MANIFEST

   1 .shipit
   2 AUTHORS
   3 Bio/Align/AlignI.pm
   4 Bio/Align/DNAStatistics.pm
   5 Bio/Align/Graphics.pm
   6 Bio/Align/PairwiseStatistics.pm
   7 Bio/Align/ProteinStatistics.pm
   8 Bio/Align/StatisticsI.pm
   9 Bio/Align/Utilities.pm
  10 Bio/AlignIO.pm
  11 Bio/AlignIO/arp.pm
  12 Bio/AlignIO/bl2seq.pm
  13 Bio/AlignIO/clustalw.pm
  14 Bio/AlignIO/emboss.pm
  15 Bio/AlignIO/fasta.pm
  16 Bio/AlignIO/Handler/GenericAlignHandler.pm
  17 Bio/AlignIO/largemultifasta.pm
  18 Bio/AlignIO/maf.pm
  19 Bio/AlignIO/mase.pm
  20 Bio/AlignIO/mega.pm
  21 Bio/AlignIO/meme.pm
  22 Bio/AlignIO/metafasta.pm
  23 Bio/AlignIO/msf.pm
  24 Bio/AlignIO/nexml.pm
  25 Bio/AlignIO/nexus.pm
  26 Bio/AlignIO/pfam.pm
  27 Bio/AlignIO/phylip.pm
  28 Bio/AlignIO/po.pm
  29 Bio/AlignIO/proda.pm
  30 Bio/AlignIO/prodom.pm
  31 Bio/AlignIO/psi.pm
  32 Bio/AlignIO/selex.pm
  33 Bio/AlignIO/stockholm.pm
  34 Bio/AlignIO/xmfa.pm
  35 Bio/AnalysisI.pm
  36 Bio/AnalysisParserI.pm
  37 Bio/AnalysisResultI.pm
  38 Bio/AnnotatableI.pm
  39 Bio/Annotation/AnnotationFactory.pm
  40 Bio/Annotation/Collection.pm
  41 Bio/Annotation/Comment.pm
  42 Bio/Annotation/DBLink.pm
  43 Bio/Annotation/OntologyTerm.pm
  44 Bio/Annotation/Reference.pm
  45 Bio/Annotation/Relation.pm
  46 Bio/Annotation/SimpleValue.pm
  47 Bio/Annotation/StructuredValue.pm
  48 Bio/Annotation/TagTree.pm
  49 Bio/Annotation/Target.pm
  50 Bio/Annotation/Tree.pm
  51 Bio/Annotation/TypeManager.pm
  52 Bio/AnnotationCollectionI.pm
  53 Bio/AnnotationI.pm
  54 Bio/Assembly/Contig.pm
  55 Bio/Assembly/ContigAnalysis.pm
  56 Bio/Assembly/IO.pm
  57 Bio/Assembly/IO/ace.pm
  58 Bio/Assembly/IO/bowtie.pm
  59 Bio/Assembly/IO/maq.pm
  60 Bio/Assembly/IO/phrap.pm
  61 Bio/Assembly/IO/sam.pm
  62 Bio/Assembly/IO/tigr.pm
  63 Bio/Assembly/Scaffold.pm
  64 Bio/Assembly/ScaffoldI.pm
  65 Bio/Assembly/Singlet.pm
  66 Bio/Assembly/Tools/ContigSpectrum.pm
  67 Bio/Biblio.pm
  68 Bio/Biblio/Article.pm
  69 Bio/Biblio/BiblioBase.pm
  70 Bio/Biblio/Book.pm
  71 Bio/Biblio/BookArticle.pm
  72 Bio/Biblio/IO.pm
  73 Bio/Biblio/IO/medline2ref.pm
  74 Bio/Biblio/IO/medlinexml.pm
  75 Bio/Biblio/IO/pubmed2ref.pm
  76 Bio/Biblio/IO/pubmedxml.pm
  77 Bio/Biblio/Journal.pm
  78 Bio/Biblio/JournalArticle.pm
  79 Bio/Biblio/MedlineArticle.pm
  80 Bio/Biblio/MedlineBook.pm
  81 Bio/Biblio/MedlineBookArticle.pm
  82 Bio/Biblio/MedlineJournal.pm
  83 Bio/Biblio/MedlineJournalArticle.pm
  84 Bio/Biblio/Organisation.pm
  85 Bio/Biblio/Patent.pm
  86 Bio/Biblio/Person.pm
  87 Bio/Biblio/Proceeding.pm
  88 Bio/Biblio/Provider.pm
  89 Bio/Biblio/PubmedArticle.pm
  90 Bio/Biblio/PubmedBookArticle.pm
  91 Bio/Biblio/PubmedJournalArticle.pm
  92 Bio/Biblio/Ref.pm
  93 Bio/Biblio/Service.pm
  94 Bio/Biblio/TechReport.pm
  95 Bio/Biblio/Thesis.pm
  96 Bio/Biblio/WebResource.pm
  97 Bio/Cluster/ClusterFactory.pm
  98 Bio/Cluster/FamilyI.pm
  99 Bio/Cluster/SequenceFamily.pm
 100 Bio/Cluster/UniGene.pm
 101 Bio/Cluster/UniGeneI.pm
 102 Bio/ClusterI.pm
 103 Bio/ClusterIO.pm
 104 Bio/ClusterIO/dbsnp.pm
 105 Bio/ClusterIO/unigene.pm
 106 Bio/CodonUsage/IO.pm
 107 Bio/CodonUsage/Table.pm
 108 Bio/Coordinate/Chain.pm
 109 Bio/Coordinate/Collection.pm
 110 Bio/Coordinate/ExtrapolatingPair.pm
 111 Bio/Coordinate/GeneMapper.pm
 112 Bio/Coordinate/Graph.pm
 113 Bio/Coordinate/MapperI.pm
 114 Bio/Coordinate/Pair.pm
 115 Bio/Coordinate/Result.pm
 116 Bio/Coordinate/Result/Gap.pm
 117 Bio/Coordinate/Result/Match.pm
 118 Bio/Coordinate/ResultI.pm
 119 Bio/Coordinate/Utils.pm
 120 Bio/Das/FeatureTypeI.pm
 121 Bio/Das/SegmentI.pm
 122 Bio/DasI.pm
 123 Bio/DB/Ace.pm
 124 Bio/DB/Biblio/biofetch.pm
 125 Bio/DB/Biblio/eutils.pm
 126 Bio/DB/Biblio/soap.pm
 127 Bio/DB/BiblioI.pm
 128 Bio/DB/BioFetch.pm
 129 Bio/DB/CUTG.pm
 130 Bio/DB/DBFetch.pm
 131 Bio/DB/EMBL.pm
 132 Bio/DB/EntrezGene.pm
 133 Bio/DB/EUtilities.pm
 134 Bio/DB/Expression.pm
 135 Bio/DB/Expression/geo.pm
 136 Bio/DB/Failover.pm
 137 Bio/DB/Fasta.pm
 138 Bio/DB/FileCache.pm
 139 Bio/DB/Flat.pm
 140 Bio/DB/Flat/BDB.pm
 141 Bio/DB/Flat/BDB/embl.pm
 142 Bio/DB/Flat/BDB/fasta.pm
 143 Bio/DB/Flat/BDB/genbank.pm
 144 Bio/DB/Flat/BDB/swiss.pm
 145 Bio/DB/Flat/BinarySearch.pm
 146 Bio/DB/GenBank.pm
 147 Bio/DB/GenericWebAgent.pm
 148 Bio/DB/GenPept.pm
 149 Bio/DB/GFF.pm
 150 Bio/DB/GFF/Adaptor/ace.pm
 151 Bio/DB/GFF/Adaptor/berkeleydb.pm
 152 Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
 153 Bio/DB/GFF/Adaptor/biofetch.pm
 154 Bio/DB/GFF/Adaptor/biofetch_oracle.pm
 155 Bio/DB/GFF/Adaptor/dbi.pm
 156 Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
 157 Bio/DB/GFF/Adaptor/dbi/iterator.pm
 158 Bio/DB/GFF/Adaptor/dbi/mysql.pm
 159 Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
 160 Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
 161 Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
 162 Bio/DB/GFF/Adaptor/dbi/oracle.pm
 163 Bio/DB/GFF/Adaptor/dbi/oracleace.pm
 164 Bio/DB/GFF/Adaptor/dbi/pg.pm
 165 Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
 166 Bio/DB/GFF/Adaptor/memory.pm
 167 Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
 168 Bio/DB/GFF/Adaptor/memory/iterator.pm
 169 Bio/DB/GFF/Aggregator.pm
 170 Bio/DB/GFF/Aggregator/alignment.pm
 171 Bio/DB/GFF/Aggregator/clone.pm
 172 Bio/DB/GFF/Aggregator/coding.pm
 173 Bio/DB/GFF/Aggregator/gene.pm
 174 Bio/DB/GFF/Aggregator/match.pm
 175 Bio/DB/GFF/Aggregator/none.pm
 176 Bio/DB/GFF/Aggregator/orf.pm
 177 Bio/DB/GFF/Aggregator/processed_transcript.pm
 178 Bio/DB/GFF/Aggregator/so_transcript.pm
 179 Bio/DB/GFF/Aggregator/transcript.pm
 180 Bio/DB/GFF/Aggregator/ucsc_acembly.pm
 181 Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
 182 Bio/DB/GFF/Aggregator/ucsc_genscan.pm
 183 Bio/DB/GFF/Aggregator/ucsc_refgene.pm
 184 Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
 185 Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
 186 Bio/DB/GFF/Aggregator/ucsc_softberry.pm
 187 Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
 188 Bio/DB/GFF/Aggregator/ucsc_unigene.pm
 189 Bio/DB/GFF/Featname.pm
 190 Bio/DB/GFF/Feature.pm
 191 Bio/DB/GFF/Homol.pm
 192 Bio/DB/GFF/RelSegment.pm
 193 Bio/DB/GFF/Segment.pm
 194 Bio/DB/GFF/Typename.pm
 195 Bio/DB/GFF/Util/Binning.pm
 196 Bio/DB/GFF/Util/Rearrange.pm
 197 Bio/DB/HIV.pm
 198 Bio/DB/HIV/HIVAnnotProcessor.pm
 199 Bio/DB/HIV/HIVQueryHelper.pm
 200 Bio/DB/HIV/lanl-schema.xml
 201 Bio/DB/InMemoryCache.pm
 202 Bio/DB/LocationI.pm
 203 Bio/DB/MeSH.pm
 204 Bio/DB/NCBIHelper.pm
 205 Bio/DB/Qual.pm
 206 Bio/DB/Query/GenBank.pm
 207 Bio/DB/Query/HIVQuery.pm
 208 Bio/DB/Query/WebQuery.pm
 209 Bio/DB/QueryI.pm
 210 Bio/DB/RandomAccessI.pm
 211 Bio/DB/ReferenceI.pm
 212 Bio/DB/RefSeq.pm
 213 Bio/DB/Registry.pm
 214 Bio/DB/SeqFeature.pm
