Setting PATH to /opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/ccs/bin:/usr/bin:/usr/sbin Start 2009-10-01T01:27:00 ActivePerl-1003 CPAN-1.9402 Going to read '/export/home/fly1064/var/cpan/Metadata' Database was generated on Wed, 30 Sep 2009 10:27:06 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 Will not use Archive::Tar, need 1.00 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 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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 >>> /export/home/fly1064/bin/perl Makefile.PL # running Build.PL /export/home/fly1064/bin/perl Build.PL Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: DB_File is not installed (I think I'm being run by CPAN/CPANPLUS, so will rely on it to handle prerequisite installation) I'll get CPAN to prepend the installation of this Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite List::MoreUtils is not installed (wanted for Back- or reverse-translation of sequences, used by Bio::Tools::SeqPattern and Bio::Tools::SeqPattern::BackTranslate) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation - DBD::mysql is not installed - DB_File is not installed - DBD::Pg is not installed Checking features: Network...................enabled BioDBSeqFeature_mysql.....disabled BioDBGFF..................enabled BioDBSeqFeature_BDB.......disabled BioDBSeqFeature_SQLite....enabled BioDBSeqFeature_Pg........disabled 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] - will not run internet-requiring tests Creating new 'Build' script for 'BioPerl' version '1.006001' ---- Unsatisfied dependencies detected during ---- ---- CJFIELDS/BioPerl-1.6.1.tar.gz ---- DB_File [requires] Running make test Delayed until after prerequisites Running test for module 'DB_File' ______________________ D i s t r o P r e f s ______________________ DB_File.yml[0] Running make for P/PM/PMQS/DB_File-1.820.tar.gz Disabled via prefs file '/export/home/fly1064/etc/distroprefs/DB_File.yml' doc 0 PMQS/DB_File-1.820.tar.gz [disabled] -- NA Disabled via prefs file '/export/home/fly1064/etc/distroprefs/DB_File.yml' doc 0 Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz Has already been unwrapped into directory /export/home/fly1064/var/cpan/build/BioPerl-1.6.1-EpZlV0 CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.1.tar.gz' failed when processing 'PMQS/DB_File-1.820.tar.gz' with 'unwrapped => NO Disabled via prefs file '/export/home/fly1064/etc/distroprefs/DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> make /export/home/fly1064/bin/perl Build --makefile_env_macros 1 Copying Bio/PopGen/MarkerI.pm -> blib/lib/Bio/PopGen/MarkerI.pm Copying Bio/Matrix/PSM/Psm.pm -> blib/lib/Bio/Matrix/PSM/Psm.pm Copying Bio/MolEvol/CodonModel.pm -> blib/lib/Bio/MolEvol/CodonModel.pm Copying Bio/Tools/Spidey/Exon.pm -> blib/lib/Bio/Tools/Spidey/Exon.pm Copying Bio/Matrix/PSM/ProtMatrix.pm -> blib/lib/Bio/Matrix/PSM/ProtMatrix.pm Copying Bio/WebAgent.pm -> blib/lib/Bio/WebAgent.pm Copying Bio/LiveSeq/ChainI.pm -> blib/lib/Bio/LiveSeq/ChainI.pm Copying Bio/AlignIO/mega.pm -> blib/lib/Bio/AlignIO/mega.pm Copying Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm Copying Bio/LiveSeq/Mutation.pm -> blib/lib/Bio/LiveSeq/Mutation.pm Copying Bio/TreeIO/pag.pm -> blib/lib/Bio/TreeIO/pag.pm Copying Bio/Tools/HMMER/Set.pm -> blib/lib/Bio/Tools/HMMER/Set.pm Copying Bio/Map/PositionWithSequence.pm -> blib/lib/Bio/Map/PositionWithSequence.pm Copying Bio/SeqIO/chaos.pm -> blib/lib/Bio/SeqIO/chaos.pm Copying Bio/Factory/ObjectFactory.pm -> blib/lib/Bio/Factory/ObjectFactory.pm Copying Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm Copying Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm Copying Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm Copying Bio/SearchIO/megablast.pm -> blib/lib/Bio/SearchIO/megablast.pm Copying Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm Copying Bio/TreeIO.pm -> blib/lib/Bio/TreeIO.pm Copying Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm Copying Bio/Search/HSP/PSLHSP.pm -> blib/lib/Bio/Search/HSP/PSLHSP.pm Copying Bio/Cluster/UniGeneI.pm -> blib/lib/Bio/Cluster/UniGeneI.pm Copying Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm Copying Bio/Map/Physical.pm -> blib/lib/Bio/Map/Physical.pm Copying Bio/Tools/GuessSeqFormat.pm -> blib/lib/Bio/Tools/GuessSeqFormat.pm Copying Bio/Search/Result/HmmpfamResult.pm -> blib/lib/Bio/Search/Result/HmmpfamResult.pm Copying Bio/Biblio/PubmedBookArticle.pm -> blib/lib/Bio/Biblio/PubmedBookArticle.pm Copying Bio/Search/HSP/WABAHSP.pm -> blib/lib/Bio/Search/HSP/WABAHSP.pm Copying Bio/Align/Utilities.pm -> blib/lib/Bio/Align/Utilities.pm Copying Bio/Expression/ProbeI.pm -> blib/lib/Bio/Expression/ProbeI.pm Copying Bio/Tools/Run/ParametersI.pm -> blib/lib/Bio/Tools/Run/ParametersI.pm Copying Bio/DB/Flat.pm -> blib/lib/Bio/DB/Flat.pm Copying Bio/SeqFeature/Lite.pm -> blib/lib/Bio/SeqFeature/Lite.pm Copying Bio/DB/SwissProt.pm -> blib/lib/Bio/DB/SwissProt.pm Copying Bio/SearchIO/fasta.pm -> blib/lib/Bio/SearchIO/fasta.pm Copying Bio/Tools/EUtilities/Query/GlobalQuery.pm -> blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm Copying Bio/TreeIO/nexus.pm -> blib/lib/Bio/TreeIO/nexus.pm Copying Bio/Biblio/Provider.pm -> blib/lib/Bio/Biblio/Provider.pm Copying Bio/Coordinate/Graph.pm -> blib/lib/Bio/Coordinate/Graph.pm Copying Bio/Search/HSP/ModelHSP.pm -> blib/lib/Bio/Search/HSP/ModelHSP.pm Copying Bio/Tree/DistanceFactory.pm -> blib/lib/Bio/Tree/DistanceFactory.pm Copying Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm Copying Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm Copying Bio/LocationI.pm -> blib/lib/Bio/LocationI.pm Copying Bio/Root/RootI.pm -> blib/lib/Bio/Root/RootI.pm Copying Bio/Taxonomy.pm -> blib/lib/Bio/Taxonomy.pm Copying Bio/Matrix/PSM/PsmI.pm -> blib/lib/Bio/Matrix/PSM/PsmI.pm Copying Bio/TreeIO/TreeEventBuilder.pm -> blib/lib/Bio/TreeIO/TreeEventBuilder.pm Copying Bio/DBLinkContainerI.pm -> blib/lib/Bio/DBLinkContainerI.pm Copying Bio/Location/Fuzzy.pm -> blib/lib/Bio/Location/Fuzzy.pm Copying Bio/SeqIO.pm -> blib/lib/Bio/SeqIO.pm Copying Bio/FeatureIO/bed.pm -> blib/lib/Bio/FeatureIO/bed.pm Copying Bio/AnalysisI.pm -> blib/lib/Bio/AnalysisI.pm Copying Bio/LiveSeq/AARange.pm -> blib/lib/Bio/LiveSeq/AARange.pm Copying Bio/DB/Biblio/biofetch.pm -> blib/lib/Bio/DB/Biblio/biofetch.pm Copying Bio/Index/Swissprot.pm -> blib/lib/Bio/Index/Swissprot.pm Copying Bio/Annotation/OntologyTerm.pm -> blib/lib/Bio/Annotation/OntologyTerm.pm Copying Bio/Map/SimpleMap.pm -> blib/lib/Bio/Map/SimpleMap.pm Copying Bio/Coordinate/Result/Gap.pm -> blib/lib/Bio/Coordinate/Result/Gap.pm Copying Bio/Tools/TandemRepeatsFinder.pm -> blib/lib/Bio/Tools/TandemRepeatsFinder.pm Copying Bio/Seq/Meta/Array.pm -> blib/lib/Bio/Seq/Meta/Array.pm Copying Bio/Tools/Run/RemoteBlast.pm -> blib/lib/Bio/Tools/Run/RemoteBlast.pm Copying Bio/FeatureIO.pm -> blib/lib/Bio/FeatureIO.pm Copying Bio/DB/BiblioI.pm -> blib/lib/Bio/DB/BiblioI.pm Copying Bio/MapIO.pm -> blib/lib/Bio/MapIO.pm Copying Bio/Map/Clone.pm -> blib/lib/Bio/Map/Clone.pm Copying Bio/SearchIO/Writer/HSPTableWriter.pm -> blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm Copying Bio/SearchIO/blasttable.pm -> blib/lib/Bio/SearchIO/blasttable.pm Copying Bio/Expression/DataSet.pm -> blib/lib/Bio/Expression/DataSet.pm Copying Bio/SeqFeature/Collection.pm -> blib/lib/Bio/SeqFeature/Collection.pm Copying Bio/DB/Expression/geo.pm -> blib/lib/Bio/DB/Expression/geo.pm Copying Bio/Tree/TreeI.pm -> blib/lib/Bio/Tree/TreeI.pm Copying Bio/Index/BlastTable.pm -> blib/lib/Bio/Index/BlastTable.pm Copying Bio/Map/MappableI.pm -> blib/lib/Bio/Map/MappableI.pm Copying Bio/Seq/BaseSeqProcessor.pm -> blib/lib/Bio/Seq/BaseSeqProcessor.pm Copying Bio/PullParserI.pm -> blib/lib/Bio/PullParserI.pm Copying Bio/SeqIO/fastq.pm -> blib/lib/Bio/SeqIO/fastq.pm Copying Bio/LiveSeq/SeqI.pm -> blib/lib/Bio/LiveSeq/SeqI.pm Copying Bio/Restriction/IO/prototype.pm -> blib/lib/Bio/Restriction/IO/prototype.pm Copying Bio/Tools/Analysis/Protein/ELM.pm -> blib/lib/Bio/Tools/Analysis/Protein/ELM.pm Copying Bio/Phenotype/Phenotype.pm -> blib/lib/Bio/Phenotype/Phenotype.pm Copying Bio/Seq/TraceI.pm -> blib/lib/Bio/Seq/TraceI.pm Copying Bio/Seq/PrimaryQual.pm -> blib/lib/Bio/Seq/PrimaryQual.pm Copying Bio/DB/Failover.pm -> blib/lib/Bio/DB/Failover.pm Copying Bio/Map/CytoMap.pm -> blib/lib/Bio/Map/CytoMap.pm Copying Bio/Variation/Allele.pm -> blib/lib/Bio/Variation/Allele.pm Copying Bio/LiveSeq/IO/Loader.pm -> blib/lib/Bio/LiveSeq/IO/Loader.pm Copying Bio/Search/Hit/PsiBlastHit.pm -> blib/lib/Bio/Search/Hit/PsiBlastHit.pm Copying Bio/LiveSeq/Repeat_Unit.pm -> blib/lib/Bio/LiveSeq/Repeat_Unit.pm Copying Bio/Restriction/Enzyme/MultiCut.pm -> blib/lib/Bio/Restriction/Enzyme/MultiCut.pm Copying Bio/DB/GFF/Adaptor/memory.pm -> blib/lib/Bio/DB/GFF/Adaptor/memory.pm Copying Bio/DB/UpdateableSeqI.pm -> blib/lib/Bio/DB/UpdateableSeqI.pm Copying Bio/DB/SeqFeature/Store/DBI/Pg.pm -> blib/lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm Copying Bio/Annotation/Target.pm -> blib/lib/Bio/Annotation/Target.pm Copying Bio/Restriction/IO/base.pm -> blib/lib/Bio/Restriction/IO/base.pm Copying Bio/DB/RefSeq.pm -> blib/lib/Bio/DB/RefSeq.pm Copying Bio/DB/GFF/Adaptor/memory/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/memory/iterator.pm Copying Bio/Tools/RepeatMasker.pm -> blib/lib/Bio/Tools/RepeatMasker.pm Copying Bio/AlignIO/xmfa.pm -> blib/lib/Bio/AlignIO/xmfa.pm Copying Bio/FeatureIO/vecscreen_simple.pm -> blib/lib/Bio/FeatureIO/vecscreen_simple.pm Copying Bio/Coordinate/Result/Match.pm -> blib/lib/Bio/Coordinate/Result/Match.pm Copying Bio/Search/Result/HMMERResult.pm -> blib/lib/Bio/Search/Result/HMMERResult.pm Copying Bio/SearchIO/wise.pm -> blib/lib/Bio/SearchIO/wise.pm Copying Bio/Seq/PrimedSeq.pm -> blib/lib/Bio/Seq/PrimedSeq.pm Copying Bio/Tools/RNAMotif.pm -> blib/lib/Bio/Tools/RNAMotif.pm Copying Bio/Structure/Chain.pm -> blib/lib/Bio/Structure/Chain.pm Copying Bio/DB/TFBS.pm -> blib/lib/Bio/DB/TFBS.pm Copying Bio/AlignIO/prodom.pm -> blib/lib/Bio/AlignIO/prodom.pm Copying Bio/Assembly/ContigAnalysis.pm -> blib/lib/Bio/Assembly/ContigAnalysis.pm Copying Bio/Root/Test.pm -> blib/lib/Bio/Root/Test.pm Copying Bio/Coordinate/ExtrapolatingPair.pm -> blib/lib/Bio/Coordinate/ExtrapolatingPair.pm Copying Bio/Ontology/DocumentRegistry.pm -> blib/lib/Bio/Ontology/DocumentRegistry.pm Copying Bio/SimpleAnalysisI.pm -> blib/lib/Bio/SimpleAnalysisI.pm Copying Bio/IdCollectionI.pm -> blib/lib/Bio/IdCollectionI.pm Copying Bio/Tools/Gel.pm -> blib/lib/Bio/Tools/Gel.pm Copying Bio/Tree/AlleleNode.pm -> blib/lib/Bio/Tree/AlleleNode.pm Copying Bio/DB/NCBIHelper.pm -> blib/lib/Bio/DB/NCBIHelper.pm Copying Bio/Biblio/BiblioBase.pm -> blib/lib/Bio/Biblio/BiblioBase.pm Copying Bio/Biblio/IO.pm -> blib/lib/Bio/Biblio/IO.pm Copying Bio/Root/Build.pm -> blib/lib/Bio/Root/Build.pm Copying Bio/Map/FPCMarker.pm -> blib/lib/Bio/Map/FPCMarker.pm Copying Bio/DB/GFF/Feature.pm -> blib/lib/Bio/DB/GFF/Feature.pm Copying Bio/Phenotype/OMIM/MiniMIMentry.pm -> blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm Copying Bio/UpdateableSeqI.pm -> blib/lib/Bio/UpdateableSeqI.pm Copying Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm Copying Bio/Event/EventHandlerI.pm -> blib/lib/Bio/Event/EventHandlerI.pm Copying Bio/Biblio/Thesis.pm -> blib/lib/Bio/Biblio/Thesis.pm Copying Bio/DB/Fasta.pm -> blib/lib/Bio/DB/Fasta.pm Copying Bio/SeqIO/table.pm -> blib/lib/Bio/SeqIO/table.pm Copying Bio/Tools/EUtilities/Summary.pm -> blib/lib/Bio/Tools/EUtilities/Summary.pm Copying Bio/TreeIO/lintree.pm -> blib/lib/Bio/TreeIO/lintree.pm Copying Bio/Biblio.pm -> blib/lib/Bio/Biblio.pm Copying Bio/Phenotype/OMIM/OMIMparser.pm -> blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm Copying Bio/DB/GFF/Adaptor/dbi/pg_fts.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm Copying Bio/Restriction/Enzyme.pm -> blib/lib/Bio/Restriction/Enzyme.pm Copying Bio/Matrix/PSM/InstanceSite.pm -> blib/lib/Bio/Matrix/PSM/InstanceSite.pm Copying Bio/SeqIO/game/seqHandler.pm -> blib/lib/Bio/SeqIO/game/seqHandler.pm Copying Bio/Assembly/Tools/ContigSpectrum.pm -> blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm Copying Bio/Tree/TreeFunctionsI.pm -> blib/lib/Bio/Tree/TreeFunctionsI.pm Copying Bio/Matrix/MatrixI.pm -> blib/lib/Bio/Matrix/MatrixI.pm Copying Bio/SeqIO/largefasta.pm -> blib/lib/Bio/SeqIO/largefasta.pm Copying Bio/Annotation/SimpleValue.pm -> blib/lib/Bio/Annotation/SimpleValue.pm Copying Bio/AlignIO/emboss.pm -> blib/lib/Bio/AlignIO/emboss.pm Copying Bio/Align/AlignI.pm -> blib/lib/Bio/Align/AlignI.pm Copying Bio/Search/Result/BlastPullResult.pm -> blib/lib/Bio/Search/Result/BlastPullResult.pm Copying Bio/Tools/EUtilities/Cookie.pm -> blib/lib/Bio/Tools/EUtilities/Cookie.pm Copying Bio/DB/Query/WebQuery.pm -> blib/lib/Bio/DB/Query/WebQuery.pm Copying Bio/Ontology/OntologyI.pm -> blib/lib/Bio/Ontology/OntologyI.pm Copying Bio/SearchIO/hmmer.pm -> blib/lib/Bio/SearchIO/hmmer.pm Copying Bio/SeqIO/ctf.pm -> blib/lib/Bio/SeqIO/ctf.pm Copying Bio/Tools/SeqPattern.pm -> blib/lib/Bio/Tools/SeqPattern.pm Copying Bio/DB/GFF/Aggregator/gene.pm -> blib/lib/Bio/DB/GFF/Aggregator/gene.pm Copying Bio/DB/SeqFeature/Store/bdb.pm -> blib/lib/Bio/DB/SeqFeature/Store/bdb.pm Copying Bio/SearchIO/psl.pm -> blib/lib/Bio/SearchIO/psl.pm Copying Bio/LiveSeq/DNA.pm -> blib/lib/Bio/LiveSeq/DNA.pm Copying Bio/Map/EntityI.pm -> blib/lib/Bio/Map/EntityI.pm Copying Bio/Index/AbstractSeq.pm -> blib/lib/Bio/Index/AbstractSeq.pm Copying Bio/DB/SeqFeature/NormalizedFeatureI.pm -> blib/lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm Copying Bio/AlignIO.pm -> blib/lib/Bio/AlignIO.pm Copying Bio/Tree/NodeI.pm -> blib/lib/Bio/Tree/NodeI.pm Copying Bio/SeqFeature/Gene/Exon.pm -> blib/lib/Bio/SeqFeature/Gene/Exon.pm Copying Bio/Tools/Prints.pm -> blib/lib/Bio/Tools/Prints.pm Copying Bio/Matrix/PSM/IO.pm -> blib/lib/Bio/Matrix/PSM/IO.pm Copying Bio/TreeIO/svggraph.pm -> blib/lib/Bio/TreeIO/svggraph.pm Copying Bio/Taxonomy/Tree.pm -> blib/lib/Bio/Taxonomy/Tree.pm Copying Bio/Ontology/RelationshipType.pm -> blib/lib/Bio/Ontology/RelationshipType.pm Copying Bio/Cluster/UniGene.pm -> blib/lib/Bio/Cluster/UniGene.pm Copying Bio/SeqIO/swissdriver.pm -> blib/lib/Bio/SeqIO/swissdriver.pm Copying Bio/CodonUsage/Table.pm -> blib/lib/Bio/CodonUsage/Table.pm Copying Bio/DB/ReferenceI.pm -> blib/lib/Bio/DB/ReferenceI.pm Copying Bio/SeqFeature/Generic.pm -> blib/lib/Bio/SeqFeature/Generic.pm Copying Bio/PopGen/PopulationI.pm -> blib/lib/Bio/PopGen/PopulationI.pm Copying Bio/SeqFeature/Annotated.pm -> blib/lib/Bio/SeqFeature/Annotated.pm Copying Bio/SearchIO/infernal.pm -> blib/lib/Bio/SearchIO/infernal.pm Copying Bio/SeqFeature/SimilarityPair.pm -> blib/lib/Bio/SeqFeature/SimilarityPair.pm Copying Bio/Search/Hit/BlastPullHit.pm -> blib/lib/Bio/Search/Hit/BlastPullHit.pm Copying Bio/SeqIO/raw.pm -> blib/lib/Bio/SeqIO/raw.pm Copying Bio/PopGen/TagHaplotype.pm -> blib/lib/Bio/PopGen/TagHaplotype.pm Copying Bio/Search/Processor.pm -> blib/lib/Bio/Search/Processor.pm Copying Bio/Tools/Analysis/Protein/GOR4.pm -> blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm Copying Bio/Seq.pm -> blib/lib/Bio/Seq.pm Copying Bio/Tools/EUtilities/Info.pm -> blib/lib/Bio/Tools/EUtilities/Info.pm Copying Bio/Biblio/Article.pm -> blib/lib/Bio/Biblio/Article.pm Copying Bio/Tools/HMMER/Results.pm -> blib/lib/Bio/Tools/HMMER/Results.pm Copying Bio/Biblio/Organisation.pm -> blib/lib/Bio/Biblio/Organisation.pm Copying Bio/Search/BlastUtils.pm -> blib/lib/Bio/Search/BlastUtils.pm Copying Bio/Tree/RandomFactory.pm -> blib/lib/Bio/Tree/RandomFactory.pm Copying Bio/Structure/IO/pdb.pm -> blib/lib/Bio/Structure/IO/pdb.pm Copying Bio/Tools/Phylo/PAML/Result.pm -> blib/lib/Bio/Tools/Phylo/PAML/Result.pm Copying Bio/DescribableI.pm -> blib/lib/Bio/DescribableI.pm Copying Bio/Structure/StructureI.pm -> blib/lib/Bio/Structure/StructureI.pm Copying Bio/Search/Result/ResultI.pm -> blib/lib/Bio/Search/Result/ResultI.pm Copying Bio/Symbol/AlphabetI.pm -> blib/lib/Bio/Symbol/AlphabetI.pm Copying Bio/RangeI.pm -> blib/lib/Bio/RangeI.pm Copying Bio/Matrix/PSM/InstanceSiteI.pm -> blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm Copying Bio/DB/SeqVersion/gi.pm -> blib/lib/Bio/DB/SeqVersion/gi.pm Copying Bio/Location/SplitLocationI.pm -> blib/lib/Bio/Location/SplitLocationI.pm Copying Bio/SeqFeature/Gene/NC_Feature.pm -> blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm Copying Bio/SeqIO/metafasta.pm -> blib/lib/Bio/SeqIO/metafasta.pm