1# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.012.
2AUTHORS
3Changes
4HACKING.md
5LICENSE
6MANIFEST
7META.json
8META.yml
9Makefile.PL
10README.md
11bin/bp_aacomp
12bin/bp_bioflat_index
13bin/bp_biogetseq
14bin/bp_dbsplit
15bin/bp_extract_feature_seq
16bin/bp_fastam9_to_table
17bin/bp_fetch
18bin/bp_filter_search
19bin/bp_find-blast-matches
20bin/bp_gccalc
21bin/bp_genbank2gff3
22bin/bp_index
23bin/bp_local_taxonomydb_query
24bin/bp_make_mrna_protein
25bin/bp_mask_by_search
26bin/bp_mrtrans
27bin/bp_mutate
28bin/bp_nexus2nh
29bin/bp_nrdb
30bin/bp_oligo_count
31bin/bp_process_gadfly
32bin/bp_process_sgd
33bin/bp_revtrans-motif
34bin/bp_search2alnblocks
35bin/bp_search2gff
36bin/bp_search2table
37bin/bp_search2tribe
38bin/bp_seq_length
39bin/bp_seqconvert
40bin/bp_seqcut
41bin/bp_seqpart
42bin/bp_seqret
43bin/bp_seqretsplit
44bin/bp_split_seq
45bin/bp_sreformat
46bin/bp_taxid4species
47bin/bp_taxonomy2tree
48bin/bp_translate_seq
49bin/bp_tree2pag
50bin/bp_unflatten_seq
51dist.ini
52examples/Bio-DB-GFF/load_ucsc.pl
53examples/align/FastAlign.pl
54examples/align/align_on_codons.pl
55examples/align/aligntutorial.pl
56examples/align/simplealign.pl
57examples/classify_hits_kingdom
58examples/contributed/nmrpdb_parse.pl
59examples/contributed/prosite2perl.pl
60examples/contributed/rebase2list.pl
61examples/db/est_tissue_query.pl
62examples/db/get_seqs.pl
63examples/db/rfetch.pl
64examples/db/use_registry.pl
65examples/generate_random_seq.pl
66examples/longorf.pl
67examples/make_primers.pl
68examples/quality/svgtrace.pl
69examples/rev_and_trans.pl
70examples/revcom_dir.pl
71examples/root/README
72examples/root/exceptions1.pl
73examples/root/exceptions2.pl
74examples/root/exceptions3.pl
75examples/root/exceptions4.pl
76examples/searchio/blast_example.pl
77examples/searchio/custom_writer.pl
78examples/searchio/hitwriter.pl
79examples/searchio/hspwriter.pl
80examples/searchio/htmlwriter.pl
81examples/searchio/psiblast_features.pl
82examples/searchio/psiblast_iterations.pl
83examples/searchio/rawwriter.pl
84examples/searchio/resultwriter.pl
85examples/searchio/waba2gff.pl
86examples/searchio/waba2gff3.pl
87examples/tk/gsequence.pl
88examples/tk/hitdisplay.pl
89examples/tools/extract_genes.pl
90examples/tools/gb_to_gff.pl
91examples/tools/gff2ps.pl
92examples/tools/parse_codeml.pl
93examples/tools/reverse-translate.pl
94examples/tools/run_genscan.pl
95examples/tools/run_primer3.pl
96examples/tools/seq_pattern.pl
97examples/tools/standaloneblast.pl
98examples/tree/paup2phylip.pl
99lib/Bio/Align/AlignI.pm
100lib/Bio/Align/DNAStatistics.pm
101lib/Bio/Align/PairwiseStatistics.pm
102lib/Bio/Align/ProteinStatistics.pm
103lib/Bio/Align/StatisticsI.pm
104lib/Bio/Align/Utilities.pm
105lib/Bio/AlignIO.pm
106lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
107lib/Bio/AlignIO/arp.pm
108lib/Bio/AlignIO/bl2seq.pm
109lib/Bio/AlignIO/clustalw.pm
110lib/Bio/AlignIO/emboss.pm
111lib/Bio/AlignIO/fasta.pm
112lib/Bio/AlignIO/largemultifasta.pm
113lib/Bio/AlignIO/maf.pm
114lib/Bio/AlignIO/mase.pm
115lib/Bio/AlignIO/mega.pm
116lib/Bio/AlignIO/meme.pm
117lib/Bio/AlignIO/metafasta.pm
118lib/Bio/AlignIO/msf.pm
119lib/Bio/AlignIO/nexus.pm
120lib/Bio/AlignIO/pfam.pm
121lib/Bio/AlignIO/phylip.pm
