1279 lines
49 KiB
Plaintext
1279 lines
49 KiB
Plaintext
%%DATADIR%%/models/README
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%%DATADIR%%/models/biblio.dia
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%%DATADIR%%/models/bio_liveseq_variation.dia
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%%DATADIR%%/models/bio_map.dia
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%%DATADIR%%/models/bioperl.dia
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%%DATADIR%%/models/bio_restriction.dia
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%%DATADIR%%/models/coordinatemapper.dia
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%%DATADIR%%/models/map_proposal.txt
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%%DATADIR%%/models/maps_and_markers.dia
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%%DATADIR%%/models/popgen.dia
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%%DATADIR%%/models/population_proposal.txt
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%%DATADIR%%/scripts/Bio-DB-EUtilities/einfo.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/README
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%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/meta_gff.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS
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%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS
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%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
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%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
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%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
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%%DATADIR%%/scripts/DB-HIV/hivq.PLS
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%%DATADIR%%/scripts/DB/TAG
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%%DATADIR%%/scripts/DB/biofetch_genbank_proxy.PLS
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%%DATADIR%%/scripts/DB/bioflat_index.PLS
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%%DATADIR%%/scripts/DB/biogetseq.PLS
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%%DATADIR%%/scripts/DB/flanks.PLS
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%%DATADIR%%/scripts/README
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%%DATADIR%%/scripts/biblio/TAG
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%%DATADIR%%/scripts/das/README
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%%DATADIR%%/scripts/index/TAG
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%%DATADIR%%/scripts/index/bp_fetch.PLS
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%%DATADIR%%/scripts/index/bp_index.PLS
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%%DATADIR%%/scripts/index/bp_seqret.PLS
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%%DATADIR%%/scripts/popgen/composite_LD.PLS
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%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
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%%DATADIR%%/scripts/searchio/README
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%%DATADIR%%/scripts/searchio/filter_search.PLS
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%%DATADIR%%/scripts/searchio/hmmer_to_table.PLS
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%%DATADIR%%/scripts/searchio/parse_hmmsearch.PLS
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%%DATADIR%%/scripts/searchio/search2table.PLS
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%%DATADIR%%/scripts/seq/TAG
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%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
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%%DATADIR%%/scripts/seq/make_mrna_protein.PLS
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%%DATADIR%%/scripts/seq/seqconvert.PLS
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%%DATADIR%%/scripts/seq/seqretsplit.PLS
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%%DATADIR%%/scripts/seq/split_seq.PLS
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%%DATADIR%%/scripts/seqstats/TAG
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%%DATADIR%%/scripts/seqstats/aacomp.PLS
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%%DATADIR%%/scripts/seqstats/chaos_plot.PLS
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%%DATADIR%%/scripts/seqstats/gccalc.PLS
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%%DATADIR%%/scripts/seqstats/oligo_count.PLS
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%%DATADIR%%/scripts/seq/translate_seq.PLS
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%%DATADIR%%/scripts/seq/unflatten_seq.PLS
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%%DATADIR%%/scripts/taxa/TAG
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%%DATADIR%%/scripts/taxa/taxid4species.PLS
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%%DATADIR%%/scripts/taxa/taxonomy2tree.PLS
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%%DATADIR%%/scripts/utilities/README
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%%DATADIR%%/scripts/utilities/TAG
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%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
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%%DATADIR%%/scripts/utilities/bp_nrdb.PLS
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%%DATADIR%%/scripts/utilities/bp_sreformat.PLS
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%%DATADIR%%/scripts/utilities/dbsplit.PLS
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%%DATADIR%%/scripts/utilities/download_query_genbank.PLS
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%%DATADIR%%/scripts/utilities/mask_by_search.PLS
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%%DATADIR%%/scripts/utilities/mutate.PLS
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%%DATADIR%%/scripts/utilities/pairwise_kaks.PLS
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%%DATADIR%%/scripts/utilities/remote_blast.PLS
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%%DATADIR%%/scripts/utilities/revtrans-motif.PLS
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%%DATADIR%%/scripts/utilities/search2BSML.PLS
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%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
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%%DATADIR%%/scripts/utilities/search2gff.PLS
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%%DATADIR%%/scripts/utilities/search2tribe.PLS
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%%DATADIR%%/scripts/utilities/seq_length.PLS
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%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
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%%EXAMPLESDIR%%/align/align_on_codons.pl
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%%EXAMPLESDIR%%/align/aligntutorial.pl
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%%EXAMPLESDIR%%/align/clustalw.pl
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%%EXAMPLESDIR%%/align/simplealign.pl
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%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl
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%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl
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%%EXAMPLESDIR%%/biblio/biblio_soap.pl