Copying Bio/Tools/Phylo/Gerp.pm -> blib/lib/Bio/Tools/Phylo/Gerp.pm Copying Bio/SeqEvolution/EvolutionI.pm -> blib/lib/Bio/SeqEvolution/EvolutionI.pm Copying Bio/DB/HIV/HIVAnnotProcessor.pm -> blib/lib/Bio/DB/HIV/HIVAnnotProcessor.pm Copying Bio/OntologyIO.pm -> blib/lib/Bio/OntologyIO.pm Copying Bio/Ontology/RelationshipI.pm -> blib/lib/Bio/Ontology/RelationshipI.pm Copying Bio/Ontology/OBOterm.pm -> blib/lib/Bio/Ontology/OBOterm.pm Copying Bio/Search/HSP/PsiBlastHSP.pm -> blib/lib/Bio/Search/HSP/PsiBlastHSP.pm Copying Bio/SearchIO/rnamotif.pm -> blib/lib/Bio/SearchIO/rnamotif.pm Copying Bio/Index/GenBank.pm -> blib/lib/Bio/Index/GenBank.pm Copying Bio/Tools/EUtilities/EUtilDataI.pm -> blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm Copying Bio/Restriction/IO/itype2.pm -> blib/lib/Bio/Restriction/IO/itype2.pm Copying Bio/PhyloNetwork/muVector.pm -> blib/lib/Bio/PhyloNetwork/muVector.pm Copying Bio/Biblio/MedlineJournalArticle.pm -> blib/lib/Bio/Biblio/MedlineJournalArticle.pm Copying Bio/CodonUsage/IO.pm -> blib/lib/Bio/CodonUsage/IO.pm Copying Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm -> blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm Copying Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm Copying Bio/Expression/Platform.pm -> blib/lib/Bio/Expression/Platform.pm Copying Bio/Taxonomy/Node.pm -> blib/lib/Bio/Taxonomy/Node.pm Copying Bio/Variation/IO/xml.pm -> blib/lib/Bio/Variation/IO/xml.pm Copying Bio/DB/GFF/Aggregator/alignment.pm -> blib/lib/Bio/DB/GFF/Aggregator/alignment.pm Copying Bio/Matrix/Generic.pm -> blib/lib/Bio/Matrix/Generic.pm Copying Bio/FeatureHolderI.pm -> blib/lib/Bio/FeatureHolderI.pm Copying Bio/Tools/dpAlign.pm -> blib/lib/Bio/Tools/dpAlign.pm Copying Bio/Search/Tiling/MapTileUtils.pm -> blib/lib/Bio/Search/Tiling/MapTileUtils.pm Copying Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm Copying Bio/SeqFeature/Gene/TranscriptI.pm -> blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm Copying Bio/Restriction/IO.pm -> blib/lib/Bio/Restriction/IO.pm Copying Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm Copying Bio/Cluster/FamilyI.pm -> blib/lib/Bio/Cluster/FamilyI.pm Copying Bio/DB/RandomAccessI.pm -> blib/lib/Bio/DB/RandomAccessI.pm Copying Bio/SeqIO/qual.pm -> blib/lib/Bio/SeqIO/qual.pm Copying Bio/SeqIO/kegg.pm -> blib/lib/Bio/SeqIO/kegg.pm Copying Bio/SearchIO/axt.pm -> blib/lib/Bio/SearchIO/axt.pm Copying Bio/SeqIO/pln.pm -> blib/lib/Bio/SeqIO/pln.pm Copying Bio/Ontology/TermI.pm -> blib/lib/Bio/Ontology/TermI.pm Copying Bio/AnalysisResultI.pm -> blib/lib/Bio/AnalysisResultI.pm Copying Bio/Search/Result/BlastResult.pm -> blib/lib/Bio/Search/Result/BlastResult.pm Copying Bio/Map/PositionHandlerI.pm -> blib/lib/Bio/Map/PositionHandlerI.pm Copying Bio/PopGen/Simulation/Coalescent.pm -> blib/lib/Bio/PopGen/Simulation/Coalescent.pm Copying Bio/Assembly/ScaffoldI.pm -> blib/lib/Bio/Assembly/ScaffoldI.pm Copying Bio/Annotation/AnnotationFactory.pm -> blib/lib/Bio/Annotation/AnnotationFactory.pm Copying Bio/Taxon.pm -> blib/lib/Bio/Taxon.pm Copying Bio/SeqIO/locuslink.pm -> blib/lib/Bio/SeqIO/locuslink.pm Copying Bio/Phenotype/MeSH/Twig.pm -> blib/lib/Bio/Phenotype/MeSH/Twig.pm Copying Bio/Tools/Sim4/Exon.pm -> blib/lib/Bio/Tools/Sim4/Exon.pm Copying Bio/Structure/Atom.pm -> blib/lib/Bio/Structure/Atom.pm Copying Bio/PopGen/Genotype.pm -> blib/lib/Bio/PopGen/Genotype.pm Copying Bio/Tools/pICalculator.pm -> blib/lib/Bio/Tools/pICalculator.pm Copying Bio/Tools/Phylo/Molphy/Result.pm -> blib/lib/Bio/Tools/Phylo/Molphy/Result.pm Copying Bio/DB/GFF/Aggregator/match.pm -> blib/lib/Bio/DB/GFF/Aggregator/match.pm Copying Bio/DB/GFF/Aggregator/ucsc_softberry.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm Copying Bio/Map/PositionI.pm -> blib/lib/Bio/Map/PositionI.pm Copying Bio/Biblio/BookArticle.pm -> blib/lib/Bio/Biblio/BookArticle.pm Copying Bio/Search/Tiling/TilingI.pm -> blib/lib/Bio/Search/Tiling/TilingI.pm Copying Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm Copying Bio/Restriction/IO/withrefm.pm -> blib/lib/Bio/Restriction/IO/withrefm.pm Copying Bio/DB/Flat/BDB/swiss.pm -> blib/lib/Bio/DB/Flat/BDB/swiss.pm Copying Bio/Tools/SeqStats.pm -> blib/lib/Bio/Tools/SeqStats.pm Copying Bio/LiveSeq/Transcript.pm -> blib/lib/Bio/LiveSeq/Transcript.pm Copying Bio/Ontology/OntologyEngineI.pm -> blib/lib/Bio/Ontology/OntologyEngineI.pm Copying Bio/Ontology/Term.pm -> blib/lib/Bio/Ontology/Term.pm Copying Bio/Search/HSP/FastaHSP.pm -> blib/lib/Bio/Search/HSP/FastaHSP.pm Copying Bio/Tools/Primer/Assessor/Base.pm -> blib/lib/Bio/Tools/Primer/Assessor/Base.pm Copying Bio/Tools/Match.pm -> blib/lib/Bio/Tools/Match.pm Copying Bio/DB/Taxonomy/list.pm -> blib/lib/Bio/DB/Taxonomy/list.pm Copying Bio/DB/Flat/BDB.pm -> blib/lib/Bio/DB/Flat/BDB.pm Copying Bio/AlignIO/mase.pm -> blib/lib/Bio/AlignIO/mase.pm Copying Bio/SeqFeature/Gene/Transcript.pm -> blib/lib/Bio/SeqFeature/Gene/Transcript.pm Copying Bio/SeqFeature/Tools/TypeMapper.pm -> blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm Copying Bio/SeqIO/scf.pm -> blib/lib/Bio/SeqIO/scf.pm Copying Bio/MapIO/mapmaker.pm -> blib/lib/Bio/MapIO/mapmaker.pm Copying Bio/Ontology/OntologyStore.pm -> blib/lib/Bio/Ontology/OntologyStore.pm Copying 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blib/lib/Bio/Tools/Blat.pm Copying Bio/FeatureIO/ptt.pm -> blib/lib/Bio/FeatureIO/ptt.pm Copying Bio/DB/SeqFeature/Store/memory.pm -> blib/lib/Bio/DB/SeqFeature/Store/memory.pm Copying Bio/Symbol/SymbolI.pm -> blib/lib/Bio/Symbol/SymbolI.pm Copying Bio/Tools/EUtilities/Query.pm -> blib/lib/Bio/Tools/EUtilities/Query.pm Copying Bio/Tools/EPCR.pm -> blib/lib/Bio/Tools/EPCR.pm Copying Bio/Location/NarrowestCoordPolicy.pm -> blib/lib/Bio/Location/NarrowestCoordPolicy.pm Copying Bio/Tools/pSW.pm -> blib/lib/Bio/Tools/pSW.pm Copying Bio/SeqIO/bsml_sax.pm -> blib/lib/Bio/SeqIO/bsml_sax.pm Copying Bio/SeqIO/gbdriver.pm -> blib/lib/Bio/SeqIO/gbdriver.pm Copying Bio/AnnotatableI.pm -> blib/lib/Bio/AnnotatableI.pm Copying Bio/Tools/EUtilities/Link/LinkSet.pm -> blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm Copying Bio/Biblio/Proceeding.pm -> blib/lib/Bio/Biblio/Proceeding.pm Copying Bio/Tools/Run/GenericParameters.pm -> blib/lib/Bio/Tools/Run/GenericParameters.pm Copying Bio/TreeIO/newick.pm -> blib/lib/Bio/TreeIO/newick.pm Copying Bio/Biblio/Book.pm -> blib/lib/Bio/Biblio/Book.pm Copying Bio/SeqFeature/Gene/GeneStructure.pm -> blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm Copying Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm Copying Bio/Tree/Statistics.pm -> blib/lib/Bio/Tree/Statistics.pm Copying Bio/Align/PairwiseStatistics.pm -> blib/lib/Bio/Align/PairwiseStatistics.pm Copying Bio/Assembly/IO.pm -> blib/lib/Bio/Assembly/IO.pm Copying Bio/SeqIO/tinyseq.pm -> blib/lib/Bio/SeqIO/tinyseq.pm Copying Bio/Ontology/TermFactory.pm -> blib/lib/Bio/Ontology/TermFactory.pm Copying Bio/Tools/SeqWords.pm -> blib/lib/Bio/Tools/SeqWords.pm Copying Bio/DB/GFF/Adaptor/dbi/oracleace.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm Copying Bio/Expression/FeatureI.pm -> blib/lib/Bio/Expression/FeatureI.pm Copying Bio/Map/OrderedPositionWithDistance.pm -> blib/lib/Bio/Map/OrderedPositionWithDistance.pm Copying Bio/DB/SeqFeature/Store/berkeleydb.pm -> blib/lib/Bio/DB/SeqFeature/Store/berkeleydb.pm Copying Bio/Matrix/PSM/ProtPsm.pm -> blib/lib/Bio/Matrix/PSM/ProtPsm.pm Copying Bio/Biblio/IO/pubmed2ref.pm -> blib/lib/Bio/Biblio/IO/pubmed2ref.pm Copying Bio/SeqIO/game.pm -> blib/lib/Bio/SeqIO/game.pm Copying Bio/Index/Abstract.pm -> blib/lib/Bio/Index/Abstract.pm Copying Bio/Search/Iteration/IterationI.pm -> blib/lib/Bio/Search/Iteration/IterationI.pm Copying Bio/SearchIO/blastxml.pm -> blib/lib/Bio/SearchIO/blastxml.pm Copying Bio/Tools/HMMER/Domain.pm -> blib/lib/Bio/Tools/HMMER/Domain.pm Copying Bio/DB/GFF/Adaptor/dbi/oracle.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm Copying Bio/PhyloNetwork/TreeFactoryX.pm -> blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm Copying Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm Copying Bio/Biblio/IO/medlinexml.pm -> blib/lib/Bio/Biblio/IO/medlinexml.pm Copying Bio/Coordinate/GeneMapper.pm -> blib/lib/Bio/Coordinate/GeneMapper.pm Copying Bio/SeqIO/flybase_chadoxml.pm -> blib/lib/Bio/SeqIO/flybase_chadoxml.pm Copying Bio/Location/FuzzyLocationI.pm -> blib/lib/Bio/Location/FuzzyLocationI.pm Copying Bio/DB/TFBS/transfac_pro.pm -> blib/lib/Bio/DB/TFBS/transfac_pro.pm Copying Bio/SeqIO/ace.pm -> blib/lib/Bio/SeqIO/ace.pm Copying Bio/Search/Hit/Fasta.pm -> blib/lib/Bio/Search/Hit/Fasta.pm Copying Bio/Root/Exception.pm -> blib/lib/Bio/Root/Exception.pm Copying Bio/Factory/TreeFactoryI.pm -> blib/lib/Bio/Factory/TreeFactoryI.pm Copying Bio/Expression/Contact.pm -> blib/lib/Bio/Expression/Contact.pm Copying Bio/SearchIO/cross_match.pm -> blib/lib/Bio/SearchIO/cross_match.pm Copying Bio/Assembly/IO/ace.pm -> blib/lib/Bio/Assembly/IO/ace.pm Copying Bio/Expression/Sample.pm -> blib/lib/Bio/Expression/Sample.pm Copying Bio/Map/RelativeI.pm -> blib/lib/Bio/Map/RelativeI.pm Copying Bio/DB/Biblio/soap.pm -> blib/lib/Bio/DB/Biblio/soap.pm Copying Bio/SeqIO/tab.pm -> blib/lib/Bio/SeqIO/tab.pm Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS 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 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 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 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 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 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 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 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 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 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 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 Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS 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 Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl Copying Bio/DB/HIV/lanl-schema.xml -> blib/lib/Bio/DB/HIV/lanl-schema.xml Writing config notes to blib/lib/Bio/ConfigData.pm Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 Manifying blib/script/bp_hivq.pl -> blib/bindoc/bp_hivq.pl.1 Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 Manifying blib/script/bp_einfo.pl -> blib/bindoc/bp_einfo.pl.1 Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 Manifying blib/script/bp_revtrans-motif.pl -> blib/bindoc/bp_revtrans-motif.pl.1 Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 Manifying blib/lib/Bio/SeqIO/interpro.pm -> blib/libdoc/Bio::SeqIO::interpro.3 Manifying blib/lib/Bio/Tools/SiRNA/Ruleset/tuschl.pm -> blib/libdoc/Bio::Tools::SiRNA::Ruleset::tuschl.3 Manifying blib/lib/Bio/Expression/FeatureGroup.pm -> blib/libdoc/Bio::Expression::FeatureGroup.3 Manifying blib/lib/Bio/OntologyIO/dagflat.pm -> blib/libdoc/Bio::OntologyIO::dagflat.3 Manifying blib/lib/Bio/Seq/SeqFactory.pm -> blib/libdoc/Bio::Seq::SeqFactory.3 Manifying blib/lib/Bio/Location/CoordinatePolicyI.pm -> blib/libdoc/Bio::Location::CoordinatePolicyI.3 Manifying blib/lib/Bio/Root/Storable.pm -> blib/libdoc/Bio::Root::Storable.3 Manifying blib/lib/Bio/Location/Atomic.pm -> blib/libdoc/Bio::Location::Atomic.3 Manifying blib/lib/Bio/SearchIO/SearchWriterI.pm -> blib/libdoc/Bio::SearchIO::SearchWriterI.3 Manifying blib/lib/Bio/FeatureIO.pm -> blib/libdoc/Bio::FeatureIO.3 Manifying blib/lib/Bio/Biblio/IO.pm -> blib/libdoc/Bio::Biblio::IO.3 Manifying blib/lib/Bio/Variation/RNAChange.pm -> blib/libdoc/Bio::Variation::RNAChange.3 Manifying blib/lib/Bio/Root/Exception.pm -> blib/libdoc/Bio::Root::Exception.3 Manifying blib/lib/Bio/Factory/LocationFactoryI.pm -> blib/libdoc/Bio::Factory::LocationFactoryI.3 Manifying blib/lib/Bio/Biblio/Ref.pm -> blib/libdoc/Bio::Biblio::Ref.3 Manifying blib/lib/Bio/Search/HSP/WABAHSP.pm -> blib/libdoc/Bio::Search::HSP::WABAHSP.3 Manifying blib/lib/Bio/SeqIO/embl.pm -> blib/libdoc/Bio::SeqIO::embl.3 Manifying blib/lib/Bio/Factory/DriverFactory.pm -> blib/libdoc/Bio::Factory::DriverFactory.3 Manifying blib/lib/Bio/Tools/Genemark.pm -> blib/libdoc/Bio::Tools::Genemark.3 Manifying blib/lib/Bio/Biblio/MedlineArticle.pm -> blib/libdoc/Bio::Biblio::MedlineArticle.3 Manifying blib/lib/Bio/LiveSeq/ChainI.pm -> blib/libdoc/Bio::LiveSeq::ChainI.3 Manifying blib/lib/Bio/Tools/PrositeScan.pm -> blib/libdoc/Bio::Tools::PrositeScan.3 Manifying blib/lib/Bio/LiveSeq/Intron.pm -> blib/libdoc/Bio::LiveSeq::Intron.3 Manifying blib/lib/Bio/Matrix/IO/scoring.pm -> blib/libdoc/Bio::Matrix::IO::scoring.3 Manifying blib/lib/Bio/Seq/LargeLocatableSeq.pm -> blib/libdoc/Bio::Seq::LargeLocatableSeq.3 Manifying blib/lib/Bio/AlignIO/msf.pm -> blib/libdoc/Bio::AlignIO::msf.3 Manifying blib/lib/Bio/Tools/Glimmer.pm -> blib/libdoc/Bio::Tools::Glimmer.3 Manifying blib/lib/Bio/SeqIO/flybase_chadoxml.pm -> blib/libdoc/Bio::SeqIO::flybase_chadoxml.3 Manifying blib/lib/Bio/Map/RelativeI.pm -> blib/libdoc/Bio::Map::RelativeI.3 Manifying blib/lib/Bio/Tools/Profile.pm -> blib/libdoc/Bio::Tools::Profile.3 Manifying blib/lib/Bio/LiveSeq/Mutator.pm -> blib/libdoc/Bio::LiveSeq::Mutator.3 Manifying blib/lib/Bio/Tools/Primer/Pair.pm -> blib/libdoc/Bio::Tools::Primer::Pair.3 Manifying blib/lib/Bio/Annotation/TypeManager.pm -> blib/libdoc/Bio::Annotation::TypeManager.3 Manifying blib/lib/Bio/Expression/ProbeI.pm -> blib/libdoc/Bio::Expression::ProbeI.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/alignment.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::alignment.3 Manifying blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -> blib/libdoc/Bio::SearchIO::IteratedSearchResultEventBuilder.3 Manifying blib/lib/Bio/Map/LinkagePosition.pm -> blib/libdoc/Bio::Map::LinkagePosition.3 Manifying blib/lib/Bio/Tools/Primer/Assessor/Base.pm -> blib/libdoc/Bio::Tools::Primer::Assessor::Base.3 Manifying blib/lib/Bio/ClusterIO/unigene.pm -> blib/libdoc/Bio::ClusterIO::unigene.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch_oracle.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/pg.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::pg.3 Manifying blib/lib/Bio/DB/GFF/Util/Binning.pm -> blib/libdoc/Bio::DB::GFF::Util::Binning.3 Manifying blib/lib/Bio/Index/Abstract.pm -> blib/libdoc/Bio::Index::Abstract.3 Manifying blib/lib/Bio/PopGen/GenotypeI.pm -> blib/libdoc/Bio::PopGen::GenotypeI.3 Manifying blib/lib/Bio/Cluster/ClusterFactory.pm -> blib/libdoc/Bio::Cluster::ClusterFactory.3 Manifying blib/lib/Bio/Tools/pSW.pm -> blib/libdoc/Bio::Tools::pSW.3 Manifying blib/lib/Bio/FeatureIO/interpro.pm -> blib/libdoc/Bio::FeatureIO::interpro.3 Manifying blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm -> blib/libdoc/Bio::SeqFeature::Gene::TranscriptI.3 Manifying blib/lib/Bio/TreeIO/tabtree.pm -> blib/libdoc/Bio::TreeIO::tabtree.3 Manifying blib/lib/Bio/DB/SeqFeature/Store.pm -> blib/libdoc/Bio::DB::SeqFeature::Store.3 Manifying blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm -> blib/libdoc/Bio::SeqFeature::Gene::NC_Feature.3 Manifying blib/lib/Bio/Biblio/Provider.pm -> blib/libdoc/Bio::Biblio::Provider.3 Manifying blib/lib/Bio/Phenotype/PhenotypeI.pm -> blib/libdoc/Bio::Phenotype::PhenotypeI.3 Manifying blib/lib/Bio/SeqIO/bsml_sax.pm -> blib/libdoc/Bio::SeqIO::bsml_sax.3 Manifying blib/lib/Bio/Map/OrderedPosition.pm -> blib/libdoc/Bio::Map::OrderedPosition.3 Manifying blib/lib/Bio/Search/BlastUtils.pm -> blib/libdoc/Bio::Search::BlastUtils.3 Manifying blib/lib/Bio/SearchIO/blastxml.pm -> blib/libdoc/Bio::SearchIO::blastxml.3 Manifying blib/lib/Bio/DB/Expression/geo.pm -> blib/libdoc/Bio::DB::Expression::geo.3 Manifying blib/lib/Bio/Tools/FootPrinter.pm -> blib/libdoc/Bio::Tools::FootPrinter.3 Manifying blib/lib/Bio/Coordinate/ResultI.pm -> blib/libdoc/Bio::Coordinate::ResultI.3 Manifying blib/lib/Bio/Factory/ApplicationFactoryI.pm -> blib/libdoc/Bio::Factory::ApplicationFactoryI.3 Manifying blib/lib/Bio/SeqIO/scf.pm -> blib/libdoc/Bio::SeqIO::scf.3 Manifying blib/lib/Bio/Tools/EUtilities/Info.pm -> blib/libdoc/Bio::Tools::EUtilities::Info.3 Manifying blib/lib/Bio/PopGen/PopStats.pm -> blib/libdoc/Bio::PopGen::PopStats.3 Manifying blib/lib/Bio/SeqEvolution/Factory.pm -> blib/libdoc/Bio::SeqEvolution::Factory.3 Manifying blib/lib/Bio/DB/Query/GenBank.pm -> blib/libdoc/Bio::DB::Query::GenBank.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::FeatureFileLoader.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_unigene.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::SQLite.