Start 2009-06-19T02:05:06
ActivePerl-1003 CPAN-1.94
Going to read '/Users/fly1003/var/cpan/Metadata'
  Database was generated on Thu, 18 Jun 2009 10:26:58 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz
Checksum for /Users/fly1003/var/cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz ok
BioPerl-1.6.0/
BioPerl-1.6.0/AUTHORS
BioPerl-1.6.0/Bio/
BioPerl-1.6.0/Bio/Align/
BioPerl-1.6.0/Bio/Align/AlignI.pm
BioPerl-1.6.0/Bio/Align/DNAStatistics.pm
BioPerl-1.6.0/Bio/Align/PairwiseStatistics.pm
BioPerl-1.6.0/Bio/Align/ProteinStatistics.pm
BioPerl-1.6.0/Bio/Align/StatisticsI.pm
BioPerl-1.6.0/Bio/Align/Utilities.pm
BioPerl-1.6.0/Bio/AlignIO/
BioPerl-1.6.0/Bio/AlignIO/arp.pm
BioPerl-1.6.0/Bio/AlignIO/bl2seq.pm
BioPerl-1.6.0/Bio/AlignIO/clustalw.pm
BioPerl-1.6.0/Bio/AlignIO/emboss.pm
BioPerl-1.6.0/Bio/AlignIO/fasta.pm
BioPerl-1.6.0/Bio/AlignIO/Handler/
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BioPerl-1.6.0/Bio/AlignIO/largemultifasta.pm
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BioPerl-1.6.0/Bio/Assembly/
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BioPerl-1.6.0/Bio/Coordinate/Utils.pm
BioPerl-1.6.0/Bio/Das/
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BioPerl-1.6.0/Bio/Das/SegmentI.pm
BioPerl-1.6.0/Bio/DasI.pm
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BioPerl-1.6.0/Bio/DB/Flat/
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BioPerl-1.6.0/Bio/DB/GFF/
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/berkeleydb/
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/dbi.pm
BioPerl-1.6.0/Bio/DB/GFF/Adaptor/memory/
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/clone.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/coding.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/gene.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/match.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/none.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/transcript.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
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BioPerl-1.6.0/Bio/DB/GFF/Feature.pm
BioPerl-1.6.0/Bio/DB/GFF/Homol.pm
BioPerl-1.6.0/Bio/DB/GFF/RelSegment.pm
BioPerl-1.6.0/Bio/DB/GFF/Segment.pm
BioPerl-1.6.0/Bio/DB/GFF/Typename.pm
BioPerl-1.6.0/Bio/DB/GFF/Util/
BioPerl-1.6.0/Bio/DB/GFF/Util/Binning.pm
BioPerl-1.6.0/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.0/Bio/DB/GFF.pm
BioPerl-1.6.0/Bio/DB/HIV/
BioPerl-1.6.0/Bio/DB/HIV/HIVAnnotProcessor.pm
BioPerl-1.6.0/Bio/DB/HIV/HIVQueryHelper.pm
BioPerl-1.6.0/Bio/DB/HIV/lanl-schema.xml
BioPerl-1.6.0/Bio/DB/HIV.pm
BioPerl-1.6.0/Bio/DB/InMemoryCache.pm
BioPerl-1.6.0/Bio/DB/LocationI.pm
BioPerl-1.6.0/Bio/DB/MeSH.pm
BioPerl-1.6.0/Bio/DB/NCBIHelper.pm
BioPerl-1.6.0/Bio/DB/Qual.pm
BioPerl-1.6.0/Bio/DB/Query/
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BioPerl-1.6.0/Bio/DB/Query/HIVQuery.pm
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BioPerl-1.6.0/Bio/DB/RandomAccessI.pm
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BioPerl-1.6.0/Bio/DB/RefSeq.pm
BioPerl-1.6.0/Bio/DB/Registry.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/
BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedFeature.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedFeatureI.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/Segment.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/Store/
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BioPerl-1.6.0/Bio/DB/Taxonomy/
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BioPerl-1.6.0/Bio/DB/TFBS/
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BioPerl-1.6.0/Bio/Expression/
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BioPerl-1.6.0/Bio/Expression/FeatureGroup/
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BioPerl-1.6.0/Bio/Expression/FeatureI.pm
BioPerl-1.6.0/Bio/Expression/FeatureSet/
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BioPerl-1.6.0/Bio/Expression/Platform.pm
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BioPerl-1.6.0/Bio/Expression/Sample.pm
BioPerl-1.6.0/Bio/Factory/
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BioPerl-1.6.0/Bio/Factory/ApplicationFactoryI.pm
BioPerl-1.6.0/Bio/Factory/DriverFactory.pm
BioPerl-1.6.0/Bio/Factory/FTLocationFactory.pm
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BioPerl-1.6.0/Bio/Factory/SeqAnalysisParserFactoryI.pm
BioPerl-1.6.0/Bio/Factory/SequenceFactoryI.pm
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BioPerl-1.6.0/Bio/Factory/SequenceStreamI.pm
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BioPerl-1.6.0/Bio/LiveSeq/Translation.pm
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BioPerl-1.6.0/Bio/Map/
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BioPerl-1.6.0/t/Tools/Run/
BioPerl-1.6.0/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.0/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.0/t/Tools/Run/WrapperBase.t
BioPerl-1.6.0/t/Tools/Seg.t
BioPerl-1.6.0/t/Tools/Sigcleave.t
BioPerl-1.6.0/t/Tools/Signalp/
BioPerl-1.6.0/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.0/t/Tools/Signalp.t
BioPerl-1.6.0/t/Tools/Sim4.t
BioPerl-1.6.0/t/Tools/SiRNA.t
BioPerl-1.6.0/t/Tools/Spidey/
BioPerl-1.6.0/t/Tools/Spidey/Spidey.t
BioPerl-1.6.0/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.0/t/Tools/TargetP.t
BioPerl-1.6.0/t/Tools/Tmhmm.t
BioPerl-1.6.0/t/Tools/tRNAscanSE.t
BioPerl-1.6.0/t/Tree/
BioPerl-1.6.0/t/Tree/Compatible.t
BioPerl-1.6.0/t/Tree/Node.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/
BioPerl-1.6.0/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.0/t/Tree/RandomTreeFactory.t
BioPerl-1.6.0/t/Tree/Tree.t
BioPerl-1.6.0/t/Tree/TreeIO/
BioPerl-1.6.0/t/Tree/TreeIO/lintree.t
BioPerl-1.6.0/t/Tree/TreeIO/newick.t
BioPerl-1.6.0/t/Tree/TreeIO/nexus.t
BioPerl-1.6.0/t/Tree/TreeIO/nhx.t
BioPerl-1.6.0/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.0/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.0/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.0/t/Tree/TreeIO.t
BioPerl-1.6.0/t/Tree/TreeStatistics.t
BioPerl-1.6.0/t/Variation/
BioPerl-1.6.0/t/Variation/AAChange.t
BioPerl-1.6.0/t/Variation/AAReverseMutate.t
BioPerl-1.6.0/t/Variation/Allele.t
BioPerl-1.6.0/t/Variation/DNAMutation.t
BioPerl-1.6.0/t/Variation/RNAChange.t
BioPerl-1.6.0/t/Variation/SeqDiff.t
BioPerl-1.6.0/t/Variation/SNP.t
BioPerl-1.6.0/t/Variation/Variation_IO.t

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz

>>> /Users/fly1003/bin/perl Makefile.PL
# running Build.PL 
/Users/fly1003/bin/perl Build.PL
Checking whether your kit is complete...
