mirror of
https://git.FreeBSD.org/ports.git
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1076 lines
43 KiB
Plaintext
1076 lines
43 KiB
Plaintext
bin/bp_aacomp
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bin/bp_bioflat_index
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bin/bp_biogetseq
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bin/bp_dbsplit
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bin/bp_extract_feature_seq
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bin/bp_fastam9_to_table
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bin/bp_fetch
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bin/bp_filter_search
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bin/bp_find-blast-matches
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bin/bp_gccalc
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bin/bp_genbank2gff3
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bin/bp_index
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bin/bp_local_taxonomydb_query
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bin/bp_make_mrna_protein
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bin/bp_mask_by_search
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bin/bp_mrtrans
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bin/bp_mutate
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bin/bp_nexus2nh
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bin/bp_nrdb
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bin/bp_oligo_count
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bin/bp_process_gadfly
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bin/bp_process_sgd
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bin/bp_revtrans-motif
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bin/bp_search2alnblocks
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bin/bp_search2gff
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bin/bp_search2table
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bin/bp_search2tribe
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bin/bp_seq_length
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bin/bp_seqconvert
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bin/bp_seqcut
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bin/bp_seqpart
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bin/bp_seqret
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bin/bp_seqretsplit
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bin/bp_split_seq
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bin/bp_sreformat
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bin/bp_taxid4species
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bin/bp_taxonomy2tree
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bin/bp_translate_seq
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bin/bp_tree2pag
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bin/bp_unflatten_seq
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%%SITE_PERL%%/Bio/Align/AlignI.pm
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%%SITE_PERL%%/Bio/Align/DNAStatistics.pm
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%%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm
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%%SITE_PERL%%/Bio/Align/ProteinStatistics.pm
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%%SITE_PERL%%/Bio/Align/StatisticsI.pm
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%%SITE_PERL%%/Bio/Align/Utilities.pm
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%%SITE_PERL%%/Bio/AlignIO.pm
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%%SITE_PERL%%/Bio/AlignIO/Handler/GenericAlignHandler.pm
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%%SITE_PERL%%/Bio/AlignIO/arp.pm
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%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
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%%SITE_PERL%%/Bio/AlignIO/clustalw.pm
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%%SITE_PERL%%/Bio/AlignIO/emboss.pm
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%%SITE_PERL%%/Bio/AlignIO/fasta.pm
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%%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm
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%%SITE_PERL%%/Bio/AlignIO/maf.pm
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%%SITE_PERL%%/Bio/AlignIO/mase.pm
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%%SITE_PERL%%/Bio/AlignIO/mega.pm
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%%SITE_PERL%%/Bio/AlignIO/meme.pm
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%%SITE_PERL%%/Bio/AlignIO/metafasta.pm
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%%SITE_PERL%%/Bio/AlignIO/msf.pm
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%%SITE_PERL%%/Bio/AlignIO/nexus.pm
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%%SITE_PERL%%/Bio/AlignIO/pfam.pm
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%%SITE_PERL%%/Bio/AlignIO/phylip.pm
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%%SITE_PERL%%/Bio/AlignIO/po.pm
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%%SITE_PERL%%/Bio/AlignIO/proda.pm
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%%SITE_PERL%%/Bio/AlignIO/prodom.pm
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%%SITE_PERL%%/Bio/AlignIO/psi.pm
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%%SITE_PERL%%/Bio/AlignIO/selex.pm
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%%SITE_PERL%%/Bio/AlignIO/xmfa.pm
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%%SITE_PERL%%/Bio/AnalysisI.pm
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%%SITE_PERL%%/Bio/AnalysisParserI.pm
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%%SITE_PERL%%/Bio/AnalysisResultI.pm
