl
scripts/taxa/bp_taxid4species.pl
scripts/utilities/bp_dbsplit.pl
scripts/utilities/bp_mutate.pl
scripts/utilities/bp_pairwise_kaks.pl
scripts/utilities/bp_remote_blast.pl
scripts/utilities/bp_seq_length.pl