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Domcut.3 Manifying blib/lib/Bio/SearchIO/blast.pm -> blib/libdoc/Bio::SearchIO::blast.3 Manifying blib/lib/Bio/Structure/Model.pm -> blib/libdoc/Bio::Structure::Model.3 Manifying blib/lib/Bio/Tools/Hmmpfam.pm -> blib/libdoc/Bio::Tools::Hmmpfam.3 Manifying blib/lib/Bio/CodonUsage/Table.pm -> blib/libdoc/Bio::CodonUsage::Table.3 Manifying blib/lib/Bio/Factory/SequenceStreamI.pm -> blib/libdoc/Bio::Factory::SequenceStreamI.3 Manifying blib/lib/Bio/LiveSeq/Prim_Transcript.pm -> blib/libdoc/Bio::LiveSeq::Prim_Transcript.3 Manifying blib/lib/Bio/MolEvol/CodonModel.pm -> blib/libdoc/Bio::MolEvol::CodonModel.3 Manifying blib/lib/Bio/Annotation/TagTree.pm -> blib/libdoc/Bio::Annotation::TagTree.3 Manifying blib/lib/Bio/DB/EMBL.pm -> blib/libdoc/Bio::DB::EMBL.3 Manifying blib/lib/Bio/Map/Microsatellite.pm -> blib/libdoc/Bio::Map::Microsatellite.3 Manifying blib/lib/Bio/Tools/Alignment/Trim.pm -> blib/libdoc/Bio::Tools::Alignment::Trim.3 Manifying blib/lib/Bio/Tools/Geneid.pm -> blib/libdoc/Bio::Tools::Geneid.3 Manifying blib/lib/Bio/Restriction/IO/prototype.pm -> blib/libdoc/Bio::Restriction::IO::prototype.3 Manifying blib/lib/Bio/Structure/Entry.pm -> blib/libdoc/Bio::Structure::Entry.3 Manifying blib/lib/Bio/Map/Contig.pm -> blib/libdoc/Bio::Map::Contig.3 Manifying blib/lib/Bio/Range.pm -> blib/libdoc/Bio::Range.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_refgene.3 Manifying blib/lib/Bio/Assembly/Contig.pm -> blib/libdoc/Bio::Assembly::Contig.3 Manifying blib/lib/Bio/Tools/AnalysisResult.pm -> blib/libdoc/Bio::Tools::AnalysisResult.3 Manifying blib/lib/Bio/IdentifiableI.pm -> blib/libdoc/Bio::IdentifiableI.3 Manifying blib/lib/Bio/Map/Mappable.pm -> blib/libdoc/Bio::Map::Mappable.3 Manifying blib/lib/Bio/Search/Tiling/MapTiling.pm -> blib/libdoc/Bio::Search::Tiling::MapTiling.3 Manifying blib/lib/Bio/Matrix/PSM/ProtPsm.pm -> blib/libdoc/Bio::Matrix::PSM::ProtPsm.3 Manifying blib/lib/Bio/Taxonomy/Taxon.pm -> blib/libdoc/Bio::Taxonomy::Taxon.3 Manifying blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeature.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/orf.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::orf.3 Manifying blib/lib/Bio/TreeIO/svggraph.pm -> blib/libdoc/Bio::TreeIO::svggraph.3 Manifying blib/lib/Bio/PopGen/IO/hapmap.pm -> blib/libdoc/Bio::PopGen::IO::hapmap.3 Manifying blib/lib/Bio/Restriction/IO/withrefm.pm -> blib/libdoc/Bio::Restriction::IO::withrefm.3 Manifying blib/lib/Bio/Tree/DistanceFactory.pm -> blib/libdoc/Bio::Tree::DistanceFactory.3 Manifying blib/lib/Bio/SeqFeature/Gene/Exon.pm -> blib/libdoc/Bio::SeqFeature::Gene::Exon.3 Manifying blib/lib/Bio/DB/Query/WebQuery.pm -> blib/libdoc/Bio::DB::Query::WebQuery.3 Manifying blib/lib/Bio/Search/Result/CrossMatchResult.pm -> blib/libdoc/Bio::Search::Result::CrossMatchResult.3 Manifying blib/lib/Bio/DB/Universal.pm -> blib/libdoc/Bio::DB::Universal.3 Manifying blib/lib/Bio/Tree/NodeI.pm -> blib/libdoc/Bio::Tree::NodeI.3 Manifying blib/lib/Bio/Tools/Phylo/Gerp.pm -> blib/libdoc/Bio::Tools::Phylo::Gerp.3 Manifying blib/lib/Bio/SeqIO/MultiFile.pm -> blib/libdoc/Bio::SeqIO::MultiFile.3 Manifying blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm -> blib/libdoc/Bio::Seq::SeqFastaSpeedFactory.3 Manifying blib/lib/Bio/Tools/EUtilities/Link.pm -> blib/libdoc/Bio::Tools::EUtilities::Link.3 Manifying blib/lib/Bio/Tools/Tmhmm.pm -> blib/libdoc/Bio::Tools::Tmhmm.3 Manifying blib/lib/Bio/Restriction/Enzyme/MultiSite.pm -> blib/libdoc/Bio::Restriction::Enzyme::MultiSite.3 Manifying blib/lib/Bio/Tools/EUtilities/Cookie.pm -> blib/libdoc/Bio::Tools::EUtilities::Cookie.3 Manifying blib/lib/Bio/OntologyIO/InterProParser.pm -> blib/libdoc/Bio::OntologyIO::InterProParser.3 Manifying blib/lib/Bio/SeqIO/chadoxml.pm -> blib/libdoc/Bio::SeqIO::chadoxml.3 Manifying blib/lib/Bio/Index/Qual.pm -> blib/libdoc/Bio::Index::Qual.3 Manifying blib/lib/Bio/Matrix/PSM/IO/masta.pm -> blib/libdoc/Bio::Matrix::PSM::IO::masta.3 Manifying blib/lib/Bio/Annotation/Reference.pm -> blib/libdoc/Bio::Annotation::Reference.3 Manifying blib/lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeatureI.3 Manifying blib/lib/Bio/Variation/IO.pm -> blib/libdoc/Bio::Variation::IO.3 Manifying blib/lib/Bio/SearchIO/XML/PsiBlastHandler.pm -> blib/libdoc/Bio::SearchIO::XML::PsiBlastHandler.3 Manifying blib/lib/Bio/Matrix/PSM/IO/meme.pm -> blib/libdoc/Bio::Matrix::PSM::IO::meme.3 Manifying blib/lib/Bio/Seq/MetaI.pm -> blib/libdoc/Bio::Seq::MetaI.3 Manifying blib/lib/Bio/TreeIO/pag.pm -> blib/libdoc/Bio::TreeIO::pag.3 Manifying blib/lib/Bio/LiveSeq/IO/Loader.pm -> blib/libdoc/Bio::LiveSeq::IO::Loader.3 Manifying blib/lib/Bio/AlignIO/arp.pm -> blib/libdoc/Bio::AlignIO::arp.3 Manifying blib/lib/Bio/Ontology/SimpleOntologyEngine.pm -> blib/libdoc/Bio::Ontology::SimpleOntologyEngine.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/NetPhos.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::NetPhos.3 Manifying blib/lib/Bio/Ontology/TermI.pm -> blib/libdoc/Bio::Ontology::TermI.3 Manifying blib/lib/Bio/SeqFeature/PositionProxy.pm -> blib/libdoc/Bio::SeqFeature::PositionProxy.3 Manifying blib/lib/Bio/SeqEvolution/DNAPoint.pm -> blib/libdoc/Bio::SeqEvolution::DNAPoint.3 Manifying blib/lib/Bio/SeqIO/ace.pm -> blib/libdoc/Bio::SeqIO::ace.3 Manifying blib/lib/Bio/Map/CytoPosition.pm -> blib/libdoc/Bio::Map::CytoPosition.3 Manifying blib/lib/Bio/Tools/ERPIN.pm -> blib/libdoc/Bio::Tools::ERPIN.3 Manifying blib/lib/Bio/Cluster/UniGene.pm -> blib/libdoc/Bio::Cluster::UniGene.3 Manifying blib/lib/Bio/DB/LocationI.pm -> blib/libdoc/Bio::DB::LocationI.3 Manifying blib/lib/Bio/SeqI.pm -> blib/libdoc/Bio::SeqI.3 Manifying blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm -> blib/libdoc/Bio::Tools::SeqPattern::Backtranslate.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/Iterator.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::Iterator.3 Manifying blib/lib/Bio/DB/SeqFeature.pm -> blib/libdoc/Bio::DB::SeqFeature.3 Manifying blib/lib/Bio/Search/Hit/GenericHit.pm -> blib/libdoc/Bio::Search::Hit::GenericHit.3 Manifying blib/lib/Bio/Tools/EUtilities/EUtilParameters.pm -> blib/libdoc/Bio::Tools::EUtilities::EUtilParameters.3 Manifying blib/lib/Bio/Matrix/PSM/IO/mast.pm -> blib/libdoc/Bio::Matrix::PSM::IO::mast.3 Manifying blib/lib/Bio/SearchIO/blasttable.pm -> blib/libdoc/Bio::SearchIO::blasttable.3 Manifying blib/lib/Bio/Tools/Genewise.pm -> blib/libdoc/Bio::Tools::Genewise.3 Manifying blib/lib/Bio/Tools/Primer3.pm -> blib/libdoc/Bio::Tools::Primer3.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb.3 Manifying blib/lib/Bio/Map/EntityI.pm -> blib/libdoc/Bio::Map::EntityI.3 Manifying blib/lib/Bio/Tools/Spidey/Results.pm -> blib/libdoc/Bio::Tools::Spidey::Results.3 Manifying blib/lib/Bio/SearchIO/waba.pm -> blib/libdoc/Bio::SearchIO::waba.3 Manifying blib/lib/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedTableFeatureI.3 Manifying blib/lib/Bio/Biblio/IO/pubmed2ref.pm -> blib/libdoc/Bio::Biblio::IO::pubmed2ref.3 Manifying blib/lib/Bio/Species.pm -> blib/libdoc/Bio::Species.3 Manifying blib/lib/Bio/Matrix/PSM/InstanceSite.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSite.3 Manifying blib/lib/Bio/Variation/AAReverseMutate.pm -> blib/libdoc/Bio::Variation::AAReverseMutate.3 Manifying blib/lib/Bio/Tools/SiRNA/Ruleset/saigo.pm -> blib/libdoc/Bio::Tools::SiRNA::Ruleset::saigo.3 Manifying blib/lib/Bio/Tools/Sim4/Exon.pm -> blib/libdoc/Bio::Tools::Sim4::Exon.3 Manifying blib/lib/Bio/Tools/Run/StandAloneWUBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneWUBlast.3 Manifying blib/lib/Bio/Restriction/EnzymeCollection.pm -> blib/libdoc/Bio::Restriction::EnzymeCollection.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/memory.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/processed_transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::processed_transcript.3 Manifying blib/lib/Bio/DB/Ace.pm -> blib/libdoc/Bio::DB::Ace.3 Manifying blib/lib/Bio/LiveSeq/DNA.pm -> blib/libdoc/Bio::LiveSeq::DNA.3 Manifying blib/lib/Bio/Tools/HMMER/Results.pm -> blib/libdoc/Bio::Tools::HMMER::Results.3 Manifying blib/lib/Bio/Seq.pm -> blib/libdoc/Bio::Seq.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_softberry.3 Manifying blib/lib/Bio/Ontology/OBOEngine.pm -> blib/libdoc/Bio::Ontology::OBOEngine.3 Manifying blib/lib/Bio/SeqIO/ztr.pm -> blib/libdoc/Bio::SeqIO::ztr.3 Manifying blib/lib/Bio/MapIO.pm -> blib/libdoc/Bio::MapIO.3 Manifying blib/lib/Bio/DB/DBFetch.pm -> blib/libdoc/Bio::DB::DBFetch.3 Manifying blib/lib/Bio/Root/Test.pm -> blib/libdoc/Bio::Root::Test.3 Manifying blib/lib/Bio/Biblio/BookArticle.pm -> blib/libdoc/Bio::Biblio::BookArticle.3 Manifying blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 Manifying blib/lib/Bio/Tools/Coil.pm -> blib/libdoc/Bio::Tools::Coil.3 Manifying blib/lib/Bio/PopGen/Population.pm -> blib/libdoc/Bio::PopGen::Population.3 Manifying blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm -> blib/libdoc/Bio::Matrix::PSM::PsmHeaderI.3 Manifying blib/lib/Bio/Restriction/EnzymeI.pm -> blib/libdoc/Bio::Restriction::EnzymeI.3 Manifying blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm -> blib/libdoc/Bio::SeqFeature::Gene::GeneStructureI.3 Manifying blib/lib/Bio/Biblio/MedlineBook.pm -> blib/libdoc/Bio::Biblio::MedlineBook.3 Manifying blib/lib/Bio/Biblio/Proceeding.pm -> blib/libdoc/Bio::Biblio::Proceeding.3 Manifying blib/lib/Bio/Index/Fastq.pm -> blib/libdoc/Bio::Index::Fastq.3 Manifying blib/lib/Bio/SeqUtils.pm -> blib/libdoc/Bio::SeqUtils.3 Manifying blib/lib/Bio/DB/Failover.pm -> blib/libdoc/Bio::DB::Failover.3 Manifying blib/lib/Bio/SeqIO/asciitree.pm -> blib/libdoc/Bio::SeqIO::asciitree.3 Manifying blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -> blib/libdoc/Bio::Matrix::PSM::SiteMatrixI.3 Manifying blib/lib/Bio/Tools/Gel.pm -> blib/libdoc/Bio::Tools::Gel.3 Manifying blib/lib/Bio/DB/Registry.pm -> blib/libdoc/Bio::DB::Registry.3 Manifying blib/lib/Bio/SeqIO/game/featHandler.pm -> blib/libdoc/Bio::SeqIO::game::featHandler.3 Manifying blib/lib/Bio/Search/HSP/BlastHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastHSP.3 Manifying blib/lib/Bio/Factory/SequenceFactoryI.pm -> blib/libdoc/Bio::Factory::SequenceFactoryI.3 Manifying blib/lib/Bio/Biblio/TechReport.pm -> blib/libdoc/Bio::Biblio::TechReport.3 Manifying blib/lib/Bio/Tools/Blat.pm -> blib/libdoc/Bio::Tools::Blat.3 Manifying blib/lib/Bio/Tools/Protparam.pm -> blib/libdoc/Bio::Tools::Protparam.3 Manifying blib/lib/Bio/PhyloNetwork.pm -> blib/libdoc/Bio::PhyloNetwork.3 Manifying blib/lib/Bio/SeqIO/metafasta.pm -> blib/libdoc/Bio::SeqIO::metafasta.3 Manifying blib/lib/Bio/Expression/Sample.pm -> blib/libdoc/Bio::Expression::Sample.3 Manifying blib/lib/Bio/Map/CytoMarker.pm -> blib/libdoc/Bio::Map::CytoMarker.3 Manifying blib/lib/Bio/Tools/TargetP.pm -> blib/libdoc/Bio::Tools::TargetP.3 Manifying blib/lib/Bio/DB/NCBIHelper.pm -> blib/libdoc/Bio::DB::NCBIHelper.3 Manifying blib/lib/Bio/SeqIO/table.pm -> blib/libdoc/Bio::SeqIO::table.3 Manifying blib/lib/Bio/Root/Root.pm -> blib/libdoc/Bio::Root::Root.3 Manifying blib/lib/Bio/Tools/Spidey/Exon.pm -> blib/libdoc/Bio::Tools::Spidey::Exon.3 Manifying blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm -> blib/libdoc/Bio::Tools::EUtilities::EUtilDataI.3 Manifying blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/libdoc/Bio::AlignIO::Handler::GenericAlignHandler.3 Manifying blib/lib/Bio/Event/EventGeneratorI.pm -> blib/libdoc/Bio::Event::EventGeneratorI.3 Manifying blib/lib/Bio/SearchIO/exonerate.pm -> blib/libdoc/Bio::SearchIO::exonerate.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/ace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::ace.3 Manifying blib/lib/Bio/DB/QueryI.pm -> blib/libdoc/Bio::DB::QueryI.3 Manifying blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -> blib/libdoc/Bio::Factory::SeqAnalysisParserFactory.3 Manifying blib/lib/Bio/AlignIO/maf.pm -> blib/libdoc/Bio::AlignIO::maf.3 Manifying blib/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneNCBIBlast.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Sopma.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Sopma.3 Manifying blib/lib/Bio/Search/Hit/BlastHit.pm -> blib/libdoc/Bio::Search::Hit::BlastHit.3 Manifying blib/lib/Bio/DB/SeqHound.pm -> blib/libdoc/Bio::DB::SeqHound.3 Manifying blib/lib/Bio/SeqIO/game/gameHandler.pm -> blib/libdoc/Bio::SeqIO::game::gameHandler.3 Manifying blib/lib/Bio/SeqFeature/Generic.pm -> blib/libdoc/Bio::SeqFeature::Generic.3 Manifying blib/lib/Bio/Search/SearchUtils.pm -> blib/libdoc/Bio::Search::SearchUtils.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 Manifying blib/lib/Bio/Factory/ObjectBuilderI.pm -> blib/libdoc/Bio::Factory::ObjectBuilderI.3 Manifying blib/lib/Bio/Map/Relative.pm -> blib/libdoc/Bio::Map::Relative.3 Manifying blib/lib/Bio/Map/Position.pm -> blib/libdoc/Bio::Map::Position.3 Manifying blib/lib/Bio/Symbol/DNAAlphabet.pm -> blib/libdoc/Bio::Symbol::DNAAlphabet.3 Manifying blib/lib/Bio/Root/Utilities.pm -> blib/libdoc/Bio::Root::Utilities.3 Manifying blib/lib/Bio/Matrix/MatrixI.pm -> blib/libdoc/Bio::Matrix::MatrixI.3 Manifying blib/lib/Bio/AlignIO/largemultifasta.pm -> blib/libdoc/Bio::AlignIO::largemultifasta.3 Manifying blib/lib/Bio/DB/MeSH.pm -> blib/libdoc/Bio::DB::MeSH.3 Manifying blib/lib/Bio/SeqIO/pir.pm -> blib/libdoc/Bio::SeqIO::pir.3 Manifying blib/lib/Bio/Variation/IO/flat.pm -> blib/libdoc/Bio::Variation::IO::flat.3 Manifying blib/lib/Bio/Coordinate/GeneMapper.pm -> blib/libdoc/Bio::Coordinate::GeneMapper.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_twinscan.3 Manifying blib/lib/Bio/SearchIO/fasta.pm -> blib/libdoc/Bio::SearchIO::fasta.3 Manifying blib/lib/Bio/SeqFeature/Computation.pm -> blib/libdoc/Bio::SeqFeature::Computation.3 Manifying blib/lib/Bio/Annotation/Target.pm -> blib/libdoc/Bio::Annotation::Target.3 Manifying blib/lib/Bio/Tools/ipcress.pm -> blib/libdoc/Bio::Tools::ipcress.3 Manifying blib/lib/Bio/ClusterIO/dbsnp.pm -> blib/libdoc/Bio::ClusterIO::dbsnp.3 Manifying blib/lib/Bio/Search/HSP/PSLHSP.pm -> blib/libdoc/Bio::Search::HSP::PSLHSP.3 Manifying blib/lib/Bio/ClusterI.pm -> blib/libdoc/Bio::ClusterI.3 Manifying blib/lib/Bio/DB/GFF/Typename.pm -> blib/libdoc/Bio::DB::GFF::Typename.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/coding.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::coding.3 Manifying blib/lib/Bio/Index/Blast.pm -> blib/libdoc/Bio::Index::Blast.3 Manifying blib/lib/Bio/Tree/NodeNHX.pm -> blib/libdoc/Bio::Tree::NodeNHX.3 Manifying blib/lib/Bio/Biblio/Organisation.pm -> blib/libdoc/Bio::Biblio::Organisation.3 Manifying blib/lib/Bio/Ontology/OBOterm.pm -> blib/libdoc/Bio::Ontology::OBOterm.3 Manifying blib/lib/Bio/Structure/Residue.pm -> blib/libdoc/Bio::Structure::Residue.3 Manifying blib/lib/Bio/AnalysisResultI.pm -> blib/libdoc/Bio::AnalysisResultI.3 Manifying blib/lib/Bio/Coordinate/Result/Gap.pm -> blib/libdoc/Bio::Coordinate::Result::Gap.3 Manifying blib/lib/Bio/DB/Expression.pm -> blib/libdoc/Bio::DB::Expression.3 Manifying blib/lib/Bio/SeqIO/excel.pm -> blib/libdoc/Bio::SeqIO::excel.3 Manifying blib/lib/Bio/Tree/Compatible.pm -> blib/libdoc/Bio::Tree::Compatible.3 Manifying blib/lib/Bio/AlignIO/emboss.pm -> blib/libdoc/Bio::AlignIO::emboss.3 Manifying blib/lib/Bio/Search/HSP/HmmpfamHSP.pm -> blib/libdoc/Bio::Search::HSP::HmmpfamHSP.3 Manifying blib/lib/Bio/Tools/Prints.pm -> blib/libdoc/Bio::Tools::Prints.3 Manifying blib/lib/Bio/Search/Iteration/GenericIteration.pm -> blib/libdoc/Bio::Search::Iteration::GenericIteration.3 Manifying blib/lib/Bio/SeqFeature/Primer.pm -> blib/libdoc/Bio::SeqFeature::Primer.3 Manifying blib/lib/Bio/Cluster/SequenceFamily.pm -> blib/libdoc/Bio::Cluster::SequenceFamily.3 Manifying blib/lib/Bio/Assembly/ScaffoldI.pm -> blib/libdoc/Bio::Assembly::ScaffoldI.3 Manifying blib/lib/Bio/Assembly/Singlet.pm -> blib/libdoc/Bio::Assembly::Singlet.3 Manifying blib/lib/Bio/Search/HSP/HSPI.pm -> blib/libdoc/Bio::Search::HSP::HSPI.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::mysql.3 Manifying blib/lib/Bio/SeqIO/game/gameSubs.pm -> blib/libdoc/Bio::SeqIO::game::gameSubs.3 Manifying blib/lib/Bio/Biblio/MedlineJournalArticle.pm -> blib/libdoc/Bio::Biblio::MedlineJournalArticle.3 Manifying blib/lib/Bio/Das/FeatureTypeI.pm -> blib/libdoc/Bio::Das::FeatureTypeI.3 Manifying blib/lib/Bio/PhyloNetwork/FactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::FactoryX.3 Manifying blib/lib/Bio/Search/HSP/HSPFactory.pm -> blib/libdoc/Bio::Search::HSP::HSPFactory.3 Manifying blib/lib/Bio/SeqIO/gbdriver.pm -> blib/libdoc/Bio::SeqIO::gbdriver.3 Manifying blib/lib/Bio/Symbol/Symbol.pm -> blib/libdoc/Bio::Symbol::Symbol.3 Manifying blib/lib/Bio/Tools/Prediction/Exon.pm -> blib/libdoc/Bio::Tools::Prediction::Exon.3 Manifying blib/lib/Bio/DB/BiblioI.pm -> blib/libdoc/Bio::DB::BiblioI.