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%%SITE_PERL%%/Bio/AnnotatableI.pm
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%%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm
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%%SITE_PERL%%/Bio/Annotation/Collection.pm
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%%SITE_PERL%%/Bio/Annotation/Comment.pm
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%%SITE_PERL%%/Bio/Annotation/DBLink.pm
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%%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm
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%%SITE_PERL%%/Bio/Annotation/Reference.pm
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%%SITE_PERL%%/Bio/Annotation/Relation.pm
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%%SITE_PERL%%/Bio/Annotation/SimpleValue.pm
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%%SITE_PERL%%/Bio/Annotation/StructuredValue.pm
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%%SITE_PERL%%/Bio/Annotation/TagTree.pm
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%%SITE_PERL%%/Bio/Annotation/Target.pm
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%%SITE_PERL%%/Bio/Annotation/Tree.pm
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%%SITE_PERL%%/Bio/Annotation/TypeManager.pm
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%%SITE_PERL%%/Bio/AnnotationCollectionI.pm
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%%SITE_PERL%%/Bio/AnnotationI.pm
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%%SITE_PERL%%/Bio/CodonUsage/IO.pm
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%%SITE_PERL%%/Bio/CodonUsage/Table.pm
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%%SITE_PERL%%/Bio/DB/DBFetch.pm
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%%SITE_PERL%%/Bio/DB/Failover.pm
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%%SITE_PERL%%/Bio/DB/Fasta.pm
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%%SITE_PERL%%/Bio/DB/FileCache.pm
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%%SITE_PERL%%/Bio/DB/Flat.pm
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%%SITE_PERL%%/Bio/DB/Flat/BDB.pm
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%%SITE_PERL%%/Bio/DB/Flat/BDB/embl.pm
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%%SITE_PERL%%/Bio/DB/Flat/BDB/fasta.pm
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%%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm
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%%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm
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%%SITE_PERL%%/Bio/DB/Flat/BinarySearch.pm
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%%SITE_PERL%%/Bio/DB/GFF/Util/Binning.pm
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%%SITE_PERL%%/Bio/DB/GFF/Util/Rearrange.pm
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%%SITE_PERL%%/Bio/DB/GenericWebAgent.pm
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%%SITE_PERL%%/Bio/DB/InMemoryCache.pm
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%%SITE_PERL%%/Bio/DB/IndexedBase.pm
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%%SITE_PERL%%/Bio/DB/LocationI.pm
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%%SITE_PERL%%/Bio/DB/Qual.pm
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%%SITE_PERL%%/Bio/DB/Query/WebQuery.pm
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%%SITE_PERL%%/Bio/DB/QueryI.pm
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%%SITE_PERL%%/Bio/DB/RandomAccessI.pm
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%%SITE_PERL%%/Bio/DB/ReferenceI.pm
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%%SITE_PERL%%/Bio/DB/Registry.pm
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%%SITE_PERL%%/Bio/DB/SeqI.pm
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%%SITE_PERL%%/Bio/DB/Taxonomy.pm
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%%SITE_PERL%%/Bio/DB/Taxonomy/flatfile.pm
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%%SITE_PERL%%/Bio/DB/Taxonomy/greengenes.pm
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%%SITE_PERL%%/Bio/DB/Taxonomy/list.pm
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%%SITE_PERL%%/Bio/DB/Taxonomy/silva.pm
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%%SITE_PERL%%/Bio/DB/UpdateableSeqI.pm
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%%SITE_PERL%%/Bio/DB/WebDBSeqI.pm
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%%SITE_PERL%%/Bio/DBLinkContainerI.pm
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%%SITE_PERL%%/Bio/Das/FeatureTypeI.pm
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%%SITE_PERL%%/Bio/Das/SegmentI.pm
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%%SITE_PERL%%/Bio/DasI.pm
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%%SITE_PERL%%/Bio/DescribableI.pm
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%%SITE_PERL%%/Bio/Event/EventGeneratorI.pm
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%%SITE_PERL%%/Bio/Event/EventHandlerI.pm
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%%SITE_PERL%%/Bio/Factory/AnalysisI.pm
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%%SITE_PERL%%/Bio/Factory/ApplicationFactoryI.pm
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%%SITE_PERL%%/Bio/Factory/DriverFactory.pm
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%%SITE_PERL%%/Bio/Factory/FTLocationFactory.pm
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%%SITE_PERL%%/Bio/Factory/LocationFactoryI.pm
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%%SITE_PERL%%/Bio/Factory/ObjectBuilderI.pm
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%%SITE_PERL%%/Bio/Factory/ObjectFactory.pm
