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bin/bp_filter_search.pl
bin/bp_genbank2gff.pl
bin/bp_bulk_load_gff.pl
bin/bp_nrdb.pl
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%%EXAMPLESDIR%%/tools/gb_to_gff.pl
%%EXAMPLESDIR%%/tk/gsequence.pl
%%EXAMPLESDIR%%/tk/hitdisplay.pl
%%EXAMPLESDIR%%/tree/paup2phylip.pl
%%EXAMPLESDIR%%/sirna/TAG
%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
%%EXAMPLESDIR%%/searchio/waba2gff.pl
%%EXAMPLESDIR%%/searchio/custom_writer.pl
%%EXAMPLESDIR%%/searchio/hitwriter.pl
%%EXAMPLESDIR%%/searchio/hspwriter.pl
%%EXAMPLESDIR%%/searchio/htmlwriter.pl
%%EXAMPLESDIR%%/searchio/psiblast_features.pl
%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
%%EXAMPLESDIR%%/searchio/rawwriter.pl
%%EXAMPLESDIR%%/searchio/resultwriter.pl
%%EXAMPLESDIR%%/searchio/blast_example.pl
%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
%%EXAMPLESDIR%%/root/lib/Error.pm
%%EXAMPLESDIR%%/root/lib/TestInterface.pm
%%EXAMPLESDIR%%/root/lib/TestObject.pm
%%EXAMPLESDIR%%/root/README
%%EXAMPLESDIR%%/root/exceptions1.pl
%%EXAMPLESDIR%%/root/exceptions2.pl
%%EXAMPLESDIR%%/root/exceptions3.pl
%%EXAMPLESDIR%%/root/exceptions4.pl
%%EXAMPLESDIR%%/db/gb2features.pl
%%EXAMPLESDIR%%/db/dbfetch
%%EXAMPLESDIR%%/db/est_tissue_query.pl
%%EXAMPLESDIR%%/db/get_seqs.pl
%%EXAMPLESDIR%%/db/getGenBank.pl
%%EXAMPLESDIR%%/db/rfetch.pl
%%EXAMPLESDIR%%/db/use_registry.pl
%%EXAMPLESDIR%%/biblio/biblio_examples.pl
%%EXAMPLESDIR%%/biblio/biblio_soap.pl
%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
%%EXAMPLESDIR%%/biographics/all_glyphs.pl
%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl
%%EXAMPLESDIR%%/biographics/feature_data.gff
%%EXAMPLESDIR%%/biographics/feature_data.txt
%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl
%%EXAMPLESDIR%%/biographics/render_sequence.pl
%%EXAMPLESDIR%%/cluster/dbsnp.pl
%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
%%EXAMPLESDIR%%/contributed/prosite2perl.pl
%%EXAMPLESDIR%%/contributed/rebase2list.pl
%%EXAMPLESDIR%%/liveseq/change_gene.pl
%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
%%EXAMPLESDIR%%/subsequence.cgi
%%EXAMPLESDIR%%/longorf.pl
%%EXAMPLESDIR%%/make_mrna_protein.pl
%%EXAMPLESDIR%%/bioperl.pl
%%EXAMPLESDIR%%/make_primers.pl
%%EXAMPLESDIR%%/rev_and_trans.pl
%%EXAMPLESDIR%%/revcom_dir.pl
%%EXAMPLESDIR%%/generate_random_seq.pl
%%DATADIR%%/scripts/index/TAG
%%DATADIR%%/scripts/index/bp_fetch.PLS
%%DATADIR%%/scripts/index/bp_index.PLS
%%DATADIR%%/scripts/utilities/seq_length.PLS
%%DATADIR%%/scripts/utilities/README
%%DATADIR%%/scripts/utilities/TAG
%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
%%DATADIR%%/scripts/utilities/bp_sreformat.PLS
%%DATADIR%%/scripts/utilities/dbsplit.PLS
%%DATADIR%%/scripts/utilities/mask_by_search.PLS
%%DATADIR%%/scripts/utilities/mutate.PLS
%%DATADIR%%/scripts/utilities/pairwise_kaks.PLS
%%DATADIR%%/scripts/utilities/remote_blast.PLS
%%DATADIR%%/scripts/utilities/search2BSML.PLS
%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
%%DATADIR%%/scripts/utilities/search2gff.PLS
%%DATADIR%%/scripts/utilities/search2tribe.PLS
%%DATADIR%%/scripts/utilities/bp_nrdb.PLS
%%DATADIR%%/scripts/DB/TAG
%%DATADIR%%/scripts/DB/biofetch_genbank_proxy.PLS
%%DATADIR%%/scripts/DB/bioflat_index.PLS
%%DATADIR%%/scripts/DB/biogetseq.PLS
%%DATADIR%%/scripts/DB/flanks.PLS
%%DATADIR%%/scripts/biblio/TAG
%%DATADIR%%/scripts/biblio/biblio.PLS
%%DATADIR%%/scripts/das/README
%%DATADIR%%/scripts/das/TAG
%%DATADIR%%/scripts/graphics/frend.PLS
%%DATADIR%%/scripts/graphics/README
%%DATADIR%%/scripts/graphics/TAG
%%DATADIR%%/scripts/graphics/feature_draw.PLS
%%DATADIR%%/scripts/graphics/search_overview.PLS
%%DATADIR%%/scripts/tree/TAG
%%DATADIR%%/scripts/tree/blast2tree.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/README
%%DATADIR%%/scripts/Bio-DB-GFF/TAG
