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_chaos_plot
• bin/bp_classify_hits_kingdom
• 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/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/SeqWithQuality.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/interpro.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/Symbol/Alphabet.pm
• lib/Bio/Symbol/AlphabetI.pm
• lib/Bio/Symbol/DNAAlphabet.pm
• lib/Bio/Symbol/ProteinAlphabet.pm
• lib/Bio/Symbol/README.Symbol
• lib/Bio/Symbol/Symbol.pm
• lib/Bio/Symbol/SymbolI.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/README
• 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
• maintenance/README
• maintenance/authors.pl
• 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/symlink_script.pl
• maintenance/version.pl
• models/README
• 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
• 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/Alphabet.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
• t/SearchIO/Writer/HSPTableWriter.t
• t/SearchIO/Writer/HTMLWriter.t
• t/SearchIO/Writer/HitTableWriter.t
• t/SearchIO/Writer/TextWriter.t
• t/SearchIO/axt.t
• t/SearchIO/blast.t
• t/SearchIO/blast_pull.t
• t/SearchIO/blasttable.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/infernal.t
• t/SearchIO/megablast.t
• t/SearchIO/psl.t
• t/SearchIO/rnamotif.t
• t/SearchIO/sim4.t
• t/SearchIO/waba.t
• t/SearchIO/wise.t
• t/Seq/DBLink.t
• t/Seq/EncodedSeq.t
• t/Seq/LargeLocatableSeq.t
• t/Seq/LargePSeq.t
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• t/Seq/MetaSeq.t
• t/Seq/PrimaryQual.t
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• t/Seq/PrimedSeq.t
• t/Seq/Quality.t
• t/Seq/Seq.t
• t/Seq/SimulatedRead.t
• t/Seq/WithQuality.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
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• t/SeqFeature/RangeI.t
• t/SeqFeature/SeqAnalysisParser.t
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• t/SeqFeature/Unflattener.t
• t/SeqIO/Handler.t
• t/SeqIO/MultiFile.t
• t/SeqIO/Multiple_fasta.t
• t/SeqIO/SeqBuilder.t
• t/SeqIO/SeqIO.t
• t/SeqIO/Splicedseq.t
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• t/SeqIO/bsml.t
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• t/SeqIO/embl.t
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• t/SeqIO/fastq.t
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• t/SeqIO/gbxml.t
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• t/SeqIO/qual.t
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• t/SeqIO/tigr.t
• t/SeqIO/tigrxml.t
• t/SeqIO/tinyseq.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
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• t/SeqTools/SeqUtils.t
• t/SeqTools/SeqWords.t
• t/Species.t
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• t/Tools/Alignment/Consed.t
• t/Tools/AmpliconSearch.t
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• t/Tools/Genpred.t
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• t/Tools/Phylo/Phylip/ProtDist.t
• t/Tools/Primer3.t
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• t/Tools/PrositeScan.t
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• t/Tools/QRNA.t
• t/Tools/RandDistFunctions.t
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• t/Tools/Seg.t
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• t/Tools/Signalp.t
• t/Tools/Signalp/ExtendedSignalp.t
• t/Tools/Sim4.t
• t/Tools/Spidey/Spidey.t
• t/Tools/TandemRepeatsFinder.t
• t/Tools/TargetP.t
• t/Tools/Tmhmm.t
• t/Tools/ePCR.t
• t/Tools/pICalculator.t
• t/Tools/tRNAscanSE.t
• t/Tree/Compatible.t
• t/Tree/Node.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/nexus.t
• t/Tree/TreeIO/nhx.t
• t/Tree/TreeIO/phyloxml.t
• t/Tree/TreeIO/tabtree.t
• t/Tree/TreeStatistics.t
• t/author-mojibake.t
• t/author-pod-syntax.t
• t/data/13-pilE-F.scf
• t/data/1ZZ19XR301R-Alignment.tblastn
• t/data/2008.blasttable
• t/data/503384.MEGABLAST.0
• t/data/503384.MEGABLAST.2
• t/data/5X_1895.FASTXY
• t/data/AAC12660.fa
• t/data/AB077698.gb
• t/data/AE003528_ecoli.bls
• t/data/AE003644_Adh-genomic.gb
• t/data/AF032047.gbk
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• t/data/AHCYL1.kegg
• t/data/ATF14F8.gbk
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• t/data/AnnIX-v003.gbk
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• t/data/BC000007.gbk
