PATH=/home/fly1600/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome2/bin:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/java/jre/bin:/opt/gnome/bin
Start 2012-08-07T06:01:04
ActivePerl-1600 CPAN-1.9402
Going to read '/home/fly1600/var/cpan/Metadata'
  Database was generated on Sat, 04 Aug 2012 21:39:03 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz ok
BioPerl-1.6.1
BioPerl-1.6.1/AUTHORS
BioPerl-1.6.1/BioPerl.pm
BioPerl-1.6.1/BUGS
BioPerl-1.6.1/Build.PL
BioPerl-1.6.1/Changes
BioPerl-1.6.1/DEPENDENCIES
BioPerl-1.6.1/DEPRECATED
BioPerl-1.6.1/INSTALL
BioPerl-1.6.1/INSTALL.SKIP
BioPerl-1.6.1/INSTALL.WIN
BioPerl-1.6.1/LICENSE
BioPerl-1.6.1/Makefile.PL
BioPerl-1.6.1/MANIFEST
BioPerl-1.6.1/MANIFEST.SKIP
BioPerl-1.6.1/META.yml
BioPerl-1.6.1/README
BioPerl-1.6.1/Bio
BioPerl-1.6.1/Bio/AlignIO.pm
BioPerl-1.6.1/Bio/AnalysisI.pm
BioPerl-1.6.1/Bio/AnalysisParserI.pm
BioPerl-1.6.1/Bio/AnalysisResultI.pm
BioPerl-1.6.1/Bio/AnnotatableI.pm
BioPerl-1.6.1/Bio/AnnotationCollectionI.pm
BioPerl-1.6.1/Bio/AnnotationI.pm
BioPerl-1.6.1/Bio/Biblio.pm
BioPerl-1.6.1/Bio/ClusterI.pm
BioPerl-1.6.1/Bio/ClusterIO.pm
BioPerl-1.6.1/Bio/DasI.pm
BioPerl-1.6.1/Bio/DBLinkContainerI.pm
BioPerl-1.6.1/Bio/DescribableI.pm
BioPerl-1.6.1/Bio/FeatureHolderI.pm
BioPerl-1.6.1/Bio/FeatureIO.pm
BioPerl-1.6.1/Bio/HandlerBaseI.pm
BioPerl-1.6.1/Bio/IdCollectionI.pm
BioPerl-1.6.1/Bio/IdentifiableI.pm
BioPerl-1.6.1/Bio/LocatableSeq.pm
BioPerl-1.6.1/Bio/LocationI.pm
BioPerl-1.6.1/Bio/MapIO.pm
BioPerl-1.6.1/Bio/OntologyIO.pm
BioPerl-1.6.1/Bio/ParameterBaseI.pm
BioPerl-1.6.1/Bio/Perl.pm
BioPerl-1.6.1/Bio/PhyloNetwork.pm
BioPerl-1.6.1/Bio/PrimarySeq.pm
BioPerl-1.6.1/Bio/PrimarySeqI.pm
BioPerl-1.6.1/Bio/PullParserI.pm
BioPerl-1.6.1/Bio/Range.pm
BioPerl-1.6.1/Bio/RangeI.pm
BioPerl-1.6.1/Bio/SearchDist.pm
BioPerl-1.6.1/Bio/SearchIO.pm
BioPerl-1.6.1/Bio/Seq.pm
BioPerl-1.6.1/Bio/SeqAnalysisParserI.pm
BioPerl-1.6.1/Bio/SeqFeatureI.pm
BioPerl-1.6.1/Bio/SeqI.pm
BioPerl-1.6.1/Bio/SeqIO.pm
BioPerl-1.6.1/Bio/SeqUtils.pm
BioPerl-1.6.1/Bio/SimpleAlign.pm
BioPerl-1.6.1/Bio/SimpleAnalysisI.pm
BioPerl-1.6.1/Bio/Species.pm
BioPerl-1.6.1/Bio/Taxon.pm
BioPerl-1.6.1/Bio/Taxonomy.pm
BioPerl-1.6.1/Bio/TreeIO.pm
BioPerl-1.6.1/Bio/UpdateableSeqI.pm
BioPerl-1.6.1/Bio/WebAgent.pm
BioPerl-1.6.1/Bio/Align
BioPerl-1.6.1/Bio/Align/AlignI.pm
BioPerl-1.6.1/Bio/Align/DNAStatistics.pm
BioPerl-1.6.1/Bio/Align/PairwiseStatistics.pm
BioPerl-1.6.1/Bio/Align/ProteinStatistics.pm
BioPerl-1.6.1/Bio/Align/StatisticsI.pm
BioPerl-1.6.1/Bio/Align/Utilities.pm
BioPerl-1.6.1/Bio/AlignIO
BioPerl-1.6.1/Bio/AlignIO/arp.pm
BioPerl-1.6.1/Bio/AlignIO/bl2seq.pm
BioPerl-1.6.1/Bio/AlignIO/clustalw.pm
BioPerl-1.6.1/Bio/AlignIO/emboss.pm
BioPerl-1.6.1/Bio/AlignIO/fasta.pm
BioPerl-1.6.1/Bio/AlignIO/largemultifasta.pm
BioPerl-1.6.1/Bio/AlignIO/maf.pm
BioPerl-1.6.1/Bio/AlignIO/mase.pm
BioPerl-1.6.1/Bio/AlignIO/mega.pm
BioPerl-1.6.1/Bio/AlignIO/meme.pm
BioPerl-1.6.1/Bio/AlignIO/metafasta.pm
BioPerl-1.6.1/Bio/AlignIO/msf.pm
BioPerl-1.6.1/Bio/AlignIO/nexus.pm
BioPerl-1.6.1/Bio/AlignIO/pfam.pm
BioPerl-1.6.1/Bio/AlignIO/phylip.pm
BioPerl-1.6.1/Bio/AlignIO/po.pm
BioPerl-1.6.1/Bio/AlignIO/proda.pm
BioPerl-1.6.1/Bio/AlignIO/prodom.pm
BioPerl-1.6.1/Bio/AlignIO/psi.pm
BioPerl-1.6.1/Bio/AlignIO/selex.pm
BioPerl-1.6.1/Bio/AlignIO/stockholm.pm
BioPerl-1.6.1/Bio/AlignIO/xmfa.pm
BioPerl-1.6.1/Bio/AlignIO/Handler
BioPerl-1.6.1/Bio/AlignIO/Handler/GenericAlignHandler.pm
BioPerl-1.6.1/Bio/Annotation
BioPerl-1.6.1/Bio/Annotation/AnnotationFactory.pm
BioPerl-1.6.1/Bio/Annotation/Collection.pm
BioPerl-1.6.1/Bio/Annotation/Comment.pm
BioPerl-1.6.1/Bio/Annotation/DBLink.pm
BioPerl-1.6.1/Bio/Annotation/OntologyTerm.pm
BioPerl-1.6.1/Bio/Annotation/Reference.pm
BioPerl-1.6.1/Bio/Annotation/Relation.pm
BioPerl-1.6.1/Bio/Annotation/SimpleValue.pm
BioPerl-1.6.1/Bio/Annotation/StructuredValue.pm
BioPerl-1.6.1/Bio/Annotation/TagTree.pm
BioPerl-1.6.1/Bio/Annotation/Target.pm
BioPerl-1.6.1/Bio/Annotation/Tree.pm
BioPerl-1.6.1/Bio/Annotation/TypeManager.pm
BioPerl-1.6.1/Bio/Assembly
BioPerl-1.6.1/Bio/Assembly/Contig.pm
BioPerl-1.6.1/Bio/Assembly/ContigAnalysis.pm
BioPerl-1.6.1/Bio/Assembly/IO.pm
BioPerl-1.6.1/Bio/Assembly/Scaffold.pm
BioPerl-1.6.1/Bio/Assembly/ScaffoldI.pm
BioPerl-1.6.1/Bio/Assembly/Singlet.pm
BioPerl-1.6.1/Bio/Assembly/IO
BioPerl-1.6.1/Bio/Assembly/IO/ace.pm
BioPerl-1.6.1/Bio/Assembly/IO/phrap.pm
BioPerl-1.6.1/Bio/Assembly/IO/tigr.pm
BioPerl-1.6.1/Bio/Assembly/Tools
BioPerl-1.6.1/Bio/Assembly/Tools/ContigSpectrum.pm
BioPerl-1.6.1/Bio/Biblio
BioPerl-1.6.1/Bio/Biblio/Article.pm
BioPerl-1.6.1/Bio/Biblio/BiblioBase.pm
BioPerl-1.6.1/Bio/Biblio/Book.pm
BioPerl-1.6.1/Bio/Biblio/BookArticle.pm
BioPerl-1.6.1/Bio/Biblio/IO.pm
BioPerl-1.6.1/Bio/Biblio/Journal.pm
BioPerl-1.6.1/Bio/Biblio/JournalArticle.pm
BioPerl-1.6.1/Bio/Biblio/MedlineArticle.pm
BioPerl-1.6.1/Bio/Biblio/MedlineBook.pm
BioPerl-1.6.1/Bio/Biblio/MedlineBookArticle.pm
BioPerl-1.6.1/Bio/Biblio/MedlineJournal.pm
BioPerl-1.6.1/Bio/Biblio/MedlineJournalArticle.pm
BioPerl-1.6.1/Bio/Biblio/Organisation.pm
BioPerl-1.6.1/Bio/Biblio/Patent.pm
BioPerl-1.6.1/Bio/Biblio/Person.pm
BioPerl-1.6.1/Bio/Biblio/Proceeding.pm
BioPerl-1.6.1/Bio/Biblio/Provider.pm
BioPerl-1.6.1/Bio/Biblio/PubmedArticle.pm
BioPerl-1.6.1/Bio/Biblio/PubmedBookArticle.pm
BioPerl-1.6.1/Bio/Biblio/PubmedJournalArticle.pm
BioPerl-1.6.1/Bio/Biblio/Ref.pm
BioPerl-1.6.1/Bio/Biblio/Service.pm
BioPerl-1.6.1/Bio/Biblio/TechReport.pm
BioPerl-1.6.1/Bio/Biblio/Thesis.pm
BioPerl-1.6.1/Bio/Biblio/WebResource.pm
BioPerl-1.6.1/Bio/Biblio/IO
BioPerl-1.6.1/Bio/Biblio/IO/medline2ref.pm
BioPerl-1.6.1/Bio/Biblio/IO/medlinexml.pm
BioPerl-1.6.1/Bio/Biblio/IO/pubmed2ref.pm
BioPerl-1.6.1/Bio/Biblio/IO/pubmedxml.pm
BioPerl-1.6.1/Bio/Cluster
BioPerl-1.6.1/Bio/Cluster/ClusterFactory.pm
BioPerl-1.6.1/Bio/Cluster/FamilyI.pm
BioPerl-1.6.1/Bio/Cluster/SequenceFamily.pm
BioPerl-1.6.1/Bio/Cluster/UniGene.pm
BioPerl-1.6.1/Bio/Cluster/UniGeneI.pm
BioPerl-1.6.1/Bio/ClusterIO
BioPerl-1.6.1/Bio/ClusterIO/dbsnp.pm
BioPerl-1.6.1/Bio/ClusterIO/unigene.pm
BioPerl-1.6.1/Bio/CodonUsage
BioPerl-1.6.1/Bio/CodonUsage/IO.pm
BioPerl-1.6.1/Bio/CodonUsage/Table.pm
BioPerl-1.6.1/Bio/Coordinate
BioPerl-1.6.1/Bio/Coordinate/Chain.pm
BioPerl-1.6.1/Bio/Coordinate/Collection.pm
BioPerl-1.6.1/Bio/Coordinate/ExtrapolatingPair.pm
BioPerl-1.6.1/Bio/Coordinate/GeneMapper.pm
BioPerl-1.6.1/Bio/Coordinate/Graph.pm
BioPerl-1.6.1/Bio/Coordinate/MapperI.pm
BioPerl-1.6.1/Bio/Coordinate/Pair.pm
BioPerl-1.6.1/Bio/Coordinate/Result.pm
BioPerl-1.6.1/Bio/Coordinate/ResultI.pm
BioPerl-1.6.1/Bio/Coordinate/Utils.pm
BioPerl-1.6.1/Bio/Coordinate/Result
BioPerl-1.6.1/Bio/Coordinate/Result/Gap.pm
BioPerl-1.6.1/Bio/Coordinate/Result/Match.pm
BioPerl-1.6.1/Bio/Das
BioPerl-1.6.1/Bio/Das/FeatureTypeI.pm
BioPerl-1.6.1/Bio/Das/SegmentI.pm
BioPerl-1.6.1/Bio/DB
BioPerl-1.6.1/Bio/DB/Ace.pm
BioPerl-1.6.1/Bio/DB/BiblioI.pm
BioPerl-1.6.1/Bio/DB/BioFetch.pm
BioPerl-1.6.1/Bio/DB/CUTG.pm
BioPerl-1.6.1/Bio/DB/DBFetch.pm
BioPerl-1.6.1/Bio/DB/EMBL.pm
BioPerl-1.6.1/Bio/DB/EntrezGene.pm
BioPerl-1.6.1/Bio/DB/EUtilities.pm
BioPerl-1.6.1/Bio/DB/Expression.pm
BioPerl-1.6.1/Bio/DB/Failover.pm
BioPerl-1.6.1/Bio/DB/Fasta.pm
BioPerl-1.6.1/Bio/DB/FileCache.pm
BioPerl-1.6.1/Bio/DB/Flat.pm
BioPerl-1.6.1/Bio/DB/GenBank.pm
BioPerl-1.6.1/Bio/DB/GenericWebAgent.pm
BioPerl-1.6.1/Bio/DB/GenPept.pm
BioPerl-1.6.1/Bio/DB/GFF.pm
BioPerl-1.6.1/Bio/DB/HIV.pm
BioPerl-1.6.1/Bio/DB/InMemoryCache.pm
BioPerl-1.6.1/Bio/DB/LocationI.pm
BioPerl-1.6.1/Bio/DB/MeSH.pm
BioPerl-1.6.1/Bio/DB/NCBIHelper.pm
BioPerl-1.6.1/Bio/DB/Qual.pm
BioPerl-1.6.1/Bio/DB/QueryI.pm
BioPerl-1.6.1/Bio/DB/RandomAccessI.pm
BioPerl-1.6.1/Bio/DB/ReferenceI.pm
BioPerl-1.6.1/Bio/DB/RefSeq.pm
BioPerl-1.6.1/Bio/DB/Registry.pm
BioPerl-1.6.1/Bio/DB/SeqFeature.pm
BioPerl-1.6.1/Bio/DB/SeqHound.pm
BioPerl-1.6.1/Bio/DB/SeqI.pm
BioPerl-1.6.1/Bio/DB/SeqVersion.pm
BioPerl-1.6.1/Bio/DB/SwissProt.pm
BioPerl-1.6.1/Bio/DB/Taxonomy.pm
BioPerl-1.6.1/Bio/DB/TFBS.pm
BioPerl-1.6.1/Bio/DB/Universal.pm
BioPerl-1.6.1/Bio/DB/UpdateableSeqI.pm
BioPerl-1.6.1/Bio/DB/WebDBSeqI.pm
BioPerl-1.6.1/Bio/DB/Biblio
BioPerl-1.6.1/Bio/DB/Biblio/biofetch.pm
BioPerl-1.6.1/Bio/DB/Biblio/eutils.pm
BioPerl-1.6.1/Bio/DB/Biblio/soap.pm
BioPerl-1.6.1/Bio/DB/Expression
BioPerl-1.6.1/Bio/DB/Expression/geo.pm
BioPerl-1.6.1/Bio/DB/Flat
BioPerl-1.6.1/Bio/DB/Flat/BDB.pm
BioPerl-1.6.1/Bio/DB/Flat/BinarySearch.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB
BioPerl-1.6.1/Bio/DB/Flat/BDB/embl.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/fasta.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/genbank.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/swiss.pm
BioPerl-1.6.1/Bio/DB/GFF
BioPerl-1.6.1/Bio/DB/GFF/Aggregator.pm
BioPerl-1.6.1/Bio/DB/GFF/Featname.pm
BioPerl-1.6.1/Bio/DB/GFF/Feature.pm
BioPerl-1.6.1/Bio/DB/GFF/Homol.pm
BioPerl-1.6.1/Bio/DB/GFF/RelSegment.pm
BioPerl-1.6.1/Bio/DB/GFF/Segment.pm
BioPerl-1.6.1/Bio/DB/GFF/Typename.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/ace.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/berkeleydb.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/biofetch.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/berkeleydb
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/iterator.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysql.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/oracle.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/pg.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory/iterator.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/alignment.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/clone.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/coding.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/gene.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/match.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/none.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/transcript.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
BioPerl-1.6.1/Bio/DB/GFF/Util
BioPerl-1.6.1/Bio/DB/GFF/Util/Binning.pm
BioPerl-1.6.1/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.1/Bio/DB/HIV
BioPerl-1.6.1/Bio/DB/HIV/HIVAnnotProcessor.pm
BioPerl-1.6.1/Bio/DB/HIV/HIVQueryHelper.pm
BioPerl-1.6.1/Bio/DB/HIV/lanl-schema.xml
BioPerl-1.6.1/Bio/DB/Query
BioPerl-1.6.1/Bio/DB/Query/GenBank.pm
BioPerl-1.6.1/Bio/DB/Query/HIVQuery.pm
BioPerl-1.6.1/Bio/DB/Query/WebQuery.pm
BioPerl-1.6.1/Bio/DB/SeqFeature
BioPerl-1.6.1/Bio/DB/SeqFeature/NormalizedFeature.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/NormalizedFeatureI.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Segment.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/bdb.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/berkeleydb.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/berkeleydb3.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/GFF2Loader.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/GFF3Loader.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/Loader.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/LoadHelper.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/memory.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/Iterator.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/Pg.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
BioPerl-1.6.1/Bio/DB/SeqVersion
BioPerl-1.6.1/Bio/DB/SeqVersion/gi.pm
BioPerl-1.6.1/Bio/DB/Taxonomy
BioPerl-1.6.1/Bio/DB/Taxonomy/entrez.pm
BioPerl-1.6.1/Bio/DB/Taxonomy/flatfile.pm
BioPerl-1.6.1/Bio/DB/Taxonomy/list.pm
BioPerl-1.6.1/Bio/DB/TFBS
BioPerl-1.6.1/Bio/DB/TFBS/transfac_pro.pm
BioPerl-1.6.1/Bio/Event
BioPerl-1.6.1/Bio/Event/EventGeneratorI.pm
BioPerl-1.6.1/Bio/Event/EventHandlerI.pm
BioPerl-1.6.1/Bio/Expression
BioPerl-1.6.1/Bio/Expression/Contact.pm
BioPerl-1.6.1/Bio/Expression/DataSet.pm
BioPerl-1.6.1/Bio/Expression/FeatureGroup.pm
BioPerl-1.6.1/Bio/Expression/FeatureI.pm
BioPerl-1.6.1/Bio/Expression/Platform.pm
BioPerl-1.6.1/Bio/Expression/ProbeI.pm
BioPerl-1.6.1/Bio/Expression/Sample.pm
BioPerl-1.6.1/Bio/Expression/FeatureGroup
BioPerl-1.6.1/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
BioPerl-1.6.1/Bio/Expression/FeatureSet
BioPerl-1.6.1/Bio/Expression/FeatureSet/FeatureSetMas50.pm
BioPerl-1.6.1/Bio/Factory
BioPerl-1.6.1/Bio/Factory/AnalysisI.pm
BioPerl-1.6.1/Bio/Factory/ApplicationFactoryI.pm
BioPerl-1.6.1/Bio/Factory/DriverFactory.pm
BioPerl-1.6.1/Bio/Factory/FTLocationFactory.pm
BioPerl-1.6.1/Bio/Factory/LocationFactoryI.pm
BioPerl-1.6.1/Bio/Factory/MapFactoryI.pm
BioPerl-1.6.1/Bio/Factory/ObjectBuilderI.pm
BioPerl-1.6.1/Bio/Factory/ObjectFactory.pm
BioPerl-1.6.1/Bio/Factory/ObjectFactoryI.pm
BioPerl-1.6.1/Bio/Factory/SeqAnalysisParserFactory.pm
BioPerl-1.6.1/Bio/Factory/SeqAnalysisParserFactoryI.pm
BioPerl-1.6.1/Bio/Factory/SequenceFactoryI.pm
BioPerl-1.6.1/Bio/Factory/SequenceProcessorI.pm
BioPerl-1.6.1/Bio/Factory/SequenceStreamI.pm
