Setting PATH to /opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/ccs/bin:/usr/bin:/usr/sbin
Start 2009-06-13T02:35:51
ActivePerl-818 CPAN-1.94
Going to read '/export/home/fly818/var/cpan/Metadata'
  Database was generated on Fri, 12 Jun 2009 10:27:07 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz
Checksum for /net/nas/data/cpan/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/
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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/DB/GFF/Aggregator/orf.pm
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/so_transcript.pm
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
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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
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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
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BioPerl-1.6.0/Bio/DB/HIV/lanl-schema.xml
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BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedFeature.pm
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BioPerl-1.6.0/examples/tools/standaloneblast.pl
BioPerl-1.6.0/examples/tree/
BioPerl-1.6.0/examples/tree/paup2phylip.pl
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BioPerl-1.6.0/INSTALL.WIN
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BioPerl-1.6.0/README
BioPerl-1.6.0/scripts/
BioPerl-1.6.0/scripts/biblio/
BioPerl-1.6.0/scripts/biblio/biblio.PLS
BioPerl-1.6.0/scripts/biblio/TAG
BioPerl-1.6.0/scripts/Bio-DB-GFF/
BioPerl-1.6.0/scripts/Bio-DB-GFF/bulk_load_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/fast_load_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/genbank2gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/genbank2gff3.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/generate_histogram.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/load_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/meta_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/process_gadfly.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/process_sgd.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/process_wormbase.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/README
BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/
BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
BioPerl-1.6.0/scripts/das/
BioPerl-1.6.0/scripts/das/README
BioPerl-1.6.0/scripts/das/TAG
BioPerl-1.6.0/scripts/DB/
BioPerl-1.6.0/scripts/DB/biofetch_genbank_proxy.PLS
BioPerl-1.6.0/scripts/DB/bioflat_index.PLS
BioPerl-1.6.0/scripts/DB/biogetseq.PLS
BioPerl-1.6.0/scripts/DB/flanks.PLS
BioPerl-1.6.0/scripts/DB/TAG
BioPerl-1.6.0/scripts/index/
BioPerl-1.6.0/scripts/index/bp_fetch.PLS
BioPerl-1.6.0/scripts/index/bp_index.PLS
BioPerl-1.6.0/scripts/index/bp_seqret.PLS
BioPerl-1.6.0/scripts/index/TAG
BioPerl-1.6.0/scripts/popgen/
BioPerl-1.6.0/scripts/popgen/composite_LD.PLS
BioPerl-1.6.0/scripts/popgen/heterogeneity_test.PLS
BioPerl-1.6.0/scripts/README
BioPerl-1.6.0/scripts/searchio/
BioPerl-1.6.0/scripts/searchio/fastam9_to_table.PLS
BioPerl-1.6.0/scripts/searchio/filter_search.PLS
BioPerl-1.6.0/scripts/searchio/hmmer_to_table.PLS
BioPerl-1.6.0/scripts/searchio/parse_hmmsearch.PLS
BioPerl-1.6.0/scripts/searchio/README
BioPerl-1.6.0/scripts/searchio/search2table.PLS
BioPerl-1.6.0/scripts/searchio/TAG
BioPerl-1.6.0/scripts/seq/
BioPerl-1.6.0/scripts/seq/extract_feature_seq.PLS
BioPerl-1.6.0/scripts/seq/make_mrna_protein.PLS
BioPerl-1.6.0/scripts/seq/seqconvert.PLS
BioPerl-1.6.0/scripts/seq/seqretsplit.PLS
BioPerl-1.6.0/scripts/seq/split_seq.PLS
BioPerl-1.6.0/scripts/seq/TAG
BioPerl-1.6.0/scripts/seq/translate_seq.PLS
BioPerl-1.6.0/scripts/seq/unflatten_seq.PLS
BioPerl-1.6.0/scripts/seqstats/
BioPerl-1.6.0/scripts/seqstats/aacomp.PLS
BioPerl-1.6.0/scripts/seqstats/chaos_plot.PLS
BioPerl-1.6.0/scripts/seqstats/gccalc.PLS
BioPerl-1.6.0/scripts/seqstats/oligo_count.PLS
BioPerl-1.6.0/scripts/seqstats/TAG
BioPerl-1.6.0/scripts/taxa/
BioPerl-1.6.0/scripts/taxa/classify_hits_kingdom.PLS
BioPerl-1.6.0/scripts/taxa/local_taxonomydb_query.PLS
BioPerl-1.6.0/scripts/taxa/query_entrez_taxa.PLS
BioPerl-1.6.0/scripts/taxa/TAG
BioPerl-1.6.0/scripts/taxa/taxid4species.PLS
BioPerl-1.6.0/scripts/taxa/taxonomy2tree.PLS
BioPerl-1.6.0/scripts/tree/
BioPerl-1.6.0/scripts/tree/blast2tree.PLS
BioPerl-1.6.0/scripts/tree/nexus2nh.PLS
BioPerl-1.6.0/scripts/tree/TAG
BioPerl-1.6.0/scripts/tree/tree2pag.PLS
BioPerl-1.6.0/scripts/utilities/
BioPerl-1.6.0/scripts/utilities/bp_mrtrans.PLS
BioPerl-1.6.0/scripts/utilities/bp_nrdb.PLS
BioPerl-1.6.0/scripts/utilities/bp_sreformat.PLS
BioPerl-1.6.0/scripts/utilities/dbsplit.PLS
BioPerl-1.6.0/scripts/utilities/download_query_genbank.PLS
BioPerl-1.6.0/scripts/utilities/mask_by_search.PLS
BioPerl-1.6.0/scripts/utilities/mutate.PLS
BioPerl-1.6.0/scripts/utilities/pairwise_kaks.PLS
BioPerl-1.6.0/scripts/utilities/README
BioPerl-1.6.0/scripts/utilities/remote_blast.PLS
BioPerl-1.6.0/scripts/utilities/search2alnblocks.PLS
BioPerl-1.6.0/scripts/utilities/search2BSML.PLS
BioPerl-1.6.0/scripts/utilities/search2gff.PLS
BioPerl-1.6.0/scripts/utilities/search2tribe.PLS
BioPerl-1.6.0/scripts/utilities/seq_length.PLS
BioPerl-1.6.0/scripts/utilities/TAG
BioPerl-1.6.0/t/
BioPerl-1.6.0/t/Align/
BioPerl-1.6.0/t/Align/AlignStats.t
BioPerl-1.6.0/t/Align/AlignUtil.t
BioPerl-1.6.0/t/Align/SimpleAlign.t
BioPerl-1.6.0/t/Align/TreeBuild.t
BioPerl-1.6.0/t/Align/Utilities.t
BioPerl-1.6.0/t/AlignIO/
BioPerl-1.6.0/t/AlignIO/AlignIO.t
BioPerl-1.6.0/t/AlignIO/arp.t
BioPerl-1.6.0/t/AlignIO/bl2seq.t
BioPerl-1.6.0/t/AlignIO/clustalw.t
BioPerl-1.6.0/t/AlignIO/emboss.t
BioPerl-1.6.0/t/AlignIO/fasta.t
BioPerl-1.6.0/t/AlignIO/largemultifasta.t
BioPerl-1.6.0/t/AlignIO/maf.t
BioPerl-1.6.0/t/AlignIO/mase.t
BioPerl-1.6.0/t/AlignIO/mega.t
BioPerl-1.6.0/t/AlignIO/meme.t
BioPerl-1.6.0/t/AlignIO/metafasta.t
BioPerl-1.6.0/t/AlignIO/msf.t
BioPerl-1.6.0/t/AlignIO/nexus.t
BioPerl-1.6.0/t/AlignIO/pfam.t
BioPerl-1.6.0/t/AlignIO/phylip.t
BioPerl-1.6.0/t/AlignIO/po.t
BioPerl-1.6.0/t/AlignIO/prodom.t
BioPerl-1.6.0/t/AlignIO/psi.t
BioPerl-1.6.0/t/AlignIO/selex.t
BioPerl-1.6.0/t/AlignIO/stockholm.t
BioPerl-1.6.0/t/AlignIO/xmfa.t
BioPerl-1.6.0/t/Alphabet.t
BioPerl-1.6.0/t/Annotation/
BioPerl-1.6.0/t/Annotation/Annotation.t
BioPerl-1.6.0/t/Annotation/AnnotationAdaptor.t
BioPerl-1.6.0/t/Assembly/
BioPerl-1.6.0/t/Assembly/Assembly.t
BioPerl-1.6.0/t/Assembly/ContigSpectrum.t
BioPerl-1.6.0/t/Biblio/
BioPerl-1.6.0/t/Biblio/Biblio.t
BioPerl-1.6.0/t/Biblio/biofetch.t
BioPerl-1.6.0/t/Biblio/eutils.t
BioPerl-1.6.0/t/Biblio/References.t
BioPerl-1.6.0/t/ClusterIO/
BioPerl-1.6.0/t/ClusterIO/ClusterIO.t
BioPerl-1.6.0/t/ClusterIO/SequenceFamily.t
BioPerl-1.6.0/t/ClusterIO/unigene.t
BioPerl-1.6.0/t/Coordinate/
BioPerl-1.6.0/t/Coordinate/CoordinateGraph.t
BioPerl-1.6.0/t/Coordinate/CoordinateMapper.t
BioPerl-1.6.0/t/Coordinate/GeneCoordinateMapper.t
BioPerl-1.6.0/t/data/
BioPerl-1.6.0/t/data/13-pilE-F.scf
BioPerl-1.6.0/t/data/1A11.pdb
BioPerl-1.6.0/t/data/1A3I.pdb
BioPerl-1.6.0/t/data/1BPT.pdb
BioPerl-1.6.0/t/data/2008.blasttable
BioPerl-1.6.0/t/data/503384.MEGABLAST.0
BioPerl-1.6.0/t/data/503384.MEGABLAST.2
BioPerl-1.6.0/t/data/5X_1895.FASTXY
BioPerl-1.6.0/t/data/8HVP.pdb
BioPerl-1.6.0/t/data/a_thaliana.blastn
BioPerl-1.6.0/t/data/AAC12660.fa
BioPerl-1.6.0/t/data/aaml.mlc
BioPerl-1.6.0/t/data/aaml_pairwise.mlc
BioPerl-1.6.0/t/data/AB077698.gb
BioPerl-1.6.0/t/data/acefile.ace.1