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%%EXAMPLESDIR%%/bioperl.pl
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%%EXAMPLESDIR%%/cluster/dbsnp.pl
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%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
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%%EXAMPLESDIR%%/contributed/prosite2perl.pl
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%%EXAMPLESDIR%%/contributed/rebase2list.pl
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%%EXAMPLESDIR%%/db/dbfetch
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%%EXAMPLESDIR%%/db/est_tissue_query.pl
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%%EXAMPLESDIR%%/db/gb2features.pl
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%%EXAMPLESDIR%%/db/getGenBank.pl
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%%EXAMPLESDIR%%/db/get_seqs.pl
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%%EXAMPLESDIR%%/db/rfetch.pl
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%%EXAMPLESDIR%%/db/use_registry.pl
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%%EXAMPLESDIR%%/generate_random_seq.pl
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%%EXAMPLESDIR%%/liveseq/change_gene.pl
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%%EXAMPLESDIR%%/longorf.pl
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%%EXAMPLESDIR%%/make_primers.pl
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%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
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%%EXAMPLESDIR%%/quality/svgtrace.pl
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%%EXAMPLESDIR%%/rev_and_trans.pl
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%%EXAMPLESDIR%%/revcom_dir.pl
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%%EXAMPLESDIR%%/root/README
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%%EXAMPLESDIR%%/root/exceptions2.pl
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%%EXAMPLESDIR%%/root/exceptions3.pl
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%%EXAMPLESDIR%%/root/exceptions4.pl
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%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
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%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
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%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
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%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
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%%EXAMPLESDIR%%/root/lib/TestInterface.pm
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%%EXAMPLESDIR%%/root/lib/TestObject.pm
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%%EXAMPLESDIR%%/searchio/blast_example.pl
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%%EXAMPLESDIR%%/searchio/custom_writer.pl
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%%EXAMPLESDIR%%/searchio/hitwriter.pl
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%%EXAMPLESDIR%%/searchio/hspwriter.pl
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%%EXAMPLESDIR%%/searchio/htmlwriter.pl
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%%EXAMPLESDIR%%/searchio/psiblast_features.pl
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%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
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%%EXAMPLESDIR%%/searchio/rawwriter.pl
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%%EXAMPLESDIR%%/searchio/resultwriter.pl
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%%EXAMPLESDIR%%/searchio/waba2gff3.pl
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%%EXAMPLESDIR%%/searchio/waba2gff.pl
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%%EXAMPLESDIR%%/sirna/TAG
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%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
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%%EXAMPLESDIR%%/structure/structure-io.pl
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%%EXAMPLESDIR%%/subsequence.cgi
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%%EXAMPLESDIR%%/tk/gsequence.pl
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%%EXAMPLESDIR%%/tk/hitdisplay.pl
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%%EXAMPLESDIR%%/tools/extract_genes.pl
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%%EXAMPLESDIR%%/tools/gb_to_gff.pl
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%%EXAMPLESDIR%%/tools/gff2ps.pl
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%%EXAMPLESDIR%%/tools/parse_codeml.pl
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%%EXAMPLESDIR%%/tools/psw.pl
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%%EXAMPLESDIR%%/tools/reverse-translate.pl
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%%EXAMPLESDIR%%/tools/run_genscan.pl
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%%EXAMPLESDIR%%/tools/run_primer3.pl
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%%EXAMPLESDIR%%/tools/seq_pattern.pl
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%%EXAMPLESDIR%%/tools/standaloneblast.pl
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%%EXAMPLESDIR%%/tree/paup2phylip.pl
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%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
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%%PORTDOCS%%%%DOCSDIR%%/BUGS
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/LICENSE
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/META.yml
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Makefile.PL
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/README
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/deob_index.pl
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_flowchart.png
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_help.html
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/lib/Deobfuscator.pm
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%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/00.load.t
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%%PORTDOCS%%%%DOCSDIR%%/doc/README
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%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
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%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
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%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
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%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
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%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
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%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
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%%PORTDOCS%%@dirrm %%DOCSDIR%%
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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/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/xmfa.pm
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%%SITE_PERL%%/Bio/Align/ProteinStatistics.pm
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bin/bp_aacomp.pl
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bin/bp_biblio.pl
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bin/bp_biofetch_genbank_proxy.pl
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bin/bp_bioflat_index.pl
