maintenance/big_split/file_classification.csv

   1 ,"AUTHORS"
   2 "Bio-Analysis","Bio/AnalysisI.pm"
   3 ,"Bio/Draw/Pictogram.pm"
   4 "Bio-Taxonomy","Bio/Taxonomy/Tree.pm"
   5 "Bio-Taxonomy","Bio/Taxonomy/FactoryI.pm"
   6 "Bio-Taxonomy","Bio/Taxonomy/Node.pm"
   7 "Bio-Taxonomy","Bio/Taxonomy/Taxon.pm"
   8 ,"Bio/HandlerBaseI.pm"
   9 ,"Bio/DescribableI.pm"
  10 ,"Bio/Nexml/Factory.pm"
  11 ,"Bio/MapIO/mapmaker.pm"
  12 ,"Bio/MapIO/fpc.pm"
  13 "Bio-SeqEvolution","Bio/SeqEvolution/DNAPoint.pm"
  14 "Bio-SeqEvolution","Bio/SeqEvolution/EvolutionI.pm"
  15 "Bio-SeqEvolution","Bio/SeqEvolution/Factory.pm"
  16 "Bio-SeqIO","Bio/SeqIO.pm"
  17 ,"Bio/OntologyIO.pm"
  18 ,"Bio/PhyloNetwork.pm"
  19 ,"Bio/DBLinkContainerI.pm"
  20 "Bio-Map","Bio/Map/Contig.pm"
  21 "Bio-Map","Bio/Map/CytoMap.pm"
  22 "Bio-Map","Bio/Map/MapI.pm"
  23 "Bio-Map","Bio/Map/Gene.pm"
  24 "Bio-Map","Bio/Map/SimpleMap.pm"
  25 "Bio-Map","Bio/Map/LinkagePosition.pm"
  26 "Bio-Map","Bio/Map/CytoMarker.pm"
  27 "Bio-Map","Bio/Map/PositionI.pm"
  28 "Bio-Map","Bio/Map/Microsatellite.pm"
  29 "Bio-Map","Bio/Map/OrderedPositionWithDistance.pm"
  30 "Bio-Map","Bio/Map/Prediction.pm"
  31 "Bio-Map","Bio/Map/Physical.pm"
  32 "Bio-Map","Bio/Map/PositionHandler.pm"
  33 "Bio-Map","Bio/Map/Position.pm"
  34 "Bio-Map","Bio/Map/PositionWithSequence.pm"
  35 "Bio-Map","Bio/Map/GenePosition.pm"
  36 "Bio-Map","Bio/Map/MarkerI.pm"
  37 "Bio-Map","Bio/Map/RelativeI.pm"
  38 "Bio-Map","Bio/Map/MappableI.pm"
  39 "Bio-Map","Bio/Map/GeneMap.pm"
  40 "Bio-Map","Bio/Map/TranscriptionFactor.pm"
  41 "Bio-Map","Bio/Map/Clone.pm"
  42 "Bio-Map","Bio/Map/Mappable.pm"
  43 "Bio-Map","Bio/Map/OrderedPosition.pm"
  44 "Bio-Map","Bio/Map/Marker.pm"
  45 "Bio-Map","Bio/Map/LinkageMap.pm"
  46 "Bio-Map","Bio/Map/GeneRelative.pm"
  47 "Bio-Map","Bio/Map/Relative.pm"
  48 "Bio-Map","Bio/Map/CytoPosition.pm"
  49 "Bio-Map","Bio/Map/FPCMarker.pm"
  50 "Bio-Map","Bio/Map/PositionHandlerI.pm"
  51 "Bio-Map","Bio/Map/EntityI.pm"
  52 "Bio-Restriction","Bio/Restriction/EnzymeCollection.pm"
  53 "Bio-Restriction","Bio/Restriction/IO/withrefm.pm"
  54 "Bio-Restriction","Bio/Restriction/IO/itype2.pm"
  55 "Bio-Restriction","Bio/Restriction/IO/prototype.pm"
  56 "Bio-Restriction","Bio/Restriction/IO/bairoch.pm"
  57 "Bio-Restriction","Bio/Restriction/IO/base.pm"
  58 "Bio-Restriction","Bio/Restriction/Enzyme/MultiSite.pm"
  59 "Bio-Restriction","Bio/Restriction/Enzyme/MultiCut.pm"
  60 "Bio-Restriction","Bio/Restriction/IO.pm"
  61 "Bio-Restriction","Bio/Restriction/Analysis.pm"
  62 "Bio-Restriction","Bio/Restriction/Enzyme.pm"
  63 "Bio-Restriction","Bio/Restriction/EnzymeI.pm"
  64 ,"Bio/LocationI.pm"
  65 "Bio-Tree","Bio/TreeIO/phyloxml.pm"
  66 "Bio-Tree","Bio/TreeIO/pag.pm"
  67 "Bio-Tree","Bio/TreeIO/lintree.pm"
  68 "Bio-Tree","Bio/TreeIO/svggraph.pm"
  69 "Bio-Tree","Bio/TreeIO/nexml.pm"
  70 "Bio-Tree","Bio/TreeIO/nhx.pm"
  71 "Bio-Tree","Bio/TreeIO/nexus.pm"
  72 "Bio-Tree","Bio/TreeIO/tabtree.pm"
  73 "Bio-Tree","Bio/TreeIO/newick.pm"
  74 "Bio-Tree","Bio/TreeIO/cluster.pm"
  75 "Bio-Tree","Bio/TreeIO/TreeEventBuilder.pm"
  76 "Bio-Analysis","Bio/AnalysisResultI.pm"
  77 ,"Bio/Range.pm"
  78 "Bio-Tree","Bio/TreeIO.pm"
  79 ,"Bio/IdentifiableI.pm"
  80 "Bio-Das","Bio/Das/SegmentI.pm"
  81 "Bio-Das","Bio/Das/FeatureTypeI.pm"
  82 ,"Bio/PullParserI.pm"
  83 "Bio-Analysis","Bio/Factory/AnalysisI.pm"
  84 ,"Bio/Factory/SequenceProcessorI.pm"
  85 ,"Bio/Factory/SequenceStreamI.pm"
  86 ,"Bio/Factory/ObjectFactoryI.pm"
  87 ,"Bio/Factory/TreeFactoryI.pm"
  88 ,"Bio/Factory/SeqAnalysisParserFactoryI.pm"
  89 ,"Bio/Factory/MapFactoryI.pm"
  90 ,"Bio/Factory/SequenceFactoryI.pm"
  91 ,"Bio/Factory/SeqAnalysisParserFactory.pm"
  92 ,"Bio/Factory/ObjectBuilderI.pm"
  93 ,"Bio/Factory/ApplicationFactoryI.pm"
  94 ,"Bio/Factory/FTLocationFactory.pm"
  95 ,"Bio/Factory/ObjectFactory.pm"
  96 ,"Bio/Factory/DriverFactory.pm"
  97 ,"Bio/Factory/LocationFactoryI.pm"
  98 ,"Bio/Species.pm"
  99 ,"Bio/NexmlIO.pm"
 100 "Bio-Cluster","Bio/Cluster/UniGene.pm"
 101 "Bio-Cluster","Bio/Cluster/UniGeneI.pm"
 102 "Bio-Cluster","Bio/Cluster/FamilyI.pm"
 103 "Bio-Cluster","Bio/Cluster/SequenceFamily.pm"
 104 "Bio-Cluster","Bio/Cluster/ClusterFactory.pm"
 105 ,"Bio/SimpleAlign.pm"
 106 "Bio-Cluster","Bio/ClusterI.pm"
 107 "Bio-Coordinate","Bio/Coordinate/Graph.pm"
 108 "Bio-Coordinate","Bio/Coordinate/GeneMapper.pm"
 109 "Bio-Coordinate","Bio/Coordinate/Chain.pm"
 110 "Bio-Coordinate","Bio/Coordinate/Collection.pm"
 111 "Bio-Coordinate","Bio/Coordinate/Result.pm"
 112 "Bio-Coordinate","Bio/Coordinate/ResultI.pm"
 113 "Bio-Coordinate","Bio/Coordinate/Pair.pm"
 114 "Bio-Coordinate","Bio/Coordinate/MapperI.pm"
 115 "Bio-Coordinate","Bio/Coordinate/ExtrapolatingPair.pm"
 116 "Bio-Coordinate","Bio/Coordinate/Utils.pm"
 117 "Bio-Coordinate","Bio/Coordinate/Result/Gap.pm"
 118 "Bio-Coordinate","Bio/Coordinate/Result/Match.pm"
 119 ,"Bio/Seq.pm"
 120 "Bio-Tree","Bio/Tree/Draw/Cladogram.pm"
 121 "Bio-Tree","Bio/Tree/DistanceFactory.pm"
 122 "Bio-Tree","Bio/Tree/Compatible.pm"
 123 "Bio-Tree","Bio/Tree/TreeI.pm"
 124 "Bio-Tree","Bio/Tree/Tree.pm"
 125 "Bio-Tree","Bio/Tree/AnnotatableNode.pm"
 126 "Bio-Tree","Bio/Tree/NodeI.pm"
 127 "Bio-Tree","Bio/Tree/AlleleNode.pm"
 128 "Bio-Tree","Bio/Tree/Statistics.pm"
 129 "Bio-Tree","Bio/Tree/RandomFactory.pm"
 130 "Bio-Tree","Bio/Tree/Node.pm"
 131 "Bio-Tree","Bio/Tree/TreeFunctionsI.pm"
 132 "Bio-Tree","Bio/Tree/NodeNHX.pm"
 133 ,"Bio/Structure/IO/pdb.pm"
 134 "Bio-Structure","Bio/Structure/Atom.pm"
 135 "Bio-Structure","Bio/Structure/Residue.pm"
 136 "Bio-Structure","Bio/Structure/StructureI.pm"
 137 "Bio-Structure","Bio/Structure/Chain.pm"
 138 "Bio-Structure","Bio/Structure/IO.pm"
 139 "Bio-Structure","Bio/Structure/Model.pm"
 140 "Bio-Structure","Bio/Structure/Entry.pm"
 141 "Bio-Structure","Bio/Structure/SecStr/DSSP/Res.pm"
 142 "Bio-Structure","Bio/Structure/SecStr/STRIDE/Res.pm"
 143 "Bio-SeqFeature-Annotated","Bio/SeqFeature/Annotated.pm"
 144 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/ExonI.pm"
 145 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/UTR.pm"
 146 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Exon.pm"
 147 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Transcript.pm"
 148 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/GeneStructure.pm"
 149 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/GeneStructureI.pm"
 150 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Poly_A_site.pm"
 151 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/NC_Feature.pm"
 152 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Promoter.pm"
 153 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Intron.pm"
 154 "Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/TranscriptI.pm"
 155 ,"Bio/SeqFeature/Generic.pm"
 156 ,"Bio/SeqFeature/SiRNA/Pair.pm"
 157 ,"Bio/SeqFeature/SiRNA/Oligo.pm"
 158 ,"Bio/SeqFeature/FeaturePair.pm"
 159 ,"Bio/SeqFeature/Similarity.pm"
 160 ,"Bio/SeqFeature/Computation.pm"
 161 ,"Bio/SeqFeature/Collection.pm"
 162 ,"Bio/SeqFeature/Primer.pm"
 163 ,"Bio/SeqFeature/SimilarityPair.pm"
 164 ,"Bio/SeqFeature/AnnotationAdaptor.pm"
 165 ,"Bio/SeqFeature/PositionProxy.pm"
 166 ,"Bio/SeqFeature/TypedSeqFeatureI.pm"
 167 ,"Bio/SeqFeature/Lite.pm"
 168 ,"Bio/SeqFeature/CollectionI.pm"
 169 ,"Bio/SeqFeature/Tools/Unflattener.pm"
 170 ,"Bio/SeqFeature/Tools/IDHandler.pm"
 171 ,"Bio/SeqFeature/Tools/FeatureNamer.pm"
 172 ,"Bio/SeqFeature/Tools/TypeMapper.pm"
 173 "Bio-Variation","Bio/Variation/AAReverseMutate.pm"
 174 "Bio-Variation","Bio/Variation/IO/flat.pm"
 175 "Bio-Variation","Bio/Variation/IO/xml.pm"
 176 "Bio-Variation","Bio/Variation/AAChange.pm"
 177 "Bio-Variation","Bio/Variation/SNP.pm"
 178 "Bio-Variation","Bio/Variation/README"
 179 "Bio-Variation","Bio/Variation/SeqDiff.pm"
 180 "Bio-Variation","Bio/Variation/IO.pm"
 181 "Bio-Variation","Bio/Variation/RNAChange.pm"
 182 "Bio-Variation","Bio/Variation/DNAMutation.pm"
 183 "Bio-Variation","Bio/Variation/Allele.pm"
 184 "Bio-Variation","Bio/Variation/VariantI.pm"
 185 ,"Bio/AnnotationCollectionI.pm"
 186 ,"Bio/Perl.pm"
 187 ,"Bio/MolEvol/CodonModel.pm"
 188 "Bio-Align","Bio/AlignIO/proda.pm"
 189 "Bio-Align","Bio/AlignIO/stockholm.pm"
 190 "Bio-Align","Bio/AlignIO/clustalw.pm"
 191 "Bio-Align","Bio/AlignIO/xmfa.pm"
 192 "Bio-Align","Bio/AlignIO/selex.pm"
 193 "Bio-Align","Bio/AlignIO/fasta.pm"
 194 "Bio-Align","Bio/AlignIO/bl2seq.pm"
 195 "Bio-Align","Bio/AlignIO/emboss.pm"
 196 "Bio-Align","Bio/AlignIO/arp.pm"
 197 "Bio-Align","Bio/AlignIO/prodom.pm"
 198 "Bio-Align","Bio/AlignIO/po.pm"
 199 "Bio-Align","Bio/AlignIO/nexml.pm"
 200 "Bio-Align","Bio/AlignIO/meme.pm"
 201 "Bio-Align","Bio/AlignIO/mega.pm"
 202 "Bio-Align","Bio/AlignIO/pfam.pm"
 203 "Bio-Align","Bio/AlignIO/largemultifasta.pm"
 204 "Bio-Align","Bio/AlignIO/maf.pm"
 205 "Bio-Align","Bio/AlignIO/nexus.pm"
 206 "Bio-Align","Bio/AlignIO/msf.pm"
 207 "Bio-Align","Bio/AlignIO/psi.pm"
 208 "Bio-Align","Bio/AlignIO/phylip.pm"
 209 "Bio-Align","Bio/AlignIO/Handler/GenericAlignHandler.pm"
 210 "Bio-Align","Bio/AlignIO/mase.pm"
 211 "Bio-Align","Bio/AlignIO/metafasta.pm"
 212 ,"Bio/SeqFeatureI.pm"
 213 "Bio-Align","Bio/Align/DNAStatistics.pm"
 214 "Bio-Align","Bio/Align/ProteinStatistics.pm"
 215 "Bio-Align","Bio/Align/AlignI.pm"
 216 "Bio-Align","Bio/Align/PairwiseStatistics.pm"
 217 "Bio-Align","Bio/Align/Utilities.pm"
 218 "Bio-Align","Bio/Align/Graphics.pm"
 219 "Bio-Align","Bio/Align/StatisticsI.pm"
 220 ,"Bio/UpdateableSeqI.pm"
 221 ,"Bio/CodonUsage/IO.pm"
 222 ,"Bio/CodonUsage/Table.pm"
 223 ,"Bio/ClusterIO/unigene.pm"
 224 ,"Bio/ClusterIO/dbsnp.pm"
 225 ,"Bio/PrimarySeq.pm"
 226 ,"Bio/SearchIO.pm"
 227 "Bio-Seq-Meta","Bio/Seq/MetaI.pm"
 228 "Bio-Seq","Bio/Seq/LargeSeqI.pm"
 229 "Bio-Seq","Bio/Seq/EncodedSeq.pm"
 230 "Bio-Seq","Bio/Seq/LargeSeq.pm"
 231 "Bio-Seq","Bio/Seq/QualI.pm"
 232 "Bio-Seq","Bio/Seq/SeqWithQuality.pm"
 233 "Bio-Seq","Bio/Seq/LargeLocatableSeq.pm"
 234 "Bio-Seq","Bio/Seq/Quality.pm"
 235 "Bio-Seq","Bio/Seq/TraceI.pm"
 236 "Bio-Seq","Bio/Seq/SequenceTrace.pm"
 237 "Bio-Seq-Meta","Bio/Seq/Meta.pm"
 238 "Bio-Seq","Bio/Seq/PrimedSeq.pm"
 239 "Bio-Seq","Bio/Seq/SeqFastaSpeedFactory.pm"
 240 "Bio-Seq","Bio/Seq/SeqBuilder.pm"
