Fix for #154, per @stuartrbaker

[bioperl-live.git] / MANIFEST

.travis.yml
AUTHORS
Bio/Align/AlignI.pm
Bio/Align/DNAStatistics.pm
Bio/Align/Graphics.pm
Bio/Align/PairwiseStatistics.pm
Bio/Align/ProteinStatistics.pm
Bio/Align/StatisticsI.pm
Bio/Align/Utilities.pm
Bio/AlignIO.pm
Bio/AlignIO/arp.pm
Bio/AlignIO/bl2seq.pm
Bio/AlignIO/clustalw.pm
Bio/AlignIO/emboss.pm
Bio/AlignIO/fasta.pm
Bio/AlignIO/Handler/GenericAlignHandler.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/Comment.pm
Bio/Annotation/DBLink.pm
Bio/Annotation/OntologyTerm.pm
Bio/Annotation/Reference.pm
Bio/Annotation/Relation.pm
Bio/Annotation/SimpleValue.pm
Bio/Annotation/StructuredValue.pm
Bio/Annotation/TagTree.pm
Bio/Annotation/Target.pm
Bio/Annotation/Tree.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/Das/FeatureTypeI.pm
Bio/Das/SegmentI.pm
Bio/DasI.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/Fasta.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/GenericWebAgent.pm
Bio/DB/GenPept.pm
Bio/DB/GFF.pm
Bio/DB/GFF/Adaptor/ace.pm
Bio/DB/GFF/Adaptor/berkeleydb.pm
Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
Bio/DB/GFF/Adaptor/biofetch.pm
Bio/DB/GFF/Adaptor/biofetch_oracle.pm
Bio/DB/GFF/Adaptor/dbi.pm
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio/DB/GFF/Adaptor/dbi/iterator.pm
Bio/DB/GFF/Adaptor/dbi/mysql.pm
Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
Bio/DB/GFF/Adaptor/dbi/oracle.pm
Bio/DB/GFF/Adaptor/dbi/oracleace.pm
Bio/DB/GFF/Adaptor/dbi/pg.pm
Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
Bio/DB/GFF/Adaptor/memory.pm
Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
Bio/DB/GFF/Adaptor/memory/iterator.pm
Bio/DB/GFF/Aggregator.pm
Bio/DB/GFF/Aggregator/alignment.pm
Bio/DB/GFF/Aggregator/clone.pm
Bio/DB/GFF/Aggregator/coding.pm
Bio/DB/GFF/Aggregator/gene.pm
Bio/DB/GFF/Aggregator/match.pm
Bio/DB/GFF/Aggregator/none.pm
Bio/DB/GFF/Aggregator/orf.pm
Bio/DB/GFF/Aggregator/processed_transcript.pm
Bio/DB/GFF/Aggregator/so_transcript.pm
Bio/DB/GFF/Aggregator/transcript.pm
Bio/DB/GFF/Aggregator/ucsc_acembly.pm
Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
Bio/DB/GFF/Aggregator/ucsc_genscan.pm
Bio/DB/GFF/Aggregator/ucsc_refgene.pm
Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
Bio/DB/GFF/Aggregator/ucsc_softberry.pm
Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
Bio/DB/GFF/Aggregator/ucsc_unigene.pm
Bio/DB/GFF/Featname.pm
Bio/DB/GFF/Feature.pm
Bio/DB/GFF/Homol.pm
Bio/DB/GFF/RelSegment.pm
Bio/DB/GFF/Segment.pm
Bio/DB/GFF/Typename.pm
Bio/DB/GFF/Util/Binning.pm
Bio/DB/GFF/Util/Rearrange.pm
Bio/DB/HIV.pm
Bio/DB/HIV/HIVAnnotProcessor.pm
Bio/DB/HIV/HIVQueryHelper.pm
Bio/DB/HIV/lanl-schema.xml
Bio/DB/IndexedBase.pm
Bio/DB/InMemoryCache.pm
Bio/DB/LocationI.pm
Bio/DB/MeSH.pm
Bio/DB/NCBIHelper.pm
Bio/DB/Qual.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/ReferenceI.pm
Bio/DB/RefSeq.pm
Bio/DB/Registry.pm
Bio/DB/SeqFeature.pm
Bio/DB/SeqFeature/NormalizedFeature.pm
Bio/DB/SeqFeature/NormalizedFeatureI.pm
Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
Bio/DB/SeqFeature/Segment.pm
Bio/DB/SeqFeature/Store.pm
Bio/DB/SeqFeature/Store/bdb.pm
Bio/DB/SeqFeature/Store/berkeleydb.pm
Bio/DB/SeqFeature/Store/berkeleydb3.pm
Bio/DB/SeqFeature/Store/DBI/Iterator.pm
Bio/DB/SeqFeature/Store/DBI/mysql.pm
Bio/DB/SeqFeature/Store/DBI/Pg.pm
Bio/DB/SeqFeature/Store/DBI/SQLite.pm
Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
Bio/DB/SeqFeature/Store/GFF2Loader.pm
Bio/DB/SeqFeature/Store/GFF3Loader.pm
Bio/DB/SeqFeature/Store/Loader.pm
Bio/DB/SeqFeature/Store/LoadHelper.pm
Bio/DB/SeqFeature/Store/memory.pm
Bio/DB/SeqHound.pm
Bio/DB/SeqI.pm
Bio/DB/SeqVersion.pm
Bio/DB/SeqVersion/gi.pm
Bio/DB/SwissProt.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/Taxonomy/sqlite.pm
Bio/DB/TFBS.pm
Bio/DB/TFBS/transfac_pro.pm
Bio/DB/Universal.pm
Bio/DB/UpdateableSeqI.pm
Bio/DB/WebDBSeqI.pm
Bio/DBLinkContainerI.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/AARange.pm
Bio/LiveSeq/Chain.pm
Bio/LiveSeq/ChainI.pm
Bio/LiveSeq/DNA.pm
Bio/LiveSeq/Exon.pm
Bio/LiveSeq/Gene.pm
Bio/LiveSeq/Intron.pm
Bio/LiveSeq/IO/BioPerl.pm
Bio/LiveSeq/IO/Loader.pm
Bio/LiveSeq/IO/README
Bio/LiveSeq/Mutation.pm
Bio/LiveSeq/Mutator.pm
Bio/LiveSeq/Prim_Transcript.pm
Bio/LiveSeq/Range.pm
Bio/LiveSeq/Repeat_Region.pm
Bio/LiveSeq/Repeat_Unit.pm
Bio/LiveSeq/SeqI.pm
Bio/LiveSeq/Transcript.pm
Bio/LiveSeq/Translation.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/PhylipDist.pm
Bio/Matrix/PSM/InstanceSite.pm
Bio/Matrix/PSM/InstanceSiteI.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/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/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/dagflat.pm
Bio/OntologyIO/goflat.pm
Bio/OntologyIO/Handlers/BaseSAXHandler.pm
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
Bio/OntologyIO/Handlers/InterProHandler.pm
Bio/OntologyIO/InterProParser.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/Measure.pm
Bio/Phenotype/MeSH/Term.pm
Bio/Phenotype/MeSH/Twig.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/PhyloNetwork.pm
Bio/PhyloNetwork/Factory.pm
Bio/PhyloNetwork/FactoryX.pm
Bio/PhyloNetwork/GraphViz.pm
Bio/PhyloNetwork/muVector.pm
Bio/PhyloNetwork/RandomFactory.pm
Bio/PhyloNetwork/TreeFactory.pm
Bio/PhyloNetwork/TreeFactoryMulti.pm
Bio/PhyloNetwork/TreeFactoryX.pm
Bio/PopGen/Genotype.pm
Bio/PopGen/GenotypeI.pm