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::GOR4.3 Manifying blib/lib/Bio/Map/Marker.pm -> blib/libdoc/Bio::Map::Marker.3 Manifying blib/lib/Bio/Root/Version.pm -> blib/libdoc/Bio::Root::Version.3 Manifying blib/lib/Bio/SeqIO.pm -> blib/libdoc/Bio::SeqIO.3 Manifying blib/lib/Bio/Location/FuzzyLocationI.pm -> blib/libdoc/Bio::Location::FuzzyLocationI.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_genscan.3 Manifying blib/lib/Bio/PopGen/IO/phase.pm -> blib/libdoc/Bio::PopGen::IO::phase.3 Manifying blib/lib/Bio/Align/DNAStatistics.pm -> blib/libdoc/Bio::Align::DNAStatistics.3 Manifying blib/lib/Bio/Biblio/PubmedJournalArticle.pm -> blib/libdoc/Bio::Biblio::PubmedJournalArticle.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary.3 Manifying blib/lib/Bio/Tools/Eponine.pm -> blib/libdoc/Bio::Tools::Eponine.3 Manifying blib/lib/Bio/Variation/Allele.pm -> blib/libdoc/Bio::Variation::Allele.3 Manifying blib/lib/Bio/Phenotype/Phenotype.pm -> blib/libdoc/Bio::Phenotype::Phenotype.3 Manifying blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/libdoc/Bio::Factory::SeqAnalysisParserFactoryI.3 Manifying blib/lib/Bio/SeqIO/swiss.pm -> blib/libdoc/Bio::SeqIO::swiss.3 Manifying blib/lib/Bio/DB/ReferenceI.pm -> blib/libdoc/Bio::DB::ReferenceI.3 Manifying blib/lib/Bio/ClusterIO.pm -> blib/libdoc/Bio::ClusterIO.3 Manifying blib/lib/Bio/DB/Taxonomy/entrez.pm -> blib/libdoc/Bio::DB::Taxonomy::entrez.3 Manifying blib/lib/Bio/Map/GenePosition.pm -> blib/libdoc/Bio::Map::GenePosition.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_sanger22.3 Manifying blib/lib/Bio/Map/FPCMarker.pm -> blib/libdoc/Bio::Map::FPCMarker.3 Manifying blib/lib/Bio/AlignIO/mase.pm -> blib/libdoc/Bio::AlignIO::mase.3 Manifying blib/lib/Bio/OntologyIO/soflat.pm -> blib/libdoc/Bio::OntologyIO::soflat.3 Manifying blib/lib/Bio/MapIO/fpc.pm -> blib/libdoc/Bio::MapIO::fpc.3 Manifying blib/lib/Bio/Coordinate/Result/Match.pm -> blib/libdoc/Bio::Coordinate::Result::Match.3 Manifying blib/lib/Bio/Search/Hit/PsiBlastHit.pm -> blib/libdoc/Bio::Search::Hit::PsiBlastHit.3 Manifying blib/lib/Bio/Restriction/IO/bairoch.pm -> blib/libdoc/Bio::Restriction::IO::bairoch.3 Manifying blib/lib/Bio/PopGen/IO/csv.pm -> blib/libdoc/Bio::PopGen::IO::csv.3 Manifying blib/lib/Bio/Biblio/IO/medlinexml.pm -> blib/libdoc/Bio::Biblio::IO::medlinexml.3 Manifying blib/lib/Bio/Search/Result/WABAResult.pm -> blib/libdoc/Bio::Search::Result::WABAResult.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/none.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::none.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::berkeleydb3.3 Manifying blib/lib/Bio/Search/Result/HmmpfamResult.pm -> blib/libdoc/Bio::Search::Result::HmmpfamResult.3 Manifying blib/lib/Bio/DB/GenBank.pm -> blib/libdoc/Bio::DB::GenBank.3 Manifying blib/lib/Bio/AlignIO/psi.pm -> blib/libdoc/Bio::AlignIO::psi.3 Manifying blib/lib/Bio/SeqIO/agave.pm -> blib/libdoc/Bio::SeqIO::agave.3 Manifying blib/lib/Bio/SeqIO/swissdriver.pm -> blib/libdoc/Bio::SeqIO::swissdriver.3 Manifying blib/lib/Bio/Variation/VariantI.pm -> blib/libdoc/Bio::Variation::VariantI.3 Manifying blib/lib/Bio/SeqFeature/Similarity.pm -> blib/libdoc/Bio::SeqFeature::Similarity.3 Manifying blib/lib/Bio/DescribableI.pm -> blib/libdoc/Bio::DescribableI.3 Manifying blib/lib/Bio/Biblio/IO/medline2ref.pm -> blib/libdoc/Bio::Biblio::IO::medline2ref.3 Manifying blib/lib/Bio/Ontology/OntologyStore.pm -> blib/libdoc/Bio::Ontology::OntologyStore.3 Manifying blib/lib/Bio/SeqFeature/Gene/Promoter.pm -> blib/libdoc/Bio::SeqFeature::Gene::Promoter.3 Manifying blib/lib/Bio/PhyloNetwork/Factory.pm -> blib/libdoc/Bio::PhyloNetwork::Factory.3 Manifying blib/lib/Bio/HandlerBaseI.pm -> blib/libdoc/Bio::HandlerBaseI.3 Manifying blib/lib/Bio/Ontology/Path.pm -> blib/libdoc/Bio::Ontology::Path.3 Manifying blib/lib/Bio/Ontology/TermFactory.pm -> blib/libdoc/Bio::Ontology::TermFactory.3 Manifying blib/lib/Bio/Restriction/Analysis.pm -> blib/libdoc/Bio::Restriction::Analysis.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_acembly.3 Manifying blib/lib/Bio/Factory/ObjectFactoryI.pm -> blib/libdoc/Bio::Factory::ObjectFactoryI.3 Manifying blib/lib/Bio/Annotation/SimpleValue.pm -> blib/libdoc/Bio::Annotation::SimpleValue.3 Manifying blib/lib/Bio/Align/StatisticsI.pm -> blib/libdoc/Bio::Align::StatisticsI.3 Manifying blib/lib/Bio/Tree/TreeFunctionsI.pm -> blib/libdoc/Bio::Tree::TreeFunctionsI.3 Manifying blib/lib/Bio/Restriction/IO/itype2.pm -> blib/libdoc/Bio::Restriction::IO::itype2.3 Manifying blib/lib/Bio/SeqIO/entrezgene.pm -> blib/libdoc/Bio::SeqIO::entrezgene.3 Manifying blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm -> blib/libdoc/Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 Manifying blib/lib/Bio/SeqIO/tigrxml.pm -> blib/libdoc/Bio::SeqIO::tigrxml.3 Manifying blib/lib/Bio/TreeIO/nexus.pm -> blib/libdoc/Bio::TreeIO::nexus.3 Manifying blib/lib/Bio/Tools/RandomDistFunctions.pm -> blib/libdoc/Bio::Tools::RandomDistFunctions.3 Manifying blib/lib/Bio/DB/Flat.pm -> blib/libdoc/Bio::DB::Flat.3 Manifying blib/lib/Bio/SeqIO/phd.pm -> blib/libdoc/Bio::SeqIO::phd.3 Manifying blib/lib/Bio/Tools/Fgenesh.pm -> blib/libdoc/Bio::Tools::Fgenesh.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary/DocSum.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::DocSum.3 Manifying blib/lib/Bio/Matrix/PhylipDist.pm -> blib/libdoc/Bio::Matrix::PhylipDist.3 Manifying blib/lib/Bio/DB/CUTG.pm -> blib/libdoc/Bio::DB::CUTG.3 Manifying blib/lib/Bio/Map/CytoMap.pm -> blib/libdoc/Bio::Map::CytoMap.3 Manifying blib/lib/Bio/DB/TFBS/transfac_pro.pm -> blib/libdoc/Bio::DB::TFBS::transfac_pro.3 Manifying blib/lib/Bio/Expression/Platform.pm -> blib/libdoc/Bio::Expression::Platform.3 Manifying blib/lib/Bio/DB/GFF/RelSegment.pm -> blib/libdoc/Bio::DB::GFF::RelSegment.3 Manifying blib/lib/Bio/Tools/ECnumber.pm -> blib/libdoc/Bio::Tools::ECnumber.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory::feature_serializer.3 Manifying blib/lib/Bio/Tools/Alignment/Consed.pm -> blib/libdoc/Bio::Tools::Alignment::Consed.3 Manifying blib/lib/Bio/OntologyIO/obo.pm -> blib/libdoc/Bio::OntologyIO::obo.3 Manifying blib/lib/Bio/Tree/Tree.pm -> blib/libdoc/Bio::Tree::Tree.3 Manifying blib/lib/Bio/FeatureHolderI.pm -> blib/libdoc/Bio::FeatureHolderI.3 Manifying blib/lib/Bio/Tree/AlleleNode.pm -> blib/libdoc/Bio::Tree::AlleleNode.3 Manifying blib/lib/Bio/Tools/IUPAC.pm -> blib/libdoc/Bio::Tools::IUPAC.3 Manifying blib/lib/Bio/LiveSeq/Range.pm -> blib/libdoc/Bio::LiveSeq::Range.3 Manifying blib/lib/Bio/Tree/AnnotatableNode.pm -> blib/libdoc/Bio::Tree::AnnotatableNode.3 Manifying blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm -> blib/libdoc/Bio::SearchIO::Writer::GbrowseGFF.3 Manifying blib/lib/Bio/PrimarySeqI.pm -> blib/libdoc/Bio::PrimarySeqI.3 Manifying blib/lib/Bio/Tools/isPcr.pm -> blib/libdoc/Bio::Tools::isPcr.3 Manifying blib/lib/Bio/Tools/EPCR.pm -> blib/libdoc/Bio::Tools::EPCR.3 Manifying blib/lib/Bio/Index/Stockholm.pm -> blib/libdoc/Bio::Index::Stockholm.3 Manifying blib/lib/Bio/Tools/Phylo/Molphy/Result.pm -> blib/libdoc/Bio::Tools::Phylo::Molphy::Result.3 Manifying blib/lib/Bio/Align/AlignI.pm -> blib/libdoc/Bio::Align::AlignI.3 Manifying blib/lib/Bio/Seq/LargePrimarySeq.pm -> blib/libdoc/Bio::Seq::LargePrimarySeq.3 Manifying blib/lib/Bio/AlignIO/proda.pm -> blib/libdoc/Bio::AlignIO::proda.3 Manifying blib/lib/Bio/Tools/Genomewise.pm -> blib/libdoc/Bio::Tools::Genomewise.3 Manifying blib/lib/Bio/PhyloNetwork/muVector.pm -> blib/libdoc/Bio::PhyloNetwork::muVector.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::pg_fts.3 Manifying blib/lib/Bio/DB/Flat/BDB/swiss.pm -> blib/libdoc/Bio::DB::Flat::BDB::swiss.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/memory.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::memory.3 Manifying blib/lib/Bio/SeqIO/game.pm -> blib/libdoc/Bio::SeqIO::game.3 Manifying blib/lib/Bio/SeqIO/FTHelper.pm -> blib/libdoc/Bio::SeqIO::FTHelper.3 Manifying blib/lib/Bio/LocatableSeq.pm -> blib/libdoc/Bio::LocatableSeq.3 Manifying blib/lib/Bio/Tools/EUtilities/Info/FieldInfo.pm -> blib/libdoc/Bio::Tools::EUtilities::Info::FieldInfo.3 Manifying blib/lib/Bio/Search/HSP/GenericHSP.pm -> blib/libdoc/Bio::Search::HSP::GenericHSP.3 Manifying blib/lib/Bio/SearchIO/XML/BlastHandler.pm -> blib/libdoc/Bio::SearchIO::XML::BlastHandler.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/berkeleydb.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::berkeleydb.3 Manifying blib/lib/Bio/SearchIO/Writer/BSMLResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::BSMLResultWriter.3 Manifying blib/lib/Bio/FeatureIO/gff.pm -> blib/libdoc/Bio::FeatureIO::gff.3 Manifying blib/lib/Bio/Tools/CodonTable.pm -> blib/libdoc/Bio::Tools::CodonTable.3 Manifying blib/lib/Bio/AlignIO/bl2seq.pm -> blib/libdoc/Bio::AlignIO::bl2seq.3 Manifying blib/lib/Bio/SeqIO/fasta.pm -> blib/libdoc/Bio::SeqIO::fasta.3 Manifying blib/lib/Bio/Cluster/FamilyI.pm -> blib/libdoc/Bio::Cluster::FamilyI.3 Manifying blib/lib/Bio/Ontology/Term.pm -> blib/libdoc/Bio::Ontology::Term.3 Manifying blib/lib/Bio/Location/Fuzzy.pm -> blib/libdoc/Bio::Location::Fuzzy.3 Manifying blib/lib/Bio/Factory/FTLocationFactory.pm -> blib/libdoc/Bio::Factory::FTLocationFactory.3 Manifying blib/lib/Bio/TreeIO/TreeEventBuilder.pm -> blib/libdoc/Bio::TreeIO::TreeEventBuilder.3 Manifying blib/lib/Bio/DB/GFF/Aggregator.pm -> blib/libdoc/Bio::DB::GFF::Aggregator.3 Manifying blib/lib/Bio/LiveSeq/Repeat_Region.pm -> blib/libdoc/Bio::LiveSeq::Repeat_Region.3 Manifying blib/lib/Bio/Restriction/Enzyme/MultiCut.pm -> blib/libdoc/Bio::Restriction::Enzyme::MultiCut.3 Manifying blib/lib/Bio/Matrix/PSM/IO.pm -> blib/libdoc/Bio::Matrix::PSM::IO.3 Manifying blib/lib/Bio/Map/MappableI.pm -> blib/libdoc/Bio::Map::MappableI.3 Manifying blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMentry.3 Manifying blib/lib/Bio/Seq/TraceI.pm -> blib/libdoc/Bio::Seq::TraceI.3 Manifying blib/lib/Bio/Map/PositionI.pm -> blib/libdoc/Bio::Map::PositionI.3 Manifying blib/lib/Bio/AlignIO/stockholm.pm -> blib/libdoc/Bio::AlignIO::stockholm.3 Manifying blib/lib/Bio/AlignIO/selex.pm -> blib/libdoc/Bio::AlignIO::selex.3 Manifying blib/lib/Bio/DB/GenericWebAgent.pm -> blib/libdoc/Bio::DB::GenericWebAgent.3 Manifying blib/lib/Bio/SeqFeature/SiRNA/Oligo.pm -> blib/libdoc/Bio::SeqFeature::SiRNA::Oligo.3 Manifying blib/lib/Bio/Ontology/OntologyI.pm -> blib/libdoc/Bio::Ontology::OntologyI.3 Manifying blib/lib/Bio/Das/SegmentI.pm -> blib/libdoc/Bio::Das::SegmentI.3 Manifying blib/lib/Bio/WebAgent.pm -> blib/libdoc/Bio::WebAgent.3 Manifying blib/lib/Bio/TreeIO/cluster.pm -> blib/libdoc/Bio::TreeIO::cluster.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/bdb.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::bdb.3 Manifying blib/lib/Bio/Seq/BaseSeqProcessor.pm -> blib/libdoc/Bio::Seq::BaseSeqProcessor.3 Manifying blib/lib/Bio/DB/GFF/Util/Rearrange.pm -> blib/libdoc/Bio::DB::GFF::Util::Rearrange.3 Manifying blib/lib/Bio/AnalysisI.pm -> blib/libdoc/Bio::AnalysisI.3 Manifying blib/lib/Bio/OntologyIO/simplehierarchy.pm -> blib/libdoc/Bio::OntologyIO::simplehierarchy.3 Manifying blib/lib/Bio/DB/HIV/HIVAnnotProcessor.pm -> blib/libdoc/Bio::DB::HIV::HIVAnnotProcessor.3 Manifying blib/lib/Bio/Search/HSP/PsiBlastHSP.pm -> blib/libdoc/Bio::Search::HSP::PsiBlastHSP.3 Manifying blib/lib/Bio/AlignIO/phylip.pm -> blib/libdoc/Bio::AlignIO::phylip.3 Manifying blib/lib/Bio/Ontology/DocumentRegistry.pm -> blib/libdoc/Bio::Ontology::DocumentRegistry.3 Manifying blib/lib/Bio/Coordinate/Chain.pm -> blib/libdoc/Bio::Coordinate::Chain.3 Manifying blib/lib/Bio/Matrix/PSM/Psm.pm -> blib/libdoc/Bio::Matrix::PSM::Psm.3 Manifying blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::InterProHandler.3 Manifying blib/lib/Bio/Align/PairwiseStatistics.pm -> blib/libdoc/Bio::Align::PairwiseStatistics.3 Manifying blib/lib/Bio/Tools/SiRNA.pm -> blib/libdoc/Bio::Tools::SiRNA.3 Manifying blib/lib/Bio/Ontology/OntologyEngineI.pm -> blib/libdoc/Bio::Ontology::OntologyEngineI.3 Manifying blib/lib/Bio/AlignIO/pfam.pm -> blib/libdoc/Bio::AlignIO::pfam.3 Manifying blib/lib/Bio/Taxonomy/FactoryI.pm -> blib/libdoc/Bio::Taxonomy::FactoryI.3 Manifying blib/lib/Bio/SeqFeature/Lite.pm -> blib/libdoc/Bio::SeqFeature::Lite.3 Manifying blib/lib/Bio/TreeIO/lintree.pm -> blib/libdoc/Bio::TreeIO::lintree.3 Manifying blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm -> blib/libdoc/Bio::Tools::EUtilities::Query::GlobalQuery.3 Manifying blib/lib/Bio/Tools/Infernal.pm -> blib/libdoc/Bio::Tools::Infernal.3 Manifying blib/lib/Bio/SearchIO/hmmer_pull.pm -> blib/libdoc/Bio::SearchIO::hmmer_pull.3 Manifying blib/lib/Bio/DB/SeqVersion.pm -> blib/libdoc/Bio::DB::SeqVersion.3 Manifying blib/lib/Bio/Tools/Phylo/PAML.pm -> blib/libdoc/Bio::Tools::Phylo::PAML.3 Manifying blib/lib/Bio/Search/StatisticsI.pm -> blib/libdoc/Bio::Search::StatisticsI.3 Manifying blib/lib/Bio/SimpleAlign.pm -> blib/libdoc/Bio::SimpleAlign.3 Manifying blib/lib/Bio/Factory/TreeFactoryI.pm -> blib/libdoc/Bio::Factory::TreeFactoryI.3 Manifying blib/lib/Bio/Tools/RepeatMasker.pm -> blib/libdoc/Bio::Tools::RepeatMasker.3 Manifying blib/lib/Bio/Map/GeneMap.pm -> blib/libdoc/Bio::Map::GeneMap.3 Manifying blib/lib/Bio/DB/RandomAccessI.pm -> blib/libdoc/Bio::DB::RandomAccessI.3 Manifying blib/lib/Bio/PopGen/Marker.pm -> blib/libdoc/Bio::PopGen::Marker.3 Manifying blib/lib/Bio/Matrix/Generic.pm -> blib/libdoc/Bio::Matrix::Generic.3 Manifying blib/lib/Bio/Root/HTTPget.pm -> blib/libdoc/Bio::Root::HTTPget.3 Manifying blib/lib/Bio/Index/SwissPfam.pm -> blib/libdoc/Bio::Index::SwissPfam.3 Manifying blib/lib/Bio/TreeIO.pm -> blib/libdoc/Bio::TreeIO.3 Manifying blib/lib/Bio/Search/Hit/PullHitI.pm -> blib/libdoc/Bio::Search::Hit::PullHitI.3 Manifying blib/lib/Bio/Tools/EUtilities/Query.pm -> blib/libdoc/Bio::Tools::EUtilities::Query.3 Manifying blib/lib/Bio/PopGen/Individual.pm -> blib/libdoc/Bio::PopGen::Individual.3 Manifying blib/lib/Bio/Tools/GuessSeqFormat.pm -> blib/libdoc/Bio::Tools::GuessSeqFormat.3 Manifying blib/lib/Bio/AlignIO/xmfa.pm -> blib/libdoc/Bio::AlignIO::xmfa.3 Manifying blib/lib/Bio/Map/LinkageMap.pm -> blib/libdoc/Bio::Map::LinkageMap.3 Manifying blib/lib/Bio/SearchIO/rnamotif.pm -> blib/libdoc/Bio::SearchIO::rnamotif.3 Manifying blib/lib/Bio/SeqFeature/Gene/ExonI.pm -> blib/libdoc/Bio::SeqFeature::Gene::ExonI.3 Manifying blib/lib/Bio/Biblio/Thesis.pm -> blib/libdoc/Bio::Biblio::Thesis.3 Manifying blib/lib/Bio/Search/GenericStatistics.pm -> blib/libdoc/Bio::Search::GenericStatistics.3 Manifying blib/lib/Bio/SeqIO/alf.pm -> blib/libdoc/Bio::SeqIO::alf.3 Manifying blib/lib/Bio/Factory/SequenceProcessorI.pm -> blib/libdoc/Bio::Factory::SequenceProcessorI.3 Manifying blib/lib/Bio/Search/Processor.pm -> blib/libdoc/Bio::Search::Processor.3 Manifying blib/lib/Bio/AnalysisParserI.pm -> blib/libdoc/Bio::AnalysisParserI.3 Manifying blib/lib/Bio/Search/Result/BlastPullResult.pm -> blib/libdoc/Bio::Search::Result::BlastPullResult.3 Manifying blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMparser.3 Manifying blib/lib/Bio/Biblio/Book.pm -> blib/libdoc/Bio::Biblio::Book.3 Manifying blib/lib/Bio/DB/Biblio/eutils.pm -> blib/libdoc/Bio::DB::Biblio::eutils.3 Manifying blib/lib/Bio/DBLinkContainerI.pm -> blib/libdoc/Bio::DBLinkContainerI.3 Manifying blib/lib/Bio/Index/AbstractSeq.pm -> blib/libdoc/Bio::Index::AbstractSeq.3 Manifying blib/lib/Bio/Location/Split.pm -> blib/libdoc/Bio::Location::Split.3 Manifying blib/lib/Bio/Symbol/ProteinAlphabet.pm -> blib/libdoc/Bio::Symbol::ProteinAlphabet.3 Manifying blib/lib/Bio/Annotation/StructuredValue.pm -> blib/libdoc/Bio::Annotation::StructuredValue.3 Manifying blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm -> blib/libdoc/Bio::SeqFeature::Gene::GeneStructure.3 Manifying blib/lib/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3 Manifying blib/lib/Bio/Tools/EMBOSS/Palindrome.pm -> blib/libdoc/Bio::Tools::EMBOSS::Palindrome.3 Manifying blib/lib/Bio/SearchIO/cross_match.pm -> blib/libdoc/Bio::SearchIO::cross_match.3 Manifying blib/lib/Bio/Map/GeneRelative.pm -> blib/libdoc/Bio::Map::GeneRelative.3 Manifying blib/lib/Bio/Map/MarkerI.pm -> blib/libdoc/Bio::Map::MarkerI.3 Manifying blib/lib/Bio/SeqIO/tinyseq.pm -> blib/libdoc/Bio::SeqIO::tinyseq.3 Manifying blib/lib/Bio/SearchIO/erpin.pm -> blib/libdoc/Bio::SearchIO::erpin.3 Manifying blib/lib/Bio/Ontology/PathI.pm -> blib/libdoc/Bio::Ontology::PathI.3 Manifying blib/lib/Bio/Expression/DataSet.pm -> blib/libdoc/Bio::Expression::DataSet.3 Manifying blib/lib/Bio/PopGen/Simulation/Coalescent.pm -> blib/libdoc/Bio::PopGen::Simulation::Coalescent.3 Manifying blib/lib/Bio/DB/SeqVersion/gi.pm -> blib/libdoc/Bio::DB::SeqVersion::gi.3 Manifying blib/lib/Bio/Tools/TandemRepeatsFinder.pm -> blib/libdoc/Bio::Tools::TandemRepeatsFinder.3 Manifying blib/lib/Bio/Taxonomy.pm -> blib/libdoc/Bio::Taxonomy.