 241 "Bio-Seq","Bio/Seq/RichSeqI.pm"
 242 "Bio-Seq","Bio/Seq/BaseSeqProcessor.pm"
 243 "Bio-Seq","Bio/Seq/PrimaryQual.pm"
 244 "Bio-Seq-Meta","Bio/Seq/Meta/Array.pm"
 245 "Bio-Seq","Bio/Seq/LargePrimarySeq.pm"
 246 "Bio-Seq","Bio/Seq/SeqFactory.pm"
 247 "Bio-Seq","Bio/Seq/RichSeq.pm"
 248 ,"Bio/IdCollectionI.pm"
 249 "Bio-Analysis","Bio/AnalysisParserI.pm"
 250 "Bio-Ontology","Bio/Ontology/GOterm.pm"
 251 "Bio-Ontology","Bio/Ontology/DocumentRegistry.pm"
 252 "Bio-Ontology","Bio/Ontology/RelationshipFactory.pm"
 253 "Bio-Ontology","Bio/Ontology/Ontology.pm"
 254 "Bio-Ontology","Bio/Ontology/InterProTerm.pm"
 255 "Bio-Ontology","Bio/Ontology/TermI.pm"
 256 "Bio-Ontology","Bio/Ontology/Path.pm"
 257 "Bio-Ontology","Bio/Ontology/TermFactory.pm"
 258 "Bio-Ontology","Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm"
 259 "Bio-Ontology","Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm"
 260 "Bio-Ontology","Bio/Ontology/Relationship.pm"
 261 "Bio-Ontology","Bio/Ontology/RelationshipI.pm"
 262 "Bio-Ontology","Bio/Ontology/Term.pm"
 263 "Bio-Ontology","Bio/Ontology/OBOEngine.pm"
 264 "Bio-Ontology","Bio/Ontology/OntologyEngineI.pm"
 265 "Bio-Ontology","Bio/Ontology/OntologyI.pm"
 266 "Bio-Ontology","Bio/Ontology/PathI.pm"
 267 "Bio-Ontology","Bio/Ontology/SimpleOntologyEngine.pm"
 268 "Bio-Ontology","Bio/Ontology/OBOterm.pm"
 269 "Bio-Ontology","Bio/Ontology/RelationshipType.pm"
 270 "Bio-Ontology","Bio/Ontology/OntologyStore.pm"
 271 ,"Bio/AnnotatableI.pm"
 272 "Bio-Assembly","Bio/Assembly/Contig.pm"
 273 "Bio-Assembly","Bio/Assembly/IO/maq.pm"
 274 "Bio-Assembly","Bio/Assembly/IO/ace.pm"
 275 "Bio-Assembly","Bio/Assembly/IO/phrap.pm"
 276 "Bio-Assembly","Bio/Assembly/IO/sam.pm"
 277 "Bio-Assembly","Bio/Assembly/IO/tigr.pm"
 278 "Bio-Assembly","Bio/Assembly/IO/bowtie.pm"
 279 "Bio-Assembly","Bio/Assembly/ScaffoldI.pm"
 280 "Bio-Assembly","Bio/Assembly/IO.pm"
 281 "Bio-Assembly","Bio/Assembly/Singlet.pm"
 282 "Bio-Assembly","Bio/Assembly/ContigAnalysis.pm"
 283 "Bio-Assembly","Bio/Assembly/Scaffold.pm"
 284 "Bio-Assembly","Bio/Assembly/Tools/ContigSpectrum.pm"
 285 ,"Bio/Symbol/DNAAlphabet.pm"
 286 ,"Bio/Symbol/README.Symbol"
 287 ,"Bio/Symbol/Symbol.pm"
 288 ,"Bio/Symbol/AlphabetI.pm"
 289 ,"Bio/Symbol/ProteinAlphabet.pm"
 290 ,"Bio/Symbol/Alphabet.pm"
 291 ,"Bio/Symbol/SymbolI.pm"
 292 ,"Bio/MapIO.pm"
 293 ,"Bio/WebAgent.pm"
 294 "Bio-Annotation","Bio/Annotation/SimpleValue.pm"
 295 "Bio-Annotation","Bio/Annotation/Relation.pm"
 296 "Bio-Annotation","Bio/Annotation/OntologyTerm.pm"
 297 "Bio-Annotation","Bio/Annotation/TypeManager.pm"
 298 "Bio-Annotation","Bio/Annotation/Tree.pm"
 299 "Bio-Annotation","Bio/Annotation/AnnotationFactory.pm"
 300 "Bio-Annotation","Bio/Annotation/Collection.pm"
 301 "Bio-Annotation","Bio/Annotation/StructuredValue.pm"
 302 "Bio-Annotation","Bio/Annotation/Reference.pm"
 303 "Bio-Annotation","Bio/Annotation/TagTree.pm"
 304 "Bio-Annotation","Bio/Annotation/DBLink.pm"
 305 "Bio-Annotation","Bio/Annotation/Target.pm"
 306 "Bio-Annotation","Bio/Annotation/Comment.pm"
 307 "Bio-Phenotype","Bio/Phenotype/PhenotypeI.pm"
 308 "Bio-Phenotype","Bio/Phenotype/MeSH/Twig.pm"
 309 "Bio-Phenotype","Bio/Phenotype/MeSH/Term.pm"
 310 "Bio-Phenotype","Bio/Phenotype/Phenotype.pm"
 311 "Bio-Phenotype","Bio/Phenotype/Measure.pm"
 312 "Bio-Phenotype","Bio/Phenotype/Correlate.pm"
 313 "Bio-Phenotype","Bio/Phenotype/OMIM/MiniMIMentry.pm"
 314 "Bio-Phenotype","Bio/Phenotype/OMIM/OMIMentry.pm"
 315 "Bio-Phenotype","Bio/Phenotype/OMIM/OMIMparser.pm"
 316 "Bio-Phenotype","Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm"
 317 "Bio-Index","Bio/Index/BlastTable.pm"
 318 "Bio-Index","Bio/Index/Qual.pm"
 319 "Bio-HMMER","Bio/Index/Hmmer.pm"
 320 "Bio-Index","Bio/Index/Swissprot.pm"
 321 "Bio-Index","Bio/Index/Fasta.pm"
 322 "Bio-Index","Bio/Index/SwissPfam.pm"
 323 "Bio-Index","Bio/Index/AbstractSeq.pm"
 324 "Bio-Index","Bio/Index/Stockholm.pm"
 325 "Bio-Index","Bio/Index/EMBL.pm"
 326 "Bio-Index","Bio/Index/Blast.pm"
 327 "Bio-Index","Bio/Index/Abstract.pm"
 328 "Bio-Index","Bio/Index/GenBank.pm"
 329 "Bio-Index","Bio/Index/Fastq.pm"
 330 "Bio-PhyloNetwork","Bio/PhyloNetwork/TreeFactoryMulti.pm"
 331 "Bio-PhyloNetwork","Bio/PhyloNetwork/TreeFactoryX.pm"
 332 "Bio-PhyloNetwork","Bio/PhyloNetwork/TreeFactory.pm"
 333 "Bio-PhyloNetwork","Bio/PhyloNetwork/FactoryX.pm"
 334 "Bio-PhyloNetwork","Bio/PhyloNetwork/RandomFactory.pm"
 335 "Bio-PhyloNetwork","Bio/PhyloNetwork/GraphViz.pm"
 336 "Bio-PhyloNetwork","Bio/PhyloNetwork/muVector.pm"
 337 "Bio-PhyloNetwork","Bio/PhyloNetwork/Factory.pm"
 338 "Bio-Matrix","Bio/Matrix/IO/mlagan.pm"
 339 "Bio-Matrix","Bio/Matrix/IO/phylip.pm"
 340 "Bio-Matrix","Bio/Matrix/IO/scoring.pm"
 341 "Bio-Matrix","Bio/Matrix/Generic.pm"
 342 "Bio-Matrix","Bio/Matrix/Scoring.pm"
 343 "Bio-Matrix","Bio/Matrix/IO.pm"
 344 "Bio-Matrix","Bio/Matrix/PhylipDist.pm"
 345 "Bio-Matrix","Bio/Matrix/Mlagan.pm"
 346 "Bio-Matrix","Bio/Matrix/MatrixI.pm"
 347 "Bio-Matrix","Bio/Matrix/PSM/IO/mast.pm"
 348 "Bio-Matrix","Bio/Matrix/PSM/IO/psiblast.pm"
 349 "Bio-Matrix","Bio/Matrix/PSM/IO/masta.pm"
 350 "Bio-Matrix","Bio/Matrix/PSM/IO/meme.pm"
 351 "Bio-Matrix","Bio/Matrix/PSM/IO/transfac.pm"
 352 "Bio-Matrix","Bio/Matrix/PSM/SiteMatrixI.pm"
 353 "Bio-Matrix","Bio/Matrix/PSM/SiteMatrix.pm"
 354 "Bio-Matrix","Bio/Matrix/PSM/ProtMatrix.pm"
 355 "Bio-Matrix","Bio/Matrix/PSM/IO.pm"
 356 "Bio-Matrix","Bio/Matrix/PSM/ProtPsm.pm"
 357 "Bio-Matrix","Bio/Matrix/PSM/InstanceSiteI.pm"
 358 "Bio-Matrix","Bio/Matrix/PSM/Psm.pm"
 359 "Bio-Matrix","Bio/Matrix/PSM/PsmHeaderI.pm"
 360 "Bio-Matrix","Bio/Matrix/PSM/InstanceSite.pm"
 361 "Bio-Matrix","Bio/Matrix/PSM/PsmHeader.pm"
 362 "Bio-Matrix","Bio/Matrix/PSM/PsmI.pm"
 363 ,"Bio/RangeI.pm"
 364 "Bio-Search","Bio/SearchIO/axt.pm"
 365 "Bio-Search","Bio/SearchIO/rnamotif.pm"
 366 "Bio-Search","Bio/SearchIO/SearchResultEventBuilder.pm"
 367 "Bio-HMMER","Bio/SearchIO/hmmer_pull.pm"
 368 "Bio-Search","Bio/SearchIO/fasta.pm"
 369 "Bio-Search","Bio/SearchIO/SearchWriterI.pm"
 370 "Bio-Search","Bio/SearchIO/psl.pm"
 371 "Bio-Search","Bio/SearchIO/erpin.pm"
 372 "Bio-Search","Bio/SearchIO/IteratedSearchResultEventBuilder.pm"
 373 "Bio-Search","Bio/SearchIO/cross_match.pm"
 374 "Bio-Search","Bio/SearchIO/EventHandlerI.pm"
 375 "Bio-Search","Bio/SearchIO/exonerate.pm"
 376 "Bio-Search","Bio/SearchIO/gmap_f9.pm"
 377 "Bio-HMMER","Bio/SearchIO/hmmer3.pm"
 378 "Bio-Search","Bio/SearchIO/infernal.pm"
 379 "Bio-Search","Bio/SearchIO/Writer/GbrowseGFF.pm"
 380 "Bio-Search","Bio/SearchIO/Writer/HSPTableWriter.pm"
 381 "Bio-Search","Bio/SearchIO/Writer/BSMLResultWriter.pm"
 382 "Bio-Search","Bio/SearchIO/Writer/HitTableWriter.pm"
 383 "Bio-Search","Bio/SearchIO/Writer/HTMLResultWriter.pm"
 384 "Bio-Search","Bio/SearchIO/Writer/TextResultWriter.pm"
 385 "Bio-Search","Bio/SearchIO/Writer/ResultTableWriter.pm"
 386 "Bio-Search","Bio/SearchIO/megablast.pm"
 387 "Bio-Search","Bio/SearchIO/blastxml.pm"
 388 "Bio-Search","Bio/SearchIO/FastHitEventBuilder.pm"
 389 "Bio-Search","Bio/SearchIO/wise.pm"
 390 "Bio-Search","Bio/SearchIO/blast_pull.pm"
 391 "Bio-Search","Bio/SearchIO/waba.pm"
 392 "Bio-HMMER","Bio/SearchIO/hmmer.pm"
 393 "Bio-Search","Bio/SearchIO/blasttable.pm"
 394 "Bio-Search","Bio/SearchIO/blast.pm"
 395 "Bio-Search","Bio/SearchIO/sim4.pm"
 396 "Bio-Search","Bio/SearchIO/XML/BlastHandler.pm"
 397 "Bio-Search","Bio/SearchIO/XML/PsiBlastHandler.pm"
 398 "Bio-FeatureIO","Bio/FeatureIO/gtf.pm"
 399 "Bio-FeatureIO","Bio/FeatureIO/interpro.pm"
 400 "Bio-FeatureIO","Bio/FeatureIO/bed.pm"
 401 "Bio-FeatureIO","Bio/FeatureIO/gff.pm"
 402 "Bio-FeatureIO","Bio/FeatureIO/vecscreen_simple.pm"
 403 "Bio-FeatureIO","Bio/FeatureIO/ptt.pm"
 404 ,"Bio/ParameterBaseI.pm"
 405 "Bio-Search","Bio/Search/Tiling/MapTiling.pm"
 406 "Bio-Search","Bio/Search/Tiling/MapTileUtils.pm"
 407 "Bio-Search","Bio/Search/Tiling/TilingI.pm"
 408 "Bio-Search","Bio/Search/SearchUtils.pm"
 409 "Bio-Search","Bio/Search/GenericDatabase.pm"
 410 "Bio-Search","Bio/Search/Iteration/GenericIteration.pm"
 411 "Bio-Search","Bio/Search/Iteration/IterationI.pm"
 412 "Bio-Search","Bio/Search/BlastStatistics.pm"
 413 "Bio-Search","Bio/Search/Processor.pm"
 414 "Bio-Search","Bio/Search/Hit/BlastHit.pm"
 415 "Bio-Search","Bio/Search/Hit/GenericHit.pm"
 416 "Bio-Search","Bio/Search/Hit/Fasta.pm"
 417 "Bio-Search","Bio/Search/Hit/ModelHit.pm"
 418 "Bio-Search","Bio/Search/Hit/HitI.pm"
 419 "Bio-HMMER","Bio/Search/Hit/hmmer3Hit.pm"
 420 "Bio-HMMER","Bio/Search/Hit/HMMERHit.pm"
 421 "Bio-Search","Bio/Search/Hit/PsiBlastHit.pm"
 422 "Bio-Search","Bio/Search/Hit/BlastPullHit.pm"
 423 "Bio-Search","Bio/Search/Hit/HitFactory.pm"
 424 "Bio-Search","Bio/Search/Hit/PullHitI.pm"
 425 "Bio-Search","Bio/Search/Hit/HmmpfamHit.pm"
 426 "Bio-Search","Bio/Search/BlastUtils.pm"
 427 "Bio-Search","Bio/Search/GenericStatistics.pm"
 428 "Bio-Search","Bio/Search/StatisticsI.pm"
 429 "Bio-Search","Bio/Search/HSP/GenericHSP.pm"
 430 "Bio-Search","Bio/Search/HSP/HSPI.pm"
 431 "Bio-Search","Bio/Search/HSP/FastaHSP.pm"
 432 "Bio-Search","Bio/Search/HSP/BlastHSP.pm"
 433 "Bio-Search","Bio/Search/HSP/WABAHSP.pm"
 434 "Bio-Search","Bio/Search/HSP/HmmpfamHSP.pm"
 435 "Bio-Search","Bio/Search/HSP/BlastPullHSP.pm"
 436 "Bio-Search","Bio/Search/HSP/ModelHSP.pm"
 437 "Bio-Search","Bio/Search/HSP/HSPFactory.pm"
 438 "Bio-HMMER","Bio/Search/HSP/HMMERHSP.pm"
 439 "Bio-HMMER","Bio/Search/HSP/hmmer3HSP.pm"
 440 "Bio-Search","Bio/Search/HSP/PSLHSP.pm"
 441 "Bio-Search","Bio/Search/HSP/PsiBlastHSP.pm"
 442 "Bio-Search","Bio/Search/HSP/PullHSPI.pm"
 443 "Bio-HMMER","Bio/Search/Result/hmmer3Result.pm"
 444 "Bio-Search","Bio/Search/Result/BlastResult.pm"
 445 "Bio-Search","Bio/Search/Result/ResultFactory.pm"
 446 "Bio-Search","Bio/Search/Result/CrossMatchResult.pm"
 447 "Bio-Search","Bio/Search/Result/WABAResult.pm"
 448 "Bio-Search","Bio/Search/Result/ResultI.pm"
 449 "Bio-Search","Bio/Search/Result/BlastPullResult.pm"
 450 "Bio-Search","Bio/Search/Result/HmmpfamResult.pm"
 451 "Bio-HMMER","Bio/Search/Result/HMMERResult.pm"
 452 "Bio-Search","Bio/Search/Result/GenericResult.pm"
 453 "Bio-Search","Bio/Search/Result/PullResultI.pm"
 454 "Bio-Search","Bio/Search/DatabaseI.pm"
 455 ,"Bio/PrimarySeqI.pm"
 456 ,"Bio/FeatureHolderI.pm"