BioPerl-1.6.0/t/data/acefile.singlets
BioPerl-1.6.0/t/data/adh.mb_tree.nexus
BioPerl-1.6.0/t/data/AE003528_ecoli.bls
BioPerl-1.6.0/t/data/AE003644_Adh-genomic.gb
BioPerl-1.6.0/t/data/AF032047.gbk
BioPerl-1.6.0/t/data/AF165282.gb
BioPerl-1.6.0/t/data/AF305198.gb
BioPerl-1.6.0/t/data/AHCYL1.kegg
BioPerl-1.6.0/t/data/alleles.fas
BioPerl-1.6.0/t/data/alnfile.fasta
BioPerl-1.6.0/t/data/amino.fa
BioPerl-1.6.0/t/data/AnnIX-v003.gbk
BioPerl-1.6.0/t/data/ar.embl
BioPerl-1.6.0/t/data/assembly_with_singlets.ace
BioPerl-1.6.0/t/data/ATF14F8.gbk
BioPerl-1.6.0/t/data/atp1.matrix
BioPerl-1.6.0/t/data/ay007676.gb
BioPerl-1.6.0/t/data/AY095303S1.gbk
BioPerl-1.6.0/t/data/ay116458.gb
BioPerl-1.6.0/t/data/ay149291.gb
BioPerl-1.6.0/t/data/AY763288.gb
BioPerl-1.6.0/t/data/BAB68554.gb
BioPerl-1.6.0/t/data/barns-combined.nex
BioPerl-1.6.0/t/data/baseml.pairwise
BioPerl-1.6.0/t/data/baseml.usertree
BioPerl-1.6.0/t/data/basic-bush.nex
BioPerl-1.6.0/t/data/basic-ladder.nex
BioPerl-1.6.0/t/data/BC000007.gbk
BioPerl-1.6.0/t/data/BEL16-LTR_AG.embl
BioPerl-1.6.0/t/data/biodbgff/
BioPerl-1.6.0/t/data/biodbgff/test.gff
BioPerl-1.6.0/t/data/biodbgff/test.gff3
BioPerl-1.6.0/t/data/biofpc.cor
BioPerl-1.6.0/t/data/biofpc.fpc
BioPerl-1.6.0/t/data/Bird_Ovomucoids.nex
BioPerl-1.6.0/t/data/BK000016-tpa.gbk
BioPerl-1.6.0/t/data/bl2seq.blastn
BioPerl-1.6.0/t/data/bl2seq.blastn.rev
BioPerl-1.6.0/t/data/bl2seq.blastx.out
BioPerl-1.6.0/t/data/bl2seq.bug940.out
BioPerl-1.6.0/t/data/bl2seq.out
BioPerl-1.6.0/t/data/bl2seq.tblastx.out
BioPerl-1.6.0/t/data/blast.report
BioPerl-1.6.0/t/data/blast_no_hit_desc.txt
BioPerl-1.6.0/t/data/blastp2215.blast
BioPerl-1.6.0/t/data/blat.psLayout3
BioPerl-1.6.0/t/data/BLOSUM50
BioPerl-1.6.0/t/data/blosum62.bla
BioPerl-1.6.0/t/data/BN000066-tpa.embl
BioPerl-1.6.0/t/data/bootstrap.tre
BioPerl-1.6.0/t/data/BOSS_DROME.FASTP_v35_04
BioPerl-1.6.0/t/data/branchSite.mlc
BioPerl-1.6.0/t/data/brassica_ATH.WUBLASTN
BioPerl-1.6.0/t/data/bug1986.blast2
BioPerl-1.6.0/t/data/bug1986.blastp
BioPerl-1.6.0/t/data/bug2120.phd
BioPerl-1.6.0/t/data/bug2246.blast
BioPerl-1.6.0/t/data/bug2335.fastq
BioPerl-1.6.0/t/data/bug2391.megablast
BioPerl-1.6.0/t/data/bug2399.tblastn
BioPerl-1.6.0/t/data/bug2453.maf
BioPerl-1.6.0/t/data/bug2473.fasta
BioPerl-1.6.0/t/data/c200-vs-yeast.BLASTN
BioPerl-1.6.0/t/data/c200-vs-yeast.BLASTN.m8
BioPerl-1.6.0/t/data/calm.swiss
BioPerl-1.6.0/t/data/catalase-webblast.BLASTP
BioPerl-1.6.0/t/data/cds-266.fas
BioPerl-1.6.0/t/data/CG11099.fasaln
BioPerl-1.6.0/t/data/CG2865.fasaln
BioPerl-1.6.0/t/data/chad100.scf
BioPerl-1.6.0/t/data/char-interleave.nex
BioPerl-1.6.0/t/data/char-matrix-spaces.nex
BioPerl-1.6.0/t/data/codeml.mlc
BioPerl-1.6.0/t/data/codeml315.mlc
BioPerl-1.6.0/t/data/codeml4.mlc
BioPerl-1.6.0/t/data/codeml_lysozyme/
BioPerl-1.6.0/t/data/codeml_lysozyme/2NG.dN
BioPerl-1.6.0/t/data/codeml_lysozyme/2NG.dS
BioPerl-1.6.0/t/data/codeml_lysozyme/2NG.tt
BioPerl-1.6.0/t/data/codeml_lysozyme/4fold.nuc
BioPerl-1.6.0/t/data/codeml_lysozyme/lnf
BioPerl-1.6.0/t/data/codeml_lysozyme/lysozymeSmall.ctl
BioPerl-1.6.0/t/data/codeml_lysozyme/lysozymeSmall.trees
BioPerl-1.6.0/t/data/codeml_lysozyme/lysozymeSmall.txt
BioPerl-1.6.0/t/data/codeml_lysozyme/mlc
BioPerl-1.6.0/t/data/codeml_lysozyme/rst
BioPerl-1.6.0/t/data/codeml_lysozyme/rst1
BioPerl-1.6.0/t/data/codeml_lysozyme/rub
BioPerl-1.6.0/t/data/codeml_nssites.mlc
BioPerl-1.6.0/t/data/compLD_missingtest.prettybase
BioPerl-1.6.0/t/data/compLD_test.prettybase
BioPerl-1.6.0/t/data/component.ontology.test
BioPerl-1.6.0/t/data/component.ontology.test2
BioPerl-1.6.0/t/data/consed_project/
BioPerl-1.6.0/t/data/consed_project/edit_dir/
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.contigs
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.log
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.log
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.problems
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.qual
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.fasta.screen.view
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.newtags
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.phrap.out
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project.screen.out
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_project_to_alu.cross
BioPerl-1.6.0/t/data/consed_project/edit_dir/test_projectNewChromats.fof
BioPerl-1.6.0/t/data/consed_project/phd_dir/
BioPerl-1.6.0/t/data/consed_project/phd_dir/ML4922R.phd.1
BioPerl-1.6.0/t/data/consed_project/phd_dir/ML4924F.phd.1
BioPerl-1.6.0/t/data/consed_project/phd_dir/ML4924R.phd.1
BioPerl-1.6.0/t/data/consed_project/phd_dir/ML4947F.phd.1
BioPerl-1.6.0/t/data/contigspectrumtest.asm
BioPerl-1.6.0/t/data/crab.dat.cn
BioPerl-1.6.0/t/data/crab.nj
BioPerl-1.6.0/t/data/crab.njb
BioPerl-1.6.0/t/data/crypto.sim4-0
BioPerl-1.6.0/t/data/crypto.sim4-3
BioPerl-1.6.0/t/data/crypto.sim4-4
BioPerl-1.6.0/t/data/ctgdemo.fpc
BioPerl-1.6.0/t/data/cys1_dicdi.water
BioPerl-1.6.0/t/data/cysprot.fa
BioPerl-1.6.0/t/data/cysprot.msf
BioPerl-1.6.0/t/data/cysprot.needle
BioPerl-1.6.0/t/data/cysprot.tblastn
BioPerl-1.6.0/t/data/cysprot.water
BioPerl-1.6.0/t/data/cysprot1.fa
BioPerl-1.6.0/t/data/cysprot1.FASTA
BioPerl-1.6.0/t/data/cysprot1a.fa
BioPerl-1.6.0/t/data/cysprot1a.msf
BioPerl-1.6.0/t/data/cysprot1b.fa
BioPerl-1.6.0/t/data/cysprot1b.hmmsearch
BioPerl-1.6.0/t/data/cysprot1b.msf
BioPerl-1.6.0/t/data/cysprot1b.newick
BioPerl-1.6.0/t/data/cysprot_vs_gadfly.FASTA
BioPerl-1.6.0/t/data/D10483.gbk
BioPerl-1.6.0/t/data/D12555.gbk
BioPerl-1.6.0/t/data/dbfa/
BioPerl-1.6.0/t/data/dbfa/1.fa
BioPerl-1.6.0/t/data/dbfa/2.fa
BioPerl-1.6.0/t/data/dbfa/3.fa
BioPerl-1.6.0/t/data/dbfa/4.fa
BioPerl-1.6.0/t/data/dbfa/5.fa
BioPerl-1.6.0/t/data/dbfa/6.fa
BioPerl-1.6.0/t/data/dbfa/7.fa
BioPerl-1.6.0/t/data/dbqual/
BioPerl-1.6.0/t/data/dbqual/1.qual
BioPerl-1.6.0/t/data/dbqual/2.qual
BioPerl-1.6.0/t/data/dbqual/3.qual
BioPerl-1.6.0/t/data/dcr1_sp.WUBLASTP
BioPerl-1.6.0/t/data/directives.gff3
BioPerl-1.6.0/t/data/dmel_2Lchunk.gb
BioPerl-1.6.0/t/data/dna1.fa
BioPerl-1.6.0/t/data/dna2.fa
BioPerl-1.6.0/t/data/dnaE-bsub-prot.fa
BioPerl-1.6.0/t/data/dnaE-bsub.fa
BioPerl-1.6.0/t/data/dnaEbsub_ecoli.wublastx
BioPerl-1.6.0/t/data/dnaEbsub_ecoli.wutblastn
BioPerl-1.6.0/t/data/dnaEbsub_ecoli.wutblastx
BioPerl-1.6.0/t/data/DQ018368.gb
BioPerl-1.6.0/t/data/dq519393.gb
BioPerl-1.6.0/t/data/ECAPAH02.embl
BioPerl-1.6.0/t/data/echofilter.wublastn
BioPerl-1.6.0/t/data/ecoli-trna-qrna.out
BioPerl-1.6.0/t/data/ecoli_domains.rps.xml
BioPerl-1.6.0/t/data/ecoli_domains.rpsblast
BioPerl-1.6.0/t/data/ecolitst.bls
BioPerl-1.6.0/t/data/ecolitst.fa
BioPerl-1.6.0/t/data/ecolitst.noseqs.wublastp
BioPerl-1.6.0/t/data/ecolitst.wublastp
BioPerl-1.6.0/t/data/empty.bl2seq
BioPerl-1.6.0/t/data/ENr111.mfa.example.elems
BioPerl-1.6.0/t/data/entrezgene.dat
BioPerl-1.6.0/t/data/eutils/
BioPerl-1.6.0/t/data/eutils/egquery.xml
BioPerl-1.6.0/t/data/eutils/einfo.xml
BioPerl-1.6.0/t/data/eutils/einfo_dbs.xml
BioPerl-1.6.0/t/data/eutils/elink_acheck.xml
BioPerl-1.6.0/t/data/eutils/elink_acheck_corr.xml
BioPerl-1.6.0/t/data/eutils/elink_dball.xml
BioPerl-1.6.0/t/data/eutils/elink_lcheck.xml
BioPerl-1.6.0/t/data/eutils/elink_lcheck_corr.xml
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BioPerl-1.6.0/t/Tools/rnamotif.t
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

>>> /export/home/fly818/bin/perl Makefile.PL
# running Build.PL 
/export/home/fly818/bin/perl Build.PL
Checking whether your kit is complete...