Looks good

Checking prerequisites...
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 GraphViz is not installed
   (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)

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

    - DBD::mysql is not installed
Checking features:
  Network..................enabled
  BioDBSeqFeature_mysql....disabled
  BioDBGFF.................enabled
  BioDBSeqFeature_BDB......enabled

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

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

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n]   - will not run internet-requiring tests
Creating new 'Build' script for 'BioPerl' version '1.006000'
>>> make
/Users/fly1003/bin/perl Build --makefile_env_macros 1
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Copying Bio/LiveSeq/Mutation.pm -> blib/lib/Bio/LiveSeq/Mutation.pm
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Copying Bio/Search/HSP/PSLHSP.pm -> blib/lib/Bio/Search/HSP/PSLHSP.pm
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Copying Bio/Expression/ProbeI.pm -> blib/lib/Bio/Expression/ProbeI.pm
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Copying Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm
Copying Bio/LocationI.pm -> blib/lib/Bio/LocationI.pm
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Copying Bio/DB/Failover.pm -> blib/lib/Bio/DB/Failover.pm
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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/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
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Copying Bio/DB/SeqFeature/Store/GFF2Loader.pm -> blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm
Copying Bio/DB/Flat/BDB/embl.pm -> blib/lib/Bio/DB/Flat/BDB/embl.pm
Copying Bio/Search/HSP/BlastHSP.pm -> blib/lib/Bio/Search/HSP/BlastHSP.pm
Copying Bio/LiveSeq/Mutator.pm -> blib/lib/Bio/LiveSeq/Mutator.pm
Copying Bio/Phenotype/Measure.pm -> blib/lib/Bio/Phenotype/Measure.pm
Copying Bio/DB/GFF/RelSegment.pm -> blib/lib/Bio/DB/GFF/RelSegment.pm
Copying Bio/SeqFeature/Gene/Intron.pm -> blib/lib/Bio/SeqFeature/Gene/Intron.pm
Copying Bio/Tools/Eponine.pm -> blib/lib/Bio/Tools/Eponine.pm
Copying Bio/DB/SeqFeature/Store/GFF3Loader.pm -> blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm
Copying Bio/Seq/LargeSeqI.pm -> blib/lib/Bio/Seq/LargeSeqI.pm
Copying Bio/SeqIO/lasergene.pm -> blib/lib/Bio/SeqIO/lasergene.pm
Copying Bio/Map/OrderedPosition.pm -> blib/lib/Bio/Map/OrderedPosition.pm
Copying Bio/Annotation/TypeManager.pm -> blib/lib/Bio/Annotation/TypeManager.pm
Copying Bio/DB/GFF/Aggregator/ucsc_ensgene.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
Copying Bio/SeqIO/MultiFile.pm -> blib/lib/Bio/SeqIO/MultiFile.pm
Copying Bio/Tools/Tmhmm.pm -> blib/lib/Bio/Tools/Tmhmm.pm
Copying Bio/PopGen/IO/hapmap.pm -> blib/lib/Bio/PopGen/IO/hapmap.pm
Copying Bio/FeatureIO/gtf.pm -> blib/lib/Bio/FeatureIO/gtf.pm
Copying Bio/Factory/SeqAnalysisParserFactory.pm -> blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm
Copying Bio/Map/CytoMarker.pm -> blib/lib/Bio/Map/CytoMarker.pm
Copying Bio/AlignIO/selex.pm -> blib/lib/Bio/AlignIO/selex.pm
Copying Bio/SeqFeature/Gene/UTR.pm -> blib/lib/Bio/SeqFeature/Gene/UTR.pm
Copying Bio/Search/Result/PullResultI.pm -> blib/lib/Bio/Search/Result/PullResultI.pm
Copying Bio/Seq/SeqBuilder.pm -> blib/lib/Bio/Seq/SeqBuilder.pm
Copying Bio/Biblio/Service.pm -> blib/lib/Bio/Biblio/Service.pm
Copying Bio/Search/HSP/BlastPullHSP.pm -> blib/lib/Bio/Search/HSP/BlastPullHSP.pm
Copying Bio/Biblio/MedlineJournal.pm -> blib/lib/Bio/Biblio/MedlineJournal.pm
Copying Bio/DB/GenPept.pm -> blib/lib/Bio/DB/GenPept.pm
Copying Bio/Map/TranscriptionFactor.pm -> blib/lib/Bio/Map/TranscriptionFactor.pm
Copying Bio/Search/DatabaseI.pm -> blib/lib/Bio/Search/DatabaseI.pm
Copying Bio/Index/Blast.pm -> blib/lib/Bio/Index/Blast.pm
Copying Bio/SeqIO/game/featHandler.pm -> blib/lib/Bio/SeqIO/game/featHandler.pm
Copying Bio/Tools/Blat.pm -> 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/Tools/HMM.pm -> blib/lib/Bio/Tools/HMM.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/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/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/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/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/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/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Deleting blib/script/taxid4species.PLS.bak
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.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/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/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/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/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/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/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/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/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/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Deleting blib/script/taxonomy2tree.PLS.bak
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.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/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/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/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/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Deleting blib/script/aacomp.PLS.bak
blib/script/aacomp.PLS -> blib/script/bp_aacomp.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/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
Deleting blib/script/seqretsplit.PLS.bak
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.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/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_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1
Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.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_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1
Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1
Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1
Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.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_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1
Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.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_mutate.pl -> blib/bindoc/bp_mutate.pl.1
Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1
Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1
Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.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_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1
Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.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_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_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.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_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/Seq/SeqFactory.pm -> blib/libdoc/Bio::Seq::SeqFactory.3
Manifying blib/lib/Bio/OntologyIO/dagflat.pm -> blib/libdoc/Bio::OntologyIO::dagflat.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/SearchIO/SearchWriterI.pm -> blib/libdoc/Bio::SearchIO::SearchWriterI.3
Manifying blib/lib/Bio/Location/Atomic.pm -> blib/libdoc/Bio::Location::Atomic.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/SeqIO/embl.pm -> blib/libdoc/Bio::SeqIO::embl.3
Manifying blib/lib/Bio/Search/HSP/WABAHSP.pm -> blib/libdoc/Bio::Search::HSP::WABAHSP.3
Manifying blib/lib/Bio/Biblio/Ref.pm -> blib/libdoc/Bio::Biblio::Ref.3
Manifying blib/lib/Bio/Tools/Genemark.pm -> blib/libdoc/Bio::Tools::Genemark.3
Manifying blib/lib/Bio/Factory/DriverFactory.pm -> blib/libdoc/Bio::Factory::DriverFactory.3
Manifying blib/lib/Bio/Biblio/MedlineArticle.pm -> blib/libdoc/Bio::Biblio::MedlineArticle.3
Manifying blib/lib/Bio/Tools/PrositeScan.pm -> blib/libdoc/Bio::Tools::PrositeScan.3
Manifying blib/lib/Bio/LiveSeq/ChainI.pm -> blib/libdoc/Bio::LiveSeq::ChainI.3
Manifying blib/lib/Bio/Matrix/IO/scoring.pm -> blib/libdoc/Bio::Matrix::IO::scoring.3
Manifying blib/lib/Bio/LiveSeq/Intron.pm -> blib/libdoc/Bio::LiveSeq::Intron.3
Manifying blib/lib/Bio/Seq/LargeLocatableSeq.pm -> blib/libdoc/Bio::Seq::LargeLocatableSeq.3
Manifying blib/lib/Bio/Tools/Glimmer.pm -> blib/libdoc/Bio::Tools::Glimmer.3
Manifying blib/lib/Bio/AlignIO/msf.pm -> blib/libdoc/Bio::AlignIO::msf.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/Tools/Primer/Pair.pm -> blib/libdoc/Bio::Tools::Primer::Pair.3
Manifying blib/lib/Bio/LiveSeq/Mutator.pm -> blib/libdoc/Bio::LiveSeq::Mutator.3
Manifying blib/lib/Bio/Expression/ProbeI.pm -> blib/libdoc/Bio::Expression::ProbeI.3
Manifying blib/lib/Bio/Annotation/TypeManager.pm -> blib/libdoc/Bio::Annotation::TypeManager.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/DB/GFF/Adaptor/biofetch_oracle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch_oracle.3
Manifying blib/lib/Bio/ClusterIO/unigene.pm -> blib/libdoc/Bio::ClusterIO::unigene.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/SeqIO/bsml_sax.pm -> blib/libdoc/Bio::SeqIO::bsml_sax.3
Manifying blib/lib/Bio/Phenotype/PhenotypeI.pm -> blib/libdoc/Bio::Phenotype::PhenotypeI.3
Manifying blib/lib/Bio/Map/OrderedPosition.pm -> blib/libdoc/Bio::Map::OrderedPosition.3
Manifying blib/lib/Bio/SearchIO/blastxml.pm -> blib/libdoc/Bio::SearchIO::blastxml.3
Manifying blib/lib/Bio/Search/BlastUtils.pm -> blib/libdoc/Bio::Search::BlastUtils.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/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/Tools/Hmmpfam.pm -> blib/libdoc/Bio::Tools::Hmmpfam.3
Manifying blib/lib/Bio/Structure/Model.pm -> blib/libdoc/Bio::Structure::Model.3
Manifying blib/lib/Bio/Factory/SequenceStreamI.pm -> blib/libdoc/Bio::Factory::SequenceStreamI.3
Manifying blib/lib/Bio/CodonUsage/Table.pm -> blib/libdoc/Bio::CodonUsage::Table.3
Manifying blib/lib/Bio/MolEvol/CodonModel.pm -> blib/libdoc/Bio::MolEvol::CodonModel.3
Manifying blib/lib/Bio/LiveSeq/Prim_Transcript.pm -> blib/libdoc/Bio::LiveSeq::Prim_Transcript.3
Manifying blib/lib/Bio/Annotation/TagTree.pm -> blib/libdoc/Bio::Annotation::TagTree.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/Map/Microsatellite.pm -> blib/libdoc/Bio::Map::Microsatellite.3
Manifying blib/lib/Bio/DB/EMBL.pm -> blib/libdoc/Bio::DB::EMBL.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/Tools/AnalysisResult.pm -> blib/libdoc/Bio::Tools::AnalysisResult.3
Manifying blib/lib/Bio/Assembly/Contig.pm -> blib/libdoc/Bio::Assembly::Contig.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/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/SeqIO/chadoxml.pm -> blib/libdoc/Bio::SeqIO::chadoxml.3
Manifying blib/lib/Bio/OntologyIO/InterProParser.pm -> blib/libdoc/Bio::OntologyIO::InterProParser.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/DB/SeqFeature/NormalizedFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeatureI.3
Manifying blib/lib/Bio/Annotation/Reference.pm -> blib/libdoc/Bio::Annotation::Reference.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/TreeIO/pag.pm -> blib/libdoc/Bio::TreeIO::pag.3
Manifying blib/lib/Bio/Seq/MetaI.pm -> blib/libdoc/Bio::Seq::MetaI.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/SeqFeature/PositionProxy.pm -> blib/libdoc/Bio::SeqFeature::PositionProxy.3
Manifying blib/lib/Bio/Ontology/TermI.pm -> blib/libdoc/Bio::Ontology::TermI.3
Manifying blib/lib/Bio/SeqIO/ace.pm -> blib/libdoc/Bio::SeqIO::ace.3
Manifying blib/lib/Bio/SeqEvolution/DNAPoint.pm -> blib/libdoc/Bio::SeqEvolution::DNAPoint.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/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/Tools/Primer3.pm -> blib/libdoc/Bio::Tools::Primer3.3
Manifying blib/lib/Bio/Tools/Genewise.pm -> blib/libdoc/Bio::Tools::Genewise.3
Manifying blib/lib/Bio/SearchIO/blasttable.pm -> blib/libdoc/Bio::SearchIO::blasttable.3
Manifying blib/lib/Bio/Map/EntityI.pm -> blib/libdoc/Bio::Map::EntityI.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb.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/Tools/HMMER/Results.pm -> blib/libdoc/Bio::Tools::HMMER::Results.3
Manifying blib/lib/Bio/LiveSeq/DNA.pm -> blib/libdoc/Bio::LiveSeq::DNA.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/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/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.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/SeqIO/asciitree.pm -> blib/libdoc/Bio::SeqIO::asciitree.3
Manifying blib/lib/Bio/DB/Failover.pm -> blib/libdoc/Bio::DB::Failover.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/SeqIO/game/featHandler.pm -> blib/libdoc/Bio::SeqIO::game::featHandler.3
Manifying blib/lib/Bio/DB/Registry.pm -> blib/libdoc/Bio::DB::Registry.3
Manifying blib/lib/Bio/Search/HSP/BlastHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastHSP.3
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Manifying blib/lib/Bio/Tools/Blat.pm -> blib/libdoc/Bio::Tools::Blat.3
Manifying blib/lib/Bio/Biblio/TechReport.pm -> blib/libdoc/Bio::Biblio::TechReport.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/Tools/TargetP.pm -> blib/libdoc/Bio::Tools::TargetP.3
