Files

• AUTHORS
• Changes
• HACKING.md
• LICENSE
• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README.md
• bin/bp_aacomp
• bin/bp_bioflat_index
• bin/bp_biogetseq
• bin/bp_dbsplit
• bin/bp_extract_feature_seq
• bin/bp_fastam9_to_table
• bin/bp_fetch
• bin/bp_filter_search
• bin/bp_find-blast-matches
• bin/bp_gccalc
• bin/bp_genbank2gff3
• bin/bp_index
• bin/bp_local_taxonomydb_query
• bin/bp_make_mrna_protein
• bin/bp_mask_by_search
• bin/bp_mrtrans
• bin/bp_mutate
• bin/bp_nexus2nh
• bin/bp_nrdb
• bin/bp_oligo_count
• bin/bp_process_gadfly
• bin/bp_process_sgd
• bin/bp_revtrans-motif
• bin/bp_search2alnblocks
• bin/bp_search2gff
• bin/bp_search2table
• bin/bp_search2tribe
• bin/bp_seq_length
• bin/bp_seqconvert
• bin/bp_seqcut
• bin/bp_seqpart
• bin/bp_seqret
• bin/bp_seqretsplit
• bin/bp_split_seq
• bin/bp_sreformat
• bin/bp_taxid4species
• bin/bp_taxonomy2tree
• bin/bp_translate_seq
• bin/bp_tree2pag
• bin/bp_unflatten_seq
• dist.ini
• examples/Bio-DB-GFF/load_ucsc.pl
• examples/align/FastAlign.pl
• examples/align/align_on_codons.pl
• examples/align/aligntutorial.pl
• examples/align/simplealign.pl
• examples/classify_hits_kingdom
• examples/contributed/nmrpdb_parse.pl
• examples/contributed/prosite2perl.pl
• examples/contributed/rebase2list.pl
• examples/db/est_tissue_query.pl
• examples/db/get_seqs.pl
• examples/db/rfetch.pl
• examples/db/use_registry.pl
• examples/generate_random_seq.pl
• examples/longorf.pl
• examples/make_primers.pl
• examples/quality/svgtrace.pl
• examples/rev_and_trans.pl
• examples/revcom_dir.pl
• examples/root/README
• examples/root/exceptions1.pl
• examples/root/exceptions2.pl
• examples/root/exceptions3.pl
• examples/root/exceptions4.pl
• 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/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/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
• lib/Bio/Align/AlignI.pm
• lib/Bio/Align/DNAStatistics.pm
• lib/Bio/Align/PairwiseStatistics.pm
• lib/Bio/Align/ProteinStatistics.pm
• lib/Bio/Align/StatisticsI.pm
• lib/Bio/Align/Utilities.pm
• lib/Bio/AlignIO.pm
• lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
• lib/Bio/AlignIO/arp.pm
• lib/Bio/AlignIO/bl2seq.pm
• lib/Bio/AlignIO/clustalw.pm
• lib/Bio/AlignIO/emboss.pm
• lib/Bio/AlignIO/fasta.pm
• lib/Bio/AlignIO/largemultifasta.pm
• lib/Bio/AlignIO/maf.pm
• lib/Bio/AlignIO/mase.pm
• lib/Bio/AlignIO/mega.pm
• lib/Bio/AlignIO/meme.pm
• lib/Bio/AlignIO/metafasta.pm
• lib/Bio/AlignIO/msf.pm
• lib/Bio/AlignIO/nexus.pm
• lib/Bio/AlignIO/pfam.pm
• lib/Bio/AlignIO/phylip.pm
• lib/Bio/AlignIO/po.pm
• lib/Bio/AlignIO/proda.pm