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Mitoprot.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Mitoprot.3 Manifying blib/lib/Bio/Search/DatabaseI.pm -> blib/libdoc/Bio::Search::DatabaseI.3 Manifying blib/lib/Bio/Tools/Phylo/Gumby.pm -> blib/libdoc/Bio::Tools::Phylo::Gumby.3 Manifying blib/lib/Bio/DasI.pm -> blib/libdoc/Bio::DasI.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::LoadHelper.3 Manifying blib/lib/Bio/SeqIO/tigr.pm -> blib/libdoc/Bio::SeqIO::tigr.3 Manifying blib/lib/Bio/Index/GenBank.pm -> blib/libdoc/Bio::Index::GenBank.3 Manifying blib/lib/Bio/FeatureIO/ptt.pm -> blib/libdoc/Bio::FeatureIO::ptt.3 Manifying blib/lib/Bio/PhyloNetwork/RandomFactory.pm -> blib/libdoc/Bio::PhyloNetwork::RandomFactory.3 Manifying blib/lib/Bio/DB/Biblio/soap.pm -> blib/libdoc/Bio::DB::Biblio::soap.3 Manifying blib/lib/Bio/SearchIO/hmmer.pm -> blib/libdoc/Bio::SearchIO::hmmer.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/Loader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::Loader.3 Manifying blib/lib/Bio/Tools/tRNAscanSE.pm -> blib/libdoc/Bio::Tools::tRNAscanSE.3 Manifying blib/lib/Bio/Assembly/IO/tigr.pm -> blib/libdoc/Bio::Assembly::IO::tigr.3 Manifying blib/lib/Bio/Biblio/JournalArticle.pm -> blib/libdoc/Bio::Biblio::JournalArticle.3 Manifying blib/lib/Bio/Tools/Sim4/Results.pm -> blib/libdoc/Bio::Tools::Sim4::Results.3 Manifying blib/lib/Bio/Index/Hmmer.pm -> blib/libdoc/Bio::Index::Hmmer.3 Manifying blib/lib/Bio/MapIO/mapmaker.pm -> blib/libdoc/Bio::MapIO::mapmaker.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch.3 Manifying blib/lib/Bio/Tools/Prediction/Gene.pm -> blib/libdoc/Bio::Tools::Prediction::Gene.3 Manifying blib/lib/Bio/Root/Test/Warn.pm -> blib/libdoc/Bio::Root::Test::Warn.3 Manifying blib/lib/Bio/AlignIO/meme.pm -> blib/libdoc/Bio::AlignIO::meme.3 Manifying blib/lib/Bio/Tools/SeqPattern.pm -> blib/libdoc/Bio::Tools::SeqPattern.3 Manifying blib/lib/Bio/Seq/RichSeq.pm -> blib/libdoc/Bio::Seq::RichSeq.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::ItemContainerI.3 Manifying blib/lib/Bio/Search/HSP/HMMERHSP.pm -> blib/libdoc/Bio::Search::HSP::HMMERHSP.3 Manifying blib/lib/Bio/SeqIO/ctf.pm -> blib/libdoc/Bio::SeqIO::ctf.3 Manifying blib/lib/Bio/DB/Taxonomy/list.pm -> blib/libdoc/Bio::DB::Taxonomy::list.3 Manifying blib/lib/Bio/Location/NarrowestCoordPolicy.pm -> blib/libdoc/Bio::Location::NarrowestCoordPolicy.3 Manifying blib/lib/Bio/Tools/Sigcleave.pm -> blib/libdoc/Bio::Tools::Sigcleave.3 Manifying blib/lib/Bio/DB/Taxonomy.pm -> blib/libdoc/Bio::DB::Taxonomy.3 Manifying blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm -> blib/libdoc/Bio::Assembly::Tools::ContigSpectrum.3 Manifying blib/lib/Bio/Ontology/GOterm.pm -> blib/libdoc/Bio::Ontology::GOterm.3 Manifying blib/lib/Bio/DB/Flat/BDB/embl.pm -> blib/libdoc/Bio::DB::Flat::BDB::embl.3 Manifying blib/lib/Bio/Tools/MZEF.pm -> blib/libdoc/Bio::Tools::MZEF.3 Manifying blib/lib/Bio/Phenotype/MeSH/Twig.pm -> blib/libdoc/Bio::Phenotype::MeSH::Twig.3 Manifying blib/lib/Bio/Tools/Primer/Feature.pm -> blib/libdoc/Bio::Tools::Primer::Feature.3 Manifying blib/lib/Bio/DB/GFF/Featname.pm -> blib/libdoc/Bio::DB::GFF::Featname.3 Manifying blib/lib/Bio/LiveSeq/SeqI.pm -> blib/libdoc/Bio::LiveSeq::SeqI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::oracleace.3 Manifying blib/lib/Bio/SeqFeature/FeaturePair.pm -> blib/libdoc/Bio::SeqFeature::FeaturePair.3 Manifying blib/lib/Bio/LiveSeq/Repeat_Unit.pm -> blib/libdoc/Bio::LiveSeq::Repeat_Unit.3 Manifying blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -> blib/libdoc/Bio::SeqIO::Handler::GenericRichSeqHandler.3 Manifying blib/lib/Bio/OntologyIO.pm -> blib/libdoc/Bio::OntologyIO.3 Manifying blib/lib/Bio/Variation/SNP.pm -> blib/libdoc/Bio::Variation::SNP.3 Manifying blib/lib/Bio/PhyloNetwork/TreeFactory.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactory.3 Manifying blib/lib/Bio/Tools/pICalculator.pm -> blib/libdoc/Bio::Tools::pICalculator.3 Manifying blib/lib/Bio/DB/GenPept.pm -> blib/libdoc/Bio::DB::GenPept.3 Manifying blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -> blib/libdoc/Bio::Matrix::PSM::SiteMatrix.3 Manifying blib/lib/Bio/DB/GFF.pm -> blib/libdoc/Bio::DB::GFF.3 Manifying blib/lib/Bio/Ontology/RelationshipFactory.pm -> blib/libdoc/Bio::Ontology::RelationshipFactory.3 Manifying blib/lib/Bio/Biblio/WebResource.pm -> blib/libdoc/Bio::Biblio::WebResource.3 Manifying blib/lib/Bio/ParameterBaseI.pm -> blib/libdoc/Bio::ParameterBaseI.3 Manifying blib/lib/Bio/Search/Hit/HitFactory.pm -> blib/libdoc/Bio::Search::Hit::HitFactory.3 Manifying blib/lib/Bio/DB/SeqFeature/Segment.pm -> blib/libdoc/Bio::DB::SeqFeature::Segment.3 Manifying blib/lib/Bio/Index/Fasta.pm -> blib/libdoc/Bio::Index::Fasta.3 Manifying blib/lib/Bio/FeatureIO/bed.pm -> blib/libdoc/Bio::FeatureIO::bed.3 Manifying blib/lib/Bio/ConfigData.pm -> blib/libdoc/Bio::ConfigData.3 Manifying blib/lib/Bio/Ontology/InterProTerm.pm -> blib/libdoc/Bio::Ontology::InterProTerm.3 Manifying blib/lib/Bio/PopGen/Simulation/GeneticDrift.pm -> blib/libdoc/Bio::PopGen::Simulation::GeneticDrift.3 Manifying blib/lib/Bio/AlignIO/metafasta.pm -> blib/libdoc/Bio::AlignIO::metafasta.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::caching_handle.3 Manifying blib/lib/Bio/Restriction/Enzyme.pm -> blib/libdoc/Bio::Restriction::Enzyme.3 Manifying blib/lib/Bio/Tools/QRNA.pm -> blib/libdoc/Bio::Tools::QRNA.3 Manifying blib/lib/Bio/Tools/Phylo/PAML/Result.pm -> blib/libdoc/Bio::Tools::Phylo::PAML::Result.3 Manifying blib/lib/Bio/Location/AvWithinCoordPolicy.pm -> blib/libdoc/Bio::Location::AvWithinCoordPolicy.3 Manifying blib/lib/Bio/Symbol/AlphabetI.pm -> blib/libdoc/Bio::Symbol::AlphabetI.3 Manifying blib/lib/Bio/Tools/Genscan.pm -> blib/libdoc/Bio::Tools::Genscan.3 Manifying blib/lib/Bio/Annotation/Relation.pm -> blib/libdoc/Bio::Annotation::Relation.3 Manifying blib/lib/Bio/Tree/Draw/Cladogram.pm -> blib/libdoc/Bio::Tree::Draw::Cladogram.3 Manifying blib/lib/Bio/Biblio/IO/pubmedxml.pm -> blib/libdoc/Bio::Biblio::IO::pubmedxml.3 Manifying blib/lib/Bio/DB/GFF/Homol.pm -> blib/libdoc/Bio::DB::GFF::Homol.3 Manifying blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -> blib/libdoc/Bio::SearchIO::FastHitEventBuilder.3 Manifying blib/lib/Bio/SeqFeature/SiRNA/Pair.pm -> blib/libdoc/Bio::SeqFeature::SiRNA::Pair.3 Manifying blib/lib/Bio/Factory/MapFactoryI.pm -> blib/libdoc/Bio::Factory::MapFactoryI.3 Manifying blib/lib/Bio/SeqEvolution/EvolutionI.pm -> blib/libdoc/Bio::SeqEvolution::EvolutionI.3 Manifying blib/lib/Bio/Tools/OddCodes.pm -> blib/libdoc/Bio::Tools::OddCodes.3 Manifying blib/lib/Bio/SearchIO/psl.pm -> blib/libdoc/Bio::SearchIO::psl.3 Manifying blib/lib/Bio/Map/TranscriptionFactor.pm -> blib/libdoc/Bio::Map::TranscriptionFactor.3 Manifying blib/lib/Bio/RangeI.pm -> blib/libdoc/Bio::RangeI.3 Manifying blib/lib/Bio/SeqAnalysisParserI.pm -> blib/libdoc/Bio::SeqAnalysisParserI.3 Manifying blib/lib/Bio/Map/Clone.pm -> blib/libdoc/Bio::Map::Clone.3 Manifying blib/lib/Bio/SeqIO/chaos.pm -> blib/libdoc/Bio::SeqIO::chaos.3 Manifying blib/lib/Bio/Restriction/IO.pm -> blib/libdoc/Bio::Restriction::IO.3 Manifying blib/lib/Bio/DB/TFBS.pm -> blib/libdoc/Bio::DB::TFBS.3 Manifying blib/lib/Bio/Structure/IO/pdb.pm -> blib/libdoc/Bio::Structure::IO::pdb.3 Manifying blib/lib/Bio/Align/Utilities.pm -> blib/libdoc/Bio::Align::Utilities.3 Manifying blib/lib/Bio/LiveSeq/Transcript.pm -> blib/libdoc/Bio::LiveSeq::Transcript.3 Manifying blib/lib/Bio/AlignIO/po.pm -> blib/libdoc/Bio::AlignIO::po.3 Manifying blib/lib/Bio/Index/EMBL.pm -> blib/libdoc/Bio::Index::EMBL.3 Manifying blib/lib/Bio/Expression/FeatureI.pm -> blib/libdoc/Bio::Expression::FeatureI.3 Manifying blib/lib/Bio/Seq/QualI.pm -> blib/libdoc/Bio::Seq::QualI.3 Manifying blib/lib/Bio/TreeIO/nhx.pm -> blib/libdoc/Bio::TreeIO::nhx.3 Manifying blib/lib/Bio/Tools/Promoterwise.pm -> blib/libdoc/Bio::Tools::Promoterwise.3 Manifying blib/lib/Bio/PopGen/IO.pm -> blib/libdoc/Bio::PopGen::IO.3 Manifying blib/lib/Bio/Assembly/Scaffold.pm -> blib/libdoc/Bio::Assembly::Scaffold.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/memory/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory::iterator.3 Manifying blib/lib/Bio/SeqIO/locuslink.pm -> blib/libdoc/Bio::SeqIO::locuslink.3 Manifying blib/lib/Bio/Tools/Est2Genome.pm -> blib/libdoc/Bio::Tools::Est2Genome.3 Manifying blib/lib/Bio/Structure/Atom.pm -> blib/libdoc/Bio::Structure::Atom.3 Manifying blib/lib/Bio/Search/GenericDatabase.pm -> blib/libdoc/Bio::Search::GenericDatabase.3 Manifying blib/lib/Bio/Search/HSP/PullHSPI.pm -> blib/libdoc/Bio::Search::HSP::PullHSPI.3 Manifying blib/lib/Bio/DB/GFF/Segment.pm -> blib/libdoc/Bio::DB::GFF::Segment.3 Manifying blib/lib/Bio/Root/RootI.pm -> blib/libdoc/Bio::Root::RootI.3 Manifying blib/lib/Bio/Tools/EUtilities/HistoryI.pm -> blib/libdoc/Bio::Tools::EUtilities::HistoryI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::iterator.3 Manifying blib/lib/Bio/Assembly/ContigAnalysis.pm -> blib/libdoc/Bio::Assembly::ContigAnalysis.3 Manifying blib/lib/Bio/SeqIO/genbank.pm -> blib/libdoc/Bio::SeqIO::genbank.3 Manifying blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::BaseSAXHandler.3 Manifying blib/lib/Bio/Search/Hit/HmmpfamHit.pm -> blib/libdoc/Bio::Search::Hit::HmmpfamHit.3 Manifying blib/lib/Bio/Tools/HMMER/Set.pm -> blib/libdoc/Bio::Tools::HMMER::Set.3 Manifying blib/lib/Bio/CodonUsage/IO.pm -> blib/libdoc/Bio::CodonUsage::IO.3 Manifying blib/lib/Bio/Variation/IO/xml.pm -> blib/libdoc/Bio::Variation::IO::xml.3 Manifying blib/lib/Bio/Matrix/PSM/PsmI.pm -> blib/libdoc/Bio::Matrix::PSM::PsmI.3 Manifying blib/lib/Bio/Biblio/Service.pm -> blib/libdoc/Bio::Biblio::Service.3 Manifying blib/lib/Bio/Seq/RichSeqI.pm -> blib/libdoc/Bio::Seq::RichSeqI.3 Manifying blib/lib/Bio/Biblio/PubmedBookArticle.pm -> blib/libdoc/Bio::Biblio::PubmedBookArticle.3 Manifying blib/lib/Bio/TreeIO/phyloxml.pm -> blib/libdoc/Bio::TreeIO::phyloxml.3 Manifying blib/lib/Bio/Search/Hit/Fasta.pm -> blib/libdoc/Bio::Search::Hit::Fasta.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary/Item.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::Item.3 Manifying blib/lib/Bio/Coordinate/MapperI.pm -> blib/libdoc/Bio::Coordinate::MapperI.3 Manifying blib/lib/Bio/SearchIO/infernal.pm -> blib/libdoc/Bio::SearchIO::infernal.3 Manifying blib/lib/Bio/Map/MapI.pm -> blib/libdoc/Bio::Map::MapI.3 Manifying blib/lib/Bio/SeqIO/gcg.pm -> blib/libdoc/Bio::SeqIO::gcg.3 Manifying blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HSPTableWriter.3 Manifying blib/lib/Bio/Seq/PrimaryQual.pm -> blib/libdoc/Bio::Seq::PrimaryQual.3 Manifying blib/lib/Bio/Tools/Signalp.pm -> blib/libdoc/Bio::Tools::Signalp.3 Manifying blib/lib/Bio/FeatureIO/vecscreen_simple.pm -> blib/libdoc/Bio::FeatureIO::vecscreen_simple.3 Manifying blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/libdoc/Bio::Tools::EUtilities::Info::LinkInfo.3 Manifying blib/lib/Bio/DB/Flat/BDB.pm -> blib/libdoc/Bio::DB::Flat::BDB.3 Manifying blib/lib/Bio/Seq/Meta.pm -> blib/libdoc/Bio::Seq::Meta.3 Manifying blib/lib/Bio/SeqFeature/Gene/Intron.pm -> blib/libdoc/Bio::SeqFeature::Gene::Intron.3 Manifying blib/lib/Bio/Seq/SequenceTrace.pm -> blib/libdoc/Bio::Seq::SequenceTrace.3 Manifying blib/lib/Bio/Annotation/Collection.pm -> blib/libdoc/Bio::Annotation::Collection.3 Manifying blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HitTableWriter.3 Manifying blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::ResultTableWriter.3 Manifying blib/lib/Bio/Seq/PrimedSeq.pm -> blib/libdoc/Bio::Seq::PrimedSeq.3 Manifying blib/lib/Bio/Tools/Phylo/Molphy.pm -> blib/libdoc/Bio::Tools::Phylo::Molphy.3 Manifying blib/lib/Bio/AnnotationCollectionI.pm -> blib/libdoc/Bio::AnnotationCollectionI.3 Manifying blib/lib/Bio/Location/SplitLocationI.pm -> blib/libdoc/Bio::Location::SplitLocationI.3 Manifying blib/lib/Bio/Tree/RandomFactory.pm -> blib/libdoc/Bio::Tree::RandomFactory.3 Manifying blib/lib/Bio/Biblio/Patent.pm -> blib/libdoc/Bio::Biblio::Patent.3 Manifying blib/lib/Bio/Tree/TreeI.pm -> blib/libdoc/Bio::Tree::TreeI.3 Manifying blib/lib/Bio/Biblio/BiblioBase.pm -> blib/libdoc/Bio::Biblio::BiblioBase.3 Manifying blib/lib/Bio/Tools/Run/StandAloneBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneBlast.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::transcript.3 Manifying blib/lib/Bio/PullParserI.pm -> blib/libdoc/Bio::PullParserI.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Scansite.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Scansite.3 Manifying blib/lib/Bio/Biblio/MedlineBookArticle.pm -> blib/libdoc/Bio::Biblio::MedlineBookArticle.3 Manifying blib/lib/Bio/DB/Taxonomy/flatfile.pm -> blib/libdoc/Bio::DB::Taxonomy::flatfile.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysql.3 Manifying blib/lib/Bio/SeqFeature/SimilarityPair.pm -> blib/libdoc/Bio::SeqFeature::SimilarityPair.3 Manifying blib/lib/Bio/Index/BlastTable.pm -> blib/libdoc/Bio::Index::BlastTable.3 Manifying blib/lib/Bio/Search/HSP/BlastPullHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastPullHSP.3 Manifying blib/lib/Bio/SeqIO/pln.pm -> blib/libdoc/Bio::SeqIO::pln.3 Manifying blib/lib/Bio/Expression/Contact.pm -> blib/libdoc/Bio::Expression::Contact.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_ensgene.3 Manifying blib/lib/Bio/Event/EventHandlerI.pm -> blib/libdoc/Bio::Event::EventHandlerI.3 Manifying blib/lib/Bio/LocationI.pm -> blib/libdoc/Bio::LocationI.3 Manifying blib/lib/Bio/Variation/AAChange.pm -> blib/libdoc/Bio::Variation::AAChange.3 Manifying 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blib/libdoc/Bio::Seq::EncodedSeq.3 Manifying blib/lib/Bio/Tree/Statistics.pm -> blib/libdoc/Bio::Tree::Statistics.3 Manifying blib/lib/Bio/Tools/Match.pm -> blib/libdoc/Bio::Tools::Match.3 Manifying blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HTMLResultWriter.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 Manifying blib/lib/Bio/Tools/Primer/AssessorI.pm -> blib/libdoc/Bio::Tools::Primer::AssessorI.3 Manifying blib/lib/Bio/Root/Build.pm -> blib/libdoc/Bio::Root::Build.3 Manifying blib/lib/Bio/Map/PositionWithSequence.pm -> blib/libdoc/Bio::Map::PositionWithSequence.3 Manifying blib/lib/Bio/Matrix/IO/phylip.pm -> blib/libdoc/Bio::Matrix::IO::phylip.3 Manifying blib/lib/Bio/DB/SeqI.pm -> blib/libdoc/Bio::DB::SeqI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3 Manifying blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/libdoc/Bio::SeqFeature::Tools::FeatureNamer.3 Manifying blib/lib/Bio/Coordinate/Pair.pm -> blib/libdoc/Bio::Coordinate::Pair.3 Manifying blib/lib/Bio/SeqFeature/Annotated.pm -> blib/libdoc/Bio::SeqFeature::Annotated.3 Manifying blib/lib/Bio/DB/Query/HIVQuery.pm -> blib/libdoc/Bio::DB::Query::HIVQuery.3 Manifying blib/lib/Bio/Structure/SecStr/DSSP/Res.pm -> blib/libdoc/Bio::Structure::SecStr::DSSP::Res.3 Manifying blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/libdoc/Bio::Tools::Phylo::PAML::ModelResult.3 Manifying blib/lib/Bio/PopGen/PopulationI.pm -> blib/libdoc/Bio::PopGen::PopulationI.3 Manifying blib/lib/Bio/LiveSeq/Translation.pm -> blib/libdoc/Bio::LiveSeq::Translation.3 Manifying blib/lib/Bio/SeqIO/embldriver.pm -> blib/libdoc/Bio::SeqIO::embldriver.3 Manifying blib/lib/Bio/SearchIO/gmap_f9.pm -> blib/libdoc/Bio::SearchIO::gmap_f9.3 Manifying blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -> blib/libdoc/Bio::SearchIO::SearchResultEventBuilder.3 Manifying blib/lib/Bio/Factory/ObjectFactory.pm -> blib/libdoc/Bio::Factory::ObjectFactory.3 Manifying blib/lib/Bio/DB/SwissProt.pm -> blib/libdoc/Bio::DB::SwissProt.