 457 ,"Bio/AnnotationI.pm"
 458 "Bio-Biblio","Bio/Biblio/Organisation.pm"
 459 "Bio-Biblio","Bio/Biblio/Ref.pm"
 460 "Bio-Biblio","Bio/Biblio/PubmedArticle.pm"
 461 "Bio-Biblio","Bio/Biblio/IO/pubmed2ref.pm"
 462 "Bio-Biblio","Bio/Biblio/IO/pubmedxml.pm"
 463 "Bio-Biblio","Bio/Biblio/IO/medline2ref.pm"
 464 "Bio-Biblio","Bio/Biblio/IO/medlinexml.pm"
 465 "Bio-Biblio","Bio/Biblio/WebResource.pm"
 466 "Bio-Biblio","Bio/Biblio/TechReport.pm"
 467 "Bio-Biblio","Bio/Biblio/Service.pm"
 468 "Bio-Biblio","Bio/Biblio/Journal.pm"
 469 "Bio-Biblio","Bio/Biblio/MedlineArticle.pm"
 470 "Bio-Biblio","Bio/Biblio/Patent.pm"
 471 "Bio-Biblio","Bio/Biblio/IO.pm"
 472 "Bio-Biblio","Bio/Biblio/JournalArticle.pm"
 473 "Bio-Biblio","Bio/Biblio/BookArticle.pm"
 474 "Bio-Biblio","Bio/Biblio/Thesis.pm"
 475 "Bio-Biblio","Bio/Biblio/MedlineJournalArticle.pm"
 476 "Bio-Biblio","Bio/Biblio/Article.pm"
 477 "Bio-Biblio","Bio/Biblio/Book.pm"
 478 "Bio-Biblio","Bio/Biblio/MedlineBookArticle.pm"
 479 "Bio-Biblio","Bio/Biblio/Proceeding.pm"
 480 "Bio-Biblio","Bio/Biblio/Person.pm"
 481 "Bio-Biblio","Bio/Biblio/PubmedJournalArticle.pm"
 482 "Bio-Biblio","Bio/Biblio/Provider.pm"
 483 "Bio-Biblio","Bio/Biblio/BiblioBase.pm"
 484 "Bio-Biblio","Bio/Biblio/PubmedBookArticle.pm"
 485 "Bio-Biblio","Bio/Biblio/MedlineBook.pm"
 486 "Bio-Biblio","Bio/Biblio/MedlineJournal.pm"
 487 "Bio-DB","Bio/DB/HIV.pm"
 488 ,"Bio/DB/RandomAccessI.pm"
 489 ,"Bio/DB/Taxonomy/flatfile.pm"
 490 ,"Bio/DB/Taxonomy/entrez.pm"
 491 ,"Bio/DB/Taxonomy/list.pm"
 492 ,"Bio/DB/QueryI.pm"
 493 ,"Bio/DB/SwissProt.pm"
 494 ,"Bio/DB/EntrezGene.pm"
 495 ,"Bio/DB/Registry.pm"
 496 ,"Bio/DB/MeSH.pm"
 497 ,"Bio/DB/HIV/HIVQueryHelper.pm"
 498 ,"Bio/DB/HIV/HIVAnnotProcessor.pm"
 499 ,"Bio/DB/HIV/lanl-schema.xml"
 500 ,"Bio/DB/CUTG.pm"
 501 ,"Bio/DB/Flat.pm"
 502 ,"Bio/DB/InMemoryCache.pm"
 503 ,"Bio/DB/BiblioI.pm"
 504 ,"Bio/DB/LocationI.pm"
 505 ,"Bio/DB/Qual.pm"
 506 ,"Bio/DB/WebDBSeqI.pm"
 507 ,"Bio/DB/TFBS.pm"
 508 ,"Bio/DB/Fasta.pm"
 509 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedFeature.pm"
 510 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Segment.pm"
 511 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedFeatureI.pm"
 512 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/berkeleydb.pm"
 513 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/LoadHelper.pm"
 514 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/GFF2Loader.pm"
 515 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/Loader.pm"
 516 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/Iterator.pm"
 517 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/mysql.pm"
 518 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/SQLite.pm"
 519 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/Pg.pm"
 520 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/berkeleydb3.pm"
 521 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/GFF3Loader.pm"
 522 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/FeatureFileLoader.pm"
 523 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/bdb.pm"
 524 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/memory.pm"
 525 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store.pm"
 526 "Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedTableFeatureI.pm"
 527 "AcePerl","Bio/DB/Ace.pm"
 528 ,"Bio/DB/GenPept.pm"
 529 ,"Bio/DB/Flat/BDB.pm"
 530 ,"Bio/DB/Flat/BinarySearch.pm"
 531 ,"Bio/DB/Flat/BDB/swiss.pm"
 532 ,"Bio/DB/Flat/BDB/fasta.pm"
 533 ,"Bio/DB/Flat/BDB/genbank.pm"
 534 ,"Bio/DB/Flat/BDB/embl.pm"
 535 ,"Bio/DB/SeqVersion.pm"
 536 ,"Bio/DB/NCBIHelper.pm"
 537 ,"Bio/DB/BioFetch.pm"
 538 ,"Bio/DB/DBFetch.pm"
 539 "Bio-DB-GFF","Bio/DB/GFF/Homol.pm"
 540 "Bio-DB-GFF","Bio/DB/GFF/Feature.pm"
 541 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/berkeleydb.pm"
 542 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/memory/feature_serializer.pm"
 543 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/memory/iterator.pm"
 544 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi.pm"
 545 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm"
 546 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/ace.pm"
 547 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm"
 548 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm"
 549 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/caching_handle.pm"
 550 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysql.pm"
 551 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/pg.pm"
 552 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/oracleace.pm"
 553 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/pg_fts.pm"
 554 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/oracle.pm"
 555 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysqlace.pm"
 556 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/iterator.pm"
 557 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/biofetch_oracle.pm"
 558 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/memory.pm"
 559 "Bio-DB-GFF","Bio/DB/GFF/Adaptor/biofetch.pm"
 560 "Bio-DB-GFF","Bio/DB/GFF/Typename.pm"
 561 "Bio-DB-GFF","Bio/DB/GFF/Segment.pm"
 562 "Bio-DB-GFF","Bio/DB/GFF/Util/Binning.pm"
 563 "Bio-DB-GFF","Bio/DB/GFF/Util/Rearrange.pm"
 564 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm"
 565 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/coding.pm"
 566 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_twinscan.pm"
 567 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/none.pm"
 568 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/clone.pm"
 569 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/gene.pm"
 570 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/transcript.pm"
 571 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/processed_transcript.pm"
 572 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_acembly.pm"
 573 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/orf.pm"
 574 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/alignment.pm"
 575 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_ensgene.pm"
 576 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_refgene.pm"
 577 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_genscan.pm"
 578 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_softberry.pm"
 579 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_sanger22.pm"
 580 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_unigene.pm"
 581 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/match.pm"
 582 "Bio-DB-GFF","Bio/DB/GFF/Aggregator/so_transcript.pm"
 583 "Bio-DB-GFF","Bio/DB/GFF/RelSegment.pm"
 584 "Bio-DB-GFF","Bio/DB/GFF/Aggregator.pm"
 585 "Bio-DB-GFF","Bio/DB/GFF/Featname.pm"
 586 ,"Bio/DB/UpdateableSeqI.pm"
 587 ,"Bio/DB/GenericWebAgent.pm"
 588 ,"Bio/DB/SeqFeature.pm"
 589 ,"Bio/DB/RefSeq.pm"
 590 ,"Bio/DB/Failover.pm"
 591 ,"Bio/DB/EMBL.pm"
 592 ,"Bio/DB/Query/WebQuery.pm"
 593 ,"Bio/DB/Query/GenBank.pm"
 594 ,"Bio/DB/Query/HIVQuery.pm"
 595 ,"Bio/DB/Expression/geo.pm"
 596 ,"Bio/DB/Biblio/eutils.pm"
 597 ,"Bio/DB/Biblio/soap.pm"
 598 ,"Bio/DB/Biblio/biofetch.pm"
 599 ,"Bio/DB/SeqI.pm"
 600 ,"Bio/DB/FileCache.pm"
 601 ,"Bio/DB/GenBank.pm"
 602 ,"Bio/DB/TFBS/transfac_pro.pm"
 603 ,"Bio/DB/Universal.pm"
 604 ,"Bio/DB/Expression.pm"
 605 ,"Bio/DB/EUtilities.pm"
 606 ,"Bio/DB/SeqVersion/gi.pm"
 607 ,"Bio/DB/ReferenceI.pm"
 608 ,"Bio/DB/Taxonomy.pm"
 609 ,"Bio/DB/GFF.pm"
 610 ,"Bio/SeqI.pm"
 611 "Bio-PopGen","Bio/PopGen/HtSNP.pm"
 612 "Bio-PopGen","Bio/PopGen/TagHaplotype.pm"
 613 "Bio-PopGen","Bio/PopGen/GenotypeI.pm"
 614 "Bio-PopGen","Bio/PopGen/PopStats.pm"
 615 "Bio-PopGen","Bio/PopGen/IO/phase.pm"
 616 "Bio-PopGen","Bio/PopGen/IO/hapmap.pm"
 617 "Bio-PopGen","Bio/PopGen/IO/csv.pm"
 618 "Bio-PopGen","Bio/PopGen/IO/prettybase.pm"
 619 "Bio-PopGen","Bio/PopGen/PopulationI.pm"
 620 "Bio-PopGen","Bio/PopGen/IO.pm"
 621 "Bio-PopGen","Bio/PopGen/IndividualI.pm"
 622 "Bio-PopGen","Bio/PopGen/Statistics.pm"
 623 "Bio-PopGen","Bio/PopGen/Population.pm"
 624 "Bio-PopGen","Bio/PopGen/Individual.pm"
 625 "Bio-PopGen","Bio/PopGen/MarkerI.pm"
 626 "Bio-PopGen","Bio/PopGen/Simulation/Coalescent.pm"
 627 "Bio-PopGen","Bio/PopGen/Simulation/GeneticDrift.pm"
 628 "Bio-PopGen","Bio/PopGen/Utilities.pm"
 629 "Bio-PopGen","Bio/PopGen/Marker.pm"
 630 "Bio-PopGen","Bio/PopGen/Genotype.pm"
 631 "Bio-Cluster","Bio/ClusterIO.pm"
 632 "Bio-Align","Bio/AlignIO.pm"
 633 "Bio-Biblio","Bio/Biblio.pm"
 634 "Bio-FeatureIO","Bio/FeatureIO.pm"
 635 "Bio-Location","Bio/Location/Split.pm"
 636 "Bio-Location","Bio/Location/NarrowestCoordPolicy.pm"
 637 "Bio-Location","Bio/Location/FuzzyLocationI.pm"
 638 "Bio-Location","Bio/Location/SplitLocationI.pm"
 639 "Bio-Location","Bio/Location/Simple.pm"
 640 "Bio-Location","Bio/Location/CoordinatePolicyI.pm"
 641 "Bio-Location","Bio/Location/WidestCoordPolicy.pm"
 642 "Bio-Location","Bio/Location/Atomic.pm"
 643 "Bio-Location","Bio/Location/Fuzzy.pm"
 644 "Bio-Location","Bio/Location/AvWithinCoordPolicy.pm"
 645 ,"Bio/LocatableSeq.pm"
 646 "Bio-LiveSeq","Bio/LiveSeq/DNA.pm"
 647 "Bio-LiveSeq","Bio/LiveSeq/Exon.pm"
 648 "Bio-LiveSeq","Bio/LiveSeq/IO/README"
 649 "Bio-LiveSeq","Bio/LiveSeq/IO/Loader.pm"
 650 "Bio-LiveSeq","Bio/LiveSeq/IO/BioPerl.pm"
 651 "Bio-LiveSeq","Bio/LiveSeq/Gene.pm"
 652 "Bio-LiveSeq","Bio/LiveSeq/Range.pm"
 653 "Bio-LiveSeq","Bio/LiveSeq/Transcript.pm"
 654 "Bio-LiveSeq","Bio/LiveSeq/Mutation.pm"
 655 "Bio-LiveSeq","Bio/LiveSeq/Chain.pm"
 656 "Bio-LiveSeq","Bio/LiveSeq/ChainI.pm"
 657 "Bio-LiveSeq","Bio/LiveSeq/AARange.pm"
 658 "Bio-LiveSeq","Bio/LiveSeq/Repeat_Unit.pm"
 659 "Bio-LiveSeq","Bio/LiveSeq/Repeat_Region.pm"
 660 "Bio-LiveSeq","Bio/LiveSeq/Mutator.pm"
 661 "Bio-LiveSeq","Bio/LiveSeq/Prim_Transcript.pm"
 662 "Bio-LiveSeq","Bio/LiveSeq/SeqI.pm"
 663 "Bio-LiveSeq","Bio/LiveSeq/Intron.pm"
 664 "Bio-LiveSeq","Bio/LiveSeq/Translation.pm"
 665 ,"Bio/Taxon.pm"
 666 "Bio-Ontology","Bio/OntologyIO/obo.pm"
 667 "Bio-Ontology","Bio/OntologyIO/InterProParser.pm"
 668 "Bio-Ontology","Bio/OntologyIO/Handlers/InterProHandler.pm"
 669 "Bio-Ontology","Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm"
 670 "Bio-Ontology","Bio/OntologyIO/Handlers/BaseSAXHandler.pm"
 671 "Bio-Ontology","Bio/OntologyIO/soflat.pm"