Bio/PopGen/HtSNP.pm
Bio/PopGen/Individual.pm
Bio/PopGen/IndividualI.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/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/Build.pm
Bio/Root/Exception.pm
Bio/Root/HTTPget.pm
Bio/Root/IO.pm
Bio/Root/Root.pm
Bio/Root/RootI.pm
Bio/Root/Storable.pm
Bio/Root/Test.pm
Bio/Root/TestObject.pm
Bio/Root/Utilities.pm
Bio/Root/Version.pm
Bio/Search/BlastStatistics.pm
Bio/Search/BlastUtils.pm
Bio/Search/DatabaseI.pm
Bio/Search/GenericDatabase.pm
Bio/Search/GenericStatistics.pm
Bio/Search/Hit/BlastHit.pm
Bio/Search/Hit/BlastPullHit.pm
Bio/Search/Hit/Fasta.pm
Bio/Search/Hit/GenericHit.pm
Bio/Search/Hit/HitFactory.pm
Bio/Search/Hit/HitI.pm
Bio/Search/Hit/hmmer3Hit.pm
Bio/Search/Hit/HMMERHit.pm
Bio/Search/Hit/HmmpfamHit.pm
Bio/Search/Hit/ModelHit.pm
Bio/Search/Hit/PsiBlastHit.pm
Bio/Search/Hit/PullHitI.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/HmmpfamHSP.pm
Bio/Search/HSP/HSPFactory.pm
Bio/Search/HSP/HSPI.pm
Bio/Search/HSP/ModelHSP.pm
Bio/Search/HSP/PsiBlastHSP.pm
Bio/Search/HSP/PSLHSP.pm
Bio/Search/HSP/PullHSPI.pm
Bio/Search/HSP/WABAHSP.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/hmmer3Result.pm
Bio/Search/Result/HMMERResult.pm
Bio/Search/Result/HmmpfamResult.pm
Bio/Search/Result/INFERNALResult.pm
Bio/Search/Result/PullResultI.pm
Bio/Search/Result/ResultFactory.pm
Bio/Search/Result/ResultI.pm
Bio/Search/Result/WABAResult.pm
Bio/Search/SearchUtils.pm
Bio/Search/StatisticsI.pm
Bio/Search/Tiling/MapTileUtils.pm
Bio/Search/Tiling/MapTiling.pm
Bio/Search/Tiling/TilingI.pm
Bio/SearchDist.pm
Bio/SearchIO.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/EventHandlerI.pm
Bio/SearchIO/exonerate.pm
Bio/SearchIO/fasta.pm
Bio/SearchIO/FastHitEventBuilder.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/IteratedSearchResultEventBuilder.pm
Bio/SearchIO/megablast.pm
Bio/SearchIO/psl.pm
Bio/SearchIO/rnamotif.pm
Bio/SearchIO/SearchResultEventBuilder.pm
Bio/SearchIO/SearchWriterI.pm
Bio/SearchIO/sim4.pm
Bio/SearchIO/waba.pm
Bio/SearchIO/wise.pm
Bio/SearchIO/Writer/GbrowseGFF.pm
Bio/SearchIO/Writer/HitTableWriter.pm
Bio/SearchIO/Writer/HSPTableWriter.pm
Bio/SearchIO/Writer/HTMLResultWriter.pm
Bio/SearchIO/Writer/ResultTableWriter.pm
Bio/SearchIO/Writer/TextResultWriter.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/SequenceTrace.pm
Bio/Seq/SeqWithQuality.pm
Bio/Seq/SimulatedRead.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/FeaturePair.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/Lite.pm
Bio/SeqFeature/PositionProxy.pm
Bio/SeqFeature/Primer.pm
Bio/SeqFeature/Similarity.pm
Bio/SeqFeature/SimilarityPair.pm
Bio/SeqFeature/SiRNA/Oligo.pm
Bio/SeqFeature/SiRNA/Pair.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/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/FTHelper.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/Handler/GenericRichSeqHandler.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/MultiFile.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/README.Symbol
Bio/Symbol/Symbol.pm
Bio/Symbol/SymbolI.pm
Bio/Taxon.pm
Bio/Taxonomy.pm
Bio/Taxonomy/FactoryI.pm
Bio/Taxonomy/Node.pm
Bio/Taxonomy/Taxon.pm
Bio/Taxonomy/Tree.pm
Bio/Tools/AlignFactory.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/dpAlign.pm
Bio/Tools/ECnumber.pm
Bio/Tools/EMBOSS/Palindrome.pm
Bio/Tools/EPCR.pm
Bio/Tools/Eponine.pm
Bio/Tools/ERPIN.pm
Bio/Tools/Est2Genome.pm
Bio/Tools/ESTScan.pm
Bio/Tools/Fgenesh.pm
Bio/Tools/FootPrinter.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/GFF.pm
Bio/Tools/Glimmer.pm
Bio/Tools/Grail.pm
Bio/Tools/GuessSeqFormat.pm
Bio/Tools/HMMER/Domain.pm
Bio/Tools/HMMER/Results.pm
Bio/Tools/HMMER/Set.pm
Bio/Tools/Hmmpfam.pm
Bio/Tools/Infernal.pm
Bio/Tools/ipcress.pm
Bio/Tools/isPcr.pm
Bio/Tools/IUPAC.pm
Bio/Tools/Lucy.pm
Bio/Tools/Match.pm
Bio/Tools/MZEF.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/Codeml.pm
Bio/Tools/Phylo/PAML/ModelResult.pm
Bio/Tools/Phylo/PAML/Result.pm
Bio/Tools/Phylo/Phylip/ProtDist.pm
Bio/Tools/pICalculator.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/PrositeScan.pm
Bio/Tools/Protparam.pm
Bio/Tools/Pseudowise.pm
Bio/Tools/pSW.pm
Bio/Tools/QRNA.pm
Bio/Tools/RandomDistFunctions.pm
Bio/Tools/RepeatMasker.pm
Bio/Tools/RNAMotif.pm
Bio/Tools/Run/GenericParameters.pm
Bio/Tools/Run/ParametersI.pm
Bio/Tools/Run/README
Bio/Tools/Run/RemoteBlast.pm
Bio/Tools/Seg.pm
Bio/Tools/SeqPattern.pm
Bio/Tools/SeqPattern/Backtranslate.pm
Bio/Tools/SeqStats.pm
Bio/Tools/SeqWords.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/SiRNA.pm
Bio/Tools/SiRNA/Ruleset/saigo.pm
Bio/Tools/SiRNA/Ruleset/tuschl.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/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/cluster.pm
Bio/TreeIO/lintree.pm
Bio/TreeIO/newick.pm
Bio/TreeIO/NewickParser.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/TreeIO/TreeEventBuilder.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/SeqDiff.pm
Bio/Variation/SNP.pm
Bio/Variation/VariantI.pm
Bio/WebAgent.pm
BioPerl.pm
BUGS
Build.PL
Changes
deobfuscator/Deobfuscator/bin/deob_index.pl
deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl
deobfuscator/Deobfuscator/Build.PL
deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png
deobfuscator/Deobfuscator/cgi-bin/deob_help.html
deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
deobfuscator/Deobfuscator/Changes