 215 Bio/DB/SeqFeature/NormalizedFeature.pm
 216 Bio/DB/SeqFeature/NormalizedFeatureI.pm
 217 Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
 218 Bio/DB/SeqFeature/Segment.pm
 219 Bio/DB/SeqFeature/Store.pm
 220 Bio/DB/SeqFeature/Store/bdb.pm
 221 Bio/DB/SeqFeature/Store/berkeleydb.pm
 222 Bio/DB/SeqFeature/Store/berkeleydb3.pm
 223 Bio/DB/SeqFeature/Store/DBI/Iterator.pm
 224 Bio/DB/SeqFeature/Store/DBI/mysql.pm
 225 Bio/DB/SeqFeature/Store/DBI/Pg.pm
 226 Bio/DB/SeqFeature/Store/DBI/SQLite.pm
 227 Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
 228 Bio/DB/SeqFeature/Store/GFF2Loader.pm
 229 Bio/DB/SeqFeature/Store/GFF3Loader.pm
 230 Bio/DB/SeqFeature/Store/Loader.pm
 231 Bio/DB/SeqFeature/Store/LoadHelper.pm
 232 Bio/DB/SeqFeature/Store/memory.pm
 233 Bio/DB/SeqHound.pm
 234 Bio/DB/SeqI.pm
 235 Bio/DB/SeqVersion.pm
 236 Bio/DB/SeqVersion/gi.pm
 237 Bio/DB/SwissProt.pm
 238 Bio/DB/Taxonomy.pm
 239 Bio/DB/Taxonomy/entrez.pm
 240 Bio/DB/Taxonomy/flatfile.pm
 241 Bio/DB/Taxonomy/list.pm
 242 Bio/DB/TFBS.pm
 243 Bio/DB/TFBS/transfac_pro.pm
 244 Bio/DB/Universal.pm
 245 Bio/DB/UpdateableSeqI.pm
 246 Bio/DB/WebDBSeqI.pm
 247 Bio/DBLinkContainerI.pm
 248 Bio/DescribableI.pm
 249 Bio/Draw/Pictogram.pm
 250 Bio/Event/EventGeneratorI.pm
 251 Bio/Event/EventHandlerI.pm
 252 Bio/Factory/AnalysisI.pm
 253 Bio/Factory/ApplicationFactoryI.pm
 254 Bio/Factory/DriverFactory.pm
 255 Bio/Factory/FTLocationFactory.pm
 256 Bio/Factory/LocationFactoryI.pm
 257 Bio/Factory/MapFactoryI.pm
 258 Bio/Factory/ObjectBuilderI.pm
 259 Bio/Factory/ObjectFactory.pm
 260 Bio/Factory/ObjectFactoryI.pm
 261 Bio/Factory/SeqAnalysisParserFactory.pm
 262 Bio/Factory/SeqAnalysisParserFactoryI.pm
 263 Bio/Factory/SequenceFactoryI.pm
 264 Bio/Factory/SequenceProcessorI.pm
 265 Bio/Factory/SequenceStreamI.pm
 266 Bio/Factory/TreeFactoryI.pm
 267 Bio/FeatureHolderI.pm
 268 Bio/FeatureIO.pm
 269 Bio/FeatureIO/bed.pm
 270 Bio/FeatureIO/gff.pm
 271 Bio/FeatureIO/gtf.pm
 272 Bio/FeatureIO/interpro.pm
 273 Bio/FeatureIO/ptt.pm
 274 Bio/FeatureIO/vecscreen_simple.pm
 275 Bio/HandlerBaseI.pm
 276 Bio/IdCollectionI.pm
 277 Bio/IdentifiableI.pm
 278 Bio/Index/Abstract.pm
 279 Bio/Index/AbstractSeq.pm
 280 Bio/Index/Blast.pm
 281 Bio/Index/BlastTable.pm
 282 Bio/Index/EMBL.pm
 283 Bio/Index/Fasta.pm
 284 Bio/Index/Fastq.pm
 285 Bio/Index/GenBank.pm
 286 Bio/Index/Hmmer.pm
 287 Bio/Index/Qual.pm
 288 Bio/Index/Stockholm.pm
 289 Bio/Index/SwissPfam.pm
 290 Bio/Index/Swissprot.pm
 291 Bio/LiveSeq/AARange.pm
 292 Bio/LiveSeq/Chain.pm
 293 Bio/LiveSeq/ChainI.pm
 294 Bio/LiveSeq/DNA.pm
 295 Bio/LiveSeq/Exon.pm
 296 Bio/LiveSeq/Gene.pm
 297 Bio/LiveSeq/Intron.pm
 298 Bio/LiveSeq/IO/BioPerl.pm
 299 Bio/LiveSeq/IO/Loader.pm
 300 Bio/LiveSeq/IO/README
 301 Bio/LiveSeq/Mutation.pm
 302 Bio/LiveSeq/Mutator.pm
 303 Bio/LiveSeq/Prim_Transcript.pm
 304 Bio/LiveSeq/Range.pm
 305 Bio/LiveSeq/Repeat_Region.pm
 306 Bio/LiveSeq/Repeat_Unit.pm
 307 Bio/LiveSeq/SeqI.pm
 308 Bio/LiveSeq/Transcript.pm
 309 Bio/LiveSeq/Translation.pm
 310 Bio/LocatableSeq.pm
 311 Bio/Location/Atomic.pm
 312 Bio/Location/AvWithinCoordPolicy.pm
 313 Bio/Location/CoordinatePolicyI.pm
 314 Bio/Location/Fuzzy.pm
 315 Bio/Location/FuzzyLocationI.pm
 316 Bio/Location/NarrowestCoordPolicy.pm
 317 Bio/Location/Simple.pm
 318 Bio/Location/Split.pm
 319 Bio/Location/SplitLocationI.pm
 320 Bio/Location/WidestCoordPolicy.pm
 321 Bio/LocationI.pm
 322 Bio/Map/Clone.pm
 323 Bio/Map/Contig.pm
 324 Bio/Map/CytoMap.pm
 325 Bio/Map/CytoMarker.pm
 326 Bio/Map/CytoPosition.pm
 327 Bio/Map/EntityI.pm
 328 Bio/Map/FPCMarker.pm
 329 Bio/Map/Gene.pm
 330 Bio/Map/GeneMap.pm
 331 Bio/Map/GenePosition.pm
 332 Bio/Map/GeneRelative.pm
 333 Bio/Map/LinkageMap.pm
 334 Bio/Map/LinkagePosition.pm
 335 Bio/Map/MapI.pm
 336 Bio/Map/Mappable.pm
 337 Bio/Map/MappableI.pm
 338 Bio/Map/Marker.pm
 339 Bio/Map/MarkerI.pm
 340 Bio/Map/Microsatellite.pm
 341 Bio/Map/OrderedPosition.pm
 342 Bio/Map/OrderedPositionWithDistance.pm
 343 Bio/Map/Physical.pm
 344 Bio/Map/Position.pm
 345 Bio/Map/PositionHandler.pm
 346 Bio/Map/PositionHandlerI.pm
 347 Bio/Map/PositionI.pm
 348 Bio/Map/PositionWithSequence.pm
 349 Bio/Map/Prediction.pm
 350 Bio/Map/Relative.pm
 351 Bio/Map/RelativeI.pm
 352 Bio/Map/SimpleMap.pm
 353 Bio/Map/TranscriptionFactor.pm
 354 Bio/MapIO.pm
 355 Bio/MapIO/fpc.pm
 356 Bio/MapIO/mapmaker.pm
 357 Bio/Matrix/Generic.pm
 358 Bio/Matrix/IO.pm
 359 Bio/Matrix/IO/mlagan.pm
 360 Bio/Matrix/IO/phylip.pm
 361 Bio/Matrix/IO/scoring.pm
 362 Bio/Matrix/MatrixI.pm
 363 Bio/Matrix/Mlagan.pm
 364 Bio/Matrix/PhylipDist.pm
 365 Bio/Matrix/PSM/InstanceSite.pm
 366 Bio/Matrix/PSM/InstanceSiteI.pm
 367 Bio/Matrix/PSM/IO.pm
 368 Bio/Matrix/PSM/IO/mast.pm
 369 Bio/Matrix/PSM/IO/masta.pm
 370 Bio/Matrix/PSM/IO/meme.pm
 371 Bio/Matrix/PSM/IO/psiblast.pm
 372 Bio/Matrix/PSM/IO/transfac.pm
 373 Bio/Matrix/PSM/ProtMatrix.pm
 374 Bio/Matrix/PSM/ProtPsm.pm
 375 Bio/Matrix/PSM/Psm.pm
 376 Bio/Matrix/PSM/PsmHeader.pm
 377 Bio/Matrix/PSM/PsmHeaderI.pm
 378 Bio/Matrix/PSM/PsmI.pm
 379 Bio/Matrix/PSM/SiteMatrix.pm
 380 Bio/Matrix/PSM/SiteMatrixI.pm
 381 Bio/Matrix/Scoring.pm
 382 Bio/MolEvol/CodonModel.pm
 383 Bio/Nexml/Factory.pm
 384 Bio/NexmlIO.pm
 385 Bio/Ontology/DocumentRegistry.pm
 386 Bio/Ontology/GOterm.pm
 387 Bio/Ontology/InterProTerm.pm
 388 Bio/Ontology/OBOEngine.pm
 389 Bio/Ontology/OBOterm.pm
 390 Bio/Ontology/Ontology.pm
 391 Bio/Ontology/OntologyEngineI.pm
 392 Bio/Ontology/OntologyI.pm
 393 Bio/Ontology/OntologyStore.pm
 394 Bio/Ontology/Path.pm
 395 Bio/Ontology/PathI.pm
 396 Bio/Ontology/Relationship.pm
 397 Bio/Ontology/RelationshipFactory.pm
 398 Bio/Ontology/RelationshipI.pm
 399 Bio/Ontology/RelationshipType.pm
 400 Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
 401 Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
 402 Bio/Ontology/SimpleOntologyEngine.pm
 403 Bio/Ontology/Term.pm
 404 Bio/Ontology/TermFactory.pm
 405 Bio/Ontology/TermI.pm
 406 Bio/OntologyIO.pm
 407 Bio/OntologyIO/dagflat.pm
 408 Bio/OntologyIO/goflat.pm
 409 Bio/OntologyIO/Handlers/BaseSAXHandler.pm
 410 Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
 411 Bio/OntologyIO/Handlers/InterProHandler.pm
 412 Bio/OntologyIO/InterProParser.pm
 413 Bio/OntologyIO/obo.pm
 414 Bio/OntologyIO/simplehierarchy.pm
 415 Bio/OntologyIO/soflat.pm
 416 Bio/ParameterBaseI.pm
 417 Bio/Perl.pm
 418 Bio/Phenotype/Correlate.pm
 419 Bio/Phenotype/Measure.pm
 420 Bio/Phenotype/MeSH/Term.pm
 421 Bio/Phenotype/MeSH/Twig.pm
 422 Bio/Phenotype/OMIM/MiniMIMentry.pm
 423 Bio/Phenotype/OMIM/OMIMentry.pm
 424 Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
 425 Bio/Phenotype/OMIM/OMIMparser.pm
 426 Bio/Phenotype/Phenotype.pm
 427 Bio/Phenotype/PhenotypeI.pm