 672 "Bio-Ontology","Bio/OntologyIO/dagflat.pm"
 673 "Bio-Ontology","Bio/OntologyIO/simplehierarchy.pm"
 674 "Bio-Ontology","Bio/OntologyIO/goflat.pm"
 675 ,"Bio/Event/EventHandlerI.pm"
 676 ,"Bio/Event/EventGeneratorI.pm"
 677 ,"Bio/Root/Test/Warn.pm"
 678 ,"Bio/Root/Root.pm"
 679 ,"Bio/Root/Exception.pm"
 680 ,"Bio/Root/Version.pm"
 681 ,"Bio/Root/RootI.pm"
 682 ,"Bio/Root/IO.pm"
 683 ,"Bio/Root/Build.pm"
 684 ,"Bio/Root/HTTPget.pm"
 685 ,"Bio/Root/Utilities.pm"
 686 ,"Bio/Root/Test.pm"
 687 ,"Bio/Root/Storable.pm"
 688 ,"Bio/SimpleAnalysisI.pm"
 689 ,"Bio/SearchDist.pm"
 690 ,"Bio/SeqAnalysisParserI.pm"
 691 ,"Bio/DasI.pm"
 692 "Bio-SeqIO","Bio/SeqIO/lasergene.pm"
 693 "Bio-SeqIO","Bio/SeqIO/bsml_sax.pm"
 694 "Bio-SeqIO","Bio/SeqIO/agave.pm"
 695 "Bio-SeqIO","Bio/SeqIO/interpro.pm"
 696 "Bio-SeqIO","Bio/SeqIO/gbxml.pm"
 697 "Bio-SeqIO","Bio/SeqIO/swiss.pm"
 698 "Bio-SeqIO","Bio/SeqIO/fasta.pm"
 699 "Bio-SeqIO","Bio/SeqIO/chadoxml.pm"
 700 "Bio-SeqIO","Bio/SeqIO/MultiFile.pm"
 701 "Bio-SeqIO","Bio/SeqIO/kegg.pm"
 702 "Bio-SeqIO","Bio/SeqIO/bsml.pm"
 703 "Bio-SeqIO","Bio/SeqIO/game.pm"
 704 "Bio-SeqIO","Bio/SeqIO/tinyseq/tinyseqHandler.pm"
 705 "Bio-SeqIO","Bio/SeqIO/game/gameHandler.pm"
 706 "Bio-SeqIO","Bio/SeqIO/game/featHandler.pm"
 707 "Bio-SeqIO","Bio/SeqIO/game/gameWriter.pm"
 708 "Bio-SeqIO","Bio/SeqIO/game/gameSubs.pm"
 709 "Bio-SeqIO","Bio/SeqIO/game/seqHandler.pm"
 710 "Bio-SeqIO","Bio/SeqIO/FTHelper.pm"
 711 "Bio-SeqIO","Bio/SeqIO/ace.pm"
 712 "Bio-SeqIO","Bio/SeqIO/tinyseq.pm"
 713 "Bio-SeqIO","Bio/SeqIO/entrezgene.pm"
 714 "Bio-SeqIO","Bio/SeqIO/qual.pm"
 715 "Bio-SeqIO","Bio/SeqIO/tigrxml.pm"
 716 "Bio-SeqIO","Bio/SeqIO/largefasta.pm"
 717 "Bio-SeqIO","Bio/SeqIO/tab.pm"
 718 "Bio-SeqIO","Bio/SeqIO/nexml.pm"
 719 "Bio-SeqIO","Bio/SeqIO/ctf.pm"
 720 "Bio-SeqIO","Bio/SeqIO/genbank.pm"
 721 "Bio-SeqIO","Bio/SeqIO/msout.pm"
 722 "Bio-SeqIO","Bio/SeqIO/excel.pm"
 723 "Bio-SeqIO","Bio/SeqIO/gbdriver.pm"
 724 "Bio-SeqIO","Bio/SeqIO/ztr.pm"
 725 "Bio-SeqIO","Bio/SeqIO/pln.pm"
 726 "Bio-SeqIO","Bio/SeqIO/embl.pm"
 727 "Bio-SeqIO","Bio/SeqIO/fastq.pm"
 728 "Bio-SeqIO","Bio/SeqIO/pir.pm"
 729 "Bio-SeqIO","Bio/SeqIO/raw.pm"
 730 "Bio-SeqIO","Bio/SeqIO/asciitree.pm"
 731 "Bio-SeqIO","Bio/SeqIO/seqxml.pm"
 732 "Bio-SeqIO","Bio/SeqIO/chaos.pm"
 733 "Bio-SeqIO","Bio/SeqIO/gcg.pm"
 734 "Bio-SeqIO","Bio/SeqIO/tigr.pm"
 735 "Bio-SeqIO","Bio/SeqIO/scf.pm"
 736 "Bio-SeqIO","Bio/SeqIO/embldriver.pm"
 737 "Bio-SeqIO","Bio/SeqIO/table.pm"
 738 "Bio-SeqIO","Bio/SeqIO/locuslink.pm"
 739 "Bio-SeqIO","Bio/SeqIO/chaosxml.pm"
 740 "Bio-SeqIO","Bio/SeqIO/exp.pm"
 741 "Bio-SeqIO","Bio/SeqIO/abi.pm"
 742 "Bio-SeqIO","Bio/SeqIO/Handler/GenericRichSeqHandler.pm"
 743 "Bio-SeqIO","Bio/SeqIO/strider.pm"
 744 "Bio-SeqIO","Bio/SeqIO/alf.pm"
 745 "Bio-SeqIO","Bio/SeqIO/swissdriver.pm"
 746 "Bio-SeqIO","Bio/SeqIO/phd.pm"
 747 "Bio-SeqIO","Bio/SeqIO/metafasta.pm"
 748 "Bio-SeqIO","Bio/SeqIO/flybase_chadoxml.pm"
 749 "Bio-Taxonomy","Bio/Taxonomy.pm"
 750 ,"Bio/Tools/CodonTable.pm"
 751 ,"Bio/Tools/Prints.pm"
 752 ,"Bio/Tools/Eponine.pm"
 753 ,"Bio/Tools/Glimmer.pm"
 754 "Bio-HMMER","Bio/Tools/HMMER/Results.pm"
 755 "Bio-HMMER","Bio/Tools/HMMER/Set.pm"
 756 "Bio-HMMER","Bio/Tools/HMMER/Domain.pm"
 757 ,"Bio/Tools/Lucy.pm"
 758 ,"Bio/Tools/SeqWords.pm"
 759 ,"Bio/Tools/GuessSeqFormat.pm"
 760 ,"Bio/Tools/TargetP.pm"
 761 ,"Bio/Tools/SeqPattern.pm"
 762 ,"Bio/Tools/pSW.pm"
 763 ,"Bio/Tools/Hmmpfam.pm"
 764 ,"Bio/Tools/Genewise.pm"
 765 ,"Bio/Tools/QRNA.pm"
 766 ,"Bio/Tools/Profile.pm"
 767 ,"Bio/Tools/Primer/Feature.pm"
 768 ,"Bio/Tools/Primer/AssessorI.pm"
 769 ,"Bio/Tools/Primer/Pair.pm"
 770 ,"Bio/Tools/Primer/Assessor/Base.pm"
 771 ,"Bio/Tools/Run/ParametersI.pm"
 772 ,"Bio/Tools/Run/RemoteBlast.pm"
 773 ,"Bio/Tools/Run/WrapperBase/CommandExts.pm"
 774 ,"Bio/Tools/Run/README"
 775 "Bio-HMMER","Bio/Tools/Run/hmmer3.pm"
 776 ,"Bio/Tools/Run/WrapperBase.pm"
 777 ,"Bio/Tools/Run/GenericParameters.pm"
 778 ,"Bio/Tools/Run/StandAloneWUBlast.pm"
 779 ,"Bio/Tools/Run/StandAloneBlast.pm"
 780 ,"Bio/Tools/Run/StandAloneNCBIBlast.pm"
 781 ,"Bio/Tools/Signalp/ExtendedSignalp.pm"
 782 ,"Bio/Tools/SiRNA/Ruleset/tuschl.pm"
 783 ,"Bio/Tools/SiRNA/Ruleset/saigo.pm"
 784 ,"Bio/Tools/Genscan.pm"
 785 ,"Bio/Tools/Genemark.pm"
 786 ,"Bio/Tools/OddCodes.pm"
 787 ,"Bio/Tools/ipcress.pm"
 788 ,"Bio/Tools/Est2Genome.pm"
 789 ,"Bio/Tools/Sim4/Results.pm"
 790 ,"Bio/Tools/Sim4/Exon.pm"
 791 ,"Bio/Tools/SeqStats.pm"
 792 ,"Bio/Tools/ERPIN.pm"
 793 ,"Bio/Tools/RNAMotif.pm"
 794 ,"Bio/Tools/dpAlign.pm"
 795 ,"Bio/Tools/Alignment/Trim.pm"
 796 ,"Bio/Tools/Alignment/Consed.pm"
 797 ,"Bio/Tools/Primer3.pm"
 798 ,"Bio/Tools/AnalysisResult.pm"
 799 ,"Bio/Tools/Match.pm"
 800 ,"Bio/Tools/Phylo/Molphy/Result.pm"
 801 ,"Bio/Tools/Phylo/Gumby.pm"
 802 ,"Bio/Tools/Phylo/PAML/Codeml.pm"
 803 ,"Bio/Tools/Phylo/PAML/ModelResult.pm"
 804 ,"Bio/Tools/Phylo/PAML/Result.pm"
 805 ,"Bio/Tools/Phylo/Phylip/ProtDist.pm"
 806 ,"Bio/Tools/Phylo/Molphy.pm"
 807 ,"Bio/Tools/Phylo/Gerp.pm"
 808 ,"Bio/Tools/Phylo/PAML.pm"
 809 ,"Bio/Tools/Gel.pm"
 810 ,"Bio/Tools/Genomewise.pm"
 811 ,"Bio/Tools/Signalp.pm"
 812 ,"Bio/Tools/Infernal.pm"
 813 ,"Bio/Tools/EUtilities/Summary/DocSum.pm"
 814 ,"Bio/Tools/EUtilities/Summary/ItemContainerI.pm"
 815 ,"Bio/Tools/EUtilities/Summary/Item.pm"
 816 ,"Bio/Tools/EUtilities/Info/LinkInfo.pm"
 817 ,"Bio/Tools/EUtilities/Info/FieldInfo.pm"
 818 ,"Bio/Tools/EUtilities/HistoryI.pm"
 819 ,"Bio/Tools/EUtilities/Info.pm"
 820 ,"Bio/Tools/EUtilities/EUtilParameters.pm"
 821 ,"Bio/Tools/EUtilities/EUtilDataI.pm"
 822 ,"Bio/Tools/EUtilities/History.pm"
 823 ,"Bio/Tools/EUtilities/Cookie.pm"
 824 ,"Bio/Tools/EUtilities/Link.pm"
 825 ,"Bio/Tools/EUtilities/Summary.pm"
 826 ,"Bio/Tools/EUtilities/Query/GlobalQuery.pm"
 827 ,"Bio/Tools/EUtilities/Query.pm"
 828 ,"Bio/Tools/EUtilities/Link/LinkSet.pm"
 829 ,"Bio/Tools/EUtilities/Link/UrlLink.pm"
 830 ,"Bio/Tools/FootPrinter.pm"
 831 ,"Bio/Tools/TandemRepeatsFinder.pm"
 832 ,"Bio/Tools/Analysis/SimpleAnalysisBase.pm"
 833 ,"Bio/Tools/Analysis/DNA/ESEfinder.pm"
 834 ,"Bio/Tools/Analysis/Protein/Domcut.pm"
 835 ,"Bio/Tools/Analysis/Protein/Sopma.pm"
 836 ,"Bio/Tools/Analysis/Protein/NetPhos.pm"
 837 ,"Bio/Tools/Analysis/Protein/Scansite.pm"
 838 ,"Bio/Tools/Analysis/Protein/ELM.pm"
 839 ,"Bio/Tools/Analysis/Protein/GOR4.pm"
 840 ,"Bio/Tools/Analysis/Protein/HNN.pm"
 841 ,"Bio/Tools/AlignFactory.pm"
 842 ,"Bio/Tools/Promoterwise.pm"
 843 ,"Bio/Tools/Geneid.pm"
 844 ,"Bio/Tools/Sigcleave.pm"
 845 ,"Bio/Tools/IUPAC.pm"
 846 ,"Bio/Tools/SiRNA.pm"
 847 ,"Bio/Tools/pICalculator.pm"
 848 ,"Bio/Tools/SeqPattern/Backtranslate.pm"
 849 ,"Bio/Tools/Blat.pm"
 850 ,"Bio/Tools/ECnumber.pm"
 851 ,"Bio/Tools/tRNAscanSE.pm"
 852 ,"Bio/Tools/Fgenesh.pm"
 853 ,"Bio/Tools/Prediction/Exon.pm"
 854 ,"Bio/Tools/Prediction/Gene.pm"
 855 ,"Bio/Tools/Pseudowise.pm"
 856 ,"Bio/Tools/RepeatMasker.pm"
 857 ,"Bio/Tools/Tmhmm.pm"
 858 ,"Bio/Tools/Grail.pm"
 859 ,"Bio/Tools/MZEF.pm"
 860 ,"Bio/Tools/Protparam.pm"
 861 ,"Bio/Tools/isPcr.pm"
 862 ,"Bio/Tools/EPCR.pm"
 863 ,"Bio/Tools/Coil.pm"
 864 ,"Bio/Tools/Spidey/Results.pm"
 865 ,"Bio/Tools/Spidey/Exon.pm"
 866 ,"Bio/Tools/EMBOSS/Palindrome.pm"
 867 ,"Bio/Tools/EUtilities.pm"
 868 ,"Bio/Tools/Seg.pm"
 869 ,"Bio/Tools/PrositeScan.pm"
 870 ,"Bio/Tools/RandomDistFunctions.pm"
 871 ,"Bio/Tools/ESTScan.pm"
 872 ,"Bio/Tools/GFF.pm"
 873 ,"Bio/SeqUtils.pm"
 874 ,"BioPerl.pm"
 875 ,"BUGS"
 876 ,"Build.PL"
 877 ,"Changes"
 878 ,"DEPENDENCIES"
 879 ,"DEPRECATED"
 880 ,"doc/README"
 881 ,"doc/makedoc.PL"
 882 ,"doc/Deobfuscator/excluded_modules.txt"
 883 ,"doc/Deobfuscator/t/00.load.t"
 884 ,"doc/Deobfuscator/t/pod.t"
 885 ,"doc/Deobfuscator/LICENSE"
 886 ,"doc/Deobfuscator/META.yml"
 887 ,"doc/Deobfuscator/README"
 888 ,"doc/Deobfuscator/bin/deob_index.pl"
 889 ,"doc/Deobfuscator/Makefile.PL"
 890 ,"doc/Deobfuscator/Build.PL"
 891 ,"doc/Deobfuscator/lib/Deobfuscator.pm"
 892 ,"doc/Deobfuscator/cgi-bin/deob_detail.cgi"
 893 ,"doc/Deobfuscator/cgi-bin/deob_interface.cgi"
 894 ,"doc/Deobfuscator/cgi-bin/deob_help.html"
 895 ,"doc/Deobfuscator/cgi-bin/deob_flowchart.png"
 896 ,"doc/Deobfuscator/Changes"
 897 ,"doc/Deobfuscator/MANIFEST"
 898 ,"examples/bioperl.pl"
 899 ,"examples/subsequence.cgi"
 900 ,"examples/searchio/resultwriter.pl"
 901 ,"examples/searchio/waba2gff3.pl"
 902 ,"examples/searchio/custom_writer.pl"
 903 ,"examples/searchio/psiblast_iterations.pl"
 904 ,"examples/searchio/psiblast_features.pl"
 905 ,"examples/searchio/waba2gff.pl"
 906 ,"examples/searchio/htmlwriter.pl"
 907 ,"examples/searchio/blast_example.pl"
 908 ,"examples/searchio/hitwriter.pl"
 909 ,"examples/searchio/hspwriter.pl"
 910 ,"examples/searchio/rawwriter.pl"
 911 ,"examples/root/exceptions3.pl"
 912 ,"examples/root/README"
 913 ,"examples/root/exceptions1.pl"
 914 ,"examples/root/exceptions2.pl"
 915 ,"examples/root/exceptions4.pl"
 916 ,"examples/sirna/rnai_finder.cgi"
 917 ,"examples/sirna/TAG"
 918 ,"examples/cluster/dbsnp.pl"
 919 ,"examples/quality/svgtrace.pl"
 920 ,"examples/longorf.pl"
 921 ,"examples/revcom_dir.pl"
 922 ,"examples/align/simplealign.pl"
 923 ,"examples/align/clustalw.pl"
 924 ,"examples/align/aligntutorial.pl"
 925 ,"examples/align/align_on_codons.pl"
 926 ,"examples/biblio/biblio-eutils-example.pl"
 927 ,"examples/biblio/biblio_soap.pl"
 928 ,"examples/biblio/biblio-soap-example.pl"
 929 ,"examples/generate_random_seq.pl"
 930 ,"examples/rev_and_trans.pl"
 931 ,"examples/liveseq/change_gene.pl"
 932 ,"examples/structure/structure-io.pl"
 933 ,"examples/tools/run_genscan.pl"
 934 ,"examples/tools/extract_genes.pl"
 935 ,"examples/tools/standaloneblast.pl"
 936 ,"examples/tools/gff2ps.pl"
 937 ,"examples/tools/parse_codeml.pl"
 938 ,"examples/tools/gb_to_gff.pl"
 939 ,"examples/tools/seq_pattern.pl"
 940 ,"examples/tools/run_primer3.pl"
 941 ,"examples/tools/psw.pl"
 942 ,"examples/tools/reverse-translate.pl"
 943 ,"examples/contributed/nmrpdb_parse.pl"
 944 ,"examples/contributed/rebase2list.pl"
 945 ,"examples/contributed/prosite2perl.pl"
 946 ,"examples/Bio-DB-GFF/load_ucsc.pl"
 947 ,"examples/make_primers.pl"
 948 ,"examples/db/get_seqs.pl"
 949 ,"examples/db/use_registry.pl"
 950 ,"examples/db/getGenBank.pl"
 951 ,"examples/db/est_tissue_query.pl"