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/gene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::gene.3 Manifying blib/lib/Bio/Phenotype/Correlate.pm -> blib/libdoc/Bio::Phenotype::Correlate.3 Manifying blib/lib/Bio/Tools/Run/ParametersI.pm -> blib/libdoc/Bio::Tools::Run::ParametersI.3 Manifying blib/lib/Bio/SeqIO/largefasta.pm -> blib/libdoc/Bio::SeqIO::largefasta.3 Manifying blib/lib/Bio/AlignIO.pm -> blib/libdoc/Bio::AlignIO.3 Manifying blib/lib/Bio/Search/Tiling/MapTileUtils.pm -> blib/libdoc/Bio::Search::Tiling::MapTileUtils.3 Manifying blib/lib/Bio/SeqIO/chaosxml.pm -> blib/libdoc/Bio::SeqIO::chaosxml.3 Manifying blib/lib/Bio/PhyloNetwork/TreeFactoryMulti.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactoryMulti.3 Manifying blib/lib/Bio/Taxonomy/Node.pm -> blib/libdoc/Bio::Taxonomy::Node.3 Manifying blib/lib/Bio/Search/Result/ResultI.pm -> blib/libdoc/Bio::Search::Result::ResultI.3 Manifying blib/lib/Bio/SearchIO/axt.pm -> blib/libdoc/Bio::SearchIO::axt.3 Manifying blib/lib/Bio/DB/UpdateableSeqI.pm -> blib/libdoc/Bio::DB::UpdateableSeqI.3 Manifying blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -> blib/libdoc/Bio::SeqFeature::Tools::IDHandler.3 Manifying blib/lib/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm -> blib/libdoc/Bio::Expression::FeatureGroup::FeatureGroupMas50.3 Manifying blib/lib/Bio/DB/Flat/BDB/genbank.pm -> blib/libdoc/Bio::DB::Flat::BDB::genbank.3 Manifying blib/lib/Bio/SearchIO/blast_pull.pm -> blib/libdoc/Bio::SearchIO::blast_pull.3 Manifying blib/lib/Bio/DB/Flat/BinarySearch.pm -> blib/libdoc/Bio::DB::Flat::BinarySearch.3 Manifying blib/lib/Bio/Map/PositionHandlerI.pm -> blib/libdoc/Bio::Map::PositionHandlerI.3 Manifying blib/lib/Bio/Tools/EUtilities/Link/UrlLink.pm -> blib/libdoc/Bio::Tools::EUtilities::Link::UrlLink.3 Manifying blib/lib/Bio/SearchIO/megablast.pm -> blib/libdoc/Bio::SearchIO::megablast.3 Manifying blib/lib/Bio/Annotation/DBLink.pm -> blib/libdoc/Bio::Annotation::DBLink.3 Manifying blib/lib/Bio/Tree/Node.pm -> blib/libdoc/Bio::Tree::Node.3 Manifying blib/lib/Bio/LiveSeq/Exon.pm -> blib/libdoc/Bio::LiveSeq::Exon.3 Manifying blib/lib/Bio/Tools/EUtilities.pm -> blib/libdoc/Bio::Tools::EUtilities.3 Manifying blib/lib/Bio/SeqIO/exp.pm -> blib/libdoc/Bio::SeqIO::exp.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/match.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::match.3 Manifying blib/lib/Bio/SeqIO/bsml.pm -> blib/libdoc/Bio::SeqIO::bsml.3 Manifying blib/lib/Bio/AlignIO/prodom.pm -> blib/libdoc/Bio::AlignIO::prodom.3 Manifying blib/lib/Bio/Tools/ESTScan.pm -> blib/libdoc/Bio::Tools::ESTScan.3 Manifying blib/lib/Bio/Cluster/UniGeneI.pm -> blib/libdoc/Bio::Cluster::UniGeneI.3 Manifying blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm -> blib/libdoc/Bio::Tools::Signalp::ExtendedSignalp.3 Manifying blib/lib/Bio/Biblio/Journal.pm -> blib/libdoc/Bio::Biblio::Journal.3 Manifying blib/lib/Bio/Matrix/Scoring.pm -> blib/libdoc/Bio::Matrix::Scoring.3 Manifying blib/lib/Bio/Structure/Chain.pm -> blib/libdoc/Bio::Structure::Chain.3 Manifying blib/lib/Bio/Phenotype/Measure.pm -> blib/libdoc/Bio::Phenotype::Measure.3 Manifying blib/lib/Bio/UpdateableSeqI.pm -> blib/libdoc/Bio::UpdateableSeqI.3 Manifying blib/lib/Bio/DB/HIV/HIVQueryHelper.pm -> blib/libdoc/Bio::DB::HIV::HIVQueryHelper.3 Manifying blib/lib/Bio/Search/Tiling/TilingI.pm -> blib/libdoc/Bio::Search::Tiling::TilingI.3 Manifying blib/lib/Bio/SearchDist.pm -> blib/libdoc/Bio::SearchDist.3 Manifying blib/lib/Bio/Coordinate/Graph.pm -> blib/libdoc/Bio::Coordinate::Graph.3 Manifying blib/lib/Bio/IdCollectionI.pm -> blib/libdoc/Bio::IdCollectionI.3 Manifying blib/lib/Bio/Search/Hit/HitI.pm -> blib/libdoc/Bio::Search::Hit::HitI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi.3 Manifying blib/lib/Bio/Search/Result/BlastResult.pm -> blib/libdoc/Bio::Search::Result::BlastResult.3 Manifying blib/lib/Bio/Seq/LargeSeq.pm -> blib/libdoc/Bio::Seq::LargeSeq.3 Manifying blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm -> blib/libdoc/Bio::Expression::FeatureSet::FeatureSetMas50.3 Manifying blib/lib/Bio/SeqIO/game/seqHandler.pm -> blib/libdoc/Bio::SeqIO::game::seqHandler.3 Manifying blib/lib/Bio/Align/ProteinStatistics.pm -> blib/libdoc/Bio::Align::ProteinStatistics.3 Manifying blib/lib/Bio/DB/GFF/Feature.pm -> blib/libdoc/Bio::DB::GFF::Feature.3 Manifying blib/lib/Bio/Annotation/Comment.pm -> blib/libdoc/Bio::Annotation::Comment.3 Manifying blib/lib/Bio/Coordinate/Result.pm -> blib/libdoc/Bio::Coordinate::Result.3 Manifying blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm -> blib/libdoc/Bio::SeqFeature::Gene::Poly_A_site.3 Manifying blib/lib/Bio/Root/IO.pm -> blib/libdoc/Bio::Root::IO.3 Manifying blib/lib/Bio/Search/Hit/HMMERHit.pm -> blib/libdoc/Bio::Search::Hit::HMMERHit.3 Manifying blib/lib/Bio/DB/Fasta.pm -> blib/libdoc/Bio::DB::Fasta.3 Manifying blib/lib/Bio/DB/Biblio/biofetch.pm -> blib/libdoc/Bio::DB::Biblio::biofetch.3 Manifying blib/lib/Bio/Seq/Quality.pm -> blib/libdoc/Bio::Seq::Quality.3 Manifying blib/lib/Bio/SeqIO/strider.pm -> blib/libdoc/Bio::SeqIO::strider.3 Manifying blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactoryX.3 Manifying blib/lib/Bio/Matrix/Mlagan.pm -> blib/libdoc/Bio::Matrix::Mlagan.3 Manifying blib/lib/Bio/SearchIO/sim4.pm -> blib/libdoc/Bio::SearchIO::sim4.3 Manifying blib/lib/Bio/Assembly/IO.pm -> blib/libdoc/Bio::Assembly::IO.3 Manifying blib/lib/Bio/SeqFeature/Gene/UTR.pm -> blib/libdoc/Bio::SeqFeature::Gene::UTR.3 Manifying blib/lib/Bio/Index/Swissprot.pm -> blib/libdoc/Bio::Index::Swissprot.3 Manifying blib/lib/Bio/Tools/SeqStats.pm -> blib/libdoc/Bio::Tools::SeqStats.3 Manifying blib/lib/Bio/Structure/StructureI.pm -> blib/libdoc/Bio::Structure::StructureI.3 Manifying 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blib/lib/Bio/Symbol/Alphabet.pm -> blib/libdoc/Bio::Symbol::Alphabet.3 Manifying blib/lib/Bio/Coordinate/ExtrapolatingPair.pm -> blib/libdoc/Bio::Coordinate::ExtrapolatingPair.3 Manifying blib/lib/Bio/Search/Result/PullResultI.pm -> blib/libdoc/Bio::Search::Result::PullResultI.3 Manifying blib/lib/Bio/SeqIO/tab.pm -> blib/libdoc/Bio::SeqIO::tab.3 Manifying blib/lib/Bio/Coordinate/Collection.pm -> blib/libdoc/Bio::Coordinate::Collection.3 Manifying blib/lib/Bio/LiveSeq/Gene.pm -> blib/libdoc/Bio::LiveSeq::Gene.3 Manifying blib/lib/Bio/Annotation/AnnotationFactory.pm -> blib/libdoc/Bio::Annotation::AnnotationFactory.3 Manifying blib/lib/Bio/Search/Hit/BlastPullHit.pm -> blib/libdoc/Bio::Search::Hit::BlastPullHit.3 Manifying blib/lib/Bio/OntologyIO/goflat.pm -> blib/libdoc/Bio::OntologyIO::goflat.3 Manifying blib/lib/Bio/Location/Simple.pm -> blib/libdoc/Bio::Location::Simple.3 Manifying blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm -> blib/libdoc/Bio::Tools::Phylo::Phylip::ProtDist.3 Manifying blib/lib/Bio/SeqFeature/Collection.pm -> blib/libdoc/Bio::SeqFeature::Collection.3 Manifying blib/lib/Bio/Biblio.pm -> blib/libdoc/Bio::Biblio.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/clone.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::clone.3 Manifying blib/lib/Bio/SeqFeature/Gene/Transcript.pm -> blib/libdoc/Bio::SeqFeature::Gene::Transcript.3 Manifying blib/lib/Bio/SeqFeatureI.pm -> blib/libdoc/Bio::SeqFeatureI.3 Manifying blib/lib/Bio/PopGen/IndividualI.pm -> blib/libdoc/Bio::PopGen::IndividualI.3 Manifying blib/lib/Bio/Tools/Lucy.pm -> blib/libdoc/Bio::Tools::Lucy.3 Manifying blib/lib/Bio/Tools/Run/WrapperBase.pm -> blib/libdoc/Bio::Tools::Run::WrapperBase.3 Manifying blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -> blib/libdoc/Bio::SeqFeature::Tools::TypeMapper.3 Manifying blib/lib/Bio/Biblio/MedlineJournal.pm -> blib/libdoc/Bio::Biblio::MedlineJournal.3 Manifying blib/lib/Bio/SeqIO/kegg.pm -> blib/libdoc/Bio::SeqIO::kegg.3 Manifying blib/lib/Bio/Matrix/PSM/ProtMatrix.pm -> blib/libdoc/Bio::Matrix::PSM::ProtMatrix.3 Manifying blib/lib/Bio/AlignIO/fasta.pm -> blib/libdoc/Bio::AlignIO::fasta.3 Manifying blib/lib/Bio/Matrix/PSM/PsmHeader.pm -> blib/libdoc/Bio::Matrix::PSM::PsmHeader.3 Manifying blib/lib/Bio/SeqFeature/Tools/Unflattener.pm -> blib/libdoc/Bio::SeqFeature::Tools::Unflattener.3 Manifying blib/lib/Bio/Location/WidestCoordPolicy.pm -> blib/libdoc/Bio::Location::WidestCoordPolicy.3 Manifying blib/lib/Bio/Search/Result/GenericResult.pm -> blib/libdoc/Bio::Search::Result::GenericResult.3 Manifying blib/lib/Bio/Map/PositionHandler.pm -> blib/libdoc/Bio::Map::PositionHandler.3 Manifying blib/lib/Bio/Tools/GFF.pm -> blib/libdoc/Bio::Tools::GFF.3 Manifying blib/lib/Bio/Ontology/Ontology.pm -> blib/libdoc/Bio::Ontology::Ontology.3 Manifying blib/lib/Bio/Biblio/PubmedArticle.pm -> blib/libdoc/Bio::Biblio::PubmedArticle.3 Manifying blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::TextResultWriter.3 Manifying blib/lib/Bio/Seq/LargeSeqI.pm -> blib/libdoc/Bio::Seq::LargeSeqI.3 Manifying blib/lib/Bio/AlignIO/nexus.pm -> blib/libdoc/Bio::AlignIO::nexus.3 Manifying blib/lib/Bio/SearchIO/EventHandlerI.pm -> blib/libdoc/Bio::SearchIO::EventHandlerI.3 Manifying blib/lib/Bio/Tools/Seg.pm -> blib/libdoc/Bio::Tools::Seg.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlace.3 Manifying blib/lib/Bio/DB/BioFetch.pm -> blib/libdoc/Bio::DB::BioFetch.3 Manifying blib/lib/Bio/Assembly/IO/phrap.pm -> blib/libdoc/Bio::Assembly::IO::phrap.3 Manifying blib/lib/Bio/Taxon.pm -> blib/libdoc/Bio::Taxon.3 Manifying blib/lib/Bio/Tools/RNAMotif.pm -> blib/libdoc/Bio::Tools::RNAMotif.3 Manifying blib/lib/Bio/Ontology/RelationshipI.pm -> blib/libdoc/Bio::Ontology::RelationshipI.3 Manifying blib/lib/Bio/Factory/AnalysisI.pm -> blib/libdoc/Bio::Factory::AnalysisI.3 Manifying blib/lib/Bio/PopGen/Genotype.pm -> blib/libdoc/Bio::PopGen::Genotype.3 Manifying blib/lib/Bio/Map/OrderedPositionWithDistance.pm -> blib/libdoc/Bio::Map::OrderedPositionWithDistance.3 Manifying blib/lib/Bio/Coordinate/Utils.pm -> blib/libdoc/Bio::Coordinate::Utils.3 Manifying blib/lib/Bio/Tools/EUtilities/History.pm -> blib/libdoc/Bio::Tools::EUtilities::History.3 Manifying blib/lib/Bio/PopGen/Statistics.pm -> blib/libdoc/Bio::PopGen::Statistics.3 Manifying blib/lib/Bio/DB/EntrezGene.pm -> blib/libdoc/Bio::DB::EntrezGene.3 Manifying blib/lib/Bio/AnnotationI.pm -> blib/libdoc/Bio::AnnotationI.3 Manifying blib/lib/Bio/Ontology/Relationship.pm -> blib/libdoc/Bio::Ontology::Relationship.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/HNN.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::HNN.3 Manifying blib/lib/Bio/Seq/SeqBuilder.pm -> blib/libdoc/Bio::Seq::SeqBuilder.3 Manifying blib/lib/Bio/Tools/SeqWords.pm -> blib/libdoc/Bio::Tools::SeqWords.3 Manifying blib/lib/Bio/SeqIO/raw.pm -> blib/libdoc/Bio::SeqIO::raw.3 Manifying blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -> blib/libdoc/Bio::SeqFeature::TypedSeqFeatureI.3 Manifying blib/lib/Bio/Search/Iteration/IterationI.pm -> blib/libdoc/Bio::Search::Iteration::IterationI.3 Manifying blib/lib/Bio/Search/Result/ResultFactory.pm -> blib/libdoc/Bio::Search::Result::ResultFactory.3 Manifying blib/lib/Bio/LiveSeq/Chain.pm -> blib/libdoc/Bio::LiveSeq::Chain.3 Manifying blib/lib/Bio/PopGen/HtSNP.pm -> blib/libdoc/Bio::PopGen::HtSNP.3 Manifying blib/lib/Bio/LiveSeq/Mutation.pm -> blib/libdoc/Bio::LiveSeq::Mutation.3 Manifying blib/lib/Bio/Map/SimpleMap.pm -> blib/libdoc/Bio::Map::SimpleMap.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::GFF2Loader.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::Pg.3 Manifying blib/lib/Bio/Search/Hit/ModelHit.pm -> blib/libdoc/Bio::Search::Hit::ModelHit.3 Manifying blib/lib/Bio/Tools/HMMER/Domain.pm -> blib/libdoc/Bio::Tools::HMMER::Domain.3 Manifying blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSiteI.3 Manifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libdoc/Bio::Structure::SecStr::STRIDE::Res.3 Manifying blib/lib/Bio/Map/Physical.pm -> blib/libdoc/Bio::Map::Physical.3 Manifying blib/lib/Bio/DB/InMemoryCache.pm -> blib/libdoc/Bio::DB::InMemoryCache.3 Manifying blib/lib/Bio/Perl.pm -> blib/libdoc/Bio::Perl.3 Manifying blib/lib/Bio/SeqIO/game/gameWriter.pm -> blib/libdoc/Bio::SeqIO::game::gameWriter.3 Manifying blib/lib/Bio/SeqIO/abi.pm -> blib/libdoc/Bio::SeqIO::abi.3 Manifying blib/lib/Bio/LiveSeq/AARange.pm -> blib/libdoc/Bio::LiveSeq::AARange.3 Manifying blib/lib/Bio/PrimarySeq.pm -> blib/libdoc/Bio::PrimarySeq.3 Manifying blib/lib/Bio/DB/Flat/BDB/fasta.pm -> blib/libdoc/Bio::DB::Flat::BDB::fasta.3 Manifying blib/lib/Bio/Tools/Run/GenericParameters.pm -> blib/libdoc/Bio::Tools::Run::GenericParameters.3 Manifying blib/lib/Bio/SeqIO/lasergene.pm -> blib/libdoc/Bio::SeqIO::lasergene.3 Manifying blib/lib/Bio/PopGen/IO/prettybase.pm -> blib/libdoc/Bio::PopGen::IO::prettybase.3 Manifying blib/lib/Bio/Assembly/IO/ace.pm -> blib/libdoc/Bio::Assembly::IO::ace.3 Manifying blib/lib/Bio/Symbol/SymbolI.pm -> blib/libdoc/Bio::Symbol::SymbolI.3 Manifying blib/lib/Bio/SimpleAnalysisI.pm -> blib/libdoc/Bio::SimpleAnalysisI.3 Manifying blib/lib/Bio/Matrix/PSM/IO/transfac.pm -> blib/libdoc/Bio::Matrix::PSM::IO::transfac.3 Manifying blib/lib/Bio/LiveSeq/IO/BioPerl.pm -> blib/libdoc/Bio::LiveSeq::IO::BioPerl.3 Manifying blib/lib/Bio/Annotation/OntologyTerm.pm -> blib/libdoc/Bio::Annotation::OntologyTerm.3 Manifying blib/lib/Bio/Tools/Run/RemoteBlast.pm -> blib/libdoc/Bio::Tools::Run::RemoteBlast.3 Manifying blib/lib/Bio/Phenotype/MeSH/Term.pm -> blib/libdoc/Bio::Phenotype::MeSH::Term.3 Manifying blib/lib/Bio/Tools/Pseudowise.pm -> blib/libdoc/Bio::Tools::Pseudowise.3 Manifying blib/lib/Bio/DB/HIV.pm -> blib/libdoc/Bio::DB::HIV.3 Manifying blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -> blib/libdoc/Bio::SeqFeature::AnnotationAdaptor.3 Manifying blib/lib/Bio/Matrix/IO.pm -> blib/libdoc/Bio::Matrix::IO.3 Manifying blib/lib/Bio/Map/Gene.pm -> blib/libdoc/Bio::Map::Gene.3 Manifying blib/lib/Bio/Map/Prediction.pm -> blib/libdoc/Bio::Map::Prediction.3 Manifying blib/lib/Bio/Biblio/Person.pm -> blib/libdoc/Bio::Biblio::Person.3 Manifying blib/lib/Bio/Search/BlastStatistics.pm -> blib/libdoc/Bio::Search::BlastStatistics.3 Manifying blib/lib/Bio/PopGen/MarkerI.pm -> blib/libdoc/Bio::PopGen::MarkerI.3 Manifying blib/lib/Bio/Tools/Grail.pm -> blib/libdoc/Bio::Tools::Grail.3 Manifying blib/lib/Bio/Search/HSP/ModelHSP.pm -> blib/libdoc/Bio::Search::HSP::ModelHSP.3 Manifying blib/lib/Bio/DB/WebDBSeqI.pm Build: blib/script/bp_bulk_load_gff.pl: cannot resolve L in paragraph 26. 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blib/libhtml/site/lib/Bio/LiveSeq/Intron.html HTMLifying blib/lib/Bio/Matrix/IO/scoring.pm -> blib/libhtml/site/lib/Bio/Matrix/IO/scoring.html HTMLifying blib/lib/Bio/Seq/LargeLocatableSeq.pm -> blib/libhtml/site/lib/Bio/Seq/LargeLocatableSeq.html HTMLifying blib/lib/Bio/AlignIO/msf.pm -> blib/libhtml/site/lib/Bio/AlignIO/msf.html HTMLifying blib/lib/Bio/Tools/Glimmer.pm -> blib/libhtml/site/lib/Bio/Tools/Glimmer.html HTMLifying blib/lib/Bio/SeqIO/flybase_chadoxml.pm -> blib/libhtml/site/lib/Bio/SeqIO/flybase_chadoxml.html HTMLifying blib/lib/Bio/Map/RelativeI.pm -> blib/libhtml/site/lib/Bio/Map/RelativeI.html HTMLifying blib/lib/Bio/Tools/Profile.pm -> blib/libhtml/site/lib/Bio/Tools/Profile.html HTMLifying blib/lib/Bio/LiveSeq/Mutator.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Mutator.html HTMLifying blib/lib/Bio/Tools/Primer/Pair.pm -> blib/libhtml/site/lib/Bio/Tools/Primer/Pair.html HTMLifying blib/lib/Bio/Annotation/TypeManager.pm -> 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blib/libhtml/site/lib/Bio/Factory/ApplicationFactoryI.html HTMLifying blib/lib/Bio/SeqIO/scf.pm -> blib/libhtml/site/lib/Bio/SeqIO/scf.html HTMLifying blib/lib/Bio/Tools/EUtilities/Info.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Info.html HTMLifying blib/lib/Bio/PopGen/PopStats.pm -> blib/libhtml/site/lib/Bio/PopGen/PopStats.html HTMLifying blib/lib/Bio/SeqEvolution/Factory.pm -> blib/libhtml/site/lib/Bio/SeqEvolution/Factory.html HTMLifying blib/lib/Bio/DB/Query/GenBank.pm -> blib/libhtml/site/lib/Bio/DB/Query/GenBank.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/DBI/SQLite.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm -> 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blib/libhtml/site/lib/Bio/IdentifiableI.html HTMLifying blib/lib/Bio/Map/Mappable.pm -> blib/libhtml/site/lib/Bio/Map/Mappable.html HTMLifying blib/lib/Bio/Search/Tiling/MapTiling.pm -> blib/libhtml/site/lib/Bio/Search/Tiling/MapTiling.html HTMLifying blib/lib/Bio/Matrix/PSM/ProtPsm.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/ProtPsm.html HTMLifying blib/lib/Bio/Taxonomy/Taxon.pm -> blib/libhtml/site/lib/Bio/Taxonomy/Taxon.html HTMLifying blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm -> blib/libhtml/site/lib/Bio/DB/SeqFBuild: blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm: cannot resolve L in paragraph 160. 