Manifying blib/lib/Bio/Map/CytoMarker.pm -> blib/libdoc/Bio::Map::CytoMarker.3
Manifying blib/lib/Bio/Expression/Sample.pm -> blib/libdoc/Bio::Expression::Sample.3
Manifying blib/lib/Bio/SeqIO/table.pm -> blib/libdoc/Bio::SeqIO::table.3
Manifying blib/lib/Bio/DB/NCBIHelper.pm -> blib/libdoc/Bio::DB::NCBIHelper.3
Manifying blib/lib/Bio/Tools/Spidey/Exon.pm -> blib/libdoc/Bio::Tools::Spidey::Exon.3
Manifying blib/lib/Bio/Root/Root.pm -> blib/libdoc/Bio::Root::Root.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/QueryI.pm -> blib/libdoc/Bio::DB::QueryI.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/ace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::ace.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
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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/Factory/ObjectBuilderI.pm -> blib/libdoc/Bio::Factory::ObjectBuilderI.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlopt.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/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/ClusterIO/dbsnp.pm -> blib/libdoc/Bio::ClusterIO::dbsnp.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/Tree/NodeNHX.pm -> blib/libdoc/Bio::Tree::NodeNHX.3
Manifying blib/lib/Bio/Index/Blast.pm -> blib/libdoc/Bio::Index::Blast.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/SeqIO/excel.pm -> blib/libdoc/Bio::SeqIO::excel.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/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
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Manifying blib/lib/Bio/Cluster/SequenceFamily.pm -> blib/libdoc/Bio::Cluster::SequenceFamily.3
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Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::mysql.3
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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/SeqIO/gbdriver.pm -> blib/libdoc/Bio::SeqIO::gbdriver.3
Manifying blib/lib/Bio/Search/HSP/HSPFactory.pm -> blib/libdoc/Bio::Search::HSP::HSPFactory.3
Manifying blib/lib/Bio/PhyloNetwork/FactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::FactoryX.3
Manifying blib/lib/Bio/Das/FeatureTypeI.pm -> blib/libdoc/Bio::Das::FeatureTypeI.3
Manifying blib/lib/Bio/Symbol/Symbol.pm -> blib/libdoc/Bio::Symbol::Symbol.3
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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
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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
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Manifying blib/lib/Bio/Map/GenePosition.pm -> blib/libdoc/Bio::Map::GenePosition.3
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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/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_sanger22.3
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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
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Manifying blib/lib/Bio/AlignIO/psi.pm -> blib/libdoc/Bio::AlignIO::psi.3
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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
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Manifying blib/lib/Bio/PhyloNetwork/Factory.pm -> blib/libdoc/Bio::PhyloNetwork::Factory.3
Manifying blib/lib/Bio/HandlerBaseI.pm -> blib/libdoc/Bio::HandlerBaseI.3
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Manifying blib/lib/Bio/Ontology/TermFactory.pm -> blib/libdoc/Bio::Ontology::TermFactory.3
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Manifying blib/lib/Bio/Factory/ObjectFactoryI.pm -> blib/libdoc/Bio::Factory::ObjectFactoryI.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_acembly.3
Manifying blib/lib/Bio/Annotation/SimpleValue.pm -> blib/libdoc/Bio::Annotation::SimpleValue.3
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Manifying blib/lib/Bio/Matrix/PhylipDist.pm -> blib/libdoc/Bio::Matrix::PhylipDist.3
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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/Matrix/Generic.pm -> blib/libdoc/Bio::Matrix::Generic.3
Manifying blib/lib/Bio/PopGen/Marker.pm -> blib/libdoc/Bio::PopGen::Marker.3
Manifying blib/lib/Bio/Root/HTTPget.pm -> blib/libdoc/Bio::Root::HTTPget.3
Manifying blib/lib/Bio/TreeIO.pm -> blib/libdoc/Bio::TreeIO.3
Manifying blib/lib/Bio/Index/SwissPfam.pm -> blib/libdoc/Bio::Index::SwissPfam.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/Tools/GuessSeqFormat.pm -> blib/libdoc/Bio::Tools::GuessSeqFormat.3
Manifying blib/lib/Bio/PopGen/Individual.pm -> blib/libdoc/Bio::PopGen::Individual.3
Manifying blib/lib/Bio/AlignIO/xmfa.pm -> blib/libdoc/Bio::AlignIO::xmfa.3
Manifying blib/lib/Bio/SearchIO/rnamotif.pm -> blib/libdoc/Bio::SearchIO::rnamotif.3
Manifying blib/lib/Bio/Map/LinkageMap.pm -> blib/libdoc/Bio::Map::LinkageMap.3
Manifying blib/lib/Bio/SeqFeature/Gene/ExonI.pm -> blib/libdoc/Bio::SeqFeature::Gene::ExonI.3
Manifying blib/lib/Bio/SeqIO/alf.pm -> blib/libdoc/Bio::SeqIO::alf.3
Manifying blib/lib/Bio/Biblio/Thesis.pm -> blib/libdoc/Bio::Biblio::Thesis.3
Manifying blib/lib/Bio/Factory/SequenceProcessorI.pm -> blib/libdoc/Bio::Factory::SequenceProcessorI.3
Manifying blib/lib/Bio/Search/GenericStatistics.pm -> blib/libdoc/Bio::Search::GenericStatistics.3
Manifying blib/lib/Bio/AnalysisParserI.pm -> blib/libdoc/Bio::AnalysisParserI.3
Manifying blib/lib/Bio/Search/Processor.pm -> blib/libdoc/Bio::Search::Processor.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/SeqFeature/Gene/GeneStructure.pm -> blib/libdoc/Bio::SeqFeature::Gene::GeneStructure.3
Manifying blib/lib/Bio/Annotation/StructuredValue.pm -> blib/libdoc/Bio::Annotation::StructuredValue.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/Phenotype/OMIM/OMIMentryAllelicVariant.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMentryAllelicVariant.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/DB/SeqVersion/gi.pm -> blib/libdoc/Bio::DB::SeqVersion::gi.3
Manifying blib/lib/Bio/Expression/DataSet.pm -> blib/libdoc/Bio::Expression::DataSet.3
Manifying blib/lib/Bio/Ontology/PathI.pm -> blib/libdoc/Bio::Ontology::PathI.3
Manifying blib/lib/Bio/PopGen/Simulation/Coalescent.pm -> blib/libdoc/Bio::PopGen::Simulation::Coalescent.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/FeatureIO/ptt.pm -> blib/libdoc/Bio::FeatureIO::ptt.3
Manifying blib/lib/Bio/Index/GenBank.pm -> blib/libdoc/Bio::Index::GenBank.3
Manifying blib/lib/Bio/SearchIO/hmmer.pm -> blib/libdoc/Bio::SearchIO::hmmer.3
Manifying blib/lib/Bio/DB/Biblio/soap.pm -> blib/libdoc/Bio::DB::Biblio::soap.3