 428 Bio/PhyloNetwork.pm
 429 Bio/PhyloNetwork/Factory.pm
 430 Bio/PhyloNetwork/FactoryX.pm
 431 Bio/PhyloNetwork/GraphViz.pm
 432 Bio/PhyloNetwork/muVector.pm
 433 Bio/PhyloNetwork/RandomFactory.pm
 434 Bio/PhyloNetwork/TreeFactory.pm
 435 Bio/PhyloNetwork/TreeFactoryMulti.pm
 436 Bio/PhyloNetwork/TreeFactoryX.pm
 437 Bio/PopGen/Genotype.pm
 438 Bio/PopGen/GenotypeI.pm
 439 Bio/PopGen/HtSNP.pm
 440 Bio/PopGen/Individual.pm
 441 Bio/PopGen/IndividualI.pm
 442 Bio/PopGen/IO.pm
 443 Bio/PopGen/IO/csv.pm
 444 Bio/PopGen/IO/hapmap.pm
 445 Bio/PopGen/IO/phase.pm
 446 Bio/PopGen/IO/prettybase.pm
 447 Bio/PopGen/Marker.pm
 448 Bio/PopGen/MarkerI.pm
 449 Bio/PopGen/PopStats.pm
 450 Bio/PopGen/Population.pm
 451 Bio/PopGen/PopulationI.pm
 452 Bio/PopGen/Simulation/Coalescent.pm
 453 Bio/PopGen/Simulation/GeneticDrift.pm
 454 Bio/PopGen/Statistics.pm
 455 Bio/PopGen/TagHaplotype.pm
 456 Bio/PopGen/Utilities.pm
 457 Bio/PrimarySeq.pm
 458 Bio/PrimarySeqI.pm
 459 Bio/PullParserI.pm
 460 Bio/Range.pm
 461 Bio/RangeI.pm
 462 Bio/Restriction/Analysis.pm
 463 Bio/Restriction/Enzyme.pm
 464 Bio/Restriction/Enzyme/MultiCut.pm
 465 Bio/Restriction/Enzyme/MultiSite.pm
 466 Bio/Restriction/EnzymeCollection.pm
 467 Bio/Restriction/EnzymeI.pm
 468 Bio/Restriction/IO.pm
 469 Bio/Restriction/IO/bairoch.pm
 470 Bio/Restriction/IO/base.pm
 471 Bio/Restriction/IO/itype2.pm
 472 Bio/Restriction/IO/prototype.pm
 473 Bio/Restriction/IO/withrefm.pm
 474 Bio/Root/Build.pm
 475 Bio/Root/Exception.pm
 476 Bio/Root/HTTPget.pm
 477 Bio/Root/IO.pm
 478 Bio/Root/Root.pm
 479 Bio/Root/RootI.pm
 480 Bio/Root/Storable.pm
 481 Bio/Root/Test.pm
 482 Bio/Root/Test/Warn.pm
 483 Bio/Root/Utilities.pm
 484 Bio/Root/Version.pm
 485 Bio/Search/BlastStatistics.pm
 486 Bio/Search/BlastUtils.pm
 487 Bio/Search/DatabaseI.pm
 488 Bio/Search/GenericDatabase.pm
 489 Bio/Search/GenericStatistics.pm
 490 Bio/Search/Hit/BlastHit.pm
 491 Bio/Search/Hit/BlastPullHit.pm
 492 Bio/Search/Hit/Fasta.pm
 493 Bio/Search/Hit/GenericHit.pm
 494 Bio/Search/Hit/HitFactory.pm
 495 Bio/Search/Hit/HitI.pm
 496 Bio/Search/Hit/hmmer3Hit.pm
 497 Bio/Search/Hit/HMMERHit.pm
 498 Bio/Search/Hit/HmmpfamHit.pm
 499 Bio/Search/Hit/ModelHit.pm
 500 Bio/Search/Hit/PsiBlastHit.pm
 501 Bio/Search/Hit/PullHitI.pm
 502 Bio/Search/HSP/BlastHSP.pm
 503 Bio/Search/HSP/BlastPullHSP.pm
 504 Bio/Search/HSP/FastaHSP.pm
 505 Bio/Search/HSP/GenericHSP.pm
 506 Bio/Search/HSP/hmmer3HSP.pm
 507 Bio/Search/HSP/HMMERHSP.pm
 508 Bio/Search/HSP/HmmpfamHSP.pm
 509 Bio/Search/HSP/HSPFactory.pm
 510 Bio/Search/HSP/HSPI.pm
 511 Bio/Search/HSP/ModelHSP.pm
 512 Bio/Search/HSP/PsiBlastHSP.pm
 513 Bio/Search/HSP/PSLHSP.pm
 514 Bio/Search/HSP/PullHSPI.pm
 515 Bio/Search/HSP/WABAHSP.pm
 516 Bio/Search/Iteration/GenericIteration.pm
 517 Bio/Search/Iteration/IterationI.pm
 518 Bio/Search/Processor.pm
 519 Bio/Search/Result/BlastPullResult.pm
 520 Bio/Search/Result/BlastResult.pm
 521 Bio/Search/Result/CrossMatchResult.pm
 522 Bio/Search/Result/GenericResult.pm
 523 Bio/Search/Result/hmmer3Result.pm
 524 Bio/Search/Result/HMMERResult.pm
 525 Bio/Search/Result/HmmpfamResult.pm
 526 Bio/Search/Result/PullResultI.pm
 527 Bio/Search/Result/ResultFactory.pm
 528 Bio/Search/Result/ResultI.pm
 529 Bio/Search/Result/WABAResult.pm
 530 Bio/Search/SearchUtils.pm
 531 Bio/Search/StatisticsI.pm
 532 Bio/Search/Tiling/MapTileUtils.pm
 533 Bio/Search/Tiling/MapTiling.pm
 534 Bio/Search/Tiling/TilingI.pm
 535 Bio/SearchDist.pm
 536 Bio/SearchIO.pm
 537 Bio/SearchIO/axt.pm
 538 Bio/SearchIO/blast.pm
 539 Bio/SearchIO/blast_pull.pm
 540 Bio/SearchIO/blasttable.pm
 541 Bio/SearchIO/blastxml.pm
 542 Bio/SearchIO/cross_match.pm
 543 Bio/SearchIO/erpin.pm
 544 Bio/SearchIO/EventHandlerI.pm
 545 Bio/SearchIO/exonerate.pm
 546 Bio/SearchIO/fasta.pm
 547 Bio/SearchIO/FastHitEventBuilder.pm
 548 Bio/SearchIO/gmap_f9.pm
 549 Bio/SearchIO/hmmer.pm
 550 Bio/SearchIO/hmmer3.pm
 551 Bio/SearchIO/hmmer_pull.pm
 552 Bio/SearchIO/infernal.pm
 553 Bio/SearchIO/IteratedSearchResultEventBuilder.pm
 554 Bio/SearchIO/megablast.pm
 555 Bio/SearchIO/psl.pm
 556 Bio/SearchIO/rnamotif.pm
 557 Bio/SearchIO/SearchResultEventBuilder.pm
 558 Bio/SearchIO/SearchWriterI.pm
 559 Bio/SearchIO/sim4.pm
 560 Bio/SearchIO/waba.pm
 561 Bio/SearchIO/wise.pm
 562 Bio/SearchIO/Writer/BSMLResultWriter.pm
 563 Bio/SearchIO/Writer/GbrowseGFF.pm
 564 Bio/SearchIO/Writer/HitTableWriter.pm
 565 Bio/SearchIO/Writer/HSPTableWriter.pm
 566 Bio/SearchIO/Writer/HTMLResultWriter.pm
 567 Bio/SearchIO/Writer/ResultTableWriter.pm
 568 Bio/SearchIO/Writer/TextResultWriter.pm
 569 Bio/SearchIO/XML/BlastHandler.pm
 570 Bio/SearchIO/XML/PsiBlastHandler.pm
 571 Bio/Seq.pm
 572 Bio/Seq/BaseSeqProcessor.pm
 573 Bio/Seq/EncodedSeq.pm
 574 Bio/Seq/LargeLocatableSeq.pm
 575 Bio/Seq/LargePrimarySeq.pm
 576 Bio/Seq/LargeSeq.pm
 577 Bio/Seq/LargeSeqI.pm
 578 Bio/Seq/Meta.pm
 579 Bio/Seq/Meta/Array.pm
 580 Bio/Seq/MetaI.pm
 581 Bio/Seq/PrimaryQual.pm
 582 Bio/Seq/PrimedSeq.pm
 583 Bio/Seq/QualI.pm
 584 Bio/Seq/Quality.pm
 585 Bio/Seq/RichSeq.pm
 586 Bio/Seq/RichSeqI.pm
 587 Bio/Seq/SeqBuilder.pm
 588 Bio/Seq/SeqFactory.pm
 589 Bio/Seq/SeqFastaSpeedFactory.pm
 590 Bio/Seq/SequenceTrace.pm
 591 Bio/Seq/SeqWithQuality.pm
 592 Bio/Seq/TraceI.pm
 593 Bio/SeqAnalysisParserI.pm
 594 Bio/SeqEvolution/DNAPoint.pm
 595 Bio/SeqEvolution/EvolutionI.pm
 596 Bio/SeqEvolution/Factory.pm
 597 Bio/SeqFeature/Annotated.pm
 598 Bio/SeqFeature/AnnotationAdaptor.pm
 599 Bio/SeqFeature/Collection.pm
 600 Bio/SeqFeature/CollectionI.pm
 601 Bio/SeqFeature/Computation.pm
 602 Bio/SeqFeature/FeaturePair.pm
 603 Bio/SeqFeature/Gene/Exon.pm
 604 Bio/SeqFeature/Gene/ExonI.pm
 605 Bio/SeqFeature/Gene/GeneStructure.pm
 606 Bio/SeqFeature/Gene/GeneStructureI.pm
 607 Bio/SeqFeature/Gene/Intron.pm
 608 Bio/SeqFeature/Gene/NC_Feature.pm
 609 Bio/SeqFeature/Gene/Poly_A_site.pm
 610 Bio/SeqFeature/Gene/Promoter.pm
 611 Bio/SeqFeature/Gene/Transcript.pm
 612 Bio/SeqFeature/Gene/TranscriptI.pm
 613 Bio/SeqFeature/Gene/UTR.pm
 614 Bio/SeqFeature/Generic.pm
 615 Bio/SeqFeature/Lite.pm
 616 Bio/SeqFeature/PositionProxy.pm
 617 Bio/SeqFeature/Primer.pm
 618 Bio/SeqFeature/Similarity.pm
 619 Bio/SeqFeature/SimilarityPair.pm
 620 Bio/SeqFeature/SiRNA/Oligo.pm
 621 Bio/SeqFeature/SiRNA/Pair.pm
 622 Bio/SeqFeature/Tools/FeatureNamer.pm
 623 Bio/SeqFeature/Tools/IDHandler.pm
 624 Bio/SeqFeature/Tools/TypeMapper.pm
 625 Bio/SeqFeature/Tools/Unflattener.pm
 626 Bio/SeqFeature/TypedSeqFeatureI.pm
 627 Bio/SeqFeatureI.pm
 628 Bio/SeqI.pm
 629 Bio/SeqIO.pm
 630 Bio/SeqIO/abi.pm
 631 Bio/SeqIO/ace.pm
 632 Bio/SeqIO/agave.pm
 633 Bio/SeqIO/alf.pm
 634 Bio/SeqIO/asciitree.pm
 635 Bio/SeqIO/bsml.pm
 636 Bio/SeqIO/bsml_sax.pm
 637 Bio/SeqIO/chadoxml.pm
 638 Bio/SeqIO/chaos.pm
