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1.10
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desc
@@


1.10
log
@- Update to 1.6.1

Approved by:	maintainer (via Email)
@
text
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@


1.9
log
@- Update to 1.6.0

PR:		ports/131989
Submitted by:	maintainer
@
text
@d1 191
a191 63
bin/bp_sreformat.pl
bin/bp_seqconvert.pl
bin/bp_parse_hmmsearch.pl
bin/bp_seqret.pl
bin/bp_tree2pag.pl
bin/bp_meta_gff.pl
bin/bp_nexus2nh.pl
bin/bp_filter_search.pl
bin/bp_flanks.pl
bin/bp_seqfeature_gff3.pl
bin/bp_generate_histogram.pl
bin/bp_heterogeneity_test.pl
bin/bp_split_seq.pl
bin/bp_load_gff.pl
bin/bp_biogetseq.pl
bin/bp_fetch.pl
bin/bp_mutate.pl
bin/bp_process_sgd.pl
bin/bp_index.pl
bin/bp_dbsplit.pl
bin/bp_oligo_count.pl
bin/bp_seq_length.pl
bin/bp_seqfeature_load.pl
bin/bp_process_gadfly.pl
bin/bp_hmmer_to_table.pl
bin/bp_fastam9_to_table.pl
bin/bp_genbank2gff.pl
bin/bp_biofetch_genbank_proxy.pl
bin/bp_extract_feature_seq.pl
bin/bp_search2gff.pl
bin/bp_taxid4species.pl
bin/bp_bulk_load_gff.pl
bin/bp_blast2tree.pl
bin/bp_make_mrna_protein.pl
bin/bp_unflatten_seq.pl
bin/bp_search2tribe.pl
bin/bp_bioflat_index.pl
bin/bp_seqfeature_delete.pl
bin/bp_query_entrez_taxa.pl
bin/bp_pairwise_kaks.pl
bin/bp_fast_load_gff.pl
bin/bp_chaos_plot.pl
bin/bp_taxonomy2tree.pl
bin/bp_mrtrans.pl
bin/bp_search2alnblocks.pl
bin/bp_download_query_genbank.pl
bin/bp_nrdb.pl
bin/bp_mask_by_search.pl
bin/bp_gccalc.pl
bin/bp_composite_LD.pl
bin/bp_classify_hits_kingdom.pl
bin/bp_aacomp.pl
bin/bp_process_wormbase.pl
bin/bp_local_taxonomydb_query.pl
bin/bp_biblio.pl
bin/bp_seqretsplit.pl
bin/bp_remote_blast.pl
bin/bp_genbank2gff3.pl
bin/bp_search2table.pl
bin/bp_search2BSML.pl
bin/bp_translate_seq.pl
bin/bp_pg_bulk_load_gff.pl
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%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/Deobfuscator
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc
%%PORTDOCS%%@@dirrm %%DOCSDIR%%
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@


1.8
log
@- add missing MAN1 and MAN3
- apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST
- update the usage of NOPORTDOCS