 952 ,"examples/db/gb2features.pl"
 953 ,"examples/db/rfetch.pl"
 954 ,"examples/db/dbfetch"
 955 ,"examples/tk/hitdisplay.pl"
 956 ,"examples/tk/gsequence.pl"
 957 ,"examples/popgen/parse_calc_stats.pl"
 958 ,"examples/tree/paup2phylip.pl"
 959 ,"ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5"
 960 ,"ide/bioperl-mode/dist/bioperl-mode-xemacs.tar"
 961 ,"ide/bioperl-mode/dist/SKIP"
 962 ,"ide/bioperl-mode/dist/bioperl-mode.tar"
 963 ,"ide/bioperl-mode/dist/package-me"
 964 ,"ide/bioperl-mode/dist/bioperl-mode.tar.md5"
 965 ,"ide/bioperl-mode/dist/Changes"
 966 ,"ide/bioperl-mode/site-lisp/bioperl-mode.el"
 967 ,"ide/bioperl-mode/site-lisp/pod.el"
 968 ,"ide/bioperl-mode/site-lisp/bioperl-skel.el"
 969 ,"ide/bioperl-mode/site-lisp/bioperl-init.el"
 970 ,"ide/bioperl-mode/README"
 971 ,"ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm"
 972 ,"ide/bioperl-mode/etc/images/bpmode-tool.xpm"
 973 ,"ide/bioperl.komodo"
 974 ,"ide/bioperl.lisp"
 975 ,"INSTALL"
 976 ,"INSTALL.SKIP"
 977 ,"INSTALL.WIN"
 978 ,"LICENSE"
 979 ,"maintenance/modules.pl"
 980 ,"maintenance/pod.pl"
 981 ,"maintenance/split"
 982 ,"maintenance/deprecated.pl"
 983 ,"maintenance/version.pl"
 984 ,"maintenance/authors.pl"
 985 ,"maintenance/perltidy.conf"
 986 ,"maintenance/README"
 987 ,"maintenance/symlink_script.pl"
 988 ,"maintenance/dependencies.pl"
 989 ,"maintenance/all_files"
 990 ,"maintenance/ncbi_blast_switches.pl"
 991 ,"maintenance/cvs2cl_by_file.pl"
 992 ,"maintenance/check_URLs.pl"
 993 ,"maintenance/check_NAME.pl"
 994 ,"maintenance/module_usage.pl"
 995 ,"MANIFEST"
 996 ,"MANIFEST.SKIP"
 997 ,"models/map_proposal.txt"
 998 ,"models/popgen.dia"
 999 ,"models/biblio.dia"
1000 ,"models/bioperl.dia"
1001 ,"models/README"
1002 ,"models/maps_and_markers.dia"
1003 ,"models/bio_liveseq_variation.dia"
1004 ,"models/bio_restriction.dia"
1005 ,"models/bio_map.dia"
1006 ,"models/coordinatemapper.dia"
1007 ,"models/population_proposal.txt"
1008 ,"README"
1009 ,"scripts/searchio/parse_hmmsearch.PLS"
1010 ,"scripts/searchio/filter_search.PLS"
1011 "Bio-HMMER","scripts/searchio/hmmer_to_table.PLS"
1012 ,"scripts/searchio/README"
1013 ,"scripts/searchio/fastam9_to_table.PLS"
1014 ,"scripts/searchio/search2table.PLS"
1015 ,"scripts/searchio/TAG"
1016 ,"scripts/utilities/search2tribe.PLS"
1017 ,"scripts/utilities/bp_mrtrans.PLS"
1018 ,"scripts/utilities/mutate.PLS"
1019 ,"scripts/utilities/dbsplit.PLS"
1020 ,"scripts/utilities/remote_blast.PLS"
1021 ,"scripts/utilities/README"
1022 ,"scripts/utilities/mask_by_search.PLS"
1023 ,"scripts/utilities/bp_sreformat.PLS"
1024 ,"scripts/utilities/revtrans-motif.PLS"
1025 ,"scripts/utilities/seq_length.PLS"
1026 ,"scripts/utilities/search2alnblocks.PLS"
1027 ,"scripts/utilities/bp_nrdb.PLS"
1028 ,"scripts/utilities/search2BSML.PLS"
1029 ,"scripts/utilities/pairwise_kaks.PLS"
1030 ,"scripts/utilities/TAG"
1031 ,"scripts/utilities/search2gff.PLS"
1032 ,"scripts/utilities/download_query_genbank.PLS"
1033 ,"scripts/taxa/classify_hits_kingdom.PLS"
1034 ,"scripts/taxa/taxonomy2tree.PLS"
1035 ,"scripts/taxa/query_entrez_taxa.PLS"
1036 ,"scripts/taxa/taxid4species.PLS"
1037 ,"scripts/taxa/local_taxonomydb_query.PLS"
1038 ,"scripts/taxa/TAG"
1039 ,"scripts/index/bp_index.PLS"
1040 ,"scripts/index/bp_seqret.PLS"
1041 ,"scripts/index/bp_fetch.PLS"
1042 ,"scripts/index/TAG"
1043 ,"scripts/README"
1044 ,"scripts/das/das_server.pl"
1045 ,"scripts/das/README"
1046 ,"scripts/das/TAG"
1047 ,"scripts/biblio/biblio.PLS"
1048 ,"scripts/biblio/TAG"
1049 ,"scripts/bioperl_netinstall.pl"
1050 "Bio-DB-GFF","scripts/Bio-DB-GFF/generate_histogram.PLS"
1051 "Bio-DB-GFF","scripts/Bio-DB-GFF/genbank2gff3.PLS"
1052 "Bio-DB-GFF","scripts/Bio-DB-GFF/process_sgd.PLS"
1053 "Bio-DB-GFF","scripts/Bio-DB-GFF/genbank2gff.PLS"
1054 "Bio-DB-GFF","scripts/Bio-DB-GFF/process_gadfly.PLS"
1055 "Bio-DB-GFF","scripts/Bio-DB-GFF/meta_gff.PLS"
1056 "Bio-DB-GFF","scripts/Bio-DB-GFF/README"
1057 "Bio-DB-GFF","scripts/Bio-DB-GFF/process_wormbase.PLS"
1058 "Bio-DB-GFF","scripts/Bio-DB-GFF/fast_load_gff.PLS"
1059 "Bio-DB-GFF","scripts/Bio-DB-GFF/load_gff.PLS"
1060 "Bio-DB-GFF","scripts/Bio-DB-GFF/bulk_load_gff.PLS"
1061 ,"scripts/DB/biofetch_genbank_proxy.PLS"
1062 ,"scripts/DB/biogetseq.PLS"
1063 ,"scripts/DB/flanks.PLS"
1064 ,"scripts/DB/bioflat_index.PLS"
1065 ,"scripts/DB/TAG"
1066 ,"scripts/popgen/composite_LD.PLS"
1067 ,"scripts/popgen/heterogeneity_test.PLS"
1068 ,"scripts/Bio-DB-EUtilities/einfo.PLS"
1069 ,"scripts/tree/blast2tree.PLS"
1070 ,"scripts/tree/tree2pag.PLS"
1071 ,"scripts/tree/nexus2nh.PLS"
1072 ,"scripts/tree/TAG"
1073 ,"scripts/seqstats/aacomp.PLS"
1074 ,"scripts/seqstats/oligo_count.PLS"
1075 ,"scripts/seqstats/gccalc.PLS"
1076 ,"scripts/seqstats/chaos_plot.PLS"
1077 ,"scripts/seqstats/TAG"
1078 ,"scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS"
1079 ,"scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS"
1080 ,"scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS"
1081 ,"scripts/DB-HIV/hivq.PLS"
1082 ,"scripts/seq/split_seq.PLS"
1083 ,"scripts/seq/seqconvert.PLS"
1084 ,"scripts/seq/unflatten_seq.PLS"
1085 ,"scripts/seq/translate_seq.PLS"
1086 ,"scripts/seq/make_mrna_protein.PLS"
1087 ,"scripts/seq/extract_feature_seq.PLS"
1088 ,"scripts/seq/seqretsplit.PLS"
1089 ,"scripts/seq/TAG"
1090 ,"t/Draw/Pictogram.t"
1091 ,"t/Perl.t"
1092 ,"t/Map/MicrosatelliteMarker.t"
1093 ,"t/Map/Map.t"
1094 ,"t/Map/Linkage.t"
1095 ,"t/Map/MapIO.t"
1096 ,"t/Map/Physical.t"
1097 ,"t/Map/Cyto.t"
1098 ,"t/TaxonTree.t"
1099 ,"t/Restriction/Analysis.t"
1100 ,"t/Restriction/Analysis-refac.t"
1101 ,"t/Restriction/Gel.t"
1102 ,"t/Restriction/IO.t"
1103 ,"t/SearchDist.t"
1104 ,"t/Symbol.t"
1105 ,"t/Coordinate/CoordinateGraph.t"
1106 ,"t/Coordinate/CoordinateMapper.t"
1107 ,"t/Coordinate/GeneCoordinateMapper.t"
1108 ,"t/Tree/TreeStatistics.t"
1109 ,"t/Tree/TreeIO/newick.t"
1110 ,"t/Tree/TreeIO/svggraph.t"
1111 ,"t/Tree/TreeIO/nhx.t"
1112 ,"t/Tree/TreeIO/nexus.t"
1113 ,"t/Tree/TreeIO/lintree.t"
1114 ,"t/Tree/TreeIO/tabtree.t"
1115 ,"t/Tree/TreeIO/nexml.t"
1116 ,"t/Tree/TreeIO/phyloxml.t"
1117 ,"t/Tree/Node.t"
1118 ,"t/Tree/Compatible.t"
1119 ,"t/Tree/TreeIO.t"
1120 ,"t/Tree/PhyloNetwork/RandomFactory.t"
1121 ,"t/Tree/PhyloNetwork/TreeFactory.t"
1122 ,"t/Tree/PhyloNetwork/GraphViz.t"
1123 ,"t/Tree/PhyloNetwork/Factory.t"
1124 ,"t/Tree/PhyloNetwork/PhyloNetwork.t"
1125 ,"t/Tree/PhyloNetwork/MuVector.t"
1126 ,"t/Tree/RandomTreeFactory.t"
1127 ,"t/Tree/Tree.t"
1128 ,"t/Structure/IO.t"
1129 ,"t/Structure/Structure.t"
1130 ,"t/SeqFeature/SeqFeaturePrimer.t"
1131 ,"t/SeqFeature/SeqFeatCollection.t"
1132 ,"t/SeqFeature/SeqFeatAnnotated.t"
1133 ,"t/SeqFeature/LocationFactory.t"
1134 ,"t/SeqFeature/Location.t"
1135 ,"t/SeqFeature/FeatureIO.t"
1136 ,"t/SeqFeature/RangeI.t"
1137 ,"t/SeqFeature/SeqFeature.t"
1138 ,"t/SeqFeature/Unflattener2.t"
1139 ,"t/SeqFeature/Primer.t"
1140 ,"t/SeqFeature/Range.t"
1141 ,"t/SeqFeature/SeqAnalysisParser.t"
1142 ,"t/SeqFeature/Clone.t"
1143 ,"t/SeqFeature/Unflattener.t"
1144 ,"t/Variation/RNAChange.t"
1145 ,"t/Variation/DNAMutation.t"
1146 ,"t/Variation/Variation_IO.t"
1147 ,"t/Variation/Allele.t"
1148 ,"t/Variation/SeqDiff.t"
1149 ,"t/Variation/AAReverseMutate.t"
1150 ,"t/Variation/SNP.t"
1151 ,"t/Variation/AAChange.t"
1152 ,"t/SeqIO.t"
1153 ,"t/AlignIO/phylip.t"
1154 ,"t/AlignIO/pfam.t"
1155 ,"t/AlignIO/psi.t"
1156 ,"t/AlignIO/mega.t"
1157 ,"t/AlignIO/largemultifasta.t"
1158 ,"t/AlignIO/fasta.t"
1159 ,"t/AlignIO/mase.t"
1160 ,"t/AlignIO/AlignIO.t"
1161 ,"t/AlignIO/arp.t"
1162 ,"t/AlignIO/po.t"
1163 ,"t/AlignIO/prodom.t"
1164 ,"t/AlignIO/xmfa.t"
1165 ,"t/AlignIO/nexus.t"
1166 ,"t/AlignIO/bl2seq.t"
1167 ,"t/AlignIO/selex.t"
1168 ,"t/AlignIO/nexml.t"
1169 ,"t/AlignIO/stockholm.t"
1170 ,"t/AlignIO/clustalw.t"
1171 ,"t/AlignIO/metafasta.t"
1172 ,"t/AlignIO/emboss.t"
1173 ,"t/AlignIO/maf.t"
1174 ,"t/AlignIO/msf.t"
1175 ,"t/AlignIO/meme.t"
1176 ,"t/Align/Utilities.t"
1177 ,"t/Align/AlignUtil.t"
1178 ,"t/Align/Graphics.t"
1179 ,"t/Align/AlignStats.t"
1180 ,"t/Align/TreeBuild.t"
1181 ,"t/Align/SimpleAlign.t"
1182 ,"t/ClusterIO/SequenceFamily.t"
1183 ,"t/ClusterIO/unigene.t"
1184 ,"t/ClusterIO/ClusterIO.t"
1185 ,"t/Seq/LargePSeq.t"
1186 ,"t/Seq/PrimarySeq.t"
1187 ,"t/Seq/LocatableSeq.t"
1188 ,"t/Seq/DBLink.t"
1189 ,"t/Seq/LargeLocatableSeq.t"
1190 ,"t/Seq/Seq.t"
1191 ,"t/Seq/WithQuality.t"
1192 ,"t/Seq/EncodedSeq.t"
1193 ,"t/Seq/PrimedSeq.t"
1194 ,"t/Seq/Quality.t"
1195 ,"t/Seq/MetaSeq.t"
1196 ,"t/Seq/PrimaryQual.t"
1197 ,"t/Ontology/OntologyStore.t"
1198 ,"t/Ontology/IO/obo.t"
1199 ,"t/Ontology/IO/go.t"
1200 ,"t/Ontology/IO/interpro.t"
1201 ,"t/Ontology/GOterm.t"
1202 ,"t/Ontology/Relationship.t"
1203 ,"t/Ontology/Term.t"
1204 ,"t/Ontology/RelationshipType.t"
1205 ,"t/Ontology/Ontology.t"
1206 ,"t/Ontology/GraphAdaptor.t"
1207 ,"t/Ontology/OntologyEngine.t"
1208 ,"t/Assembly/IO/sam.t"
1209 ,"t/Assembly/IO/bowtie.t"
1210 ,"t/Assembly/ContigSpectrum.t"
1211 ,"t/Assembly/core.t"
1212 ,"t/Annotation/Annotation.t"
1213 ,"t/Annotation/AnnotationAdaptor.t"
1214 ,"t/Phenotype/OMIMentry.t"
1215 ,"t/Phenotype/Correlate.t"
1216 ,"t/Phenotype/Phenotype.t"
1217 ,"t/Phenotype/Measure.t"
1218 ,"t/Phenotype/OMIMparser.t"
1219 ,"t/Phenotype/MeSH.t"
1220 ,"t/Phenotype/MiniMIMentry.t"
1221 ,"t/Phenotype/OMIMentryAllelicVariant.t"
1222 ,"t/SeqTools/SeqPattern.t"
1223 ,"t/SeqTools/OddCodes.t"
1224 ,"t/SeqTools/SeqUtils.t"
1225 ,"t/SeqTools/CodonTable.t"
1226 ,"t/SeqTools/Backtranslate.t"
1227 ,"t/SeqTools/GuessSeqFormat.t"
1228 ,"t/SeqTools/SeqStats.t"
1229 ,"t/SeqTools/ECnumber.t"
1230 ,"t/SeqTools/SeqWords.t"
1231 ,"t/SeqEvolution.t"
1232 ,"t/Matrix/IO/psm.t"
1233 ,"t/Matrix/IO/masta.t"
1234 ,"t/Matrix/ProtPsm.t"
1235 ,"t/Matrix/InstanceSite.t"
1236 ,"t/Matrix/Matrix.t"
1237 ,"t/Matrix/ProtMatrix.t"
1238 ,"t/Matrix/SiteMatrix.t"
1239 ,"t/Alphabet.t"
1240 ,"t/SearchIO/gmap_f9.t"
1241 ,"t/SearchIO/SearchIO.t"
1242 ,"t/SearchIO/fasta.t"
1243 ,"t/SearchIO/sim4.t"
1244 ,"t/SearchIO/psl.t"
1245 ,"t/SearchIO/cross_match.t"
1246 ,"t/SearchIO/waba.t"
1247 ,"t/SearchIO/erpin.t"
1248 "Bio-HMMER","t/SearchIO/hmmer.t"
1249 ,"t/SearchIO/Tiling.t"
1250 ,"t/SearchIO/exonerate.t"
1251 ,"t/SearchIO/blast_pull.t"
1252 ,"t/SearchIO/Writer/GbrowseGFF.t"
1253 ,"t/SearchIO/Writer/HTMLWriter.t"
1254 ,"t/SearchIO/Writer/HSPTableWriter.t"