Looks good

Checking prerequisites...
 - ERROR: DB_File is not installed

CPAN: File::HomeDir loaded ok (v0.86)
(I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand)
CPAN: Storable loaded ok (v2.20)
Going to read /export/home/fly818/.cpan/Metadata
  Database was generated on Thu, 11 Jun 2009 10:27:00 GMT
Running install for module 'DB_File'
CPAN: YAML loaded ok (v0.68)
Running make for P/PM/PMQS/DB_File-1.820.tar.gz
CPAN: Digest::SHA loaded ok (v5.47)
CPAN: Compress::Zlib loaded ok (v2.015)
Checksum for /export/home/fly818/.cpan/sources/authors/id/P/PM/PMQS/DB_File-1.820.tar.gz ok
x DB_File-1.820, 0 bytes, 0 tape blocks
x DB_File-1.820/MANIFEST, 499 bytes, 1 tape blocks
x DB_File-1.820/Changes, 14109 bytes, 28 tape blocks
x DB_File-1.820/DB_File.pm, 63535 bytes, 125 tape blocks
x DB_File-1.820/DB_File_BS, 164 bytes, 1 tape blocks
x DB_File-1.820/config.in, 3117 bytes, 7 tape blocks
x DB_File-1.820/ppport.h, 9567 bytes, 19 tape blocks
x DB_File-1.820/DB_File.xs, 47755 bytes, 94 tape blocks
x DB_File-1.820/t, 0 bytes, 0 tape blocks
x DB_File-1.820/t/db-recno.t, 37821 bytes, 74 tape blocks
x DB_File-1.820/t/pod.t, 260 bytes, 1 tape blocks
x DB_File-1.820/t/db-hash.t, 28424 bytes, 56 tape blocks
x DB_File-1.820/t/db-btree.t, 36903 bytes, 73 tape blocks
x DB_File-1.820/version.c, 2287 bytes, 5 tape blocks
x DB_File-1.820/fallback.h, 11405 bytes, 23 tape blocks
x DB_File-1.820/fallback.xs, 2645 bytes, 6 tape blocks
x DB_File-1.820/README, 21274 bytes, 42 tape blocks
x DB_File-1.820/dbinfo, 3228 bytes, 7 tape blocks
x DB_File-1.820/patches, 0 bytes, 0 tape blocks
x DB_File-1.820/patches/5.004, 2561 bytes, 6 tape blocks
x DB_File-1.820/patches/5.005_01, 7252 bytes, 15 tape blocks
x DB_File-1.820/patches/5.6.0, 10120 bytes, 20 tape blocks
x DB_File-1.820/patches/5.005_03, 8602 bytes, 17 tape blocks
x DB_File-1.820/patches/5.004_05, 6712 bytes, 14 tape blocks
x DB_File-1.820/patches/5.004_04, 6678 bytes, 14 tape blocks
x DB_File-1.820/patches/5.004_01, 6944 bytes, 14 tape blocks
x DB_File-1.820/patches/5.004_03, 7212 bytes, 15 tape blocks
x DB_File-1.820/patches/5.005, 7168 bytes, 14 tape blocks
x DB_File-1.820/patches/5.004_02, 6944 bytes, 14 tape blocks
x DB_File-1.820/patches/5.005_02, 9240 bytes, 19 tape blocks
x DB_File-1.820/META.yml, 533 bytes, 2 tape blocks
x DB_File-1.820/typemap, 1177 bytes, 3 tape blocks
x DB_File-1.820/hints, 0 bytes, 0 tape blocks
x DB_File-1.820/hints/sco.pl, 146 bytes, 1 tape blocks
x DB_File-1.820/hints/dynixptx.pl, 101 bytes, 1 tape blocks
x DB_File-1.820/Makefile.PL, 8433 bytes, 17 tape blocks
CPAN: File::Temp loaded ok (v0.21)

  CPAN.pm: Going to build P/PM/PMQS/DB_File-1.820.tar.gz

Parsing config.in...
Looks Good.
Checking if your kit is complete...
Looks good
Note (probably harmless): No library found for -ldb
Writing Makefile for DB_File
cp DB_File.pm blib/lib/DB_File.pm
AutoSplitting blib/lib/DB_File.pm (blib/lib/auto/DB_File)
cc -c  -I/usr/local/BerkeleyDB/include -D_POSIX_PTHREAD_SEMANTICS -D_REENTRANT -DUSE_SITECUSTOMIZE -DNO_HASH_SEED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O   -DVERSION=\"1.820\" -DXS_VERSION=\"1.82\" -KPIC "-I/export/home/fly818/ap818/lib/CORE"  -D_NOT_CORE  -DmDB_Prefix_t=size_t -DmDB_Hash_t=u_int32_t   version.c
"version.c", line 30: cannot find include file: <db.h>
cc: acomp failed for version.c
make: *** [version.o] Error 2
  PMQS/DB_File-1.820.tar.gz
  /usr/local/bin/make -- NOT OK
Running make test
  Can't test without successful make
Running make install
  Make had returned bad status, install seems impossible


*** (back in Bioperl Build.PL) ***
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n]  - ERROR: You chose to install DB_File but it failed to install
 * Optional prerequisite Bio::ASN1::EntrezGene is not installed
   (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!])
 * Optional prerequisite XML::SAX::Writer is not installed
   (wanted for writing xml, used by Bio::SeqIO::tigrxml)
 * Optional prerequisite GraphViz is not installed
   (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)

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

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

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'
---- Unsatisfied dependencies detected during ----
----       CJFIELDS/BioPerl-1.6.0.tar.gz      ----
    DB_File [requires]
Running make test
  Delayed until after prerequisites
Running test for module 'DB_File'

______________________ D i s t r o P r e f s ______________________
                           DB_File.yml[0]                           
Running make for P/PM/PMQS/DB_File-1.820.tar.gz
Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0
  PMQS/DB_File-1.820.tar.gz
  [disabled] -- NA Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0
Running make for C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz
  Has already been unwrapped into directory /export/home/fly818/var/cpan/build/BioPerl-1.6.0-f1Opum

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

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.0.tar.gz' failed when processing 'PMQS/DB_File-1.820.tar.gz' with 'unwrapped => NO Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> make
/export/home/fly818/bin/perl Build --makefile_env_macros 1
Copying Bio/PopGen/MarkerI.pm -> blib/lib/Bio/PopGen/MarkerI.pm
Copying Bio/Matrix/PSM/Psm.pm -> blib/lib/Bio/Matrix/PSM/Psm.pm
Copying Bio/MolEvol/CodonModel.pm -> blib/lib/Bio/MolEvol/CodonModel.pm
Copying Bio/Tools/Spidey/Exon.pm -> blib/lib/Bio/Tools/Spidey/Exon.pm
Copying Bio/Matrix/PSM/ProtMatrix.pm -> blib/lib/Bio/Matrix/PSM/ProtMatrix.pm
Copying Bio/WebAgent.pm -> blib/lib/Bio/WebAgent.pm
Copying Bio/LiveSeq/ChainI.pm -> blib/lib/Bio/LiveSeq/ChainI.pm
Copying Bio/AlignIO/mega.pm -> blib/lib/Bio/AlignIO/mega.pm
Copying Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm
Copying Bio/LiveSeq/Mutation.pm -> blib/lib/Bio/LiveSeq/Mutation.pm
Copying Bio/TreeIO/pag.pm -> blib/lib/Bio/TreeIO/pag.pm
Copying Bio/Tools/HMMER/Set.pm -> blib/lib/Bio/Tools/HMMER/Set.pm
Copying Bio/Map/PositionWithSequence.pm -> blib/lib/Bio/Map/PositionWithSequence.pm
Copying Bio/SeqIO/chaos.pm -> blib/lib/Bio/SeqIO/chaos.pm
Copying Bio/Factory/ObjectFactory.pm -> blib/lib/Bio/Factory/ObjectFactory.pm
Copying Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm
Copying Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
Copying Bio/SearchIO/megablast.pm -> blib/lib/Bio/SearchIO/megablast.pm
Copying Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm
Copying Bio/TreeIO.pm -> blib/lib/Bio/TreeIO.pm
Copying Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
Copying Bio/Search/HSP/PSLHSP.pm -> blib/lib/Bio/Search/HSP/PSLHSP.pm
Copying Bio/Cluster/UniGeneI.pm -> blib/lib/Bio/Cluster/UniGeneI.pm
Copying Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
Copying Bio/Map/Physical.pm -> blib/lib/Bio/Map/Physical.pm
Copying Bio/Tools/GuessSeqFormat.pm -> blib/lib/Bio/Tools/GuessSeqFormat.pm
Copying Bio/Search/Result/HmmpfamResult.pm -> blib/lib/Bio/Search/Result/HmmpfamResult.pm
Copying Bio/Biblio/PubmedBookArticle.pm -> blib/lib/Bio/Biblio/PubmedBookArticle.pm
Copying Bio/Search/HSP/WABAHSP.pm -> blib/lib/Bio/Search/HSP/WABAHSP.pm
Copying Bio/Align/Utilities.pm -> blib/lib/Bio/Align/Utilities.pm
Copying Bio/Tools/Run/ParametersI.pm -> blib/lib/Bio/Tools/Run/ParametersI.pm
Copying Bio/Expression/ProbeI.pm -> blib/lib/Bio/Expression/ProbeI.pm
Copying Bio/DB/Flat.pm -> blib/lib/Bio/DB/Flat.pm
Copying Bio/SeqFeature/Lite.pm -> blib/lib/Bio/SeqFeature/Lite.pm
Copying Bio/DB/SwissProt.pm -> blib/lib/Bio/DB/SwissProt.pm
Copying Bio/SearchIO/fasta.pm -> blib/lib/Bio/SearchIO/fasta.pm
Copying Bio/Tools/EUtilities/Query/GlobalQuery.pm -> blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm
Copying Bio/TreeIO/nexus.pm -> blib/lib/Bio/TreeIO/nexus.pm
Copying Bio/Biblio/Provider.pm -> blib/lib/Bio/Biblio/Provider.pm
Copying Bio/Coordinate/Graph.pm -> blib/lib/Bio/Coordinate/Graph.pm
Copying Bio/Search/HSP/ModelHSP.pm -> blib/lib/Bio/Search/HSP/ModelHSP.pm
Copying Bio/Tree/DistanceFactory.pm -> blib/lib/Bio/Tree/DistanceFactory.pm
Copying Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
Copying Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm
Copying Bio/LocationI.pm -> blib/lib/Bio/LocationI.pm
Copying Bio/Root/RootI.pm -> blib/lib/Bio/Root/RootI.pm
Copying Bio/Taxonomy.pm -> blib/lib/Bio/Taxonomy.pm
Copying Bio/Matrix/PSM/PsmI.pm -> blib/lib/Bio/Matrix/PSM/PsmI.pm
Copying Bio/TreeIO/TreeEventBuilder.pm -> blib/lib/Bio/TreeIO/TreeEventBuilder.pm
Copying Bio/DBLinkContainerI.pm -> blib/lib/Bio/DBLinkContainerI.pm
Copying Bio/Location/Fuzzy.pm -> blib/lib/Bio/Location/Fuzzy.pm