PR:		71322
Submitted by:	leeym
Approved by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>
@
text
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%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
%%SITE_PERL%%/Bio/Biblio/Organisation.pm
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%%SITE_PERL%%/Bio/Biblio/Patent.pm
%%SITE_PERL%%/Bio/Biblio/MedlineJournal.pm
%%SITE_PERL%%/Bio/Biblio/Proceeding.pm
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%%SITE_PERL%%/Bio/OntologyIO/goflat.pm
a445 1
%%SITE_PERL%%/Bio/OntologyIO/dagflat.pm
d447 2
d450 203
a652 19
%%SITE_PERL%%/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
%%SITE_PERL%%/Bio/OntologyIO/Handlers/InterProHandler.pm
%%SITE_PERL%%/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
%%SITE_PERL%%/Bio/Location/NarrowestCoordPolicy.pm
%%SITE_PERL%%/Bio/Location/Simple.pm
%%SITE_PERL%%/Bio/Location/Split.pm
%%SITE_PERL%%/Bio/Location/SplitLocationI.pm
%%SITE_PERL%%/Bio/Location/AvWithinCoordPolicy.pm
%%SITE_PERL%%/Bio/Location/FuzzyLocationI.pm
%%SITE_PERL%%/Bio/Location/WidestCoordPolicy.pm
%%SITE_PERL%%/Bio/Location/CoordinatePolicyI.pm
%%SITE_PERL%%/Bio/Location/Atomic.pm
%%SITE_PERL%%/Bio/Location/Fuzzy.pm
%%SITE_PERL%%/Bio/SeqIO/bsml.pm
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%%SITE_PERL%%/Bio/SeqIO/pir.pm
%%SITE_PERL%%/Bio/SeqIO/phd.pm
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d654 2
a655 4
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%%SITE_PERL%%/Bio/SeqIO/exp.pm
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%%SITE_PERL%%/Bio/SeqIO/ztr.pm
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a674 6
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%%SITE_PERL%%/Bio/SeqIO/game/gameWriter.pm
d918 1
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d922 1
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/embl2picture.pl
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_blast1.pl
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/blastn.out
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/README
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/OBDA_Access.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/PAML.html
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/SearchIO.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/SeqIO.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/SimpleWebAnalysis.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/e-novative.css
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/Trees.pdf
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/PAML.pdf
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Trees.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Flat_Databases.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Graphics-HOWTO.sgml
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/SeqIO.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/SimpleWebAnalysis.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Feature-Annotation.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/txt/Flat_Databases.txt
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/txt/SimpleWebAnalysis.txt
d942 12
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%%EXAMPLESDIR%%/align/align_on_codons.pl
%%EXAMPLESDIR%%/align/aligntutorial.pl
%%EXAMPLESDIR%%/align/clustalw.pl
%%EXAMPLESDIR%%/align/simplealign.pl
d955 1
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%%EXAMPLESDIR%%/tree/paup2phylip.pl
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%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
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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/TestInterface.pm
%%EXAMPLESDIR%%/root/lib/TestObject.pm
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%%EXAMPLESDIR%%/biographics/all_glyphs.pl
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%%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
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%%DATADIR%%/scripts/index/bp_index.PLS
%%DATADIR%%/scripts/utilities/seq_length.PLS
%%DATADIR%%/scripts/utilities/README
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%%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
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%%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
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%%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
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%%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
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%%DATADIR%%/scripts/seq/TAG
%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
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%%DATADIR%%/scripts/taxa/local_taxonomydb_query.PLS
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%%DATADIR%%/scripts/popgen/composite_LD.PLS
%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
%%DATADIR%%/scripts/install_bioperl_scripts.pl
%%DATADIR%%/models/population_proposal.txt
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%%DATADIR%%/models/bio_liveseq_variation.dia
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%%DATADIR%%/models/bio_restriction.dia
%%DATADIR%%/models/bioperl.dia
%%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/Tools/Prediction
@@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
@@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
@@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
@@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
@@dirrm %%SITE_PERL%%/Bio/Tools/Phylo
@@dirrm %%SITE_PERL%%/Bio/Tools/BPlite
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@@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
@@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
@@dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
@@dirrm %%SITE_PERL%%/Bio/DB/GFF
@@dirrm %%SITE_PERL%%/Bio/DB
@@dirrm %%SITE_PERL%%/Bio/Biblio/IO
@@dirrm %%SITE_PERL%%/Bio/Biblio
@@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
@@dirrm %%SITE_PERL%%/Bio/OntologyIO
@@dirrm %%SITE_PERL%%/Bio/Location
@@dirrm %%SITE_PERL%%/Bio/SeqIO/game
@@dirrm %%SITE_PERL%%/Bio/SeqIO
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%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/faq
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/examples/graphics
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/examples
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/figs/graphics
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/figs
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/html/images
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/html
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/pdf
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/sgml
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto/txt
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/doc/howto
d1229 3
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@@dirrm %%EXAMPLESDIR%%/align
d1234 2
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@@dirrm %%EXAMPLESDIR%%/tree
a1237 3
@@dirrm %%EXAMPLESDIR%%/root/lib/Bio
@@dirrm %%EXAMPLESDIR%%/root/lib
@@dirrm %%EXAMPLESDIR%%/root
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a1242 2
@@dirrm %%EXAMPLESDIR%%/popgen
@@dirrm %%EXAMPLESDIR%%/biographics
d1246 1
a1246 1
@@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
d1248 6
d1255 1
a1255 2
@@dirrm %%DATADIR%%/scripts/utilities
@@dirrm %%DATADIR%%/scripts/DB
a1256 4
@@dirrm %%DATADIR%%/scripts/das
@@dirrm %%DATADIR%%/scripts/graphics
@@dirrm %%DATADIR%%/scripts/tree
@@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
d1261 1
a1261 1
@@dirrm %%DATADIR%%/scripts/popgen
a1262 1
@@dirrm %%DATADIR%%/models
@