1255 ,"t/SearchIO/Writer/HitTableWriter.t"
1256 ,"t/SearchIO/wise.t"
1257 ,"t/SearchIO/rnamotif.t"
1258 ,"t/SearchIO/CigarString.t"
1259 ,"t/SearchIO/blastxml.t"
1260 ,"t/SearchIO/SimilarityPair.t"
1261 ,"t/SearchIO/blasttable.t"
1262 ,"t/SearchIO/blast.t"
1263 ,"t/SearchIO/infernal.t"
1264 "Bio-HMMER","t/SearchIO/hmmer3.t"
1265 "Bio-HMMER","t/SearchIO/hmmer_pull.t"
1266 ,"t/SearchIO/megablast.t"
1267 ,"t/Species.t"
1268 ,"t/Biblio/Biblio.t"
1269 ,"t/Biblio/References.t"
1270 ,"t/Biblio/biofetch.t"
1271 ,"t/Biblio/eutils.t"
1272 ,"t/nexml.t"
1273 ,"t/lib/Error.pm"
1274 ,"t/lib/Test/Harness.pm"
1275 ,"t/lib/Test/Harness/Iterator.pm"
1276 ,"t/lib/Test/Harness/Results.pm"
1277 ,"t/lib/Test/Harness/Util.pm"
1278 ,"t/lib/Test/Harness/Point.pm"
1279 ,"t/lib/Test/Harness/Assert.pm"
1280 ,"t/lib/Test/Harness/Straps.pm"
1281 ,"t/lib/Test/Harness/TAP.pod"
1282 ,"t/lib/Test/Builder.pm"
1283 ,"t/lib/Test/Exception.pm"
1284 ,"t/lib/Test/More.pm"
1285 ,"t/lib/Test/Simple.pm"
1286 ,"t/lib/Test/Builder/Module.pm"
1287 ,"t/lib/Test/Builder/Tester/Color.pm"
1288 ,"t/lib/Test/Builder/Tester.pm"
1289 ,"t/lib/Test/Warn.pm"
1290 ,"t/lib/Test/Tutorial.pod"
1291 ,"t/lib/Sub/Uplevel.pm"
1292 ,"t/lib/Tree/DAG_Node.pm"
1293 ,"t/lib/Array/Compare.pm"
1294 ,"t/PopGen/TagHaplotype.t"
1295 ,"t/PopGen/HtSNP.t"
1296 ,"t/PopGen/PopGen.t"
1297 ,"t/PopGen/Coalescent.t"
1298 ,"t/PopGen/PopGenSims.t"
1299 ,"t/PopGen/MK.t"
1300 ,"t/PodSyntax.t"
1301 ,"t/data/test_badlf.gcg"
1302 ,"t/data/cysprot1.FASTA"
1303 ,"t/data/U71225.gb.win"
1304 ,"t/data/contigspectrumtest.tigr"
1305 ,"t/data/worm_fam_2785.cdna"
1306 ,"t/data/traittree.nexus"
1307 ,"t/data/mixedmast.dat"
1308 ,"t/data/test.genbank"
1309 ,"t/data/testaln.selex"
1310 ,"t/data/test.waba"
1311 ,"t/data/U71225.gb"
1312 ,"t/data/no_FH.embl"
1313 ,"t/data/mus.bls.xml"
1314 ,"t/data/signalp.hmm.summary"
1315 ,"t/data/test.mase"
1316 ,"t/data/pictogram.fa"
1317 ,"t/data/hybrid1.gff3"
1318 ,"t/data/omim_genemap_test_nolinebreak"
1319 ,"t/data/barns-combined.nex"
1320 ,"t/data/blastp2215.blast"
1321 ,"t/data/protpars.phy"
1322 ,"t/data/ecolitst.noseqs.wublastp"
1323 ,"t/data/hmmpfam_cs.out"
1324 ,"t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml"
1325 ,"t/data/2008.blasttable"
1326 ,"t/data/bug2901.fa"
1327 ,"t/data/compLD_test.prettybase"
1328 ,"t/data/tblastn.out"
1329 ,"t/data/alnfile.fasta"
1330 ,"t/data/char-interleave.nex"
1331 ,"t/data/pseudowise.out"
1332 ,"t/data/gmap_f9-multiple_results.txt"
1333 ,"t/data/yn00.mlc"
1334 ,"t/data/characters+trees.nexml.xml"
1335 ,"t/data/BOSS_DROME.FASTP_v35_04"
1336 ,"t/data/myco_sites.gff"
1337 ,"t/data/cysprot1b.hmmsearch"
1338 ,"t/data/bug2399.tblastn"
1339 ,"t/data/ecoli_domains.rps.xml"
1340 ,"t/data/test.fastq"
1341 ,"t/data/test.interpro-go.xml"
1342 ,"t/data/AF165282.gb"
1343 ,"t/data/primedseq.fa"
1344 ,"t/data/no-genes.genscan"
1345 ,"t/data/testaln.phylip"
1346 ,"t/data/bl2seq.bug940.out"
1347 ,"t/data/branchSite.mlc"
1348 ,"t/data/BK000016-tpa.gbk"
1349 ,"t/data/lucy.info"
1350 ,"t/data/sbay_c127.fas"
1351 ,"t/data/ecolitst.wublastp"
1352 ,"t/data/fgenesh.out"
1353 ,"t/data/503384.MEGABLAST.0"
1354 ,"t/data/HUMBETGLOA.fa"
1355 ,"t/data/aaml.mlc"
1356 ,"t/data/02_dogfish_no_taxrefs.xml"
1357 ,"t/data/roa1.dat"
1358 ,"t/data/crypto.sim4-0"
1359 ,"t/data/frac_problems2.blast"
1360 ,"t/data/ECAPAH02.embl"
1361 ,"t/data/acefile.singlets"
1362 ,"t/data/HUMBETGLOA.FASTA"
1363 ,"t/data/test.genbank.noseq"
1364 ,"t/data/mutations.dat"
1365 ,"t/data/baseml.pairwise"
1366 ,"t/data/Glimmer3.detail"
1367 ,"t/data/hs_owlmonkey.fasta"
1368 ,"t/data/cysprot1b.fa"
1369 ,"t/data/c200-vs-yeast.BLASTN"
1370 ,"t/data/map_hem/HEM12-HEM13.fa"
1371 ,"t/data/map_hem/HEM12-HEM14.fa"
1372 ,"t/data/map_hem/HEM3-HEM14.meme.txt"
1373 ,"t/data/map_hem/HEM2-HEM13.fa"
1374 ,"t/data/map_hem/HEM4-HEM14.meme.txt"
1375 ,"t/data/map_hem/HEM14.ups.fa_.revcom"
1376 ,"t/data/map_hem/HEM2.ups.fa_.revcom"
1377 ,"t/data/map_hem/HEM14-HEM15.meme.txt"
1378 ,"t/data/map_hem/HEM3-HEM4.meme.txt"
1379 ,"t/data/map_hem/HEM13-HEM15.meme.txt"
1380 ,"t/data/map_hem/HEM1.ups.fa_"
1381 ,"t/data/map_hem/HEM15.ups.fa_.revcom"
1382 ,"t/data/map_hem/HEM1-HEM12.fa.revcom"
1383 ,"t/data/map_hem/HEM3-HEM15.fa"
1384 ,"t/data/map_hem/HEM12-HEM14.meme.txt"
1385 ,"t/data/map_hem/HEM4.ups.fa_.revcom"
1386 ,"t/data/map_hem/HEM1-HEM4.fa"
1387 ,"t/data/map_hem/HEM3-HEM12.meme.txt"
1388 ,"t/data/map_hem/HEM12-HEM15.fa"
1389 ,"t/data/map_hem/HEM3.ups.fa_.revcom"
1390 ,"t/data/map_hem/HEM2-HEM15.meme.txt"
1391 ,"t/data/map_hem/HEM4-HEM12.fa"
1392 ,"t/data/map_hem/HEM1-HEM4.meme.txt"
1393 ,"t/data/map_hem/HEM15.ups.fa_"
1394 ,"t/data/map_hem/HEM1-HEM2.meme.txt"
1395 ,"t/data/map_hem/HEM14-HEM15.fa"
1396 ,"t/data/map_hem/HEM2-HEM4.fa"
1397 ,"t/data/map_hem/HEM1.ups.fa_.revcom"
1398 ,"t/data/map_hem/HEM13.ups.fa_"
1399 ,"t/data/map_hem/HEM4-HEM13.fa"
1400 ,"t/data/map_hem/HEM2-HEM14.meme.txt"
1401 ,"t/data/map_hem/HEM4-HEM15.fa"
1402 ,"t/data/map_hem/HEM12-HEM15.meme.txt"
1403 ,"t/data/map_hem/HEM2-HEM12.fa"
1404 ,"t/data/map_hem/HEM4-HEM12.meme.txt"
1405 ,"t/data/map_hem/HEM1-HEM14.fa"
1406 ,"t/data/map_hem/HEM1-HEM2.fa.revcom"
1407 ,"t/data/map_hem/HEM1-HEM12.fa"
1408 ,"t/data/map_hem/HEM2-HEM3.fa"
1409 ,"t/data/map_hem/HEM2-HEM4.meme.txt"
1410 ,"t/data/map_hem/HEM1-HEM3.meme.txt"
1411 ,"t/data/map_hem/HEM3-HEM12.fa"
1412 ,"t/data/map_hem/HEM2-HEM3.meme.txt"
1413 ,"t/data/map_hem/HEM3-HEM15.meme.txt"
1414 ,"t/data/map_hem/HEM13-HEM15.fa"
1415 ,"t/data/map_hem/HEM1-HEM13.fa"
1416 ,"t/data/map_hem/HEM13-HEM14.meme.txt"
1417 ,"t/data/map_hem/HEM1-HEM12.meme.txt"
1418 ,"t/data/map_hem/HEM4.ups.fa_"
1419 ,"t/data/map_hem/HEM1-HEM2.fa"
1420 ,"t/data/map_hem/HEM3-HEM4.fa"
1421 ,"t/data/map_hem/HEM1-HEM14.meme.txt"
1422 ,"t/data/map_hem/HEM1-HEM15.fa"
1423 ,"t/data/map_hem/HEM2.ups.fa_"
1424 ,"t/data/map_hem/HEM2-HEM15.fa"
1425 ,"t/data/map_hem/HEM13.ups.fa_.revcom"
1426 ,"t/data/map_hem/HEM1-HEM3.fa"
1427 ,"t/data/map_hem/HEM3-HEM14.fa"
1428 ,"t/data/map_hem/HEM2-HEM12.meme.txt"
1429 ,"t/data/map_hem/yeast.nc.1.freq"
1430 ,"t/data/map_hem/HEM4-HEM13.meme.txt"
1431 ,"t/data/map_hem/HEM4-HEM14.fa"
1432 ,"t/data/map_hem/HEM2-HEM13.meme.txt"
1433 ,"t/data/map_hem/HEM1-HEM13.meme.txt"
1434 ,"t/data/map_hem/HEM14.ups.fa_"
1435 ,"t/data/map_hem/HEM4-HEM15.meme.txt"
1436 ,"t/data/map_hem/HEM3.ups.fa_"
1437 ,"t/data/map_hem/HEM12.ups.fa_.revcom"
1438 ,"t/data/map_hem/HEM13-HEM14.fa"
1439 ,"t/data/map_hem/HEM3-HEM13.meme.txt"
1440 ,"t/data/map_hem/HEM2-HEM14.fa"
1441 ,"t/data/map_hem/HEM1-HEM15.meme.txt"
1442 ,"t/data/map_hem/HEM12.ups.fa_"
1443 ,"t/data/map_hem/HEM3-HEM13.fa"
1444 ,"t/data/map_hem/HEM12-HEM13.meme.txt"
1445 ,"t/data/04_labeled_ancestors.xml"
1446 ,"t/data/testaln.metafasta"
1447 ,"t/data/codeml_lysozyme/lysozymeSmall.ctl"
1448 ,"t/data/codeml_lysozyme/lysozymeSmall.trees"
1449 ,"t/data/codeml_lysozyme/mlc"
1450 ,"t/data/codeml_lysozyme/2NG.tt"
1451 ,"t/data/codeml_lysozyme/2NG.dS"
1452 ,"t/data/codeml_lysozyme/4fold.nuc"
1453 ,"t/data/codeml_lysozyme/lnf"
1454 ,"t/data/codeml_lysozyme/rst1"
1455 ,"t/data/codeml_lysozyme/rst"
1456 ,"t/data/codeml_lysozyme/lysozymeSmall.txt"
1457 ,"t/data/codeml_lysozyme/2NG.dN"
1458 ,"t/data/codeml_lysozyme/rub"
1459 ,"t/data/transfac.dat"
1460 ,"t/data/test_singlets.cns.fastq"
1461 ,"t/data/exonerate.output.works"
1462 ,"t/data/ZABJ4EA7014.CH878695.1.blast.txt"
1463 ,"t/data/omim_text_test"
1464 ,"t/data/SwissProt.dat"
1465 ,"t/data/biofpc.fpc"
1466 ,"t/data/bug2982.embl"
1467 ,"t/data/phylipdist.out"
1468 ,"t/data/repeatmasker.fa.out"
1469 ,"t/data/AE003528_ecoli.bls"
1470 ,"t/data/multi.phd"
1471 ,"t/data/fastq/tricky.fastq"
1472 ,"t/data/fastq/error_double_seq.fastq"
1473 ,"t/data/fastq/error_qual_del.fastq"
1474 ,"t/data/fastq/error_double_qual.fastq"
1475 ,"t/data/fastq/error_trunc_at_plus.fastq"
1476 ,"t/data/fastq/test3_illumina.fastq"
1477 ,"t/data/fastq/error_long_qual.fastq"
1478 ,"t/data/fastq/error_qual_null.fastq"
1479 ,"t/data/fastq/example.fasta"
1480 ,"t/data/fastq/evil_wrapping.fastq"
1481 ,"t/data/fastq/error_trunc_at_qual.fastq"
1482 ,"t/data/fastq/sanger_93.fastq"
1483 ,"t/data/fastq/error_qual_vtab.fastq"
1484 ,"t/data/fastq/sanger_faked.fastq"
1485 ,"t/data/fastq/error_diff_ids.fastq"
1486 ,"t/data/fastq/test2_solexa.fastq"
1487 ,"t/data/fastq/error_trunc_in_qual.fastq"
1488 ,"t/data/fastq/solexa_example.fastq"
1489 ,"t/data/fastq/error_qual_escape.fastq"
1490 ,"t/data/fastq/error_no_qual.fastq"
1491 ,"t/data/fastq/error_trunc_in_title.fastq"
1492 ,"t/data/fastq/solexa_faked.fastq"
1493 ,"t/data/fastq/error_trunc_in_plus.fastq"
1494 ,"t/data/fastq/error_qual_unit_sep.fastq"
1495 ,"t/data/fastq/error_trunc_in_seq.fastq"
1496 ,"t/data/fastq/error_qual_tab.fastq"
1497 ,"t/data/fastq/error_spaces.fastq"
1498 ,"t/data/fastq/test1_sanger.fastq"
1499 ,"t/data/fastq/example.qual"
1500 ,"t/data/fastq/wrapping_issues.fastq"
1501 ,"t/data/fastq/illumina_faked.fastq"
1502 ,"t/data/fastq/error_tabs.fastq"
1503 ,"t/data/fastq/error_qual_space.fastq"
1504 ,"t/data/fastq/bug2335.fastq"
1505 ,"t/data/fastq/error_short_qual.fastq"
1506 ,"t/data/fastq/error_trunc_at_seq.fastq"
1507 ,"t/data/fastq/example.fastq"
1508 ,"t/data/genomic-seq.mzef"
1509 ,"t/data/mapmaker.txt"
1510 ,"t/data/hmmsearch3.out"
1511 ,"t/data/HUMBETGLOA.grailexp"
1512 ,"t/data/interpro_ebi.xml"
1513 ,"t/data/T7.aln"
1514 ,"t/data/BEL16-LTR_AG.embl"
1515 ,"t/data/revcomp_mrna.gb"
1516 ,"t/data/test.locuslink"
1517 ,"t/data/mutations.old.xml"
1518 ,"t/data/tmp.fst"
1519 ,"t/data/test2.infernal"
1520 ,"t/data/hmmpfam.out"
1521 ,"t/data/bl2seq.blastn.rev"
1522 ,"t/data/footprinter.out"
1523 ,"t/data/component.ontology.test2"
1524 ,"t/data/bug3021.gmap"
1525 ,"t/data/503384.MEGABLAST.2"
1526 ,"t/data/characters.nexml.old.xml"
1527 ,"t/data/test.ref.fas"
1528 ,"t/data/dna1.fa"
1529 ,"t/data/test.metafasta"
1530 ,"t/data/neighbor.dist"
1531 ,"t/data/test.txt"
1532 ,"t/data/lysozyme6.protml"
1533 ,"t/data/knownGene.gff3"
1534 ,"t/data/tree_nonewline.nexus"
1535 ,"t/data/test.exp"
1536 ,"t/data/ecoli-trna-qrna.out"
1537 ,"t/data/pfam_tests.stk"
1538 ,"t/data/plague_yeast.bls.xml"
1539 ,"t/data/test_clear_range.fastq"
1540 ,"t/data/PAM250"
1541 ,"t/data/U83300.bsml"
1542 ,"t/data/BAB68554.gb"
1543 ,"t/data/test.interpro"
1544 ,"t/data/BC000007.gbk"