BioPerl-1.6.1/Bio/Factory/TreeFactoryI.pm
BioPerl-1.6.1/Bio/FeatureIO
BioPerl-1.6.1/Bio/FeatureIO/bed.pm
BioPerl-1.6.1/Bio/FeatureIO/gff.pm
BioPerl-1.6.1/Bio/FeatureIO/gtf.pm
BioPerl-1.6.1/Bio/FeatureIO/interpro.pm
BioPerl-1.6.1/Bio/FeatureIO/ptt.pm
BioPerl-1.6.1/Bio/FeatureIO/vecscreen_simple.pm
BioPerl-1.6.1/Bio/Index
BioPerl-1.6.1/Bio/Index/Abstract.pm
BioPerl-1.6.1/Bio/Index/AbstractSeq.pm
BioPerl-1.6.1/Bio/Index/Blast.pm
BioPerl-1.6.1/Bio/Index/BlastTable.pm
BioPerl-1.6.1/Bio/Index/EMBL.pm
BioPerl-1.6.1/Bio/Index/Fasta.pm
BioPerl-1.6.1/Bio/Index/Fastq.pm
BioPerl-1.6.1/Bio/Index/GenBank.pm
BioPerl-1.6.1/Bio/Index/Hmmer.pm
BioPerl-1.6.1/Bio/Index/Qual.pm
BioPerl-1.6.1/Bio/Index/Stockholm.pm
BioPerl-1.6.1/Bio/Index/SwissPfam.pm
BioPerl-1.6.1/Bio/Index/Swissprot.pm
BioPerl-1.6.1/Bio/LiveSeq
BioPerl-1.6.1/Bio/LiveSeq/AARange.pm
BioPerl-1.6.1/Bio/LiveSeq/Chain.pm
BioPerl-1.6.1/Bio/LiveSeq/ChainI.pm
BioPerl-1.6.1/Bio/LiveSeq/DNA.pm
BioPerl-1.6.1/Bio/LiveSeq/Exon.pm
BioPerl-1.6.1/Bio/LiveSeq/Gene.pm
BioPerl-1.6.1/Bio/LiveSeq/Intron.pm
BioPerl-1.6.1/Bio/LiveSeq/Mutation.pm
BioPerl-1.6.1/Bio/LiveSeq/Mutator.pm
BioPerl-1.6.1/Bio/LiveSeq/Prim_Transcript.pm
BioPerl-1.6.1/Bio/LiveSeq/Range.pm
BioPerl-1.6.1/Bio/LiveSeq/Repeat_Region.pm
BioPerl-1.6.1/Bio/LiveSeq/Repeat_Unit.pm
BioPerl-1.6.1/Bio/LiveSeq/SeqI.pm
BioPerl-1.6.1/Bio/LiveSeq/Transcript.pm
BioPerl-1.6.1/Bio/LiveSeq/Translation.pm
BioPerl-1.6.1/Bio/LiveSeq/IO
BioPerl-1.6.1/Bio/LiveSeq/IO/BioPerl.pm
BioPerl-1.6.1/Bio/LiveSeq/IO/Loader.pm
BioPerl-1.6.1/Bio/LiveSeq/IO/README
BioPerl-1.6.1/Bio/Location
BioPerl-1.6.1/Bio/Location/Atomic.pm
BioPerl-1.6.1/Bio/Location/AvWithinCoordPolicy.pm
BioPerl-1.6.1/Bio/Location/CoordinatePolicyI.pm
BioPerl-1.6.1/Bio/Location/Fuzzy.pm
BioPerl-1.6.1/Bio/Location/FuzzyLocationI.pm
BioPerl-1.6.1/Bio/Location/NarrowestCoordPolicy.pm
BioPerl-1.6.1/Bio/Location/Simple.pm
BioPerl-1.6.1/Bio/Location/Split.pm
BioPerl-1.6.1/Bio/Location/SplitLocationI.pm
BioPerl-1.6.1/Bio/Location/WidestCoordPolicy.pm
BioPerl-1.6.1/Bio/Map
BioPerl-1.6.1/Bio/Map/Clone.pm
BioPerl-1.6.1/Bio/Map/Contig.pm
BioPerl-1.6.1/Bio/Map/CytoMap.pm
BioPerl-1.6.1/Bio/Map/CytoMarker.pm
BioPerl-1.6.1/Bio/Map/CytoPosition.pm
BioPerl-1.6.1/Bio/Map/EntityI.pm
BioPerl-1.6.1/Bio/Map/FPCMarker.pm
BioPerl-1.6.1/Bio/Map/Gene.pm
BioPerl-1.6.1/Bio/Map/GeneMap.pm
BioPerl-1.6.1/Bio/Map/GenePosition.pm
BioPerl-1.6.1/Bio/Map/GeneRelative.pm
BioPerl-1.6.1/Bio/Map/LinkageMap.pm
BioPerl-1.6.1/Bio/Map/LinkagePosition.pm
BioPerl-1.6.1/Bio/Map/MapI.pm
BioPerl-1.6.1/Bio/Map/Mappable.pm
BioPerl-1.6.1/Bio/Map/MappableI.pm
BioPerl-1.6.1/Bio/Map/Marker.pm
BioPerl-1.6.1/Bio/Map/MarkerI.pm
BioPerl-1.6.1/Bio/Map/Microsatellite.pm
BioPerl-1.6.1/Bio/Map/OrderedPosition.pm
BioPerl-1.6.1/Bio/Map/OrderedPositionWithDistance.pm
BioPerl-1.6.1/Bio/Map/Physical.pm
BioPerl-1.6.1/Bio/Map/Position.pm
BioPerl-1.6.1/Bio/Map/PositionHandler.pm
BioPerl-1.6.1/Bio/Map/PositionHandlerI.pm
BioPerl-1.6.1/Bio/Map/PositionI.pm
BioPerl-1.6.1/Bio/Map/PositionWithSequence.pm
BioPerl-1.6.1/Bio/Map/Prediction.pm
BioPerl-1.6.1/Bio/Map/Relative.pm
BioPerl-1.6.1/Bio/Map/RelativeI.pm
BioPerl-1.6.1/Bio/Map/SimpleMap.pm
BioPerl-1.6.1/Bio/Map/TranscriptionFactor.pm
BioPerl-1.6.1/Bio/MapIO
BioPerl-1.6.1/Bio/MapIO/fpc.pm
BioPerl-1.6.1/Bio/MapIO/mapmaker.pm
BioPerl-1.6.1/Bio/Matrix
BioPerl-1.6.1/Bio/Matrix/Generic.pm
BioPerl-1.6.1/Bio/Matrix/IO.pm
BioPerl-1.6.1/Bio/Matrix/MatrixI.pm
BioPerl-1.6.1/Bio/Matrix/Mlagan.pm
BioPerl-1.6.1/Bio/Matrix/PhylipDist.pm
BioPerl-1.6.1/Bio/Matrix/Scoring.pm
BioPerl-1.6.1/Bio/Matrix/IO
BioPerl-1.6.1/Bio/Matrix/IO/mlagan.pm
BioPerl-1.6.1/Bio/Matrix/IO/phylip.pm
BioPerl-1.6.1/Bio/Matrix/IO/scoring.pm
BioPerl-1.6.1/Bio/Matrix/PSM
BioPerl-1.6.1/Bio/Matrix/PSM/InstanceSite.pm
BioPerl-1.6.1/Bio/Matrix/PSM/InstanceSiteI.pm
BioPerl-1.6.1/Bio/Matrix/PSM/IO.pm
BioPerl-1.6.1/Bio/Matrix/PSM/ProtMatrix.pm
BioPerl-1.6.1/Bio/Matrix/PSM/ProtPsm.pm
BioPerl-1.6.1/Bio/Matrix/PSM/Psm.pm
BioPerl-1.6.1/Bio/Matrix/PSM/PsmHeader.pm
BioPerl-1.6.1/Bio/Matrix/PSM/PsmHeaderI.pm
BioPerl-1.6.1/Bio/Matrix/PSM/PsmI.pm
BioPerl-1.6.1/Bio/Matrix/PSM/SiteMatrix.pm
BioPerl-1.6.1/Bio/Matrix/PSM/SiteMatrixI.pm
BioPerl-1.6.1/Bio/Matrix/PSM/IO
BioPerl-1.6.1/Bio/Matrix/PSM/IO/mast.pm
BioPerl-1.6.1/Bio/Matrix/PSM/IO/masta.pm
BioPerl-1.6.1/Bio/Matrix/PSM/IO/meme.pm
BioPerl-1.6.1/Bio/Matrix/PSM/IO/psiblast.pm
BioPerl-1.6.1/Bio/Matrix/PSM/IO/transfac.pm
BioPerl-1.6.1/Bio/MolEvol
BioPerl-1.6.1/Bio/MolEvol/CodonModel.pm
BioPerl-1.6.1/Bio/Ontology
BioPerl-1.6.1/Bio/Ontology/DocumentRegistry.pm
BioPerl-1.6.1/Bio/Ontology/GOterm.pm
BioPerl-1.6.1/Bio/Ontology/InterProTerm.pm
BioPerl-1.6.1/Bio/Ontology/OBOEngine.pm
BioPerl-1.6.1/Bio/Ontology/OBOterm.pm
BioPerl-1.6.1/Bio/Ontology/Ontology.pm
BioPerl-1.6.1/Bio/Ontology/OntologyEngineI.pm
BioPerl-1.6.1/Bio/Ontology/OntologyI.pm
BioPerl-1.6.1/Bio/Ontology/OntologyStore.pm
BioPerl-1.6.1/Bio/Ontology/Path.pm
BioPerl-1.6.1/Bio/Ontology/PathI.pm
BioPerl-1.6.1/Bio/Ontology/Relationship.pm
BioPerl-1.6.1/Bio/Ontology/RelationshipFactory.pm
BioPerl-1.6.1/Bio/Ontology/RelationshipI.pm
BioPerl-1.6.1/Bio/Ontology/RelationshipType.pm
BioPerl-1.6.1/Bio/Ontology/SimpleOntologyEngine.pm
BioPerl-1.6.1/Bio/Ontology/Term.pm
BioPerl-1.6.1/Bio/Ontology/TermFactory.pm
BioPerl-1.6.1/Bio/Ontology/TermI.pm
BioPerl-1.6.1/Bio/Ontology/SimpleGOEngine
BioPerl-1.6.1/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
BioPerl-1.6.1/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
BioPerl-1.6.1/Bio/OntologyIO
BioPerl-1.6.1/Bio/OntologyIO/dagflat.pm
BioPerl-1.6.1/Bio/OntologyIO/goflat.pm
BioPerl-1.6.1/Bio/OntologyIO/InterProParser.pm
BioPerl-1.6.1/Bio/OntologyIO/obo.pm
BioPerl-1.6.1/Bio/OntologyIO/simplehierarchy.pm
BioPerl-1.6.1/Bio/OntologyIO/soflat.pm
BioPerl-1.6.1/Bio/OntologyIO/Handlers
BioPerl-1.6.1/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
BioPerl-1.6.1/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
BioPerl-1.6.1/Bio/OntologyIO/Handlers/InterProHandler.pm
BioPerl-1.6.1/Bio/Phenotype
BioPerl-1.6.1/Bio/Phenotype/Correlate.pm
BioPerl-1.6.1/Bio/Phenotype/Measure.pm
BioPerl-1.6.1/Bio/Phenotype/Phenotype.pm
BioPerl-1.6.1/Bio/Phenotype/PhenotypeI.pm
BioPerl-1.6.1/Bio/Phenotype/MeSH
BioPerl-1.6.1/Bio/Phenotype/MeSH/Term.pm
BioPerl-1.6.1/Bio/Phenotype/MeSH/Twig.pm
BioPerl-1.6.1/Bio/Phenotype/OMIM
BioPerl-1.6.1/Bio/Phenotype/OMIM/MiniMIMentry.pm
BioPerl-1.6.1/Bio/Phenotype/OMIM/OMIMentry.pm
BioPerl-1.6.1/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
BioPerl-1.6.1/Bio/Phenotype/OMIM/OMIMparser.pm
BioPerl-1.6.1/Bio/PhyloNetwork
BioPerl-1.6.1/Bio/PhyloNetwork/Factory.pm
BioPerl-1.6.1/Bio/PhyloNetwork/FactoryX.pm
BioPerl-1.6.1/Bio/PhyloNetwork/GraphViz.pm
BioPerl-1.6.1/Bio/PhyloNetwork/muVector.pm
BioPerl-1.6.1/Bio/PhyloNetwork/RandomFactory.pm
BioPerl-1.6.1/Bio/PhyloNetwork/TreeFactory.pm
BioPerl-1.6.1/Bio/PhyloNetwork/TreeFactoryMulti.pm
BioPerl-1.6.1/Bio/PhyloNetwork/TreeFactoryX.pm
BioPerl-1.6.1/Bio/PopGen
BioPerl-1.6.1/Bio/PopGen/Genotype.pm
BioPerl-1.6.1/Bio/PopGen/GenotypeI.pm
BioPerl-1.6.1/Bio/PopGen/HtSNP.pm
BioPerl-1.6.1/Bio/PopGen/Individual.pm
BioPerl-1.6.1/Bio/PopGen/IndividualI.pm
BioPerl-1.6.1/Bio/PopGen/IO.pm
BioPerl-1.6.1/Bio/PopGen/Marker.pm
BioPerl-1.6.1/Bio/PopGen/MarkerI.pm
BioPerl-1.6.1/Bio/PopGen/PopStats.pm
BioPerl-1.6.1/Bio/PopGen/Population.pm
BioPerl-1.6.1/Bio/PopGen/PopulationI.pm
BioPerl-1.6.1/Bio/PopGen/Statistics.pm
BioPerl-1.6.1/Bio/PopGen/TagHaplotype.pm
BioPerl-1.6.1/Bio/PopGen/Utilities.pm
BioPerl-1.6.1/Bio/PopGen/IO
BioPerl-1.6.1/Bio/PopGen/IO/csv.pm
BioPerl-1.6.1/Bio/PopGen/IO/hapmap.pm
BioPerl-1.6.1/Bio/PopGen/IO/phase.pm
BioPerl-1.6.1/Bio/PopGen/IO/prettybase.pm
BioPerl-1.6.1/Bio/PopGen/Simulation
BioPerl-1.6.1/Bio/PopGen/Simulation/Coalescent.pm
BioPerl-1.6.1/Bio/PopGen/Simulation/GeneticDrift.pm
BioPerl-1.6.1/Bio/Restriction
BioPerl-1.6.1/Bio/Restriction/Analysis.pm
BioPerl-1.6.1/Bio/Restriction/Enzyme.pm
BioPerl-1.6.1/Bio/Restriction/EnzymeCollection.pm
BioPerl-1.6.1/Bio/Restriction/EnzymeI.pm
BioPerl-1.6.1/Bio/Restriction/IO.pm
BioPerl-1.6.1/Bio/Restriction/Enzyme
BioPerl-1.6.1/Bio/Restriction/Enzyme/MultiCut.pm
BioPerl-1.6.1/Bio/Restriction/Enzyme/MultiSite.pm
BioPerl-1.6.1/Bio/Restriction/IO
BioPerl-1.6.1/Bio/Restriction/IO/bairoch.pm
BioPerl-1.6.1/Bio/Restriction/IO/base.pm
BioPerl-1.6.1/Bio/Restriction/IO/itype2.pm
BioPerl-1.6.1/Bio/Restriction/IO/prototype.pm
BioPerl-1.6.1/Bio/Restriction/IO/withrefm.pm
BioPerl-1.6.1/Bio/Root
BioPerl-1.6.1/Bio/Root/Build.pm
BioPerl-1.6.1/Bio/Root/Exception.pm
BioPerl-1.6.1/Bio/Root/HTTPget.pm
BioPerl-1.6.1/Bio/Root/IO.pm
BioPerl-1.6.1/Bio/Root/Root.pm
BioPerl-1.6.1/Bio/Root/RootI.pm
BioPerl-1.6.1/Bio/Root/Storable.pm
BioPerl-1.6.1/Bio/Root/Test.pm
BioPerl-1.6.1/Bio/Root/Utilities.pm
BioPerl-1.6.1/Bio/Root/Version.pm
BioPerl-1.6.1/Bio/Root/Test
BioPerl-1.6.1/Bio/Root/Test/Warn.pm
BioPerl-1.6.1/Bio/Search
BioPerl-1.6.1/Bio/Search/BlastStatistics.pm
BioPerl-1.6.1/Bio/Search/BlastUtils.pm
BioPerl-1.6.1/Bio/Search/DatabaseI.pm
BioPerl-1.6.1/Bio/Search/GenericDatabase.pm
BioPerl-1.6.1/Bio/Search/GenericStatistics.pm
BioPerl-1.6.1/Bio/Search/Processor.pm
BioPerl-1.6.1/Bio/Search/SearchUtils.pm
BioPerl-1.6.1/Bio/Search/StatisticsI.pm
BioPerl-1.6.1/Bio/Search/Hit
BioPerl-1.6.1/Bio/Search/Hit/BlastHit.pm
BioPerl-1.6.1/Bio/Search/Hit/BlastPullHit.pm
BioPerl-1.6.1/Bio/Search/Hit/Fasta.pm
BioPerl-1.6.1/Bio/Search/Hit/GenericHit.pm
BioPerl-1.6.1/Bio/Search/Hit/HitFactory.pm
BioPerl-1.6.1/Bio/Search/Hit/HitI.pm
BioPerl-1.6.1/Bio/Search/Hit/HMMERHit.pm
BioPerl-1.6.1/Bio/Search/Hit/HmmpfamHit.pm
BioPerl-1.6.1/Bio/Search/Hit/ModelHit.pm
BioPerl-1.6.1/Bio/Search/Hit/PsiBlastHit.pm
BioPerl-1.6.1/Bio/Search/Hit/PullHitI.pm
BioPerl-1.6.1/Bio/Search/HSP
BioPerl-1.6.1/Bio/Search/HSP/BlastHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/BlastPullHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/FastaHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/GenericHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/HMMERHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/HmmpfamHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/HSPFactory.pm
BioPerl-1.6.1/Bio/Search/HSP/HSPI.pm
BioPerl-1.6.1/Bio/Search/HSP/ModelHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/PsiBlastHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/PSLHSP.pm
BioPerl-1.6.1/Bio/Search/HSP/PullHSPI.pm
BioPerl-1.6.1/Bio/Search/HSP/WABAHSP.pm
BioPerl-1.6.1/Bio/Search/Iteration
BioPerl-1.6.1/Bio/Search/Iteration/GenericIteration.pm
BioPerl-1.6.1/Bio/Search/Iteration/IterationI.pm
BioPerl-1.6.1/Bio/Search/Result
BioPerl-1.6.1/Bio/Search/Result/BlastPullResult.pm
BioPerl-1.6.1/Bio/Search/Result/BlastResult.pm
BioPerl-1.6.1/Bio/Search/Result/CrossMatchResult.pm
BioPerl-1.6.1/Bio/Search/Result/GenericResult.pm
BioPerl-1.6.1/Bio/Search/Result/HMMERResult.pm
BioPerl-1.6.1/Bio/Search/Result/HmmpfamResult.pm
BioPerl-1.6.1/Bio/Search/Result/PullResultI.pm
BioPerl-1.6.1/Bio/Search/Result/ResultFactory.pm
BioPerl-1.6.1/Bio/Search/Result/ResultI.pm
BioPerl-1.6.1/Bio/Search/Result/WABAResult.pm
BioPerl-1.6.1/Bio/Search/Tiling
BioPerl-1.6.1/Bio/Search/Tiling/MapTileUtils.pm
BioPerl-1.6.1/Bio/Search/Tiling/MapTiling.pm
BioPerl-1.6.1/Bio/Search/Tiling/TilingI.pm
BioPerl-1.6.1/Bio/SearchIO
BioPerl-1.6.1/Bio/SearchIO/axt.pm
BioPerl-1.6.1/Bio/SearchIO/blast.pm
BioPerl-1.6.1/Bio/SearchIO/blast_pull.pm
BioPerl-1.6.1/Bio/SearchIO/blasttable.pm
BioPerl-1.6.1/Bio/SearchIO/blastxml.pm
BioPerl-1.6.1/Bio/SearchIO/cross_match.pm
BioPerl-1.6.1/Bio/SearchIO/erpin.pm
BioPerl-1.6.1/Bio/SearchIO/EventHandlerI.pm
BioPerl-1.6.1/Bio/SearchIO/exonerate.pm
BioPerl-1.6.1/Bio/SearchIO/fasta.pm
BioPerl-1.6.1/Bio/SearchIO/FastHitEventBuilder.pm
BioPerl-1.6.1/Bio/SearchIO/gmap_f9.pm
BioPerl-1.6.1/Bio/SearchIO/hmmer.pm
BioPerl-1.6.1/Bio/SearchIO/hmmer_pull.pm
BioPerl-1.6.1/Bio/SearchIO/infernal.pm
BioPerl-1.6.1/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
BioPerl-1.6.1/Bio/SearchIO/megablast.pm
BioPerl-1.6.1/Bio/SearchIO/psl.pm
BioPerl-1.6.1/Bio/SearchIO/rnamotif.pm
BioPerl-1.6.1/Bio/SearchIO/SearchResultEventBuilder.pm
BioPerl-1.6.1/Bio/SearchIO/SearchWriterI.pm
BioPerl-1.6.1/Bio/SearchIO/sim4.pm
BioPerl-1.6.1/Bio/SearchIO/waba.pm
BioPerl-1.6.1/Bio/SearchIO/wise.pm
BioPerl-1.6.1/Bio/SearchIO/Writer
BioPerl-1.6.1/Bio/SearchIO/Writer/BSMLResultWriter.pm
BioPerl-1.6.1/Bio/SearchIO/Writer/GbrowseGFF.pm
BioPerl-1.6.1/Bio/SearchIO/Writer/HitTableWriter.pm
BioPerl-1.6.1/Bio/SearchIO/Writer/HSPTableWriter.pm
BioPerl-1.6.1/Bio/SearchIO/Writer/HTMLResultWriter.pm
BioPerl-1.6.1/Bio/SearchIO/Writer/ResultTableWriter.pm
BioPerl-1.6.1/Bio/SearchIO/Writer/TextResultWriter.pm
BioPerl-1.6.1/Bio/SearchIO/XML
BioPerl-1.6.1/Bio/SearchIO/XML/BlastHandler.pm
BioPerl-1.6.1/Bio/SearchIO/XML/PsiBlastHandler.pm
BioPerl-1.6.1/Bio/Seq
BioPerl-1.6.1/Bio/Seq/BaseSeqProcessor.pm
BioPerl-1.6.1/Bio/Seq/EncodedSeq.pm