• lib/Bio/AlignIO/prodom.pm
• lib/Bio/AlignIO/psi.pm
• lib/Bio/AlignIO/selex.pm
• lib/Bio/AlignIO/xmfa.pm
• lib/Bio/AnalysisI.pm
• lib/Bio/AnalysisParserI.pm
• lib/Bio/AnalysisResultI.pm
• lib/Bio/AnnotatableI.pm
• lib/Bio/Annotation/AnnotationFactory.pm
• lib/Bio/Annotation/Collection.pm
• lib/Bio/Annotation/Comment.pm
• lib/Bio/Annotation/DBLink.pm
• lib/Bio/Annotation/OntologyTerm.pm
• lib/Bio/Annotation/Reference.pm
• lib/Bio/Annotation/Relation.pm
• lib/Bio/Annotation/SimpleValue.pm
• lib/Bio/Annotation/StructuredValue.pm
• lib/Bio/Annotation/TagTree.pm
• lib/Bio/Annotation/Target.pm
• lib/Bio/Annotation/Tree.pm
• lib/Bio/Annotation/TypeManager.pm
• lib/Bio/AnnotationCollectionI.pm
• lib/Bio/AnnotationI.pm
• lib/Bio/CodonUsage/IO.pm
• lib/Bio/CodonUsage/Table.pm
• lib/Bio/DB/DBFetch.pm
• lib/Bio/DB/Failover.pm
• lib/Bio/DB/Fasta.pm
• lib/Bio/DB/FileCache.pm
• lib/Bio/DB/Flat.pm
• lib/Bio/DB/Flat/BDB.pm
• lib/Bio/DB/Flat/BDB/embl.pm
• lib/Bio/DB/Flat/BDB/fasta.pm
• lib/Bio/DB/Flat/BDB/genbank.pm
• lib/Bio/DB/Flat/BDB/swiss.pm
• lib/Bio/DB/Flat/BinarySearch.pm
• lib/Bio/DB/GFF/Util/Binning.pm
• lib/Bio/DB/GFF/Util/Rearrange.pm
• lib/Bio/DB/GenericWebAgent.pm
• lib/Bio/DB/InMemoryCache.pm
• lib/Bio/DB/IndexedBase.pm
• lib/Bio/DB/LocationI.pm
• lib/Bio/DB/Qual.pm
• lib/Bio/DB/Query/WebQuery.pm
• lib/Bio/DB/QueryI.pm
• lib/Bio/DB/RandomAccessI.pm
• lib/Bio/DB/ReferenceI.pm
• lib/Bio/DB/Registry.pm
• lib/Bio/DB/SeqI.pm
• lib/Bio/DB/Taxonomy.pm
• lib/Bio/DB/Taxonomy/flatfile.pm
• lib/Bio/DB/Taxonomy/greengenes.pm
• lib/Bio/DB/Taxonomy/list.pm
• lib/Bio/DB/Taxonomy/silva.pm
• lib/Bio/DB/UpdateableSeqI.pm
• lib/Bio/DB/WebDBSeqI.pm
• lib/Bio/DBLinkContainerI.pm
• lib/Bio/Das/FeatureTypeI.pm
• lib/Bio/Das/SegmentI.pm
• lib/Bio/DasI.pm
• lib/Bio/DescribableI.pm
• lib/Bio/Event/EventGeneratorI.pm
• lib/Bio/Event/EventHandlerI.pm
• lib/Bio/Factory/AnalysisI.pm
• lib/Bio/Factory/ApplicationFactoryI.pm
• lib/Bio/Factory/DriverFactory.pm
• lib/Bio/Factory/FTLocationFactory.pm
• lib/Bio/Factory/LocationFactoryI.pm
• lib/Bio/Factory/ObjectBuilderI.pm
• lib/Bio/Factory/ObjectFactory.pm
• lib/Bio/Factory/ObjectFactoryI.pm
• lib/Bio/Factory/SeqAnalysisParserFactory.pm
• lib/Bio/Factory/SeqAnalysisParserFactoryI.pm
• lib/Bio/Factory/SequenceFactoryI.pm
• lib/Bio/Factory/SequenceProcessorI.pm
• lib/Bio/Factory/SequenceStreamI.pm
• lib/Bio/Factory/TreeFactoryI.pm
• lib/Bio/FeatureHolderI.pm
• lib/Bio/HandlerBaseI.pm
• lib/Bio/IdCollectionI.pm
• lib/Bio/IdentifiableI.pm
• lib/Bio/Index/Abstract.pm
• lib/Bio/Index/AbstractSeq.pm
• lib/Bio/Index/Blast.pm
• lib/Bio/Index/BlastTable.pm
• lib/Bio/Index/EMBL.pm