Copying Bio/SeqIO.pm -> blib/lib/Bio/SeqIO.pm
Copying Bio/FeatureIO/bed.pm -> blib/lib/Bio/FeatureIO/bed.pm
Copying Bio/AnalysisI.pm -> blib/lib/Bio/AnalysisI.pm
Copying Bio/LiveSeq/AARange.pm -> blib/lib/Bio/LiveSeq/AARange.pm
Copying Bio/DB/Biblio/biofetch.pm -> blib/lib/Bio/DB/Biblio/biofetch.pm
Copying Bio/Index/Swissprot.pm -> blib/lib/Bio/Index/Swissprot.pm
Copying Bio/Annotation/OntologyTerm.pm -> blib/lib/Bio/Annotation/OntologyTerm.pm
Copying Bio/Map/SimpleMap.pm -> blib/lib/Bio/Map/SimpleMap.pm
Copying Bio/Coordinate/Result/Gap.pm -> blib/lib/Bio/Coordinate/Result/Gap.pm
Copying Bio/Tools/TandemRepeatsFinder.pm -> blib/lib/Bio/Tools/TandemRepeatsFinder.pm
Copying Bio/Seq/Meta/Array.pm -> blib/lib/Bio/Seq/Meta/Array.pm
Copying Bio/Tools/Run/RemoteBlast.pm -> blib/lib/Bio/Tools/Run/RemoteBlast.pm
Copying Bio/DB/BiblioI.pm -> blib/lib/Bio/DB/BiblioI.pm
Copying Bio/FeatureIO.pm -> blib/lib/Bio/FeatureIO.pm
Copying Bio/MapIO.pm -> blib/lib/Bio/MapIO.pm
Copying Bio/Map/Clone.pm -> blib/lib/Bio/Map/Clone.pm
Copying Bio/SearchIO/Writer/HSPTableWriter.pm -> blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm
Copying Bio/SearchIO/blasttable.pm -> blib/lib/Bio/SearchIO/blasttable.pm
Copying Bio/Expression/DataSet.pm -> blib/lib/Bio/Expression/DataSet.pm
Copying Bio/SeqFeature/Collection.pm -> blib/lib/Bio/SeqFeature/Collection.pm
Copying Bio/DB/Expression/geo.pm -> blib/lib/Bio/DB/Expression/geo.pm
Copying Bio/Tree/TreeI.pm -> blib/lib/Bio/Tree/TreeI.pm
Copying Bio/Index/BlastTable.pm -> blib/lib/Bio/Index/BlastTable.pm
Copying Bio/Map/MappableI.pm -> blib/lib/Bio/Map/MappableI.pm
Copying Bio/Seq/BaseSeqProcessor.pm -> blib/lib/Bio/Seq/BaseSeqProcessor.pm
Copying Bio/PullParserI.pm -> blib/lib/Bio/PullParserI.pm
Copying Bio/SeqIO/fastq.pm -> blib/lib/Bio/SeqIO/fastq.pm
Copying Bio/LiveSeq/SeqI.pm -> blib/lib/Bio/LiveSeq/SeqI.pm
Copying Bio/Restriction/IO/prototype.pm -> blib/lib/Bio/Restriction/IO/prototype.pm
Copying Bio/Tools/Analysis/Protein/ELM.pm -> blib/lib/Bio/Tools/Analysis/Protein/ELM.pm
Copying Bio/Seq/TraceI.pm -> blib/lib/Bio/Seq/TraceI.pm
Copying Bio/Phenotype/Phenotype.pm -> blib/lib/Bio/Phenotype/Phenotype.pm
Copying Bio/Seq/PrimaryQual.pm -> blib/lib/Bio/Seq/PrimaryQual.pm
Copying Bio/DB/Failover.pm -> blib/lib/Bio/DB/Failover.pm
Copying Bio/Map/CytoMap.pm -> blib/lib/Bio/Map/CytoMap.pm
Copying Bio/Variation/Allele.pm -> blib/lib/Bio/Variation/Allele.pm
Copying Bio/LiveSeq/IO/Loader.pm -> blib/lib/Bio/LiveSeq/IO/Loader.pm
Copying Bio/Search/Hit/PsiBlastHit.pm -> blib/lib/Bio/Search/Hit/PsiBlastHit.pm
Copying Bio/LiveSeq/Repeat_Unit.pm -> blib/lib/Bio/LiveSeq/Repeat_Unit.pm
Copying Bio/Restriction/Enzyme/MultiCut.pm -> blib/lib/Bio/Restriction/Enzyme/MultiCut.pm
Copying Bio/DB/GFF/Adaptor/memory.pm -> blib/lib/Bio/DB/GFF/Adaptor/memory.pm
Copying Bio/DB/UpdateableSeqI.pm -> blib/lib/Bio/DB/UpdateableSeqI.pm
Copying Bio/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
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Copying Bio/AlignIO/stockholm.pm -> blib/lib/Bio/AlignIO/stockholm.pm
Copying Bio/PopGen/Individual.pm -> blib/lib/Bio/PopGen/Individual.pm
Copying Bio/DB/GFF/Adaptor/dbi/mysqlace.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
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Copying Bio/DasI.pm -> blib/lib/Bio/DasI.pm
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Copying Bio/OntologyIO/simplehierarchy.pm -> blib/lib/Bio/OntologyIO/simplehierarchy.pm
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Copying Bio/SeqUtils.pm -> blib/lib/Bio/SeqUtils.pm
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Copying Bio/Biblio/PubmedArticle.pm -> blib/lib/Bio/Biblio/PubmedArticle.pm
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Copying Bio/SeqIO/bsml_sax.pm -> blib/lib/Bio/SeqIO/bsml_sax.pm
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Copying Bio/AnnotatableI.pm -> blib/lib/Bio/AnnotatableI.pm
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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
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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
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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
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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
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Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
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Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
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Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
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Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
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Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
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Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
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Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
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Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
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Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
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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
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Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
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Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
Deleting blib/script/mask_by_search.PLS.bak
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Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
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Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
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Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
Deleting blib/script/classify_hits_kingdom.PLS.bak
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Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
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Deleting blib/script/process_wormbase.PLS.bak
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Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
Deleting blib/script/local_taxonomydb_query.PLS.bak
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Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
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Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
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Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
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Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Deleting blib/script/genbank2gff3.PLS.bak
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Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
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Copying Bio/DB/HIV/lanl-schema.xml -> blib/lib/Bio/DB/HIV/lanl-schema.xml
Writing config notes to blib/lib/Bio/ConfigData.pm
Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1
Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1
Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1
Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1
Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1
Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1
Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1
Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1
Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1
Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1
Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1
Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1
Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1
Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1
Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1
Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1
Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1
Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1
Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1
Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1
Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1
Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1
Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1
Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1
Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1
Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1
Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1
Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1
Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1
Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1
Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1
Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1
Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1
Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1
Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1
Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1
Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1
Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1
Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1
Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1
Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1
Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1
Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1
Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1
Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1
Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1
Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1
Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1
Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1
Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1
Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1
Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1
Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1
Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.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/OntologyIO/dagflat.pm -> blib/libdoc/Bio::OntologyIO::dagflat.3
Manifying blib/lib/Bio/Seq/SeqFactory.pm -> blib/libdoc/Bio::Seq::SeqFactory.3
Manifying blib/lib/Bio/Location/CoordinatePolicyI.pm -> blib/libdoc/Bio::Location::CoordinatePolicyI.3
Manifying blib/lib/Bio/Root/Storable.pm -> blib/libdoc/Bio::Root::Storable.3
Manifying blib/lib/Bio/Location/Atomic.pm -> blib/libdoc/Bio::Location::Atomic.3
Manifying blib/lib/Bio/SearchIO/SearchWriterI.pm -> blib/libdoc/Bio::SearchIO::SearchWriterI.3
Manifying blib/lib/Bio/FeatureIO.pm -> blib/libdoc/Bio::FeatureIO.3
Manifying blib/lib/Bio/Biblio/IO.pm -> blib/libdoc/Bio::Biblio::IO.3
Manifying blib/lib/Bio/Variation/RNAChange.pm -> blib/libdoc/Bio::Variation::RNAChange.3
Manifying blib/lib/Bio/Root/Exception.pm -> blib/libdoc/Bio::Root::Exception.3
Manifying blib/lib/Bio/Factory/LocationFactoryI.pm -> blib/libdoc/Bio::Factory::LocationFactoryI.3
Manifying blib/lib/Bio/Biblio/Ref.pm -> blib/libdoc/Bio::Biblio::Ref.3
Manifying blib/lib/Bio/Search/HSP/WABAHSP.pm -> blib/libdoc/Bio::Search::HSP::WABAHSP.3
Manifying blib/lib/Bio/SeqIO/embl.pm -> blib/libdoc/Bio::SeqIO::embl.3
Manifying blib/lib/Bio/Factory/DriverFactory.pm -> blib/libdoc/Bio::Factory::DriverFactory.3
Manifying blib/lib/Bio/Tools/Genemark.pm -> blib/libdoc/Bio::Tools::Genemark.3
Manifying blib/lib/Bio/Biblio/MedlineArticle.pm -> blib/libdoc/Bio::Biblio::MedlineArticle.3
Manifying blib/lib/Bio/LiveSeq/ChainI.pm -> blib/libdoc/Bio::LiveSeq::ChainI.3
Manifying blib/lib/Bio/Tools/PrositeScan.pm -> blib/libdoc/Bio::Tools::PrositeScan.3
Manifying blib/lib/Bio/LiveSeq/Intron.pm -> blib/libdoc/Bio::LiveSeq::Intron.3
Manifying blib/lib/Bio/Matrix/IO/scoring.pm -> blib/libdoc/Bio::Matrix::IO::scoring.3
Manifying blib/lib/Bio/Seq/LargeLocatableSeq.pm -> blib/libdoc/Bio::Seq::LargeLocatableSeq.3
Manifying blib/lib/Bio/AlignIO/msf.pm -> blib/libdoc/Bio::AlignIO::msf.3
Manifying blib/lib/Bio/Tools/Glimmer.pm -> blib/libdoc/Bio::Tools::Glimmer.3
Manifying blib/lib/Bio/SeqIO/flybase_chadoxml.pm -> blib/libdoc/Bio::SeqIO::flybase_chadoxml.3
Manifying blib/lib/Bio/Map/RelativeI.pm -> blib/libdoc/Bio::Map::RelativeI.3
Manifying blib/lib/Bio/Tools/Profile.pm -> blib/libdoc/Bio::Tools::Profile.3
Manifying blib/lib/Bio/LiveSeq/Mutator.pm -> blib/libdoc/Bio::LiveSeq::Mutator.3
Manifying blib/lib/Bio/Tools/Primer/Pair.pm -> blib/libdoc/Bio::Tools::Primer::Pair.3
Manifying blib/lib/Bio/Annotation/TypeManager.pm -> blib/libdoc/Bio::Annotation::TypeManager.3
Manifying blib/lib/Bio/Expression/ProbeI.pm -> blib/libdoc/Bio::Expression::ProbeI.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/alignment.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::alignment.3
Manifying blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -> blib/libdoc/Bio::SearchIO::IteratedSearchResultEventBuilder.3
Manifying blib/lib/Bio/Map/LinkagePosition.pm -> blib/libdoc/Bio::Map::LinkagePosition.3
Manifying blib/lib/Bio/Tools/Primer/Assessor/Base.pm -> blib/libdoc/Bio::Tools::Primer::Assessor::Base.3
Manifying blib/lib/Bio/ClusterIO/unigene.pm -> blib/libdoc/Bio::ClusterIO::unigene.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch_oracle.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/pg.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::pg.3
Manifying blib/lib/Bio/DB/GFF/Util/Binning.pm -> blib/libdoc/Bio::DB::GFF::Util::Binning.3
Manifying blib/lib/Bio/Index/Abstract.pm -> blib/libdoc/Bio::Index::Abstract.3
Manifying blib/lib/Bio/PopGen/GenotypeI.pm -> blib/libdoc/Bio::PopGen::GenotypeI.3
Manifying blib/lib/Bio/Cluster/ClusterFactory.pm -> blib/libdoc/Bio::Cluster::ClusterFactory.3
Manifying blib/lib/Bio/Tools/pSW.pm -> blib/libdoc/Bio::Tools::pSW.3
Manifying blib/lib/Bio/FeatureIO/interpro.pm -> blib/libdoc/Bio::FeatureIO::interpro.3
Manifying blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm -> blib/libdoc/Bio::SeqFeature::Gene::TranscriptI.3
Manifying blib/lib/Bio/TreeIO/tabtree.pm -> blib/libdoc/Bio::TreeIO::tabtree.3
Manifying blib/lib/Bio/DB/SeqFeature/Store.pm -> blib/libdoc/Bio::DB::SeqFeature::Store.3
Manifying blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm -> blib/libdoc/Bio::SeqFeature::Gene::NC_Feature.3
Manifying blib/lib/Bio/Biblio/Provider.pm -> blib/libdoc/Bio::Biblio::Provider.3
Manifying blib/lib/Bio/Phenotype/PhenotypeI.pm -> blib/libdoc/Bio::Phenotype::PhenotypeI.3
Manifying blib/lib/Bio/SeqIO/bsml_sax.pm -> blib/libdoc/Bio::SeqIO::bsml_sax.3
Manifying blib/lib/Bio/Map/OrderedPosition.pm -> blib/libdoc/Bio::Map::OrderedPosition.3
Manifying blib/lib/Bio/Search/BlastUtils.pm -> blib/libdoc/Bio::Search::BlastUtils.3
Manifying blib/lib/Bio/SearchIO/blastxml.pm -> blib/libdoc/Bio::SearchIO::blastxml.3
Manifying blib/lib/Bio/DB/Expression/geo.pm -> blib/libdoc/Bio::DB::Expression::geo.3
Manifying blib/lib/Bio/Tools/FootPrinter.pm -> blib/libdoc/Bio::Tools::FootPrinter.3
Manifying blib/lib/Bio/Coordinate/ResultI.pm -> blib/libdoc/Bio::Coordinate::ResultI.3
Manifying blib/lib/Bio/Factory/ApplicationFactoryI.pm -> blib/libdoc/Bio::Factory::ApplicationFactoryI.3
Manifying blib/lib/Bio/SeqIO/scf.pm -> blib/libdoc/Bio::SeqIO::scf.3
Manifying blib/lib/Bio/Tools/EUtilities/Info.pm -> blib/libdoc/Bio::Tools::EUtilities::Info.3
Manifying blib/lib/Bio/PopGen/PopStats.pm -> blib/libdoc/Bio::PopGen::PopStats.3
Manifying blib/lib/Bio/SeqEvolution/Factory.pm -> blib/libdoc/Bio::SeqEvolution::Factory.3
Manifying blib/lib/Bio/DB/Query/GenBank.pm -> blib/libdoc/Bio::DB::Query::GenBank.3
Manifying blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::FeatureFileLoader.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_unigene.3
Manifying blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Domcut.3
Manifying blib/lib/Bio/SearchIO/blast.pm -> blib/libdoc/Bio::SearchIO::blast.3
Manifying blib/lib/Bio/Structure/Model.pm -> blib/libdoc/Bio::Structure::Model.3
Manifying blib/lib/Bio/Tools/Hmmpfam.pm -> blib/libdoc/Bio::Tools::Hmmpfam.3
Manifying blib/lib/Bio/CodonUsage/Table.pm -> blib/libdoc/Bio::CodonUsage::Table.3
Manifying blib/lib/Bio/Factory/SequenceStreamI.pm -> blib/libdoc/Bio::Factory::SequenceStreamI.3
Manifying blib/lib/Bio/LiveSeq/Prim_Transcript.pm -> blib/libdoc/Bio::LiveSeq::Prim_Transcript.3
Manifying blib/lib/Bio/MolEvol/CodonModel.pm -> blib/libdoc/Bio::MolEvol::CodonModel.3
Manifying blib/lib/Bio/Annotation/TagTree.pm -> blib/libdoc/Bio::Annotation::TagTree.3
Manifying blib/lib/Bio/DB/EMBL.pm -> blib/libdoc/Bio::DB::EMBL.3
Manifying blib/lib/Bio/Map/Microsatellite.pm -> blib/libdoc/Bio::Map::Microsatellite.3
Manifying blib/lib/Bio/Tools/Alignment/Trim.pm -> blib/libdoc/Bio::Tools::Alignment::Trim.3
Manifying blib/lib/Bio/Tools/Geneid.pm -> blib/libdoc/Bio::Tools::Geneid.3
Manifying blib/lib/Bio/Restriction/IO/prototype.pm -> blib/libdoc/Bio::Restriction::IO::prototype.3
Manifying blib/lib/Bio/Structure/Entry.pm -> blib/libdoc/Bio::Structure::Entry.3
Manifying blib/lib/Bio/Map/Contig.pm -> blib/libdoc/Bio::Map::Contig.3
Manifying blib/lib/Bio/Range.pm -> blib/libdoc/Bio::Range.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_refgene.3