BioPerl-1.6.1/Bio/Seq/LargeLocatableSeq.pm
BioPerl-1.6.1/Bio/Seq/LargePrimarySeq.pm
BioPerl-1.6.1/Bio/Seq/LargeSeq.pm
BioPerl-1.6.1/Bio/Seq/LargeSeqI.pm
BioPerl-1.6.1/Bio/Seq/Meta.pm
BioPerl-1.6.1/Bio/Seq/MetaI.pm
BioPerl-1.6.1/Bio/Seq/PrimaryQual.pm
BioPerl-1.6.1/Bio/Seq/PrimedSeq.pm
BioPerl-1.6.1/Bio/Seq/QualI.pm
BioPerl-1.6.1/Bio/Seq/Quality.pm
BioPerl-1.6.1/Bio/Seq/RichSeq.pm
BioPerl-1.6.1/Bio/Seq/RichSeqI.pm
BioPerl-1.6.1/Bio/Seq/SeqBuilder.pm
BioPerl-1.6.1/Bio/Seq/SeqFactory.pm
BioPerl-1.6.1/Bio/Seq/SeqFastaSpeedFactory.pm
BioPerl-1.6.1/Bio/Seq/SequenceTrace.pm
BioPerl-1.6.1/Bio/Seq/SeqWithQuality.pm
BioPerl-1.6.1/Bio/Seq/TraceI.pm
BioPerl-1.6.1/Bio/Seq/Meta
BioPerl-1.6.1/Bio/Seq/Meta/Array.pm
BioPerl-1.6.1/Bio/SeqEvolution
BioPerl-1.6.1/Bio/SeqEvolution/DNAPoint.pm
BioPerl-1.6.1/Bio/SeqEvolution/EvolutionI.pm
BioPerl-1.6.1/Bio/SeqEvolution/Factory.pm
BioPerl-1.6.1/Bio/SeqFeature
BioPerl-1.6.1/Bio/SeqFeature/Annotated.pm
BioPerl-1.6.1/Bio/SeqFeature/AnnotationAdaptor.pm
BioPerl-1.6.1/Bio/SeqFeature/Collection.pm
BioPerl-1.6.1/Bio/SeqFeature/CollectionI.pm
BioPerl-1.6.1/Bio/SeqFeature/Computation.pm
BioPerl-1.6.1/Bio/SeqFeature/FeaturePair.pm
BioPerl-1.6.1/Bio/SeqFeature/Generic.pm
BioPerl-1.6.1/Bio/SeqFeature/Lite.pm
BioPerl-1.6.1/Bio/SeqFeature/PositionProxy.pm
BioPerl-1.6.1/Bio/SeqFeature/Primer.pm
BioPerl-1.6.1/Bio/SeqFeature/Similarity.pm
BioPerl-1.6.1/Bio/SeqFeature/SimilarityPair.pm
BioPerl-1.6.1/Bio/SeqFeature/TypedSeqFeatureI.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene
BioPerl-1.6.1/Bio/SeqFeature/Gene/Exon.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/ExonI.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/GeneStructure.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/GeneStructureI.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/Intron.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/NC_Feature.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/Poly_A_site.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/Promoter.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/Transcript.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/TranscriptI.pm
BioPerl-1.6.1/Bio/SeqFeature/Gene/UTR.pm
BioPerl-1.6.1/Bio/SeqFeature/SiRNA
BioPerl-1.6.1/Bio/SeqFeature/SiRNA/Oligo.pm
BioPerl-1.6.1/Bio/SeqFeature/SiRNA/Pair.pm
BioPerl-1.6.1/Bio/SeqFeature/Tools
BioPerl-1.6.1/Bio/SeqFeature/Tools/FeatureNamer.pm
BioPerl-1.6.1/Bio/SeqFeature/Tools/IDHandler.pm
BioPerl-1.6.1/Bio/SeqFeature/Tools/TypeMapper.pm
BioPerl-1.6.1/Bio/SeqFeature/Tools/Unflattener.pm
BioPerl-1.6.1/Bio/SeqIO
BioPerl-1.6.1/Bio/SeqIO/abi.pm
BioPerl-1.6.1/Bio/SeqIO/ace.pm
BioPerl-1.6.1/Bio/SeqIO/agave.pm
BioPerl-1.6.1/Bio/SeqIO/alf.pm
BioPerl-1.6.1/Bio/SeqIO/asciitree.pm
BioPerl-1.6.1/Bio/SeqIO/bsml.pm
BioPerl-1.6.1/Bio/SeqIO/bsml_sax.pm
BioPerl-1.6.1/Bio/SeqIO/chadoxml.pm
BioPerl-1.6.1/Bio/SeqIO/chaos.pm
BioPerl-1.6.1/Bio/SeqIO/chaosxml.pm
BioPerl-1.6.1/Bio/SeqIO/ctf.pm
BioPerl-1.6.1/Bio/SeqIO/embl.pm
BioPerl-1.6.1/Bio/SeqIO/embldriver.pm
BioPerl-1.6.1/Bio/SeqIO/entrezgene.pm
BioPerl-1.6.1/Bio/SeqIO/excel.pm
BioPerl-1.6.1/Bio/SeqIO/exp.pm
BioPerl-1.6.1/Bio/SeqIO/fasta.pm
BioPerl-1.6.1/Bio/SeqIO/fastq.pm
BioPerl-1.6.1/Bio/SeqIO/flybase_chadoxml.pm
BioPerl-1.6.1/Bio/SeqIO/FTHelper.pm
BioPerl-1.6.1/Bio/SeqIO/game.pm
BioPerl-1.6.1/Bio/SeqIO/gbdriver.pm
BioPerl-1.6.1/Bio/SeqIO/gcg.pm
BioPerl-1.6.1/Bio/SeqIO/genbank.pm
BioPerl-1.6.1/Bio/SeqIO/interpro.pm
BioPerl-1.6.1/Bio/SeqIO/kegg.pm
BioPerl-1.6.1/Bio/SeqIO/largefasta.pm
BioPerl-1.6.1/Bio/SeqIO/lasergene.pm
BioPerl-1.6.1/Bio/SeqIO/locuslink.pm
BioPerl-1.6.1/Bio/SeqIO/metafasta.pm
BioPerl-1.6.1/Bio/SeqIO/MultiFile.pm
BioPerl-1.6.1/Bio/SeqIO/phd.pm
BioPerl-1.6.1/Bio/SeqIO/pir.pm
BioPerl-1.6.1/Bio/SeqIO/pln.pm
BioPerl-1.6.1/Bio/SeqIO/qual.pm
BioPerl-1.6.1/Bio/SeqIO/raw.pm
BioPerl-1.6.1/Bio/SeqIO/scf.pm
BioPerl-1.6.1/Bio/SeqIO/strider.pm
BioPerl-1.6.1/Bio/SeqIO/swiss.pm
BioPerl-1.6.1/Bio/SeqIO/swissdriver.pm
BioPerl-1.6.1/Bio/SeqIO/tab.pm
BioPerl-1.6.1/Bio/SeqIO/table.pm
BioPerl-1.6.1/Bio/SeqIO/tigr.pm
BioPerl-1.6.1/Bio/SeqIO/tigrxml.pm
BioPerl-1.6.1/Bio/SeqIO/tinyseq.pm
BioPerl-1.6.1/Bio/SeqIO/ztr.pm
BioPerl-1.6.1/Bio/SeqIO/game
BioPerl-1.6.1/Bio/SeqIO/game/featHandler.pm
BioPerl-1.6.1/Bio/SeqIO/game/gameHandler.pm
BioPerl-1.6.1/Bio/SeqIO/game/gameSubs.pm
BioPerl-1.6.1/Bio/SeqIO/game/gameWriter.pm
BioPerl-1.6.1/Bio/SeqIO/game/seqHandler.pm
BioPerl-1.6.1/Bio/SeqIO/Handler
BioPerl-1.6.1/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
BioPerl-1.6.1/Bio/SeqIO/tinyseq
BioPerl-1.6.1/Bio/SeqIO/tinyseq/tinyseqHandler.pm
BioPerl-1.6.1/Bio/Structure
BioPerl-1.6.1/Bio/Structure/Atom.pm
BioPerl-1.6.1/Bio/Structure/Chain.pm
BioPerl-1.6.1/Bio/Structure/Entry.pm
BioPerl-1.6.1/Bio/Structure/IO.pm
BioPerl-1.6.1/Bio/Structure/Model.pm
BioPerl-1.6.1/Bio/Structure/Residue.pm
BioPerl-1.6.1/Bio/Structure/StructureI.pm
BioPerl-1.6.1/Bio/Structure/IO
BioPerl-1.6.1/Bio/Structure/IO/pdb.pm
BioPerl-1.6.1/Bio/Structure/SecStr
BioPerl-1.6.1/Bio/Structure/SecStr/DSSP
BioPerl-1.6.1/Bio/Structure/SecStr/DSSP/Res.pm
BioPerl-1.6.1/Bio/Structure/SecStr/STRIDE
BioPerl-1.6.1/Bio/Structure/SecStr/STRIDE/Res.pm
BioPerl-1.6.1/Bio/Symbol
BioPerl-1.6.1/Bio/Symbol/Alphabet.pm
BioPerl-1.6.1/Bio/Symbol/AlphabetI.pm
BioPerl-1.6.1/Bio/Symbol/DNAAlphabet.pm
BioPerl-1.6.1/Bio/Symbol/ProteinAlphabet.pm
BioPerl-1.6.1/Bio/Symbol/README.Symbol
BioPerl-1.6.1/Bio/Symbol/Symbol.pm
BioPerl-1.6.1/Bio/Symbol/SymbolI.pm
BioPerl-1.6.1/Bio/Taxonomy
BioPerl-1.6.1/Bio/Taxonomy/FactoryI.pm
BioPerl-1.6.1/Bio/Taxonomy/Node.pm
BioPerl-1.6.1/Bio/Taxonomy/Taxon.pm
BioPerl-1.6.1/Bio/Taxonomy/Tree.pm
BioPerl-1.6.1/Bio/Tools
BioPerl-1.6.1/Bio/Tools/AlignFactory.pm
BioPerl-1.6.1/Bio/Tools/AnalysisResult.pm
BioPerl-1.6.1/Bio/Tools/Blat.pm
BioPerl-1.6.1/Bio/Tools/CodonTable.pm
BioPerl-1.6.1/Bio/Tools/Coil.pm
BioPerl-1.6.1/Bio/Tools/dpAlign.pm
BioPerl-1.6.1/Bio/Tools/ECnumber.pm
BioPerl-1.6.1/Bio/Tools/EPCR.pm
BioPerl-1.6.1/Bio/Tools/Eponine.pm
BioPerl-1.6.1/Bio/Tools/ERPIN.pm
BioPerl-1.6.1/Bio/Tools/Est2Genome.pm
BioPerl-1.6.1/Bio/Tools/ESTScan.pm
BioPerl-1.6.1/Bio/Tools/EUtilities.pm
BioPerl-1.6.1/Bio/Tools/Fgenesh.pm
BioPerl-1.6.1/Bio/Tools/FootPrinter.pm
BioPerl-1.6.1/Bio/Tools/Gel.pm
BioPerl-1.6.1/Bio/Tools/Geneid.pm
BioPerl-1.6.1/Bio/Tools/Genemark.pm
BioPerl-1.6.1/Bio/Tools/Genewise.pm
BioPerl-1.6.1/Bio/Tools/Genomewise.pm
BioPerl-1.6.1/Bio/Tools/Genscan.pm
BioPerl-1.6.1/Bio/Tools/GFF.pm
BioPerl-1.6.1/Bio/Tools/Glimmer.pm
BioPerl-1.6.1/Bio/Tools/Grail.pm
BioPerl-1.6.1/Bio/Tools/GuessSeqFormat.pm
BioPerl-1.6.1/Bio/Tools/Hmmpfam.pm
BioPerl-1.6.1/Bio/Tools/Infernal.pm
BioPerl-1.6.1/Bio/Tools/ipcress.pm
BioPerl-1.6.1/Bio/Tools/isPcr.pm
BioPerl-1.6.1/Bio/Tools/IUPAC.pm
BioPerl-1.6.1/Bio/Tools/Lucy.pm
BioPerl-1.6.1/Bio/Tools/Match.pm
BioPerl-1.6.1/Bio/Tools/MZEF.pm
BioPerl-1.6.1/Bio/Tools/OddCodes.pm
BioPerl-1.6.1/Bio/Tools/pICalculator.pm
BioPerl-1.6.1/Bio/Tools/Primer3.pm
BioPerl-1.6.1/Bio/Tools/Prints.pm
BioPerl-1.6.1/Bio/Tools/Profile.pm
BioPerl-1.6.1/Bio/Tools/Promoterwise.pm
BioPerl-1.6.1/Bio/Tools/PrositeScan.pm
BioPerl-1.6.1/Bio/Tools/Protparam.pm
BioPerl-1.6.1/Bio/Tools/Pseudowise.pm
BioPerl-1.6.1/Bio/Tools/pSW.pm
BioPerl-1.6.1/Bio/Tools/QRNA.pm
BioPerl-1.6.1/Bio/Tools/RandomDistFunctions.pm
BioPerl-1.6.1/Bio/Tools/RepeatMasker.pm
BioPerl-1.6.1/Bio/Tools/RNAMotif.pm
BioPerl-1.6.1/Bio/Tools/Seg.pm
BioPerl-1.6.1/Bio/Tools/SeqPattern.pm
BioPerl-1.6.1/Bio/Tools/SeqStats.pm
BioPerl-1.6.1/Bio/Tools/SeqWords.pm
BioPerl-1.6.1/Bio/Tools/Sigcleave.pm
BioPerl-1.6.1/Bio/Tools/Signalp.pm
BioPerl-1.6.1/Bio/Tools/SiRNA.pm
BioPerl-1.6.1/Bio/Tools/TandemRepeatsFinder.pm
BioPerl-1.6.1/Bio/Tools/TargetP.pm
BioPerl-1.6.1/Bio/Tools/Tmhmm.pm
BioPerl-1.6.1/Bio/Tools/tRNAscanSE.pm
BioPerl-1.6.1/Bio/Tools/Alignment
BioPerl-1.6.1/Bio/Tools/Alignment/Consed.pm
BioPerl-1.6.1/Bio/Tools/Alignment/Trim.pm
BioPerl-1.6.1/Bio/Tools/Analysis
BioPerl-1.6.1/Bio/Tools/Analysis/SimpleAnalysisBase.pm
BioPerl-1.6.1/Bio/Tools/Analysis/DNA
BioPerl-1.6.1/Bio/Tools/Analysis/DNA/ESEfinder.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/Domcut.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/ELM.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/GOR4.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/HNN.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/Mitoprot.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/NetPhos.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/Scansite.pm
BioPerl-1.6.1/Bio/Tools/Analysis/Protein/Sopma.pm
BioPerl-1.6.1/Bio/Tools/EMBOSS
BioPerl-1.6.1/Bio/Tools/EMBOSS/Palindrome.pm
BioPerl-1.6.1/Bio/Tools/EUtilities
BioPerl-1.6.1/Bio/Tools/EUtilities/Cookie.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/EUtilDataI.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/EUtilParameters.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/History.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/HistoryI.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Info.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Link.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Query.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Summary.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Info
BioPerl-1.6.1/Bio/Tools/EUtilities/Info/FieldInfo.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Info/LinkInfo.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Link
BioPerl-1.6.1/Bio/Tools/EUtilities/Link/LinkSet.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Link/UrlLink.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Query
BioPerl-1.6.1/Bio/Tools/EUtilities/Query/GlobalQuery.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Summary
BioPerl-1.6.1/Bio/Tools/EUtilities/Summary/DocSum.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Summary/Item.pm
BioPerl-1.6.1/Bio/Tools/EUtilities/Summary/ItemContainerI.pm
BioPerl-1.6.1/Bio/Tools/HMMER
BioPerl-1.6.1/Bio/Tools/HMMER/Domain.pm
BioPerl-1.6.1/Bio/Tools/HMMER/Results.pm
BioPerl-1.6.1/Bio/Tools/HMMER/Set.pm
BioPerl-1.6.1/Bio/Tools/Phylo
BioPerl-1.6.1/Bio/Tools/Phylo/Gerp.pm
BioPerl-1.6.1/Bio/Tools/Phylo/Gumby.pm
BioPerl-1.6.1/Bio/Tools/Phylo/Molphy.pm
BioPerl-1.6.1/Bio/Tools/Phylo/PAML.pm
BioPerl-1.6.1/Bio/Tools/Phylo/Molphy
BioPerl-1.6.1/Bio/Tools/Phylo/Molphy/Result.pm
BioPerl-1.6.1/Bio/Tools/Phylo/PAML
BioPerl-1.6.1/Bio/Tools/Phylo/PAML/ModelResult.pm
BioPerl-1.6.1/Bio/Tools/Phylo/PAML/Result.pm
BioPerl-1.6.1/Bio/Tools/Phylo/Phylip
BioPerl-1.6.1/Bio/Tools/Phylo/Phylip/ProtDist.pm
BioPerl-1.6.1/Bio/Tools/Prediction
BioPerl-1.6.1/Bio/Tools/Prediction/Exon.pm
BioPerl-1.6.1/Bio/Tools/Prediction/Gene.pm
BioPerl-1.6.1/Bio/Tools/Primer
BioPerl-1.6.1/Bio/Tools/Primer/AssessorI.pm
BioPerl-1.6.1/Bio/Tools/Primer/Feature.pm
BioPerl-1.6.1/Bio/Tools/Primer/Pair.pm
BioPerl-1.6.1/Bio/Tools/Primer/Assessor
BioPerl-1.6.1/Bio/Tools/Primer/Assessor/Base.pm
BioPerl-1.6.1/Bio/Tools/Run
BioPerl-1.6.1/Bio/Tools/Run/GenericParameters.pm
BioPerl-1.6.1/Bio/Tools/Run/ParametersI.pm
BioPerl-1.6.1/Bio/Tools/Run/README
BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm
BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm
BioPerl-1.6.1/Bio/Tools/Run/StandAloneNCBIBlast.pm
BioPerl-1.6.1/Bio/Tools/Run/StandAloneWUBlast.pm
BioPerl-1.6.1/Bio/Tools/Run/WrapperBase.pm
BioPerl-1.6.1/Bio/Tools/SeqPattern
BioPerl-1.6.1/Bio/Tools/SeqPattern/Backtranslate.pm
BioPerl-1.6.1/Bio/Tools/Signalp
BioPerl-1.6.1/Bio/Tools/Signalp/ExtendedSignalp.pm
BioPerl-1.6.1/Bio/Tools/Sim4
BioPerl-1.6.1/Bio/Tools/Sim4/Exon.pm
BioPerl-1.6.1/Bio/Tools/Sim4/Results.pm
BioPerl-1.6.1/Bio/Tools/SiRNA
BioPerl-1.6.1/Bio/Tools/SiRNA/Ruleset
BioPerl-1.6.1/Bio/Tools/SiRNA/Ruleset/saigo.pm
BioPerl-1.6.1/Bio/Tools/SiRNA/Ruleset/tuschl.pm
BioPerl-1.6.1/Bio/Tools/Spidey
BioPerl-1.6.1/Bio/Tools/Spidey/Exon.pm
BioPerl-1.6.1/Bio/Tools/Spidey/Results.pm
BioPerl-1.6.1/Bio/Tree
BioPerl-1.6.1/Bio/Tree/AlleleNode.pm
BioPerl-1.6.1/Bio/Tree/AnnotatableNode.pm
BioPerl-1.6.1/Bio/Tree/Compatible.pm
BioPerl-1.6.1/Bio/Tree/DistanceFactory.pm
BioPerl-1.6.1/Bio/Tree/Node.pm
BioPerl-1.6.1/Bio/Tree/NodeI.pm
BioPerl-1.6.1/Bio/Tree/NodeNHX.pm
BioPerl-1.6.1/Bio/Tree/RandomFactory.pm
BioPerl-1.6.1/Bio/Tree/Statistics.pm
BioPerl-1.6.1/Bio/Tree/Tree.pm
BioPerl-1.6.1/Bio/Tree/TreeFunctionsI.pm
BioPerl-1.6.1/Bio/Tree/TreeI.pm
BioPerl-1.6.1/Bio/Tree/Draw
BioPerl-1.6.1/Bio/Tree/Draw/Cladogram.pm
BioPerl-1.6.1/Bio/TreeIO
BioPerl-1.6.1/Bio/TreeIO/cluster.pm
BioPerl-1.6.1/Bio/TreeIO/lintree.pm
BioPerl-1.6.1/Bio/TreeIO/newick.pm
BioPerl-1.6.1/Bio/TreeIO/nexus.pm
BioPerl-1.6.1/Bio/TreeIO/nhx.pm
BioPerl-1.6.1/Bio/TreeIO/pag.pm
BioPerl-1.6.1/Bio/TreeIO/phyloxml.pm
BioPerl-1.6.1/Bio/TreeIO/svggraph.pm
BioPerl-1.6.1/Bio/TreeIO/tabtree.pm
BioPerl-1.6.1/Bio/TreeIO/TreeEventBuilder.pm
BioPerl-1.6.1/Bio/Variation
BioPerl-1.6.1/Bio/Variation/AAChange.pm
BioPerl-1.6.1/Bio/Variation/AAReverseMutate.pm
BioPerl-1.6.1/Bio/Variation/Allele.pm
BioPerl-1.6.1/Bio/Variation/DNAMutation.pm