• lib/Bio/Index/Fasta.pm
• lib/Bio/Index/Fastq.pm
• lib/Bio/Index/GenBank.pm
• lib/Bio/Index/Qual.pm
• lib/Bio/Index/SwissPfam.pm
• lib/Bio/Index/Swissprot.pm
• lib/Bio/LocatableSeq.pm
• lib/Bio/Location/Atomic.pm
• lib/Bio/Location/AvWithinCoordPolicy.pm
• lib/Bio/Location/CoordinatePolicyI.pm
• lib/Bio/Location/Fuzzy.pm
• lib/Bio/Location/FuzzyLocationI.pm
• lib/Bio/Location/NarrowestCoordPolicy.pm
• lib/Bio/Location/Simple.pm
• lib/Bio/Location/Split.pm
• lib/Bio/Location/SplitLocationI.pm
• lib/Bio/Location/WidestCoordPolicy.pm
• lib/Bio/LocationI.pm
• lib/Bio/Matrix/Generic.pm
• lib/Bio/Matrix/IO.pm
• lib/Bio/Matrix/IO/mlagan.pm
• lib/Bio/Matrix/IO/phylip.pm
• lib/Bio/Matrix/IO/scoring.pm
• lib/Bio/Matrix/MatrixI.pm
• lib/Bio/Matrix/Mlagan.pm
• lib/Bio/Matrix/PSM/IO.pm
• lib/Bio/Matrix/PSM/IO/mast.pm
• lib/Bio/Matrix/PSM/IO/masta.pm
• lib/Bio/Matrix/PSM/IO/meme.pm
• lib/Bio/Matrix/PSM/IO/psiblast.pm
• lib/Bio/Matrix/PSM/IO/transfac.pm
• lib/Bio/Matrix/PSM/InstanceSite.pm
• lib/Bio/Matrix/PSM/InstanceSiteI.pm
• lib/Bio/Matrix/PSM/ProtMatrix.pm
• lib/Bio/Matrix/PSM/ProtPsm.pm
• lib/Bio/Matrix/PSM/Psm.pm
• lib/Bio/Matrix/PSM/PsmHeader.pm
• lib/Bio/Matrix/PSM/PsmHeaderI.pm
• lib/Bio/Matrix/PSM/PsmI.pm
• lib/Bio/Matrix/PSM/SiteMatrix.pm
• lib/Bio/Matrix/PSM/SiteMatrixI.pm
• lib/Bio/Matrix/PhylipDist.pm
• lib/Bio/Matrix/Scoring.pm
• lib/Bio/Ontology/DocumentRegistry.pm
• lib/Bio/Ontology/GOterm.pm
• lib/Bio/Ontology/InterProTerm.pm
• lib/Bio/Ontology/OBOEngine.pm
• lib/Bio/Ontology/OBOterm.pm
• lib/Bio/Ontology/Ontology.pm
• lib/Bio/Ontology/OntologyEngineI.pm
• lib/Bio/Ontology/OntologyI.pm
• lib/Bio/Ontology/OntologyStore.pm
• lib/Bio/Ontology/Path.pm
• lib/Bio/Ontology/PathI.pm
• lib/Bio/Ontology/Relationship.pm
• lib/Bio/Ontology/RelationshipFactory.pm
• lib/Bio/Ontology/RelationshipI.pm
• lib/Bio/Ontology/RelationshipType.pm
• lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
• lib/Bio/Ontology/SimpleOntologyEngine.pm
• lib/Bio/Ontology/Term.pm
• lib/Bio/Ontology/TermFactory.pm
• lib/Bio/Ontology/TermI.pm
• lib/Bio/OntologyIO.pm
• lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
• lib/Bio/OntologyIO/Handlers/InterProHandler.pm
• lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
• lib/Bio/OntologyIO/InterProParser.pm
• lib/Bio/OntologyIO/dagflat.pm
• lib/Bio/OntologyIO/goflat.pm
• lib/Bio/OntologyIO/obo.pm
• lib/Bio/OntologyIO/simplehierarchy.pm
• lib/Bio/OntologyIO/soflat.pm
• lib/Bio/ParameterBaseI.pm
• lib/Bio/PrimarySeq.pm
• lib/Bio/PrimarySeqI.pm
• lib/Bio/PullParserI.pm
• lib/Bio/Range.pm
• lib/Bio/RangeI.pm
• lib/Bio/Root/Exception.pm