122lib/Bio/AlignIO/po.pm
123lib/Bio/AlignIO/proda.pm
124lib/Bio/AlignIO/prodom.pm
125lib/Bio/AlignIO/psi.pm
126lib/Bio/AlignIO/selex.pm
127lib/Bio/AlignIO/xmfa.pm
128lib/Bio/AnalysisI.pm
129lib/Bio/AnalysisParserI.pm
130lib/Bio/AnalysisResultI.pm
131lib/Bio/AnnotatableI.pm
132lib/Bio/Annotation/AnnotationFactory.pm
133lib/Bio/Annotation/Collection.pm
134lib/Bio/Annotation/Comment.pm
135lib/Bio/Annotation/DBLink.pm
136lib/Bio/Annotation/OntologyTerm.pm
137lib/Bio/Annotation/Reference.pm
138lib/Bio/Annotation/Relation.pm
139lib/Bio/Annotation/SimpleValue.pm
140lib/Bio/Annotation/StructuredValue.pm
141lib/Bio/Annotation/TagTree.pm
142lib/Bio/Annotation/Target.pm
143lib/Bio/Annotation/Tree.pm
144lib/Bio/Annotation/TypeManager.pm
145lib/Bio/AnnotationCollectionI.pm
146lib/Bio/AnnotationI.pm
147lib/Bio/CodonUsage/IO.pm
148lib/Bio/CodonUsage/Table.pm
149lib/Bio/DB/DBFetch.pm
150lib/Bio/DB/Failover.pm
151lib/Bio/DB/Fasta.pm
152lib/Bio/DB/FileCache.pm
153lib/Bio/DB/Flat.pm
154lib/Bio/DB/Flat/BDB.pm
155lib/Bio/DB/Flat/BDB/embl.pm
156lib/Bio/DB/Flat/BDB/fasta.pm
157lib/Bio/DB/Flat/BDB/genbank.pm
158lib/Bio/DB/Flat/BDB/swiss.pm
159lib/Bio/DB/Flat/BinarySearch.pm
160lib/Bio/DB/GFF/Util/Binning.pm
161lib/Bio/DB/GFF/Util/Rearrange.pm
162lib/Bio/DB/GenericWebAgent.pm
163lib/Bio/DB/InMemoryCache.pm
164lib/Bio/DB/IndexedBase.pm
165lib/Bio/DB/LocationI.pm
166lib/Bio/DB/Qual.pm
167lib/Bio/DB/Query/WebQuery.pm
168lib/Bio/DB/QueryI.pm
169lib/Bio/DB/RandomAccessI.pm
170lib/Bio/DB/ReferenceI.pm
171lib/Bio/DB/Registry.pm
172lib/Bio/DB/SeqI.pm
173lib/Bio/DB/Taxonomy.pm
174lib/Bio/DB/Taxonomy/flatfile.pm
175lib/Bio/DB/Taxonomy/greengenes.pm
176lib/Bio/DB/Taxonomy/list.pm
177lib/Bio/DB/Taxonomy/silva.pm
178lib/Bio/DB/UpdateableSeqI.pm
179lib/Bio/DB/WebDBSeqI.pm
180lib/Bio/DBLinkContainerI.pm
181lib/Bio/Das/FeatureTypeI.pm
182lib/Bio/Das/SegmentI.pm
183lib/Bio/DasI.pm
184lib/Bio/DescribableI.pm
185lib/Bio/Event/EventGeneratorI.pm
186lib/Bio/Event/EventHandlerI.pm
187lib/Bio/Factory/AnalysisI.pm
188lib/Bio/Factory/ApplicationFactoryI.pm
189lib/Bio/Factory/DriverFactory.pm
190lib/Bio/Factory/FTLocationFactory.pm
191lib/Bio/Factory/LocationFactoryI.pm
192lib/Bio/Factory/ObjectBuilderI.pm
193lib/Bio/Factory/ObjectFactory.pm
194lib/Bio/Factory/ObjectFactoryI.pm
195lib/Bio/Factory/SeqAnalysisParserFactory.pm
196lib/Bio/Factory/SeqAnalysisParserFactoryI.pm
197lib/Bio/Factory/SequenceFactoryI.pm
198lib/Bio/Factory/SequenceProcessorI.pm
199lib/Bio/Factory/SequenceStreamI.pm
200lib/Bio/Factory/TreeFactoryI.pm
201lib/Bio/FeatureHolderI.pm
202lib/Bio/HandlerBaseI.pm
203lib/Bio/IdCollectionI.pm
204lib/Bio/IdentifiableI.pm
205lib/Bio/Index/Abstract.pm
206lib/Bio/Index/AbstractSeq.pm
207lib/Bio/Index/Blast.pm
208lib/Bio/Index/BlastTable.pm
209lib/Bio/Index/EMBL.pm
210lib/Bio/Index/Fasta.pm
211lib/Bio/Index/Fastq.pm
212lib/Bio/Index/GenBank.pm
213lib/Bio/Index/Qual.pm
214lib/Bio/Index/SwissPfam.pm
215lib/Bio/Index/Swissprot.pm
216lib/Bio/LocatableSeq.pm
217lib/Bio/Location/Atomic.pm
218lib/Bio/Location/AvWithinCoordPolicy.pm
219lib/Bio/Location/CoordinatePolicyI.pm
220lib/Bio/Location/Fuzzy.pm
221lib/Bio/Location/FuzzyLocationI.pm
222lib/Bio/Location/NarrowestCoordPolicy.pm
223lib/Bio/Location/Simple.pm