%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/load_ucsc.pl
%%DATADIR%%/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/process_ncbi_human.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS
%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
%%DATADIR%%/scripts/searchio/filter_search.PLS
%%DATADIR%%/scripts/seq/TAG
%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
%%DATADIR%%/scripts/seq/seqconvert.PLS
%%DATADIR%%/scripts/seq/split_seq.PLS
%%DATADIR%%/scripts/seq/translate_seq.PLS
%%DATADIR%%/scripts/seqstats/TAG
%%DATADIR%%/scripts/seqstats/aacomp.PLS
%%DATADIR%%/scripts/seqstats/chaos_plot.PLS
%%DATADIR%%/scripts/seqstats/gccalc.PLS
%%DATADIR%%/scripts/seqstats/oligo_count.PLS
%%DATADIR%%/scripts/taxa/TAG
%%DATADIR%%/scripts/taxa/local_taxonomydb_query.PLS
%%DATADIR%%/scripts/taxa/taxid4species.PLS
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%%DATADIR%%/models/population_proposal.txt
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%%DATADIR%%/models/bio_liveseq_variation.dia
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%%DATADIR%%/models/coordinatemapper.dia
%%DATADIR%%/models/map_proposal.txt
%%DATADIR%%/models/maps_and_markers.dia
%%DATADIR%%/models/popgen.dia
%%DATADIR%%/models/biblio.dia
@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
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@dirrm %%SITE_PERL%%/Bio/MapIO
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@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
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@dirrm %%SITE_PERL%%/Bio/Factory
@dirrm %%SITE_PERL%%/Bio/Variation/IO
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@dirrm %%SITE_PERL%%/Bio/Tools/Prediction
@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
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@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
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@dirrm %%SITE_PERL%%/Bio/Tools/Analysis
@dirrm %%SITE_PERL%%/Bio/Tools/HMMER
@dirrm %%SITE_PERL%%/Bio/Tools
@dirrm %%SITE_PERL%%/Bio/Graphics/FeatureFile
@dirrm %%SITE_PERL%%/Bio/Graphics/Glyph
@dirrm %%SITE_PERL%%/Bio/Graphics
@dirrm %%SITE_PERL%%/Bio/Taxonomy
@dirrm %%SITE_PERL%%/Bio/DB/Biblio
@dirrm %%SITE_PERL%%/Bio/DB/Query
@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
@dirrm %%SITE_PERL%%/Bio/DB/Flat
@dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
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@dirrm %%SITE_PERL%%/Bio/Biblio/IO
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@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
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@dirrm %%EXAMPLESDIR%%/align
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@dirrm %%EXAMPLESDIR%%/searchio
@dirrm %%EXAMPLESDIR%%/root/lib/Bio
@dirrm %%EXAMPLESDIR%%/root/lib
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@dirrm %%EXAMPLESDIR%%/db
@dirrm %%EXAMPLESDIR%%/biblio
@dirrm %%EXAMPLESDIR%%/popgen
@dirrm %%EXAMPLESDIR%%/biographics
@dirrm %%EXAMPLESDIR%%/cluster
@dirrm %%EXAMPLESDIR%%/contributed
@dirrm %%EXAMPLESDIR%%/liveseq
@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
@dirrm %%EXAMPLESDIR%%
@dirrm %%DATADIR%%/scripts/index
@dirrm %%DATADIR%%/scripts/utilities
@dirrm %%DATADIR%%/scripts/DB
@dirrm %%DATADIR%%/scripts/biblio
@dirrm %%DATADIR%%/scripts/das
@dirrm %%DATADIR%%/scripts/graphics
@dirrm %%DATADIR%%/scripts/tree
@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
@dirrm %%DATADIR%%/scripts/searchio
@dirrm %%DATADIR%%/scripts/seq
@dirrm %%DATADIR%%/scripts/seqstats
@dirrm %%DATADIR%%/scripts/taxa
@dirrm %%DATADIR%%/scripts/popgen
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@dirrm %%DATADIR%%/models
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