Manifying blib/lib/Bio/PhyloNetwork/RandomFactory.pm -> blib/libdoc/Bio::PhyloNetwork::RandomFactory.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/Tools/Sim4/Results.pm -> blib/libdoc/Bio::Tools::Sim4::Results.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/Index/Hmmer.pm -> blib/libdoc/Bio::Index::Hmmer.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch.3
Manifying blib/lib/Bio/MapIO/mapmaker.pm -> blib/libdoc/Bio::MapIO::mapmaker.3
Manifying blib/lib/Bio/Tools/Prediction/Gene.pm -> blib/libdoc/Bio::Tools::Prediction::Gene.3
Manifying blib/lib/Bio/AlignIO/meme.pm -> blib/libdoc/Bio::AlignIO::meme.3
Manifying blib/lib/Bio/Root/Test/Warn.pm -> blib/libdoc/Bio::Root::Test::Warn.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/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/Tools/Sigcleave.pm -> blib/libdoc/Bio::Tools::Sigcleave.3
Manifying blib/lib/Bio/Location/NarrowestCoordPolicy.pm -> blib/libdoc/Bio::Location::NarrowestCoordPolicy.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/SeqIO/Handler/GenericRichSeqHandler.pm -> blib/libdoc/Bio::SeqIO::Handler::GenericRichSeqHandler.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/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/DB/GFF.pm -> blib/libdoc/Bio::DB::GFF.3
Manifying blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -> blib/libdoc/Bio::Matrix::PSM::SiteMatrix.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/Ontology/RelationshipFactory.pm -> blib/libdoc/Bio::Ontology::RelationshipFactory.3
Manifying blib/lib/Bio/DB/SeqFeature/Segment.pm -> blib/libdoc/Bio::DB::SeqFeature::Segment.3
Manifying blib/lib/Bio/Search/Hit/HitFactory.pm -> blib/libdoc/Bio::Search::Hit::HitFactory.3
Manifying blib/lib/Bio/Index/Fasta.pm -> blib/libdoc/Bio::Index::Fasta.3
Manifying blib/lib/Bio/ConfigData.pm -> blib/libdoc/Bio::ConfigData.3
Manifying blib/lib/Bio/FeatureIO/bed.pm -> blib/libdoc/Bio::FeatureIO::bed.3
Manifying blib/lib/Bio/Ontology/InterProTerm.pm -> blib/libdoc/Bio::Ontology::InterProTerm.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/PopGen/Simulation/GeneticDrift.pm -> blib/libdoc/Bio::PopGen::Simulation::GeneticDrift.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/Tree/Draw/Cladogram.pm -> blib/libdoc/Bio::Tree::Draw::Cladogram.3
Manifying blib/lib/Bio/Annotation/Relation.pm -> blib/libdoc/Bio::Annotation::Relation.3
Manifying blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -> blib/libdoc/Bio::SearchIO::FastHitEventBuilder.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/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/Tools/OddCodes.pm -> blib/libdoc/Bio::Tools::OddCodes.3
Manifying blib/lib/Bio/SeqEvolution/EvolutionI.pm -> blib/libdoc/Bio::SeqEvolution::EvolutionI.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/SeqAnalysisParserI.pm -> blib/libdoc/Bio::SeqAnalysisParserI.3
Manifying blib/lib/Bio/RangeI.pm -> blib/libdoc/Bio::RangeI.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/DB/TFBS.pm -> blib/libdoc/Bio::DB::TFBS.3
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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/AlignIO/po.pm -> blib/libdoc/Bio::AlignIO::po.3
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Manifying blib/lib/Bio/Index/EMBL.pm -> blib/libdoc/Bio::Index::EMBL.3
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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
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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
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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/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/Root/RootI.pm -> blib/libdoc/Bio::Root::RootI.3
Manifying blib/lib/Bio/SeqIO/genbank.pm -> blib/libdoc/Bio::SeqIO::genbank.3
Manifying blib/lib/Bio/Assembly/ContigAnalysis.pm -> blib/libdoc/Bio::Assembly::ContigAnalysis.3
Manifying blib/lib/Bio/Tools/HMMER/Set.pm -> blib/libdoc/Bio::Tools::HMMER::Set.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/Variation/IO/xml.pm -> blib/libdoc/Bio::Variation::IO::xml.3
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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
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Manifying blib/lib/Bio/Biblio/PubmedBookArticle.pm -> blib/libdoc/Bio::Biblio::PubmedBookArticle.3
Manifying blib/lib/Bio/Tools/EUtilities/Summary/Item.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::Item.3
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Manifying blib/lib/Bio/SearchIO/infernal.pm -> blib/libdoc/Bio::SearchIO::infernal.3
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Manifying blib/lib/Bio/Biblio/Patent.pm -> blib/libdoc/Bio::Biblio::Patent.3
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HTMLifying blib/lib/Bio/Cluster/UniGeneI.pm -> blib/libhtml/site/lib/Bio/Cluster/UniGeneI.html
HTMLifying blib/lib/Bio/Biblio/Journal.pm -> blib/libhtml/site/lib/Bio/Biblio/Journal.html
HTMLifying blib/lib/Bio/Matrix/Scoring.pm -> blib/libhtml/site/lib/Bio/Matrix/Scoring.html
HTMLifying blib/lib/Bio/Structure/Chain.pm -> blib/libhtml/site/lib/Bio/Structure/Chain.html
HTMLifying blib/lib/Bio/DB/HIV/HIVQueryHelper.pm -> blib/libhtml/site/lib/Bio/DB/HIV/HIVQueryHelper.html
HTMLifying blib/lib/Bio/UpdateableSeqI.pm -> blib/libhtml/site/lib/Bio/UpdateableSeqI.html
HTMLifying blib/lib/Bio/Phenotype/Measure.pm -> blib/libhtml/site/lib/Bio/Phenotype/Measure.html
HTMLifying blib/lib/Bio/SearchDist.pm -> blib/libhtml/site/lib/Bio/SearchDist.html
HTMLifying blib/lib/Bio/Coordinate/Graph.pm -> blib/libhtml/site/lib/Bio/Coordinate/Graph.html
HTMLifying blib/lib/Bio/IdCollectionI.pm -> blib/libhtml/site/lib/Bio/IdCollectionI.html
HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi.html
HTMLifying blib/lib/Bio/Search/Hit/HitI.pm -> blib/libhtml/site/lib/Bio/Search/Hit/HitI.html
HTMLifying blib/lib/Bio/Search/Result/BlastResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/BlastResult.html
HTMLifying blib/lib/Bio/Seq/LargeSeq.pm -> blib/libhtml/site/lib/Bio/Seq/LargeSeq.html
HTMLifying blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm -> blib/libhtml/site/lib/Bio/Expression/FeatureSet/FeatureSetMas50.html
HTMLifying blib/lib/Bio/SeqIO/game/seqHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/seqHandler.html
HTMLifying blib/lib/Bio/Align/ProteinStatistics.pm -> blib/libhtml/site/lib/Bio/Align/ProteinStatistics.Build: blib/lib/Bio/DB/GFF/Feature.pm: cannot resolve L<bioperl> in paragraph 295.
Build: blib/lib/Bio/DB/Fasta.pm: cannot resolve L<bioperl> in paragraph 123.
Build: blib/lib/Bio/Search/Hit/HMMERHit.pm: cannot resolve L<score()|score> in paragraph 66.