• lib/Bio/Root/HTTPget.pm
• lib/Bio/Root/IO.pm
• lib/Bio/Root/Root.pm
• lib/Bio/Root/RootI.pm
• lib/Bio/Root/Storable.pm
• lib/Bio/Root/Test.pm
• lib/Bio/Root/TestObject.pm
• lib/Bio/Root/Utilities.pm
• lib/Bio/Root/Version.pm
• lib/Bio/Search/BlastStatistics.pm
• lib/Bio/Search/BlastUtils.pm
• lib/Bio/Search/DatabaseI.pm
• lib/Bio/Search/GenericDatabase.pm
• lib/Bio/Search/GenericStatistics.pm
• lib/Bio/Search/HSP/BlastHSP.pm
• lib/Bio/Search/HSP/BlastPullHSP.pm
• lib/Bio/Search/HSP/FastaHSP.pm
• lib/Bio/Search/HSP/GenericHSP.pm
• lib/Bio/Search/HSP/HSPFactory.pm
• lib/Bio/Search/HSP/HSPI.pm
• lib/Bio/Search/HSP/ModelHSP.pm
• lib/Bio/Search/HSP/PSLHSP.pm
• lib/Bio/Search/HSP/PsiBlastHSP.pm
• lib/Bio/Search/HSP/PullHSPI.pm
• lib/Bio/Search/HSP/WABAHSP.pm
• lib/Bio/Search/Hit/BlastHit.pm
• lib/Bio/Search/Hit/BlastPullHit.pm
• lib/Bio/Search/Hit/Fasta.pm
• lib/Bio/Search/Hit/GenericHit.pm
• lib/Bio/Search/Hit/HitFactory.pm
• lib/Bio/Search/Hit/HitI.pm
• lib/Bio/Search/Hit/ModelHit.pm
• lib/Bio/Search/Hit/PsiBlastHit.pm
• lib/Bio/Search/Hit/PullHitI.pm
• lib/Bio/Search/Iteration/GenericIteration.pm
• lib/Bio/Search/Iteration/IterationI.pm
• lib/Bio/Search/Processor.pm
• lib/Bio/Search/Result/BlastPullResult.pm
• lib/Bio/Search/Result/BlastResult.pm
• lib/Bio/Search/Result/CrossMatchResult.pm
• lib/Bio/Search/Result/GenericResult.pm
• lib/Bio/Search/Result/INFERNALResult.pm
• lib/Bio/Search/Result/PullResultI.pm
• lib/Bio/Search/Result/ResultFactory.pm
• lib/Bio/Search/Result/ResultI.pm
• lib/Bio/Search/Result/WABAResult.pm
• lib/Bio/Search/SearchUtils.pm
• lib/Bio/Search/StatisticsI.pm
• lib/Bio/Search/Tiling/MapTileUtils.pm
• lib/Bio/Search/Tiling/MapTiling.pm
• lib/Bio/Search/Tiling/TilingI.pm
• lib/Bio/SearchIO.pm
• lib/Bio/SearchIO/EventHandlerI.pm
• lib/Bio/SearchIO/FastHitEventBuilder.pm
• lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
• lib/Bio/SearchIO/SearchResultEventBuilder.pm
• lib/Bio/SearchIO/SearchWriterI.pm
• lib/Bio/SearchIO/Writer/GbrowseGFF.pm
• lib/Bio/SearchIO/Writer/HSPTableWriter.pm
• lib/Bio/SearchIO/Writer/HTMLResultWriter.pm
• lib/Bio/SearchIO/Writer/HitTableWriter.pm
• lib/Bio/SearchIO/Writer/ResultTableWriter.pm
• lib/Bio/SearchIO/Writer/TextResultWriter.pm
• lib/Bio/SearchIO/axt.pm
• lib/Bio/SearchIO/blast.pm
• lib/Bio/SearchIO/blast_pull.pm
• lib/Bio/SearchIO/blasttable.pm
• lib/Bio/SearchIO/cross_match.pm
• lib/Bio/SearchIO/erpin.pm
• lib/Bio/SearchIO/exonerate.pm
• lib/Bio/SearchIO/fasta.pm
• lib/Bio/SearchIO/gmap_f9.pm
• lib/Bio/SearchIO/infernal.pm
• lib/Bio/SearchIO/megablast.pm
• lib/Bio/SearchIO/psl.pm
• lib/Bio/SearchIO/rnamotif.pm