224lib/Bio/Location/Split.pm
225lib/Bio/Location/SplitLocationI.pm
226lib/Bio/Location/WidestCoordPolicy.pm
227lib/Bio/LocationI.pm
228lib/Bio/Matrix/Generic.pm
229lib/Bio/Matrix/IO.pm
230lib/Bio/Matrix/IO/mlagan.pm
231lib/Bio/Matrix/IO/phylip.pm
232lib/Bio/Matrix/IO/scoring.pm
233lib/Bio/Matrix/MatrixI.pm
234lib/Bio/Matrix/Mlagan.pm
235lib/Bio/Matrix/PSM/IO.pm
236lib/Bio/Matrix/PSM/IO/mast.pm
237lib/Bio/Matrix/PSM/IO/masta.pm
238lib/Bio/Matrix/PSM/IO/meme.pm
239lib/Bio/Matrix/PSM/IO/psiblast.pm
240lib/Bio/Matrix/PSM/IO/transfac.pm
241lib/Bio/Matrix/PSM/InstanceSite.pm
242lib/Bio/Matrix/PSM/InstanceSiteI.pm
243lib/Bio/Matrix/PSM/ProtMatrix.pm
244lib/Bio/Matrix/PSM/ProtPsm.pm
245lib/Bio/Matrix/PSM/Psm.pm
246lib/Bio/Matrix/PSM/PsmHeader.pm
247lib/Bio/Matrix/PSM/PsmHeaderI.pm
248lib/Bio/Matrix/PSM/PsmI.pm
249lib/Bio/Matrix/PSM/SiteMatrix.pm
250lib/Bio/Matrix/PSM/SiteMatrixI.pm
251lib/Bio/Matrix/PhylipDist.pm
252lib/Bio/Matrix/Scoring.pm
253lib/Bio/Ontology/DocumentRegistry.pm
254lib/Bio/Ontology/GOterm.pm
255lib/Bio/Ontology/InterProTerm.pm
256lib/Bio/Ontology/OBOEngine.pm
257lib/Bio/Ontology/OBOterm.pm
258lib/Bio/Ontology/Ontology.pm
259lib/Bio/Ontology/OntologyEngineI.pm
260lib/Bio/Ontology/OntologyI.pm
261lib/Bio/Ontology/OntologyStore.pm
262lib/Bio/Ontology/Path.pm
263lib/Bio/Ontology/PathI.pm
264lib/Bio/Ontology/Relationship.pm
265lib/Bio/Ontology/RelationshipFactory.pm
266lib/Bio/Ontology/RelationshipI.pm
267lib/Bio/Ontology/RelationshipType.pm
268lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
269lib/Bio/Ontology/SimpleOntologyEngine.pm
270lib/Bio/Ontology/Term.pm
271lib/Bio/Ontology/TermFactory.pm
272lib/Bio/Ontology/TermI.pm
273lib/Bio/OntologyIO.pm
274lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
275lib/Bio/OntologyIO/Handlers/InterProHandler.pm
276lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
277lib/Bio/OntologyIO/InterProParser.pm
278lib/Bio/OntologyIO/dagflat.pm
279lib/Bio/OntologyIO/goflat.pm
280lib/Bio/OntologyIO/obo.pm
281lib/Bio/OntologyIO/simplehierarchy.pm
282lib/Bio/OntologyIO/soflat.pm
283lib/Bio/ParameterBaseI.pm
284lib/Bio/PrimarySeq.pm
285lib/Bio/PrimarySeqI.pm
286lib/Bio/PullParserI.pm
287lib/Bio/Range.pm
288lib/Bio/RangeI.pm
289lib/Bio/Root/Exception.pm
290lib/Bio/Root/HTTPget.pm
291lib/Bio/Root/IO.pm
292lib/Bio/Root/Root.pm
293lib/Bio/Root/RootI.pm
294lib/Bio/Root/Storable.pm
295lib/Bio/Root/Test.pm
296lib/Bio/Root/TestObject.pm
297lib/Bio/Root/Utilities.pm
298lib/Bio/Root/Version.pm
299lib/Bio/Search/BlastStatistics.pm
300lib/Bio/Search/BlastUtils.pm
301lib/Bio/Search/DatabaseI.pm
302lib/Bio/Search/GenericDatabase.pm
303lib/Bio/Search/GenericStatistics.pm
304lib/Bio/Search/HSP/BlastHSP.pm
305lib/Bio/Search/HSP/BlastPullHSP.pm
306lib/Bio/Search/HSP/FastaHSP.pm
307lib/Bio/Search/HSP/GenericHSP.pm
308lib/Bio/Search/HSP/HSPFactory.pm
309lib/Bio/Search/HSP/HSPI.pm
310lib/Bio/Search/HSP/ModelHSP.pm
311lib/Bio/Search/HSP/PSLHSP.pm
312lib/Bio/Search/HSP/PsiBlastHSP.pm
313lib/Bio/Search/HSP/PullHSPI.pm
314lib/Bio/Search/HSP/WABAHSP.pm
315lib/Bio/Search/Hit/BlastHit.pm
316lib/Bio/Search/Hit/BlastPullHit.pm
317lib/Bio/Search/Hit/Fasta.pm
318lib/Bio/Search/Hit/GenericHit.pm
319lib/Bio/Search/Hit/HitFactory.pm
320lib/Bio/Search/Hit/HitI.pm