1.7
log
@Major update from 0.7.2 to 1.4 by new maintainer.  This is almost a complete
rework of the port.

See the page http://news.open-bio.org/archives/cat_bioperl.html for the
changes between 1.2 and 1.4.  The older changes are in the CVS tree.

From the new maintainer:

	Note that this new port just handles the installation of bioperl and
	not of additional extra stuff (bioperl-gui, bioperl-corba-server,
	bioperl-corba-client). This is unlike the behaviour of the current
	port.

	The extra stuff, though still functional, had very little adoption
	among users, and does not appear to be currently supported/maintained.

PR:		ports/47303 (and subsequent)
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (new maintainer)
@
text
@d762 205
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share/doc/bioperl/AUTHORS
share/doc/bioperl/BUGS
share/doc/bioperl/Changes
share/doc/bioperl/DEPRECATED
share/doc/bioperl/FAQ
share/doc/bioperl/INSTALL
share/doc/bioperl/LICENSE
share/doc/bioperl/PLATFORMS
share/doc/bioperl/README
share/doc/bioperl/doc/faq/faq.html
share/doc/bioperl/doc/faq/faq.dtd
share/doc/bioperl/doc/faq/faq.pl
share/doc/bioperl/doc/faq/faq.xml
share/doc/bioperl/doc/howto/examples/graphics/render_features.pl
share/doc/bioperl/doc/howto/examples/graphics/data1.txt
share/doc/bioperl/doc/howto/examples/graphics/embl2picture.pl
share/doc/bioperl/doc/howto/examples/graphics/factor7.embl
share/doc/bioperl/doc/howto/examples/graphics/render_blast1.pl
share/doc/bioperl/doc/howto/examples/graphics/render_blast2.pl
share/doc/bioperl/doc/howto/examples/graphics/render_blast3.pl
share/doc/bioperl/doc/howto/examples/graphics/render_blast4.pl
share/doc/bioperl/doc/howto/examples/graphics/blastn.out
share/doc/bioperl/doc/howto/examples/README
share/doc/bioperl/doc/howto/figs/graphics/fig1.png
share/doc/bioperl/doc/howto/figs/graphics/fig2.png
share/doc/bioperl/doc/howto/figs/graphics/fig3.png
share/doc/bioperl/doc/howto/figs/graphics/fig4.png
share/doc/bioperl/doc/howto/figs/graphics/fig5.png
share/doc/bioperl/doc/howto/figs/graphics/fig6.png
share/doc/bioperl/doc/howto/figs/README
share/doc/bioperl/doc/howto/html/images/tip.png
share/doc/bioperl/doc/howto/html/Flat_Databases.html
share/doc/bioperl/doc/howto/html/Graphics-HOWTO.html
share/doc/bioperl/doc/howto/html/OBDA_Access.html
share/doc/bioperl/doc/howto/html/PAML.html
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share/doc/bioperl/doc/howto/html/SearchIO.html
share/doc/bioperl/doc/howto/html/SeqIO.html
share/doc/bioperl/doc/howto/html/SimpleWebAnalysis.html
share/doc/bioperl/doc/howto/html/e-novative.css
share/doc/bioperl/doc/howto/pdf/Trees.pdf
share/doc/bioperl/doc/howto/pdf/Graphics-HOWTO.pdf
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share/doc/bioperl/doc/howto/pdf/SimpleWebAnalysis.pdf
share/doc/bioperl/doc/howto/pdf/Flat_Databases.pdf
share/doc/bioperl/doc/howto/sgml/Trees.sgml
share/doc/bioperl/doc/howto/sgml/Flat_Databases.sgml
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share/doc/bioperl/doc/howto/sgml/OBDA_Access.sgml
share/doc/bioperl/doc/howto/sgml/PAML.sgml
share/doc/bioperl/doc/howto/sgml/README
share/doc/bioperl/doc/howto/sgml/SearchIO.sgml
share/doc/bioperl/doc/howto/sgml/SeqIO.sgml
share/doc/bioperl/doc/howto/sgml/SimpleWebAnalysis.sgml