BioPerl-1.6.1/Bio/Variation/IO.pm
BioPerl-1.6.1/Bio/Variation/README
BioPerl-1.6.1/Bio/Variation/RNAChange.pm
BioPerl-1.6.1/Bio/Variation/SeqDiff.pm
BioPerl-1.6.1/Bio/Variation/SNP.pm
BioPerl-1.6.1/Bio/Variation/VariantI.pm
BioPerl-1.6.1/Bio/Variation/IO
BioPerl-1.6.1/Bio/Variation/IO/flat.pm
BioPerl-1.6.1/Bio/Variation/IO/xml.pm
BioPerl-1.6.1/doc
BioPerl-1.6.1/doc/makedoc.PL
BioPerl-1.6.1/doc/README
BioPerl-1.6.1/doc/Deobfuscator
BioPerl-1.6.1/doc/Deobfuscator/Build.PL
BioPerl-1.6.1/doc/Deobfuscator/Changes
BioPerl-1.6.1/doc/Deobfuscator/excluded_modules.txt
BioPerl-1.6.1/doc/Deobfuscator/LICENSE
BioPerl-1.6.1/doc/Deobfuscator/Makefile.PL
BioPerl-1.6.1/doc/Deobfuscator/MANIFEST
BioPerl-1.6.1/doc/Deobfuscator/META.yml
BioPerl-1.6.1/doc/Deobfuscator/README
BioPerl-1.6.1/doc/Deobfuscator/bin
BioPerl-1.6.1/doc/Deobfuscator/bin/deob_index.pl
BioPerl-1.6.1/doc/Deobfuscator/cgi-bin
BioPerl-1.6.1/doc/Deobfuscator/cgi-bin/deob_detail.cgi
BioPerl-1.6.1/doc/Deobfuscator/cgi-bin/deob_flowchart.png
BioPerl-1.6.1/doc/Deobfuscator/cgi-bin/deob_help.html
BioPerl-1.6.1/doc/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.6.1/doc/Deobfuscator/lib
BioPerl-1.6.1/doc/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.6.1/doc/Deobfuscator/t
BioPerl-1.6.1/doc/Deobfuscator/t/00.load.t
BioPerl-1.6.1/doc/Deobfuscator/t/pod.t
BioPerl-1.6.1/examples
BioPerl-1.6.1/examples/bioperl.pl
BioPerl-1.6.1/examples/generate_random_seq.pl
BioPerl-1.6.1/examples/longorf.pl
BioPerl-1.6.1/examples/make_primers.pl
BioPerl-1.6.1/examples/rev_and_trans.pl
BioPerl-1.6.1/examples/revcom_dir.pl
BioPerl-1.6.1/examples/subsequence.cgi
BioPerl-1.6.1/examples/align
BioPerl-1.6.1/examples/align/align_on_codons.pl
BioPerl-1.6.1/examples/align/aligntutorial.pl
BioPerl-1.6.1/examples/align/clustalw.pl
BioPerl-1.6.1/examples/align/simplealign.pl
BioPerl-1.6.1/examples/biblio
BioPerl-1.6.1/examples/biblio/biblio-eutils-example.pl
BioPerl-1.6.1/examples/biblio/biblio-soap-example.pl
BioPerl-1.6.1/examples/biblio/biblio_soap.pl
BioPerl-1.6.1/examples/Bio-DB-GFF
BioPerl-1.6.1/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.1/examples/cluster
BioPerl-1.6.1/examples/cluster/dbsnp.pl
BioPerl-1.6.1/examples/contributed
BioPerl-1.6.1/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.1/examples/contributed/prosite2perl.pl
BioPerl-1.6.1/examples/contributed/rebase2list.pl
BioPerl-1.6.1/examples/db
BioPerl-1.6.1/examples/db/dbfetch
BioPerl-1.6.1/examples/db/est_tissue_query.pl
BioPerl-1.6.1/examples/db/gb2features.pl
BioPerl-1.6.1/examples/db/get_seqs.pl
BioPerl-1.6.1/examples/db/getGenBank.pl
BioPerl-1.6.1/examples/db/rfetch.pl
BioPerl-1.6.1/examples/db/use_registry.pl
BioPerl-1.6.1/examples/liveseq
BioPerl-1.6.1/examples/liveseq/change_gene.pl
BioPerl-1.6.1/examples/popgen
BioPerl-1.6.1/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.1/examples/quality
BioPerl-1.6.1/examples/quality/svgtrace.pl
BioPerl-1.6.1/examples/root
BioPerl-1.6.1/examples/root/exceptions1.pl
BioPerl-1.6.1/examples/root/exceptions2.pl
BioPerl-1.6.1/examples/root/exceptions3.pl
BioPerl-1.6.1/examples/root/exceptions4.pl
BioPerl-1.6.1/examples/root/README
BioPerl-1.6.1/examples/root/lib
BioPerl-1.6.1/examples/root/lib/TestInterface.pm
BioPerl-1.6.1/examples/root/lib/TestObject.pm
BioPerl-1.6.1/examples/root/lib/Bio
BioPerl-1.6.1/examples/root/lib/Bio/PrimarySeq.pm
BioPerl-1.6.1/examples/root/lib/Bio/PrimarySeqI.pm
BioPerl-1.6.1/examples/root/lib/Bio/Seq.pm
BioPerl-1.6.1/examples/root/lib/Bio/SeqI.pm
BioPerl-1.6.1/examples/searchio
BioPerl-1.6.1/examples/searchio/blast_example.pl
BioPerl-1.6.1/examples/searchio/custom_writer.pl
BioPerl-1.6.1/examples/searchio/hitwriter.pl
BioPerl-1.6.1/examples/searchio/hspwriter.pl
BioPerl-1.6.1/examples/searchio/htmlwriter.pl
BioPerl-1.6.1/examples/searchio/psiblast_features.pl
BioPerl-1.6.1/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.1/examples/searchio/rawwriter.pl
BioPerl-1.6.1/examples/searchio/resultwriter.pl
BioPerl-1.6.1/examples/searchio/waba2gff.pl
BioPerl-1.6.1/examples/searchio/waba2gff3.pl
BioPerl-1.6.1/examples/sirna
BioPerl-1.6.1/examples/sirna/rnai_finder.cgi
BioPerl-1.6.1/examples/sirna/TAG
BioPerl-1.6.1/examples/structure
BioPerl-1.6.1/examples/structure/structure-io.pl
BioPerl-1.6.1/examples/tk
BioPerl-1.6.1/examples/tk/gsequence.pl
BioPerl-1.6.1/examples/tk/hitdisplay.pl
BioPerl-1.6.1/examples/tools
BioPerl-1.6.1/examples/tools/extract_genes.pl
BioPerl-1.6.1/examples/tools/gb_to_gff.pl
BioPerl-1.6.1/examples/tools/gff2ps.pl
BioPerl-1.6.1/examples/tools/parse_codeml.pl
BioPerl-1.6.1/examples/tools/psw.pl
BioPerl-1.6.1/examples/tools/reverse-translate.pl
BioPerl-1.6.1/examples/tools/run_genscan.pl
BioPerl-1.6.1/examples/tools/run_primer3.pl
BioPerl-1.6.1/examples/tools/seq_pattern.pl
BioPerl-1.6.1/examples/tools/standaloneblast.pl
BioPerl-1.6.1/examples/tree
BioPerl-1.6.1/examples/tree/paup2phylip.pl
BioPerl-1.6.1/ide
BioPerl-1.6.1/ide/bioperl.komodo
BioPerl-1.6.1/ide/bioperl-mode
BioPerl-1.6.1/ide/bioperl-mode/README
BioPerl-1.6.1/ide/bioperl-mode/dist
BioPerl-1.6.1/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.6.1/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.6.1/ide/bioperl-mode/dist/bioperl-mode.tar
BioPerl-1.6.1/ide/bioperl-mode/dist/bioperl-mode.tar.md5
BioPerl-1.6.1/ide/bioperl-mode/dist/package-me
BioPerl-1.6.1/ide/bioperl-mode/dist/SKIP
BioPerl-1.6.1/ide/bioperl-mode/etc
BioPerl-1.6.1/ide/bioperl-mode/etc/images
BioPerl-1.6.1/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.6.1/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.6.1/ide/bioperl-mode/site-lisp
BioPerl-1.6.1/ide/bioperl-mode/site-lisp/bioperl-init.el
BioPerl-1.6.1/ide/bioperl-mode/site-lisp/bioperl-mode.el
BioPerl-1.6.1/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.6.1/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.6.1/maintenance
BioPerl-1.6.1/maintenance/authors.pl
BioPerl-1.6.1/maintenance/check_NAME.pl
BioPerl-1.6.1/maintenance/check_URLs.pl
BioPerl-1.6.1/maintenance/cvs2cl_by_file.pl
BioPerl-1.6.1/maintenance/dependencies.pl
BioPerl-1.6.1/maintenance/deprecated.pl
BioPerl-1.6.1/maintenance/module_usage.pl
BioPerl-1.6.1/maintenance/modules.pl
BioPerl-1.6.1/maintenance/ncbi_blast_switches.pl
BioPerl-1.6.1/maintenance/perltidy.conf
BioPerl-1.6.1/maintenance/pod.pl
BioPerl-1.6.1/maintenance/README
BioPerl-1.6.1/maintenance/symlink_script.pl
BioPerl-1.6.1/maintenance/version.pl
BioPerl-1.6.1/models
BioPerl-1.6.1/models/biblio.dia
BioPerl-1.6.1/models/bio_liveseq_variation.dia
BioPerl-1.6.1/models/bio_map.dia
BioPerl-1.6.1/models/bio_restriction.dia
BioPerl-1.6.1/models/bioperl.dia
BioPerl-1.6.1/models/coordinatemapper.dia
BioPerl-1.6.1/models/map_proposal.txt
BioPerl-1.6.1/models/maps_and_markers.dia
BioPerl-1.6.1/models/popgen.dia
BioPerl-1.6.1/models/population_proposal.txt
BioPerl-1.6.1/models/README
BioPerl-1.6.1/scripts
BioPerl-1.6.1/scripts/README
BioPerl-1.6.1/scripts/biblio
BioPerl-1.6.1/scripts/biblio/biblio.PLS
BioPerl-1.6.1/scripts/biblio/TAG
BioPerl-1.6.1/scripts/Bio-DB-EUtilities
BioPerl-1.6.1/scripts/Bio-DB-EUtilities/einfo.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF
BioPerl-1.6.1/scripts/Bio-DB-GFF/bulk_load_gff.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/fast_load_gff.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/genbank2gff.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/genbank2gff3.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/generate_histogram.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/load_gff.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/meta_gff.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/process_gadfly.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/process_sgd.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/process_wormbase.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/README
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
BioPerl-1.6.1/scripts/das
BioPerl-1.6.1/scripts/das/README
BioPerl-1.6.1/scripts/das/TAG
BioPerl-1.6.1/scripts/DB
BioPerl-1.6.1/scripts/DB/biofetch_genbank_proxy.PLS
BioPerl-1.6.1/scripts/DB/bioflat_index.PLS
BioPerl-1.6.1/scripts/DB/biogetseq.PLS
BioPerl-1.6.1/scripts/DB/flanks.PLS
BioPerl-1.6.1/scripts/DB/TAG
BioPerl-1.6.1/scripts/DB-HIV
BioPerl-1.6.1/scripts/DB-HIV/hivq.PLS
BioPerl-1.6.1/scripts/index
BioPerl-1.6.1/scripts/index/bp_fetch.PLS
BioPerl-1.6.1/scripts/index/bp_index.PLS
BioPerl-1.6.1/scripts/index/bp_seqret.PLS
BioPerl-1.6.1/scripts/index/TAG
BioPerl-1.6.1/scripts/popgen
BioPerl-1.6.1/scripts/popgen/composite_LD.PLS
BioPerl-1.6.1/scripts/popgen/heterogeneity_test.PLS
BioPerl-1.6.1/scripts/searchio
BioPerl-1.6.1/scripts/searchio/fastam9_to_table.PLS
BioPerl-1.6.1/scripts/searchio/filter_search.PLS
BioPerl-1.6.1/scripts/searchio/hmmer_to_table.PLS
BioPerl-1.6.1/scripts/searchio/parse_hmmsearch.PLS
BioPerl-1.6.1/scripts/searchio/README
BioPerl-1.6.1/scripts/searchio/search2table.PLS
BioPerl-1.6.1/scripts/searchio/TAG
BioPerl-1.6.1/scripts/seq
BioPerl-1.6.1/scripts/seq/extract_feature_seq.PLS
BioPerl-1.6.1/scripts/seq/make_mrna_protein.PLS
BioPerl-1.6.1/scripts/seq/seqconvert.PLS
BioPerl-1.6.1/scripts/seq/seqretsplit.PLS
BioPerl-1.6.1/scripts/seq/split_seq.PLS
BioPerl-1.6.1/scripts/seq/TAG
BioPerl-1.6.1/scripts/seq/translate_seq.PLS
BioPerl-1.6.1/scripts/seq/unflatten_seq.PLS
BioPerl-1.6.1/scripts/seqstats
BioPerl-1.6.1/scripts/seqstats/aacomp.PLS
BioPerl-1.6.1/scripts/seqstats/chaos_plot.PLS
BioPerl-1.6.1/scripts/seqstats/gccalc.PLS
BioPerl-1.6.1/scripts/seqstats/oligo_count.PLS
BioPerl-1.6.1/scripts/seqstats/TAG
BioPerl-1.6.1/scripts/taxa
BioPerl-1.6.1/scripts/taxa/classify_hits_kingdom.PLS
BioPerl-1.6.1/scripts/taxa/local_taxonomydb_query.PLS
BioPerl-1.6.1/scripts/taxa/query_entrez_taxa.PLS
BioPerl-1.6.1/scripts/taxa/TAG
BioPerl-1.6.1/scripts/taxa/taxid4species.PLS
BioPerl-1.6.1/scripts/taxa/taxonomy2tree.PLS
BioPerl-1.6.1/scripts/tree
BioPerl-1.6.1/scripts/tree/blast2tree.PLS
BioPerl-1.6.1/scripts/tree/nexus2nh.PLS
BioPerl-1.6.1/scripts/tree/TAG
BioPerl-1.6.1/scripts/tree/tree2pag.PLS
BioPerl-1.6.1/scripts/utilities
BioPerl-1.6.1/scripts/utilities/bp_mrtrans.PLS
BioPerl-1.6.1/scripts/utilities/bp_nrdb.PLS
BioPerl-1.6.1/scripts/utilities/bp_sreformat.PLS
BioPerl-1.6.1/scripts/utilities/dbsplit.PLS
BioPerl-1.6.1/scripts/utilities/download_query_genbank.PLS
BioPerl-1.6.1/scripts/utilities/mask_by_search.PLS
BioPerl-1.6.1/scripts/utilities/mutate.PLS
BioPerl-1.6.1/scripts/utilities/pairwise_kaks.PLS
BioPerl-1.6.1/scripts/utilities/README
BioPerl-1.6.1/scripts/utilities/remote_blast.PLS
BioPerl-1.6.1/scripts/utilities/revtrans-motif.PLS
BioPerl-1.6.1/scripts/utilities/search2alnblocks.PLS
BioPerl-1.6.1/scripts/utilities/search2BSML.PLS
BioPerl-1.6.1/scripts/utilities/search2gff.PLS
BioPerl-1.6.1/scripts/utilities/search2tribe.PLS
BioPerl-1.6.1/scripts/utilities/seq_length.PLS
BioPerl-1.6.1/scripts/utilities/TAG
BioPerl-1.6.1/t
BioPerl-1.6.1/t/Alphabet.t
BioPerl-1.6.1/t/Perl.t
BioPerl-1.6.1/t/PodSyntax.t
BioPerl-1.6.1/t/SearchDist.t
BioPerl-1.6.1/t/SeqEvolution.t
BioPerl-1.6.1/t/SeqIO.t
BioPerl-1.6.1/t/Species.t
BioPerl-1.6.1/t/Symbol.t
BioPerl-1.6.1/t/TaxonTree.t
BioPerl-1.6.1/t/Align
BioPerl-1.6.1/t/Align/AlignStats.t
BioPerl-1.6.1/t/Align/AlignUtil.t
BioPerl-1.6.1/t/Align/SimpleAlign.t
BioPerl-1.6.1/t/Align/TreeBuild.t
BioPerl-1.6.1/t/Align/Utilities.t
BioPerl-1.6.1/t/AlignIO
BioPerl-1.6.1/t/AlignIO/AlignIO.t
BioPerl-1.6.1/t/AlignIO/arp.t
BioPerl-1.6.1/t/AlignIO/bl2seq.t
BioPerl-1.6.1/t/AlignIO/clustalw.t
BioPerl-1.6.1/t/AlignIO/emboss.t
BioPerl-1.6.1/t/AlignIO/fasta.t
BioPerl-1.6.1/t/AlignIO/largemultifasta.t
BioPerl-1.6.1/t/AlignIO/maf.t
BioPerl-1.6.1/t/AlignIO/mase.t
BioPerl-1.6.1/t/AlignIO/mega.t
BioPerl-1.6.1/t/AlignIO/meme.t
BioPerl-1.6.1/t/AlignIO/metafasta.t
BioPerl-1.6.1/t/AlignIO/msf.t
BioPerl-1.6.1/t/AlignIO/nexus.t
BioPerl-1.6.1/t/AlignIO/pfam.t
BioPerl-1.6.1/t/AlignIO/phylip.t
BioPerl-1.6.1/t/AlignIO/po.t
BioPerl-1.6.1/t/AlignIO/prodom.t
BioPerl-1.6.1/t/AlignIO/psi.t
BioPerl-1.6.1/t/AlignIO/selex.t
BioPerl-1.6.1/t/AlignIO/stockholm.t
BioPerl-1.6.1/t/AlignIO/xmfa.t
BioPerl-1.6.1/t/Annotation
BioPerl-1.6.1/t/Annotation/Annotation.t
BioPerl-1.6.1/t/Annotation/AnnotationAdaptor.t
BioPerl-1.6.1/t/Assembly
BioPerl-1.6.1/t/Assembly/Assembly.t
BioPerl-1.6.1/t/Assembly/ContigSpectrum.t
BioPerl-1.6.1/t/Biblio
BioPerl-1.6.1/t/Biblio/Biblio.t
BioPerl-1.6.1/t/Biblio/biofetch.t
BioPerl-1.6.1/t/Biblio/eutils.t
BioPerl-1.6.1/t/Biblio/References.t
BioPerl-1.6.1/t/ClusterIO
BioPerl-1.6.1/t/ClusterIO/ClusterIO.t
BioPerl-1.6.1/t/ClusterIO/SequenceFamily.t
BioPerl-1.6.1/t/ClusterIO/unigene.t
BioPerl-1.6.1/t/Coordinate
BioPerl-1.6.1/t/Coordinate/CoordinateGraph.t
BioPerl-1.6.1/t/Coordinate/CoordinateMapper.t
BioPerl-1.6.1/t/Coordinate/GeneCoordinateMapper.t
BioPerl-1.6.1/t/data
BioPerl-1.6.1/t/data/13-pilE-F.scf
BioPerl-1.6.1/t/data/1A11.pdb