• t/data/BEL16-LTR_AG.embl
• t/data/BK000016-tpa.gbk
• t/data/BLOSUM50
• t/data/BN000066-tpa.embl
• t/data/BOSS_DROME.FASTP_v35_04
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• t/data/D10483.gbk
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• t/data/ECAPAH02.embl
• t/data/EG352462.gbxml
• t/data/ENr111.mfa.example.elems
• t/data/GO.defs.test
• t/data/GO.defs.test2
• t/data/Genscan.FastA
• t/data/Glimmer2.out
• t/data/Glimmer3.detail
• t/data/Glimmer3.predict
• t/data/GlimmerHMM.out
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• t/data/HM138502.gbk
• t/data/HUMBETGLOA.FASTA
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• t/data/HUMBETGLOA.grail
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• t/data/MmCT
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• t/data/NT_021877.gbk
• t/data/ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt
• t/data/O_sat.wgs
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• t/data/Q8GBD3.swiss
• t/data/Rab1.chaos-xml
• t/data/SPAN_Family4nl.nex
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• t/data/SwissProt.dat
• t/data/Treebase-chlamy-dna.nex
• t/data/U58726.gb
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• t/data/UnaSmithHIV-both.nex
• t/data/X98338_Adh-mRNA.gb
• t/data/YP_007988852.gp
• t/data/ZABJ4EA7014.CH878695.1.blast.txt
• t/data/a_thaliana.blastn
• t/data/acefile.ace.1
• t/data/acefile.singlets
• t/data/adh.mb_tree.nexus
• t/data/alleles.fas
• t/data/alnfile.fasta
• t/data/amino.fa
• t/data/amphora.newick
• t/data/atp1.matrix
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• t/data/badfasta.fa
• t/data/barns-combined.nex
• t/data/basic-bush.nex
• t/data/basic-ladder.nex
• t/data/biorecipe.nhx
• t/data/bl2seq+.blastn
• t/data/bl2seq.blastn
• t/data/bl2seq.blastn.rev
• t/data/bl2seq.blastx.out
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• t/data/blast.report
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• t/data/bootstrap.tre
• t/data/brassica_ATH.WUBLASTN
• t/data/bug1986.blast2
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• 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
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• t/data/cmsearch.multi.out
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• t/data/cmsearch_output.txt
• t/data/codeml45b.mlc
• t/data/component.ontology.test
• t/data/component.ontology.test2
• t/data/consed_project/edit_dir/test_project.contigs
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• 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.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.screen.out
• t/data/consed_project/edit_dir/test_projectNewChromats.fof
• t/data/consed_project/edit_dir/test_project_to_alu.cross
• 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/crab.dat.cn
• t/data/crab.nj
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• t/data/crypto.sim4-0
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• t/data/cys1_dicdi.water
• t/data/cysprot.fa
• t/data/cysprot.msf
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• t/data/cysprot.tblastn
• t/data/cysprot.water
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• t/data/cysprot_vs_gadfly.FASTA
• t/data/dbfa/1.fa
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• t/data/dbfa/mixed_alphabet.fasta
• t/data/dbqual/1.qual
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• t/data/dcr1_sp.WUBLASTP
• t/data/dmel_2Lchunk.gb
• t/data/dna2.fa
• t/data/dnaE-bsub-prot.fa
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• t/data/dnaEbsub_ecoli.wublastx
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• t/data/dnaEbsub_ecoli.wutblastx
• t/data/dq519393.gb
• t/data/echofilter.wublastn
• t/data/ecoli-trna-qrna.out
• t/data/ecoli_domains.rpsblast
• t/data/ecolitst.bls
• t/data/ecolitst.noseqs.wublastp
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• t/data/empty.bl2seq
• t/data/ex1.nucl.nhx
• t/data/example.vcf
• t/data/exonerate.output.dontwork
• t/data/exonerate.output.negativescore.works
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• t/data/exonerate.whitespace_before_query.works
• t/data/expected.blast.out
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• t/data/fastq/RT98876.fastq
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• t/data/fastq/error_trunc_in_title.fastq
• t/data/fastq/evil_wrapping.fastq