321lib/Bio/Search/Hit/ModelHit.pm
322lib/Bio/Search/Hit/PsiBlastHit.pm
323lib/Bio/Search/Hit/PullHitI.pm
324lib/Bio/Search/Iteration/GenericIteration.pm
325lib/Bio/Search/Iteration/IterationI.pm
326lib/Bio/Search/Processor.pm
327lib/Bio/Search/Result/BlastPullResult.pm
328lib/Bio/Search/Result/BlastResult.pm
329lib/Bio/Search/Result/CrossMatchResult.pm
330lib/Bio/Search/Result/GenericResult.pm
331lib/Bio/Search/Result/INFERNALResult.pm
332lib/Bio/Search/Result/PullResultI.pm
333lib/Bio/Search/Result/ResultFactory.pm
334lib/Bio/Search/Result/ResultI.pm
335lib/Bio/Search/Result/WABAResult.pm
336lib/Bio/Search/SearchUtils.pm
337lib/Bio/Search/StatisticsI.pm
338lib/Bio/Search/Tiling/MapTileUtils.pm
339lib/Bio/Search/Tiling/MapTiling.pm
340lib/Bio/Search/Tiling/TilingI.pm
341lib/Bio/SearchIO.pm
342lib/Bio/SearchIO/EventHandlerI.pm
343lib/Bio/SearchIO/FastHitEventBuilder.pm
344lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
345lib/Bio/SearchIO/SearchResultEventBuilder.pm
346lib/Bio/SearchIO/SearchWriterI.pm
347lib/Bio/SearchIO/Writer/GbrowseGFF.pm
348lib/Bio/SearchIO/Writer/HSPTableWriter.pm
349lib/Bio/SearchIO/Writer/HTMLResultWriter.pm
350lib/Bio/SearchIO/Writer/HitTableWriter.pm
351lib/Bio/SearchIO/Writer/ResultTableWriter.pm
352lib/Bio/SearchIO/Writer/TextResultWriter.pm
353lib/Bio/SearchIO/axt.pm
354lib/Bio/SearchIO/blast.pm
355lib/Bio/SearchIO/blast_pull.pm
356lib/Bio/SearchIO/blasttable.pm
357lib/Bio/SearchIO/cross_match.pm
358lib/Bio/SearchIO/erpin.pm
359lib/Bio/SearchIO/exonerate.pm
360lib/Bio/SearchIO/fasta.pm
361lib/Bio/SearchIO/gmap_f9.pm
362lib/Bio/SearchIO/infernal.pm
363lib/Bio/SearchIO/megablast.pm
364lib/Bio/SearchIO/psl.pm
365lib/Bio/SearchIO/rnamotif.pm
366lib/Bio/SearchIO/sim4.pm
367lib/Bio/SearchIO/waba.pm
368lib/Bio/SearchIO/wise.pm
369lib/Bio/Seq.pm
370lib/Bio/Seq/BaseSeqProcessor.pm
371lib/Bio/Seq/EncodedSeq.pm
372lib/Bio/Seq/LargeLocatableSeq.pm
373lib/Bio/Seq/LargePrimarySeq.pm
374lib/Bio/Seq/LargeSeq.pm
375lib/Bio/Seq/LargeSeqI.pm
376lib/Bio/Seq/Meta.pm
377lib/Bio/Seq/Meta/Array.pm
378lib/Bio/Seq/MetaI.pm
379lib/Bio/Seq/PrimaryQual.pm
380lib/Bio/Seq/PrimedSeq.pm
381lib/Bio/Seq/QualI.pm
382lib/Bio/Seq/Quality.pm
383lib/Bio/Seq/RichSeq.pm
384lib/Bio/Seq/RichSeqI.pm
385lib/Bio/Seq/SeqBuilder.pm
386lib/Bio/Seq/SeqFactory.pm
387lib/Bio/Seq/SeqFastaSpeedFactory.pm
388lib/Bio/Seq/SequenceTrace.pm
389lib/Bio/Seq/SimulatedRead.pm
390lib/Bio/Seq/TraceI.pm
391lib/Bio/SeqAnalysisParserI.pm
392lib/Bio/SeqFeature/Amplicon.pm
393lib/Bio/SeqFeature/AnnotationAdaptor.pm
394lib/Bio/SeqFeature/Collection.pm
395lib/Bio/SeqFeature/CollectionI.pm
396lib/Bio/SeqFeature/Computation.pm
397lib/Bio/SeqFeature/FeaturePair.pm
398lib/Bio/SeqFeature/Gene/Exon.pm
399lib/Bio/SeqFeature/Gene/ExonI.pm
400lib/Bio/SeqFeature/Gene/GeneStructure.pm
401lib/Bio/SeqFeature/Gene/GeneStructureI.pm
402lib/Bio/SeqFeature/Gene/Intron.pm
403lib/Bio/SeqFeature/Gene/NC_Feature.pm
404lib/Bio/SeqFeature/Gene/Poly_A_site.pm
405lib/Bio/SeqFeature/Gene/Promoter.pm
406lib/Bio/SeqFeature/Gene/Transcript.pm
407lib/Bio/SeqFeature/Gene/TranscriptI.pm
408lib/Bio/SeqFeature/Gene/UTR.pm
409lib/Bio/SeqFeature/Generic.pm
410lib/Bio/SeqFeature/Lite.pm
411lib/Bio/SeqFeature/PositionProxy.pm