 639 Bio/SeqIO/chaosxml.pm
 640 Bio/SeqIO/ctf.pm
 641 Bio/SeqIO/embl.pm
 642 Bio/SeqIO/embldriver.pm
 643 Bio/SeqIO/entrezgene.pm
 644 Bio/SeqIO/excel.pm
 645 Bio/SeqIO/exp.pm
 646 Bio/SeqIO/fasta.pm
 647 Bio/SeqIO/fastq.pm
 648 Bio/SeqIO/flybase_chadoxml.pm
 649 Bio/SeqIO/FTHelper.pm
 650 Bio/SeqIO/game.pm
 651 Bio/SeqIO/game/featHandler.pm
 652 Bio/SeqIO/game/gameHandler.pm
 653 Bio/SeqIO/game/gameSubs.pm
 654 Bio/SeqIO/game/gameWriter.pm
 655 Bio/SeqIO/game/seqHandler.pm
 656 Bio/SeqIO/gbdriver.pm
 657 Bio/SeqIO/gbxml.pm
 658 Bio/SeqIO/gcg.pm
 659 Bio/SeqIO/genbank.pm
 660 Bio/SeqIO/Handler/GenericRichSeqHandler.pm
 661 Bio/SeqIO/interpro.pm
 662 Bio/SeqIO/kegg.pm
 663 Bio/SeqIO/largefasta.pm
 664 Bio/SeqIO/lasergene.pm
 665 Bio/SeqIO/locuslink.pm
 666 Bio/SeqIO/mbsout.pm
 667 Bio/SeqIO/metafasta.pm
 668 Bio/SeqIO/msout.pm
 669 Bio/SeqIO/MultiFile.pm
 670 Bio/SeqIO/nexml.pm
 671 Bio/SeqIO/phd.pm
 672 Bio/SeqIO/pir.pm
 673 Bio/SeqIO/pln.pm
 674 Bio/SeqIO/qual.pm
 675 Bio/SeqIO/raw.pm
 676 Bio/SeqIO/scf.pm
 677 Bio/SeqIO/seqxml.pm
 678 Bio/SeqIO/strider.pm
 679 Bio/SeqIO/swiss.pm
 680 Bio/SeqIO/swissdriver.pm
 681 Bio/SeqIO/tab.pm
 682 Bio/SeqIO/table.pm
 683 Bio/SeqIO/tigr.pm
 684 Bio/SeqIO/tigrxml.pm
 685 Bio/SeqIO/tinyseq.pm
 686 Bio/SeqIO/tinyseq/tinyseqHandler.pm
 687 Bio/SeqIO/ztr.pm
 688 Bio/SeqUtils.pm
 689 Bio/SimpleAlign.pm
 690 Bio/SimpleAnalysisI.pm
 691 Bio/Species.pm
 692 Bio/Structure/Atom.pm
 693 Bio/Structure/Chain.pm
 694 Bio/Structure/Entry.pm
 695 Bio/Structure/IO.pm
 696 Bio/Structure/IO/pdb.pm
 697 Bio/Structure/Model.pm
 698 Bio/Structure/Residue.pm
 699 Bio/Structure/SecStr/DSSP/Res.pm
 700 Bio/Structure/SecStr/STRIDE/Res.pm
 701 Bio/Structure/StructureI.pm
 702 Bio/Symbol/Alphabet.pm
 703 Bio/Symbol/AlphabetI.pm
 704 Bio/Symbol/DNAAlphabet.pm
 705 Bio/Symbol/ProteinAlphabet.pm
 706 Bio/Symbol/README.Symbol
 707 Bio/Symbol/Symbol.pm
 708 Bio/Symbol/SymbolI.pm
 709 Bio/Taxon.pm
 710 Bio/Taxonomy.pm
 711 Bio/Taxonomy/FactoryI.pm
 712 Bio/Taxonomy/Node.pm
 713 Bio/Taxonomy/Taxon.pm
 714 Bio/Taxonomy/Tree.pm
 715 Bio/Tools/AlignFactory.pm
 716 Bio/Tools/Alignment/Consed.pm
 717 Bio/Tools/Alignment/Trim.pm
 718 Bio/Tools/Analysis/DNA/ESEfinder.pm
 719 Bio/Tools/Analysis/Protein/Domcut.pm
 720 Bio/Tools/Analysis/Protein/ELM.pm
 721 Bio/Tools/Analysis/Protein/GOR4.pm
 722 Bio/Tools/Analysis/Protein/HNN.pm
 723 Bio/Tools/Analysis/Protein/Mitoprot.pm
 724 Bio/Tools/Analysis/Protein/NetPhos.pm
 725 Bio/Tools/Analysis/Protein/Scansite.pm
 726 Bio/Tools/Analysis/Protein/Sopma.pm
 727 Bio/Tools/Analysis/SimpleAnalysisBase.pm
 728 Bio/Tools/AnalysisResult.pm
 729 Bio/Tools/Blat.pm
 730 Bio/Tools/CodonTable.pm
 731 Bio/Tools/Coil.pm
 732 Bio/Tools/dpAlign.pm
 733 Bio/Tools/ECnumber.pm
 734 Bio/Tools/EMBOSS/Palindrome.pm
 735 Bio/Tools/EPCR.pm
 736 Bio/Tools/Eponine.pm
 737 Bio/Tools/ERPIN.pm
 738 Bio/Tools/Est2Genome.pm
 739 Bio/Tools/ESTScan.pm
 740 Bio/Tools/EUtilities.pm
 741 Bio/Tools/EUtilities/EUtilDataI.pm
 742 Bio/Tools/EUtilities/EUtilParameters.pm
 743 Bio/Tools/EUtilities/History.pm
 744 Bio/Tools/EUtilities/HistoryI.pm
 745 Bio/Tools/EUtilities/Info.pm
 746 Bio/Tools/EUtilities/Info/FieldInfo.pm
 747 Bio/Tools/EUtilities/Info/LinkInfo.pm
 748 Bio/Tools/EUtilities/Link.pm
 749 Bio/Tools/EUtilities/Link/LinkSet.pm
 750 Bio/Tools/EUtilities/Link/UrlLink.pm
 751 Bio/Tools/EUtilities/Query.pm
 752 Bio/Tools/EUtilities/Query/GlobalQuery.pm
 753 Bio/Tools/EUtilities/Summary.pm
 754 Bio/Tools/EUtilities/Summary/DocSum.pm
 755 Bio/Tools/EUtilities/Summary/Item.pm
 756 Bio/Tools/EUtilities/Summary/ItemContainerI.pm
 757 Bio/Tools/Fgenesh.pm
 758 Bio/Tools/FootPrinter.pm
 759 Bio/Tools/Gel.pm
 760 Bio/Tools/Geneid.pm
 761 Bio/Tools/Genemark.pm
 762 Bio/Tools/Genewise.pm
 763 Bio/Tools/Genomewise.pm
 764 Bio/Tools/Genscan.pm
 765 Bio/Tools/GFF.pm
 766 Bio/Tools/Glimmer.pm
 767 Bio/Tools/Grail.pm
 768 Bio/Tools/GuessSeqFormat.pm
 769 Bio/Tools/HMMER/Domain.pm
 770 Bio/Tools/HMMER/Results.pm
 771 Bio/Tools/HMMER/Set.pm
 772 Bio/Tools/Hmmpfam.pm
 773 Bio/Tools/Infernal.pm
 774 Bio/Tools/ipcress.pm
 775 Bio/Tools/isPcr.pm
 776 Bio/Tools/IUPAC.pm
 777 Bio/Tools/Lucy.pm
 778 Bio/Tools/Match.pm
 779 Bio/Tools/MZEF.pm
 780 Bio/Tools/OddCodes.pm
 781 Bio/Tools/Phylo/Gerp.pm
 782 Bio/Tools/Phylo/Gumby.pm
 783 Bio/Tools/Phylo/Molphy.pm
 784 Bio/Tools/Phylo/Molphy/Result.pm
 785 Bio/Tools/Phylo/PAML.pm
 786 Bio/Tools/Phylo/PAML/Codeml.pm
 787 Bio/Tools/Phylo/PAML/ModelResult.pm
 788 Bio/Tools/Phylo/PAML/Result.pm
 789 Bio/Tools/Phylo/Phylip/ProtDist.pm
 790 Bio/Tools/pICalculator.pm
 791 Bio/Tools/Prediction/Exon.pm
 792 Bio/Tools/Prediction/Gene.pm
 793 Bio/Tools/Primer/Assessor/Base.pm
 794 Bio/Tools/Primer/AssessorI.pm
 795 Bio/Tools/Primer/Feature.pm
 796 Bio/Tools/Primer/Pair.pm
 797 Bio/Tools/Primer3.pm
 798 Bio/Tools/Prints.pm
 799 Bio/Tools/Profile.pm
 800 Bio/Tools/Promoterwise.pm
 801 Bio/Tools/PrositeScan.pm
 802 Bio/Tools/Protparam.pm
 803 Bio/Tools/Pseudowise.pm
 804 Bio/Tools/pSW.pm
 805 Bio/Tools/QRNA.pm
 806 Bio/Tools/RandomDistFunctions.pm
 807 Bio/Tools/RepeatMasker.pm
 808 Bio/Tools/RNAMotif.pm
 809 Bio/Tools/Run/GenericParameters.pm
 810 Bio/Tools/Run/hmmer3.pm
 811 Bio/Tools/Run/ParametersI.pm
 812 Bio/Tools/Run/README
 813 Bio/Tools/Run/RemoteBlast.pm
 814 Bio/Tools/Run/StandAloneBlast.pm
 815 Bio/Tools/Run/StandAloneNCBIBlast.pm
 816 Bio/Tools/Run/StandAloneWUBlast.pm
 817 Bio/Tools/Run/WrapperBase.pm
 818 Bio/Tools/Run/WrapperBase/CommandExts.pm
 819 Bio/Tools/Seg.pm
 820 Bio/Tools/SeqPattern.pm
 821 Bio/Tools/SeqPattern/Backtranslate.pm
 822 Bio/Tools/SeqStats.pm
 823 Bio/Tools/SeqWords.pm
 824 Bio/Tools/Sigcleave.pm
 825 Bio/Tools/Signalp.pm
 826 Bio/Tools/Signalp/ExtendedSignalp.pm
 827 Bio/Tools/Sim4/Exon.pm
 828 Bio/Tools/Sim4/Results.pm
 829 Bio/Tools/SiRNA.pm
 830 Bio/Tools/SiRNA/Ruleset/saigo.pm
 831 Bio/Tools/SiRNA/Ruleset/tuschl.pm
 832 Bio/Tools/Spidey/Exon.pm
 833 Bio/Tools/Spidey/Results.pm
 834 Bio/Tools/TandemRepeatsFinder.pm
 835 Bio/Tools/TargetP.pm
 836 Bio/Tools/Tmhmm.pm
 837 Bio/Tools/tRNAscanSE.pm
 838 Bio/Tree/AlleleNode.pm
 839 Bio/Tree/AnnotatableNode.pm
 840 Bio/Tree/Compatible.pm
 841 Bio/Tree/DistanceFactory.pm
 842 Bio/Tree/Draw/Cladogram.pm
 843 Bio/Tree/Node.pm
 844 Bio/Tree/NodeI.pm
 845 Bio/Tree/NodeNHX.pm
 846 Bio/Tree/RandomFactory.pm
 847 Bio/Tree/Statistics.pm
 848 Bio/Tree/Tree.pm
 849 Bio/Tree/TreeFunctionsI.pm
 850 Bio/Tree/TreeI.pm
 851 Bio/TreeIO.pm
 852 Bio/TreeIO/cluster.pm
 853 Bio/TreeIO/lintree.pm
 854 Bio/TreeIO/newick.pm
 855 Bio/TreeIO/nexml.pm
 856 Bio/TreeIO/nexus.pm
 857 Bio/TreeIO/nhx.pm
 858 Bio/TreeIO/pag.pm
 859 Bio/TreeIO/phyloxml.pm
 860 Bio/TreeIO/svggraph.pm
 861 Bio/TreeIO/tabtree.pm
 862 Bio/TreeIO/TreeEventBuilder.pm