share/doc/bioperl/doc/howto/sgml/Feature-Annotation.sgml
share/doc/bioperl/doc/howto/txt/Flat_Databases.txt
share/doc/bioperl/doc/howto/txt/SimpleWebAnalysis.txt
share/doc/bioperl/doc/makedoc.PL
share/examples/bioperl/align/align_on_codons.pl
share/examples/bioperl/align/aligntutorial.pl
share/examples/bioperl/align/clustalw.pl
share/examples/bioperl/align/simplealign.pl
share/examples/bioperl/tools/standaloneblast.pl
share/examples/bioperl/tools/gff2ps.pl
share/examples/bioperl/tools/parse_codeml.pl
share/examples/bioperl/tools/psw.pl
share/examples/bioperl/tools/restriction.pl
share/examples/bioperl/tools/run_genscan.pl
share/examples/bioperl/tools/seq_pattern.pl
share/examples/bioperl/tools/gb_to_gff.pl
share/examples/bioperl/tk/gsequence.pl
share/examples/bioperl/tk/hitdisplay.pl
share/examples/bioperl/tree/paup2phylip.pl
share/examples/bioperl/sirna/TAG
share/examples/bioperl/sirna/rnai_finder.cgi
share/examples/bioperl/searchio/waba2gff.pl
share/examples/bioperl/searchio/custom_writer.pl
share/examples/bioperl/searchio/hitwriter.pl
share/examples/bioperl/searchio/hspwriter.pl
share/examples/bioperl/searchio/htmlwriter.pl
share/examples/bioperl/searchio/psiblast_features.pl
share/examples/bioperl/searchio/psiblast_iterations.pl
share/examples/bioperl/searchio/rawwriter.pl
share/examples/bioperl/searchio/resultwriter.pl
share/examples/bioperl/searchio/blast_example.pl
share/examples/bioperl/root/lib/Bio/PrimarySeq.pm
share/examples/bioperl/root/lib/Bio/PrimarySeqI.pm
share/examples/bioperl/root/lib/Bio/Seq.pm
share/examples/bioperl/root/lib/Bio/SeqI.pm
share/examples/bioperl/root/lib/Error.pm
share/examples/bioperl/root/lib/TestInterface.pm
share/examples/bioperl/root/lib/TestObject.pm
share/examples/bioperl/root/README
share/examples/bioperl/root/exceptions1.pl
share/examples/bioperl/root/exceptions2.pl
share/examples/bioperl/root/exceptions3.pl
share/examples/bioperl/root/exceptions4.pl
share/examples/bioperl/db/gb2features.pl
share/examples/bioperl/db/dbfetch
share/examples/bioperl/db/est_tissue_query.pl
share/examples/bioperl/db/get_seqs.pl
share/examples/bioperl/db/getGenBank.pl
share/examples/bioperl/db/rfetch.pl
share/examples/bioperl/db/use_registry.pl
share/examples/bioperl/biblio/biblio_examples.pl
share/examples/bioperl/biblio/biblio_soap.pl
share/examples/bioperl/popgen/parse_calc_stats.pl
share/examples/bioperl/biographics/all_glyphs.pl
share/examples/bioperl/biographics/dynamic_glyphs.pl
share/examples/bioperl/biographics/feature_data.gff
share/examples/bioperl/biographics/feature_data.txt
share/examples/bioperl/biographics/lots_of_glyphs.pl
share/examples/bioperl/biographics/render_sequence.pl
share/examples/bioperl/cluster/dbsnp.pl
share/examples/bioperl/contributed/nmrpdb_parse.pl
share/examples/bioperl/contributed/prosite2perl.pl
share/examples/bioperl/contributed/rebase2list.pl
share/examples/bioperl/liveseq/change_gene.pl
share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl
share/examples/bioperl/subsequence.cgi
share/examples/bioperl/longorf.pl
share/examples/bioperl/make_mrna_protein.pl
share/examples/bioperl/bioperl.pl
share/examples/bioperl/make_primers.pl
share/examples/bioperl/rev_and_trans.pl
share/examples/bioperl/revcom_dir.pl
share/examples/bioperl/generate_random_seq.pl