• lib/Bio/SearchIO/sim4.pm
• lib/Bio/SearchIO/waba.pm
• lib/Bio/SearchIO/wise.pm
• lib/Bio/Seq.pm
• lib/Bio/Seq/BaseSeqProcessor.pm
• lib/Bio/Seq/EncodedSeq.pm
• lib/Bio/Seq/LargeLocatableSeq.pm
• lib/Bio/Seq/LargePrimarySeq.pm
• lib/Bio/Seq/LargeSeq.pm
• lib/Bio/Seq/LargeSeqI.pm
• lib/Bio/Seq/Meta.pm
• lib/Bio/Seq/Meta/Array.pm
• lib/Bio/Seq/MetaI.pm
• lib/Bio/Seq/PrimaryQual.pm
• lib/Bio/Seq/PrimedSeq.pm
• lib/Bio/Seq/QualI.pm
• lib/Bio/Seq/Quality.pm
• lib/Bio/Seq/RichSeq.pm
• lib/Bio/Seq/RichSeqI.pm
• lib/Bio/Seq/SeqBuilder.pm
• lib/Bio/Seq/SeqFactory.pm
• lib/Bio/Seq/SeqFastaSpeedFactory.pm
• lib/Bio/Seq/SequenceTrace.pm
• lib/Bio/Seq/SimulatedRead.pm
• lib/Bio/Seq/TraceI.pm
• lib/Bio/SeqAnalysisParserI.pm
• lib/Bio/SeqFeature/Amplicon.pm
• lib/Bio/SeqFeature/AnnotationAdaptor.pm
• lib/Bio/SeqFeature/Collection.pm
• lib/Bio/SeqFeature/CollectionI.pm
• lib/Bio/SeqFeature/Computation.pm
• lib/Bio/SeqFeature/FeaturePair.pm
• lib/Bio/SeqFeature/Gene/Exon.pm
• lib/Bio/SeqFeature/Gene/ExonI.pm
• lib/Bio/SeqFeature/Gene/GeneStructure.pm
• lib/Bio/SeqFeature/Gene/GeneStructureI.pm
• lib/Bio/SeqFeature/Gene/Intron.pm
• lib/Bio/SeqFeature/Gene/NC_Feature.pm
• lib/Bio/SeqFeature/Gene/Poly_A_site.pm
• lib/Bio/SeqFeature/Gene/Promoter.pm
• lib/Bio/SeqFeature/Gene/Transcript.pm
• lib/Bio/SeqFeature/Gene/TranscriptI.pm
• lib/Bio/SeqFeature/Gene/UTR.pm
• lib/Bio/SeqFeature/Generic.pm
• lib/Bio/SeqFeature/Lite.pm
• lib/Bio/SeqFeature/PositionProxy.pm
• lib/Bio/SeqFeature/Primer.pm
• lib/Bio/SeqFeature/Similarity.pm
• lib/Bio/SeqFeature/SimilarityPair.pm
• lib/Bio/SeqFeature/SubSeq.pm
• lib/Bio/SeqFeature/Tools/FeatureNamer.pm
• lib/Bio/SeqFeature/Tools/IDHandler.pm
• lib/Bio/SeqFeature/Tools/TypeMapper.pm
• lib/Bio/SeqFeature/Tools/Unflattener.pm
• lib/Bio/SeqFeature/TypedSeqFeatureI.pm
• lib/Bio/SeqFeatureI.pm
• lib/Bio/SeqI.pm
• lib/Bio/SeqIO.pm
• lib/Bio/SeqIO/FTHelper.pm
• lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
• lib/Bio/SeqIO/MultiFile.pm
• lib/Bio/SeqIO/ace.pm
• lib/Bio/SeqIO/asciitree.pm
• lib/Bio/SeqIO/bsml.pm
• lib/Bio/SeqIO/bsml_sax.pm
• lib/Bio/SeqIO/embl.pm
• lib/Bio/SeqIO/embldriver.pm
• lib/Bio/SeqIO/fasta.pm
• lib/Bio/SeqIO/fastq.pm
• lib/Bio/SeqIO/game.pm
• lib/Bio/SeqIO/game/featHandler.pm
• lib/Bio/SeqIO/game/gameHandler.pm
• lib/Bio/SeqIO/game/gameSubs.pm
• lib/Bio/SeqIO/game/gameWriter.pm
• lib/Bio/SeqIO/game/seqHandler.pm
• lib/Bio/SeqIO/gbdriver.pm
• lib/Bio/SeqIO/gbxml.pm
• lib/Bio/SeqIO/gcg.pm
• lib/Bio/SeqIO/genbank.pm
• lib/Bio/SeqIO/kegg.pm
• lib/Bio/SeqIO/largefasta.pm
• lib/Bio/SeqIO/locuslink.pm
• lib/Bio/SeqIO/mbsout.pm