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bin/bp_biogetseq.pl
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bin/bp_dbsplit.pl
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bin/bp_download_query_genbank.pl
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bin/bp_einfo.pl
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bin/bp_extract_feature_seq.pl
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bin/bp_fastam9_to_table.pl
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bin/bp_fast_load_gff.pl
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bin/bp_fetch.pl
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bin/bp_filter_search.pl
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bin/bp_flanks.pl
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bin/bp_gccalc.pl
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bin/bp_generate_histogram.pl
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bin/bp_hivq.pl
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bin/bp_hmmer_to_table.pl
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bin/bp_index.pl
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bin/bp_load_gff.pl
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bin/bp_local_taxonomydb_query.pl
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bin/bp_make_mrna_protein.pl
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bin/bp_mask_by_search.pl
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bin/bp_meta_gff.pl
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bin/bp_mrtrans.pl
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bin/bp_mutate.pl
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bin/bp_nexus2nh.pl
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bin/bp_oligo_count.pl
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bin/bp_pairwise_kaks.pl
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bin/bp_parse_hmmsearch.pl
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bin/bp_pg_bulk_load_gff.pl
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bin/bp_process_gadfly.pl
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bin/bp_process_sgd.pl
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bin/bp_process_wormbase.pl
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bin/bp_query_entrez_taxa.pl
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bin/bp_remote_blast.pl
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bin/bp_revtrans-motif.pl
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bin/bp_search2BSML.pl
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bin/bp_search2alnblocks.pl
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bin/bp_search2gff.pl
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bin/bp_search2table.pl
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bin/bp_seqconvert.pl
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bin/bp_seqfeature_delete.pl
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bin/bp_seqfeature_gff3.pl
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bin/bp_seqfeature_load.pl
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bin/bp_sreformat.pl
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bin/bp_taxid4species.pl
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bin/bp_unflatten_seq.pl
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@dirrm %%DATADIR%%/scripts/Bio-DB-EUtilities
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@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
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@dirrm %%DATADIR%%/scripts/Bio-SeqFeature-Store
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@dirrm %%DATADIR%%/scripts/DB
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@dirrm %%DATADIR%%/scripts/DB-HIV
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@dirrm %%DATADIR%%/scripts/biblio
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@dirrm %%DATADIR%%/scripts/das
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@dirrm %%DATADIR%%/scripts/index
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@dirrm %%DATADIR%%/scripts/popgen
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@dirrm %%DATADIR%%/scripts/searchio
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@dirrm %%DATADIR%%/scripts/seq
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@dirrm %%DATADIR%%/scripts/seqstats
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@dirrm %%DATADIR%%/scripts/taxa
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@dirrm %%DATADIR%%/scripts/tree
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@dirrm %%DATADIR%%/scripts/utilities
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@dirrm %%DATADIR%%/models
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@dirrm %%DATADIR%%/scripts
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@dirrm %%DATADIR%%
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@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
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@dirrm %%EXAMPLESDIR%%/biblio
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@dirrm %%EXAMPLESDIR%%/cluster
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@dirrm %%EXAMPLESDIR%%/quality
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@dirrm %%EXAMPLESDIR%%/searchio
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@dirrm %%EXAMPLESDIR%%/sirna
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@dirrm %%EXAMPLESDIR%%/structure
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@dirrm %%EXAMPLESDIR%%/tk
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@dirrm %%EXAMPLESDIR%%/tools
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@dirrm %%SITE_PERL%%/Bio/Align
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@dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
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@dirrm %%SITE_PERL%%/Bio/Search/Tiling
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@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
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@dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
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|
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|
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@dirrm %%SITE_PERL%%/Bio/Tools/Run
|
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@dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern
|
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@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
|
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@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA
|
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@dirrm %%SITE_PERL%%/Bio/Tools/Signalp
|
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@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
|
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@dirrm %%SITE_PERL%%/Bio/Tools/Spidey
|
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@dirrm %%SITE_PERL%%/Bio/Tools
|
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@dirrm %%SITE_PERL%%/Bio/Tree/Draw
|
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@dirrm %%SITE_PERL%%/Bio/Tree
|
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@dirrm %%SITE_PERL%%/Bio/TreeIO
|
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@dirrm %%SITE_PERL%%/Bio/Variation/IO
|
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@dirrm %%SITE_PERL%%/Bio/Variation
|