BioPerl-1.6.1/t/data/1A3I.pdb
BioPerl-1.6.1/t/data/1BPT.pdb
BioPerl-1.6.1/t/data/1ZZ19XR301R-Alignment.tblastn
BioPerl-1.6.1/t/data/2008.blasttable
BioPerl-1.6.1/t/data/503384.MEGABLAST.0
BioPerl-1.6.1/t/data/503384.MEGABLAST.2
BioPerl-1.6.1/t/data/5X_1895.FASTXY
BioPerl-1.6.1/t/data/8HVP.pdb
BioPerl-1.6.1/t/data/a_thaliana.blastn
BioPerl-1.6.1/t/data/AAC12660.fa
BioPerl-1.6.1/t/data/aaml.mlc
BioPerl-1.6.1/t/data/aaml_pairwise.mlc
BioPerl-1.6.1/t/data/AB077698.gb
BioPerl-1.6.1/t/data/acefile.ace.1
BioPerl-1.6.1/t/data/acefile.singlets
BioPerl-1.6.1/t/data/adh.mb_tree.nexus
BioPerl-1.6.1/t/data/AE003528_ecoli.bls
BioPerl-1.6.1/t/data/AE003644_Adh-genomic.gb
BioPerl-1.6.1/t/data/AF032047.gbk
BioPerl-1.6.1/t/data/AF165282.gb
BioPerl-1.6.1/t/data/AF305198.gb
BioPerl-1.6.1/t/data/AHCYL1.kegg
BioPerl-1.6.1/t/data/alleles.fas
BioPerl-1.6.1/t/data/alnfile.fasta
BioPerl-1.6.1/t/data/amino.fa
BioPerl-1.6.1/t/data/AnnIX-v003.gbk
BioPerl-1.6.1/t/data/ar.embl
BioPerl-1.6.1/t/data/assembly_with_singlets.ace
BioPerl-1.6.1/t/data/ATF14F8.gbk
BioPerl-1.6.1/t/data/atp1.matrix
BioPerl-1.6.1/t/data/ay007676.gb
BioPerl-1.6.1/t/data/AY095303S1.gbk
BioPerl-1.6.1/t/data/ay116458.gb
BioPerl-1.6.1/t/data/ay149291.gb
BioPerl-1.6.1/t/data/AY763288.gb
BioPerl-1.6.1/t/data/BAB68554.gb
BioPerl-1.6.1/t/data/barns-combined.nex
BioPerl-1.6.1/t/data/baseml.pairwise
BioPerl-1.6.1/t/data/baseml.usertree
BioPerl-1.6.1/t/data/basic-bush.nex
BioPerl-1.6.1/t/data/basic-ladder.nex
BioPerl-1.6.1/t/data/BC000007.gbk
BioPerl-1.6.1/t/data/BEL16-LTR_AG.embl
BioPerl-1.6.1/t/data/biofpc.cor
BioPerl-1.6.1/t/data/biofpc.fpc
BioPerl-1.6.1/t/data/Bird_Ovomucoids.nex
BioPerl-1.6.1/t/data/BK000016-tpa.gbk
BioPerl-1.6.1/t/data/bl2seq.blastn
BioPerl-1.6.1/t/data/bl2seq.blastn.rev
BioPerl-1.6.1/t/data/bl2seq.blastx.out
BioPerl-1.6.1/t/data/bl2seq.bug940.out
BioPerl-1.6.1/t/data/bl2seq.out
BioPerl-1.6.1/t/data/bl2seq.tblastx.out
BioPerl-1.6.1/t/data/blast.report
BioPerl-1.6.1/t/data/blast_no_hit_desc.txt
BioPerl-1.6.1/t/data/blastp2215.blast
BioPerl-1.6.1/t/data/blat.psLayout3
BioPerl-1.6.1/t/data/BLOSUM50
BioPerl-1.6.1/t/data/blosum62.bla
BioPerl-1.6.1/t/data/BN000066-tpa.embl
BioPerl-1.6.1/t/data/bootstrap.tre
BioPerl-1.6.1/t/data/BOSS_DROME.FASTP_v35_04
BioPerl-1.6.1/t/data/branchSite.mlc
BioPerl-1.6.1/t/data/brassica_ATH.WUBLASTN
BioPerl-1.6.1/t/data/bug1986.blast2
BioPerl-1.6.1/t/data/bug1986.blastp
BioPerl-1.6.1/t/data/bug2120.phd
BioPerl-1.6.1/t/data/bug2246.blast
BioPerl-1.6.1/t/data/bug2391.megablast
BioPerl-1.6.1/t/data/bug2399.tblastn
BioPerl-1.6.1/t/data/bug2453.maf
BioPerl-1.6.1/t/data/bug2473.fasta
BioPerl-1.6.1/t/data/bug2862.pmr
BioPerl-1.6.1/t/data/c200-vs-yeast.BLASTN
BioPerl-1.6.1/t/data/c200-vs-yeast.BLASTN.m8
BioPerl-1.6.1/t/data/calm.swiss
BioPerl-1.6.1/t/data/catalase-webblast.BLASTP
BioPerl-1.6.1/t/data/cds-266.fas
BioPerl-1.6.1/t/data/cds_sample.embl
BioPerl-1.6.1/t/data/CG11099.fasaln
BioPerl-1.6.1/t/data/CG2865.fasaln
BioPerl-1.6.1/t/data/chad100.scf
BioPerl-1.6.1/t/data/char-interleave.nex
BioPerl-1.6.1/t/data/char-matrix-spaces.nex
BioPerl-1.6.1/t/data/codeml.mlc
BioPerl-1.6.1/t/data/codeml315.mlc
BioPerl-1.6.1/t/data/codeml4.mlc
BioPerl-1.6.1/t/data/codeml_nssites.mlc
BioPerl-1.6.1/t/data/compLD_missingtest.prettybase
BioPerl-1.6.1/t/data/compLD_test.prettybase
BioPerl-1.6.1/t/data/component.ontology.test
BioPerl-1.6.1/t/data/component.ontology.test2
BioPerl-1.6.1/t/data/contig-by-hand.wublastp
BioPerl-1.6.1/t/data/contigspectrumtest.asm
BioPerl-1.6.1/t/data/crab.dat.cn
BioPerl-1.6.1/t/data/crab.nj
BioPerl-1.6.1/t/data/crab.njb
BioPerl-1.6.1/t/data/crypto.sim4-0
BioPerl-1.6.1/t/data/crypto.sim4-3
BioPerl-1.6.1/t/data/crypto.sim4-4
BioPerl-1.6.1/t/data/ctgdemo.fpc
BioPerl-1.6.1/t/data/cys1_dicdi.water
BioPerl-1.6.1/t/data/cysprot.fa
BioPerl-1.6.1/t/data/cysprot.msf
BioPerl-1.6.1/t/data/cysprot.needle
BioPerl-1.6.1/t/data/cysprot.tblastn
BioPerl-1.6.1/t/data/cysprot.water
BioPerl-1.6.1/t/data/cysprot1.fa
BioPerl-1.6.1/t/data/cysprot1.FASTA
BioPerl-1.6.1/t/data/cysprot1a.fa
BioPerl-1.6.1/t/data/cysprot1a.msf
BioPerl-1.6.1/t/data/cysprot1b.fa
BioPerl-1.6.1/t/data/cysprot1b.hmmsearch
BioPerl-1.6.1/t/data/cysprot1b.msf
BioPerl-1.6.1/t/data/cysprot1b.newick
BioPerl-1.6.1/t/data/cysprot_vs_gadfly.FASTA
BioPerl-1.6.1/t/data/D10483.gbk
BioPerl-1.6.1/t/data/D12555.gbk
BioPerl-1.6.1/t/data/dcr1_sp.WUBLASTP
BioPerl-1.6.1/t/data/directives.gff3
BioPerl-1.6.1/t/data/dmel_2Lchunk.gb
BioPerl-1.6.1/t/data/dna1.fa
BioPerl-1.6.1/t/data/dna2.fa
BioPerl-1.6.1/t/data/dnaE-bsub-prot.fa
BioPerl-1.6.1/t/data/dnaE-bsub.fa
BioPerl-1.6.1/t/data/dnaEbsub_ecoli.wublastx
BioPerl-1.6.1/t/data/dnaEbsub_ecoli.wutblastn
BioPerl-1.6.1/t/data/dnaEbsub_ecoli.wutblastx
BioPerl-1.6.1/t/data/DQ018368.gb
BioPerl-1.6.1/t/data/dq519393.gb
BioPerl-1.6.1/t/data/ECAPAH02.embl
BioPerl-1.6.1/t/data/echofilter.wublastn
BioPerl-1.6.1/t/data/ecoli-trna-qrna.out
BioPerl-1.6.1/t/data/ecoli_domains.rps.xml
BioPerl-1.6.1/t/data/ecoli_domains.rpsblast
BioPerl-1.6.1/t/data/ecolitst.bls
BioPerl-1.6.1/t/data/ecolitst.fa
BioPerl-1.6.1/t/data/ecolitst.noseqs.wublastp
BioPerl-1.6.1/t/data/ecolitst.wublastp
BioPerl-1.6.1/t/data/empty.bl2seq
BioPerl-1.6.1/t/data/ENr111.mfa.example.elems
BioPerl-1.6.1/t/data/entrezgene.dat
BioPerl-1.6.1/t/data/example.hap
BioPerl-1.6.1/t/data/example.phase
BioPerl-1.6.1/t/data/exonerate.output.dontwork
BioPerl-1.6.1/t/data/exonerate.output.works
BioPerl-1.6.1/t/data/expected.blast.out
BioPerl-1.6.1/t/data/exsignalp.out
BioPerl-1.6.1/t/data/factor7.embl
BioPerl-1.6.1/t/data/fgenesh.out
BioPerl-1.6.1/t/data/footprinter.out
BioPerl-1.6.1/t/data/frac_problems.blast
BioPerl-1.6.1/t/data/frac_problems2.blast
BioPerl-1.6.1/t/data/frac_problems3.blast
BioPerl-1.6.1/t/data/geneid_1.0.out
BioPerl-1.6.1/t/data/genemark-fragment.out
BioPerl-1.6.1/t/data/genemark.out
BioPerl-1.6.1/t/data/genewise.out
BioPerl-1.6.1/t/data/genewise_output.paracel_btk
BioPerl-1.6.1/t/data/genomewise.out
BioPerl-1.6.1/t/data/genomic-seq.epcr
BioPerl-1.6.1/t/data/genomic-seq.fasta
BioPerl-1.6.1/t/data/genomic-seq.genscan
BioPerl-1.6.1/t/data/genomic-seq.mzef
BioPerl-1.6.1/t/data/Genscan.FastA
BioPerl-1.6.1/t/data/gf-s71.needle
BioPerl-1.6.1/t/data/Glimmer2.out
BioPerl-1.6.1/t/data/glimmer3-fragment.detail
BioPerl-1.6.1/t/data/glimmer3-fragment.predict
BioPerl-1.6.1/t/data/Glimmer3.detail
BioPerl-1.6.1/t/data/Glimmer3.predict
BioPerl-1.6.1/t/data/GlimmerHMM.out
BioPerl-1.6.1/t/data/GlimmerM.out
BioPerl-1.6.1/t/data/gmap_f9-multiple_results.txt
BioPerl-1.6.1/t/data/gmap_f9-reverse-strand.txt
BioPerl-1.6.1/t/data/gmap_f9.txt
BioPerl-1.6.1/t/data/GO.defs.test
BioPerl-1.6.1/t/data/GO.defs.test2
BioPerl-1.6.1/t/data/headerless.psl
BioPerl-1.6.1/t/data/hemoglobinA.meg
BioPerl-1.6.1/t/data/hg16_chroms.gff
BioPerl-1.6.1/t/data/hmmpfam.out
BioPerl-1.6.1/t/data/hmmpfam_cs.out
BioPerl-1.6.1/t/data/hmmpfam_fake.out
BioPerl-1.6.1/t/data/hmmsearch.out
BioPerl-1.6.1/t/data/hs_est.est2genome
BioPerl-1.6.1/t/data/hs_fugu.newick
BioPerl-1.6.1/t/data/hs_owlmonkey.aln
BioPerl-1.6.1/t/data/hs_owlmonkey.fas
BioPerl-1.6.1/t/data/hs_owlmonkey.fasta
BioPerl-1.6.1/t/data/hsinsulin.blastcl3.blastn
BioPerl-1.6.1/t/data/HUMBETGLOA.fa
BioPerl-1.6.1/t/data/HUMBETGLOA.FASTA
BioPerl-1.6.1/t/data/HUMBETGLOA.gff
BioPerl-1.6.1/t/data/HUMBETGLOA.grail
BioPerl-1.6.1/t/data/HUMBETGLOA.grailexp
BioPerl-1.6.1/t/data/HUMBETGLOA.mzef
BioPerl-1.6.1/t/data/HUMBETGLOA.tblastx
BioPerl-1.6.1/t/data/humor.maf
BioPerl-1.6.1/t/data/humts1.pal
BioPerl-1.6.1/t/data/hybrid1.gff3
BioPerl-1.6.1/t/data/hybrid2.gff3
BioPerl-1.6.1/t/data/in.fasta
BioPerl-1.6.1/t/data/insulin.water
BioPerl-1.6.1/t/data/interpro_ebi.xml
BioPerl-1.6.1/t/data/interpro_short.xml
BioPerl-1.6.1/t/data/intrablock-comment.nex
BioPerl-1.6.1/t/data/Kingdoms_DNA.nex
BioPerl-1.6.1/t/data/knownGene.gff3
BioPerl-1.6.1/t/data/L77119.hmmer
BioPerl-1.6.1/t/data/little.largemultifasta
BioPerl-1.6.1/t/data/LittleChrY.dbsnp.xml
BioPerl-1.6.1/t/data/LOAD_Ccd1.dnd
BioPerl-1.6.1/t/data/long-names.nex
BioPerl-1.6.1/t/data/longnames.aln
BioPerl-1.6.1/t/data/longnames.dnd
BioPerl-1.6.1/t/data/lucy.info
BioPerl-1.6.1/t/data/lucy.qual
BioPerl-1.6.1/t/data/lucy.seq
BioPerl-1.6.1/t/data/lucy.stderr
BioPerl-1.6.1/t/data/lysozyme6.protml
BioPerl-1.6.1/t/data/lysozyme6.simple.protml
BioPerl-1.6.1/t/data/M0.mlc
BioPerl-1.6.1/t/data/M12730.gb
BioPerl-1.6.1/t/data/mapmaker.out
BioPerl-1.6.1/t/data/mapmaker.txt
BioPerl-1.6.1/t/data/mast.dat
BioPerl-1.6.1/t/data/masta.dat
BioPerl-1.6.1/t/data/match.output
BioPerl-1.6.1/t/data/Mcjanrna_rdbII.gbk
BioPerl-1.6.1/t/data/megablast_output.paracel_btk
BioPerl-1.6.1/t/data/meme.dat
BioPerl-1.6.1/t/data/mini-AE001405.gb
BioPerl-1.6.1/t/data/mini-align.aln
BioPerl-1.6.1/t/data/mixedmast.dat
BioPerl-1.6.1/t/data/MmCT
BioPerl-1.6.1/t/data/mpath.ontology.test
BioPerl-1.6.1/t/data/MSGEFTUA.gb
BioPerl-1.6.1/t/data/multi.phd
BioPerl-1.6.1/t/data/multi_1.fa
BioPerl-1.6.1/t/data/multi_2.fa
BioPerl-1.6.1/t/data/multi_blast.bls
BioPerl-1.6.1/t/data/multifa.seq
BioPerl-1.6.1/t/data/multifa.seq.qual
BioPerl-1.6.1/t/data/multiline-intrablock-comment.nex
BioPerl-1.6.1/t/data/multiseq.bls
BioPerl-1.6.1/t/data/mus.bls.xml
BioPerl-1.6.1/t/data/mutations.dat
BioPerl-1.6.1/t/data/mutations.old.dat
BioPerl-1.6.1/t/data/mutations.old.xml
BioPerl-1.6.1/t/data/mutations.xml
BioPerl-1.6.1/t/data/myco_sites.gff
BioPerl-1.6.1/t/data/NC_001284.gbk
BioPerl-1.6.1/t/data/NC_006346.gb
BioPerl-1.6.1/t/data/NC_006511-short.gbk
BioPerl-1.6.1/t/data/NC_008536.gb
BioPerl-1.6.1/t/data/nei_gojobori_test.aln
BioPerl-1.6.1/t/data/neighbor.dist
BioPerl-1.6.1/t/data/new_blastn.txt
BioPerl-1.6.1/t/data/newblast.xml
BioPerl-1.6.1/t/data/NM_002254.gb
BioPerl-1.6.1/t/data/no-genes.genscan
BioPerl-1.6.1/t/data/no_cds_example.gb
BioPerl-1.6.1/t/data/no_FH.embl
BioPerl-1.6.1/t/data/no_hsps.blastp
BioPerl-1.6.1/t/data/no_semicolon.newick
BioPerl-1.6.1/t/data/noninterleaved.phy
BioPerl-1.6.1/t/data/NT_021877.gbk
BioPerl-1.6.1/t/data/nucmatrix.txt
BioPerl-1.6.1/t/data/O_sat.wgs
BioPerl-1.6.1/t/data/omim_genemap_test
BioPerl-1.6.1/t/data/omim_genemap_test_nolinebreak
BioPerl-1.6.1/t/data/omim_text_test
BioPerl-1.6.1/t/data/P33897
BioPerl-1.6.1/t/data/P35527.gb
BioPerl-1.6.1/t/data/P39765.gb
BioPerl-1.6.1/t/data/PAM250
BioPerl-1.6.1/t/data/pep-266.aln
BioPerl-1.6.1/t/data/pfam_tests.stk
BioPerl-1.6.1/t/data/phi.out
BioPerl-1.6.1/t/data/phipsi.out
BioPerl-1.6.1/t/data/phylipdist-36.out
BioPerl-1.6.1/t/data/phylipdist.out
BioPerl-1.6.1/t/data/phyloxml_examples.xml
BioPerl-1.6.1/t/data/pictogram.fa
BioPerl-1.6.1/t/data/plague_yeast.bls.xml
BioPerl-1.6.1/t/data/polymorphism.dat
BioPerl-1.6.1/t/data/polymorphism.old.xml
BioPerl-1.6.1/t/data/polymorphism.xml
BioPerl-1.6.1/t/data/popgen_saureus.dat
BioPerl-1.6.1/t/data/popgen_saureus.multidat
BioPerl-1.6.1/t/data/popstats.prettybase
BioPerl-1.6.1/t/data/pre_rel9.swiss
BioPerl-1.6.1/t/data/Primate_mtDNA.nex
BioPerl-1.6.1/t/data/primedseq.fa
BioPerl-1.6.1/t/data/primer3_infile.txt
BioPerl-1.6.1/t/data/primer3_outfile.txt
BioPerl-1.6.1/t/data/primer3_output.txt
BioPerl-1.6.1/t/data/prints.out
BioPerl-1.6.1/t/data/promoterwise.out
BioPerl-1.6.1/t/data/protpars.phy
BioPerl-1.6.1/t/data/protpars_longid.phy
BioPerl-1.6.1/t/data/pseudowise.out
BioPerl-1.6.1/t/data/psi_xml.dat
BioPerl-1.6.1/t/data/psiblast.xml
BioPerl-1.6.1/t/data/psiblastreport.out
BioPerl-1.6.1/t/data/purine_v081.infernal
BioPerl-1.6.1/t/data/puzzle.tre
BioPerl-1.6.1/t/data/Q8GBD3.swiss
BioPerl-1.6.1/t/data/qrna-relloc.out
BioPerl-1.6.1/t/data/qualfile.qual
BioPerl-1.6.1/t/data/quoted-strings1.nex
BioPerl-1.6.1/t/data/quoted-strings2.nex
BioPerl-1.6.1/t/data/Rab1.chaos-xml
BioPerl-1.6.1/t/data/radical-whitespace.nex
BioPerl-1.6.1/t/data/radical-whitespace_02.nex
BioPerl-1.6.1/t/data/rebase.itype2
BioPerl-1.6.1/t/data/rebase.withrefm
BioPerl-1.6.1/t/data/regulation_test.obo
BioPerl-1.6.1/t/data/rel9.swiss
BioPerl-1.6.1/t/data/repeatmasker.fa.out
BioPerl-1.6.1/t/data/revcomp_mrna.gb
BioPerl-1.6.1/t/data/rfam_tests.stk
BioPerl-1.6.1/t/data/roa1.dat
BioPerl-1.6.1/t/data/roa1.genbank
BioPerl-1.6.1/t/data/roa1.swiss
BioPerl-1.6.1/t/data/roa1_v2.dat
BioPerl-1.6.1/t/data/rpsblast.bls
BioPerl-1.6.1/t/data/sample_dataset.tasm
BioPerl-1.6.1/t/data/sbay_c127.fas
BioPerl-1.6.1/t/data/sbay_c545-yeast.BLASTZ.PSL
BioPerl-1.6.1/t/data/seg.out
BioPerl-1.6.1/t/data/semicolon.newick
BioPerl-1.6.1/t/data/seqdatabase.ini
BioPerl-1.6.1/t/data/seqfile.pir
BioPerl-1.6.1/t/data/seqs.fas
BioPerl-1.6.1/t/data/sequencefamily.dat
BioPerl-1.6.1/t/data/short.blx
BioPerl-1.6.1/t/data/signalp.hmm.short
BioPerl-1.6.1/t/data/signalp.hmm.summary
BioPerl-1.6.1/t/data/signalp.negative.out
BioPerl-1.6.1/t/data/signalp.nn.short
BioPerl-1.6.1/t/data/signalp.nn.summary
BioPerl-1.6.1/t/data/signalp.positive.out
BioPerl-1.6.1/t/data/signalp.short
BioPerl-1.6.1/t/data/signalp.summary
BioPerl-1.6.1/t/data/sim4.for.for
BioPerl-1.6.1/t/data/sim4.for.rev
BioPerl-1.6.1/t/data/sim4.rev