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%%SITE_PERL%%/Bio/Factory/ObjectFactoryI.pm
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%%SITE_PERL%%/Bio/Factory/SeqAnalysisParserFactory.pm
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%%SITE_PERL%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
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%%SITE_PERL%%/Bio/Factory/SequenceFactoryI.pm
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%%SITE_PERL%%/Bio/Factory/SequenceProcessorI.pm
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%%SITE_PERL%%/Bio/Factory/SequenceStreamI.pm
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%%SITE_PERL%%/Bio/Factory/TreeFactoryI.pm
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%%SITE_PERL%%/Bio/FeatureHolderI.pm
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%%SITE_PERL%%/Bio/HandlerBaseI.pm
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%%SITE_PERL%%/Bio/IdCollectionI.pm
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%%SITE_PERL%%/Bio/IdentifiableI.pm
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%%SITE_PERL%%/Bio/Index/Abstract.pm
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%%SITE_PERL%%/Bio/Index/AbstractSeq.pm
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%%SITE_PERL%%/Bio/Index/Blast.pm
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%%SITE_PERL%%/Bio/Index/BlastTable.pm
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%%SITE_PERL%%/Bio/Index/EMBL.pm
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%%SITE_PERL%%/Bio/Index/Fasta.pm
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%%SITE_PERL%%/Bio/Index/Fastq.pm
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%%SITE_PERL%%/Bio/Index/GenBank.pm
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%%SITE_PERL%%/Bio/Index/Qual.pm
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%%SITE_PERL%%/Bio/Index/SwissPfam.pm
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%%SITE_PERL%%/Bio/Index/Swissprot.pm
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%%SITE_PERL%%/Bio/LocatableSeq.pm
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%%SITE_PERL%%/Bio/Location/Atomic.pm
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%%SITE_PERL%%/Bio/Location/AvWithinCoordPolicy.pm
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%%SITE_PERL%%/Bio/Location/CoordinatePolicyI.pm
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%%SITE_PERL%%/Bio/Location/Fuzzy.pm
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%%SITE_PERL%%/Bio/Location/FuzzyLocationI.pm
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%%SITE_PERL%%/Bio/Location/NarrowestCoordPolicy.pm
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%%SITE_PERL%%/Bio/Location/Simple.pm
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%%SITE_PERL%%/Bio/Location/Split.pm
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%%SITE_PERL%%/Bio/Location/SplitLocationI.pm
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%%SITE_PERL%%/Bio/Location/WidestCoordPolicy.pm
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%%SITE_PERL%%/Bio/LocationI.pm
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%%SITE_PERL%%/Bio/Matrix/Generic.pm
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%%SITE_PERL%%/Bio/Matrix/IO.pm
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%%SITE_PERL%%/Bio/Matrix/IO/mlagan.pm
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%%SITE_PERL%%/Bio/Matrix/IO/phylip.pm
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%%SITE_PERL%%/Bio/Matrix/IO/scoring.pm
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%%SITE_PERL%%/Bio/Matrix/MatrixI.pm
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%%SITE_PERL%%/Bio/Matrix/Mlagan.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/IO.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/IO/mast.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/IO/masta.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/IO/meme.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/IO/psiblast.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/IO/transfac.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/InstanceSite.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/InstanceSiteI.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/ProtMatrix.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/ProtPsm.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/Psm.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/PsmHeader.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/PsmHeaderI.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/PsmI.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/SiteMatrix.pm
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%%SITE_PERL%%/Bio/Matrix/PSM/SiteMatrixI.pm
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%%SITE_PERL%%/Bio/Matrix/PhylipDist.pm
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%%SITE_PERL%%/Bio/Matrix/Scoring.pm
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%%SITE_PERL%%/Bio/Ontology/DocumentRegistry.pm
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%%SITE_PERL%%/Bio/Ontology/GOterm.pm
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%%SITE_PERL%%/Bio/Ontology/InterProTerm.pm
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%%SITE_PERL%%/Bio/Ontology/OBOEngine.pm
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%%SITE_PERL%%/Bio/Ontology/OBOterm.pm
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%%SITE_PERL%%/Bio/Ontology/Ontology.pm
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%%SITE_PERL%%/Bio/Ontology/OntologyEngineI.pm
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%%SITE_PERL%%/Bio/Ontology/OntologyI.pm
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%%SITE_PERL%%/Bio/Ontology/OntologyStore.pm
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%%SITE_PERL%%/Bio/Ontology/Path.pm