Build: blib/lib/Bio/Search/Hit/HMMERHit.pm: cannot resolve L<hsp()|hsp> in paragraph 74.
Build: blib/lib/Bio/Seq/Quality.pm: cannot resolve L<force_flush> in paragraph 26.
Build: blib/lib/Bio/Search/Result/HMMERResult.pm: cannot resolve L<next_models> in paragraph 9.
Build: blib/lib/Bio/Search/Hit/BlastPullHit.pm: cannot resolve L<num_hsps> in paragraph 70.
html
HTMLifying blib/lib/Bio/DB/GFF/Feature.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Feature.html
HTMLifying blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/Poly_A_site.html
HTMLifying blib/lib/Bio/Coordinate/Result.pm -> blib/libhtml/site/lib/Bio/Coordinate/Result.html
HTMLifying blib/lib/Bio/Annotation/Comment.pm -> blib/libhtml/site/lib/Bio/Annotation/Comment.html
HTMLifying blib/lib/Bio/Root/IO.pm -> blib/libhtml/site/lib/Bio/Root/IO.html
HTMLifying blib/lib/Bio/DB/Fasta.pm -> blib/libhtml/site/lib/Bio/DB/Fasta.html
HTMLifying blib/lib/Bio/Search/Hit/HMMERHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/HMMERHit.html
HTMLifying blib/lib/Bio/DB/Biblio/biofetch.pm -> blib/libhtml/site/lib/Bio/DB/Biblio/biofetch.html
HTMLifying blib/lib/Bio/SeqIO/strider.pm -> blib/libhtml/site/lib/Bio/SeqIO/strider.html
HTMLifying blib/lib/Bio/Seq/Quality.pm -> blib/libhtml/site/lib/Bio/Seq/Quality.html
HTMLifying blib/lib/Bio/Tools/HMM.pm -> blib/libhtml/site/lib/Bio/Tools/HMM.html
HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactoryX.html
HTMLifying blib/lib/Bio/SearchIO/sim4.pm -> blib/libhtml/site/lib/Bio/SearchIO/sim4.html
HTMLifying blib/lib/Bio/Matrix/Mlagan.pm -> blib/libhtml/site/lib/Bio/Matrix/Mlagan.html
HTMLifying blib/lib/Bio/SeqFeature/Gene/UTR.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/UTR.html
HTMLifying blib/lib/Bio/Assembly/IO.pm -> blib/libhtml/site/lib/Bio/Assembly/IO.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/SeqIO/fastq.pm -> blib/libhtml/site/lib/Bio/SeqIO/fastq.html
HTMLifying blib/lib/Bio/Search/Result/HMMERResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/HMMERResult.html
HTMLifying blib/lib/Bio/SearchIO/wise.pm -> blib/libhtml/site/lib/Bio/SearchIO/wise.html
HTMLifying blib/lib/Bio/PhyloNetwork/GraphViz.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/GraphViz.html
HTMLifying blib/lib/Bio/Biblio/Article.pm -> blib/libhtml/site/lib/Bio/Biblio/Article.html
HTMLifying blib/lib/Bio/Ontology/RelationshipType.pm -> blib/libhtml/site/lib/Bio/Ontology/RelationshipType.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/Location/Simple.pm -> blib/libhtml/site/lib/Bio/Location/Simple.html
HTMLifying blib/lib/Bio/OntologyIO/goflat.pm -> blib/libhtml/site/lib/Bio/OntologyIO/goflat.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/lBuild: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm: cannot resolve L<bioperl> in paragraph 8.
ibhtml/site/lib/Bio/SeqFeature/Collection.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/Biblio.pm -> blib/libhtml/site/lib/Bio/Biblio.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/Tools/Lucy.pm -> blib/libhtml/site/lib/Bio/Tools/Lucy.html
HTMLifying blib/lib/Bio/Tools/Run/WrapperBase.pm -> blib/libhtml/site/lib/Bio/Tools/Run/WrapperBase.html
HTMLifying blib/lib/Bio/SeqIO/kegg.pm -> blib/libhtml/site/lib/Bio/SeqIO/kegg.html
HTMLifying blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Tools/TypeMapper.html
HTMLifying blib/lib/Bio/Biblio/MedlineJournal.pm -> blib/libhtml/site/lib/Bio/Biblio/MedlineJournal.html
HTMLifying blib/lib/Bio/Matrix/PSM/ProtMatrix.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/ProtMatrix.html
HTMLifying blib/lib/Bio/AlignIO/fasta.pm -> blib/libhtml/site/lib/Bio/AlignIO/fasta.html
HTMLifying blib/lib/Bio/Matrix/PSM/PsmHeader.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/PsmHeader.html
HTMLifying blib/lib/Bio/SeqFeature/Tools/Unflattener.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Tools/Unflattener.html
HTMLifying blib/lib/Bio/Search/Result/GenericResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/GenericResult.html
HTMLifying blib/lib/Bio/Location/WidestCoordPolicy.pm -> blib/libhtml/site/lib/Bio/Location/WidestCoordPolicy.html
HTMLifying blib/lib/Bio/Map/PositionHandler.pm -> blib/libhtml/site/lib/Bio/Map/PositionHandler.html
HTMLifying blib/lib/Bio/Tools/GFF.pm -> blib/libhtml/site/lib/Bio/Tools/GFF.html
HTMLifying blib/lib/Bio/Ontology/Ontology.pm -> blib/libhtml/site/lib/Bio/Ontology/Ontology.html
HTMLifying blib/lib/Bio/Biblio/PubmedArticle.pm -> blib/libhtml/site/lib/Bio/Biblio/PubmedArticle.html
HTMLifying blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -> blib/libhtml/site/lib/Bio/SearchIO/Writer/TextResultWriter.html
HTMLifying blib/lib/Bio/Seq/LargeSeqI.pm -> blib/libhtml/site/lib/Bio/Seq/LargeSeqI.html
HTMLifying blib/lib/Bio/AlignIO/nexus.pm -> blib/libhtml/site/lib/Bio/AlignIO/nexus.html
HTMLifying blib/lib/Bio/SearchIO/EventHandlerI.pm -> blib/libhtml/site/lib/Bio/SearchIO/EventHandlerI.html
HTMLifying blib/lib/Bio/Tools/Seg.pm -> blib/libhtml/site/lib/Bio/Tools/Seg.html
HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.html
HTMLifying blib/lib/Bio/DB/BioFetch.pm -> blib/libhtml/site/lib/Bio/DB/BioFetch.html
HTMLifying blib/lib/Bio/Taxon.pm -> blib/libhtml/site/lib/Bio/Taxon.html
HTMLifying blib/lib/Bio/Assembly/IO/phrap.pm -> blib/libhtml/site/lib/Bio/Assembly/IO/phrap.html
HTMLifying blib/lib/Bio/Tools/RNAMotif.pm -> blib/libhtml/site/lib/Bio/Tools/RNAMotif.html
HTMLifying blib/lib/Bio/Factory/AnalysisI.pm -> blib/libhtml/site/lib/Bio/Factory/AnalysisI.html
HTMLifying blib/lib/Bio/Ontology/RelationshipI.pm -> blib/libhtml/site/lib/Bio/Ontology/RelationshipI.html
HTMLifying blib/lib/Bio/Map/OrderedPositionWithDistance.pm -> blib/libhtml/site/lib/Bio/Map/OrderedPositionWithDistance.html
HTMLifying blib/lib/Bio/PopGen/Genotype.pm -> blib/libhtml/site/lib/Bio/PopGen/Genotype.html
HTMLifying blib/lib/Bio/Coordinate/Utils.pm -> blib/libhtml/site/lib/Bio/Coordinate/Utils.html
HTMLifying blib/lib/Bio/Tools/EUtilities/History.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/History.html
HTMLifying blib/lib/Bio/PopGen/Statistics.pm -> blib/libhtml/site/lib/Bio/PopGen/Statistics.html
HTMLifying blib/lib/Bio/DB/EntrezGene.pm -> blib/libhtml/site/lib/Bio/DB/EntrezGene.html
HTMLifying blib/lib/Bio/AnnotationI.pm -> blib/libhtml/site/lib/Bio/AnnotationI.html
HTMLifying blib/lib/Bio/Ontology/Relationship.pm ->Build: blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm: cannot resolve L<bioperl> in paragraph 181.