• lib/Bio/SeqIO/metafasta.pm
• lib/Bio/SeqIO/msout.pm
• lib/Bio/SeqIO/phd.pm
• lib/Bio/SeqIO/pir.pm
• lib/Bio/SeqIO/qual.pm
• lib/Bio/SeqIO/raw.pm
• lib/Bio/SeqIO/scf.pm
• lib/Bio/SeqIO/seqxml.pm
• lib/Bio/SeqIO/swiss.pm
• lib/Bio/SeqIO/swissdriver.pm
• lib/Bio/SeqIO/tab.pm
• lib/Bio/SeqIO/table.pm
• lib/Bio/SeqIO/tigr.pm
• lib/Bio/SeqIO/tigrxml.pm
• lib/Bio/SeqIO/tinyseq.pm
• lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm
• lib/Bio/SeqUtils.pm
• lib/Bio/SimpleAlign.pm
• lib/Bio/SimpleAnalysisI.pm
• lib/Bio/Species.pm
• lib/Bio/Taxon.pm
• lib/Bio/Tools/Alignment/Consed.pm
• lib/Bio/Tools/Alignment/Trim.pm
• lib/Bio/Tools/AmpliconSearch.pm
• lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm
• lib/Bio/Tools/AnalysisResult.pm
• lib/Bio/Tools/Blat.pm
• lib/Bio/Tools/CodonTable.pm
• lib/Bio/Tools/Coil.pm
• lib/Bio/Tools/ECnumber.pm
• lib/Bio/Tools/EMBOSS/Palindrome.pm
• lib/Bio/Tools/EPCR.pm
• lib/Bio/Tools/ESTScan.pm
• lib/Bio/Tools/Eponine.pm
• lib/Bio/Tools/Est2Genome.pm
• lib/Bio/Tools/Fgenesh.pm
• lib/Bio/Tools/FootPrinter.pm
• lib/Bio/Tools/GFF.pm
• lib/Bio/Tools/Geneid.pm
• lib/Bio/Tools/Genemark.pm
• lib/Bio/Tools/Genewise.pm
• lib/Bio/Tools/Genomewise.pm
• lib/Bio/Tools/Genscan.pm
• lib/Bio/Tools/Glimmer.pm
• lib/Bio/Tools/Grail.pm
• lib/Bio/Tools/GuessSeqFormat.pm
• lib/Bio/Tools/IUPAC.pm
• lib/Bio/Tools/Lucy.pm
• lib/Bio/Tools/MZEF.pm
• lib/Bio/Tools/Match.pm
• lib/Bio/Tools/OddCodes.pm
• lib/Bio/Tools/Phylo/Gerp.pm
• lib/Bio/Tools/Phylo/Molphy.pm
• lib/Bio/Tools/Phylo/Molphy/Result.pm
• lib/Bio/Tools/Phylo/Phylip/ProtDist.pm
• lib/Bio/Tools/Prediction/Exon.pm
• lib/Bio/Tools/Prediction/Gene.pm
• lib/Bio/Tools/Primer/Assessor/Base.pm
• lib/Bio/Tools/Primer/AssessorI.pm
• lib/Bio/Tools/Primer/Feature.pm
• lib/Bio/Tools/Primer/Pair.pm
• lib/Bio/Tools/Primer3.pm
• lib/Bio/Tools/Prints.pm
• lib/Bio/Tools/Profile.pm
• lib/Bio/Tools/Promoterwise.pm
• lib/Bio/Tools/PrositeScan.pm
• lib/Bio/Tools/Pseudowise.pm
• lib/Bio/Tools/QRNA.pm
• lib/Bio/Tools/RandomDistFunctions.pm
• lib/Bio/Tools/RepeatMasker.pm
• lib/Bio/Tools/Run/Analysis.pm
• lib/Bio/Tools/Run/AnalysisFactory.pm
• lib/Bio/Tools/Run/GenericParameters.pm
• lib/Bio/Tools/Run/ParametersI.pm
• lib/Bio/Tools/Run/Phylo/PhyloBase.pm
• lib/Bio/Tools/Run/WrapperBase.pm
• lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
• lib/Bio/Tools/Seg.pm
• lib/Bio/Tools/SeqPattern.pm
• lib/Bio/Tools/SeqPattern/Backtranslate.pm
• lib/Bio/Tools/SeqStats.pm
• lib/Bio/Tools/SeqWords.pm
• lib/Bio/Tools/Sigcleave.pm
• lib/Bio/Tools/Signalp.pm
• lib/Bio/Tools/Signalp/ExtendedSignalp.pm
• lib/Bio/Tools/Sim4/Exon.pm
• lib/Bio/Tools/Sim4/Results.pm