share/bioperl/scripts/index/TAG
share/bioperl/scripts/index/bp_fetch.PLS
share/bioperl/scripts/index/bp_index.PLS
share/bioperl/scripts/utilities/seq_length.PLS
share/bioperl/scripts/utilities/README
share/bioperl/scripts/utilities/TAG
share/bioperl/scripts/utilities/bp_mrtrans.PLS
share/bioperl/scripts/utilities/bp_sreformat.PLS
share/bioperl/scripts/utilities/dbsplit.PLS
share/bioperl/scripts/utilities/mask_by_search.PLS
share/bioperl/scripts/utilities/mutate.PLS
share/bioperl/scripts/utilities/pairwise_kaks.PLS
share/bioperl/scripts/utilities/remote_blast.PLS
share/bioperl/scripts/utilities/search2BSML.PLS
share/bioperl/scripts/utilities/search2alnblocks.PLS
share/bioperl/scripts/utilities/search2gff.PLS
share/bioperl/scripts/utilities/search2tribe.PLS
share/bioperl/scripts/utilities/bp_nrdb.PLS
share/bioperl/scripts/DB/TAG
share/bioperl/scripts/DB/biofetch_genbank_proxy.PLS
share/bioperl/scripts/DB/bioflat_index.PLS
share/bioperl/scripts/DB/biogetseq.PLS
share/bioperl/scripts/DB/flanks.PLS
share/bioperl/scripts/biblio/TAG
share/bioperl/scripts/biblio/biblio.PLS
share/bioperl/scripts/das/README
share/bioperl/scripts/das/TAG
share/bioperl/scripts/graphics/frend.PLS
share/bioperl/scripts/graphics/README
share/bioperl/scripts/graphics/TAG
share/bioperl/scripts/graphics/feature_draw.PLS
share/bioperl/scripts/graphics/search_overview.PLS
share/bioperl/scripts/tree/TAG
share/bioperl/scripts/tree/blast2tree.PLS
share/bioperl/scripts/Bio-DB-GFF/process_wormbase.PLS
share/bioperl/scripts/Bio-DB-GFF/README
share/bioperl/scripts/Bio-DB-GFF/TAG
share/bioperl/scripts/Bio-DB-GFF/bp_genbank2gff.PLS
share/bioperl/scripts/Bio-DB-GFF/bulk_load_gff.PLS
share/bioperl/scripts/Bio-DB-GFF/fast_load_gff.PLS
share/bioperl/scripts/Bio-DB-GFF/generate_histogram.PLS
share/bioperl/scripts/Bio-DB-GFF/load_ucsc.pl
share/bioperl/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS
share/bioperl/scripts/Bio-DB-GFF/process_gadfly.PLS
share/bioperl/scripts/Bio-DB-GFF/process_ncbi_human.PLS
share/bioperl/scripts/Bio-DB-GFF/process_sgd.PLS
share/bioperl/scripts/Bio-DB-GFF/load_gff.PLS
share/bioperl/scripts/searchio/filter_search.PLS
share/bioperl/scripts/seq/TAG
share/bioperl/scripts/seq/extract_feature_seq.PLS
share/bioperl/scripts/seq/seqconvert.PLS
share/bioperl/scripts/seq/split_seq.PLS
share/bioperl/scripts/seq/translate_seq.PLS
share/bioperl/scripts/seqstats/TAG
share/bioperl/scripts/seqstats/aacomp.PLS
share/bioperl/scripts/seqstats/chaos_plot.PLS
share/bioperl/scripts/seqstats/gccalc.PLS
share/bioperl/scripts/seqstats/oligo_count.PLS
share/bioperl/scripts/taxa/TAG
share/bioperl/scripts/taxa/local_taxonomydb_query.PLS
share/bioperl/scripts/taxa/taxid4species.PLS
share/bioperl/scripts/popgen/composite_LD.PLS
share/bioperl/scripts/popgen/heterogeneity_test.PLS
share/bioperl/scripts/install_bioperl_scripts.pl
share/bioperl/models/population_proposal.txt
share/bioperl/models/README
share/bioperl/models/bio_liveseq_variation.dia
share/bioperl/models/bio_map.dia
share/bioperl/models/bio_restriction.dia
share/bioperl/models/bioperl.dia
share/bioperl/models/coordinatemapper.dia
share/bioperl/models/map_proposal.txt
share/bioperl/models/maps_and_markers.dia
share/bioperl/models/popgen.dia
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@


