# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.017.
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
t/AlignIO/phylip.t
t/AlignIO/po.t
t/AlignIO/prodom.t
t/AlignIO/psi.t
t/AlignIO/selex.t
t/AlignIO/xmfa.t
t/Annotation/Annotation.t
t/Annotation/AnnotationAdaptor.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/Taxonomy/greengenes.t
t/LocalDB/Taxonomy/silva.t
t/Matrix/IO/masta.t
t/Matrix/IO/psm.t
t/Matrix/InstanceSite.t
t/Matrix/Matrix.t
t/Matrix/ProtMatrix.t
t/Matrix/ProtPsm.t
t/Matrix/SiteMatrix.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/RemoteDB/SeqRead_fail.t
t/RemoteDB/Taxonomy.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/SearchIO/CigarString.t
t/SearchIO/SearchIO.t
t/SearchIO/SimilarityPair.t
t/SearchIO/Tiling.t
t/SearchIO/Writer/GbrowseGFF.t
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t/data/wellcome_tol.nhx
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