Manifying blib/lib/Bio/Assembly/Contig.pm -> blib/libdoc/Bio::Assembly::Contig.3
Manifying blib/lib/Bio/Tools/AnalysisResult.pm -> blib/libdoc/Bio::Tools::AnalysisResult.3
Manifying blib/lib/Bio/IdentifiableI.pm -> blib/libdoc/Bio::IdentifiableI.3
Manifying blib/lib/Bio/Map/Mappable.pm -> blib/libdoc/Bio::Map::Mappable.3
Manifying blib/lib/Bio/Matrix/PSM/ProtPsm.pm -> blib/libdoc/Bio::Matrix::PSM::ProtPsm.3
Manifying blib/lib/Bio/Taxonomy/Taxon.pm -> blib/libdoc/Bio::Taxonomy::Taxon.3
Manifying blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeature.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/orf.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::orf.3
Manifying blib/lib/Bio/TreeIO/svggraph.pm -> blib/libdoc/Bio::TreeIO::svggraph.3
Manifying blib/lib/Bio/PopGen/IO/hapmap.pm -> blib/libdoc/Bio::PopGen::IO::hapmap.3
Manifying blib/lib/Bio/Restriction/IO/withrefm.pm -> blib/libdoc/Bio::Restriction::IO::withrefm.3
Manifying blib/lib/Bio/Tree/DistanceFactory.pm -> blib/libdoc/Bio::Tree::DistanceFactory.3
Manifying blib/lib/Bio/SeqFeature/Gene/Exon.pm -> blib/libdoc/Bio::SeqFeature::Gene::Exon.3
Manifying blib/lib/Bio/DB/Query/WebQuery.pm -> blib/libdoc/Bio::DB::Query::WebQuery.3
Manifying blib/lib/Bio/Search/Result/CrossMatchResult.pm -> blib/libdoc/Bio::Search::Result::CrossMatchResult.3
Manifying blib/lib/Bio/DB/Universal.pm -> blib/libdoc/Bio::DB::Universal.3
Manifying blib/lib/Bio/Tree/NodeI.pm -> blib/libdoc/Bio::Tree::NodeI.3
Manifying blib/lib/Bio/Tools/Phylo/Gerp.pm -> blib/libdoc/Bio::Tools::Phylo::Gerp.3
Manifying blib/lib/Bio/SeqIO/MultiFile.pm -> blib/libdoc/Bio::SeqIO::MultiFile.3
Manifying blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm -> blib/libdoc/Bio::Seq::SeqFastaSpeedFactory.3
Manifying blib/lib/Bio/Tools/EUtilities/Link.pm -> blib/libdoc/Bio::Tools::EUtilities::Link.3
Manifying blib/lib/Bio/Tools/Tmhmm.pm -> blib/libdoc/Bio::Tools::Tmhmm.3
Manifying blib/lib/Bio/Restriction/Enzyme/MultiSite.pm -> blib/libdoc/Bio::Restriction::Enzyme::MultiSite.3
Manifying blib/lib/Bio/Tools/EUtilities/Cookie.pm -> blib/libdoc/Bio::Tools::EUtilities::Cookie.3
Manifying blib/lib/Bio/OntologyIO/InterProParser.pm -> blib/libdoc/Bio::OntologyIO::InterProParser.3
Manifying blib/lib/Bio/SeqIO/chadoxml.pm -> blib/libdoc/Bio::SeqIO::chadoxml.3
Manifying blib/lib/Bio/Index/Qual.pm -> blib/libdoc/Bio::Index::Qual.3
Manifying blib/lib/Bio/Matrix/PSM/IO/masta.pm -> blib/libdoc/Bio::Matrix::PSM::IO::masta.3
Manifying blib/lib/Bio/Annotation/Reference.pm -> blib/libdoc/Bio::Annotation::Reference.3
Manifying blib/lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeatureI.3
Manifying blib/lib/Bio/Variation/IO.pm -> blib/libdoc/Bio::Variation::IO.3
Manifying blib/lib/Bio/SearchIO/XML/PsiBlastHandler.pm -> blib/libdoc/Bio::SearchIO::XML::PsiBlastHandler.3
Manifying blib/lib/Bio/Matrix/PSM/IO/meme.pm -> blib/libdoc/Bio::Matrix::PSM::IO::meme.3
Manifying blib/lib/Bio/Seq/MetaI.pm -> blib/libdoc/Bio::Seq::MetaI.3
Manifying blib/lib/Bio/TreeIO/pag.pm -> blib/libdoc/Bio::TreeIO::pag.3
Manifying blib/lib/Bio/LiveSeq/IO/Loader.pm -> blib/libdoc/Bio::LiveSeq::IO::Loader.3
Manifying blib/lib/Bio/AlignIO/arp.pm -> blib/libdoc/Bio::AlignIO::arp.3
Manifying blib/lib/Bio/Ontology/SimpleOntologyEngine.pm -> blib/libdoc/Bio::Ontology::SimpleOntologyEngine.3
Manifying blib/lib/Bio/Tools/Analysis/Protein/NetPhos.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::NetPhos.3
Manifying blib/lib/Bio/Ontology/TermI.pm -> blib/libdoc/Bio::Ontology::TermI.3
Manifying blib/lib/Bio/SeqFeature/PositionProxy.pm -> blib/libdoc/Bio::SeqFeature::PositionProxy.3
Manifying blib/lib/Bio/SeqEvolution/DNAPoint.pm -> blib/libdoc/Bio::SeqEvolution::DNAPoint.3
Manifying blib/lib/Bio/SeqIO/ace.pm -> blib/libdoc/Bio::SeqIO::ace.3
Manifying blib/lib/Bio/Map/CytoPosition.pm -> blib/libdoc/Bio::Map::CytoPosition.3
Manifying blib/lib/Bio/Tools/ERPIN.pm -> blib/libdoc/Bio::Tools::ERPIN.3
Manifying blib/lib/Bio/Cluster/UniGene.pm -> blib/libdoc/Bio::Cluster::UniGene.3
Manifying blib/lib/Bio/DB/LocationI.pm -> blib/libdoc/Bio::DB::LocationI.3
Manifying blib/lib/Bio/SeqI.pm -> blib/libdoc/Bio::SeqI.3
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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
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Manifying blib/lib/Bio/Tools/Genewise.pm -> blib/libdoc/Bio::Tools::Genewise.3
Manifying blib/lib/Bio/Tools/Primer3.pm -> blib/libdoc/Bio::Tools::Primer3.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb.3
Manifying blib/lib/Bio/Map/EntityI.pm -> blib/libdoc/Bio::Map::EntityI.3
Manifying blib/lib/Bio/Tools/Spidey/Results.pm -> blib/libdoc/Bio::Tools::Spidey::Results.3
Manifying blib/lib/Bio/SearchIO/waba.pm -> blib/libdoc/Bio::SearchIO::waba.3
Manifying blib/lib/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedTableFeatureI.3
Manifying blib/lib/Bio/Biblio/IO/pubmed2ref.pm -> blib/libdoc/Bio::Biblio::IO::pubmed2ref.3
Manifying blib/lib/Bio/Species.pm -> blib/libdoc/Bio::Species.3
Manifying blib/lib/Bio/Matrix/PSM/InstanceSite.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSite.3
Manifying blib/lib/Bio/Variation/AAReverseMutate.pm -> blib/libdoc/Bio::Variation::AAReverseMutate.3
Manifying blib/lib/Bio/Tools/SiRNA/Ruleset/saigo.pm -> blib/libdoc/Bio::Tools::SiRNA::Ruleset::saigo.3
Manifying blib/lib/Bio/Tools/Sim4/Exon.pm -> blib/libdoc/Bio::Tools::Sim4::Exon.3
Manifying blib/lib/Bio/Tools/Run/StandAloneWUBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneWUBlast.3
Manifying blib/lib/Bio/Restriction/EnzymeCollection.pm -> blib/libdoc/Bio::Restriction::EnzymeCollection.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/memory.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/processed_transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::processed_transcript.3
Manifying blib/lib/Bio/DB/Ace.pm -> blib/libdoc/Bio::DB::Ace.3
Manifying blib/lib/Bio/LiveSeq/DNA.pm -> blib/libdoc/Bio::LiveSeq::DNA.3
Manifying blib/lib/Bio/Tools/HMMER/Results.pm -> blib/libdoc/Bio::Tools::HMMER::Results.3
Manifying blib/lib/Bio/Seq.pm -> blib/libdoc/Bio::Seq.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_softberry.3
Manifying blib/lib/Bio/Ontology/OBOEngine.pm -> blib/libdoc/Bio::Ontology::OBOEngine.3
Manifying blib/lib/Bio/SeqIO/ztr.pm -> blib/libdoc/Bio::SeqIO::ztr.3
Manifying blib/lib/Bio/MapIO.pm -> blib/libdoc/Bio::MapIO.3
Manifying blib/lib/Bio/DB/DBFetch.pm -> blib/libdoc/Bio::DB::DBFetch.3
Manifying blib/lib/Bio/Root/Test.pm -> blib/libdoc/Bio::Root::Test.3
Manifying blib/lib/Bio/Biblio/BookArticle.pm -> blib/libdoc/Bio::Biblio::BookArticle.3
Manifying blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3
Manifying blib/lib/Bio/Tools/Coil.pm -> blib/libdoc/Bio::Tools::Coil.3
Manifying blib/lib/Bio/PopGen/Population.pm -> blib/libdoc/Bio::PopGen::Population.3
Manifying blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm -> blib/libdoc/Bio::Matrix::PSM::PsmHeaderI.3
Manifying blib/lib/Bio/Restriction/EnzymeI.pm -> blib/libdoc/Bio::Restriction::EnzymeI.3
Manifying blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm -> blib/libdoc/Bio::SeqFeature::Gene::GeneStructureI.3
Manifying blib/lib/Bio/Biblio/MedlineBook.pm -> blib/libdoc/Bio::Biblio::MedlineBook.3
Manifying blib/lib/Bio/Biblio/Proceeding.pm -> blib/libdoc/Bio::Biblio::Proceeding.3
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Manifying blib/lib/Bio/SeqUtils.pm -> blib/libdoc/Bio::SeqUtils.3
Manifying blib/lib/Bio/DB/Failover.pm -> blib/libdoc/Bio::DB::Failover.3
Manifying blib/lib/Bio/SeqIO/asciitree.pm -> blib/libdoc/Bio::SeqIO::asciitree.3
Manifying blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -> blib/libdoc/Bio::Matrix::PSM::SiteMatrixI.3
Manifying blib/lib/Bio/Tools/Gel.pm -> blib/libdoc/Bio::Tools::Gel.3
Manifying blib/lib/Bio/DB/Registry.pm -> blib/libdoc/Bio::DB::Registry.3
Manifying blib/lib/Bio/SeqIO/game/featHandler.pm -> blib/libdoc/Bio::SeqIO::game::featHandler.3
Manifying blib/lib/Bio/Search/HSP/BlastHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastHSP.3
Manifying blib/lib/Bio/Factory/SequenceFactoryI.pm -> blib/libdoc/Bio::Factory::SequenceFactoryI.3
Manifying blib/lib/Bio/Biblio/TechReport.pm -> blib/libdoc/Bio::Biblio::TechReport.3
Manifying blib/lib/Bio/Tools/Blat.pm -> blib/libdoc/Bio::Tools::Blat.3
Manifying blib/lib/Bio/Tools/Protparam.pm -> blib/libdoc/Bio::Tools::Protparam.3
Manifying blib/lib/Bio/PhyloNetwork.pm -> blib/libdoc/Bio::PhyloNetwork.3
Manifying blib/lib/Bio/SeqIO/metafasta.pm -> blib/libdoc/Bio::SeqIO::metafasta.3
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Manifying blib/lib/Bio/Map/CytoMarker.pm -> blib/libdoc/Bio::Map::CytoMarker.3