412lib/Bio/SeqFeature/Primer.pm
413lib/Bio/SeqFeature/Similarity.pm
414lib/Bio/SeqFeature/SimilarityPair.pm
415lib/Bio/SeqFeature/SubSeq.pm
416lib/Bio/SeqFeature/Tools/FeatureNamer.pm
417lib/Bio/SeqFeature/Tools/IDHandler.pm
418lib/Bio/SeqFeature/Tools/TypeMapper.pm
419lib/Bio/SeqFeature/Tools/Unflattener.pm
420lib/Bio/SeqFeature/TypedSeqFeatureI.pm
421lib/Bio/SeqFeatureI.pm
422lib/Bio/SeqI.pm
423lib/Bio/SeqIO.pm
424lib/Bio/SeqIO/FTHelper.pm
425lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
426lib/Bio/SeqIO/MultiFile.pm
427lib/Bio/SeqIO/ace.pm
428lib/Bio/SeqIO/asciitree.pm
429lib/Bio/SeqIO/bsml.pm
430lib/Bio/SeqIO/bsml_sax.pm
431lib/Bio/SeqIO/embl.pm
432lib/Bio/SeqIO/embldriver.pm
433lib/Bio/SeqIO/fasta.pm
434lib/Bio/SeqIO/fastq.pm
435lib/Bio/SeqIO/game.pm
436lib/Bio/SeqIO/game/featHandler.pm
437lib/Bio/SeqIO/game/gameHandler.pm
438lib/Bio/SeqIO/game/gameSubs.pm
439lib/Bio/SeqIO/game/gameWriter.pm
440lib/Bio/SeqIO/game/seqHandler.pm
441lib/Bio/SeqIO/gbdriver.pm
442lib/Bio/SeqIO/gbxml.pm
443lib/Bio/SeqIO/gcg.pm
444lib/Bio/SeqIO/genbank.pm
445lib/Bio/SeqIO/interpro.pm
446lib/Bio/SeqIO/kegg.pm
447lib/Bio/SeqIO/largefasta.pm
448lib/Bio/SeqIO/locuslink.pm
449lib/Bio/SeqIO/mbsout.pm
450lib/Bio/SeqIO/metafasta.pm
451lib/Bio/SeqIO/msout.pm
452lib/Bio/SeqIO/phd.pm
453lib/Bio/SeqIO/pir.pm
454lib/Bio/SeqIO/qual.pm
455lib/Bio/SeqIO/raw.pm
456lib/Bio/SeqIO/scf.pm
457lib/Bio/SeqIO/seqxml.pm
458lib/Bio/SeqIO/swiss.pm
459lib/Bio/SeqIO/swissdriver.pm
460lib/Bio/SeqIO/tab.pm
461lib/Bio/SeqIO/table.pm
462lib/Bio/SeqIO/tigr.pm
463lib/Bio/SeqIO/tigrxml.pm
464lib/Bio/SeqIO/tinyseq.pm
465lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm
466lib/Bio/SeqUtils.pm
467lib/Bio/SimpleAlign.pm
468lib/Bio/SimpleAnalysisI.pm
469lib/Bio/Species.pm
470lib/Bio/Taxon.pm
471lib/Bio/Tools/Alignment/Consed.pm
472lib/Bio/Tools/Alignment/Trim.pm
473lib/Bio/Tools/AmpliconSearch.pm
474lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm
475lib/Bio/Tools/AnalysisResult.pm
476lib/Bio/Tools/Blat.pm
477lib/Bio/Tools/CodonTable.pm
478lib/Bio/Tools/Coil.pm
479lib/Bio/Tools/ECnumber.pm
480lib/Bio/Tools/EMBOSS/Palindrome.pm
481lib/Bio/Tools/EPCR.pm
482lib/Bio/Tools/ESTScan.pm
483lib/Bio/Tools/Eponine.pm
484lib/Bio/Tools/Est2Genome.pm
485lib/Bio/Tools/Fgenesh.pm
486lib/Bio/Tools/FootPrinter.pm
487lib/Bio/Tools/GFF.pm
488lib/Bio/Tools/Geneid.pm
489lib/Bio/Tools/Genemark.pm
490lib/Bio/Tools/Genewise.pm
491lib/Bio/Tools/Genomewise.pm
492lib/Bio/Tools/Genscan.pm
493lib/Bio/Tools/Glimmer.pm
494lib/Bio/Tools/Grail.pm
495lib/Bio/Tools/GuessSeqFormat.pm
496lib/Bio/Tools/IUPAC.pm
497lib/Bio/Tools/Lucy.pm
498lib/Bio/Tools/MZEF.pm
499lib/Bio/Tools/Match.pm
500lib/Bio/Tools/OddCodes.pm
501lib/Bio/Tools/Phylo/Gerp.pm
502lib/Bio/Tools/Phylo/Molphy.pm
503lib/Bio/Tools/Phylo/Molphy/Result.pm
504lib/Bio/Tools/Phylo/Phylip/ProtDist.pm
505lib/Bio/Tools/Prediction/Exon.pm
506lib/Bio/Tools/Prediction/Gene.pm
507lib/Bio/Tools/Primer/Assessor/Base.pm
508lib/Bio/Tools/Primer/AssessorI.pm
509lib/Bio/Tools/Primer/Feature.pm
510lib/Bio/Tools/Primer/Pair.pm
511lib/Bio/Tools/Primer3.pm
512lib/Bio/Tools/Prints.pm
513lib/Bio/Tools/Profile.pm
514lib/Bio/Tools/Promoterwise.pm
515lib/Bio/Tools/PrositeScan.pm
516lib/Bio/Tools/Pseudowise.pm