Build: blib/lib/Bio/Search/Hit/ModelHit.pm: cannot resolve L<expect()|expect> in paragraph 101.
Build: blib/lib/Bio/Search/Hit/ModelHit.pm: cannot resolve L<signif()|signif> in paragraph 101.
Build: blib/lib/Bio/Tools/Run/RemoteBlast.pm: cannot resolve L<FEEDBACK> in paragraph 32.
 blib/libhtml/site/lib/Bio/Ontology/Relationship.html
HTMLifying blib/lib/Bio/Tools/Analysis/Protein/HNN.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/HNN.html
HTMLifying blib/lib/Bio/Tools/SeqWords.pm -> blib/libhtml/site/lib/Bio/Tools/SeqWords.html
HTMLifying blib/lib/Bio/SeqIO/raw.pm -> blib/libhtml/site/lib/Bio/SeqIO/raw.html
HTMLifying blib/lib/Bio/Seq/SeqBuilder.pm -> blib/libhtml/site/lib/Bio/Seq/SeqBuilder.html
HTMLifying blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -> blib/libhtml/site/lib/Bio/SeqFeature/TypedSeqFeatureI.html
HTMLifying blib/lib/Bio/Search/Iteration/IterationI.pm -> blib/libhtml/site/lib/Bio/Search/Iteration/IterationI.html
HTMLifying blib/lib/Bio/Search/Result/ResultFactory.pm -> blib/libhtml/site/lib/Bio/Search/Result/ResultFactory.html
HTMLifying blib/lib/Bio/LiveSeq/Chain.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Chain.html
HTMLifying blib/lib/Bio/PopGen/HtSNP.pm -> blib/libhtml/site/lib/Bio/PopGen/HtSNP.html
HTMLifying blib/lib/Bio/LiveSeq/Mutation.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Mutation.html
HTMLifying blib/lib/Bio/Map/SimpleMap.pm -> blib/libhtml/site/lib/Bio/Map/SimpleMap.html
HTMLifying blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/GFF2Loader.html
HTMLifying blib/lib/Bio/Tools/HMMER/Domain.pm -> blib/libhtml/site/lib/Bio/Tools/HMMER/Domain.html
HTMLifying blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/InstanceSiteI.html
HTMLifying blib/lib/Bio/Search/Hit/ModelHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/ModelHit.html
HTMLifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libhtml/site/lib/Bio/Structure/SecStr/STRIDE/Res.html
HTMLifying blib/lib/Bio/DB/InMemoryCache.pm -> blib/libhtml/site/lib/Bio/DB/InMemoryCache.html
HTMLifying blib/lib/Bio/Map/Physical.pm -> blib/libhtml/site/lib/Bio/Map/Physical.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/DB/Flat/BDB/fasta.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB/fasta.html
HTMLifying blib/lib/Bio/PrimarySeq.pm -> blib/libhtml/site/lib/Bio/PrimarySeq.html
HTMLifying blib/lib/Bio/LiveSeq/AARange.pm -> blib/libhtml/site/lib/Bio/LiveSeq/AARange.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/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/Matrix/IO.pm -> blib/libhtml/site/lib/Bio/Matrix/IO.html
HTMLifying blib/lib/Bio/Biblio/Person.pBuild: blib/lib/Bio/Search/HSP/ModelHSP.pm: cannot resolve L<seq_str()|seq_str> in paragraph 48.
Build: blib/lib/Bio/DB/RefSeq.pm: cannot resolve L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 14.
Build: blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm: cannot resolve L<bioperl> in paragraph 251.
Build: blib/lib/Bio/Structure/IO.pm: cannot resolve L<perltie> in paragraph 56.
Build: blib/lib/Bio/DB/Qual.pm: cannot resolve L<bioperl> in paragraph 118.