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%%SITE_PERL%%/Bio/Ontology/PathI.pm
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%%SITE_PERL%%/Bio/Ontology/Relationship.pm
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%%SITE_PERL%%/Bio/Ontology/RelationshipFactory.pm
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%%SITE_PERL%%/Bio/Ontology/RelationshipI.pm
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%%SITE_PERL%%/Bio/Ontology/RelationshipType.pm
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%%SITE_PERL%%/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
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%%SITE_PERL%%/Bio/Ontology/SimpleOntologyEngine.pm
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%%SITE_PERL%%/Bio/Ontology/Term.pm
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%%SITE_PERL%%/Bio/Ontology/TermFactory.pm
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%%SITE_PERL%%/Bio/Ontology/TermI.pm
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%%SITE_PERL%%/Bio/OntologyIO.pm
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%%SITE_PERL%%/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
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%%SITE_PERL%%/Bio/OntologyIO/Handlers/InterProHandler.pm
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%%SITE_PERL%%/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
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%%SITE_PERL%%/Bio/OntologyIO/InterProParser.pm
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%%SITE_PERL%%/Bio/OntologyIO/dagflat.pm
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%%SITE_PERL%%/Bio/OntologyIO/goflat.pm
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%%SITE_PERL%%/Bio/OntologyIO/obo.pm
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%%SITE_PERL%%/Bio/OntologyIO/simplehierarchy.pm
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%%SITE_PERL%%/Bio/OntologyIO/soflat.pm
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%%SITE_PERL%%/Bio/ParameterBaseI.pm
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%%SITE_PERL%%/Bio/PrimarySeq.pm
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%%SITE_PERL%%/Bio/PrimarySeqI.pm
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%%SITE_PERL%%/Bio/PullParserI.pm
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%%SITE_PERL%%/Bio/Range.pm
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%%SITE_PERL%%/Bio/RangeI.pm
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%%SITE_PERL%%/Bio/Root/Exception.pm
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%%SITE_PERL%%/Bio/Root/HTTPget.pm
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%%SITE_PERL%%/Bio/Root/IO.pm
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%%SITE_PERL%%/Bio/Root/Root.pm
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%%SITE_PERL%%/Bio/Root/RootI.pm
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%%SITE_PERL%%/Bio/Root/Storable.pm
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%%SITE_PERL%%/Bio/Root/Test.pm
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%%SITE_PERL%%/Bio/Root/TestObject.pm
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%%SITE_PERL%%/Bio/Root/Utilities.pm
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%%SITE_PERL%%/Bio/Root/Version.pm
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%%SITE_PERL%%/Bio/Search/BlastStatistics.pm
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%%SITE_PERL%%/Bio/Search/BlastUtils.pm
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%%SITE_PERL%%/Bio/Search/DatabaseI.pm
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%%SITE_PERL%%/Bio/Search/GenericDatabase.pm
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%%SITE_PERL%%/Bio/Search/GenericStatistics.pm
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%%SITE_PERL%%/Bio/Search/HSP/BlastHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/BlastPullHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/FastaHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/GenericHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/HSPFactory.pm
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%%SITE_PERL%%/Bio/Search/HSP/HSPI.pm
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%%SITE_PERL%%/Bio/Search/HSP/ModelHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/PSLHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/PsiBlastHSP.pm
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%%SITE_PERL%%/Bio/Search/HSP/PullHSPI.pm
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%%SITE_PERL%%/Bio/Search/HSP/WABAHSP.pm
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%%SITE_PERL%%/Bio/Search/Hit/BlastHit.pm
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%%SITE_PERL%%/Bio/Search/Hit/BlastPullHit.pm
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%%SITE_PERL%%/Bio/Search/Hit/Fasta.pm
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%%SITE_PERL%%/Bio/Search/Hit/GenericHit.pm
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%%SITE_PERL%%/Bio/Search/Hit/HitFactory.pm
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%%SITE_PERL%%/Bio/Search/Hit/HitI.pm
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%%SITE_PERL%%/Bio/Search/Hit/ModelHit.pm
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%%SITE_PERL%%/Bio/Search/Hit/PsiBlastHit.pm
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%%SITE_PERL%%/Bio/Search/Hit/PullHitI.pm
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%%SITE_PERL%%/Bio/Search/Iteration/GenericIteration.pm
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%%SITE_PERL%%/Bio/Search/Iteration/IterationI.pm
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%%SITE_PERL%%/Bio/Search/Processor.pm