1545 ,"t/data/quoted-strings2.nex"
1546 ,"t/data/blast_plus.blastp"
1547 ,"t/data/cysprot1a.fa"
1548 ,"t/data/genewise.out"
1549 ,"t/data/singleNSsite.mlc"
1550 ,"t/data/humts1.pal"
1551 ,"t/data/testaln.aln"
1552 ,"t/data/testaln.pfam"
1553 ,"t/data/spidey.noalignment"
1554 ,"t/data/AF305198.gb"
1555 ,"t/data/1.bed"
1556 ,"t/data/interpro.xml"
1557 ,"t/data/directives.gff3"
1558 ,"t/data/sim4.for.rev"
1559 ,"t/data/dq519393.gb"
1560 ,"t/data/tandem_repeats_finder_no_desc.dat"
1561 ,"t/data/assembly_with_singlets.ace"
1562 ,"t/data/nei_gojobori_test.aln"
1563 ,"t/data/cysprot1.fa"
1564 ,"t/data/tricky.wublast"
1565 ,"t/data/crab.nj"
1566 ,"t/data/test.tigrxml"
1567 ,"t/data/msout_infile1"
1568 ,"t/data/bug3086.embl"
1569 ,"t/data/testaln.xmfa"
1570 ,"t/data/phi.out"
1571 ,"t/data/radical-whitespace.nex"
1572 ,"t/data/targetp.out"
1573 ,"t/data/purine_v081.infernal"
1574 ,"t/data/sim4.for.for"
1575 ,"t/data/sofa.ontology"
1576 ,"t/data/long-names.nex"
1577 ,"t/data/baseml.usertree"
1578 ,"t/data/testaln.stockholm"
1579 ,"t/data/spaces.nex"
1580 ,"t/data/contig-by-hand.wublastp"
1581 ,"t/data/test.gcgblast"
1582 ,"t/data/ENr111.mfa.example.elems"
1583 ,"t/data/testaln.msf"
1584 ,"t/data/cysprot.needle"
1585 ,"t/data/X98338_Adh-mRNA.gb"
1586 ,"t/data/amino.fa"
1587 ,"t/data/GlimmerM.out"
1588 ,"t/data/polymorphism.dat"
1589 ,"t/data/dbfa/3.fa"
1590 ,"t/data/dbfa/2.fa"
1591 ,"t/data/dbfa/7.fa"
1592 ,"t/data/dbfa/6.fa"
1593 ,"t/data/dbfa/4.fa"
1594 ,"t/data/dbfa/5.fa"
1595 ,"t/data/dbfa/1.fa"
1596 ,"t/data/03_bootstraps.xml"
1597 ,"t/data/cds-266.fas"
1598 ,"t/data/quoted-strings1.nex"
1599 ,"t/data/newblast.xml"
1600 ,"t/data/stress_test_medline.xml"
1601 ,"t/data/hemoglobinA.meg"
1602 ,"t/data/testaln.list"
1603 ,"t/data/yeast.tRNAscanSE"
1604 ,"t/data/masta.dat"
1605 ,"t/data/BN000066-tpa.embl"
1606 ,"t/data/exonerate.output.dontwork"
1607 ,"t/data/test.swiss"
1608 ,"t/data/P39765.gb"
1609 ,"t/data/HUMBETGLOA.mzef"
1610 ,"t/data/primer3_outfile.txt"
1611 ,"t/data/popgen_saureus.dat"
1612 ,"t/data/dnaEbsub_ecoli.wutblastn"
1613 ,"t/data/test2.raw"
1614 ,"t/data/mini-AE001405.gb"
1615 ,"t/data/multiseq.bls"
1616 ,"t/data/P35527.gb"
1617 ,"t/data/M12730.gb"
1618 ,"t/data/Genscan.FastA"
1619 ,"t/data/characters.nexml.xml"
1620 ,"t/data/bug2391.megablast"
1621 ,"t/data/genomic-seq.genscan"
1622 ,"t/data/test.pln"
1623 ,"t/data/test_singlets.maq"
1624 ,"t/data/testaln.arp"
1625 ,"t/data/tandem_repeats_finder.dat"
1626 ,"t/data/Treebase-chlamy-dna.nex"
1627 ,"t/data/MSGEFTUA.gb"
1628 ,"t/data/crypto.sim4-3"
1629 ,"t/data/27-contig_Newbler.ace"
1630 ,"t/data/biodbgff/test.gff3"
1631 ,"t/data/biodbgff/test.gff"
1632 ,"t/data/sbay_c545-yeast.BLASTZ.PSL"
1633 ,"t/data/multifa.seq.qual"
1634 ,"t/data/pre_rel9.swiss"
1635 ,"t/data/frac_problems.blast"
1636 ,"t/data/cysprot1b.newick"
1637 ,"t/data/bug2120.phd"
1638 ,"t/data/seqxml.xml"
1639 ,"t/data/Bird_Ovomucoids.nex"
1640 ,"t/data/O_sat.wgs"
1641 ,"t/data/LittleChrY.dbsnp.xml"
1642 ,"t/data/CG11099.fasaln"
1643 ,"t/data/signalp.positive.out"
1644 ,"t/data/SPAN_Family8a.nex"
1645 ,"t/data/testdata.crossmatch"
1646 ,"t/data/catalase-webblast.BLASTP"
1647 ,"t/data/test.gcg"
1648 ,"t/data/rebase.withrefm"
1649 ,"t/data/unigene.data"
1650 ,"t/data/bug2473.fasta"
1651 ,"t/data/blat.psLayout3"
1652 ,"t/data/intrablock-comment.nex"
1653 ,"t/data/match.output"
1654 ,"t/data/dnaE-bsub.fa"
1655 ,"t/data/hmmscan.out"
1656 ,"t/data/testaln.mase"
1657 ,"t/data/longnames.dnd"
1658 ,"t/data/ecolitst.fa"
1659 ,"t/data/gf-s71.needle"
1660 ,"t/data/D12555.gbk"
1661 ,"t/data/msout_infile2.gz"
1662 ,"t/data/mutations.xml"
1663 ,"t/data/seqfile.pir"
1664 ,"t/data/test.maq"
1665 ,"t/data/phyloxml_examples.xml"
1666 ,"t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml"
1667 ,"t/data/01_basic.xml"
1668 ,"t/data/AF032047.gbk"
1669 ,"t/data/mini-align.aln"
1670 ,"t/data/sprintf.rnamotif"
1671 ,"t/data/bootstrap.tre"
1672 ,"t/data/dcr1_sp.WUBLASTP"
1673 ,"t/data/testaln.fastq"
1674 ,"t/data/prints.out"
1675 ,"t/data/consed_project/edit_dir/test_project.fasta.screen"
1676 ,"t/data/consed_project/edit_dir/test_project_to_alu.cross"
1677 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.problems"
1678 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2"
1679 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual"
1680 ,"t/data/consed_project/edit_dir/test_project.fasta"
1681 ,"t/data/consed_project/edit_dir/test_project.phrap.out"
1682 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual"
1683 ,"t/data/consed_project/edit_dir/test_projectNewChromats.fof"
1684 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.qual"
1685 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.singlets"
1686 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.log"
1687 ,"t/data/consed_project/edit_dir/test_project.fasta.log"
1688 ,"t/data/consed_project/edit_dir/test_project.newtags"
1689 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1"
1690 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.contigs"
1691 ,"t/data/consed_project/edit_dir/test_project.screen.out"
1692 ,"t/data/consed_project/edit_dir/test_project.contigs"
1693 ,"t/data/consed_project/edit_dir/test_project.fasta.screen.view"
1694 ,"t/data/consed_project/phd_dir/ML4924R.phd.1"
1695 ,"t/data/consed_project/phd_dir/ML4947F.phd.1"
1696 ,"t/data/consed_project/phd_dir/ML4924F.phd.1"
1697 ,"t/data/consed_project/phd_dir/ML4922R.phd.1"
1698 ,"t/data/factor7.embl"
1699 ,"t/data/D10483.gbk"
1700 ,"t/data/omim_genemap_test"
1701 ,"t/data/Mcjanrna_rdbII.gbk"
1702 ,"t/data/no_hsps.blastp"
1703 ,"t/data/LOAD_Ccd1.dnd"
1704 ,"t/data/glimmer3-fragment.detail"
1705 ,"t/data/cysprot.msf"
1706 ,"t/data/rpsblast.bls"
1707 ,"t/data/AY095303S1.gbk"
1708 ,"t/data/spidey.test1"
1709 ,"t/data/test.xls"
1710 ,"t/data/mpath.ontology.test"
1711 ,"t/data/msout_infile2"
1712 ,"t/data/test.lasergene"
1713 ,"t/data/test.pir"
1714 ,"t/data/seg.out"
1715 ,"t/data/cysprot1b.msf"
1716 ,"t/data/multi_1.fa"
1717 ,"t/data/mapmaker.out"
1718 ,"t/data/testaln.psi"
1719 ,"t/data/a_thaliana.blastn"
1720 ,"t/data/urease.tre.nexus"
1721 ,"t/data/compLD_missingtest.prettybase"
1722 ,"t/data/bl2seq.out"
1723 ,"t/data/CG2865.fasaln"
1724 ,"t/data/Glimmer3.predict"
1725 ,"t/data/promoterwise.out"
1726 ,"t/data/signalp.short"
1727 ,"t/data/testaln.nexus"
1728 ,"t/data/test.meme2"
1729 ,"t/data/short.blx"
1730 ,"t/data/ay149291.gb"
1731 ,"t/data/traits.tab"
1732 ,"t/data/AAC12660.fa"
1733 ,"t/data/testaln.po"
1734 ,"t/data/genomewise.out"
1735 ,"t/data/DQ018368.gb"
1736 ,"t/data/tandem_repeats_finder.noresults"
1737 ,"t/data/test.infernal"
1738 ,"t/data/test.pfam"
1739 ,"t/data/meme.dat"
1740 ,"t/data/codeml43.mlc"
1741 ,"t/data/rfam_tests.stk"
1742 ,"t/data/megablast_output.paracel_btk"
1743 ,"t/data/ay007676.gb"
1744 ,"t/data/no_semicolon.newick"
1745 ,"t/data/chad100.scf"
1746 ,"t/data/sim4.rev"
1747 ,"t/data/radical-whitespace_02.nex"
1748 ,"t/data/phipsi.out"
1749 ,"t/data/crab.dat.cn"
1750 ,"t/data/cysprot.tblastn"
1751 ,"t/data/test.embl2sq"
1752 ,"t/data/humor.maf"
1753 ,"t/data/blast_no_hit_desc.txt"
1754 ,"t/data/sv40_small.xml"
1755 ,"t/data/hs_est.est2genome"
1756 ,"t/data/ATF14F8.gbk"
1757 ,"t/data/example.phase"
1758 ,"t/data/component.ontology.test"
1759 ,"t/data/hmmsearch.out"
1760 ,"t/data/P33897"
1761 ,"t/data/popgen_saureus.multidat"
1762 ,"t/data/sample_dataset.tigr"
1763 ,"t/data/test.nhx"
1764 ,"t/data/transfac_pro/reference.dat"
1765 ,"t/data/transfac_pro/matrix.dat"
1766 ,"t/data/transfac_pro/site.dat"
1767 ,"t/data/transfac_pro/gene.dat"
1768 ,"t/data/transfac_pro/fragment.dat"
1769 ,"t/data/transfac_pro/readme.txt"
1770 ,"t/data/transfac_pro/factor.dat"
1771 ,"t/data/swiss.dat"
1772 ,"t/data/psiblast.xml"
1773 ,"t/data/ctgdemo.fpc"
1774 ,"t/data/test.tab"
1775 ,"t/data/test.fasta"
1776 ,"t/data/AnnIX-v003.gbk"
1777 ,"t/data/headerless.psl"
1778 ,"t/data/alleles.fas"
1779 ,"t/data/hsinsulin.blastcl3.blastn"
1780 ,"t/data/signalp.nn.summary"
1781 ,"t/data/gmap_f9.txt"
1782 ,"t/data/rel9.swiss"
1783 ,"t/data/AE003644_Adh-genomic.gb"
1784 ,"t/data/NC_006346.gb"
1785 ,"t/data/rebase.itype2"
1786 ,"t/data/bug2862.pmr"
1787 ,"t/data/empty.bl2seq"
1788 ,"t/data/1A3I.pdb"
1789 ,"t/data/cys1_dicdi.water"
1790 ,"t/data/M0.mlc"
1791 ,"t/data/singlet_w_CT.ace"
1792 ,"t/data/ribosome-slippage.gb"
1793 ,"t/data/withrefm.906"
1794 ,"t/data/SPAN_Family7n.nex"
1795 ,"t/data/tab1part.mif"
1796 ,"t/data/lucy.stderr"
1797 ,"t/data/AB077698.gb"
1798 ,"t/data/new_blastn.txt"
1799 ,"t/data/bug1986.blastp"
1800 ,"t/data/AHCYL1.kegg"
1801 ,"t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml"
1802 ,"t/data/genomic-seq.epcr"
1803 ,"t/data/codeml_nan.mlc"
1804 ,"t/data/dnaE-bsub-prot.fa"
1805 ,"t/data/1ZZ19XR301R-Alignment.tblastn"
1806 ,"t/data/bug1986.blast2"
1807 ,"t/data/test.ace"
1808 ,"t/data/codeml.mlc"
1809 ,"t/data/genewise_output.paracel_btk"
1810 ,"t/data/test.embl"
1811 ,"t/data/tmhmm.out"
1812 ,"t/data/trna.strict.rnamotif"
1813 ,"t/data/dbqual/3.qual"
1814 ,"t/data/dbqual/2.qual"
1815 ,"t/data/dbqual/1.qual"
1816 ,"t/data/hs_owlmonkey.fas"
1817 ,"t/data/Glimmer2.out"
1818 ,"t/data/bl2seq.blastn"
1819 ,"t/data/mast.dat"
1820 ,"t/data/phylipdist-36.out"
1821 ,"t/data/hg16_chroms.gff"
1822 ,"t/data/signalp.negative.out"
1823 ,"t/data/insulin.water"
1824 ,"t/data/psiblastreport.out"
1825 ,"t/data/swisspfam.data"
1826 ,"t/data/AY763288.gb"
1827 ,"t/data/puzzle.tre"
1828 ,"t/data/test.meme"
1829 ,"t/data/dnaEbsub_ecoli.wublastx"
1830 ,"t/data/genomic-seq.fasta"
1831 ,"t/data/test.gcgfasta"
1832 ,"t/data/qualfile.qual"
1833 ,"t/data/qrna-relloc.out"
1834 ,"t/data/trees.nexml.xml"
1835 ,"t/data/testaln2.fasta"
1836 ,"t/data/test.game"
1837 ,"t/data/GlimmerHMM.out"
1838 ,"t/data/bug2246.blast"
1839 ,"t/data/Primate_mtDNA.nex"
1840 ,"t/data/codeml4.mlc"
1841 ,"t/data/Rab1.chaos-xml"
1842 ,"t/data/NC_001284.gbk"
1843 ,"t/data/dna2.fa"
1844 ,"t/data/protpars_longid.phy"
1845 ,"t/data/cds_sample.embl"
1846 ,"t/data/SPAN_Family4nl.nex"
1847 ,"t/data/testdbaccnums.out"
1848 ,"t/data/longnames.aln"
1849 ,"t/data/tab2part.mif"
1850 ,"t/data/gmap_f9-reverse-strand.txt"
1851 ,"t/data/test1.wublastp"
1852 ,"t/data/genemark-fragment.out"
1853 ,"t/data/Q8GBD3.swiss"
1854 ,"t/data/stress_test_pubmed.xml"
1855 ,"t/data/dnaEbsub_ecoli.wutblastx"