m -> 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/Tools/Grail.pm -> blib/libhtml/site/lib/Bio/Tools/Grail.html
HTMLifying blib/lib/Bio/PopGen/MarkerI.pm -> blib/libhtml/site/lib/Bio/PopGen/MarkerI.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/TreeIO/newick.pm -> blib/libhtml/site/lib/Bio/TreeIO/newick.html
HTMLifying blib/lib/Bio/AlignIO/clustalw.pm -> blib/libhtml/site/lib/Bio/AlignIO/clustalw.html
HTMLifying blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Link/LinkSet.html
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HTMLifying blib/lib/Bio/Search/HSP/FastaHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/FastaHSP.html
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HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/oracle.html
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  CJFIELDS/BioPerl-1.6.0.tar.gz
  make -- OK
Running make test
>>> make test TEST_VERBOSE=1
/Users/fly1003/bin/perl Build --makefile_env_macros 1 test
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Changing sharpbang in blib/script/bp_sreformat.PLS to /Users/fly1003/bin/perlDeleting blib/script/bp_sreformat.PLS.bak
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Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
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Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Changing sharpbang in blib/script/tree2pag.PLS to /Users/fly1003/bin/perlDeleting blib/script/tree2pag.PLS.bak
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Changing sharpbang in blib/script/meta_gff.PLS to /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/oligo_count.PLS.bak
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.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 /Users/fly1003/bin/perlDeleting blib/script/bp_seqfeature_load.PLS.bak
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
Changing sharpbang in blib/script/process_gadfly.PLS to /Users/fly1003/bin/perlDeleting blib/script/process_gadfly.PLS.bak
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
Changing sharpbang in blib/script/hmmer_to_table.PLS to /Users/fly1003/bin/perlDeleting blib/script/hmmer_to_table.PLS.bak
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
Changing sharpbang in blib/script/fastam9_to_table.PLS to /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/genbank2gff.PLS.bak
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Changing sharpbang in blib/script/taxid4species.PLS to /Users/fly1003/bin/perlDeleting blib/script/taxid4species.PLS.bak
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.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 /Users/fly1003/bin/perlDeleting blib/script/bulk_load_gff.PLS.bak
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
Changing sharpbang in blib/script/search2gff.PLS to /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/blast2tree.PLS.bak
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
Changing sharpbang in blib/script/make_mrna_protein.PLS to /Users/fly1003/bin/perlDeleting blib/script/make_mrna_protein.PLS.bak
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
Changing sharpbang in blib/script/unflatten_seq.PLS to /Users/fly1003/bin/perlDeleting blib/script/unflatten_seq.PLS.bak
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Changing sharpbang in blib/script/search2tribe.PLS to /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/bioflat_index.PLS.bak
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.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 /Users/fly1003/bin/perlDeleting blib/script/bp_seqfeature_delete.PLS.bak
blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
Changing sharpbang in blib/script/query_entrez_taxa.PLS to /Users/fly1003/bin/perlDeleting blib/script/query_entrez_taxa.PLS.bak
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
Changing sharpbang in blib/script/pairwise_kaks.PLS to /Users/fly1003/bin/perlDeleting blib/script/pairwise_kaks.PLS.bak
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.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 /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/chaos_plot.PLS.bak
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Changing sharpbang in blib/script/taxonomy2tree.PLS to /Users/fly1003/bin/perlDeleting blib/script/taxonomy2tree.PLS.bak
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
Changing sharpbang in blib/script/bp_mrtrans.PLS to /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/search2alnblocks.PLS.bak
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
Changing sharpbang in blib/script/download_query_genbank.PLS to /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/gccalc.PLS.bak
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
Changing sharpbang in blib/script/composite_LD.PLS to /Users/fly1003/bin/perlDeleting blib/script/composite_LD.PLS.bak
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /Users/fly1003/bin/perlDeleting blib/script/classify_hits_kingdom.PLS.bak
blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Changing sharpbang in blib/script/aacomp.PLS to /Users/fly1003/bin/perlDeleting blib/script/aacomp.PLS.bak
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
Changing sharpbang in blib/script/process_wormbase.PLS to /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/bin/perlDeleting blib/script/biblio.PLS.bak
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
Changing sharpbang in blib/script/seqretsplit.PLS to /Users/fly1003/bin/perlDeleting blib/script/seqretsplit.PLS.bak
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
Changing sharpbang in blib/script/remote_blast.PLS to /Users/fly1003/bin/perlDeleting blib/script/remote_blast.PLS.bak
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Changing sharpbang in blib/script/genbank2gff3.PLS to /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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 /Users/fly1003/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..152
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 - no_sequences
ok 11 - no_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - no_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - no_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 - no_residues
ok 34 - no_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 - added 3 seqs
ok 86 - first 2 features added
ok 87 - 3rd feature added
ok 88 - slice 1 len
ok 89 - slice 2 len
ok 90 - slice 3 len
ok 91 - slice 4 len
ok 92 - initial display id ok
ok 93 - safe display id ok
ok 94 - restored display id ok
ok 95 - sort by list ok
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102 - BIC:GGATCCATT[C/C]CTACT
ok 103 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 104 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 105 - BIC:GGATCCATT[C/G]CTACT
ok 106 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 107 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 108 - BIC:GGATCCATT[C/G]CTACT
ok 109 - BIC:GGATCCATT{C.C}CTACT
ok 110 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 111 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 112 - BIC:GGATCCATT{C.G}CTACT
ok 113 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 114 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 115 - BIC:GGATCCATT{C.G}CTACT
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
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
t/Align/TreeBuild.t .......................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign
ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI
ok 9 - Tree object gotten back isa Bio::Tree::TreeI
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
t/Align/Utilities.t .......................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/AlignIO/AlignIO.t .......................... 
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : metafasta
ok 3 - input filehandle method test : po
ok 4 - input filehandle method test : nexus
ok 5 - input filehandle method test : clustalw
ok 6 - input filehandle method test : prodom
ok 7 - input filehandle method test : fasta
ok 8 - input filehandle method test : arp
ok 9 - input filehandle method test : xmfa
ok 10 - input filehandle method test : mase
ok 11 - input filehandle method test : psi
ok 12 - input filehandle method test : phylip
ok 13 - input filehandle method test : pfam
ok 14 - input filehandle method test : selex
ok 15 - input filehandle method test : stockholm
ok 16 - input filehandle method test : msf
ok 17 - filehandle output test : metafasta
ok 18 - filehandle output test : po
ok 19 - filehandle output test : nexus
ok 20 - filehandle output test : clustalw
ok 21 - filehandle output test : fasta
ok 22 - filehandle output test : xmfa
ok 23 - filehandle output test : psi
ok 24 - filehandle output test : phylip
ok 25 - filehandle output test : pfam
ok 26 - filehandle output test : selex
ok 27 - filehandle output test : stockholm
ok 28 - filehandle output test : msf
ok
t/AlignIO/arp.t .............................. 
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4 - ARP get_nse()
ok 5
ok 6 - ARP no_sequences()
ok 7 - ARP id()
ok 8 - ARP description()
ok 9 - The object isa Bio::AnnotationCollectionI
ok 10 - The object isa Bio::AnnotationI
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::AlignIO
ok 16 - The object isa Bio::Align::AlignI
ok 17 - ARP get_nse()
ok 18 - ARP no_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - The object isa Bio::AnnotationCollectionI
ok 22 - The object isa Bio::AnnotationI
ok 23
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Align::AlignI
ok 28 - ARP get_nse()
ok 29 - ARP no_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - The object isa Bio::AnnotationCollectionI
ok 33 - The object isa Bio::AnnotationI
ok 34
ok 35
ok 36
ok 37
ok 38 - The object isa Bio::Align::AlignI
ok 39 - ARP get_nse()
ok 40 - ARP no_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - The object isa Bio::AnnotationCollectionI
ok 44 - The object isa Bio::AnnotationI
ok 45
ok 46
ok 47
ok 48
ok
t/AlignIO/bl2seq.t ........................... 
1..3
ok 1 - use Bio::AlignIO::bl2seq;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - BLAST bl2seq format test
ok
t/AlignIO/clustalw.t ......................... 
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - The object isa Bio::Align::AlignI
ok 6 - clustalw (.aln) input test
ok
t/AlignIO/emboss.t ........................... 
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Align::AlignI
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Align::AlignI
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Align::AlignI
ok 19
ok 20
ok 21 - The object isa Bio::Align::AlignI
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Align::AlignI
ok 33
ok 34
ok 35
ok 36
ok 37
ok
t/AlignIO/fasta.t ............................ 
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for end
ok 7 - fasta input test for description
ok 8 - fasta output test
ok 9 - filehandle input test  
ok 10 - filehandle output test
ok
t/AlignIO/largemultifasta.t .................. 
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for description
ok 7 - fasta output test
ok
make: *** [test] Terminated

Timeout (max run time is 300s)
/Users/fly1003/bin/perl killed by signal 15