 863 Bio/UpdateableSeqI.pm
 864 Bio/Variation/AAChange.pm
 865 Bio/Variation/AAReverseMutate.pm
 866 Bio/Variation/Allele.pm
 867 Bio/Variation/DNAMutation.pm
 868 Bio/Variation/IO.pm
 869 Bio/Variation/IO/flat.pm
 870 Bio/Variation/IO/xml.pm
 871 Bio/Variation/README
 872 Bio/Variation/RNAChange.pm
 873 Bio/Variation/SeqDiff.pm
 874 Bio/Variation/SNP.pm
 875 Bio/Variation/VariantI.pm
 876 Bio/WebAgent.pm
 877 BioPerl.pm
 878 BUGS
 879 Build.PL
 880 Changes
 881 DEPENDENCIES
 882 DEPRECATED
 883 doc/Deobfuscator/bin/deob_index.pl
 884 doc/Deobfuscator/Build.PL
 885 doc/Deobfuscator/cgi-bin/deob_detail.cgi
 886 doc/Deobfuscator/cgi-bin/deob_flowchart.png
 887 doc/Deobfuscator/cgi-bin/deob_help.html
 888 doc/Deobfuscator/cgi-bin/deob_interface.cgi
 889 doc/Deobfuscator/Changes
 890 doc/Deobfuscator/excluded_modules.txt
 891 doc/Deobfuscator/lib/Deobfuscator.pm
 892 doc/Deobfuscator/LICENSE
 893 doc/Deobfuscator/Makefile.PL
 894 doc/Deobfuscator/MANIFEST
 895 doc/Deobfuscator/META.yml
 896 doc/Deobfuscator/README
 897 doc/Deobfuscator/t/00.load.t
 898 doc/Deobfuscator/t/pod.t
 899 doc/makedoc.PL
 900 doc/README
 901 examples/align/align_on_codons.pl
 902 examples/align/aligntutorial.pl
 903 examples/align/clustalw.pl
 904 examples/align/simplealign.pl
 905 examples/biblio/biblio-eutils-example.pl
 906 examples/biblio/biblio-soap-example.pl
 907 examples/biblio/biblio_soap.pl
 908 examples/Bio-DB-GFF/load_ucsc.pl
 909 examples/bioperl.pl
 910 examples/cluster/dbsnp.pl
 911 examples/contributed/nmrpdb_parse.pl
 912 examples/contributed/prosite2perl.pl
 913 examples/contributed/rebase2list.pl
 914 examples/db/dbfetch
 915 examples/db/est_tissue_query.pl
 916 examples/db/gb2features.pl
 917 examples/db/get_seqs.pl
 918 examples/db/getGenBank.pl
 919 examples/db/rfetch.pl
 920 examples/db/use_registry.pl
 921 examples/generate_random_seq.pl
 922 examples/liveseq/change_gene.pl
 923 examples/longorf.pl
 924 examples/make_primers.pl
 925 examples/popgen/parse_calc_stats.pl
 926 examples/quality/svgtrace.pl
 927 examples/rev_and_trans.pl
 928 examples/revcom_dir.pl
 929 examples/root/exceptions1.pl
 930 examples/root/exceptions2.pl
 931 examples/root/exceptions3.pl
 932 examples/root/exceptions4.pl
 933 examples/root/lib/TestInterface.pm
 934 examples/root/lib/TestObject.pm
 935 examples/root/README
 936 examples/searchio/blast_example.pl
 937 examples/searchio/custom_writer.pl
 938 examples/searchio/hitwriter.pl
 939 examples/searchio/hspwriter.pl
 940 examples/searchio/htmlwriter.pl
 941 examples/searchio/psiblast_features.pl
 942 examples/searchio/psiblast_iterations.pl
 943 examples/searchio/rawwriter.pl
 944 examples/searchio/resultwriter.pl
 945 examples/searchio/waba2gff.pl
 946 examples/searchio/waba2gff3.pl
 947 examples/sirna/rnai_finder.cgi
 948 examples/sirna/TAG
 949 examples/structure/structure-io.pl
 950 examples/subsequence.cgi
 951 examples/tk/gsequence.pl
 952 examples/tk/hitdisplay.pl
 953 examples/tools/extract_genes.pl
 954 examples/tools/gb_to_gff.pl
 955 examples/tools/gff2ps.pl
 956 examples/tools/parse_codeml.pl
 957 examples/tools/psw.pl
 958 examples/tools/reverse-translate.pl
 959 examples/tools/run_genscan.pl
 960 examples/tools/run_primer3.pl
 961 examples/tools/seq_pattern.pl
 962 examples/tools/standaloneblast.pl
 963 examples/tree/paup2phylip.pl
 964 ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
 965 ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
 966 ide/bioperl-mode/dist/bioperl-mode.tar
 967 ide/bioperl-mode/dist/bioperl-mode.tar.md5
 968 ide/bioperl-mode/dist/Changes
 969 ide/bioperl-mode/dist/package-me
 970 ide/bioperl-mode/dist/SKIP
 971 ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
 972 ide/bioperl-mode/etc/images/bpmode-tool.xpm
 973 ide/bioperl-mode/README
 974 ide/bioperl-mode/site-lisp/bioperl-init.el
 975 ide/bioperl-mode/site-lisp/bioperl-mode.el
 976 ide/bioperl-mode/site-lisp/bioperl-skel.el
 977 ide/bioperl-mode/site-lisp/pod.el
 978 ide/bioperl.komodo
 979 INSTALL
 980 INSTALL.SKIP
 981 INSTALL.WIN
 982 LICENSE
 983 maintenance/authors.pl
 984 maintenance/big_split/file_classification.csv
 985 maintenance/big_split/rbuels_notes.txt
 986 maintenance/check_NAME.pl
 987 maintenance/check_URLs.pl
 988 maintenance/cvs2cl_by_file.pl
 989 maintenance/dependencies.pl
 990 maintenance/deprecated.pl
 991 maintenance/module_usage.pl
 992 maintenance/modules.pl
 993 maintenance/ncbi_blast_switches.pl
 994 maintenance/perltidy.conf
 995 maintenance/pod.pl
 996 maintenance/README
 997 maintenance/symlink_script.pl
 998 maintenance/version.pl
 999 MANIFEST                        This list of files
1000 models/biblio.dia
1001 models/bio_liveseq_variation.dia
1002 models/bio_map.dia
1003 models/bio_restriction.dia
1004 models/bioperl.dia
1005 models/coordinatemapper.dia
1006 models/map_proposal.txt
1007 models/maps_and_markers.dia
1008 models/popgen.dia
1009 models/population_proposal.txt
1010 models/README
1011 README
1012 scripts/biblio/biblio.PLS
1013 scripts/biblio/TAG
1014 scripts/Bio-DB-EUtilities/einfo.PLS
1015 scripts/Bio-DB-GFF/bulk_load_gff.PLS
1016 scripts/Bio-DB-GFF/fast_load_gff.PLS
1017 scripts/Bio-DB-GFF/genbank2gff.PLS
1018 scripts/Bio-DB-GFF/genbank2gff3.PLS
1019 scripts/Bio-DB-GFF/generate_histogram.PLS
1020 scripts/Bio-DB-GFF/load_gff.PLS
1021 scripts/Bio-DB-GFF/meta_gff.PLS
1022 scripts/Bio-DB-GFF/process_gadfly.PLS
1023 scripts/Bio-DB-GFF/process_sgd.PLS
1024 scripts/Bio-DB-GFF/process_wormbase.PLS
1025 scripts/Bio-DB-GFF/README
1026 scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
1027 scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
1028 scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
1029 scripts/bioperl_netinstall.pl
1030 scripts/das/das_server.pl
1031 scripts/das/README
1032 scripts/das/TAG
1033 scripts/DB-HIV/hivq.PLS
1034 scripts/DB/biofetch_genbank_proxy.PLS
1035 scripts/DB/bioflat_index.PLS
1036 scripts/DB/biogetseq.PLS
1037 scripts/DB/flanks.PLS
1038 scripts/DB/TAG
1039 scripts/index/bp_fetch.PLS
1040 scripts/index/bp_index.PLS
1041 scripts/index/bp_seqret.PLS
1042 scripts/index/TAG
1043 scripts/popgen/composite_LD.PLS
1044 scripts/popgen/heterogeneity_test.PLS
1045 scripts/README
1046 scripts/searchio/fastam9_to_table.PLS
1047 scripts/searchio/filter_search.PLS
1048 scripts/searchio/hmmer_to_table.PLS
1049 scripts/searchio/parse_hmmsearch.PLS
1050 scripts/searchio/README
1051 scripts/searchio/search2table.PLS
1052 scripts/searchio/TAG
1053 scripts/seq/extract_feature_seq.PLS
1054 scripts/seq/make_mrna_protein.PLS
1055 scripts/seq/seqconvert.PLS
1056 scripts/seq/seqretsplit.PLS
1057 scripts/seq/split_seq.PLS
1058 scripts/seq/TAG
1059 scripts/seq/translate_seq.PLS
1060 scripts/seq/unflatten_seq.PLS