BioPerl-1.6.1/t/data/singleNSsite.mlc
BioPerl-1.6.1/t/data/so.obo
BioPerl-1.6.1/t/data/sofa.ontology
BioPerl-1.6.1/t/data/spaces.nex
BioPerl-1.6.1/t/data/SPAN_Family4nl.nex
BioPerl-1.6.1/t/data/SPAN_Family7n.nex
BioPerl-1.6.1/t/data/SPAN_Family8a.nex
BioPerl-1.6.1/t/data/sparsealn.needle
BioPerl-1.6.1/t/data/spidey.noalignment
BioPerl-1.6.1/t/data/spidey.test1
BioPerl-1.6.1/t/data/sprintf.rnamotif
BioPerl-1.6.1/t/data/ssp160.embl.1
BioPerl-1.6.1/t/data/stress_test_medline.xml
BioPerl-1.6.1/t/data/stress_test_pubmed.xml
BioPerl-1.6.1/t/data/sv40_small.xml
BioPerl-1.6.1/t/data/swiss.dat
BioPerl-1.6.1/t/data/swisspfam.data
BioPerl-1.6.1/t/data/SwissProt.dat
BioPerl-1.6.1/t/data/T7.aln
BioPerl-1.6.1/t/data/tab1part.mif
BioPerl-1.6.1/t/data/tab2part.mif
BioPerl-1.6.1/t/data/tab3part.mif
BioPerl-1.6.1/t/data/tandem_repeats_finder.dat
BioPerl-1.6.1/t/data/tandem_repeats_finder.noresults
BioPerl-1.6.1/t/data/targetp.out
BioPerl-1.6.1/t/data/tblastn.out
BioPerl-1.6.1/t/data/test 2.txt
BioPerl-1.6.1/t/data/test.abi
BioPerl-1.6.1/t/data/test.ace
BioPerl-1.6.1/t/data/test.ctf
BioPerl-1.6.1/t/data/test.embl
BioPerl-1.6.1/t/data/test.embl2sq
BioPerl-1.6.1/t/data/test.exp
BioPerl-1.6.1/t/data/test.fasta
BioPerl-1.6.1/t/data/test.game
BioPerl-1.6.1/t/data/test.gcg
BioPerl-1.6.1/t/data/test.gcgblast
BioPerl-1.6.1/t/data/test.gcgfasta
BioPerl-1.6.1/t/data/test.genbank
BioPerl-1.6.1/t/data/test.genbank.noseq
BioPerl-1.6.1/t/data/test.infernal
BioPerl-1.6.1/t/data/test.interpro
BioPerl-1.6.1/t/data/test.interpro-go.xml
BioPerl-1.6.1/t/data/test.lasergene
BioPerl-1.6.1/t/data/test.locuslink
BioPerl-1.6.1/t/data/test.mase
BioPerl-1.6.1/t/data/test.meme
BioPerl-1.6.1/t/data/test.meme2
BioPerl-1.6.1/t/data/test.metafasta
BioPerl-1.6.1/t/data/test.nh
BioPerl-1.6.1/t/data/test.nhx
BioPerl-1.6.1/t/data/test.pfam
BioPerl-1.6.1/t/data/test.phd
BioPerl-1.6.1/t/data/test.pir
BioPerl-1.6.1/t/data/test.pln
BioPerl-1.6.1/t/data/test.ptt
BioPerl-1.6.1/t/data/test.raw
BioPerl-1.6.1/t/data/test.swiss
BioPerl-1.6.1/t/data/test.tab
BioPerl-1.6.1/t/data/test.tigrxml
BioPerl-1.6.1/t/data/test.tseq
BioPerl-1.6.1/t/data/test.tsv
BioPerl-1.6.1/t/data/test.txt
BioPerl-1.6.1/t/data/test.waba
BioPerl-1.6.1/t/data/test.xls
BioPerl-1.6.1/t/data/test.ztr
BioPerl-1.6.1/t/data/test1.blasttab3
BioPerl-1.6.1/t/data/test1.wublastp
BioPerl-1.6.1/t/data/test2.infernal
BioPerl-1.6.1/t/data/test2.raw
BioPerl-1.6.1/t/data/test_badlf.gcg
BioPerl-1.6.1/t/data/test_clear_range.fastq
BioPerl-1.6.1/t/data/testaln.aln
BioPerl-1.6.1/t/data/testaln.arp
BioPerl-1.6.1/t/data/testaln.fasta
BioPerl-1.6.1/t/data/testaln.list
BioPerl-1.6.1/t/data/testaln.mase
BioPerl-1.6.1/t/data/testaln.metafasta
BioPerl-1.6.1/t/data/testaln.msf
BioPerl-1.6.1/t/data/testaln.nexus
BioPerl-1.6.1/t/data/testaln.pfam
BioPerl-1.6.1/t/data/testaln.phylip
BioPerl-1.6.1/t/data/testaln.po
BioPerl-1.6.1/t/data/testaln.prodom
BioPerl-1.6.1/t/data/testaln.psi
BioPerl-1.6.1/t/data/testaln.selex
BioPerl-1.6.1/t/data/testaln.stockholm
BioPerl-1.6.1/t/data/testaln.xmfa
BioPerl-1.6.1/t/data/testaln2.arp
BioPerl-1.6.1/t/data/testaln2.fasta
BioPerl-1.6.1/t/data/testdat.exonerate
BioPerl-1.6.1/t/data/testdata.crossmatch
BioPerl-1.6.1/t/data/testdbaccnums.out
BioPerl-1.6.1/t/data/testfile.erpin
BioPerl-1.6.1/t/data/testfuzzy.genbank
BioPerl-1.6.1/t/data/tmhmm.out
BioPerl-1.6.1/t/data/tmp.fst
BioPerl-1.6.1/t/data/traits.tab
BioPerl-1.6.1/t/data/traittree.nexus
BioPerl-1.6.1/t/data/transfac.dat
BioPerl-1.6.1/t/data/tree_nonewline.nexus
BioPerl-1.6.1/t/data/Treebase-chlamy-dna.nex
BioPerl-1.6.1/t/data/tricky.wublast
BioPerl-1.6.1/t/data/trna.strict.rnamotif
BioPerl-1.6.1/t/data/U58726.gb
BioPerl-1.6.1/t/data/U71225.gb
BioPerl-1.6.1/t/data/U83300.bsml
BioPerl-1.6.1/t/data/UnaSmithHIV-both.nex
BioPerl-1.6.1/t/data/unigene.data
BioPerl-1.6.1/t/data/urease.tre.nexus
BioPerl-1.6.1/t/data/vecscreen_simple.test_output
BioPerl-1.6.1/t/data/version2.scf
BioPerl-1.6.1/t/data/version3.scf
BioPerl-1.6.1/t/data/withrefm.906
BioPerl-1.6.1/t/data/worm_fam_2785.cdna
BioPerl-1.6.1/t/data/X98338_Adh-mRNA.gb
BioPerl-1.6.1/t/data/yeast.tRNAscanSE
BioPerl-1.6.1/t/data/yn00.mlc
BioPerl-1.6.1/t/data/biodbgff
BioPerl-1.6.1/t/data/biodbgff/test.gff
BioPerl-1.6.1/t/data/biodbgff/test.gff3
BioPerl-1.6.1/t/data/codeml_lysozyme
BioPerl-1.6.1/t/data/codeml_lysozyme/2NG.dN
BioPerl-1.6.1/t/data/codeml_lysozyme/2NG.dS
BioPerl-1.6.1/t/data/codeml_lysozyme/2NG.tt
BioPerl-1.6.1/t/data/codeml_lysozyme/4fold.nuc
BioPerl-1.6.1/t/data/codeml_lysozyme/lnf
BioPerl-1.6.1/t/data/codeml_lysozyme/lysozymeSmall.ctl
BioPerl-1.6.1/t/data/codeml_lysozyme/lysozymeSmall.trees
BioPerl-1.6.1/t/data/codeml_lysozyme/lysozymeSmall.txt
BioPerl-1.6.1/t/data/codeml_lysozyme/mlc
BioPerl-1.6.1/t/data/codeml_lysozyme/rst
BioPerl-1.6.1/t/data/codeml_lysozyme/rst1
BioPerl-1.6.1/t/data/codeml_lysozyme/rub
BioPerl-1.6.1/t/data/consed_project
BioPerl-1.6.1/t/data/consed_project/edit_dir
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.contigs
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.log
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.log
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.problems
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.qual
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.fasta.screen.view
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.newtags
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.phrap.out
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project.screen.out
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_project_to_alu.cross
BioPerl-1.6.1/t/data/consed_project/edit_dir/test_projectNewChromats.fof
BioPerl-1.6.1/t/data/consed_project/phd_dir
BioPerl-1.6.1/t/data/consed_project/phd_dir/ML4922R.phd.1
BioPerl-1.6.1/t/data/consed_project/phd_dir/ML4924F.phd.1
BioPerl-1.6.1/t/data/consed_project/phd_dir/ML4924R.phd.1
BioPerl-1.6.1/t/data/consed_project/phd_dir/ML4947F.phd.1
BioPerl-1.6.1/t/data/dbfa
BioPerl-1.6.1/t/data/dbfa/1.fa
BioPerl-1.6.1/t/data/dbfa/2.fa
BioPerl-1.6.1/t/data/dbfa/3.fa
BioPerl-1.6.1/t/data/dbfa/4.fa
BioPerl-1.6.1/t/data/dbfa/5.fa
BioPerl-1.6.1/t/data/dbfa/6.fa
BioPerl-1.6.1/t/data/dbfa/7.fa
BioPerl-1.6.1/t/data/dbqual
BioPerl-1.6.1/t/data/dbqual/1.qual
BioPerl-1.6.1/t/data/dbqual/2.qual
BioPerl-1.6.1/t/data/dbqual/3.qual
BioPerl-1.6.1/t/data/eutils
BioPerl-1.6.1/t/data/eutils/egquery.xml
BioPerl-1.6.1/t/data/eutils/einfo.xml
BioPerl-1.6.1/t/data/eutils/einfo_dbs.xml
BioPerl-1.6.1/t/data/eutils/elink_acheck.xml
BioPerl-1.6.1/t/data/eutils/elink_acheck_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_dball.xml
BioPerl-1.6.1/t/data/eutils/elink_lcheck.xml
BioPerl-1.6.1/t/data/eutils/elink_lcheck_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_llinks.xml
BioPerl-1.6.1/t/data/eutils/elink_llinks_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_multidb.xml
BioPerl-1.6.1/t/data/eutils/elink_multidb_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_ncheck.xml
BioPerl-1.6.1/t/data/eutils/elink_ncheck_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_neighbor.xml
BioPerl-1.6.1/t/data/eutils/elink_neighbor_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_nhist.xml
BioPerl-1.6.1/t/data/eutils/elink_nhist_corr.xml
BioPerl-1.6.1/t/data/eutils/elink_scores.xml
BioPerl-1.6.1/t/data/eutils/epost.xml
BioPerl-1.6.1/t/data/eutils/esearch1.xml
BioPerl-1.6.1/t/data/eutils/esearch2.xml
BioPerl-1.6.1/t/data/eutils/espell.xml
BioPerl-1.6.1/t/data/eutils/esummary1.xml
BioPerl-1.6.1/t/data/eutils/esummary2.xml
BioPerl-1.6.1/t/data/fastq
BioPerl-1.6.1/t/data/fastq/bug2335.fastq
BioPerl-1.6.1/t/data/fastq/error_diff_ids.fastq
BioPerl-1.6.1/t/data/fastq/error_double_qual.fastq
BioPerl-1.6.1/t/data/fastq/error_double_seq.fastq
BioPerl-1.6.1/t/data/fastq/error_long_qual.fastq
BioPerl-1.6.1/t/data/fastq/error_no_qual.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_del.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_escape.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_null.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_space.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_tab.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_unit_sep.fastq
BioPerl-1.6.1/t/data/fastq/error_qual_vtab.fastq
BioPerl-1.6.1/t/data/fastq/error_short_qual.fastq
BioPerl-1.6.1/t/data/fastq/error_spaces.fastq
BioPerl-1.6.1/t/data/fastq/error_tabs.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_at_plus.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_at_qual.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_at_seq.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_in_plus.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_in_qual.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_in_seq.fastq
BioPerl-1.6.1/t/data/fastq/error_trunc_in_title.fastq
BioPerl-1.6.1/t/data/fastq/evil_wrapping.fastq
BioPerl-1.6.1/t/data/fastq/example.fasta
BioPerl-1.6.1/t/data/fastq/example.fastq
BioPerl-1.6.1/t/data/fastq/example.qual
BioPerl-1.6.1/t/data/fastq/illumina_faked.fastq
BioPerl-1.6.1/t/data/fastq/sanger_93.fastq
BioPerl-1.6.1/t/data/fastq/sanger_faked.fastq
BioPerl-1.6.1/t/data/fastq/solexa_example.fastq
BioPerl-1.6.1/t/data/fastq/solexa_faked.fastq
BioPerl-1.6.1/t/data/fastq/test1_sanger.fastq
BioPerl-1.6.1/t/data/fastq/test2_solexa.fastq
BioPerl-1.6.1/t/data/fastq/test3_illumina.fastq
BioPerl-1.6.1/t/data/fastq/tricky.fastq
BioPerl-1.6.1/t/data/fastq/wrapping_issues.fastq
BioPerl-1.6.1/t/data/map_hem
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM12.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM12.fa.revcom
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM12.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM13.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM13.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM14.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM14.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM2.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM2.fa.revcom
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM2.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM3.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM3.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM4.fa
BioPerl-1.6.1/t/data/map_hem/HEM1-HEM4.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM1.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM1.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM12-HEM13.fa
BioPerl-1.6.1/t/data/map_hem/HEM12-HEM13.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM12-HEM14.fa
BioPerl-1.6.1/t/data/map_hem/HEM12-HEM14.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM12-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM12-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM12.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM12.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM13-HEM14.fa
BioPerl-1.6.1/t/data/map_hem/HEM13-HEM14.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM13-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM13-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM13.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM13.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM14-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM14-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM14.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM14.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM15.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM15.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM12.fa
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM12.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM13.fa
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM13.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM14.fa
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM14.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM3.fa
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM3.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM4.fa
BioPerl-1.6.1/t/data/map_hem/HEM2-HEM4.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM2.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM2.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM12.fa
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM12.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM13.fa
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM13.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM14.fa
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM14.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM4.fa
BioPerl-1.6.1/t/data/map_hem/HEM3-HEM4.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM3.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM3.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM12.fa
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM12.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM13.fa