517lib/Bio/Tools/QRNA.pm
518lib/Bio/Tools/RandomDistFunctions.pm
519lib/Bio/Tools/RepeatMasker.pm
520lib/Bio/Tools/Run/Analysis.pm
521lib/Bio/Tools/Run/AnalysisFactory.pm
522lib/Bio/Tools/Run/GenericParameters.pm
523lib/Bio/Tools/Run/ParametersI.pm
524lib/Bio/Tools/Run/Phylo/PhyloBase.pm
525lib/Bio/Tools/Run/WrapperBase.pm
526lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
527lib/Bio/Tools/Seg.pm
528lib/Bio/Tools/SeqPattern.pm
529lib/Bio/Tools/SeqPattern/Backtranslate.pm
530lib/Bio/Tools/SeqStats.pm
531lib/Bio/Tools/SeqWords.pm
532lib/Bio/Tools/Sigcleave.pm
533lib/Bio/Tools/Signalp.pm
534lib/Bio/Tools/Signalp/ExtendedSignalp.pm
535lib/Bio/Tools/Sim4/Exon.pm
536lib/Bio/Tools/Sim4/Results.pm
537lib/Bio/Tools/Spidey/Exon.pm
538lib/Bio/Tools/Spidey/Results.pm
539lib/Bio/Tools/TandemRepeatsFinder.pm
540lib/Bio/Tools/TargetP.pm
541lib/Bio/Tools/Tmhmm.pm
542lib/Bio/Tools/ipcress.pm
543lib/Bio/Tools/isPcr.pm
544lib/Bio/Tools/pICalculator.pm
545lib/Bio/Tools/tRNAscanSE.pm
546lib/Bio/Tree/AnnotatableNode.pm
547lib/Bio/Tree/Compatible.pm
548lib/Bio/Tree/DistanceFactory.pm
549lib/Bio/Tree/Node.pm
550lib/Bio/Tree/NodeI.pm
551lib/Bio/Tree/NodeNHX.pm
552lib/Bio/Tree/RandomFactory.pm
553lib/Bio/Tree/Statistics.pm
554lib/Bio/Tree/Tree.pm
555lib/Bio/Tree/TreeFunctionsI.pm
556lib/Bio/Tree/TreeI.pm
557lib/Bio/TreeIO.pm
558lib/Bio/TreeIO/NewickParser.pm
559lib/Bio/TreeIO/TreeEventBuilder.pm
560lib/Bio/TreeIO/cluster.pm
561lib/Bio/TreeIO/lintree.pm
562lib/Bio/TreeIO/newick.pm
563lib/Bio/TreeIO/nexus.pm
564lib/Bio/TreeIO/nhx.pm
565lib/Bio/TreeIO/pag.pm
566lib/Bio/TreeIO/phyloxml.pm
567lib/Bio/TreeIO/tabtree.pm
568lib/Bio/UpdateableSeqI.pm
569lib/Bio/WebAgent.pm
570lib/BioPerl.pm
571t/00-compile.t
572t/Align/AlignStats.t
573t/Align/AlignUtil.t
574t/Align/SimpleAlign.t
575t/Align/TreeBuild.t
576t/Align/Utilities.t
577t/AlignIO/AlignIO.t
578t/AlignIO/arp.t
579t/AlignIO/bl2seq.t
580t/AlignIO/clustalw.t
581t/AlignIO/emboss.t
582t/AlignIO/fasta.t
583t/AlignIO/largemultifasta.t
584t/AlignIO/maf.t
585t/AlignIO/mase.t
586t/AlignIO/mega.t
587t/AlignIO/meme.t
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1132t/data/map_hem/HEM12.ups.fa_
1133t/data/map_hem/HEM12.ups.fa_.revcom
1134t/data/map_hem/HEM13-HEM14.fa
1135t/data/map_hem/HEM13-HEM14.meme.txt
1136t/data/map_hem/HEM13-HEM15.fa
1137t/data/map_hem/HEM13-HEM15.meme.txt
1138t/data/map_hem/HEM13.ups.fa_
1139t/data/map_hem/HEM13.ups.fa_.revcom
1140t/data/map_hem/HEM14-HEM15.fa
1141t/data/map_hem/HEM14-HEM15.meme.txt
1142t/data/map_hem/HEM14.ups.fa_
1143t/data/map_hem/HEM14.ups.fa_.revcom
1144t/data/map_hem/HEM15.ups.fa_
1145t/data/map_hem/HEM15.ups.fa_.revcom
1146t/data/map_hem/HEM2-HEM12.fa
1147t/data/map_hem/HEM2-HEM12.meme.txt
1148t/data/map_hem/HEM2-HEM13.fa
1149t/data/map_hem/HEM2-HEM13.meme.txt
1150t/data/map_hem/HEM2-HEM14.fa
1151t/data/map_hem/HEM2-HEM14.meme.txt
1152t/data/map_hem/HEM2-HEM15.fa
1153t/data/map_hem/HEM2-HEM15.meme.txt
1154t/data/map_hem/HEM2-HEM3.fa
1155t/data/map_hem/HEM2-HEM3.meme.txt
1156t/data/map_hem/HEM2-HEM4.fa
1157t/data/map_hem/HEM2-HEM4.meme.txt
1158t/data/map_hem/HEM2.ups.fa_
1159t/data/map_hem/HEM2.ups.fa_.revcom
1160t/data/map_hem/HEM3-HEM12.fa
1161t/data/map_hem/HEM3-HEM12.meme.txt