1061 scripts/seqstats/aacomp.PLS
1062 scripts/seqstats/chaos_plot.PLS
1063 scripts/seqstats/gccalc.PLS
1064 scripts/seqstats/oligo_count.PLS
1065 scripts/seqstats/TAG
1066 scripts/taxa/classify_hits_kingdom.PLS
1067 scripts/taxa/local_taxonomydb_query.PLS
1068 scripts/taxa/query_entrez_taxa.PLS
1069 scripts/taxa/TAG
1070 scripts/taxa/taxid4species.PLS
1071 scripts/taxa/taxonomy2tree.PLS
1072 scripts/tree/blast2tree.PLS
1073 scripts/tree/nexus2nh.PLS
1074 scripts/tree/TAG
1075 scripts/tree/tree2pag.PLS
1076 scripts/utilities/bp_mrtrans.PLS
1077 scripts/utilities/bp_nrdb.PLS
1078 scripts/utilities/bp_sreformat.PLS
1079 scripts/utilities/dbsplit.PLS
1080 scripts/utilities/download_query_genbank.PLS
1081 scripts/utilities/mask_by_search.PLS
1082 scripts/utilities/mutate.PLS
1083 scripts/utilities/pairwise_kaks.PLS
1084 scripts/utilities/README
1085 scripts/utilities/remote_blast.PLS
1086 scripts/utilities/revtrans-motif.PLS
1087 scripts/utilities/search2alnblocks.PLS
1088 scripts/utilities/search2BSML.PLS
1089 scripts/utilities/search2gff.PLS
1090 scripts/utilities/search2tribe.PLS
1091 scripts/utilities/seq_length.PLS
1092 scripts/utilities/TAG
1093 t/Align/AlignStats.t
1094 t/Align/AlignUtil.t
1095 t/Align/Graphics.t
1096 t/Align/SimpleAlign.t
1097 t/Align/TreeBuild.t
1098 t/Align/Utilities.t
1099 t/AlignIO/AlignIO.t
1100 t/AlignIO/arp.t
1101 t/AlignIO/bl2seq.t
1102 t/AlignIO/clustalw.t
1103 t/AlignIO/emboss.t
1104 t/AlignIO/fasta.t
1105 t/AlignIO/largemultifasta.t
1106 t/AlignIO/maf.t
1107 t/AlignIO/mase.t
1108 t/AlignIO/mega.t
1109 t/AlignIO/meme.t
1110 t/AlignIO/metafasta.t
1111 t/AlignIO/msf.t
1112 t/AlignIO/nexml.t
1113 t/AlignIO/nexus.t
1114 t/AlignIO/pfam.t
1115 t/AlignIO/phylip.t
1116 t/AlignIO/po.t
1117 t/AlignIO/prodom.t
1118 t/AlignIO/psi.t
1119 t/AlignIO/selex.t
1120 t/AlignIO/stockholm.t
1121 t/AlignIO/xmfa.t
1122 t/Alphabet.t
1123 t/Annotation/Annotation.t
1124 t/Annotation/AnnotationAdaptor.t
1125 t/Assembly/ContigSpectrum.t
1126 t/Assembly/core.t
1127 t/Assembly/IO/bowtie.t
1128 t/Assembly/IO/sam.t
1129 t/Biblio/Biblio.t
1130 t/Biblio/biofetch.t
1131 t/Biblio/eutils.t
1132 t/Biblio/References.t
1133 t/ClusterIO/ClusterIO.t
1134 t/ClusterIO/SequenceFamily.t
1135 t/ClusterIO/unigene.t
1136 t/Coordinate/CoordinateGraph.t
1137 t/Coordinate/CoordinateMapper.t
1138 t/Coordinate/GeneCoordinateMapper.t
1139 t/data/01_basic.xml
1140 t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
1141 t/data/02_dogfish_no_taxrefs.xml
1142 t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
1143 t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
1144 t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml
1145 t/data/02_mackerel_no_taxrefs.xml
1146 t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
1147 t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml
1148 t/data/03_bootstraps.xml
1149 t/data/03_bootstraps_in_tag.xml
1150 t/data/04_labeled_ancestors.xml
1151 t/data/05_ancestral_states.xml
1152 t/data/1.bed
1153 t/data/13-pilE-F.scf
1154 t/data/1A11.pdb
1155 t/data/1A3I.pdb
1156 t/data/1BPT.pdb
1157 t/data/1ZZ19XR301R-Alignment.tblastn
1158 t/data/2008.blasttable
1159 t/data/27-contig_Newbler.ace
1160 t/data/503384.MEGABLAST.0
1161 t/data/503384.MEGABLAST.2
1162 t/data/5X_1895.FASTXY
1163 t/data/8HVP.pdb
1164 t/data/a_thaliana.blastn
1165 t/data/AAC12660.fa
1166 t/data/aaml.mlc
1167 t/data/aaml_pairwise.mlc
1168 t/data/AB077698.gb
1169 t/data/acefile.ace.1
1170 t/data/acefile.singlets
1171 t/data/adh.mb_tree.nexus
1172 t/data/AE003528_ecoli.bls
1173 t/data/AE003644_Adh-genomic.gb
1174 t/data/AF032047.gbk
1175 t/data/AF165282.gb
1176 t/data/AF305198.gb
1177 t/data/AHCYL1.kegg
1178 t/data/alleles.fas
1179 t/data/alnfile.fasta
1180 t/data/amino.fa
1181 t/data/AnnIX-v003.gbk
1182 t/data/ar.embl
1183 t/data/assembly_with_singlets.ace
1184 t/data/ATF14F8.gbk
1185 t/data/atp1.matrix
1186 t/data/ay007676.gb
1187 t/data/AY095303S1.gbk
1188 t/data/ay116458.gb
1189 t/data/ay149291.gb
1190 t/data/AY763288.gb
1191 t/data/BAB68554.gb
1192 t/data/barns-combined.nex
1193 t/data/baseml.pairwise
1194 t/data/baseml.usertree
1195 t/data/basic-bush.nex
1196 t/data/basic-ladder.nex
1197 t/data/BC000007.gbk
1198 t/data/BEL16-LTR_AG.embl
1199 t/data/biodbgff/test.gff
1200 t/data/biodbgff/test.gff3
1201 t/data/biofpc.cor
1202 t/data/biofpc.fpc
1203 t/data/Bird_Ovomucoids.nex
1204 t/data/BK000016-tpa.gbk
1205 t/data/bl2seq.blastn
1206 t/data/bl2seq.blastn.rev
1207 t/data/bl2seq.blastx.out
1208 t/data/bl2seq.bug940.out
1209 t/data/bl2seq.out
1210 t/data/bl2seq.tblastx.out
1211 t/data/blast.report
1212 t/data/blast_no_hit_desc.txt
1213 t/data/blast_plus.blastp
1214 t/data/blastp2215.blast
1215 t/data/blat.psLayout3
1216 t/data/BLOSUM50
1217 t/data/blosum62.bla
1218 t/data/BN000066-tpa.embl
1219 t/data/bootstrap.tre
1220 t/data/BOSS_DROME.FASTP_v35_04
1221 t/data/branchSite.mlc
1222 t/data/brassica_ATH.WUBLASTN
1223 t/data/bug1986.blast2
1224 t/data/bug1986.blastp
1225 t/data/bug2120.phd
1226 t/data/bug2246.blast
1227 t/data/bug2391.megablast
1228 t/data/bug2399.tblastn
1229 t/data/bug2453.maf
1230 t/data/bug2473.fasta
1231 t/data/bug2862.pmr
1232 t/data/bug2869.tree
1233 t/data/bug2901.fa
1234 t/data/bug2937.fasta
1235 t/data/bug2942.blastx
1236 t/data/bug2982.embl
1237 t/data/bug2982.gb
1238 t/data/bug3021.gmap
1239 t/data/bug3086.embl
1240 t/data/c200-vs-yeast.BLASTN
1241 t/data/c200-vs-yeast.BLASTN.m8
1242 t/data/calm.swiss
1243 t/data/catalase-webblast.BLASTP
1244 t/data/cds-266.fas
1245 t/data/cds_sample.embl
1246 t/data/CG11099.fasaln
1247 t/data/CG2865.fasaln
1248 t/data/chad100.scf
1249 t/data/char-interleave.nex
1250 t/data/char-matrix-spaces.nex
1251 t/data/characters+trees.nexml.xml
1252 t/data/characters.nexml.old.xml
1253 t/data/characters.nexml.xml
1254 t/data/codeml.mlc
1255 t/data/codeml315.mlc
1256 t/data/codeml4.mlc
1257 t/data/codeml43.mlc
1258 t/data/codeml43_nssites.mlc
1259 t/data/codeml_lysozyme/2NG.dN
1260 t/data/codeml_lysozyme/2NG.dS
1261 t/data/codeml_lysozyme/2NG.tt
1262 t/data/codeml_lysozyme/4fold.nuc
1263 t/data/codeml_lysozyme/lnf
1264 t/data/codeml_lysozyme/lysozymeSmall.ctl
1265 t/data/codeml_lysozyme/lysozymeSmall.trees
1266 t/data/codeml_lysozyme/lysozymeSmall.txt
1267 t/data/codeml_lysozyme/mlc
1268 t/data/codeml_lysozyme/rst
1269 t/data/codeml_lysozyme/rst1
1270 t/data/codeml_lysozyme/rub
1271 t/data/codeml_nan.mlc
1272 t/data/codeml_nssites.mlc
1273 t/data/compLD_missingtest.prettybase
1274 t/data/compLD_test.prettybase
1275 t/data/component.ontology.test
1276 t/data/component.ontology.test2
1277 t/data/consed_project/edit_dir/test_project.contigs
1278 t/data/consed_project/edit_dir/test_project.fasta
1279 t/data/consed_project/edit_dir/test_project.fasta.log
1280 t/data/consed_project/edit_dir/test_project.fasta.screen