deobfuscator/Deobfuscator/excluded_modules.txt
deobfuscator/Deobfuscator/lib/Deobfuscator.pm
deobfuscator/Deobfuscator/LICENSE
deobfuscator/Deobfuscator/Makefile.PL
deobfuscator/Deobfuscator/MANIFEST
deobfuscator/Deobfuscator/META.yml
deobfuscator/Deobfuscator/README
deobfuscator/Deobfuscator/t/00.load.t
deobfuscator/Deobfuscator/t/pod.t
deobfuscator/makedoc.PL
DEPENDENCIES
DEPRECATED
examples/align/align_on_codons.pl
examples/align/aligntutorial.pl
examples/align/clustalw.pl
examples/align/FastAlign.pl
examples/align/simplealign.pl
examples/Bio-DB-GFF/load_ucsc.pl
examples/bioperl.pl
examples/cluster/dbsnp.pl
examples/contributed/nmrpdb_parse.pl
examples/contributed/prosite2perl.pl
examples/contributed/rebase2list.pl
examples/db/dbfetch
examples/db/est_tissue_query.pl
examples/db/gb2features.pl
examples/db/get_seqs.pl
examples/db/getGenBank.pl
examples/db/rfetch.pl
examples/db/use_registry.pl
examples/generate_random_seq.pl
examples/liveseq/change_gene.pl
examples/longorf.pl
examples/make_primers.pl
examples/popgen/parse_calc_stats.pl
examples/quality/svgtrace.pl
examples/rev_and_trans.pl
examples/revcom_dir.pl
examples/root/exceptions1.pl
examples/root/exceptions2.pl
examples/root/exceptions3.pl
examples/root/exceptions4.pl
examples/root/README
examples/searchio/blast_example.pl
examples/searchio/custom_writer.pl
examples/searchio/hitwriter.pl
examples/searchio/hspwriter.pl
examples/searchio/htmlwriter.pl
examples/searchio/psiblast_features.pl
examples/searchio/psiblast_iterations.pl
examples/searchio/rawwriter.pl
examples/searchio/resultwriter.pl
examples/searchio/waba2gff.pl
examples/searchio/waba2gff3.pl
examples/sirna/rnai_finder.cgi
examples/sirna/TAG
examples/structure/structure-io.pl
examples/subsequence.cgi
examples/tk/gsequence.pl
examples/tk/hitdisplay.pl
examples/tools/extract_genes.pl
examples/tools/gb_to_gff.pl
examples/tools/gff2ps.pl
examples/tools/parse_codeml.pl
examples/tools/psw.pl
examples/tools/reverse-translate.pl
examples/tools/run_genscan.pl
examples/tools/run_primer3.pl
examples/tools/seq_pattern.pl
examples/tools/standaloneblast.pl
examples/tree/paup2phylip.pl
ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
ide/bioperl-mode/dist/bioperl-mode.tar
ide/bioperl-mode/dist/bioperl-mode.tar.md5
ide/bioperl-mode/dist/Changes
ide/bioperl-mode/dist/package-me
ide/bioperl-mode/dist/SKIP
ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
ide/bioperl-mode/etc/images/bpmode-tool.xpm
ide/bioperl-mode/README
ide/bioperl-mode/site-lisp/bioperl-init.el
ide/bioperl-mode/site-lisp/bioperl-mode.el
ide/bioperl-mode/site-lisp/bioperl-skel.el
ide/bioperl-mode/site-lisp/pod.el
ide/bioperl.komodo
INSTALL
INSTALL.SKIP
INSTALL.WIN
LICENSE
maintenance/authors.pl
maintenance/big_split/file_classification.csv
maintenance/big_split/rbuels_notes.txt
maintenance/check_NAME.pl
maintenance/check_URLs.pl
maintenance/cvs2cl_by_file.pl
maintenance/dependencies.pl
maintenance/deprecated.pl
maintenance/find_mod_deps.pl
maintenance/module_usage.pl
maintenance/modules.pl
maintenance/ncbi_blast_switches.pl
maintenance/perltidy.conf
maintenance/pod.pl
maintenance/README
maintenance/symlink_script.pl
maintenance/version.pl
MANIFEST                        This list of files
models/biblio.dia
models/bio_liveseq_variation.dia
models/bio_map.dia
models/bio_restriction.dia
models/bioperl.dia
models/coordinatemapper.dia
models/map_proposal.txt
models/maps_and_markers.dia
models/popgen.dia
models/population_proposal.txt
models/README
README.md
scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
scripts/Bio-DB-GFF/bp_fast_load_gff.pl
scripts/Bio-DB-GFF/bp_genbank2gff.pl
scripts/Bio-DB-GFF/bp_genbank2gff3.pl
scripts/Bio-DB-GFF/bp_generate_histogram.pl
scripts/Bio-DB-GFF/bp_load_gff.pl
scripts/Bio-DB-GFF/bp_meta_gff.pl
scripts/Bio-DB-GFF/bp_process_gadfly.pl
scripts/Bio-DB-GFF/bp_process_sgd.pl
scripts/Bio-DB-GFF/bp_process_wormbase.pl
scripts/Bio-DB-GFF/README
scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
scripts/das/bp_das_server.pl
scripts/das/README
scripts/das/TAG
scripts/DB-HIV/bp_hivq.pl
scripts/DB/bp_biofetch_genbank_proxy.pl
scripts/DB/bp_bioflat_index.pl
scripts/DB/bp_biogetseq.pl
scripts/DB/bp_flanks.pl
scripts/DB/TAG
scripts/index/bp_fetch.pl
scripts/index/bp_index.pl
scripts/index/bp_seqret.pl
scripts/index/TAG
scripts/popgen/bp_composite_LD.pl
scripts/popgen/bp_heterogeneity_test.pl
scripts/README
scripts/searchio/bp_fastam9_to_table.pl
scripts/searchio/bp_filter_search.pl
scripts/searchio/bp_hmmer_to_table.pl
scripts/searchio/bp_parse_hmmsearch.pl
scripts/searchio/bp_search2table.pl
scripts/searchio/README
scripts/searchio/TAG
scripts/seq/bp_extract_feature_seq.pl
scripts/seq/bp_make_mrna_protein.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/seq/TAG
scripts/seqstats/bp_aacomp.pl
scripts/seqstats/bp_chaos_plot.pl
scripts/seqstats/bp_gccalc.pl
scripts/seqstats/bp_oligo_count.pl
scripts/seqstats/TAG
scripts/taxa/bp_classify_hits_kingdom.pl
scripts/taxa/bp_local_taxonomydb_query.pl
scripts/taxa/bp_query_entrez_taxa.pl
scripts/taxa/bp_taxid4species.pl
scripts/taxa/bp_taxonomy2tree.pl
scripts/taxa/TAG
scripts/tree/bp_blast2tree.pl
scripts/tree/bp_nexus2nh.pl
scripts/tree/bp_tree2pag.pl
scripts/tree/TAG
scripts/utilities/bp_dbsplit.pl
scripts/utilities/bp_download_query_genbank.pl
scripts/utilities/bp_find-blast-matches.pl
scripts/utilities/bp_mask_by_search.pl