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM13.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM14.fa
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM14.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM15.fa
BioPerl-1.6.1/t/data/map_hem/HEM4-HEM15.meme.txt
BioPerl-1.6.1/t/data/map_hem/HEM4.ups.fa_
BioPerl-1.6.1/t/data/map_hem/HEM4.ups.fa_.revcom
BioPerl-1.6.1/t/data/map_hem/yeast.nc.1.freq
BioPerl-1.6.1/t/data/registry
BioPerl-1.6.1/t/data/registry/bdb
BioPerl-1.6.1/t/data/registry/bdb/seqdatabase.ini
BioPerl-1.6.1/t/data/registry/flat
BioPerl-1.6.1/t/data/registry/flat/seqdatabase.ini
BioPerl-1.6.1/t/data/seqfeaturedb
BioPerl-1.6.1/t/data/seqfeaturedb/test.gff3
BioPerl-1.6.1/t/data/taxdump
BioPerl-1.6.1/t/data/taxdump/names.dmp
BioPerl-1.6.1/t/data/taxdump/nodes.dmp
BioPerl-1.6.1/t/data/transfac_pro
BioPerl-1.6.1/t/data/transfac_pro/factor.dat
BioPerl-1.6.1/t/data/transfac_pro/fragment.dat
BioPerl-1.6.1/t/data/transfac_pro/gene.dat
BioPerl-1.6.1/t/data/transfac_pro/matrix.dat
BioPerl-1.6.1/t/data/transfac_pro/readme.txt
BioPerl-1.6.1/t/data/transfac_pro/reference.dat
BioPerl-1.6.1/t/data/transfac_pro/site.dat
BioPerl-1.6.1/t/lib
BioPerl-1.6.1/t/lib/Error.pm
BioPerl-1.6.1/t/lib/Array
BioPerl-1.6.1/t/lib/Array/Compare.pm
BioPerl-1.6.1/t/lib/Sub
BioPerl-1.6.1/t/lib/Sub/Uplevel.pm
BioPerl-1.6.1/t/lib/Test
BioPerl-1.6.1/t/lib/Test/Builder.pm
BioPerl-1.6.1/t/lib/Test/Exception.pm
BioPerl-1.6.1/t/lib/Test/Harness.pm
BioPerl-1.6.1/t/lib/Test/More.pm
BioPerl-1.6.1/t/lib/Test/Simple.pm
BioPerl-1.6.1/t/lib/Test/Tutorial.pod
BioPerl-1.6.1/t/lib/Test/Warn.pm
BioPerl-1.6.1/t/lib/Test/Builder
BioPerl-1.6.1/t/lib/Test/Builder/Module.pm
BioPerl-1.6.1/t/lib/Test/Builder/Tester.pm
BioPerl-1.6.1/t/lib/Test/Builder/Tester
BioPerl-1.6.1/t/lib/Test/Builder/Tester/Color.pm
BioPerl-1.6.1/t/lib/Test/Harness
BioPerl-1.6.1/t/lib/Test/Harness/Assert.pm
BioPerl-1.6.1/t/lib/Test/Harness/Iterator.pm
BioPerl-1.6.1/t/lib/Test/Harness/Point.pm
BioPerl-1.6.1/t/lib/Test/Harness/Results.pm
BioPerl-1.6.1/t/lib/Test/Harness/Straps.pm
BioPerl-1.6.1/t/lib/Test/Harness/TAP.pod
BioPerl-1.6.1/t/lib/Test/Harness/Util.pm
BioPerl-1.6.1/t/lib/Tree
BioPerl-1.6.1/t/lib/Tree/DAG_Node.pm
BioPerl-1.6.1/t/LiveSeq
BioPerl-1.6.1/t/LiveSeq/Chain.t
BioPerl-1.6.1/t/LiveSeq/LiveSeq.t
BioPerl-1.6.1/t/LiveSeq/Mutation.t
BioPerl-1.6.1/t/LiveSeq/Mutator.t
BioPerl-1.6.1/t/LocalDB
BioPerl-1.6.1/t/LocalDB/BioDBGFF.t
BioPerl-1.6.1/t/LocalDB/BlastIndex.t
BioPerl-1.6.1/t/LocalDB/DBFasta.t
BioPerl-1.6.1/t/LocalDB/DBQual.t
BioPerl-1.6.1/t/LocalDB/Flat.t
BioPerl-1.6.1/t/LocalDB/Index.t
BioPerl-1.6.1/t/LocalDB/Registry.t
BioPerl-1.6.1/t/LocalDB/SeqFeature.t
BioPerl-1.6.1/t/LocalDB/transfac_pro.t
BioPerl-1.6.1/t/Map
BioPerl-1.6.1/t/Map/Cyto.t
BioPerl-1.6.1/t/Map/Linkage.t
BioPerl-1.6.1/t/Map/Map.t
BioPerl-1.6.1/t/Map/MapIO.t
BioPerl-1.6.1/t/Map/MicrosatelliteMarker.t
BioPerl-1.6.1/t/Map/Physical.t
BioPerl-1.6.1/t/Matrix
BioPerl-1.6.1/t/Matrix/InstanceSite.t
BioPerl-1.6.1/t/Matrix/Matrix.t
BioPerl-1.6.1/t/Matrix/ProtMatrix.t
BioPerl-1.6.1/t/Matrix/ProtPsm.t
BioPerl-1.6.1/t/Matrix/SiteMatrix.t
BioPerl-1.6.1/t/Matrix/IO
BioPerl-1.6.1/t/Matrix/IO/masta.t
BioPerl-1.6.1/t/Matrix/IO/psm.t
BioPerl-1.6.1/t/Ontology
BioPerl-1.6.1/t/Ontology/GOterm.t
BioPerl-1.6.1/t/Ontology/GraphAdaptor.t
BioPerl-1.6.1/t/Ontology/Ontology.t
BioPerl-1.6.1/t/Ontology/OntologyEngine.t
BioPerl-1.6.1/t/Ontology/OntologyStore.t
BioPerl-1.6.1/t/Ontology/Relationship.t
BioPerl-1.6.1/t/Ontology/RelationshipType.t
BioPerl-1.6.1/t/Ontology/Term.t
BioPerl-1.6.1/t/Ontology/IO
BioPerl-1.6.1/t/Ontology/IO/go.t
BioPerl-1.6.1/t/Ontology/IO/interpro.t
BioPerl-1.6.1/t/Ontology/IO/obo.t
BioPerl-1.6.1/t/Phenotype
BioPerl-1.6.1/t/Phenotype/Correlate.t
BioPerl-1.6.1/t/Phenotype/Measure.t
BioPerl-1.6.1/t/Phenotype/MeSH.t
BioPerl-1.6.1/t/Phenotype/MiniMIMentry.t
BioPerl-1.6.1/t/Phenotype/OMIMentry.t
BioPerl-1.6.1/t/Phenotype/OMIMentryAllelicVariant.t
BioPerl-1.6.1/t/Phenotype/OMIMparser.t
BioPerl-1.6.1/t/Phenotype/Phenotype.t
BioPerl-1.6.1/t/PopGen
BioPerl-1.6.1/t/PopGen/Coalescent.t
BioPerl-1.6.1/t/PopGen/HtSNP.t
BioPerl-1.6.1/t/PopGen/MK.t
BioPerl-1.6.1/t/PopGen/PopGen.t
BioPerl-1.6.1/t/PopGen/PopGenSims.t
BioPerl-1.6.1/t/PopGen/TagHaplotype.t
BioPerl-1.6.1/t/RemoteDB
BioPerl-1.6.1/t/RemoteDB/BioFetch.t
BioPerl-1.6.1/t/RemoteDB/CUTG.t
BioPerl-1.6.1/t/RemoteDB/EMBL.t
BioPerl-1.6.1/t/RemoteDB/EntrezGene.t
BioPerl-1.6.1/t/RemoteDB/EUtilities.t
BioPerl-1.6.1/t/RemoteDB/GenBank.t
BioPerl-1.6.1/t/RemoteDB/GenPept.t
BioPerl-1.6.1/t/RemoteDB/MeSH.t
BioPerl-1.6.1/t/RemoteDB/RefSeq.t
BioPerl-1.6.1/t/RemoteDB/SeqHound.t
BioPerl-1.6.1/t/RemoteDB/SeqRead_fail.t
BioPerl-1.6.1/t/RemoteDB/SeqVersion.t
BioPerl-1.6.1/t/RemoteDB/SwissProt.t
BioPerl-1.6.1/t/RemoteDB/Taxonomy.t
BioPerl-1.6.1/t/RemoteDB/HIV
BioPerl-1.6.1/t/RemoteDB/HIV/HIV.t
BioPerl-1.6.1/t/RemoteDB/HIV/HIVAnnotProcessor.t
BioPerl-1.6.1/t/RemoteDB/HIV/HIVQuery.t
BioPerl-1.6.1/t/RemoteDB/HIV/HIVQueryHelper.t
BioPerl-1.6.1/t/RemoteDB/Query
BioPerl-1.6.1/t/RemoteDB/Query/GenBank.t
BioPerl-1.6.1/t/Restriction
BioPerl-1.6.1/t/Restriction/Analysis-refac.t
BioPerl-1.6.1/t/Restriction/Analysis.t
BioPerl-1.6.1/t/Restriction/Gel.t
BioPerl-1.6.1/t/Restriction/IO.t
BioPerl-1.6.1/t/Root
BioPerl-1.6.1/t/Root/Exception.t
BioPerl-1.6.1/t/Root/RootI.t
BioPerl-1.6.1/t/Root/RootIO.t
BioPerl-1.6.1/t/Root/Storable.t
BioPerl-1.6.1/t/Root/Tempfile.t
BioPerl-1.6.1/t/Root/Utilities.t
BioPerl-1.6.1/t/SearchIO
BioPerl-1.6.1/t/SearchIO/blast.t
BioPerl-1.6.1/t/SearchIO/blast_pull.t
BioPerl-1.6.1/t/SearchIO/blasttable.t
BioPerl-1.6.1/t/SearchIO/blastxml.t
BioPerl-1.6.1/t/SearchIO/CigarString.t
BioPerl-1.6.1/t/SearchIO/cross_match.t
BioPerl-1.6.1/t/SearchIO/erpin.t
BioPerl-1.6.1/t/SearchIO/exonerate.t
BioPerl-1.6.1/t/SearchIO/fasta.t
BioPerl-1.6.1/t/SearchIO/gmap_f9.t
BioPerl-1.6.1/t/SearchIO/hmmer.t
BioPerl-1.6.1/t/SearchIO/hmmer_pull.t
BioPerl-1.6.1/t/SearchIO/infernal.t
BioPerl-1.6.1/t/SearchIO/megablast.t
BioPerl-1.6.1/t/SearchIO/psl.t
BioPerl-1.6.1/t/SearchIO/rnamotif.t
BioPerl-1.6.1/t/SearchIO/SearchIO.t
BioPerl-1.6.1/t/SearchIO/sim4.t
BioPerl-1.6.1/t/SearchIO/SimilarityPair.t
BioPerl-1.6.1/t/SearchIO/Tiling.t
BioPerl-1.6.1/t/SearchIO/waba.t
BioPerl-1.6.1/t/SearchIO/wise.t
BioPerl-1.6.1/t/SearchIO/Writer
BioPerl-1.6.1/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.1/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.1/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.1/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.1/t/Seq
BioPerl-1.6.1/t/Seq/DBLink.t
BioPerl-1.6.1/t/Seq/EncodedSeq.t
BioPerl-1.6.1/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.1/t/Seq/LargePSeq.t
BioPerl-1.6.1/t/Seq/LocatableSeq.t
BioPerl-1.6.1/t/Seq/MetaSeq.t
BioPerl-1.6.1/t/Seq/PrimaryQual.t
BioPerl-1.6.1/t/Seq/PrimarySeq.t
BioPerl-1.6.1/t/Seq/PrimedSeq.t
BioPerl-1.6.1/t/Seq/Quality.t
BioPerl-1.6.1/t/Seq/Seq.t
BioPerl-1.6.1/t/Seq/WithQuality.t
BioPerl-1.6.1/t/SeqFeature
BioPerl-1.6.1/t/SeqFeature/FeatureIO.t
BioPerl-1.6.1/t/SeqFeature/Location.t
BioPerl-1.6.1/t/SeqFeature/LocationFactory.t
BioPerl-1.6.1/t/SeqFeature/Primer.t
BioPerl-1.6.1/t/SeqFeature/Range.t
BioPerl-1.6.1/t/SeqFeature/RangeI.t
BioPerl-1.6.1/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.1/t/SeqFeature/SeqFeatAnnotated.t
BioPerl-1.6.1/t/SeqFeature/SeqFeatCollection.t
BioPerl-1.6.1/t/SeqFeature/SeqFeature.t
BioPerl-1.6.1/t/SeqFeature/SeqFeaturePrimer.t
BioPerl-1.6.1/t/SeqFeature/Unflattener.t
BioPerl-1.6.1/t/SeqFeature/Unflattener2.t
BioPerl-1.6.1/t/SeqIO
BioPerl-1.6.1/t/SeqIO/abi.t
BioPerl-1.6.1/t/SeqIO/ace.t
BioPerl-1.6.1/t/SeqIO/agave.t
BioPerl-1.6.1/t/SeqIO/alf.t
BioPerl-1.6.1/t/SeqIO/asciitree.t
BioPerl-1.6.1/t/SeqIO/bsml.t
BioPerl-1.6.1/t/SeqIO/bsml_sax.t
BioPerl-1.6.1/t/SeqIO/chadoxml.t
BioPerl-1.6.1/t/SeqIO/chaos.t
BioPerl-1.6.1/t/SeqIO/chaosxml.t
BioPerl-1.6.1/t/SeqIO/ctf.t
BioPerl-1.6.1/t/SeqIO/embl.t
BioPerl-1.6.1/t/SeqIO/entrezgene.t
BioPerl-1.6.1/t/SeqIO/excel.t
BioPerl-1.6.1/t/SeqIO/exp.t
BioPerl-1.6.1/t/SeqIO/fasta.t
BioPerl-1.6.1/t/SeqIO/fastq.t
BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.1/t/SeqIO/game.t
BioPerl-1.6.1/t/SeqIO/gcg.t
BioPerl-1.6.1/t/SeqIO/genbank.t
BioPerl-1.6.1/t/SeqIO/Handler.t
BioPerl-1.6.1/t/SeqIO/interpro.t
BioPerl-1.6.1/t/SeqIO/kegg.t
BioPerl-1.6.1/t/SeqIO/largefasta.t
BioPerl-1.6.1/t/SeqIO/lasergene.t
BioPerl-1.6.1/t/SeqIO/locuslink.t
BioPerl-1.6.1/t/SeqIO/metafasta.t
BioPerl-1.6.1/t/SeqIO/MultiFile.t
BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.1/t/SeqIO/phd.t
BioPerl-1.6.1/t/SeqIO/pir.t
BioPerl-1.6.1/t/SeqIO/pln.t
BioPerl-1.6.1/t/SeqIO/qual.t
BioPerl-1.6.1/t/SeqIO/raw.t
BioPerl-1.6.1/t/SeqIO/scf.t
BioPerl-1.6.1/t/SeqIO/SeqBuilder.t
BioPerl-1.6.1/t/SeqIO/Splicedseq.t
BioPerl-1.6.1/t/SeqIO/strider.t
BioPerl-1.6.1/t/SeqIO/swiss.t
BioPerl-1.6.1/t/SeqIO/tab.t
BioPerl-1.6.1/t/SeqIO/table.t
BioPerl-1.6.1/t/SeqIO/tigr.t
BioPerl-1.6.1/t/SeqIO/tigrxml.t
BioPerl-1.6.1/t/SeqIO/tinyseq.t
BioPerl-1.6.1/t/SeqIO/ztr.t
BioPerl-1.6.1/t/SeqTools
BioPerl-1.6.1/t/SeqTools/Backtranslate.t
BioPerl-1.6.1/t/SeqTools/CodonTable.t
BioPerl-1.6.1/t/SeqTools/ECnumber.t
BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.1/t/SeqTools/OddCodes.t
BioPerl-1.6.1/t/SeqTools/SeqPattern.t
BioPerl-1.6.1/t/SeqTools/SeqStats.t
BioPerl-1.6.1/t/SeqTools/SeqUtils.t
BioPerl-1.6.1/t/SeqTools/SeqWords.t
BioPerl-1.6.1/t/Structure
BioPerl-1.6.1/t/Structure/IO.t
BioPerl-1.6.1/t/Structure/Structure.t
BioPerl-1.6.1/t/Tools
BioPerl-1.6.1/t/Tools/ePCR.t
BioPerl-1.6.1/t/Tools/Est2Genome.t
BioPerl-1.6.1/t/Tools/FootPrinter.t
BioPerl-1.6.1/t/Tools/Geneid.t
BioPerl-1.6.1/t/Tools/Genewise.t
BioPerl-1.6.1/t/Tools/Genomewise.t
BioPerl-1.6.1/t/Tools/Genpred.t
BioPerl-1.6.1/t/Tools/GFF.t
BioPerl-1.6.1/t/Tools/Hmmer.t
BioPerl-1.6.1/t/Tools/IUPAC.t
BioPerl-1.6.1/t/Tools/Lucy.t
BioPerl-1.6.1/t/Tools/Match.t
BioPerl-1.6.1/t/Tools/pICalculator.t
BioPerl-1.6.1/t/Tools/Primer3.t
BioPerl-1.6.1/t/Tools/Promoterwise.t
BioPerl-1.6.1/t/Tools/Pseudowise.t
BioPerl-1.6.1/t/Tools/QRNA.t
BioPerl-1.6.1/t/Tools/RandDistFunctions.t
BioPerl-1.6.1/t/Tools/RepeatMasker.t
BioPerl-1.6.1/t/Tools/rnamotif.t
BioPerl-1.6.1/t/Tools/Seg.t
BioPerl-1.6.1/t/Tools/Sigcleave.t
BioPerl-1.6.1/t/Tools/Signalp.t
BioPerl-1.6.1/t/Tools/Sim4.t
BioPerl-1.6.1/t/Tools/SiRNA.t
BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.1/t/Tools/TargetP.t
BioPerl-1.6.1/t/Tools/Tmhmm.t
BioPerl-1.6.1/t/Tools/tRNAscanSE.t
BioPerl-1.6.1/t/Tools/Alignment
BioPerl-1.6.1/t/Tools/Alignment/Consed.t
BioPerl-1.6.1/t/Tools/Analysis
BioPerl-1.6.1/t/Tools/Analysis/DNA
BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.1/t/Tools/Analysis/Protein
BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.1/t/Tools/EMBOSS
BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.1/t/Tools/EUtilities
BioPerl-1.6.1/t/Tools/EUtilities/egquery.t
BioPerl-1.6.1/t/Tools/EUtilities/einfo.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t
BioPerl-1.6.1/t/Tools/EUtilities/epost.t
BioPerl-1.6.1/t/Tools/EUtilities/esearch.t
BioPerl-1.6.1/t/Tools/EUtilities/espell.t
BioPerl-1.6.1/t/Tools/EUtilities/esummary.t
BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t
BioPerl-1.6.1/t/Tools/Phylo
BioPerl-1.6.1/t/Tools/Phylo/Gerp.t
BioPerl-1.6.1/t/Tools/Phylo/Molphy.t
BioPerl-1.6.1/t/Tools/Phylo/PAML.t
BioPerl-1.6.1/t/Tools/Phylo/Phylip
BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.1/t/Tools/Run
BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.1/t/Tools/Run/WrapperBase.t
BioPerl-1.6.1/t/Tools/Signalp
BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.1/t/Tools/Spidey
BioPerl-1.6.1/t/Tools/Spidey/Spidey.t
BioPerl-1.6.1/t/Tree
BioPerl-1.6.1/t/Tree/Compatible.t
BioPerl-1.6.1/t/Tree/Node.t
BioPerl-1.6.1/t/Tree/RandomTreeFactory.t
BioPerl-1.6.1/t/Tree/Tree.t
BioPerl-1.6.1/t/Tree/TreeIO.t
BioPerl-1.6.1/t/Tree/TreeStatistics.t
BioPerl-1.6.1/t/Tree/PhyloNetwork
BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.1/t/Tree/TreeIO
BioPerl-1.6.1/t/Tree/TreeIO/lintree.t
BioPerl-1.6.1/t/Tree/TreeIO/newick.t
BioPerl-1.6.1/t/Tree/TreeIO/nexus.t
BioPerl-1.6.1/t/Tree/TreeIO/nhx.t
BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.1/t/Variation
BioPerl-1.6.1/t/Variation/AAChange.t
BioPerl-1.6.1/t/Variation/AAReverseMutate.t
BioPerl-1.6.1/t/Variation/Allele.t
BioPerl-1.6.1/t/Variation/DNAMutation.t
BioPerl-1.6.1/t/Variation/RNAChange.t
BioPerl-1.6.1/t/Variation/SeqDiff.t
BioPerl-1.6.1/t/Variation/SNP.t
BioPerl-1.6.1/t/Variation/Variation_IO.t

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

>>> /home/fly1600/ap1600/bin/perl-static Makefile.PL
# running Build.PL 
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites...
  recommends:
    *  Optional prerequisite Ace is not installed
   (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace)
    *  Optional prerequisite Bio::ASN1::EntrezGene is not installed
   (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!])
