+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/bioperl-1.7.7nb3/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/bioperl-1.7.7nb3/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for bioperl-1.7.7nb3
cp bin/bp_aacomp blib/script/bp_aacomp
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp
cp bin/bp_bioflat_index blib/script/bp_bioflat_index
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index
cp bin/bp_biogetseq blib/script/bp_biogetseq
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq
cp bin/bp_dbsplit blib/script/bp_dbsplit
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit
cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq
cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table
cp bin/bp_fetch blib/script/bp_fetch
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch
cp bin/bp_filter_search blib/script/bp_filter_search
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search
cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_find-blast-matches
cp bin/bp_gccalc blib/script/bp_gccalc
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc
cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3
cp bin/bp_index blib/script/bp_index
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index
cp bin/bp_local_taxonomydb_query blib/script/bp_local_taxonomydb_query
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query
cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_make_mrna_protein
cp bin/bp_mask_by_search blib/script/bp_mask_by_search
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search
cp bin/bp_mrtrans blib/script/bp_mrtrans
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans
cp bin/bp_mutate blib/script/bp_mutate
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate
cp bin/bp_nexus2nh blib/script/bp_nexus2nh
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nexus2nh
cp bin/bp_nrdb blib/script/bp_nrdb
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb
cp bin/bp_oligo_count blib/script/bp_oligo_count
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count
cp bin/bp_process_gadfly blib/script/bp_process_gadfly
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_gadfly
cp bin/bp_process_sgd blib/script/bp_process_sgd
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd
cp bin/bp_revtrans-motif blib/script/bp_revtrans-motif
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_revtrans-motif
cp bin/bp_search2alnblocks blib/script/bp_search2alnblocks
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks
cp bin/bp_search2gff blib/script/bp_search2gff
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff
cp bin/bp_search2table blib/script/bp_search2table
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table
cp bin/bp_search2tribe blib/script/bp_search2tribe
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe
cp bin/bp_seq_length blib/script/bp_seq_length
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length
cp bin/bp_seqconvert blib/script/bp_seqconvert
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert
cp bin/bp_seqcut blib/script/bp_seqcut
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut
cp bin/bp_seqpart blib/script/bp_seqpart
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart
cp bin/bp_seqret blib/script/bp_seqret
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret
cp bin/bp_seqretsplit blib/script/bp_seqretsplit
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqretsplit
cp bin/bp_split_seq blib/script/bp_split_seq
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq
cp bin/bp_sreformat blib/script/bp_sreformat
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat
cp bin/bp_taxid4species blib/script/bp_taxid4species
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species
cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree
cp bin/bp_translate_seq blib/script/bp_translate_seq
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq
cp bin/bp_tree2pag blib/script/bp_tree2pag
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_tree2pag
cp bin/bp_unflatten_seq blib/script/bp_unflatten_seq
"/opt/pkg/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_unflatten_seq
cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm
cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm
cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm
cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm
cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm
cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm
cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm
cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm
cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm
cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm
cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm
cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm
cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm
cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm
cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm
cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm
cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm
cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm
cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm
cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm
cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm
cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm
cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm
cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm
cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm
cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm
cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm
cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm
cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm
cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm
cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm
cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm
cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm
cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm
cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm
cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm
cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm
cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm
cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm
cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm
cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm
cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm
cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm
cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm
cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm
cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm
cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm
cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm
cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm
cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm
cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm
cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm
cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm
cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm
cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm
cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm
cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm
cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm
cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm
cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm
cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm
cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm
cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm
cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm
cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm
cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm
cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm
cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm
cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm
cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm
cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm
cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm
cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm
cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm
cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm
cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm
cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm
cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm
cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm
cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm
cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm
cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm
cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm
cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm
cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm
cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm
cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm
cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm
cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm
cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm
cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm
cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm
cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm
cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm
cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm
cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm
cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm
cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm
cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm
cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm
cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm
cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm
cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm
cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm
cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm
cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm
cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm
cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm
cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm
cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm
cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm
cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm
cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm
cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm
cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm
cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm
cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm
cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm
cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm
cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm
cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm
cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm
cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm
cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm
cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm
cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm
cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm
cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm
cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm
cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm
cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm
cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm
cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm
cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm
cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm
cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm
cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm
cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm
cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm
cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm
cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm
cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm
cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm
cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm
cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm
cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm
cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm
cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm
cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm
cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm
cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm
cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm
cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm
cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm
cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm
cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm
cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm
cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm
cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm
cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm
cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm
cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm
cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm
cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm
cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm
cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm
cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm
cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm
cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm
cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm
cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm
cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm
cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm
cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm
cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm
cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm
cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm
cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm
cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm
cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm
cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm
cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm
cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm
cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm
cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm
cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm
cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm
cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm
cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm
cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm
cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm
cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm
cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm
cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm
cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm
cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm
cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm
cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm
cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm
cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm
cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm
cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm
cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm
cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm
cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm
cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm
cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm
cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm
cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm
cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm
cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm
cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm
cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm
cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm
cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm
cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm
cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm
cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm
cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm
cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm
cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm
cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm
cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm
cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm
cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm
cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm
cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm
cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm
cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm
cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm
cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm
cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm
cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm
cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm
cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm
cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm
cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm
cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm
cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm
cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm
cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm
cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm
cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm
cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm
cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm
cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm
cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm
cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm
cp lib/BioPerl.pm blib/lib/BioPerl.pm
cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm
cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm
cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm
cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm
cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm
cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm
cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm
cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm
cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm
cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm
cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm
cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm
cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm
cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm
cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm
cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm
cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm
cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm
cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm
cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm
cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm
cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm
cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm
cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm
cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm
cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm
cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm
cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm
cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm
cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm
cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm
cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm
cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm
cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm
cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm
cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm
cp lib/Bio/Species.pm blib/lib/Bio/Species.pm
cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm
cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm
cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm
cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm
cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm
cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm
cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm
cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm
cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm
cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm
cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm
cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm
cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm
cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm
cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm
cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm
cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm
cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm
cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm
cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm
cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm
cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm
cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm
cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm
cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm
cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm
cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm
cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm
cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm
cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm
cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm
cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm
cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm
cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm
cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm
cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm
cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm
cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm
cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm
cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm
cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm
cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm
cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm
cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm
cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm
cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm
cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm
cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm
cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm
cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm
cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm
cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm
cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm
cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm
cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm
cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm
cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm
cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm
cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm
cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm
cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm
cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm
cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm
cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm
cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm
cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm
cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm
cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm
cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm
cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm
cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm
cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm
cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm
cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm
cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm
cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm
cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm
cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm
cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm
cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm
cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm
cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm
cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm
cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm
cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm
cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm
cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm
cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm
cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm
cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm
cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm
cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm
cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm
cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm
cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm
cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm
cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm
cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm
cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm
cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm
cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm
cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm
cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm
cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm
cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm
cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm
cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm
cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm
cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm
cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm
cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm
cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm
cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm
cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm
cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm
cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm
cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm
cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm
cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm
cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm
cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm
cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm
cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm
cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm
cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm
cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm
cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm
cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm
cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm
cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm
cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm
cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm
cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm
cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm
cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm
cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm
cp lib/Bio/SeqIO/interpro.pm blib/lib/Bio/SeqIO/interpro.pm
cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm
cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm
cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm
cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm
cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm
cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm
cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm
cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm
cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm
cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm
cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm
cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm
cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm
cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm
cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm
cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm
cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm
cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm
cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm
cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm
cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm
cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm
cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm
cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm
cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm
cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm
cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm
cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm
cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm
cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm
cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm
cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm
cp lib/Bio/Range.pm blib/lib/Bio/Range.pm
cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm
cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm
cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm
cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm
cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm
cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm
cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm
cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm
cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm
Manifying 40 pod documents
Manifying 472 pod documents