1162t/data/map_hem/HEM3-HEM13.fa
1163t/data/map_hem/HEM3-HEM13.meme.txt
1164t/data/map_hem/HEM3-HEM14.fa
1165t/data/map_hem/HEM3-HEM14.meme.txt
1166t/data/map_hem/HEM3-HEM15.fa
1167t/data/map_hem/HEM3-HEM15.meme.txt
1168t/data/map_hem/HEM3-HEM4.fa
1169t/data/map_hem/HEM3-HEM4.meme.txt
1170t/data/map_hem/HEM3.ups.fa_
1171t/data/map_hem/HEM3.ups.fa_.revcom
1172t/data/map_hem/HEM4-HEM12.fa
1173t/data/map_hem/HEM4-HEM12.meme.txt
1174t/data/map_hem/HEM4-HEM13.fa
1175t/data/map_hem/HEM4-HEM13.meme.txt
1176t/data/map_hem/HEM4-HEM14.fa
1177t/data/map_hem/HEM4-HEM14.meme.txt
1178t/data/map_hem/HEM4-HEM15.fa
1179t/data/map_hem/HEM4-HEM15.meme.txt
1180t/data/map_hem/HEM4.ups.fa_
1181t/data/map_hem/HEM4.ups.fa_.revcom
1182t/data/map_hem/yeast.nc.1.freq
1183t/data/mast.dat
1184t/data/masta.dat
1185t/data/match.output
1186t/data/mbsout/mbsout_infile1
1187t/data/mbsout/mbsout_infile2
1188t/data/mbsout/mbsout_infile3
1189t/data/megablast_output.paracel_btk
1190t/data/meme.dat
1191t/data/mini-AE001405.gb
1192t/data/mini-align.aln
1193t/data/mixedmast.dat
1194t/data/mpath.ontology.test
1195t/data/msout/bad_msout_infile1
1196t/data/msout/bad_msout_infile2
1197t/data/msout/msout_infile1
1198t/data/msout/msout_infile2
1199t/data/msout/msout_infile3
1200t/data/msout/msout_infile4
1201t/data/multi.blast.m8
1202t/data/multi.blast.m9
1203t/data/multi.phd
1204t/data/multi_1.fa
1205t/data/multi_2.fa
1206t/data/multi_blast.bls
1207t/data/multifa.seq
1208t/data/multifa.seq.qual
1209t/data/multiline-intrablock-comment.nex
1210t/data/multiresult_blastn+.bls
1211t/data/multiseq.bls
1212t/data/multiseq_tags.phd
1213t/data/myco_sites.gff
1214t/data/nei_gojobori_test.aln
1215t/data/neighbor.dist
1216t/data/new_blastn.txt
1217t/data/nhx-bacteria.nhx
1218t/data/no-genes.genscan
1219t/data/no_FH.embl
1220t/data/no_cds_example.gb
1221t/data/no_hsps.blastp
1222t/data/no_semicolon.newick
1223t/data/noninterleaved.phy
1224t/data/nucmatrix.txt
1225t/data/pep-266.aln
1226t/data/phi.out
1227t/data/phipsi.out
1228t/data/phylipdist-36.out
1229t/data/phylipdist.out
1230t/data/phyloxml_examples.xml
1231t/data/pre_rel9.swiss
1232t/data/primedseq.fa
1233t/data/primer3_infile.txt
1234t/data/primer3_outfile.txt
1235t/data/primer3_output.txt
1236t/data/prints.out
1237t/data/promoterwise.out
1238t/data/protpars.phy
1239t/data/protpars_longid.phy
1240t/data/ps_scan/out.PrositeScan
1241t/data/pseudowise.out
1242t/data/psi_xml.dat
1243t/data/psiblastreport.out
1244t/data/purine_v081.infernal
1245t/data/puzzle.tre
1246t/data/qrna-relloc.out
1247t/data/qualfile.qual
1248t/data/quoted-strings1.nex
1249t/data/quoted-strings2.nex
1250t/data/radical-whitespace.nex
1251t/data/radical-whitespace_02.nex
1252t/data/registry/bdb/seqdatabase.ini
1253t/data/registry/flat/seqdatabase.ini
1254t/data/regulation_test.obo
1255t/data/rel9.swiss
1256t/data/repeatmasker.fa.out
1257t/data/revcomp_mrna.gb
1258t/data/ribosome-slippage.gb
1259t/data/roa1.dat
1260t/data/roa1.gbxml
1261t/data/roa1.genbank
1262t/data/roa1.swiss
1263t/data/roa1_v2.dat
1264t/data/rpsblast.bls
1265t/data/rpsblast_no_hits.bls
1266t/data/sbay_c127.fas
1267t/data/sbay_c545-yeast.BLASTZ.PSL
1268t/data/seg.out
1269t/data/semicolon.newick
1270t/data/seqdatabase.ini
1271t/data/seqfeaturedb/test.gff3