1.6
log
@utilize SITE_PERL

PR:		58166
Submitted by:	Cheng-Lung Sung <clsung@@dragon2.net>
@
text
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%%PLIST_GUI%%@@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Tk
%%PLIST_GUI%%@@dirrm %%SITE_PERL%%/Bio/Tk
%%PLIST_CORBA_SERVER%%@@dirrm %%SITE_PERL%%/Bio/CorbaServer
%%PLIST_CORBA_CLIENT%%@@dirrm %%SITE_PERL%%/Bio/CorbaClient
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@@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
@@dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment
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@@dirrm %%SITE_PERL%%/Bio/Tools/Blast/Run
@@dirrm %%SITE_PERL%%/Bio/Tools/Blast
@@dirrm %%SITE_PERL%%/Bio/Tools/BPlite
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@@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
@@dirrm %%SITE_PERL%%/Bio/SeqFeature
@@dirrm %%SITE_PERL%%/Bio/Seq
@@dirrm %%SITE_PERL%%/Bio/Root
@@dirrm %%SITE_PERL%%/Bio/Location
@@dirrm %%SITE_PERL%%/Bio/LiveSeq/IO
@@dirrm %%SITE_PERL%%/Bio/LiveSeq
@@dirrm %%SITE_PERL%%/Bio/Index
@@dirrm %%SITE_PERL%%/Bio/Factory
@@dirrm %%SITE_PERL%%/Bio/DB
@@dirrm %%SITE_PERL%%/Bio/Annotation
@@dirrm %%SITE_PERL%%/Bio/AlignIO
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a1114 5
@@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Ext/Align
@@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Ext
@@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
@@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Bio/Ext
@@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Bio
@