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Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm: cannot resolve L in paragraph 8. eneStructureI.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/GeneStructureI.html HTMLifying blib/lib/Bio/Biblio/MedlineBook.pm -> blib/libhtml/site/lib/Bio/Biblio/MedlineBook.html HTMLifying blib/lib/Bio/Biblio/Proceeding.pm -> blib/libhtml/site/lib/Bio/Biblio/Proceeding.html HTMLifying blib/lib/Bio/Index/Fastq.pm -> blib/libhtml/site/lib/Bio/Index/Fastq.html HTMLifying blib/lib/Bio/SeqUtils.pm -> blib/libhtml/site/lib/Bio/SeqUtils.html HTMLifying blib/lib/Bio/DB/Failover.pm -> blib/libhtml/site/lib/Bio/DB/Failover.html HTMLifying blib/lib/Bio/SeqIO/asciitree.pm -> blib/libhtml/site/lib/Bio/SeqIO/asciitree.html HTMLifying blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/SiteMatrixI.html HTMLifying blib/lib/Bio/Tools/Gel.pm -> blib/libhtml/site/lib/Bio/Tools/Gel.html HTMLifying blib/lib/Bio/DB/Registry.pm -> blib/libhtml/site/lib/Bio/DB/Registry.html HTMLifying blib/lib/Bio/SeqIO/game/featHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/featHandler.html HTMLifying blib/lib/Bio/Search/HSP/BlastHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/BlastHSP.html HTMLifying blib/lib/Bio/Factory/SequenceFactoryI.pm -> blib/libhtml/site/lib/Bio/Factory/SequenceFactoryI.html HTMLifying blib/lib/Bio/Biblio/TechReport.pm -> blib/libhtml/site/lib/Bio/Biblio/TechReport.html HTMLifying blib/lib/Bio/Tools/Blat.pm -> blib/libhtml/site/lib/Bio/Tools/Blat.html HTMLifying blib/lib/Bio/Tools/Protparam.pm -> blib/libhtml/site/lib/Bio/Tools/Protparam.html HTMLifying blib/lib/Bio/PhyloNetwork.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork.html HTMLifying blib/lib/Bio/SeqIO/metafasta.pm -> blib/libhtml/site/lib/Bio/SeqIO/metafasta.html HTMLifying blib/lib/Bio/Expression/Sample.pm -> blib/libhtml/site/lib/Bio/Expression/Sample.html HTMLifying blib/lib/Bio/Map/CytoMarker.pm -> blib/libhtml/site/lib/Bio/Map/CytoMarker.html HTMLifying blib/lib/Bio/Tools/TargetP.pm -> blib/libhtml/site/lib/Bio/Tools/TargetP.html HTMLifying blib/lib/Bio/DB/NCBIHelper.pm -> blib/libhtml/site/lib/Bio/DB/NCBIHelper.html HTMLifying blib/lib/Bio/SeqIO/table.pm -> blib/libhtml/site/lib/Bio/SeqIO/table.html HTMLifying blib/lib/Bio/Root/Root.pm -> blib/libhtml/site/lib/Bio/Root/Root.html HTMLifying blib/lib/Bio/Tools/Spidey/Exon.pm -> blib/libhtml/site/lib/Bio/Tools/Spidey/Exon.html HTMLifying blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/EUtilDataI.html HTMLifying blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/libhtml/site/lib/Bio/AlignIO/Handler/GenericAlignHandler.html HTMLifying blib/lib/Bio/Event/EventGeneratorI.pm -> blib/libhtml/site/lib/Bio/Event/EventGeneratorI.html HTMLifying blib/lib/Bio/SearchIO/exonerate.pm -> blib/libhtml/site/lib/Bio/SearchIO/exonerate.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/ace.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/ace.html HTMLifying blib/lib/Bio/DB/QueryI.pm -> blib/libhtml/site/lib/Bio/DB/QueryI.html HTMLifying blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -> blib/libhtml/site/lib/Bio/Factory/SeqAnalysisParserFactory.html HTMLifying blib/lib/Bio/AlignIO/maf.pm -> blib/libhtml/site/lib/Bio/AlignIO/maf.html HTMLifying blib/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm -> blib/libhtml/site/lib/Bio/Tools/Run/StandAloneNCBIBlast.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/Sopma.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/Sopma.html HTMLifying blib/lib/Bio/Search/Hit/BlastHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/BlastHit.html HTMLifying blib/lib/Bio/DB/SeqHound.pm -> blib/libhtml/site/lib/Bio/DB/SeqHound.html HTMLifying blib/lib/Bio/SeqIO/game/gameHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/gameHandler.html HTMLifying blib/lib/Bio/SeqFeature/Generic.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Generic.html HTMLifying blib/lib/Bio/Search/SearchUtils.pm -> blib/libhtml/site/lib/Bio/Search/SearchUtils.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.html HTMLifying blib/lib/Bio/Factory/ObjectBuilderI.pm -> blib/libhtml/site/lib/Bio/Factory/ObjectBuilderI.html HBuild: blib/lib/Bio/DB/GFF/Typename.pm: cannot resolve L in paragraph 49. 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Build: blib/lib/Bio/SeqIO/swiss.pm: cannot resolve L in paragraph 44. Build: blib/lib/Bio/ClusterIO.pm: cannot resolve L in paragraph 29. Build: blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm: cannot resolve L in paragraph 15. ib/Bio/Das/FeatureTypeI.pm -> blib/libhtml/site/lib/Bio/Das/FeatureTypeI.html HTMLifying blib/lib/Bio/PhyloNetwork/FactoryX.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/FactoryX.html HTMLifying blib/lib/Bio/Search/HSP/HSPFactory.pm -> blib/libhtml/site/lib/Bio/Search/HSP/HSPFactory.html HTMLifying blib/lib/Bio/SeqIO/gbdriver.pm -> blib/libhtml/site/lib/Bio/SeqIO/gbdriver.html HTMLifying blib/lib/Bio/Symbol/Symbol.pm -> blib/libhtml/site/lib/Bio/Symbol/Symbol.html HTMLifying blib/lib/Bio/Tools/Prediction/Exon.pm -> blib/libhtml/site/lib/Bio/Tools/Prediction/Exon.html HTMLifying blib/lib/Bio/DB/BiblioI.pm -> blib/libhtml/site/lib/Bio/DB/BiblioI.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/GOR4.html HTMLifying blib/lib/Bio/Map/Marker.pm -> blib/libhtml/site/lib/Bio/Map/Marker.html HTMLifying blib/lib/Bio/Root/Version.pm -> blib/libhtml/site/lib/Bio/Root/Version.html HTMLifying blib/lib/Bio/SeqIO.pm -> blib/libhtml/site/lib/Bio/SeqIO.html HTMLifying blib/lib/Bio/Location/FuzzyLocationI.pm -> blib/libhtml/site/lib/Bio/Location/FuzzyLocationI.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.html HTMLifying blib/lib/Bio/PopGen/IO/phase.pm -> blib/libhtml/site/lib/Bio/PopGen/IO/phase.html HTMLifying blib/lib/Bio/Align/DNAStatistics.pm -> blib/libhtml/site/lib/Bio/Align/DNAStatistics.html HTMLifying blib/lib/Bio/Biblio/PubmedJournalArticle.pm -> blib/libhtml/site/lib/Bio/Biblio/PubmedJournalArticle.html HTMLifying blib/lib/Bio/Tools/EUtilities/Summary.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Summary.html HTMLifying blib/lib/Bio/Tools/Eponine.pm -> blib/libhtml/site/lib/Bio/Tools/Eponine.html HTMLifying blib/lib/Bio/Variation/Allele.pm -> blib/libhtml/site/lib/Bio/Variation/Allele.html HTMLifying blib/lib/Bio/Phenotype/Phenotype.pm -> blib/libhtml/site/lib/Bio/Phenotype/Phenotype.html HTMLifying blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/libhtml/site/lib/Bio/Factory/SeqAnalysisParserFactoryI.html HTMLifying blib/lib/Bio/SeqIO/swiss.pm -> blib/libhtml/site/lib/Bio/SeqIO/swiss.html HTMLifying blib/lib/Bio/DB/ReferenceI.pm -> blib/libhtml/site/lib/Bio/DB/ReferenceI.html HTMLifying blib/lib/Bio/ClusterIO.pm -> blib/libhtml/site/lib/Bio/ClusterIO.html HTMLifying blib/lib/Bio/DB/Taxonomy/entrez.pm -> blib/libhtml/site/lib/Bio/DB/Taxonomy/entrez.html HTMLifying blib/lib/Bio/Map/GenePosition.pm -> blib/libhtml/site/lib/Bio/Map/GenePosition.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.html HTMLifying blib/lib/Bio/Map/FPCMarker.pm -> blib/libhtml/site/lib/Bio/Map/FPCMarker.html HTMLifying blib/lib/Bio/AlignIO/mase.pm -> blib/libhtml/site/lib/Bio/AlignIO/mase.html HTMLifying blib/lib/Bio/OntologyIO/soflat.pm -> blib/libhtml/site/lib/Bio/OntologyIO/soflat.html HTMLifying blib/lib/Bio/MapIO/fpc.pm -> blib/libhtml/site/lib/Bio/MapIO/fpc.html HTMLifying blib/lib/Bio/Coordinate/Result/Match.pm -> blib/libhtml/site/lib/Bio/Coordinate/Result/Match.html HTMLifying blib/lib/Bio/Search/Hit/PsiBlastHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/PsiBlastHit.html HTMLifying blib/lib/Bio/Restriction/IO/bairoch.pm -> blib/libhtml/site/lib/Bio/Restriction/IO/bairoch.html HTMLifying blib/lib/Bio/PopGen/IO/csv.pm -> blib/libhtml/site/lib/Bio/PopGen/IO/csv.html HTMLifying blib/lib/Bio/Biblio/IO/medlinexml.pm -> blib/libhtml/site/lib/Bio/Biblio/IO/medlinexml.html HTMLifying blib/lib/Bio/Search/Result/WABAResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/WABAResult.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/none.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/none.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/berkeleydb3.html HTMLifying blib/lib/Bio/Search/Result/HmmpfamResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/HmmpfamResult.html HTMLifying blib/lib/Bio/DB/GenBank.pm -> blib/libhtml/site/lib/Bio/DB/GenBank.html HTMLifying blib/lib/Bio/AlBuild: blib/lib/Bio/DB/GFF/RelSegment.pm: cannot resolve L in paragraph 251. 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Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm: cannot resolve L in paragraph 45. Build: blib/lib/Bio/DB/SeqFeature/Store/memory.pm: cannot resolve L in paragraph 121. 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Build: blib/lib/Bio/DB/SeqFeature/Store/Loader.pm: cannot resolve L in paragraph 178. Build: blib/lib/Bio/DB/GFF/Featname.pm: cannot resolve L in paragraph 44. Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm: cannot resolve L in paragraph 8. atabaseI.html HTMLifying blib/lib/Bio/Tools/Phylo/Gumby.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/Gumby.html HTMLifying blib/lib/Bio/DasI.pm -> blib/libhtml/site/lib/Bio/DasI.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.html HTMLifying blib/lib/Bio/SeqIO/tigr.pm -> blib/libhtml/site/lib/Bio/SeqIO/tigr.html HTMLifying blib/lib/Bio/Index/GenBank.pm -> blib/libhtml/site/lib/Bio/Index/GenBank.html HTMLifying blib/lib/Bio/FeatureIO/ptt.pm -> blib/libhtml/site/lib/Bio/FeatureIO/ptt.html HTMLifying blib/lib/Bio/PhyloNetwork/RandomFactory.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/RandomFactory.html HTMLifying blib/lib/Bio/DB/Biblio/soap.pm -> blib/libhtml/site/lib/Bio/DB/Biblio/soap.html HTMLifying blib/lib/Bio/SearchIO/hmmer.pm -> blib/libhtml/site/lib/Bio/SearchIO/hmmer.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/Loader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/Loader.html HTMLifying blib/lib/Bio/Tools/tRNAscanSE.pm -> blib/libhtml/site/lib/Bio/Tools/tRNAscanSE.html HTMLifying blib/lib/Bio/Assembly/IO/tigr.pm -> blib/libhtml/site/lib/Bio/Assembly/IO/tigr.html HTMLifying blib/lib/Bio/Biblio/JournalArticle.pm -> blib/libhtml/site/lib/Bio/Biblio/JournalArticle.html HTMLifying blib/lib/Bio/Tools/Sim4/Results.pm -> blib/libhtml/site/lib/Bio/Tools/Sim4/Results.html HTMLifying blib/lib/Bio/Index/Hmmer.pm -> blib/libhtml/site/lib/Bio/Index/Hmmer.html HTMLifying blib/lib/Bio/MapIO/mapmaker.pm -> blib/libhtml/site/lib/Bio/MapIO/mapmaker.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/biofetch.html HTMLifying blib/lib/Bio/Tools/Prediction/Gene.pm -> blib/libhtml/site/lib/Bio/Tools/Prediction/Gene.html HTMLifying blib/lib/Bio/Root/Test/Warn.pm -> blib/libhtml/site/lib/Bio/Root/Test/Warn.html HTMLifying blib/lib/Bio/AlignIO/meme.pm -> blib/libhtml/site/lib/Bio/AlignIO/meme.html HTMLifying blib/lib/Bio/Tools/SeqPattern.pm -> blib/libhtml/site/lib/Bio/Tools/SeqPattern.html HTMLifying blib/lib/Bio/Seq/RichSeq.pm -> blib/libhtml/site/lib/Bio/Seq/RichSeq.html HTMLifying blib/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.html HTMLifying blib/lib/Bio/Search/HSP/HMMERHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/HMMERHSP.html HTMLifying blib/lib/Bio/SeqIO/ctf.pm -> blib/libhtml/site/lib/Bio/SeqIO/ctf.html HTMLifying blib/lib/Bio/DB/Taxonomy/list.pm -> blib/libhtml/site/lib/Bio/DB/Taxonomy/list.html HTMLifying blib/lib/Bio/Location/NarrowestCoordPolicy.pm -> blib/libhtml/site/lib/Bio/Location/NarrowestCoordPolicy.html HTMLifying blib/lib/Bio/Tools/Sigcleave.pm -> blib/libhtml/site/lib/Bio/Tools/Sigcleave.html HTMLifying blib/lib/Bio/DB/Taxonomy.pm -> blib/libhtml/site/lib/Bio/DB/Taxonomy.html HTMLifying blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm -> blib/libhtml/site/lib/Bio/Assembly/Tools/ContigSpectrum.html HTMLifying blib/lib/Bio/Ontology/GOterm.pm -> blib/libhtml/site/lib/Bio/Ontology/GOterm.html HTMLifying blib/lib/Bio/DB/Flat/BDB/embl.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB/embl.html HTMLifying blib/lib/Bio/Tools/MZEF.pm -> blib/libhtml/site/lib/Bio/Tools/MZEF.html HTMLifying blib/lib/Bio/Phenotype/MeSH/Twig.pm -> blib/libhtml/site/lib/Bio/Phenotype/MeSH/Twig.html HTMLifying blib/lib/Bio/Tools/Primer/Feature.pm -> blib/libhtml/site/lib/Bio/Tools/Primer/Feature.html HTMLifying blib/lib/Bio/DB/GFF/Featname.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Featname.html HTMLifying blib/lib/Bio/LiveSeq/SeqI.pm -> blib/libhtml/site/lib/Bio/LiveSeq/SeqI.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.html HTMLifying blib/lib/Bio/SeqFeature/FeaturePair.pm -> blib/libhtml/site/lib/Bio/SeqFeature/FeaturePair.html HTMLifying blib/lib/Bio/LiveSeq/Repeat_Unit.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Repeat_Unit.html HTMLifying blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.html HTMLifying blib/lib/BioBuild: blib/lib/Bio/DB/SeqFeature/Segment.pm: cannot resolve L in paragraph 122. 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Build: blib/lib/Bio/DB/GFF/Homol.pm: cannot resolve L in paragraph 28. /OntologyIO.pm -> blib/libhtml/site/lib/Bio/OntologyIO.html HTMLifying blib/lib/Bio/Variation/SNP.pm -> blib/libhtml/site/lib/Bio/Variation/SNP.html HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactory.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactory.html HTMLifying blib/lib/Bio/Tools/pICalculator.pm -> blib/libhtml/site/lib/Bio/Tools/pICalculator.html HTMLifying blib/lib/Bio/DB/GenPept.pm -> blib/libhtml/site/lib/Bio/DB/GenPept.html HTMLifying blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/SiteMatrix.html HTMLifying blib/lib/Bio/DB/GFF.pm -> blib/libhtml/site/lib/Bio/DB/GFF.html HTMLifying blib/lib/Bio/Ontology/RelationshipFactory.pm -> blib/libhtml/site/lib/Bio/Ontology/RelationshipFactory.html HTMLifying blib/lib/Bio/Biblio/WebResource.pm -> blib/libhtml/site/lib/Bio/Biblio/WebResource.html HTMLifying blib/lib/Bio/ParameterBaseI.pm -> blib/libhtml/site/lib/Bio/ParameterBaseI.html HTMLifying blib/lib/Bio/Search/Hit/HitFactory.pm -> blib/libhtml/site/lib/Bio/Search/Hit/HitFactory.html HTMLifying blib/lib/Bio/DB/SeqFeature/Segment.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Segment.html HTMLifying blib/lib/Bio/Index/Fasta.pm -> blib/libhtml/site/lib/Bio/Index/Fasta.html HTMLifying blib/lib/Bio/FeatureIO/bed.pm -> blib/libhtml/site/lib/Bio/FeatureIO/bed.html HTMLifying blib/lib/Bio/ConfigData.pm -> blib/libhtml/site/lib/Bio/ConfigData.html HTMLifying blib/lib/Bio/Ontology/InterProTerm.pm -> blib/libhtml/site/lib/Bio/Ontology/InterProTerm.html HTMLifying blib/lib/Bio/PopGen/Simulation/GeneticDrift.pm -> blib/libhtml/site/lib/Bio/PopGen/Simulation/GeneticDrift.html HTMLifying blib/lib/Bio/AlignIO/metafasta.pm -> blib/libhtml/site/lib/Bio/AlignIO/metafasta.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.html HTMLifying blib/lib/Bio/Restriction/Enzyme.pm -> blib/libhtml/site/lib/Bio/Restriction/Enzyme.html HTMLifying blib/lib/Bio/Tools/QRNA.pm -> blib/libhtml/site/lib/Bio/Tools/QRNA.html HTMLifying blib/lib/Bio/Tools/Phylo/PAML/Result.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/PAML/Result.html HTMLifying blib/lib/Bio/Location/AvWithinCoordPolicy.pm -> blib/libhtml/site/lib/Bio/Location/AvWithinCoordPolicy.html HTMLifying blib/lib/Bio/Symbol/AlphabetI.pm -> blib/libhtml/site/lib/Bio/Symbol/AlphabetI.html HTMLifying blib/lib/Bio/Tools/Genscan.pm -> blib/libhtml/site/lib/Bio/Tools/Genscan.html HTMLifying blib/lib/Bio/Annotation/Relation.pm -> blib/libhtml/site/lib/Bio/Annotation/Relation.html HTMLifying blib/lib/Bio/Tree/Draw/Cladogram.pm -> blib/libhtml/site/lib/Bio/Tree/Draw/Cladogram.html HTMLifying blib/lib/Bio/Biblio/IO/pubmedxml.pm -> blib/libhtml/site/lib/Bio/Biblio/IO/pubmedxml.html HTMLifying blib/lib/Bio/DB/GFF/Homol.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Homol.html HTMLifying blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -> blib/libhtml/site/lib/Bio/SearchIO/FastHitEventBuilder.html HTMLifying blib/lib/Bio/SeqFeature/SiRNA/Pair.pm -> blib/libhtml/site/lib/Bio/SeqFeature/SiRNA/Pair.html HTMLifying blib/lib/Bio/Factory/MapFactoryI.pm -> blib/libhtml/site/lib/Bio/Factory/MapFactoryI.html HTMLifying blib/lib/Bio/SeqEvolution/EvolutionI.pm -> blib/libhtml/site/lib/Bio/SeqEvolution/EvolutionI.html HTMLifying blib/lib/Bio/Tools/OddCodes.pm -> blib/libhtml/site/lib/Bio/Tools/OddCodes.html HTMLifying blib/lib/Bio/SearchIO/psl.pm -> blib/libhtml/site/lib/Bio/SearchIO/psl.html HTMLifying blib/lib/Bio/Map/TranscriptionFactor.pm -> blib/libhtml/site/lib/Bio/Map/TranscriptionFactor.html HTMLifying blib/lib/Bio/RangeI.pm -> blib/libhtml/site/lib/Bio/RangeI.html HTMLifying blib/lib/Bio/SeqAnalysisParserI.pm -> blib/libhtml/site/lib/Bio/SeqAnalysisParserI.html HTMLifying blib/lib/Bio/Map/Clone.pm -> blib/libhtml/site/lib/Bio/Map/Clone.html HTMLifying blib/lib/Bio/SeqIO/chaos.pm -> blib/libhtml/site/lib/Bio/SeqIO/chaos.html HTMLifying blib/lib/Bio/Restriction/IO.pm -> blib/libhtml/site/lib/Bio/Restriction/IO.html HTMLifying blib/lib/Bio/DB/TFBS.pm -> blib/libhtml/site/lib/Bio/DB/TFBS.html HTMLifying blib/lib/Bio/StructuBuild: blib/lib/Bio/DB/GFF/Segment.pm: cannot resolve L in paragraph 229. Build: blib/lib/Bio/SeqIO/genbank.pm: cannot resolve L in paragraph 22. 