    *  Optional prerequisite GraphViz is not installed
   (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

Checking features:
  Network...................enabled
  BioDBSeqFeature_mysql.....enabled
  BioDBGFF..................enabled
  BioDBSeqFeature_BDB.......enabled
  BioDBSeqFeature_SQLite....enabled
  BioDBSeqFeature_Pg........enabled

Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n]   - will not run the BioDBGFF or BioDBSeqFeature live database tests

Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a]   - will install all scripts

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2]
 at /home/fly1600/var/megalib/Module/Build/Base.pm line 4571.

Could not create MYMETA files
  - will not run internet-requiring tests
Creating new 'Build' script for 'BioPerl' version '1.006001'
>>> make
/home/fly1600/ap1600/bin/perl-static Build --makefile_env_macros 1
Building BioPerl
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
blib/script/hivq.PLS -> blib/script/bp_hivq.pl
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
blib/script/bp_index.PLS -> blib/script/bp_index.pl
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
blib/script/einfo.PLS -> blib/script/bp_einfo.pl
blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl
blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
blib/script/search2table.PLS -> blib/script/bp_search2table.pl
blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
  CJFIELDS/BioPerl-1.6.1.tar.gz
  make -- OK
Running make test
>>> make test TEST_VERBOSE=1
/home/fly1600/ap1600/bin/perl-static Build --makefile_env_macros 1 test
Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
Changing sharpbang in blib/script/bp_sreformat.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_sreformat.PLS.bak
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
Changing sharpbang in blib/script/seqconvert.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/seqconvert.PLS.bak
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
Changing sharpbang in blib/script/parse_hmmsearch.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/parse_hmmsearch.PLS.bak
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS
Changing sharpbang in blib/script/hivq.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/hivq.PLS.bak
blib/script/hivq.PLS -> blib/script/bp_hivq.pl
Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
Changing sharpbang in blib/script/bp_seqret.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_seqret.PLS.bak
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Changing sharpbang in blib/script/tree2pag.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/tree2pag.PLS.bak
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
Changing sharpbang in blib/script/meta_gff.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/meta_gff.PLS.bak
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
Changing sharpbang in blib/script/nexus2nh.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/nexus2nh.PLS.bak
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
Changing sharpbang in blib/script/filter_search.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/filter_search.PLS.bak
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
Changing sharpbang in blib/script/generate_histogram.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/generate_histogram.PLS.bak
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
Changing sharpbang in blib/script/heterogeneity_test.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/heterogeneity_test.PLS.bak
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
Changing sharpbang in blib/script/flanks.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/flanks.PLS.bak
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
Changing sharpbang in blib/script/split_seq.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/split_seq.PLS.bak
blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
Changing sharpbang in blib/script/load_gff.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/load_gff.PLS.bak
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
Changing sharpbang in blib/script/biogetseq.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/biogetseq.PLS.bak
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
Changing sharpbang in blib/script/bp_fetch.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_fetch.PLS.bak
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
Changing sharpbang in blib/script/mutate.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/mutate.PLS.bak
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
Changing sharpbang in blib/script/process_sgd.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/process_sgd.PLS.bak
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
Changing sharpbang in blib/script/bp_index.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_index.PLS.bak
blib/script/bp_index.PLS -> blib/script/bp_index.pl
Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
Changing sharpbang in blib/script/dbsplit.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/dbsplit.PLS.bak
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
Changing sharpbang in blib/script/oligo_count.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/oligo_count.PLS.bak
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
Changing sharpbang in blib/script/hmmer_to_table.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/hmmer_to_table.PLS.bak
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
Changing sharpbang in blib/script/process_gadfly.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/process_gadfly.PLS.bak
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
Changing sharpbang in blib/script/bp_seqfeature_load.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_seqfeature_load.PLS.bak
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
Changing sharpbang in blib/script/fastam9_to_table.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/fastam9_to_table.PLS.bak
blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
Changing sharpbang in blib/script/biofetch_genbank_proxy.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/biofetch_genbank_proxy.PLS.bak
blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
Changing sharpbang in blib/script/seq_length.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/seq_length.PLS.bak
blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
Changing sharpbang in blib/script/extract_feature_seq.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/extract_feature_seq.PLS.bak
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
Changing sharpbang in blib/script/genbank2gff.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/genbank2gff.PLS.bak
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
Changing sharpbang in blib/script/bulk_load_gff.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bulk_load_gff.PLS.bak
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Changing sharpbang in blib/script/taxid4species.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/taxid4species.PLS.bak
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
Changing sharpbang in blib/script/search2gff.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/search2gff.PLS.bak
blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
Changing sharpbang in blib/script/blast2tree.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/blast2tree.PLS.bak
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
Changing sharpbang in blib/script/unflatten_seq.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/unflatten_seq.PLS.bak
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
Changing sharpbang in blib/script/make_mrna_protein.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/make_mrna_protein.PLS.bak
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Changing sharpbang in blib/script/search2tribe.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/search2tribe.PLS.bak
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
Changing sharpbang in blib/script/bioflat_index.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bioflat_index.PLS.bak
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
Changing sharpbang in blib/script/pairwise_kaks.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/pairwise_kaks.PLS.bak
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
Changing sharpbang in blib/script/query_entrez_taxa.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/query_entrez_taxa.PLS.bak
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
Changing sharpbang in blib/script/bp_seqfeature_delete.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_seqfeature_delete.PLS.bak
blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
Changing sharpbang in blib/script/fast_load_gff.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/fast_load_gff.PLS.bak
blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
Changing sharpbang in blib/script/chaos_plot.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/chaos_plot.PLS.bak
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
Changing sharpbang in blib/script/bp_mrtrans.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_mrtrans.PLS.bak
blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
Changing sharpbang in blib/script/search2alnblocks.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/search2alnblocks.PLS.bak
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Changing sharpbang in blib/script/taxonomy2tree.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/taxonomy2tree.PLS.bak
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS
Changing sharpbang in blib/script/einfo.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/einfo.PLS.bak
blib/script/einfo.PLS -> blib/script/bp_einfo.pl
Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
Changing sharpbang in blib/script/download_query_genbank.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/download_query_genbank.PLS.bak
blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
Changing sharpbang in blib/script/bp_nrdb.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/bp_nrdb.PLS.bak
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
Changing sharpbang in blib/script/mask_by_search.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/mask_by_search.PLS.bak
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
Changing sharpbang in blib/script/gccalc.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/gccalc.PLS.bak
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/classify_hits_kingdom.PLS.bak
blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
Changing sharpbang in blib/script/composite_LD.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/composite_LD.PLS.bak
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Changing sharpbang in blib/script/aacomp.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/aacomp.PLS.bak
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
Copying scripts/utilities/revtrans-motif.PLS -> blib/script/revtrans-motif.PLS
Changing sharpbang in blib/script/revtrans-motif.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/revtrans-motif.PLS.bak
blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl
Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
Changing sharpbang in blib/script/process_wormbase.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/process_wormbase.PLS.bak
blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
Changing sharpbang in blib/script/local_taxonomydb_query.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/local_taxonomydb_query.PLS.bak
blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
Changing sharpbang in blib/script/biblio.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/biblio.PLS.bak
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
Changing sharpbang in blib/script/remote_blast.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/remote_blast.PLS.bak
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
Changing sharpbang in blib/script/seqretsplit.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/seqretsplit.PLS.bak
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Changing sharpbang in blib/script/genbank2gff3.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/genbank2gff3.PLS.bak
blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
Changing sharpbang in blib/script/search2table.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/search2table.PLS.bak
blib/script/search2table.PLS -> blib/script/bp_search2table.pl
Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
Changing sharpbang in blib/script/search2BSML.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/search2BSML.PLS.bak
blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
Changing sharpbang in blib/script/translate_seq.PLS to /home/fly1600/ap1600/bin/perl-static
Deleting blib/script/translate_seq.PLS.bak
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
t/Align/AlignStats.t ......................... 
1..43
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Align::AlignI
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - The object isa Bio::Align::AlignI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::Matrix::PhylipDist
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeqI
ok 43
ok
t/Align/AlignUtil.t .......................... 
1..33
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok
t/Align/SimpleAlign.t ........................ 
1..179
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - The object isa Bio::AlignIO
ok 7 - pfam input test
ok 8 - match_line
ok 9 - The object isa Bio::Align::AlignI
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - num_gaps
ok 21 - each_alphabetically
ok 22 - column_from_residue_number
ok 23 - display_name get/set
ok 24 - display_name get
ok 25 - consensus_string
ok 26 - consensus_string
ok 27 - consensus_string
ok 28
ok 29 - each_seq_with_id
ok 30 - is_flush
ok 31 - id get/set
ok 32 - length
ok 33 - num_residues
ok 34 - num_sequences
ok 35 - overall_percentage_identity
ok 36 - overall_percentage_identity
ok 37 - overall_percentage_identity
ok 38 - overall_percentage_identity
ok 39 - average_percentage_identity
ok 40
ok 41 - set_displayname_count
ok 42
ok 43 - set_displayname_flat
ok 44
ok 45 - set_displayname_normal
ok 46
ok 47
ok 48 - uppercase, map_chars
ok 49 - match_line
ok 50 - remove_seqs
ok 51 - remove_seqs
ok 52 - add_seq
ok 53 - add_seq
ok 54 - get_seq_by_pos
ok 55 - get_seq_by_pos
ok 56
ok 57
ok 58
ok 59 - purge
ok 60 - purge
ok 61 - IO::String consensus_iupac
ok 62 - IO::String write_aln normal
ok 63 - IO::String write_aln slice
ok 64 - IO::String write_aln slice
ok 65 - IO::String write_aln slice
ok 66 - IO::String write_aln slice
ok 67 - IO::String write_aln slice
ok 68
ok 69 - remove_columns by position
ok 70 - remove_columns by position (wrong order)
ok 71 - cigar_line
ok 72 - cigar_line
ok 73 - cigar_line
ok 74 - cigar_line
ok 75 - sort_alphabetically - before
ok 76
ok 77 - sort_alphabetically - after
ok 78 - remove_gaps
ok 79 - remove_gaps all_gaps_only
ok 80 - set_new_reference
ok 81 - set_new_reference
ok 82 - uniq_seq
ok 83 - bug 2099
ok 84 - bug 2099
ok 85 - bug 2793
ok 86 - bug 2793
ok 87 - bug 2793
ok 88 - bug 2793
ok 89 - Bad sequence, bad!
ok 90 - added 3 seqs
ok 91 - first 2 features added
ok 92 - 3rd feature added
not ok 93 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 1.  
# Overriding value [0] with value 1 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 94 - slice 1 len
ok 95 - correct masked seq
ok 96 - correct masked seq
ok 97 - correct masked seq
not ok 98 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 99 - slice 2 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 104 - slice 3 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842
#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.  
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 109 - slice 4 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113 - initial display id ok
ok 114 - safe display id ok
ok 115 - restored display id ok
ok 116 - sort by list ok
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - BIC:GGATCCATT[C/C]CTACT
ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 126 - BIC:GGATCCATT[C/G]CTACT
ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 129 - BIC:GGATCCATT[C/G]CTACT
ok 130 - BIC:GGATCCATT{C.C}CTACT
ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 133 - BIC:GGATCCATT{C.G}CTACT
ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 136 - BIC:GGATCCATT{C.G}CTACT
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174 - The object isa Bio::SimpleAlign
ok 175 - consensus string looks ok
ok 176 - looks like correct unmasked alignment (from clustalw)
ok 177 - looks like correct masked alignment (from clustalw)
ok 178
ok 179 - align after looks ok
ok
t/Align/TreeBuild.t .......................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign
ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI
ok 9 - Tree object gotten back isa Bio::Tree::TreeI
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
t/Align/Utilities.t .......................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/AlignIO/AlignIO.t .......................... 
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : metafasta
ok 3 - input filehandle method test : po
ok 4 - input filehandle method test : nexus
ok 5 - input filehandle method test : clustalw
ok 6 - input filehandle method test : prodom
ok 7 - input filehandle method test : fasta
ok 8 - input filehandle method test : arp
ok 9 - input filehandle method test : xmfa
ok 10 - input filehandle method test : mase
ok 11 - input filehandle method test : psi
ok 12 - input filehandle method test : phylip
ok 13 - input filehandle method test : pfam
ok 14 - input filehandle method test : selex
ok 15 - input filehandle method test : stockholm
ok 16 - input filehandle method test : msf
ok 17 - filehandle output test : metafasta
ok 18 - filehandle output test : po
ok 19 - filehandle output test : nexus
ok 20 - filehandle output test : clustalw
ok 21 - filehandle output test : fasta
ok 22 - filehandle output test : xmfa
ok 23 - filehandle output test : psi
ok 24 - filehandle output test : phylip
ok 25 - filehandle output test : pfam
ok 26 - filehandle output test : selex
ok 27 - filehandle output test : stockholm
ok 28 - filehandle output test : msf
ok
t/AlignIO/arp.t .............................. 
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4 - ARP get_nse()
ok 5
ok 6 - ARP num_sequences()
ok 7 - ARP id()
ok 8 - ARP description()
ok 9 - The object isa Bio::AnnotationCollectionI
ok 10 - The object isa Bio::AnnotationI
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::AlignIO
ok 16 - The object isa Bio::Align::AlignI
ok 17 - ARP get_nse()
ok 18 - ARP num_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - The object isa Bio::AnnotationCollectionI
ok 22 - The object isa Bio::AnnotationI
ok 23
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Align::AlignI
ok 28 - ARP get_nse()
ok 29 - ARP num_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - The object isa Bio::AnnotationCollectionI
ok 33 - The object isa Bio::AnnotationI
ok 34
ok 35
ok 36
ok 37
ok 38 - The object isa Bio::Align::AlignI
ok 39 - ARP get_nse()
ok 40 - ARP num_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - The object isa Bio::AnnotationCollectionI
ok 44 - The object isa Bio::AnnotationI
ok 45
ok 46
ok 47
ok 48
ok
t/AlignIO/bl2seq.t ........................... 
1..3
ok 1 - use Bio::AlignIO::bl2seq;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - BLAST bl2seq format test
ok
t/AlignIO/clustalw.t ......................... 
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - The object isa Bio::Align::AlignI
ok 6 - clustalw (.aln) input test
ok
t/AlignIO/emboss.t ........................... 
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Align::AlignI
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Align::AlignI
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Align::AlignI
ok 19
ok 20
ok 21 - The object isa Bio::Align::AlignI
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Align::AlignI
ok 33
ok 34
ok 35
ok 36
ok 37
ok
t/AlignIO/fasta.t ............................ 
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for end
ok 7 - fasta input test for description
ok 8 - fasta output test
ok 9 - filehandle input test  
ok 10 - filehandle output test
ok
t/AlignIO/largemultifasta.t .................. 
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for description
ok 7 - fasta output test
ok
t/AlignIO/maf.t .............................. 
1..11
ok 1 - use Bio::AlignIO::maf;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - maf input test
ok 4
ok 5 - The object isa Bio::Align::AlignI
ok 6 - maf input test
ok 7
ok 8 - maf input test
ok 9
ok 10 - maf input test
ok 11
ok
t/AlignIO/mase.t ............................. 
1..3
ok 1 - use Bio::AlignIO::mase;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - mase input test 
ok
t/AlignIO/mega.t ............................. 
1..6
ok 1 - use Bio::AlignIO::mega;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6 - mega output test
ok
t/AlignIO/meme.t ............................. 
1..14
ok 1 - use Bio::AlignIO::meme;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/AlignIO/metafasta.t ........................ 
1..4
ok 1 - use Bio::AlignIO::metafasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - consensus_string on metafasta
ok 4 - symbol_chars() using metafasta
ok
t/AlignIO/msf.t .............................. 
1..4
ok 1 - use Bio::AlignIO::msf;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - msf input test
ok 4 - msf output test
ok
t/AlignIO/nexus.t ............................ 
1..43
ok 1 - use Bio::AlignIO::nexus;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - nexus output test
ok 6 - The object isa Bio::AlignIO
ok 7 - The object isa Bio::Align::AlignI
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10 - The object isa Bio::AlignIO
ok 11 - The object isa Bio::Align::AlignI
ok 12 - The object isa Bio::AlignIO
ok 13 - The object isa Bio::Align::AlignI
ok 14 - The object isa Bio::AlignIO
ok 15 - The object isa Bio::Align::AlignI
ok 16 - The object isa Bio::AlignIO
ok 17 - The object isa Bio::Align::AlignI
ok 18 - The object isa Bio::AlignIO
ok 19 - The object isa Bio::Align::AlignI
ok 20 - The object isa Bio::AlignIO
ok 21 - The object isa Bio::Align::AlignI
ok 22 - The object isa Bio::AlignIO
ok 23 - The object isa Bio::Align::AlignI
ok 24 - The object isa Bio::AlignIO
ok 25 - The object isa Bio::Align::AlignI
ok 26 - The object isa Bio::AlignIO
ok 27 - The object isa Bio::Align::AlignI
ok 28 - The object isa Bio::AlignIO
ok 29 - The object isa Bio::Align::AlignI
ok 30 - The object isa Bio::AlignIO
ok 31 - The object isa Bio::Align::AlignI
ok 32 - The object isa Bio::AlignIO
ok 33 - The object isa Bio::Align::AlignI
ok 34 - The object isa Bio::AlignIO
ok 35 - The object isa Bio::Align::AlignI
ok 36 - The object isa Bio::AlignIO
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::AlignIO
ok 39 - The object isa Bio::Align::AlignI
ok 40 - The object isa Bio::AlignIO
ok 41 - The object isa Bio::Align::AlignI
ok 42 - The object isa Bio::AlignIO
ok 43 - The object isa Bio::Align::AlignI
ok
t/AlignIO/pfam.t ............................. 
1..5
ok 1 - use Bio::AlignIO::pfam;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 -  pfam output test
ok
make: *** [test] Terminated

Timeout (max run time is 300s)
/home/fly1600/ap1600/bin/perl-static killed by signal 15.