scripts/utilities/bp_mrtrans.pl
scripts/utilities/bp_mutate.pl
scripts/utilities/bp_netinstall.pl
scripts/utilities/bp_nrdb.pl
scripts/utilities/bp_pairwise_kaks.pl
scripts/utilities/bp_remote_blast.pl
scripts/utilities/bp_revtrans-motif.pl
scripts/utilities/bp_search2alnblocks.pl
scripts/utilities/bp_search2gff.pl
scripts/utilities/bp_search2tribe.pl
scripts/utilities/bp_seq_length.pl
scripts/utilities/bp_sreformat.pl
scripts/utilities/README
scripts/utilities/TAG
t/Align/AlignStats.t
t/Align/AlignUtil.t
t/Align/Graphics.t
t/Align/SimpleAlign.t
t/Align/TreeBuild.t
t/Align/Utilities.t
t/AlignIO/AlignIO.t
t/AlignIO/arp.t
t/AlignIO/bl2seq.t
t/AlignIO/clustalw.t
t/AlignIO/emboss.t
t/AlignIO/fasta.t
t/AlignIO/largemultifasta.t
t/AlignIO/maf.t
t/AlignIO/mase.t
t/AlignIO/mega.t
t/AlignIO/meme.t
t/AlignIO/metafasta.t
t/AlignIO/msf.t
t/AlignIO/nexml.t
t/AlignIO/nexus.t
t/AlignIO/pfam.t
t/AlignIO/phylip.t
t/AlignIO/po.t
t/AlignIO/prodom.t
t/AlignIO/psi.t
t/AlignIO/selex.t
t/AlignIO/stockholm.t
t/AlignIO/xmfa.t
t/Alphabet.t
t/Annotation/Annotation.t
t/Annotation/AnnotationAdaptor.t
t/Assembly/ContigSpectrum.t
t/Assembly/core.t
t/Assembly/IO/bowtie.t
t/Assembly/IO/sam.t
t/Cluster/UniGene.t
t/ClusterIO/ClusterIO.t
t/ClusterIO/SequenceFamily.t
t/ClusterIO/unigene.t
t/data/01_basic.xml
t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
t/data/02_dogfish_no_taxrefs.xml
t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml
t/data/02_mackerel_no_taxrefs.xml
t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml
t/data/03_bootstraps.xml
t/data/03_bootstraps_in_tag.xml
t/data/04_labeled_ancestors.xml
t/data/05_ancestral_states.xml
t/data/13-pilE-F.scf
t/data/1A11.pdb
t/data/1A3I.pdb
t/data/1BPT.pdb
t/data/1ZZ19XR301R-Alignment.tblastn
t/data/2008.blasttable
t/data/27-contig_Newbler.ace
t/data/503384.MEGABLAST.0
t/data/503384.MEGABLAST.2
t/data/5X_1895.FASTXY
t/data/8HVP.pdb
t/data/a_thaliana.blastn
t/data/AAC12660.fa
t/data/aaml.mlc
t/data/aaml_pairwise.mlc
t/data/AB077698.gb
t/data/acefile.ace.1
t/data/acefile.singlets
t/data/adh.mb_tree.nexus
t/data/AE003528_ecoli.bls
t/data/AE003644_Adh-genomic.gb
t/data/AF032047.gbk
t/data/AF165282.gb
t/data/AF222649-rc.gbk
t/data/AF305198.gb
t/data/AHCYL1.kegg
t/data/alleles.fas
t/data/alnfile.fasta
t/data/amino.fa
t/data/amphora.newick
t/data/AnnIX-v003.gbk
t/data/ar.embl
t/data/assembly_with_singlets.ace
t/data/ATF14F8.gbk
t/data/atp1.matrix
t/data/ay007676.gb
t/data/AY095303S1.gbk
t/data/ay116458.gb
t/data/ay149291.gb
t/data/AY763288.gb
t/data/BAB68554.gb
t/data/bad_dbfa/bug3172.fa
t/data/bad_dbfa/shotdb.fa
t/data/badfasta.fa
t/data/barns-combined.nex
t/data/baseml.pairwise
t/data/baseml.usertree
t/data/basic-bush.nex
t/data/basic-ladder.nex
t/data/BC000007.gbk
t/data/BEL16-LTR_AG.embl
t/data/biodbgff/test.gff
t/data/biodbgff/test.gff3
t/data/biofpc.cor
t/data/biofpc.fpc
t/data/biorecipe.nhx
t/data/Bird_Ovomucoids.nex
t/data/BK000016-tpa.gbk
t/data/bl2seq+.blastn
t/data/bl2seq.blastn
t/data/bl2seq.blastn.rev
t/data/bl2seq.blastx.out
t/data/bl2seq.bug940.out
t/data/bl2seq.out
t/data/bl2seq.tblastn.out
t/data/bl2seq.tblastx.out
t/data/blast.report
t/data/blast_no_hit_desc.txt
t/data/blast_plus.blastp
t/data/blastp2215.blast
t/data/blat.psLayout3
t/data/BLOSUM50
t/data/blosum62.bla
t/data/BN000066-tpa.embl
t/data/bootstrap.tre
t/data/BOSS_DROME.FASTP_v35_04
t/data/branchSite.mlc
t/data/brassica_ATH.WUBLASTN
t/data/bug1986.blast2
t/data/bug1986.blastp
t/data/bug2120.phd
t/data/bug2246.blast
t/data/bug2391.megablast
t/data/bug2399.tblastn
t/data/bug2453.maf
t/data/bug2473.fasta
t/data/bug2862.pmr
t/data/bug2869.tree
t/data/bug2901.fa
t/data/bug2937.fasta
t/data/bug2942.blastx
t/data/bug2982.embl
t/data/bug2982.gb
t/data/bug3021.gmap
t/data/bug3086.embl
t/data/bug3331.mlc
t/data/c200-vs-yeast.BLASTN
t/data/c200-vs-yeast.BLASTN.m8
t/data/calm.swiss
t/data/catalase-webblast.BLASTP
t/data/cds-266.fas
t/data/cds_sample.embl
t/data/CG11099.fasaln
t/data/CG2865.fasaln
t/data/chad100.scf
t/data/char-interleave.nex
t/data/char-matrix-spaces.nex
t/data/characters+trees.nexml.xml
t/data/characters.nexml.old.xml
t/data/cmsearch.multi.out
t/data/cmsearch.nohit.out
t/data/cmsearch_output.txt
t/data/codeml.mlc
t/data/codeml315.mlc
t/data/codeml4.mlc
t/data/codeml43.mlc
t/data/codeml43_nssites.mlc
t/data/codeml45.mlc
t/data/codeml45b.mlc
t/data/codeml_lysozyme/2NG.dN
t/data/codeml_lysozyme/2NG.dS
t/data/codeml_lysozyme/2NG.tt
t/data/codeml_lysozyme/4fold.nuc
t/data/codeml_lysozyme/lnf
t/data/codeml_lysozyme/lysozymeSmall.ctl
t/data/codeml_lysozyme/lysozymeSmall.trees
t/data/codeml_lysozyme/lysozymeSmall.txt
t/data/codeml_lysozyme/mlc
t/data/codeml_lysozyme/rst
t/data/codeml_lysozyme/rst1
t/data/codeml_lysozyme/rub
t/data/codeml_nan.mlc
t/data/codeml_nssites.mlc
t/data/compLD_missingtest.prettybase
t/data/compLD_test.prettybase
t/data/component.ontology.test
t/data/component.ontology.test2
t/data/consed_project/edit_dir/test_project.contigs
t/data/consed_project/edit_dir/test_project.fasta
t/data/consed_project/edit_dir/test_project.fasta.log
t/data/consed_project/edit_dir/test_project.fasta.screen
t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual
t/data/consed_project/edit_dir/test_project.fasta.screen.log
t/data/consed_project/edit_dir/test_project.fasta.screen.problems
t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