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Manifying blib/lib/Bio/Tools/Spidey/Exon.pm -> blib/libdoc/Bio::Tools::Spidey::Exon.3
Manifying blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm -> blib/libdoc/Bio::Tools::EUtilities::EUtilDataI.3
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Manifying blib/lib/Bio/DB/GFF/Adaptor/ace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::ace.3
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Manifying blib/lib/Bio/Search/SearchUtils.pm -> blib/libdoc/Bio::Search::SearchUtils.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlopt.3
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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/Das/FeatureTypeI.pm -> blib/libdoc/Bio::Das::FeatureTypeI.3
Manifying blib/lib/Bio/PhyloNetwork/FactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::FactoryX.3
Manifying blib/lib/Bio/Search/HSP/HSPFactory.pm -> blib/libdoc/Bio::Search::HSP::HSPFactory.3
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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/SearchIO/Writer/HSPTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HSPTableWriter.3
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Manifying blib/lib/Bio/Tools/Signalp.pm -> blib/libdoc/Bio::Tools::Signalp.3
Manifying blib/lib/Bio/FeatureIO/vecscreen_simple.pm -> blib/libdoc/Bio::FeatureIO::vecscreen_simple.3
Manifying blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/libdoc/Bio::Tools::EUtilities::Info::LinkInfo.3
Manifying blib/lib/Bio/DB/Flat/BDB.pm -> blib/libdoc/Bio::DB::Flat::BDB.3
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Manifying blib/lib/Bio/SeqFeature/Gene/Intron.pm -> blib/libdoc/Bio::SeqFeature::Gene::Intron.3
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Manifying blib/lib/Bio/Annotation/Collection.pm -> blib/libdoc/Bio::Annotation::Collection.3
Manifying blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HitTableWriter.3
Manifying blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::ResultTableWriter.3
Manifying blib/lib/Bio/Seq/PrimedSeq.pm -> blib/libdoc/Bio::Seq::PrimedSeq.3
Manifying blib/lib/Bio/Tools/Phylo/Molphy.pm -> blib/libdoc/Bio::Tools::Phylo::Molphy.3
Manifying blib/lib/Bio/AnnotationCollectionI.pm -> blib/libdoc/Bio::AnnotationCollectionI.3
Manifying blib/lib/Bio/Location/SplitLocationI.pm -> blib/libdoc/Bio::Location::SplitLocationI.3
Manifying blib/lib/Bio/Tree/RandomFactory.pm -> blib/libdoc/Bio::Tree::RandomFactory.3
Manifying blib/lib/Bio/Biblio/Patent.pm -> blib/libdoc/Bio::Biblio::Patent.3
Manifying blib/lib/Bio/Tree/TreeI.pm -> blib/libdoc/Bio::Tree::TreeI.3
Manifying blib/lib/Bio/Biblio/BiblioBase.pm -> blib/libdoc/Bio::Biblio::BiblioBase.3
Manifying blib/lib/Bio/Tools/Run/StandAloneBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneBlast.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::transcript.3
Manifying blib/lib/Bio/PullParserI.pm -> blib/libdoc/Bio::PullParserI.3
Manifying blib/lib/Bio/Tools/Analysis/Protein/Scansite.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Scansite.3
Manifying blib/lib/Bio/Biblio/MedlineBookArticle.pm -> blib/libdoc/Bio::Biblio::MedlineBookArticle.3
Manifying blib/lib/Bio/DB/Taxonomy/flatfile.pm -> blib/libdoc/Bio::DB::Taxonomy::flatfile.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysql.3
Manifying blib/lib/Bio/SeqFeature/SimilarityPair.pm -> blib/libdoc/Bio::SeqFeature::SimilarityPair.3
Manifying blib/lib/Bio/Index/BlastTable.pm -> blib/libdoc/Bio::Index::BlastTable.3
Manifying blib/lib/Bio/Search/HSP/BlastPullHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastPullHSP.3
Manifying blib/lib/Bio/SeqIO/pln.pm -> blib/libdoc/Bio::SeqIO::pln.3
Manifying blib/lib/Bio/Expression/Contact.pm -> blib/libdoc/Bio::Expression::Contact.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_ensgene.3
Manifying blib/lib/Bio/Event/EventHandlerI.pm -> blib/libdoc/Bio::Event::EventHandlerI.3
Manifying blib/lib/Bio/LocationI.pm -> blib/libdoc/Bio::LocationI.3
Manifying blib/lib/Bio/Variation/AAChange.pm -> blib/libdoc/Bio::Variation::AAChange.3
Manifying blib/lib/Bio/SeqFeature/CollectionI.pm -> blib/libdoc/Bio::SeqFeature::CollectionI.3
Manifying blib/lib/Bio/Taxonomy/Tree.pm -> blib/libdoc/Bio::Taxonomy::Tree.3
Manifying blib/lib/Bio/Annotation/Tree.pm -> blib/libdoc/Bio::Annotation::Tree.3
Manifying blib/lib/Bio/SeqIO/qual.pm -> blib/libdoc/Bio::SeqIO::qual.3
Manifying blib/lib/Bio/Tools/AlignFactory.pm -> blib/libdoc/Bio::Tools::AlignFactory.3
Manifying blib/lib/Bio/Matrix/PSM/IO/psiblast.pm -> blib/libdoc/Bio::Matrix::PSM::IO::psiblast.3
Manifying blib/lib/Bio/DB/EUtilities.pm -> blib/libdoc/Bio::DB::EUtilities.3
Manifying blib/lib/Bio/SearchIO.pm -> blib/libdoc/Bio::SearchIO.3
Manifying blib/lib/Bio/Restriction/IO/base.pm -> blib/libdoc/Bio::Restriction::IO::base.3
Manifying blib/lib/Bio/DB/FileCache.pm -> blib/libdoc/Bio::DB::FileCache.3
Manifying blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm -> blib/libdoc/Bio::Ontology::SimpleGOEngine::GraphAdaptor.3
Manifying blib/lib/Bio/Seq/EncodedSeq.pm -> blib/libdoc/Bio::Seq::EncodedSeq.3
Manifying blib/lib/Bio/Tree/Statistics.pm -> blib/libdoc/Bio::Tree::Statistics.3
Manifying blib/lib/Bio/Tools/Match.pm -> blib/libdoc/Bio::Tools::Match.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb::iterator.3
Manifying blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HTMLResultWriter.3
Manifying blib/lib/Bio/Tools/Primer/AssessorI.pm -> blib/libdoc/Bio::Tools::Primer::AssessorI.3
Manifying blib/lib/Bio/Root/Build.pm -> blib/libdoc/Bio::Root::Build.3
Manifying blib/lib/Bio/Map/PositionWithSequence.pm -> blib/libdoc/Bio::Map::PositionWithSequence.3
Manifying blib/lib/Bio/Matrix/IO/phylip.pm -> blib/libdoc/Bio::Matrix::IO::phylip.3
Manifying blib/lib/Bio/DB/SeqI.pm -> blib/libdoc/Bio::DB::SeqI.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3
Manifying blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/libdoc/Bio::SeqFeature::Tools::FeatureNamer.3
Manifying blib/lib/Bio/Coordinate/Pair.pm -> blib/libdoc/Bio::Coordinate::Pair.3
Manifying blib/lib/Bio/SeqFeature/Annotated.pm -> blib/libdoc/Bio::SeqFeature::Annotated.3
Manifying blib/lib/Bio/DB/Query/HIVQuery.pm -> blib/libdoc/Bio::DB::Query::HIVQuery.3
Manifying blib/lib/Bio/Structure/SecStr/DSSP/Res.pm -> blib/libdoc/Bio::Structure::SecStr::DSSP::Res.3
Manifying blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/libdoc/Bio::Tools::Phylo::PAML::ModelResult.3
Manifying blib/lib/Bio/PopGen/PopulationI.pm -> blib/libdoc/Bio::PopGen::PopulationI.3
Manifying blib/lib/Bio/LiveSeq/Translation.pm -> blib/libdoc/Bio::LiveSeq::Translation.3
Manifying blib/lib/Bio/SeqIO/embldriver.pm -> blib/libdoc/Bio::SeqIO::embldriver.3
Manifying blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -> blib/libdoc/Bio::SearchIO::SearchResultEventBuilder.3
Manifying blib/lib/Bio/Factory/ObjectFactory.pm -> blib/libdoc/Bio::Factory::ObjectFactory.3
Manifying blib/lib/Bio/DB/SwissProt.pm -> blib/libdoc/Bio::DB::SwissProt.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/gene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::gene.3
Manifying blib/lib/Bio/Phenotype/Correlate.pm -> blib/libdoc/Bio::Phenotype::Correlate.3
Manifying blib/lib/Bio/Tools/Run/ParametersI.pm -> blib/libdoc/Bio::Tools::Run::ParametersI.3
Manifying blib/lib/Bio/SeqIO/largefasta.pm -> blib/libdoc/Bio::SeqIO::largefasta.3
Manifying blib/lib/Bio/AlignIO.pm -> blib/libdoc/Bio::AlignIO.3
Manifying blib/lib/Bio/SeqIO/chaosxml.pm -> blib/libdoc/Bio::SeqIO::chaosxml.3
Manifying blib/lib/Bio/PhyloNetwork/TreeFactoryMulti.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactoryMulti.3
Manifying blib/lib/Bio/Taxonomy/Node.pm -> blib/libdoc/Bio::Taxonomy::Node.3
Manifying blib/lib/Bio/Search/Result/ResultI.pm -> blib/libdoc/Bio::Search::Result::ResultI.3
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Manifying blib/lib/Bio/DB/UpdateableSeqI.pm -> blib/libdoc/Bio::DB::UpdateableSeqI.3
Manifying blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -> blib/libdoc/Bio::SeqFeature::Tools::IDHandler.3
Manifying blib/lib/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm -> blib/libdoc/Bio::Expression::FeatureGroup::FeatureGroupMas50.3
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Manifying blib/lib/Bio/DB/Flat/BinarySearch.pm -> blib/libdoc/Bio::DB::Flat::BinarySearch.3
Manifying blib/lib/Bio/Map/PositionHandlerI.pm -> blib/libdoc/Bio::Map::PositionHandlerI.3
Manifying blib/lib/Bio/Tools/EUtilities/Link/UrlLink.pm -> blib/libdoc/Bio::Tools::EUtilities::Link::UrlLink.3
Manifying blib/lib/Bio/SearchIO/megablast.pm -> blib/libdoc/Bio::SearchIO::megablast.3