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%%SITE_PERL%%/Bio/Search/Result/BlastPullResult.pm
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%%SITE_PERL%%/Bio/Search/Result/BlastResult.pm
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%%SITE_PERL%%/Bio/Search/Result/CrossMatchResult.pm
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%%SITE_PERL%%/Bio/Search/Result/GenericResult.pm
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%%SITE_PERL%%/Bio/Search/Result/INFERNALResult.pm
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%%SITE_PERL%%/Bio/Search/Result/ResultI.pm
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%%SITE_PERL%%/Bio/Search/Result/WABAResult.pm
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%%SITE_PERL%%/Bio/Search/SearchUtils.pm
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%%SITE_PERL%%/Bio/Search/StatisticsI.pm
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%%SITE_PERL%%/Bio/Search/Tiling/MapTileUtils.pm
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%%SITE_PERL%%/Bio/Search/Tiling/MapTiling.pm
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%%SITE_PERL%%/Bio/Search/Tiling/TilingI.pm
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%%SITE_PERL%%/Bio/SearchIO.pm
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%%SITE_PERL%%/Bio/SearchIO/EventHandlerI.pm
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%%SITE_PERL%%/Bio/SearchIO/FastHitEventBuilder.pm
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%%SITE_PERL%%/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
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%%SITE_PERL%%/Bio/SearchIO/SearchResultEventBuilder.pm
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%%SITE_PERL%%/Bio/SearchIO/SearchWriterI.pm
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%%SITE_PERL%%/Bio/SearchIO/Writer/GbrowseGFF.pm
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%%SITE_PERL%%/Bio/SearchIO/Writer/HSPTableWriter.pm
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%%SITE_PERL%%/Bio/SearchIO/Writer/HTMLResultWriter.pm
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%%SITE_PERL%%/Bio/SearchIO/Writer/HitTableWriter.pm
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%%SITE_PERL%%/Bio/SearchIO/Writer/ResultTableWriter.pm
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%%SITE_PERL%%/Bio/SearchIO/Writer/TextResultWriter.pm
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%%SITE_PERL%%/Bio/SearchIO/axt.pm
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%%SITE_PERL%%/Bio/SearchIO/blast.pm
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%%SITE_PERL%%/Bio/SearchIO/blast_pull.pm
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%%SITE_PERL%%/Bio/SearchIO/blasttable.pm
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%%SITE_PERL%%/Bio/SearchIO/cross_match.pm
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%%SITE_PERL%%/Bio/SearchIO/erpin.pm
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%%SITE_PERL%%/Bio/SearchIO/exonerate.pm
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%%SITE_PERL%%/Bio/SearchIO/fasta.pm
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%%SITE_PERL%%/Bio/SearchIO/gmap_f9.pm
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%%SITE_PERL%%/Bio/SearchIO/infernal.pm
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%%SITE_PERL%%/Bio/SearchIO/megablast.pm
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%%SITE_PERL%%/Bio/SearchIO/psl.pm
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%%SITE_PERL%%/Bio/SearchIO/rnamotif.pm
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%%SITE_PERL%%/Bio/SearchIO/sim4.pm
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%%SITE_PERL%%/Bio/SearchIO/waba.pm
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%%SITE_PERL%%/Bio/SearchIO/wise.pm
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%%SITE_PERL%%/Bio/Seq.pm
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%%SITE_PERL%%/Bio/Seq/BaseSeqProcessor.pm
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%%SITE_PERL%%/Bio/Seq/EncodedSeq.pm
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%%SITE_PERL%%/Bio/Seq/LargeLocatableSeq.pm
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%%SITE_PERL%%/Bio/Seq/LargePrimarySeq.pm
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%%SITE_PERL%%/Bio/Seq/LargeSeq.pm
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%%SITE_PERL%%/Bio/Seq/LargeSeqI.pm
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%%SITE_PERL%%/Bio/Seq/Meta.pm
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%%SITE_PERL%%/Bio/Seq/Meta/Array.pm
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%%SITE_PERL%%/Bio/Seq/MetaI.pm
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%%SITE_PERL%%/Bio/Seq/PrimaryQual.pm
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%%SITE_PERL%%/Bio/Seq/PrimedSeq.pm
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%%SITE_PERL%%/Bio/Seq/QualI.pm
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%%SITE_PERL%%/Bio/Seq/Quality.pm
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%%SITE_PERL%%/Bio/Seq/RichSeq.pm
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%%SITE_PERL%%/Bio/Seq/RichSeqI.pm
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%%SITE_PERL%%/Bio/Seq/SeqBuilder.pm
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%%SITE_PERL%%/Bio/Seq/SeqFactory.pm
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%%SITE_PERL%%/Bio/Seq/SeqFastaSpeedFactory.pm
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%%SITE_PERL%%/Bio/Seq/SequenceTrace.pm
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%%SITE_PERL%%/Bio/Seq/SimulatedRead.pm
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%%SITE_PERL%%/Bio/SeqAnalysisParserI.pm
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