t/data/consed_project/edit_dir/test_project.fasta.screen.qual
t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
t/data/consed_project/edit_dir/test_project.fasta.screen.view
t/data/consed_project/edit_dir/test_project.newtags
t/data/consed_project/edit_dir/test_project.phrap.out
t/data/consed_project/edit_dir/test_project.screen.out
t/data/consed_project/edit_dir/test_project_to_alu.cross
t/data/consed_project/edit_dir/test_projectNewChromats.fof
t/data/consed_project/phd_dir/ML4922R.phd.1
t/data/consed_project/phd_dir/ML4924F.phd.1
t/data/consed_project/phd_dir/ML4924R.phd.1
t/data/consed_project/phd_dir/ML4947F.phd.1
t/data/contig-by-hand.wublastp
t/data/contigspectrumtest.tigr
t/data/crab.dat.cn
t/data/crab.nj
t/data/crab.njb
t/data/crypto.sim4-0
t/data/crypto.sim4-3
t/data/crypto.sim4-4
t/data/ctgdemo.fpc
t/data/cys1_dicdi.water
t/data/cysprot.fa
t/data/cysprot.msf
t/data/cysprot.needle
t/data/cysprot.tblastn
t/data/cysprot.water
t/data/cysprot1.fa
t/data/cysprot1.FASTA
t/data/cysprot1a.fa
t/data/cysprot1a.msf
t/data/cysprot1b.fa
t/data/cysprot1b.hmmsearch
t/data/cysprot1b.msf
t/data/cysprot1b.newick
t/data/cysprot_vs_gadfly.FASTA
t/data/D10483.gbk
t/data/D12555.gbk
t/data/dbfa/1.fa
t/data/dbfa/2.fa
t/data/dbfa/3.fa
t/data/dbfa/4.fa
t/data/dbfa/5.fa
t/data/dbfa/6.fa
t/data/dbfa/7.fa
t/data/dbfa/mixed_alphabet.fasta
t/data/dbqual/1.qual
t/data/dbqual/2.qual
t/data/dbqual/3.qual
t/data/dcr1_sp.WUBLASTP
t/data/dmel_2Lchunk.gb
t/data/dna1.fa
t/data/dna2.fa
t/data/dnaE-bsub-prot.fa
t/data/dnaE-bsub.fa
t/data/dnaEbsub_ecoli.wublastx
t/data/dnaEbsub_ecoli.wutblastn
t/data/dnaEbsub_ecoli.wutblastx
t/data/DQ018368.gb
t/data/dq519393.gb
t/data/ECAPAH02.embl
t/data/echofilter.wublastn
t/data/ecoli-trna-qrna.out
t/data/ecoli_domains.rpsblast
t/data/ecolitst.bls
t/data/ecolitst.fa
t/data/ecolitst.noseqs.wublastp
t/data/ecolitst.wublastp
t/data/EG352462.gbxml
t/data/empty.bl2seq
t/data/ENr111.mfa.example.elems
t/data/entrezgene.dat
t/data/entrezgene_bug3453.dat
t/data/ex1.nucl.nhx
t/data/example.hap
t/data/example.phase
t/data/example.vcf
t/data/exonerate.output.dontwork
t/data/exonerate.output.negativescore.works
t/data/exonerate.output.works
t/data/exonerate.whitespace_before_query.works
t/data/expected.blast.out
t/data/exsignalp.out
t/data/factor7.embl
t/data/Fang_2003.xml
t/data/fastq/bug2335.fastq
t/data/fastq/error_diff_ids.fastq
t/data/fastq/error_double_qual.fastq
t/data/fastq/error_double_seq.fastq
t/data/fastq/error_long_qual.fastq
t/data/fastq/error_no_qual.fastq
t/data/fastq/error_qual_del.fastq
t/data/fastq/error_qual_escape.fastq
t/data/fastq/error_qual_null.fastq
t/data/fastq/error_qual_space.fastq
t/data/fastq/error_qual_tab.fastq
t/data/fastq/error_qual_unit_sep.fastq
t/data/fastq/error_qual_vtab.fastq
t/data/fastq/error_short_qual.fastq
t/data/fastq/error_spaces.fastq
t/data/fastq/error_tabs.fastq
t/data/fastq/error_trunc_at_plus.fastq
t/data/fastq/error_trunc_at_qual.fastq
t/data/fastq/error_trunc_at_seq.fastq
t/data/fastq/error_trunc_in_plus.fastq
t/data/fastq/error_trunc_in_qual.fastq
t/data/fastq/error_trunc_in_seq.fastq
t/data/fastq/error_trunc_in_title.fastq
t/data/fastq/evil_wrapping.fastq
t/data/fastq/example.fasta
t/data/fastq/example.fastq
t/data/fastq/example.qual
t/data/fastq/illumina_faked.fastq
t/data/fastq/sanger_93.fastq
t/data/fastq/sanger_faked.fastq
t/data/fastq/solexa_example.fastq
t/data/fastq/solexa_faked.fastq
t/data/fastq/test1_sanger.fastq
t/data/fastq/test2_solexa.fastq
t/data/fastq/test3_illumina.fastq
t/data/fastq/tricky.fastq
t/data/fastq/wrapping_issues.fastq
t/data/fastq/zero_qual.fastq
t/data/fgenesh.out
t/data/footprinter.out
t/data/forward_primer.fa
t/data/forward_reverse_primers.fa
t/data/frac_problems.blast
t/data/frac_problems2.blast
t/data/frac_problems3.blast
t/data/geneid_1.0.out
t/data/genemark-fragment.out
t/data/genemark.out
t/data/genewise.out
t/data/genewise_output.paracel_btk
t/data/genomewise.out
t/data/genomic-seq.epcr
t/data/genomic-seq.fasta
t/data/genomic-seq.genscan
t/data/genomic-seq.mzef
t/data/Genscan.FastA
t/data/gf-s71.needle
t/data/Glimmer2.out
t/data/glimmer3-fragment.detail
t/data/glimmer3-fragment.predict
t/data/Glimmer3.detail
t/data/Glimmer3.predict
t/data/GlimmerHMM.out
t/data/GlimmerM.out
t/data/gmap_f9-multiple_results.txt
t/data/gmap_f9-reverse-strand.txt
t/data/gmap_f9.txt
t/data/GO.defs.test
t/data/GO.defs.test2
t/data/headerless.psl
t/data/hg16_chroms.gff
t/data/HM138502.gbk
t/data/hmmpfam.out
t/data/hmmpfam_cs.out
t/data/hmmpfam_fake.out
t/data/hmmpfam_HSPdashline.txt
t/data/hmmpfam_multiresult.out
t/data/hmmscan.out
t/data/hmmscan_multi_domain.out
t/data/hmmscan_qry_stop.txt
t/data/hmmscan_sec_struct.out
t/data/hmmsearch.out
t/data/hmmsearch3.out
t/data/hmmsearch3_multi.out
t/data/hs_est.est2genome
t/data/hs_fugu.newick
t/data/hs_owlmonkey.aln
t/data/hs_owlmonkey.fas
t/data/hs_owlmonkey.fasta
t/data/hsinsulin.blastcl3.blastn
t/data/HUMBETGLOA.fa
t/data/HUMBETGLOA.FASTA
t/data/HUMBETGLOA.gff
t/data/HUMBETGLOA.grail
t/data/HUMBETGLOA.grailexp
t/data/HUMBETGLOA.mzef
t/data/HUMBETGLOA.tblastx
t/data/humor.maf
t/data/humts1.pal
t/data/hybrid2.gff3
t/data/ids-with-spaces.phy
t/data/in.fasta
t/data/insulin.water
t/data/interpro.xml
t/data/interpro_ebi.xml
t/data/interpro_relationship.xml
t/data/interpro_sample.xml
t/data/interpro_short.xml
t/data/intrablock-comment.nex
t/data/KF527485.gbk