1272t/data/seqfile-no-desc.pir
1273t/data/seqfile.pir
1274t/data/seqs.fas
1275t/data/seqxml.xml
1276t/data/short.blx
1277t/data/signalp.hmm.short
1278t/data/signalp.hmm.summary
1279t/data/signalp.negative.out
1280t/data/signalp.nn.short
1281t/data/signalp.nn.summary
1282t/data/signalp.positive.out
1283t/data/signalp.short
1284t/data/signalp.summary
1285t/data/sim4.for.for
1286t/data/sim4.for.rev
1287t/data/sim4.rev
1288t/data/singlescore.gbk
1289t/data/so.obo
1290t/data/sofa.ontology
1291t/data/sp_subset.obo
1292t/data/spaced_fasta.fa
1293t/data/spaces.nex
1294t/data/sparsealn.needle
1295t/data/spidey.noalignment
1296t/data/spidey.test1
1297t/data/sprintf.rnamotif
1298t/data/sv40_small.xml
1299t/data/swiss.dat
1300t/data/swisspfam.data
1301t/data/tab1part.mif
1302t/data/tab2part.mif
1303t/data/tab3part.mif
1304t/data/tandem_repeats_finder.dat
1305t/data/tandem_repeats_finder.noresults
1306t/data/tandem_repeats_finder_no_desc.dat
1307t/data/targetp.out
1308t/data/taxdump/names.dmp
1309t/data/taxdump/nodes.dmp
1310t/data/taxonomy/greengenes_taxonomy_16S_candiv_gg_2011_1.txt
1311t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta
1312t/data/tblastn.out
1313't/data/test 2.txt'
1314t/data/test-1.tab
1315t/data/test-1.tab.gb
1316t/data/test-3.0-1.meme
1317t/data/test-3.0-2.meme
1318t/data/test-4.9.meme
1319t/data/test.ace
1320t/data/test.embl
1321t/data/test.embl2sq
1322t/data/test.fasta
1323t/data/test.fastq
1324t/data/test.game
1325t/data/test.gcg
1326t/data/test.gcgblast
1327t/data/test.gcgfasta
1328t/data/test.genbank
1329t/data/test.genbank.noseq
1330t/data/test.infernal
1331t/data/test.interpro
1332t/data/test.interpro-go.xml
1333t/data/test.locuslink
1334t/data/test.metafasta
1335t/data/test.nh
1336t/data/test.nhx
1337t/data/test.phd
1338t/data/test.pir
1339t/data/test.raw
1340t/data/test.swiss
1341t/data/test.tab
1342t/data/test.tigrxml
1343t/data/test.tseq
1344t/data/test.tsv
1345t/data/test.txt
1346t/data/test.waba
1347t/data/test1.blasttab3
1348t/data/test1.wublastp
1349t/data/test2.infernal
1350t/data/test2.raw
1351t/data/test_badlf.gcg
1352t/data/test_clear_range.fastq
1353t/data/test_data.axt
1354t/data/test_space.embl
1355t/data/testaln.arp
1356t/data/testaln.clustalw
1357t/data/testaln.fasta
1358t/data/testaln.fastq
1359t/data/testaln.list
1360t/data/testaln.mase
1361t/data/testaln.mega
1362t/data/testaln.metafasta
1363t/data/testaln.msf
1364t/data/testaln.nexus
1365t/data/testaln.pfam
1366t/data/testaln.phylip
1367t/data/testaln.po
1368t/data/testaln.prodom
1369t/data/testaln.psi
1370t/data/testaln.selex
1371t/data/testaln.stockholm
1372t/data/testaln.xmfa
1373t/data/testaln2.arp
1374t/data/testaln2.fasta
1375t/data/testdat.exonerate
1376t/data/testdata.crossmatch
1377t/data/testdbaccnums.out
1378t/data/testfile.erpin
1379t/data/testfuzzy.genbank
1380t/data/tmhmm.out
1381t/data/tmp.fst
1382t/data/tol-2010-02-18.nhx
1383t/data/traits.tab
1384t/data/traittree.nexus
1385t/data/transfac.dat
1386t/data/tree_nonewline.nexus
1387t/data/tricky.wublast
1388t/data/trna.strict.rnamotif
1389t/data/urease.tre.nexus
1390t/data/version2.scf
1391t/data/version3.scf
1392t/data/wellcome_tol.nhx
1393t/data/worm_fam_2785.cdna
1394t/data/yeast.tRNAscanSE
1395