1.5
log
@- Properly list run-time dependencies in RUN_DEPENDS in Makefile.
- Deploy %%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout
  pkg-plist.  (Ouch, that was embarrassing.)
- Bump PORTREVISION due to the above.
- Update my email address and the project's URL in pkg-descr.
@
text
@d1 250
a250 250
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Base.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Client.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/ORB.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/PrimarySeq.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Seq.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/SeqFeature.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Biocorba.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/biocorba.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/AnonymousSeq.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Base.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/BioEnv.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeq.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqDB.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqIterator.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqVector.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Seq.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqDB.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeature.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeatureIterator.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeatureVector.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Server.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/AnnotMap.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/BioTkPerl8_1.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/GO_Browser.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/HitDisplay.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/README
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/SeqCanvas.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/Tkpsh.pl
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Map.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_SeqSubs.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Sequence.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Utilities.pm
%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Tk/.packlist
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/bl2seq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/clustalw.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/mase.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/msf.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/pfam.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/prodom.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/selex.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/stockholm.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GDB.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/NCBIHelper.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SwissProt.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/UpdateableSeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/WebDBSeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DBLinkContainerI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/DriverFactory.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactory.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/GenBank.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Swissprot.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/AARange.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Chain.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/ChainI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/DNA.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Exon.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Gene.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/BioPerl.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/Loader.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/SRS.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Intron.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutation.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutator.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Prim_Transcript.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Range.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Region.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Unit.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/SeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Transcript.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Translation.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/AvWithinCoordPolicy.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/CoordinatePolicyI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Fuzzy.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/FuzzyLocationI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/NarrowestCoordPolicy.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Simple.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Split.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/SplitLocationI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/WidestCoordPolicy.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LocationI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IO.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargePrimarySeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargeSeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqAnalysisParserI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Exon.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/ExonI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructure.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructureI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Transcript.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/TranscriptI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Similarity.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/SimilarityPair.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/ace.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/featureHandler.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/idHandler.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/seqHandler.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/largefasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqUtils.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AnalysisResult.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPbl2seq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/HSP.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Iteration.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Sbjct.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPpsilite.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/ESTScan.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/GFF.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Genscan.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/MZEF.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/OddCodes.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Exon.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Gene.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/Clustalw.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/TCoffee.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/StandAloneBlast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAChange.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAReverseMutate.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/Allele.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/DNAMutation.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/flat.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/xml.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/README
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/RNAChange.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/SeqDiff.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/VariantI.pm
lib/perl5/site_perl/%%PERL_VER%%/bioback.pod
lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
lib/perl5/site_perl/%%PERL_VER%%/bptutorial.pl
%%PLIST_GUI%%@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Tk
%%PLIST_GUI%%@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk
%%PLIST_CORBA_SERVER%%@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer
%%PLIST_CORBA_CLIENT%%@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Location
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio
@


1.4
log
@- Update to version 0.7.1
- Add a build-time message to inform the user of available options.
@
text
@d1 33
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Base.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Client.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/ORB.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/PrimarySeq.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Seq.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/SeqFeature.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/DB/Biocorba.pm
%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/SeqIO/biocorba.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/AnonymousSeq.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Base.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/BioEnv.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeq.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqDB.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqIterator.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqVector.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Seq.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqDB.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeature.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureIterator.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureVector.pm
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Server.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/AnnotMap.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/BioTkPerl8_1.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/GO_Browser.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/HitDisplay.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/README
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/SeqCanvas.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/Tkpsh.pl
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Map.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_SeqSubs.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Sequence.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Utilities.pm
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk/.packlist
d216 4
a219 4
%%PLIST_GUI%%@@dirrm lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk
%%PLIST_GUI%%@@dirrm lib/perl5/site_perl/5.6.0/Bio/Tk
%%PLIST_CORBA_SERVER%%@@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaServer
%%PLIST_CORBA_CLIENT%%@@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaClient
@


1.3
log
@Embarrassingly long overdue update to 0.7.0, including optional support for
GUI (Tk) and CORBA extensions.
@
text
@a148 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm
@


1.2
log
@Update to version 0.6.2

PR:		21954
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
@d1 33
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lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
d119 5
d125 6
d132 2
d139 1
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d216 11
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d236 1
a236 4
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search
d238 3
d242 1
d245 1
@


1.1
log
@Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics

PR:		ports/20252
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
@d1 10
d12 2
d15 10
a24 3
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
a25 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
d27 1
a27 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
d29 2
d32 13
a44 4
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
d46 6
a51 2
lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
d53 1
a53 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
a54 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
a55 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
d57 2
a58 7
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
d60 6
d67 1
a68 4
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
d70 1
a70 5
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
d72 1
a72 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
d75 6
a80 1
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
d82 3
a84 31
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
d87 1
d89 1
a89 9
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4
a91 1
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
d93 4
a97 2
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result
d99 1
d101 1
a102 1
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
d104 1
a104 1
@@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/
d107 2
@