t/data/Kingdoms_DNA.nex
t/data/L77119.hmmer
t/data/little.largemultifasta
t/data/LittleChrY.dbsnp.xml
t/data/LOAD_Ccd1.dnd
t/data/long-names.nex
t/data/longnames.aln
t/data/longnames.dnd
t/data/lucy.info
t/data/lucy.qual
t/data/lucy.seq
t/data/lucy.stderr
t/data/lysozyme6.protml
t/data/lysozyme6.simple.protml
t/data/M0.mlc
t/data/M12730.gb
t/data/map_hem/HEM1-HEM12.fa
t/data/map_hem/HEM1-HEM12.fa.revcom
t/data/map_hem/HEM1-HEM12.meme.txt
t/data/map_hem/HEM1-HEM13.fa
t/data/map_hem/HEM1-HEM13.meme.txt
t/data/map_hem/HEM1-HEM14.fa
t/data/map_hem/HEM1-HEM14.meme.txt
t/data/map_hem/HEM1-HEM15.fa
t/data/map_hem/HEM1-HEM15.meme.txt
t/data/map_hem/HEM1-HEM2.fa
t/data/map_hem/HEM1-HEM2.fa.revcom
t/data/map_hem/HEM1-HEM2.meme.txt
t/data/map_hem/HEM1-HEM3.fa
t/data/map_hem/HEM1-HEM3.meme.txt
t/data/map_hem/HEM1-HEM4.fa
t/data/map_hem/HEM1-HEM4.meme.txt
t/data/map_hem/HEM1.ups.fa_
t/data/map_hem/HEM1.ups.fa_.revcom
t/data/map_hem/HEM12-HEM13.fa
t/data/map_hem/HEM12-HEM13.meme.txt
t/data/map_hem/HEM12-HEM14.fa
t/data/map_hem/HEM12-HEM14.meme.txt
t/data/map_hem/HEM12-HEM15.fa
t/data/map_hem/HEM12-HEM15.meme.txt
t/data/map_hem/HEM12.ups.fa_
t/data/map_hem/HEM12.ups.fa_.revcom
t/data/map_hem/HEM13-HEM14.fa
t/data/map_hem/HEM13-HEM14.meme.txt
t/data/map_hem/HEM13-HEM15.fa
t/data/map_hem/HEM13-HEM15.meme.txt
t/data/map_hem/HEM13.ups.fa_
t/data/map_hem/HEM13.ups.fa_.revcom
t/data/map_hem/HEM14-HEM15.fa
t/data/map_hem/HEM14-HEM15.meme.txt
t/data/map_hem/HEM14.ups.fa_
t/data/map_hem/HEM14.ups.fa_.revcom
t/data/map_hem/HEM15.ups.fa_
t/data/map_hem/HEM15.ups.fa_.revcom
t/data/map_hem/HEM2-HEM12.fa
t/data/map_hem/HEM2-HEM12.meme.txt
t/data/map_hem/HEM2-HEM13.fa
t/data/map_hem/HEM2-HEM13.meme.txt
t/data/map_hem/HEM2-HEM14.fa
t/data/map_hem/HEM2-HEM14.meme.txt
t/data/map_hem/HEM2-HEM15.fa
t/data/map_hem/HEM2-HEM15.meme.txt
t/data/map_hem/HEM2-HEM3.fa
t/data/map_hem/HEM2-HEM3.meme.txt
t/data/map_hem/HEM2-HEM4.fa
t/data/map_hem/HEM2-HEM4.meme.txt
t/data/map_hem/HEM2.ups.fa_
t/data/map_hem/HEM2.ups.fa_.revcom
t/data/map_hem/HEM3-HEM12.fa
t/data/map_hem/HEM3-HEM12.meme.txt
t/data/map_hem/HEM3-HEM13.fa
t/data/map_hem/HEM3-HEM13.meme.txt
t/data/map_hem/HEM3-HEM14.fa
t/data/map_hem/HEM3-HEM14.meme.txt
t/data/map_hem/HEM3-HEM15.fa
t/data/map_hem/HEM3-HEM15.meme.txt
t/data/map_hem/HEM3-HEM4.fa
t/data/map_hem/HEM3-HEM4.meme.txt
t/data/map_hem/HEM3.ups.fa_
t/data/map_hem/HEM3.ups.fa_.revcom
t/data/map_hem/HEM4-HEM12.fa
t/data/map_hem/HEM4-HEM12.meme.txt
t/data/map_hem/HEM4-HEM13.fa
t/data/map_hem/HEM4-HEM13.meme.txt
t/data/map_hem/HEM4-HEM14.fa
t/data/map_hem/HEM4-HEM14.meme.txt
t/data/map_hem/HEM4-HEM15.fa
t/data/map_hem/HEM4-HEM15.meme.txt
t/data/map_hem/HEM4.ups.fa_
t/data/map_hem/HEM4.ups.fa_.revcom
t/data/map_hem/yeast.nc.1.freq
t/data/mapmaker.out
t/data/mapmaker.txt
t/data/mast.dat
t/data/masta.dat
t/data/match.output
t/data/mbsout/mbsout_infile1
t/data/mbsout/mbsout_infile2
t/data/mbsout/mbsout_infile3
t/data/Mcjanrna_rdbII.gbk
t/data/megablast_output.paracel_btk
t/data/meme.dat
t/data/mini-AE001405.gb
t/data/mini-align.aln
t/data/mixedmast.dat
t/data/MmCT
t/data/mpath.ontology.test
t/data/MSGEFTUA.gb
t/data/msout/bad_msout_infile1
t/data/msout/bad_msout_infile2
t/data/msout/msout_infile1
t/data/msout/msout_infile2
t/data/msout/msout_infile3
t/data/msout/msout_infile4
t/data/multi.blast.m8
t/data/multi.blast.m9
t/data/multi.phd
t/data/multi_1.fa
t/data/multi_2.fa
t/data/multi_blast.bls
t/data/multifa.seq
t/data/multifa.seq.qual
t/data/multiline-intrablock-comment.nex
t/data/multiresult_blastn+.bls
t/data/multiseq.bls
t/data/multiseq_tags.phd
t/data/mutations.dat
t/data/mutations.old.dat
t/data/mutations.old.xml
t/data/mutations.xml
t/data/myco_sites.gff
t/data/NC_000007-ribosomal-slippage.gb
t/data/NC_001284.gbk
t/data/NC_002058_multDBLINK_bug3375.gb
t/data/NC_006346.gb
t/data/NC_006511-short.gbk
t/data/NC_008536.gb
t/data/nei_gojobori_test.aln
t/data/neighbor.dist
t/data/new_blastn.txt
t/data/nexml/characters.nexml.8.xml
t/data/nexml/characters.nexml.xml
t/data/nexml/trees.nexml.8.xml
t/data/nexml/trees.nexml.xml
t/data/nhmmer-3.1.out
t/data/nhx-bacteria.nhx
t/data/NM_002254.gb
t/data/no-genes.genscan
t/data/no_cds_example.gb
t/data/no_FH.embl
t/data/no_hsps.blastp
t/data/no_semicolon.newick
t/data/noninterleaved.phy
t/data/NT_021877.gbk
t/data/nucmatrix.txt
t/data/O_sat.wgs
t/data/omim_genemap_test
t/data/omim_genemap_test_nolinebreak
t/data/omim_text_test
t/data/ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt
t/data/P33897
t/data/P35527.gb
t/data/P39765.gb
t/data/PAM250
t/data/pep-266.aln
t/data/pfam_tests.stk
t/data/pfamOutput-bug3376.out
t/data/phi.out
t/data/phipsi.out
t/data/phmmer.out
t/data/phylipdist-36.out
t/data/phylipdist.out
t/data/phyloxml_examples.xml
t/data/pictogram.fa
t/data/polymorphism.dat
t/data/polymorphism.old.xml
t/data/polymorphism.xml
t/data/popgen_saureus.dat
t/data/popgen_saureus.multidat
t/data/popstats.prettybase
t/data/pre_rel9.swiss
t/data/Primate_mtDNA.nex
t/data/primedseq.fa
t/data/primer3_infile.txt
t/data/primer3_outfile.txt
t/data/primer3_output.txt
t/data/prints.out
t/data/promoterwise.out
t/data/protpars.phy
t/data/protpars_longid.phy
t/data/pseudowise.out
t/data/psi_xml.dat
t/data/psiblastreport.out
t/data/purine_v081.infernal
t/data/puzzle.tre
t/data/PX1CG.gb
t/data/Q8GBD3.swiss
t/data/qrna-relloc.out
t/data/qualfile.qual