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blib/libhtml/site/lib/Bio/Seq/PrimaryQual.html HTMLifying blib/lib/Bio/Tools/Signalp.pm -> blib/libhtml/site/lib/Bio/Tools/Signalp.html HTMLifying blib/lib/Bio/FeatureIO/vecscreen_simple.pm -Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm: cannot resolve L in paragraph 161. > blib/libhtml/site/lib/Bio/FeatureIO/vecscreen_simple.html HTMLifying blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Info/LinkInfo.html HTMLifying blib/lib/Bio/DB/Flat/BDB.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB.html HTMLifying blib/lib/Bio/Seq/Meta.pm -> blib/libhtml/site/lib/Bio/Seq/Meta.html HTMLifying blib/lib/Bio/SeqFeature/Gene/Intron.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/Intron.html HTMLifying blib/lib/Bio/Seq/SequenceTrace.pm -> blib/libhtml/site/lib/Bio/Seq/SequenceTrace.html HTMLifying blib/lib/Bio/Annotation/Collection.pm -> blib/libhtml/site/lib/Bio/Annotation/Collection.html HTMLifying blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm -> 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MLifying blib/lib/Bio/Restriction/IO/base.pm -> blib/libhtml/site/lib/Bio/Restriction/IO/base.html HTMLifying blib/lib/Bio/DB/FileCache.pm -> blib/libhtml/site/lib/Bio/DB/FileCache.html HTMLifying blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm -> blib/libhtml/site/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.html HTMLifying blib/lib/Bio/Seq/EncodedSeq.pm -> blib/libhtml/site/lib/Bio/Seq/EncodedSeq.html HTMLifying blib/lib/Bio/Tree/Statistics.pm -> blib/libhtml/site/lib/Bio/Tree/Statistics.html HTMLifying blib/lib/Bio/Tools/Match.pm -> blib/libhtml/site/lib/Bio/Tools/Match.html HTMLifying blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/libhtml/site/lib/Bio/SearchIO/Writer/HTMLResultWriter.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.html HTMLifying blib/lib/Bio/Tools/Primer/AssessorI.pm -> blib/libhtml/site/lib/Bio/Tools/Primer/AssessorI.html HTMLifying blib/lib/Bio/Root/Build.pm -> blib/libhtml/site/lib/Bio/Root/Build.html HTMLifying blib/lib/Bio/Map/PositionWithSequence.pm -> blib/libhtml/site/lib/Bio/Map/PositionWithSequence.html HTMLifying blib/lib/Bio/Matrix/IO/phylip.pm -> blib/libhtml/site/lib/Bio/Matrix/IO/phylip.html HTMLifying blib/lib/Bio/DB/SeqI.pm -> blib/libhtml/site/lib/Bio/DB/SeqI.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.html HTMLifying blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Tools/FeatureNamer.html HTMLifying blib/lib/Bio/Coordinate/Pair.pm -> blib/libhtml/site/lib/Bio/Coordinate/Pair.html HTMLifying blib/lib/Bio/SeqFeature/Annotated.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Annotated.html HTMLifying blib/lib/Bio/DB/Query/HIVQuery.pm -> blib/libhtml/site/lib/Bio/DB/Query/HIVQuery.html HTMLifying blib/lib/Bio/Structure/SecStr/DSSP/Res.pm -> blib/libhtml/site/lib/Bio/Structure/SecStr/DSSP/Res.html HTMLifying blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/PAML/ModelResult.html HTMLifying blib/lib/Bio/PopGen/PopulationI.pm -> blib/libhtml/site/lib/Bio/PopGen/PopulationI.html HTMLifying blib/lib/Bio/LiveSeq/Translation.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Translation.html HTMLifying blib/lib/Bio/SeqIO/embldriver.pm -> blib/libhtml/site/lib/Bio/SeqIO/embldriver.html HTMLifying blib/lib/Bio/SearchIO/gmap_f9.pm -> blib/libhtml/site/lib/Bio/SearchIO/gmap_f9.html HTMLifying blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -> blib/libhtml/site/lib/Bio/SearchIO/SearchResultEventBuilder.html HTMLifying blib/lib/Bio/Factory/ObjectFactory.pm -> blib/libhtml/site/lib/Bio/Factory/ObjectFactory.html HTMLifying blib/lib/Bio/DB/SwissProt.pm -> blib/libhtml/site/lib/Bio/DB/SwissProt.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/gene.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/gene.html HTMLifying blib/lib/Bio/Phenotype/Correlate.pm -> blib/libhtml/site/lib/Bio/Phenotype/Correlate.html HTMLifying blib/lib/Bio/Tools/Run/ParametersI.pm -> blib/libhtml/site/lib/Bio/Tools/Run/ParametersI.html HTMLifying blib/lib/Bio/SeqIO/largefasta.pm -> blib/libhtml/site/lib/Bio/SeqIO/largefasta.html HTMLifying blib/lib/Bio/AlignIO.pm -> blib/libhtml/site/lib/Bio/AlignIO.html HTMLifying blib/lib/Bio/Search/Tiling/MapTileUtils.pm -> blib/libhtml/site/lib/Bio/Search/Tiling/MapTileUtils.html HTMLifying blib/lib/Bio/SeqIO/chaosxml.pm -> blib/libhtml/site/lib/Bio/SeqIO/chaosxml.html HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactoryMulti.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactoryMulti.html HTMLifying blib/lib/Bio/Taxonomy/Node.pm -> blib/libhtml/site/lib/Bio/Taxonomy/Node.html HTMLifying blib/lib/Bio/Search/Result/ResultI.pm -> blib/libhtml/site/lib/Bio/Search/Result/ResultI.html HTMLifying blib/lib/Bio/SearchIO/axt.pm -> blib/libhtml/site/lib/Bio/SearchIO/axt.html HTMLifying blib/lib/Bio/DB/UpdateableSeqI.pm -> blib/libhtml/site/lib/Bio/DB/UpdateableSeqI.html HTMLifying blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Tools/IDHandlerBuild: blib/lib/Bio/Search/Hit/HitI.pm: cannot resolve L in paragraph 126. 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Build: blib/lib/Bio/Search/Hit/BlastPullHit.pm: cannot resolve L in paragraph 74. /DB/Fasta.pm -> blib/libhtml/site/lib/Bio/DB/Fasta.html HTMLifying blib/lib/Bio/DB/Biblio/biofetch.pm -> blib/libhtml/site/lib/Bio/DB/Biblio/biofetch.html HTMLifying blib/lib/Bio/Seq/Quality.pm -> blib/libhtml/site/lib/Bio/Seq/Quality.html HTMLifying blib/lib/Bio/SeqIO/strider.pm -> blib/libhtml/site/lib/Bio/SeqIO/strider.html HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactoryX.html HTMLifying blib/lib/Bio/Matrix/Mlagan.pm -> blib/libhtml/site/lib/Bio/Matrix/Mlagan.html HTMLifying blib/lib/Bio/SearchIO/sim4.pm -> blib/libhtml/site/lib/Bio/SearchIO/sim4.html HTMLifying blib/lib/Bio/Assembly/IO.pm -> blib/libhtml/site/lib/Bio/Assembly/IO.html HTMLifying blib/lib/Bio/SeqFeature/Gene/UTR.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/UTR.html HTMLifying blib/lib/Bio/Index/Swissprot.pm -> blib/libhtml/site/lib/Bio/Index/Swissprot.html HTMLifying blib/lib/Bio/Tools/SeqStats.pm -> blib/libhtml/site/lib/Bio/Tools/SeqStats.html HTMLifying blib/lib/Bio/Structure/StructureI.pm -> blib/libhtml/site/lib/Bio/Structure/StructureI.html HTMLifying blib/lib/Bio/AlignIO/mega.pm -> blib/libhtml/site/lib/Bio/AlignIO/mega.html HTMLifying blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/tinyseq/tinyseqHandler.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/so_transcript.html HTMLifying blib/lib/Bio/Tools/dpAlign.pm -> blib/libhtml/site/lib/Bio/Tools/dpAlign.html HTMLifying blib/lib/Bio/Variation/DNAMutation.pm -> blib/libhtml/site/lib/Bio/Variation/DNAMutation.html HTMLifying blib/lib/Bio/Search/Result/HMMERResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/HMMERResult.html HTMLifying blib/lib/Bio/SeqIO/fastq.pm -> blib/libhtml/site/lib/Bio/SeqIO/fastq.html HTMLifying blib/lib/Bio/PhyloNetwork/GraphViz.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/GraphViz.html HTMLifying blib/lib/Bio/SearchIO/wise.pm -> blib/libhtml/site/lib/Bio/SearchIO/wise.html HTMLifying blib/lib/Bio/Ontology/RelationshipType.pm -> blib/libhtml/site/lib/Bio/Ontology/RelationshipType.html HTMLifying blib/lib/Bio/Biblio/Article.pm -> blib/libhtml/site/lib/Bio/Biblio/Article.html HTMLifying blib/lib/Bio/Symbol/Alphabet.pm -> blib/libhtml/site/lib/Bio/Symbol/Alphabet.html HTMLifying blib/lib/Bio/Coordinate/ExtrapolatingPair.pm -> blib/libhtml/site/lib/Bio/Coordinate/ExtrapolatingPair.html HTMLifying blib/lib/Bio/Search/Result/PullResultI.pm -> blib/libhtml/site/lib/Bio/Search/Result/PullResultI.html HTMLifying blib/lib/Bio/SeqIO/tab.pm -> blib/libhtml/site/lib/Bio/SeqIO/tab.html HTMLifying blib/lib/Bio/Coordinate/Collection.pm -> blib/libhtml/site/lib/Bio/Coordinate/Collection.html HTMLifying blib/lib/Bio/LiveSeq/Gene.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Gene.html HTMLifying blib/lib/Bio/Annotation/AnnotationFactory.pm -> blib/libhtml/site/lib/Bio/Annotation/AnnotationFactory.html HTMLifying blib/lib/Bio/Search/Hit/BlastPullHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/BlastPullHit.html HTMLifying blib/lib/Bio/OntologyIO/goflat.pm -> blib/libhtml/site/lib/Bio/OntologyIO/goflat.html HTMLifying blib/lib/Bio/Location/Simple.pm -> blib/libhtml/site/lib/Bio/Location/Simple.html HTMLifying blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/Phylip/ProtDist.html HTMLifying blib/lib/Bio/SeqFeature/Collection.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Collection.html HTMLifying blib/lib/Bio/Biblio.pm -> blib/libhtml/site/lib/Bio/Biblio.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/clone.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/clone.html HTMLifying blib/lib/Bio/SeqFeature/Gene/Transcript.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/Transcript.html HTMLifying blib/lib/Bio/SeqFeatureI.pm -> blib/libhtml/site/lib/Bio/SeqFeatureI.html HTMLifying blib/lib/Bio/PopGen/IndividualI.pm -> blib/libhtml/site/lib/Bio/PopGen/IndividualI.html HTMLifying blib/lib/Bio/Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm: cannot resolve L in paragraph 8. 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blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/InstanceSiteI.html HTMLifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libhtml/site/lib/Bio/Structure/SecStr/STRIDE/Res.html HTMLifying blib/lib/Bio/Map/Physical.pm -> blib/libhtml/site/lib/Bio/Map/Physical.html HTMLifying blib/lib/Bio/DB/InMemoryCache.pm -> blib/libhtml/site/lib/Bio/DB/InMemoryCache.html HTMLifying blib/lib/Bio/Perl.pm -> blib/libhtml/site/lib/Bio/Perl.html HTMLifying blib/lib/Bio/SeqIO/game/gameWriter.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/gameWriter.html HTMLifying blib/lib/Bio/SeqIO/abi.pm -> blib/libhtml/site/lib/Bio/SeqIO/abi.html HTMLifying blib/lib/Bio/LiveSeq/AARange.pm -> blib/libhtml/site/lib/Bio/LiveSeq/AARange.html HTMLifying blib/lib/Bio/PrimarySeq.pm -> blib/libhtml/site/lib/Bio/PrimarySeq.html HTMLifying blib/lib/Bio/DB/Flat/BDB/fasta.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB/fasta.html HTMLifying blib/lib/Bio/Tools/Run/GenericParameters.pm -> blib/libhtml/site/lib/Bio/Tools/Run/GenericParameters.html HTMLifying blib/lib/Bio/SeqIO/lasergene.pm -> blib/libhtml/site/lib/Bio/SeqIO/lasergene.html HTMLifying blib/lib/Bio/PopGen/IO/prettybase.pm -> blib/libhtml/site/lib/Bio/PopGen/IO/prettybase.html HTMLifying blib/lib/Bio/Assembly/IO/ace.pm -> blib/libhtml/site/lib/Bio/Assembly/IO/ace.html HTMLifying blib/lib/Bio/Symbol/SymbolI.pm -> blib/libhtml/site/lib/Bio/Symbol/SymbolI.html HTMLifying blib/lib/Bio/SimpleAnalysisI.pm -> blib/libhtml/site/lib/Bio/SimpleAnalysisI.html HTMLifying blib/lib/Bio/Matrix/PSM/IO/transfac.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/IO/transfac.html HTMLifying blib/lib/Bio/LiveSeq/IO/BioPerl.pm -> blib/libhtml/site/lib/Bio/LiveSeq/IO/BioPerl.html HTMLifying blib/lib/Bio/Annotation/OntologyTerm.pm -> blib/libhtml/site/lib/Bio/Annotation/OntologyTerm.html HTMLifying blib/lib/Bio/Tools/Run/RemoteBlast.pm -> blib/libhtml/site/lib/Bio/Tools/Run/RemoteBlast.html HTMLifying blib/lib/Bio/Phenotype/MeSH/Term.pm -> blib/libhtml/site/lib/Bio/Phenotype/MeSH/Term.html HTMLifying blib/lib/Bio/Tools/Pseudowise.pm -> blib/libhtml/site/lib/Bio/Tools/Pseudowise.html HTMLifying blib/lib/Bio/DB/HIV.pm -> blib/libhtml/site/lib/Bio/DB/HIV.html HTMLifying blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -> blib/libhtml/site/lib/Bio/SeqFeature/AnnotationAdaptor.html HTMLifying blib/lib/Bio/Matrix/IO.pm -> blib/libhtml/site/lib/Bio/Matrix/IO.html HTMLifying blib/lib/Bio/Map/Gene.pm -> blib/libhtml/site/lib/Bio/Map/Gene.html HTMLifying blib/lib/Bio/Map/Prediction.pm -> blib/libhtml/site/lib/Bio/Map/Prediction.html HTMLifying blib/lib/Bio/Biblio/Person.pm -> blib/libhtml/site/lib/Bio/Biblio/Person.html HTMLifying blib/lib/Bio/Search/BlastStatistics.pm -> blib/libhtml/site/lib/Bio/Search/BlastStatistics.html HTMLifying blib/lib/Bio/PopGen/MarkerI.pm -> blib/libhtml/site/lib/Bio/PopGen/MarkerI.html HTMLifying blib/lib/Bio/Tools/Grail.pm -> blib/libhtml/site/lib/Bio/Tools/Grail.html HTMLifying blib/lib/Bio/Search/HSP/ModelHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/ModelHSP.html HTMLifying blib/lib/Bio/DB/WebDBSeqI.pm -> blib/libhtml/site/lib/Bio/DB/WebDBSeqI.html HTMLifying blib/lib/Bio/AlignIO/clustalw.pm -> blib/libBuild: blib/lib/Bio/Structure/IO.pm: cannot resolve L in paragraph 56. html/site/lib/Bio/AlignIO/clustalw.html HTMLifying blib/lib/Bio/TreeIO/newick.pm -> blib/libhtml/site/lib/Bio/TreeIO/newick.html HTMLifying blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Link/LinkSet.html HTMLifying blib/lib/Bio/PopGen/Utilities.pm -> blib/libhtml/site/lib/Bio/PopGen/Utilities.html HTMLifying blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/DNA/ESEfinder.html HTMLifying blib/lib/Bio/Search/HSP/FastaHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/FastaHSP.html HTMLifying blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm -> blib/libhtml/site/lib/Bio/Phenotype/OMIM/MiniMIMentry.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/ELM.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/ELM.html HTMLifying blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/SimpleAnalysisBase.html HTMLifying blib/lib/Bio/FeatureIO/gtf.pm -> blib/libhtml/site/lib/Bio/FeatureIO/gtf.html HTMLifying blib/lib/Bio/AnnotatableI.pm -> blib/libhtml/site/lib/Bio/AnnotatableI.html HTMLifying blib/lib/Bio/DB/RefSeq.pm -> blib/libhtml/site/lib/Bio/DB/RefSeq.html HTMLifying blib/lib/Bio/Seq/Meta/Array.pm -> blib/libhtml/site/lib/Bio/Seq/Meta/Array.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.html HTMLifying blib/lib/Bio/Structure/IO.pm -> blib/libhtml/site/lib/Bio/Structure/IO.html HTMLifying blib/lib/Bio/Variation/SeqDiff.pm -> blib/libhtml/site/lib/Bio/Variation/SeqDiff.html HTMLifying blib/lib/Bio/Seq/SeqWithQuality.pm -> blib/libhtml/site/lib/Bio/Seq/SeqWithQuality.html HTMLifying blib/lib/Bio/PopGen/TagHaplotype.pm -> blib/libhtml/site/lib/Bio/PopGen/TagHaplotype.html HTMLifying blib/lib/Bio/Matrix/IO/mlagan.pm -> blib/libhtml/site/lib/Bio/Matrix/IO/mlagan.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/oracle.html HTMLifying blib/lib/Bio/DB/Qual.pm -> blib/libhtml/site/lib/Bio/DB/Qual.html CJFIELDS/BioPerl-1.6.1.tar.gz make -- OK Running make test >>> make test TEST_VERBOSE=1 /export/home/fly1064/bin/perl 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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 /export/home/fly1064/bin/perlDeleting 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: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1064/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1064/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1064/var/megalib/Test/Exception.pm:258 # 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: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1064/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1064/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1064/var/megalib/Test/Exception.pm:258 # 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: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1064/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1064/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1064/var/megalib/Test/Exception.pm:258 # 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: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1064/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1064/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1064/var/megalib/Test/Exception.pm:258 # 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 make: *** [test] Terminated Timeout (max run time is 300s) /export/home/fly1064/bin/perl killed by signal 15