• t/data/fastq/example.fasta
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• t/data/fastq/example.qual
• t/data/fastq/illumina_faked.fastq
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• t/data/fastq/solexa_example.fastq
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• 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
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• t/data/forward_primer.fa
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• t/data/frac_problems.blast
• t/data/frac_problems2.blast
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• t/data/geneid_1.0.out
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• t/data/genomewise.out
• t/data/genomic-seq.epcr
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• t/data/genomic-seq.genscan
• t/data/genomic-seq.mzef
• t/data/gf-s71.needle
• t/data/glimmer3-fragment.detail
• t/data/glimmer3-fragment.predict
• t/data/gmap_f9-multiple_results.txt
• t/data/gmap_f9-reverse-strand.txt
• t/data/gmap_f9.txt
• t/data/headerless.psl
• t/data/hg16_chroms.gff
• t/data/hmmpfam.out
• t/data/hs_est.est2genome
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• t/data/hs_owlmonkey.aln
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• t/data/hs_owlmonkey.fasta
• t/data/hsinsulin.blastcl3.blastn
• 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
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• t/data/interpro_relationship.xml
• t/data/interpro_sample.xml
• t/data/interpro_short.xml
• t/data/intrablock-comment.nex
• t/data/issue255_ssearch.fasta
• t/data/little.largemultifasta
• t/data/long-names.nex
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• 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/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
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• t/data/map_hem/HEM1-HEM14.fa
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• t/data/map_hem/HEM1-HEM15.fa
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• 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/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/megablast_output.paracel_btk
• t/data/meme.dat
• t/data/mini-AE001405.gb
• t/data/mini-align.aln
• t/data/mixedmast.dat
• t/data/mpath.ontology.test
• 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/myco_sites.gff
• t/data/nei_gojobori_test.aln
• t/data/neighbor.dist
• t/data/new_blastn.txt
• t/data/nhx-bacteria.nhx
• t/data/no-genes.genscan
• t/data/no_FH.embl
• t/data/no_cds_example.gb
• t/data/no_hsps.blastp
• t/data/no_semicolon.newick
• t/data/noninterleaved.phy
• t/data/nucmatrix.txt
• t/data/pep-266.aln
• t/data/phi.out
• t/data/phipsi.out
• t/data/phylipdist-36.out
• t/data/phylipdist.out
• t/data/phyloxml_examples.xml
• t/data/pre_rel9.swiss
• 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/ps_scan/out.PrositeScan
• t/data/pseudowise.out
• t/data/psi_xml.dat
• t/data/psiblastreport.out
• t/data/purine_v081.infernal
• t/data/puzzle.tre
• t/data/qrna-relloc.out
• t/data/qualfile.qual
• t/data/quoted-strings1.nex
• t/data/quoted-strings2.nex
• t/data/radical-whitespace.nex
• t/data/radical-whitespace_02.nex
• 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/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/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-no-desc.pir
• t/data/seqfile.pir
• t/data/seqs.fas
• 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/singlescore.gbk
• t/data/so.obo
• t/data/sofa.ontology
• t/data/sp_subset.obo
• t/data/spaced_fasta.fa
• t/data/spaces.nex
• t/data/sparsealn.needle
• t/data/spidey.noalignment
• t/data/spidey.test1
• t/data/sprintf.rnamotif
• t/data/sv40_small.xml
• t/data/swiss.dat
• t/data/swisspfam.data
• 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.ace
• t/data/test.embl
• t/data/test.embl2sq
• 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.locuslink
• t/data/test.metafasta
• t/data/test.nh
• t/data/test.nhx
• t/data/test.phd
• t/data/test.pir
• t/data/test.raw
• 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/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_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/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/tree_nonewline.nexus
• 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
• travis_scripts/dependency_installs
• travis_scripts/trigger-dockerhub.sh