t/data/quoted-strings1.nex
t/data/quoted-strings2.nex
t/data/Rab1.chaos-xml
t/data/radical-whitespace.nex
t/data/radical-whitespace_02.nex
t/data/rebase.itype2
t/data/rebase.withrefm
t/data/reference_ace.ace
t/data/registry/bdb/seqdatabase.ini
t/data/registry/flat/seqdatabase.ini
t/data/regulation_test.obo
t/data/rel9.swiss
t/data/repeatmasker.fa.out
t/data/revcomp_mrna.gb
t/data/rfam_tests.stk
t/data/ribosome-slippage.gb
t/data/roa1.dat
t/data/roa1.gbxml
t/data/roa1.genbank
t/data/roa1.swiss
t/data/roa1_v2.dat
t/data/rpsblast.bls
t/data/rpsblast_no_hits.bls
t/data/sample_dataset.tigr
t/data/sbay_c127.fas
t/data/sbay_c545-yeast.BLASTZ.PSL
t/data/seg.out
t/data/semicolon.newick
t/data/seqdatabase.ini
t/data/seqfeaturedb/test.gff3
t/data/seqfile.pir
t/data/seqs.fas
t/data/sequencefamily.dat
t/data/seqxml.xml
t/data/short.blx
t/data/signalp.hmm.short
t/data/signalp.hmm.summary
t/data/signalp.negative.out
t/data/signalp.nn.short
t/data/signalp.nn.summary
t/data/signalp.positive.out
t/data/signalp.short
t/data/signalp.summary
t/data/sim4.for.for
t/data/sim4.for.rev
t/data/sim4.rev
t/data/singleNSsite.mlc
t/data/singlescore.gbk
t/data/singlet_w_CT.ace
t/data/so.obo
t/data/sofa.ontology
t/data/sp_subset.obo
t/data/spaced_fasta.fa
t/data/spaces.nex
t/data/SPAN_Family4nl.nex
t/data/SPAN_Family7n.nex
t/data/SPAN_Family8a.nex
t/data/sparsealn.needle
t/data/spidey.noalignment
t/data/spidey.test1
t/data/sprintf.rnamotif
t/data/ssp160.embl.1
t/data/sv40_small.xml
t/data/swiss.dat
t/data/swisspfam.data
t/data/SwissProt.dat
t/data/T7.aln
t/data/tab1part.mif
t/data/tab2part.mif
t/data/tab3part.mif
t/data/tandem_repeats_finder.dat
t/data/tandem_repeats_finder.noresults
t/data/tandem_repeats_finder_no_desc.dat
t/data/targetp.out
t/data/taxdump/names.dmp
t/data/taxdump/nodes.dmp
t/data/taxonomy/greengenes_taxonomy_16S_candiv_gg_2011_1.txt
t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta
t/data/tblastn.out
't/data/test 2.txt'
t/data/test-1.tab
t/data/test-1.tab.gb
t/data/test-3.0-1.meme
t/data/test-3.0-2.meme
t/data/test-4.9.meme
t/data/test.abi
t/data/test.ace
t/data/test.bam
t/data/test.bowtie
t/data/test.cns.fastq
t/data/test.ctf
t/data/test.embl
t/data/test.embl2sq
t/data/test.exp
t/data/test.fasta
t/data/test.fastq
t/data/test.game
t/data/test.gcg
t/data/test.gcgblast
t/data/test.gcgfasta
t/data/test.genbank
t/data/test.genbank.noseq
t/data/test.infernal
t/data/test.interpro
t/data/test.interpro-go.xml
t/data/test.lasergene
t/data/test.locuslink
t/data/test.maq
t/data/test.metafasta
t/data/test.nh
t/data/test.nhx
t/data/test.phd
t/data/test.pir
t/data/test.pln
t/data/test.raw
t/data/test.ref.fas
t/data/test.swiss
t/data/test.tab
t/data/test.tigrxml
t/data/test.tseq
t/data/test.tsv
t/data/test.txt
t/data/test.waba
t/data/test.xls
t/data/test.ztr
t/data/test1.blasttab3
t/data/test1.wublastp
t/data/test2.infernal
t/data/test2.raw
t/data/test_badlf.gcg
t/data/test_clear_range.fastq
t/data/test_data.axt
t/data/test_singlets.cns.fastq
t/data/test_singlets.maq
t/data/test_space.embl
t/data/testaln.arp
t/data/testaln.clustalw
t/data/testaln.fasta
t/data/testaln.fastq
t/data/testaln.list
t/data/testaln.mase
t/data/testaln.mega
t/data/testaln.metafasta
t/data/testaln.msf
t/data/testaln.nexus
t/data/testaln.pfam
t/data/testaln.phylip
t/data/testaln.po
t/data/testaln.prodom
t/data/testaln.psi
t/data/testaln.selex
t/data/testaln.stockholm
t/data/testaln.xmfa
t/data/testaln2.arp
t/data/testaln2.fasta
t/data/testdat.exonerate
t/data/testdata.crossmatch
t/data/testdbaccnums.out
t/data/testfile.erpin
t/data/testfuzzy.genbank
t/data/tiny.stk
t/data/tmhmm.out
t/data/tmp.fst
t/data/tol-2010-02-18.nhx
t/data/traits.tab
t/data/traittree.nexus
t/data/transfac.dat
t/data/transfac_pro/factor.dat
t/data/transfac_pro/fragment.dat
t/data/transfac_pro/gene.dat
t/data/transfac_pro/matrix.dat
t/data/transfac_pro/readme.txt
t/data/transfac_pro/reference.dat
t/data/transfac_pro/site.dat
t/data/tree_nonewline.nexus
t/data/Treebase-chlamy-dna.nex
t/data/trees.nexml.old.xml
t/data/tricky.wublast
t/data/trna.strict.rnamotif
t/data/U58726.gb
t/data/U71225.gb
t/data/U71225.gb.mac
t/data/U71225.gb.unix
t/data/U71225.gb.win
t/data/U83300.bsml
t/data/UnaSmithHIV-both.nex
t/data/unigene.data
t/data/urease.tre.nexus
t/data/version2.scf
t/data/version3.scf
t/data/wellcome_tol.nhx
t/data/withrefm.906
t/data/worm_fam_2785.cdna
t/data/X98338_Adh-mRNA.gb
t/data/yeast.tRNAscanSE
t/data/yn00.mlc
t/data/yn00_45.mlc
t/data/YP_007988852.gp
t/data/ZABJ4EA7014.CH878695.1.blast.txt
t/Draw/Pictogram.t
t/lib/Error.pm
t/LiveSeq/Chain.t
t/LiveSeq/LiveSeq.t
t/LiveSeq/Mutation.t
t/LiveSeq/Mutator.t
t/LocalDB/BioDBGFF.t
t/LocalDB/Fasta.t
t/LocalDB/Flat.t
t/LocalDB/Index/Blast.t
t/LocalDB/Index/BlastTable.t
t/LocalDB/Index/Index.t
t/LocalDB/Qual.t
t/LocalDB/Registry.t
t/LocalDB/SeqFeature.t
t/LocalDB/Taxonomy/greengenes.t
t/LocalDB/Taxonomy/silva.t
t/LocalDB/Taxonomy/sqlite.t
t/LocalDB/transfac_pro.t
t/Map/Cyto.t
t/Map/Linkage.t
t/Map/Map.t
t/Map/MapIO.t
t/Map/MicrosatelliteMarker.t
t/Map/Physical.t
t/Matrix/InstanceSite.t
t/Matrix/IO/masta.t
t/Matrix/IO/psm.t
t/Matrix/Matrix.t
t/Matrix/ProtMatrix.t
t/Matrix/ProtPsm.t
t/Matrix/SiteMatrix.t
t/nexml.t
t/Ontology/GOterm.t
t/Ontology/GraphAdaptor.t
t/Ontology/IO/go.t
t/Ontology/IO/interpro.t
t/Ontology/IO/obo.t
t/Ontology/Ontology.t
t/Ontology/OntologyEngine.t
t/Ontology/OntologyStore.t