1856 ,"t/data/U71225.gb.unix"
1857 ,"t/data/test.raw"
1858 ,"t/data/codeml315.mlc"
1859 ,"t/data/cysprot_vs_gadfly.FASTA"
1860 ,"t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml"
1861 ,"t/data/hs_owlmonkey.aln"
1862 ,"t/data/testdat.exonerate"
1863 ,"t/data/taxdump/names.dmp"
1864 ,"t/data/taxdump/nodes.dmp"
1865 ,"t/data/test.nh"
1866 ,"t/data/seqdatabase.ini"
1867 ,"t/data/GO.defs.test"
1868 ,"t/data/test.ztr"
1869 ,"t/data/HUMBETGLOA.grail"
1870 ,"t/data/EG352462.gbxml"
1871 ,"t/data/testfile.erpin"
1872 ,"t/data/multifa.seq"
1873 ,"t/data/eutils/elink_multidb_corr.xml"
1874 ,"t/data/eutils/elink_acheck_corr.xml"
1875 ,"t/data/eutils/elink_llinks_corr.xml"
1876 ,"t/data/eutils/elink_lcheck_corr.xml"
1877 ,"t/data/eutils/elink_ncheck.xml"
1878 ,"t/data/eutils/elink_dball.xml"
1879 ,"t/data/eutils/elink_multidb.xml"
1880 ,"t/data/eutils/elink_lcheck.xml"
1881 ,"t/data/eutils/elink_llinks.xml"
1882 ,"t/data/eutils/egquery.xml"
1883 ,"t/data/eutils/einfo.xml"
1884 ,"t/data/eutils/elink_scores.xml"
1885 ,"t/data/eutils/epost.xml"
1886 ,"t/data/eutils/espell.xml"
1887 ,"t/data/eutils/einfo_dbs.xml"
1888 ,"t/data/eutils/elink_nhist_corr.xml"
1889 ,"t/data/eutils/elink_neighbor_corr.xml"
1890 ,"t/data/eutils/esearch1.xml"
1891 ,"t/data/eutils/elink_acheck.xml"
1892 ,"t/data/eutils/elink_ncheck_corr.xml"
1893 ,"t/data/eutils/esummary1.xml"
1894 ,"t/data/eutils/elink_nhist.xml"
1895 ,"t/data/eutils/esearch2.xml"
1896 ,"t/data/eutils/elink_neighbor.xml"
1897 ,"t/data/eutils/esummary2.xml"
1898 ,"t/data/echofilter.wublastn"
1899 ,"t/data/expected.blast.out"
1900 ,"t/data/lucy.qual"
1901 ,"t/data/multiseq_tags.phd"
1902 ,"t/data/multi_blast.bls"
1903 ,"t/data/1A11.pdb"
1904 ,"t/data/cysprot.fa"
1905 ,"t/data/ssp160.embl.1"
1906 ,"t/data/acefile.ace.1"
1907 ,"t/data/in.fasta"
1908 ,"t/data/multiline-intrablock-comment.nex"
1909 ,"t/data/13-pilE-F.scf"
1910 ,"t/data/signalp.hmm.short"
1911 ,"t/data/trees.nexml.old.xml"
1912 ,"t/data/bl2seq.tblastx.out"
1913 ,"t/data/03_bootstraps_in_tag.xml"
1914 ,"t/data/02_mackerel_no_taxrefs.xml"
1915 ,"t/data/seqfeaturedb/test.gff3"
1916 ,"t/data/test 2.txt"
1917 ,"t/data/biofpc.cor"
1918 ,"t/data/pep-266.aln"
1919 ,"t/data/test.ctf"
1920 ,"t/data/test.bowtie"
1921 ,"t/data/test.bam"
1922 ,"t/data/U58726.gb"
1923 "Bio-HMMER","t/data/L77119.hmmer"
1924 ,"t/data/testfuzzy.genbank"
1925 ,"t/data/hmmpfam_fake.out"
1926 ,"t/data/bug2869.tree"
1927 ,"t/data/sparsealn.needle"
1928 ,"t/data/interpro_short.xml"
1929 ,"t/data/little.largemultifasta"
1930 ,"t/data/primer3_output.txt"
1931 ,"t/data/regulation_test.obo"
1932 ,"t/data/hmmscan_multi_domain.out"
1933 ,"t/data/hybrid2.gff3"
1934 ,"t/data/roa1.swiss"
1935 ,"t/data/testaln.fasta"
1936 ,"t/data/test.tsv"
1937 ,"t/data/bug2453.maf"
1938 ,"t/data/8HVP.pdb"
1939 ,"t/data/exsignalp.out"
1940 ,"t/data/codeml_nssites.mlc"
1941 ,"t/data/msout_infile1.gz"
1942 ,"t/data/frac_problems3.blast"
1943 ,"t/data/test.tseq"
1944 ,"t/data/bug2937.fasta"
1945 ,"t/data/version2.scf"
1946 ,"t/data/NT_021877.gbk"
1947 ,"t/data/codeml43_nssites.mlc"
1948 ,"t/data/example.hap"
1949 ,"t/data/1BPT.pdb"
1950 ,"t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml"
1951 ,"t/data/psi_xml.dat"
1952 ,"t/data/BLOSUM50"
1953 ,"t/data/multi_2.fa"
1954 ,"t/data/basic-ladder.nex"
1955 ,"t/data/primer3_infile.txt"
1956 ,"t/data/lucy.seq"
1957 ,"t/data/test.abi"
1958 ,"t/data/ecolitst.bls"
1959 ,"t/data/semicolon.newick"
1960 ,"t/data/polymorphism.old.xml"
1961 ,"t/data/NC_008536.gb"
1962 ,"t/data/registry/bdb/seqdatabase.ini"
1963 ,"t/data/registry/flat/seqdatabase.ini"
1964 ,"t/data/vecscreen_simple.test_output"
1965 ,"t/data/test1.blasttab3"
1966 ,"t/data/testaln.prodom"
1967 ,"t/data/testaln2.arp"
1968 ,"t/data/HUMBETGLOA.tblastx"
1969 ,"t/data/ar.embl"
1970 ,"t/data/NM_002254.gb"
1971 ,"t/data/genemark.out"
1972 ,"t/data/ecoli_domains.rpsblast"
1973 ,"t/data/crypto.sim4-4"
1974 ,"t/data/test.ptt"
1975 ,"t/data/basic-bush.nex"
1976 ,"t/data/char-matrix-spaces.nex"
1977 ,"t/data/5X_1895.FASTXY"
1978 ,"t/data/test.cns.fastq"
1979 ,"t/data/Kingdoms_DNA.nex"
1980 ,"t/data/test.phd"
1981 ,"t/data/Fang_2003.xml"
1982 ,"t/data/adh.mb_tree.nexus"
1983 ,"t/data/bug2982.gb"
1984 ,"t/data/UnaSmithHIV-both.nex"
1985 ,"t/data/seqs.fas"
1986 ,"t/data/c200-vs-yeast.BLASTN.m8"
1987 ,"t/data/entrezgene.dat"
1988 ,"t/data/cysprot.water"
1989 ,"t/data/05_ancestral_states.xml"
1990 ,"t/data/reference_ace.ace"
1991 ,"t/data/roa1.gbxml"
1992 ,"t/data/roa1_v2.dat"
1993 ,"t/data/hs_fugu.newick"
1994 ,"t/data/atp1.matrix"
1995 ,"t/data/calm.swiss"
1996 ,"t/data/tab3part.mif"
1997 ,"t/data/popstats.prettybase"
1998 ,"t/data/multi.blast.m8"
1999 ,"t/data/crab.njb"
2000 ,"t/data/brassica_ATH.WUBLASTN"
2001 ,"t/data/PX1CG.gb"
2002 ,"t/data/no_cds_example.gb"
2003 ,"t/data/lysozyme6.simple.protml"
2004 ,"t/data/bl2seq.blastx.out"
2005 ,"t/data/signalp.nn.short"
2006 ,"t/data/bug2942.blastx"
2007 ,"t/data/nucmatrix.txt"
2008 ,"t/data/mutations.old.dat"
2009 ,"t/data/roa1.genbank"
2010 ,"t/data/NC_006511-short.gbk"
2011 ,"t/data/MmCT"
2012 ,"t/data/dmel_2Lchunk.gb"
2013 ,"t/data/polymorphism.xml"
2014 ,"t/data/geneid_1.0.out"
2015 ,"t/data/so.obo"
2016 ,"t/data/aaml_pairwise.mlc"
2017 ,"t/data/ay116458.gb"
2018 ,"t/data/blast.report"
2019 ,"t/data/multi.blast.m9"
2020 ,"t/data/blosum62.bla"
2021 ,"t/data/sequencefamily.dat"
2022 ,"t/data/noninterleaved.phy"
2023 ,"t/data/GO.defs.test2"
2024 ,"t/data/signalp.summary"
2025 ,"t/data/cysprot1a.msf"
2026 ,"t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml"
2027 ,"t/data/HUMBETGLOA.gff"
2028 ,"t/data/glimmer3-fragment.predict"
2029 ,"t/data/version3.scf"
2030 ,"t/LocalDB/DBQual.t"
2031 ,"t/LocalDB/Registry.t"
2032 ,"t/LocalDB/transfac_pro.t"
2033 ,"t/LocalDB/Index/Blast.t"
2034 ,"t/LocalDB/Index/BlastTable.t"
2035 ,"t/LocalDB/Index/Index.t"
2036 ,"t/LocalDB/Flat.t"
2037 ,"t/LocalDB/BioDBGFF.t"
2038 ,"t/LocalDB/SeqFeature.t"
2039 ,"t/LocalDB/DBFasta.t"
2040 ,"t/LiveSeq/Mutation.t"
2041 ,"t/LiveSeq/LiveSeq.t"
2042 ,"t/LiveSeq/Chain.t"
2043 ,"t/LiveSeq/Mutator.t"
2044 ,"t/Root/Utilities.t"
2045 ,"t/Root/HTTPget.t"
2046 ,"t/Root/Exception.t"
2047 ,"t/Root/Tempfile.t"
2048 ,"t/Root/RootI.t"
2049 ,"t/Root/Storable.t"
2050 ,"t/Root/RootIO.t"
2051 ,"t/RemoteDB/Taxonomy.t"
2052 ,"t/RemoteDB/HIV/HIVAnnotProcessor.t"
2053 ,"t/RemoteDB/HIV/HIVQuery.t"
2054 ,"t/RemoteDB/HIV/HIV.t"
2055 ,"t/RemoteDB/HIV/HIVQueryHelper.t"
2056 ,"t/RemoteDB/EMBL.t"
2057 ,"t/RemoteDB/GenPept.t"
2058 ,"t/RemoteDB/EUtilities.t"
2059 ,"t/RemoteDB/EntrezGene.t"
2060 ,"t/RemoteDB/BioFetch.t"
2061 ,"t/RemoteDB/CUTG.t"
2062 ,"t/RemoteDB/Query/GenBank.t"
2063 ,"t/RemoteDB/SeqVersion.t"
2064 ,"t/RemoteDB/MeSH.t"
2065 ,"t/RemoteDB/SwissProt.t"
2066 ,"t/RemoteDB/SeqRead_fail.t"
2067 ,"t/RemoteDB/RefSeq.t"
2068 ,"t/RemoteDB/GenBank.t"
2069 ,"t/SeqIO/agave.t"
2070 ,"t/SeqIO/tinyseq.t"
2071 ,"t/SeqIO/abi.t"
2072 ,"t/SeqIO/ctf.t"
2073 ,"t/SeqIO/Multiple_fasta.t"
2074 ,"t/SeqIO/chaos.t"
2075 ,"t/SeqIO/fasta.t"
2076 ,"t/SeqIO/fastq.t"
2077 ,"t/SeqIO/seqxml.t"
2078 ,"t/SeqIO/strider.t"
2079 ,"t/SeqIO/table.t"
2080 ,"t/SeqIO/genbank.t"
2081 ,"t/SeqIO/ztr.t"
2082 ,"t/SeqIO/MultiFile.t"
2083 ,"t/SeqIO/flybase_chadoxml.t"
2084 ,"t/SeqIO/pln.t"
2085 ,"t/SeqIO/tigrxml.t"
2086 ,"t/SeqIO/embl.t"
2087 ,"t/SeqIO/excel.t"
2088 ,"t/SeqIO/Handler.t"
2089 ,"t/SeqIO/phd.t"
2090 ,"t/SeqIO/entrezgene.t"
2091 ,"t/SeqIO/locuslink.t"
2092 ,"t/SeqIO/tigr.t"
2093 ,"t/SeqIO/gbxml.t"
2094 ,"t/SeqIO/swiss.t"
2095 ,"t/SeqIO/game.t"
2096 ,"t/SeqIO/chadoxml.t"
2097 ,"t/SeqIO/Splicedseq.t"
2098 ,"t/SeqIO/tab.t"
2099 ,"t/SeqIO/ace.t"
2100 ,"t/SeqIO/kegg.t"
2101 ,"t/SeqIO/scf.t"
2102 ,"t/SeqIO/exp.t"
2103 ,"t/SeqIO/pir.t"
2104 ,"t/SeqIO/nexml.t"
2105 ,"t/SeqIO/alf.t"
2106 ,"t/SeqIO/lasergene.t"
2107 ,"t/SeqIO/chaosxml.t"
2108 ,"t/SeqIO/qual.t"
2109 ,"t/SeqIO/raw.t"
2110 ,"t/SeqIO/metafasta.t"
2111 ,"t/SeqIO/bsml.t"
2112 ,"t/SeqIO/largefasta.t"
2113 ,"t/SeqIO/interpro.t"
2114 ,"t/SeqIO/bsml_sax.t"
2115 ,"t/SeqIO/gcg.t"
2116 ,"t/SeqIO/msout.t"
2117 ,"t/SeqIO/asciitree.t"
2118 ,"t/SeqIO/SeqBuilder.t"
2119 ,"t/Tools/Sigcleave.t"
2120 ,"t/Tools/QRNA.t"
2121 ,"t/Tools/FootPrinter.t"
2122 ,"t/Tools/Lucy.t"
2123 ,"t/Tools/Sim4.t"
2124 ,"t/Tools/Run/Dummy/Config.pm"
2125 ,"t/Tools/Run/Dummy.pm"
2126 ,"t/Tools/Run/RemoteBlast_rpsblast.t"
2127 ,"t/Tools/Run/RemoteBlast.t"
2128 ,"t/Tools/Run/StandAloneBlast.t"
2129 ,"t/Tools/Run/WBCommandExts.t"
2130 ,"t/Tools/Run/WrapperBase.t"
2131 ,"t/Tools/Signalp/ExtendedSignalp.t"
2132 ,"t/Tools/SiRNA.t"
2133 ,"t/Tools/Promoterwise.t"
2134 ,"t/Tools/Match.t"
2135 "Bio-HMMER","t/Tools/Hmmer.t"
2136 ,"t/Tools/Alignment/Consed.t"
2137 ,"t/Tools/Primer3.t"
2138 ,"t/Tools/Phylo/PAML.t"
2139 ,"t/Tools/Phylo/Molphy.t"
2140 ,"t/Tools/Phylo/Phylip/ProtDist.t"
2141 ,"t/Tools/Phylo/Gerp.t"
2142 ,"t/Tools/RandDistFunctions.t"
2143 ,"t/Tools/pICalculator.t"
2144 ,"t/Tools/GFF.t"
2145 ,"t/Tools/EUtilities/elink_acheck.t"
2146 ,"t/Tools/EUtilities/elink_scores.t"
2147 ,"t/Tools/EUtilities/EUtilParameters.t"
2148 ,"t/Tools/EUtilities/elink_neighbor_history.t"
2149 ,"t/Tools/EUtilities/elink_lcheck.t"
2150 ,"t/Tools/EUtilities/espell.t"
2151 ,"t/Tools/EUtilities/elink_neighbor.t"
2152 ,"t/Tools/EUtilities/esearch.t"
2153 ,"t/Tools/EUtilities/elink_llinks.t"
2154 ,"t/Tools/EUtilities/einfo.t"
2155 ,"t/Tools/EUtilities/esummary.t"
2156 ,"t/Tools/EUtilities/epost.t"
2157 ,"t/Tools/EUtilities/elink_ncheck.t"
2158 ,"t/Tools/EUtilities/egquery.t"
2159 ,"t/Tools/Analysis/DNA/ESEfinder.t"
2160 ,"t/Tools/Analysis/Protein/Sopma.t"
2161 ,"t/Tools/Analysis/Protein/GOR4.t"
2162 ,"t/Tools/Analysis/Protein/Scansite.t"
2163 ,"t/Tools/Analysis/Protein/ELM.t"
2164 ,"t/Tools/Analysis/Protein/HNN.t"
2165 ,"t/Tools/Analysis/Protein/NetPhos.t"
2166 ,"t/Tools/Analysis/Protein/Domcut.t"
2167 ,"t/Tools/TargetP.t"
2168 ,"t/Tools/ePCR.t"
2169 ,"t/Tools/rnamotif.t"
2170 ,"t/Tools/Pseudowise.t"
2171 ,"t/Tools/RepeatMasker.t"
2172 ,"t/Tools/Geneid.t"
2173 ,"t/Tools/Est2Genome.t"
2174 ,"t/Tools/Genewise.t"
2175 ,"t/Tools/Genpred.t"
2176 ,"t/Tools/TandemRepeatsFinder.t"
2177 ,"t/Tools/Tmhmm.t"
2178 ,"t/Tools/IUPAC.t"
2179 ,"t/Tools/tRNAscanSE.t"
2180 ,"t/Tools/Signalp.t"
2181 ,"t/Tools/Spidey/Spidey.t"
2182 ,"t/Tools/Genomewise.t"
2183 ,"t/Tools/EMBOSS/Palindrome.t"
2184 ,"t/Tools/Seg.t"