1281 t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
1282 t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
1283 t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
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1285 t/data/consed_project/edit_dir/test_project.fasta.screen.log
1286 t/data/consed_project/edit_dir/test_project.fasta.screen.problems
1287 t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
1288 t/data/consed_project/edit_dir/test_project.fasta.screen.qual
1289 t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
1290 t/data/consed_project/edit_dir/test_project.fasta.screen.view
1291 t/data/consed_project/edit_dir/test_project.newtags
1292 t/data/consed_project/edit_dir/test_project.phrap.out
1293 t/data/consed_project/edit_dir/test_project.screen.out
1294 t/data/consed_project/edit_dir/test_project_to_alu.cross
1295 t/data/consed_project/edit_dir/test_projectNewChromats.fof
1296 t/data/consed_project/phd_dir/ML4922R.phd.1
1297 t/data/consed_project/phd_dir/ML4924F.phd.1
1298 t/data/consed_project/phd_dir/ML4924R.phd.1
1299 t/data/consed_project/phd_dir/ML4947F.phd.1
1300 t/data/contig-by-hand.wublastp
1301 t/data/contigspectrumtest.tigr
1302 t/data/crab.dat.cn
1303 t/data/crab.nj
1304 t/data/crab.njb
1305 t/data/crypto.sim4-0
1306 t/data/crypto.sim4-3
1307 t/data/crypto.sim4-4
1308 t/data/ctgdemo.fpc
1309 t/data/cys1_dicdi.water
1310 t/data/cysprot.fa
1311 t/data/cysprot.msf
1312 t/data/cysprot.needle
1313 t/data/cysprot.tblastn
1314 t/data/cysprot.water
1315 t/data/cysprot1.fa
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1317 t/data/cysprot1a.fa
1318 t/data/cysprot1a.msf
1319 t/data/cysprot1b.fa
1320 t/data/cysprot1b.hmmsearch
1321 t/data/cysprot1b.msf
1322 t/data/cysprot1b.newick
1323 t/data/cysprot_vs_gadfly.FASTA
1324 t/data/D10483.gbk
1325 t/data/D12555.gbk
1326 t/data/dbfa/1.fa
1327 t/data/dbfa/2.fa
1328 t/data/dbfa/3.fa
1329 t/data/dbfa/4.fa
1330 t/data/dbfa/5.fa
1331 t/data/dbfa/6.fa
1332 t/data/dbfa/7.fa
1333 t/data/dbqual/1.qual
1334 t/data/dbqual/2.qual
1335 t/data/dbqual/3.qual
1336 t/data/dcr1_sp.WUBLASTP
1337 t/data/directives.gff3
1338 t/data/dmel_2Lchunk.gb
1339 t/data/dna1.fa
1340 t/data/dna2.fa
1341 t/data/dnaE-bsub-prot.fa
1342 t/data/dnaE-bsub.fa
1343 t/data/dnaEbsub_ecoli.wublastx
1344 t/data/dnaEbsub_ecoli.wutblastn
1345 t/data/dnaEbsub_ecoli.wutblastx
1346 t/data/DQ018368.gb
1347 t/data/dq519393.gb
1348 t/data/ECAPAH02.embl
1349 t/data/echofilter.wublastn
1350 t/data/ecoli-trna-qrna.out
1351 t/data/ecoli_domains.rps.xml
1352 t/data/ecoli_domains.rpsblast
1353 t/data/ecolitst.bls
1354 t/data/ecolitst.fa
1355 t/data/ecolitst.noseqs.wublastp
1356 t/data/ecolitst.wublastp
1357 t/data/EG352462.gbxml
1358 t/data/empty.bl2seq
1359 t/data/ENr111.mfa.example.elems
1360 t/data/entrezgene.dat
1361 t/data/eutils/egquery.xml
1362 t/data/eutils/einfo.xml
1363 t/data/eutils/einfo_dbs.xml
1364 t/data/eutils/elink_acheck.xml
1365 t/data/eutils/elink_acheck_corr.xml
1366 t/data/eutils/elink_dball.xml
1367 t/data/eutils/elink_lcheck.xml
1368 t/data/eutils/elink_lcheck_corr.xml
1369 t/data/eutils/elink_llinks.xml
1370 t/data/eutils/elink_llinks_corr.xml
1371 t/data/eutils/elink_multidb.xml
1372 t/data/eutils/elink_multidb_corr.xml
1373 t/data/eutils/elink_ncheck.xml
1374 t/data/eutils/elink_ncheck_corr.xml
1375 t/data/eutils/elink_neighbor.xml
1376 t/data/eutils/elink_neighbor_corr.xml
1377 t/data/eutils/elink_nhist.xml
1378 t/data/eutils/elink_nhist_corr.xml
1379 t/data/eutils/elink_scores.xml
1380 t/data/eutils/epost.xml
1381 t/data/eutils/esearch1.xml
1382 t/data/eutils/esearch2.xml
1383 t/data/eutils/espell.xml
1384 t/data/eutils/esummary1.xml
1385 t/data/eutils/esummary2.xml
1386 t/data/example.hap
1387 t/data/example.phase
1388 t/data/exonerate.output.dontwork
1389 t/data/exonerate.output.works
1390 t/data/expected.blast.out
1391 t/data/exsignalp.out
1392 t/data/factor7.embl
1393 t/data/Fang_2003.xml
1394 t/data/fastq/bug2335.fastq
1395 t/data/fastq/error_diff_ids.fastq
1396 t/data/fastq/error_double_qual.fastq
1397 t/data/fastq/error_double_seq.fastq
1398 t/data/fastq/error_long_qual.fastq
1399 t/data/fastq/error_no_qual.fastq
1400 t/data/fastq/error_qual_del.fastq
1401 t/data/fastq/error_qual_escape.fastq
1402 t/data/fastq/error_qual_null.fastq
1403 t/data/fastq/error_qual_space.fastq
1404 t/data/fastq/error_qual_tab.fastq
1405 t/data/fastq/error_qual_unit_sep.fastq
1406 t/data/fastq/error_qual_vtab.fastq
1407 t/data/fastq/error_short_qual.fastq
1408 t/data/fastq/error_spaces.fastq
1409 t/data/fastq/error_tabs.fastq
1410 t/data/fastq/error_trunc_at_plus.fastq
1411 t/data/fastq/error_trunc_at_qual.fastq
1412 t/data/fastq/error_trunc_at_seq.fastq
1413 t/data/fastq/error_trunc_in_plus.fastq
1414 t/data/fastq/error_trunc_in_qual.fastq
1415 t/data/fastq/error_trunc_in_seq.fastq
1416 t/data/fastq/error_trunc_in_title.fastq
1417 t/data/fastq/evil_wrapping.fastq
1418 t/data/fastq/example.fasta
1419 t/data/fastq/example.fastq
1420 t/data/fastq/example.qual
1421 t/data/fastq/illumina_faked.fastq
1422 t/data/fastq/sanger_93.fastq
1423 t/data/fastq/sanger_faked.fastq
1424 t/data/fastq/solexa_example.fastq
1425 t/data/fastq/solexa_faked.fastq
1426 t/data/fastq/test1_sanger.fastq
1427 t/data/fastq/test2_solexa.fastq
1428 t/data/fastq/test3_illumina.fastq
1429 t/data/fastq/tricky.fastq
1430 t/data/fastq/wrapping_issues.fastq
1431 t/data/fgenesh.out
1432 t/data/footprinter.out
1433 t/data/frac_problems.blast
1434 t/data/frac_problems2.blast
1435 t/data/frac_problems3.blast
1436 t/data/geneid_1.0.out
1437 t/data/genemark-fragment.out
1438 t/data/genemark.out
1439 t/data/genewise.out
1440 t/data/genewise_output.paracel_btk
1441 t/data/genomewise.out
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1444 t/data/genomic-seq.genscan
1445 t/data/genomic-seq.mzef
1446 t/data/Genscan.FastA
1447 t/data/gf-s71.needle
1448 t/data/Glimmer2.out
1449 t/data/glimmer3-fragment.detail
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1451 t/data/Glimmer3.detail
1452 t/data/Glimmer3.predict
1453 t/data/GlimmerHMM.out
1454 t/data/GlimmerM.out
1455 t/data/gmap_f9-multiple_results.txt
1456 t/data/gmap_f9-reverse-strand.txt
1457 t/data/gmap_f9.txt
1458 t/data/GO.defs.test
1459 t/data/GO.defs.test2
1460 t/data/headerless.psl
1461 t/data/hemoglobinA.meg
1462 t/data/hg16_chroms.gff
1463 t/data/hmmpfam.out
1464 t/data/hmmpfam_cs.out
1465 t/data/hmmpfam_fake.out
1466 t/data/hmmscan.out
1467 t/data/hmmscan_multi_domain.out
1468 t/data/hmmsearch.out
1469 t/data/hmmsearch3.out
1470 t/data/hs_est.est2genome
1471 t/data/hs_fugu.newick
1472 t/data/hs_owlmonkey.aln
1473 t/data/hs_owlmonkey.fas
1474 t/data/hs_owlmonkey.fasta
1475 t/data/hsinsulin.blastcl3.blastn