t/Ontology/Relationship.t
t/Ontology/RelationshipType.t
t/Ontology/Term.t
t/Perl.t
t/Phenotype/Correlate.t
t/Phenotype/Measure.t
t/Phenotype/MeSH.t
t/Phenotype/MiniMIMentry.t
t/Phenotype/OMIMentry.t
t/Phenotype/OMIMentryAllelicVariant.t
t/Phenotype/OMIMparser.t
t/Phenotype/Phenotype.t
t/PodSyntax.t
t/PopGen/Coalescent.t
t/PopGen/HtSNP.t
t/PopGen/MK.t
t/PopGen/PopGen.t
t/PopGen/PopGenSims.t
t/PopGen/TagHaplotype.t
t/RemoteDB/BioFetch.t
t/RemoteDB/CUTG.t
t/RemoteDB/EMBL.t
t/RemoteDB/EntrezGene.t
t/RemoteDB/GenBank.t
t/RemoteDB/GenPept.t
t/RemoteDB/HIV/HIV.t
t/RemoteDB/HIV/HIVAnnotProcessor.t
t/RemoteDB/HIV/HIVQuery.t
t/RemoteDB/HIV/HIVQueryHelper.t
t/RemoteDB/MeSH.t
t/RemoteDB/Query/GenBank.t
t/RemoteDB/RefSeq.t
t/RemoteDB/SeqHound.t
t/RemoteDB/SeqRead_fail.t
t/RemoteDB/SeqVersion.t
t/RemoteDB/SwissProt.t
t/RemoteDB/Taxonomy.t
t/Restriction/Analysis-refac.t
t/Restriction/Analysis.t
t/Restriction/Gel.t
t/Restriction/IO.t
t/Root/Exception.t
t/Root/HTTPget.t
t/Root/IO.t
t/Root/RootI.t
t/Root/RootIO.t
t/Root/Storable.t
t/Root/Utilities.t
t/SearchDist.t
t/SearchIO/axt.t
t/SearchIO/blast.t
t/SearchIO/blast_pull.t
t/SearchIO/blasttable.t
t/SearchIO/CigarString.t
t/SearchIO/cross_match.t
t/SearchIO/erpin.t
t/SearchIO/exonerate.t
t/SearchIO/fasta.t
t/SearchIO/gmap_f9.t
t/SearchIO/hmmer.t
t/SearchIO/hmmer_pull.t
t/SearchIO/infernal.t
t/SearchIO/megablast.t
t/SearchIO/psl.t
t/SearchIO/rnamotif.t
t/SearchIO/SearchIO.t
t/SearchIO/sim4.t
t/SearchIO/SimilarityPair.t
t/SearchIO/Tiling.t
t/SearchIO/waba.t
t/SearchIO/wise.t
t/SearchIO/Writer/GbrowseGFF.t
t/SearchIO/Writer/HitTableWriter.t
t/SearchIO/Writer/HSPTableWriter.t
t/SearchIO/Writer/HTMLWriter.t
t/SearchIO/Writer/TextWriter.t
t/Seq/DBLink.t
t/Seq/EncodedSeq.t
t/Seq/LargeLocatableSeq.t
t/Seq/LargePSeq.t
t/Seq/LocatableSeq.t
t/Seq/MetaSeq.t
t/Seq/PrimaryQual.t
t/Seq/PrimarySeq.t
t/Seq/PrimedSeq.t
t/Seq/Quality.t
t/Seq/Seq.t
t/Seq/SimulatedRead.t
t/Seq/WithQuality.t
t/SeqEvolution.t
t/SeqFeature/Amplicon.t
t/SeqFeature/Clone.t
t/SeqFeature/Collection.t
t/SeqFeature/Computation.t
t/SeqFeature/FeaturePair.t
t/SeqFeature/Gene.t
t/SeqFeature/Generic.t
t/SeqFeature/Location.t
t/SeqFeature/LocationFactory.t
t/SeqFeature/Primer.t
t/SeqFeature/Range.t
t/SeqFeature/RangeI.t
t/SeqFeature/SeqAnalysisParser.t
t/SeqFeature/SubSeq.t
t/SeqFeature/Unflattener.t
t/SeqIO/abi.t
t/SeqIO/ace.t
t/SeqIO/agave.t
t/SeqIO/alf.t
t/SeqIO/asciitree.t
t/SeqIO/bsml.t
t/SeqIO/bsml_sax.t
t/SeqIO/chadoxml.t
t/SeqIO/chaos.t
t/SeqIO/chaosxml.t
t/SeqIO/ctf.t
t/SeqIO/embl.t
t/SeqIO/entrezgene.t
t/SeqIO/excel.t
t/SeqIO/exp.t
t/SeqIO/fasta.t
t/SeqIO/fastq.t
t/SeqIO/flybase_chadoxml.t
t/SeqIO/game.t
t/SeqIO/gbxml.t
t/SeqIO/gcg.t
t/SeqIO/genbank.t
t/SeqIO/Handler.t
t/SeqIO/interpro.t
t/SeqIO/kegg.t
t/SeqIO/largefasta.t
t/SeqIO/lasergene.t
t/SeqIO/locuslink.t
t/SeqIO/mbsout.t
t/SeqIO/metafasta.t
t/SeqIO/msout.t
t/SeqIO/MultiFile.t
t/SeqIO/Multiple_fasta.t
t/SeqIO/nexml.t
t/SeqIO/phd.t
t/SeqIO/pir.t
t/SeqIO/pln.t
t/SeqIO/qual.t
t/SeqIO/raw.t
t/SeqIO/scf.t
t/SeqIO/SeqBuilder.t
t/SeqIO/SeqIO.t
t/SeqIO/seqxml.t
t/SeqIO/Splicedseq.t
t/SeqIO/strider.t
t/SeqIO/swiss.t
t/SeqIO/tab.t
t/SeqIO/table.t
t/SeqIO/tigr.t
t/SeqIO/tigrxml.t
t/SeqIO/tinyseq.t
t/SeqIO/ztr.t
t/SeqTools/Backtranslate.t
t/SeqTools/CodonTable.t
t/SeqTools/ECnumber.t
t/SeqTools/GuessSeqFormat.t
t/SeqTools/OddCodes.t
t/SeqTools/SeqPattern.t
t/SeqTools/SeqStats.t
t/SeqTools/SeqUtils.t
t/SeqTools/SeqWords.t
t/Species.t
t/Structure/IO.t
t/Structure/Structure.t
t/Symbol.t
t/TaxonTree.t
t/Tools/Alignment/Consed.t
t/Tools/AmpliconSearch.t
t/Tools/Analysis/DNA/ESEfinder.t
t/Tools/Analysis/Protein/Domcut.t
t/Tools/Analysis/Protein/ELM.t
t/Tools/Analysis/Protein/GOR4.t
t/Tools/Analysis/Protein/HNN.t
t/Tools/Analysis/Protein/Mitoprot.t
t/Tools/Analysis/Protein/NetPhos.t
t/Tools/Analysis/Protein/Scansite.t
t/Tools/Analysis/Protein/Sopma.t
t/Tools/EMBOSS/Palindrome.t
t/Tools/ePCR.t
t/Tools/Est2Genome.t
t/Tools/FootPrinter.t
t/Tools/Geneid.t
t/Tools/Genewise.t
t/Tools/Genomewise.t
t/Tools/Genpred.t
t/Tools/GFF.t
t/Tools/Hmmer.t
t/Tools/IUPAC.t
t/Tools/Lucy.t
t/Tools/Match.t
t/Tools/Phylo/Gerp.t
t/Tools/Phylo/Molphy.t
t/Tools/Phylo/PAML.t
t/Tools/Phylo/Phylip/ProtDist.t
t/Tools/pICalculator.t
t/Tools/Primer3.t
t/Tools/Promoterwise.t
t/Tools/Pseudowise.t
t/Tools/QRNA.t
t/Tools/RandDistFunctions.t
t/Tools/RepeatMasker.t
t/Tools/rnamotif.t
t/Tools/Run/RemoteBlast.t
t/Tools/Run/RemoteBlast_rpsblast.t
t/Tools/Seg.t
t/Tools/Sigcleave.t
t/Tools/Signalp.t
t/Tools/Signalp/ExtendedSignalp.t
t/Tools/Sim4.t
t/Tools/SiRNA.t
t/Tools/Spidey/Spidey.t
t/Tools/TandemRepeatsFinder.t
t/Tools/TargetP.t
t/Tools/Tmhmm.t
t/Tools/tRNAscanSE.t
t/Tree/Compatible.t
t/Tree/Node.t
t/Tree/PhyloNetwork/Factory.t
t/Tree/PhyloNetwork/GraphViz.t
t/Tree/PhyloNetwork/MuVector.t
t/Tree/PhyloNetwork/PhyloNetwork.t
t/Tree/PhyloNetwork/RandomFactory.t
t/Tree/PhyloNetwork/TreeFactory.t
t/Tree/RandomTreeFactory.t
t/Tree/Tree.t
t/Tree/TreeIO.t
t/Tree/TreeIO/lintree.t
t/Tree/TreeIO/newick.t
t/Tree/TreeIO/nexml.t
t/Tree/TreeIO/nexus.t
t/Tree/TreeIO/nhx.t
t/Tree/TreeIO/phyloxml.t
t/Tree/TreeIO/svggraph.t
t/Tree/TreeIO/tabtree.t
t/Tree/TreeStatistics.t
t/Variation/AAChange.t
t/Variation/AAReverseMutate.t
t/Variation/Allele.t
t/Variation/DNAMutation.t
t/Variation/RNAChange.t
t/Variation/SeqDiff.t
t/Variation/SNP.t
t/Variation/Variation_IO.t
travis_scripts/dependency_installs