Manifying blib/lib/Bio/Annotation/DBLink.pm -> blib/libdoc/Bio::Annotation::DBLink.3
Manifying blib/lib/Bio/Tree/Node.pm -> blib/libdoc/Bio::Tree::Node.3
Manifying blib/lib/Bio/LiveSeq/Exon.pm -> blib/libdoc/Bio::LiveSeq::Exon.3
Manifying blib/lib/Bio/Tools/EUtilities.pm -> blib/libdoc/Bio::Tools::EUtilities.3
Manifying blib/lib/Bio/SeqIO/exp.pm -> blib/libdoc/Bio::SeqIO::exp.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/match.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::match.3
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Manifying blib/lib/Bio/AlignIO/prodom.pm -> blib/libdoc/Bio::AlignIO::prodom.3
Manifying blib/lib/Bio/Tools/ESTScan.pm -> blib/libdoc/Bio::Tools::ESTScan.3
Manifying blib/lib/Bio/Cluster/UniGeneI.pm -> blib/libdoc/Bio::Cluster::UniGeneI.3
Manifying blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm -> blib/libdoc/Bio::Tools::Signalp::ExtendedSignalp.3
Manifying blib/lib/Bio/Biblio/Journal.pm -> blib/libdoc/Bio::Biblio::Journal.3
Manifying blib/lib/Bio/Matrix/Scoring.pm -> blib/libdoc/Bio::Matrix::Scoring.3
Manifying blib/lib/Bio/Structure/Chain.pm -> blib/libdoc/Bio::Structure::Chain.3
Manifying blib/lib/Bio/Phenotype/Measure.pm -> blib/libdoc/Bio::Phenotype::Measure.3
Manifying blib/lib/Bio/UpdateableSeqI.pm -> blib/libdoc/Bio::UpdateableSeqI.3
Manifying blib/lib/Bio/DB/HIV/HIVQueryHelper.pm -> blib/libdoc/Bio::DB::HIV::HIVQueryHelper.3
Manifying blib/lib/Bio/SearchDist.pm -> blib/libdoc/Bio::SearchDist.3
Manifying blib/lib/Bio/Coordinate/Graph.pm -> blib/libdoc/Bio::Coordinate::Graph.3
Manifying blib/lib/Bio/IdCollectionI.pm -> blib/libdoc/Bio::IdCollectionI.3
Manifying blib/lib/Bio/Search/Hit/HitI.pm -> blib/libdoc/Bio::Search::Hit::HitI.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi.3
Manifying blib/lib/Bio/Search/Result/BlastResult.pm -> blib/libdoc/Bio::Search::Result::BlastResult.3
Manifying blib/lib/Bio/Seq/LargeSeq.pm -> blib/libdoc/Bio::Seq::LargeSeq.3
Manifying blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm -> blib/libdoc/Bio::Expression::FeatureSet::FeatureSetMas50.3
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Manifying blib/lib/Bio/Align/ProteinStatistics.pm -> blib/libdoc/Bio::Align::ProteinStatistics.3
Manifying blib/lib/Bio/DB/GFF/Feature.pm -> blib/libdoc/Bio::DB::GFF::Feature.3
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Manifying blib/lib/Bio/Coordinate/Result.pm -> blib/libdoc/Bio::Coordinate::Result.3
Manifying blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm -> blib/libdoc/Bio::SeqFeature::Gene::Poly_A_site.3
Manifying blib/lib/Bio/Root/IO.pm -> blib/libdoc/Bio::Root::IO.3
Manifying blib/lib/Bio/Search/Hit/HMMERHit.pm -> blib/libdoc/Bio::Search::Hit::HMMERHit.3
Manifying blib/lib/Bio/DB/Fasta.pm -> blib/libdoc/Bio::DB::Fasta.3
Manifying blib/lib/Bio/DB/Biblio/biofetch.pm -> blib/libdoc/Bio::DB::Biblio::biofetch.3
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Manifying blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactoryX.3
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Manifying blib/lib/Bio/Matrix/Mlagan.pm -> blib/libdoc/Bio::Matrix::Mlagan.3
Manifying blib/lib/Bio/SearchIO/sim4.pm -> blib/libdoc/Bio::SearchIO::sim4.3
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Manifying blib/lib/Bio/Tools/SeqStats.pm -> blib/libdoc/Bio::Tools::SeqStats.3
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Manifying blib/lib/Bio/AlignIO/mega.pm -> blib/libdoc/Bio::AlignIO::mega.3
Manifying blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/libdoc/Bio::SeqIO::tinyseq::tinyseqHandler.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::so_transcript.3
Manifying blib/lib/Bio/Tools/dpAlign.pm -> blib/libdoc/Bio::Tools::dpAlign.3
Manifying blib/lib/Bio/Variation/DNAMutation.pm -> blib/libdoc/Bio::Variation::DNAMutation.3
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Manifying blib/lib/Bio/SeqIO/fastq.pm -> blib/libdoc/Bio::SeqIO::fastq.3
Manifying blib/lib/Bio/PhyloNetwork/GraphViz.pm -> blib/libdoc/Bio::PhyloNetwork::GraphViz.3
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Manifying blib/lib/Bio/Ontology/RelationshipType.pm -> blib/libdoc/Bio::Ontology::RelationshipType.3
Manifying blib/lib/Bio/Biblio/Article.pm -> blib/libdoc/Bio::Biblio::Article.3
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Manifying blib/lib/Bio/Search/Result/PullResultI.pm -> blib/libdoc/Bio::Search::Result::PullResultI.3
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Manifying blib/lib/Bio/Coordinate/Collection.pm -> blib/libdoc/Bio::Coordinate::Collection.3
Manifying blib/lib/Bio/LiveSeq/Gene.pm -> blib/libdoc/Bio::LiveSeq::Gene.3
Manifying blib/lib/Bio/Annotation/AnnotationFactory.pm -> blib/libdoc/Bio::Annotation::AnnotationFactory.3
Manifying blib/lib/Bio/Search/Hit/BlastPullHit.pm -> blib/libdoc/Bio::Search::Hit::BlastPullHit.3
Manifying blib/lib/Bio/OntologyIO/goflat.pm -> blib/libdoc/Bio::OntologyIO::goflat.3
Manifying blib/lib/Bio/Location/Simple.pm -> blib/libdoc/Bio::Location::Simple.3
Manifying blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm -> blib/libdoc/Bio::Tools::Phylo::Phylip::ProtDist.3
Manifying blib/lib/Bio/SeqFeature/Collection.pm -> blib/libdoc/Bio::SeqFeature::Collection.3
Manifying blib/lib/Bio/Biblio.pm -> blib/libdoc/Bio::Biblio.3
Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3
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Manifying blib/lib/Bio/Tools/Lucy.pm -> blib/libdoc/Bio::Tools::Lucy.3
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Manifying blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -> blib/libdoc/Bio::SeqFeature::Tools::TypeMapper.3
Manifying blib/lib/Bio/Biblio/MedlineJournal.pm -> blib/libdoc/Bio::Biblio::MedlineJournal.3
Manifying blib/lib/Bio/SeqIO/kegg.pm -> blib/libdoc/Bio::SeqIO::kegg.3
Manifying blib/lib/Bio/Matrix/PSM/ProtMatrix.pm -> blib/libdoc/Bio::Matrix::PSM::ProtMatrix.3
Manifying blib/lib/Bio/AlignIO/fasta.pm -> blib/libdoc/Bio::AlignIO::fasta.3
Manifying blib/lib/Bio/Matrix/PSM/PsmHeader.pm -> blib/libdoc/Bio::Matrix::PSM::PsmHeader.3
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Manifying blib/lib/Bio/Map/PositionHandler.pm -> blib/libdoc/Bio::Map::PositionHandler.3
Manifying blib/lib/Bio/Tools/GFF.pm -> blib/libdoc/Bio::Tools::GFF.3
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Manifying blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::TextResultWriter.3
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Manifying blib/lib/Bio/AlignIO/nexus.pm -> blib/libdoc/Bio::AlignIO::nexus.3
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Manifying blib/lib/Bio/Tools/Seg.pm -> blib/libdoc/Bio::Tools::Seg.3
Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlace.3
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Manifying blib/lib/Bio/Assembly/IO/phrap.pm -> blib/libdoc/Bio::Assembly::IO::phrap.3
Manifying blib/lib/Bio/Taxon.pm -> blib/libdoc/Bio::Taxon.3
Manifying blib/lib/Bio/Tools/RNAMotif.pm -> blib/libdoc/Bio::Tools::RNAMotif.3
Manifying blib/lib/Bio/Ontology/RelationshipI.pm -> blib/libdoc/Bio::Ontology::RelationshipI.3
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Manifying blib/lib/Bio/PopGen/Genotype.pm -> blib/libdoc/Bio::PopGen::Genotype.3
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Manifying blib/lib/Bio/Coordinate/Utils.pm -> blib/libdoc/Bio::Coordinate::Utils.3
Manifying blib/lib/Bio/Tools/EUtilities/History.pm -> blib/libdoc/Bio::Tools::EUtilities::History.3
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Manifying blib/lib/Bio/Search/Hit/ModelHit.pm -> blib/libdoc/Bio::Search::Hit::ModelHit.3
Manifying blib/lib/Bio/Tools/HMMER/Domain.pm -> blib/libdoc/Bio::Tools::HMMER::Domain.3
Manifying blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSiteI.3
Manifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libdoc/Bio::Structure::SecStr::STRIDE::Res.3
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Manifying blib/lib/Bio/PrimarySeq.pm -> blib/libdoc/Bio::PrimarySeq.3
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HTMLifyBuild: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm: cannot resolve L<bioperl> in paragraph 161.
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Build: blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm: cannot resolve L<remote_database> in paragraph 82.
Build: blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm: cannot resolve L<remote_database> in paragraph 93.
Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm: cannot resolve L<bioperl> in paragraph 183.
make: *** [all] Terminated

Timeout (max run time is 300s)
/export/home/fly818/bin/perl killed by signal 15