• lib/Bio/Tools/Spidey/Exon.pm
• lib/Bio/Tools/Spidey/Results.pm
• lib/Bio/Tools/TandemRepeatsFinder.pm
• lib/Bio/Tools/TargetP.pm
• lib/Bio/Tools/Tmhmm.pm
• lib/Bio/Tools/ipcress.pm
• lib/Bio/Tools/isPcr.pm
• lib/Bio/Tools/pICalculator.pm
• lib/Bio/Tools/tRNAscanSE.pm
• lib/Bio/Tree/AnnotatableNode.pm
• lib/Bio/Tree/Compatible.pm
• lib/Bio/Tree/DistanceFactory.pm
• lib/Bio/Tree/Node.pm
• lib/Bio/Tree/NodeI.pm
• lib/Bio/Tree/NodeNHX.pm
• lib/Bio/Tree/RandomFactory.pm
• lib/Bio/Tree/Statistics.pm
• lib/Bio/Tree/Tree.pm
• lib/Bio/Tree/TreeFunctionsI.pm
• lib/Bio/Tree/TreeI.pm
• lib/Bio/TreeIO.pm
• lib/Bio/TreeIO/NewickParser.pm
• lib/Bio/TreeIO/TreeEventBuilder.pm
• lib/Bio/TreeIO/cluster.pm
• lib/Bio/TreeIO/lintree.pm
• lib/Bio/TreeIO/newick.pm
• lib/Bio/TreeIO/nexus.pm
• lib/Bio/TreeIO/nhx.pm
• lib/Bio/TreeIO/pag.pm
• lib/Bio/TreeIO/phyloxml.pm
• lib/Bio/TreeIO/tabtree.pm
• lib/Bio/UpdateableSeqI.pm
• lib/Bio/WebAgent.pm
• lib/BioPerl.pm
• t/00-compile.t
• t/Align/AlignStats.t
• t/Align/AlignUtil.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/nexus.t
• t/AlignIO/pfam.t
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• t/data/map_hem/HEM2-HEM4.fa
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• t/data/map_hem/HEM2.ups.fa_
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• t/data/map_hem/HEM3-HEM12.fa
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• t/data/map_hem/HEM3-HEM15.fa
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• t/data/map_hem/HEM3-HEM4.fa
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• t/data/map_hem/HEM3.ups.fa_
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• t/data/map_hem/HEM4-HEM15.fa
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• t/data/map_hem/HEM4.ups.fa_.revcom
• t/data/map_hem/yeast.nc.1.freq
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• t/data/masta.dat
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• t/data/mbsout/mbsout_infile2
• t/data/mbsout/mbsout_infile3
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• t/data/mixedmast.dat
• t/data/mpath.ontology.test
• t/data/msout/bad_msout_infile1
• t/data/msout/bad_msout_infile2
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• t/data/multifa.seq
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• t/data/multiresult_blastn+.bls
• t/data/multiseq.bls
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• t/data/nei_gojobori_test.aln
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• t/data/no-genes.genscan
• t/data/no_FH.embl
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• t/data/no_semicolon.newick