1476 t/data/HUMBETGLOA.fa
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1478 t/data/HUMBETGLOA.gff
1479 t/data/HUMBETGLOA.grail
1480 t/data/HUMBETGLOA.grailexp
1481 t/data/HUMBETGLOA.mzef
1482 t/data/HUMBETGLOA.tblastx
1483 t/data/humor.maf
1484 t/data/humts1.pal
1485 t/data/hybrid1.gff3
1486 t/data/hybrid2.gff3
1487 t/data/in.fasta
1488 t/data/insulin.water
1489 t/data/interpro.xml
1490 t/data/interpro_ebi.xml
1491 t/data/interpro_sample.xml
1492 t/data/interpro_short.xml
1493 t/data/intrablock-comment.nex
1494 t/data/Kingdoms_DNA.nex
1495 t/data/knownGene.gff3
1496 t/data/L77119.hmmer
1497 t/data/little.largemultifasta
1498 t/data/LittleChrY.dbsnp.xml
1499 t/data/LOAD_Ccd1.dnd
1500 t/data/long-names.nex
1501 t/data/longnames.aln
1502 t/data/longnames.dnd
1503 t/data/lucy.info
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1505 t/data/lucy.seq
1506 t/data/lucy.stderr
1507 t/data/lysozyme6.protml
1508 t/data/lysozyme6.simple.protml
1509 t/data/M0.mlc
1510 t/data/M12730.gb
1511 t/data/map_hem/HEM1-HEM12.fa
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1513 t/data/map_hem/HEM1-HEM12.meme.txt
1514 t/data/map_hem/HEM1-HEM13.fa
1515 t/data/map_hem/HEM1-HEM13.meme.txt
1516 t/data/map_hem/HEM1-HEM14.fa
1517 t/data/map_hem/HEM1-HEM14.meme.txt
1518 t/data/map_hem/HEM1-HEM15.fa
1519 t/data/map_hem/HEM1-HEM15.meme.txt
1520 t/data/map_hem/HEM1-HEM2.fa
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1522 t/data/map_hem/HEM1-HEM2.meme.txt
1523 t/data/map_hem/HEM1-HEM3.fa
1524 t/data/map_hem/HEM1-HEM3.meme.txt
1525 t/data/map_hem/HEM1-HEM4.fa
1526 t/data/map_hem/HEM1-HEM4.meme.txt
1527 t/data/map_hem/HEM1.ups.fa_
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1529 t/data/map_hem/HEM12-HEM13.fa
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1531 t/data/map_hem/HEM12-HEM14.fa
1532 t/data/map_hem/HEM12-HEM14.meme.txt
1533 t/data/map_hem/HEM12-HEM15.fa
1534 t/data/map_hem/HEM12-HEM15.meme.txt
1535 t/data/map_hem/HEM12.ups.fa_
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1537 t/data/map_hem/HEM13-HEM14.fa
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1539 t/data/map_hem/HEM13-HEM15.fa
1540 t/data/map_hem/HEM13-HEM15.meme.txt
1541 t/data/map_hem/HEM13.ups.fa_
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1543 t/data/map_hem/HEM14-HEM15.fa
1544 t/data/map_hem/HEM14-HEM15.meme.txt
1545 t/data/map_hem/HEM14.ups.fa_
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1547 t/data/map_hem/HEM15.ups.fa_
1548 t/data/map_hem/HEM15.ups.fa_.revcom
1549 t/data/map_hem/HEM2-HEM12.fa
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1551 t/data/map_hem/HEM2-HEM13.fa
1552 t/data/map_hem/HEM2-HEM13.meme.txt
1553 t/data/map_hem/HEM2-HEM14.fa
1554 t/data/map_hem/HEM2-HEM14.meme.txt
1555 t/data/map_hem/HEM2-HEM15.fa
1556 t/data/map_hem/HEM2-HEM15.meme.txt
1557 t/data/map_hem/HEM2-HEM3.fa
1558 t/data/map_hem/HEM2-HEM3.meme.txt
1559 t/data/map_hem/HEM2-HEM4.fa
1560 t/data/map_hem/HEM2-HEM4.meme.txt
1561 t/data/map_hem/HEM2.ups.fa_
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1563 t/data/map_hem/HEM3-HEM12.fa
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1565 t/data/map_hem/HEM3-HEM13.fa
1566 t/data/map_hem/HEM3-HEM13.meme.txt
1567 t/data/map_hem/HEM3-HEM14.fa
1568 t/data/map_hem/HEM3-HEM14.meme.txt
1569 t/data/map_hem/HEM3-HEM15.fa
1570 t/data/map_hem/HEM3-HEM15.meme.txt
1571 t/data/map_hem/HEM3-HEM4.fa
1572 t/data/map_hem/HEM3-HEM4.meme.txt
1573 t/data/map_hem/HEM3.ups.fa_
1574 t/data/map_hem/HEM3.ups.fa_.revcom
1575 t/data/map_hem/HEM4-HEM12.fa
1576 t/data/map_hem/HEM4-HEM12.meme.txt
1577 t/data/map_hem/HEM4-HEM13.fa
1578 t/data/map_hem/HEM4-HEM13.meme.txt
1579 t/data/map_hem/HEM4-HEM14.fa
1580 t/data/map_hem/HEM4-HEM14.meme.txt
1581 t/data/map_hem/HEM4-HEM15.fa
1582 t/data/map_hem/HEM4-HEM15.meme.txt
1583 t/data/map_hem/HEM4.ups.fa_
1584 t/data/map_hem/HEM4.ups.fa_.revcom
1585 t/data/map_hem/yeast.nc.1.freq
1586 t/data/mapmaker.out
1587 t/data/mapmaker.txt
1588 t/data/mast.dat
1589 t/data/masta.dat
1590 t/data/match.output
1591 t/data/mbsout/mbsout_infile1
1592 t/data/mbsout/mbsout_infile2
1593 t/data/mbsout/mbsout_infile3
1594 t/data/Mcjanrna_rdbII.gbk
1595 t/data/megablast_output.paracel_btk
1596 t/data/meme.dat
1597 t/data/mini-AE001405.gb
1598 t/data/mini-align.aln
1599 t/data/mixedmast.dat
1600 t/data/MmCT
1601 t/data/mpath.ontology.test
1602 t/data/MSGEFTUA.gb
1603 t/data/msout_infile1
1604 t/data/msout_infile1.gz
1605 t/data/msout_infile2
1606 t/data/msout_infile2.gz
1607 t/data/multi.blast.m8
1608 t/data/multi.blast.m9
1609 t/data/multi.phd
1610 t/data/multi_1.fa
1611 t/data/multi_2.fa
1612 t/data/multi_blast.bls
1613 t/data/multifa.seq
1614 t/data/multifa.seq.qual
1615 t/data/multiline-intrablock-comment.nex
1616 t/data/multiseq.bls
1617 t/data/multiseq_tags.phd
1618 t/data/mus.bls.xml
1619 t/data/mutations.dat
1620 t/data/mutations.old.dat
1621 t/data/mutations.old.xml
1622 t/data/mutations.xml
1623 t/data/myco_sites.gff
1624 t/data/NC_001284.gbk
1625 t/data/NC_006346.gb
1626 t/data/NC_006511-short.gbk
1627 t/data/NC_008536.gb
1628 t/data/nei_gojobori_test.aln
1629 t/data/neighbor.dist
1630 t/data/new_blastn.txt
1631 t/data/newblast.xml
1632 t/data/NM_002254.gb
1633 t/data/no-genes.genscan
1634 t/data/no_cds_example.gb
1635 t/data/no_FH.embl
1636 t/data/no_hsps.blastp
1637 t/data/no_semicolon.newick
1638 t/data/noninterleaved.phy
1639 t/data/NT_021877.gbk
1640 t/data/nucmatrix.txt
1641 t/data/O_sat.wgs
1642 t/data/omim_genemap_test
1643 t/data/omim_genemap_test_nolinebreak
1644 t/data/omim_text_test
1645 t/data/P33897
1646 t/data/P35527.gb
1647 t/data/P39765.gb
1648 t/data/PAM250
1649 t/data/pep-266.aln
1650 t/data/pfam_tests.stk
1651 t/data/phi.out
1652 t/data/phipsi.out
1653 t/data/phylipdist-36.out
1654 t/data/phylipdist.out
1655 t/data/phyloxml_examples.xml
1656 t/data/pictogram.fa
1657 t/data/plague_yeast.bls.xml
1658 t/data/polymorphism.dat
1659 t/data/polymorphism.old.xml
1660 t/data/polymorphism.xml
1661 t/data/popgen_saureus.dat
1662 t/data/popgen_saureus.multidat
1663 t/data/popstats.prettybase
1664 t/data/pre_rel9.swiss
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1961 t/RemoteDB/Query/GenBank.t
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1977 t/Root/Tempfile.t
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1982 t/SearchIO/blasttable.t
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1993 t/SearchIO/megablast.t
1994 t/SearchIO/psl.t
1995 t/SearchIO/rnamotif.t
1996 t/SearchIO/SearchIO.t
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1998 t/SearchIO/SimilarityPair.t
1999 t/SearchIO/Tiling.t
2000 t/SearchIO/waba.t
2001 t/SearchIO/wise.t
2002 t/SearchIO/Writer/GbrowseGFF.t
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