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• t/data/prints.out
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• t/data/ps_scan/out.PrositeScan
• t/data/pseudowise.out
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• t/data/purine_v081.infernal
• t/data/puzzle.tre
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• t/data/registry/bdb/seqdatabase.ini
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• t/data/regulation_test.obo
• t/data/rel9.swiss
• t/data/repeatmasker.fa.out
• t/data/revcomp_mrna.gb
• t/data/ribosome-slippage.gb
• t/data/roa1.dat
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• t/data/roa1.genbank
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• t/data/rpsblast.bls
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• t/data/sbay_c127.fas
• t/data/sbay_c545-yeast.BLASTZ.PSL
• t/data/seg.out
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• t/data/short.blx
• t/data/signalp.hmm.short
• t/data/signalp.hmm.summary
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• t/data/signalp.short
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• t/data/sim4.for.for
• t/data/sim4.for.rev
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• t/data/singlescore.gbk
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• t/data/targetp.out
• t/data/taxdump/names.dmp
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• 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
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• t/data/test-4.9.meme
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• t/data/test.genbank
• t/data/test.genbank.noseq
• t/data/test.infernal
• t/data/test.locuslink
• t/data/test.metafasta
• t/data/test.nh
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• t/data/test.tseq
• t/data/test.tsv
• t/data/test.txt
• t/data/test.waba
• t/data/test1.blasttab3
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• t/data/test2.infernal
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• t/data/testaln.selex
• t/data/testaln.stockholm
• t/data/testaln.xmfa
• t/data/testaln2.arp
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• t/data/testdat.exonerate
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• t/data/testdbaccnums.out
• t/data/testfile.erpin
• t/data/testfuzzy.genbank
• 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
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• t/data/tricky.wublast
• t/data/trna.strict.rnamotif
• t/data/urease.tre.nexus
• t/data/version2.scf
• t/data/version3.scf
• t/data/wellcome_tol.nhx
• t/data/worm_fam_2785.cdna
• t/data/yeast.tRNAscanSE