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authorMartin Wilke <miwi@FreeBSD.org>2009-06-06 04:38:36 +0800
committerMartin Wilke <miwi@FreeBSD.org>2009-06-06 04:38:36 +0800
commitf128ddfb8e824bce7cd0ef1addba5b707e8adc66 (patch)
tree3f59163d342879f3073e32d5466a9463002dd536 /biology
parent178818ef96f08d2d87f6be577b2df88cf00ebe1a (diff)
downloadfreebsd-ports-gnome-f128ddfb8e824bce7cd0ef1addba5b707e8adc66.tar.gz
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2009-05-31 biology/p5-bioperl-devel: no longer under development
2009-05-31 biology/p5-bioperl-run-devel: no longer under development 2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead 2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
Diffstat (limited to 'biology')
-rw-r--r--biology/Makefile2
-rw-r--r--biology/p5-bioperl-devel/Makefile1008
-rw-r--r--biology/p5-bioperl-devel/distinfo3
-rw-r--r--biology/p5-bioperl-devel/files/patch-Build.PL19
-rw-r--r--biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm20
-rw-r--r--biology/p5-bioperl-devel/pkg-descr11
-rw-r--r--biology/p5-bioperl-devel/pkg-plist1272
-rw-r--r--biology/p5-bioperl-run-devel/Makefile392
-rw-r--r--biology/p5-bioperl-run-devel/distinfo3
-rw-r--r--biology/p5-bioperl-run-devel/pkg-descr5
-rw-r--r--biology/p5-bioperl-run-devel/pkg-plist383
11 files changed, 0 insertions, 3118 deletions
diff --git a/biology/Makefile b/biology/Makefile
index 892e117aa36c..8f120d02a7b3 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -62,9 +62,7 @@
SUBDIR += p5-Bio-Graphics
SUBDIR += p5-Bio-Phylo
SUBDIR += p5-bioperl
- SUBDIR += p5-bioperl-devel
SUBDIR += p5-bioperl-run
- SUBDIR += p5-bioperl-run-devel
SUBDIR += paml
SUBDIR += phd2fasta
SUBDIR += phrap
diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile
deleted file mode 100644
index 9371a7171c6d..000000000000
--- a/biology/p5-bioperl-devel/Makefile
+++ /dev/null
@@ -1,1008 +0,0 @@
-# New ports collection makefile for: biology/p5-bioperl-devel
-# Date created: 21 November 2005
-# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net>
-#
-# $FreeBSD$
-#
-
-PORTNAME= bioperl
-PORTVERSION= 1.5.2
-CATEGORIES= biology perl5
-MASTER_SITES= http://bioperl.org/DIST/
-PKGNAMEPREFIX= p5-
-DISTNAME= ${PORTNAME}-${PORTVERSION}_102
-
-MAINTAINER= mauricio@arareko.net
-COMMENT= A collection of Perl modules for bioinformatics (developer release)
-
-BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VERSION}/Text/Wrap.pm:${PORTSDIR}/lang/${PERL_PORT} \
- ${LOCALBASE}/lib/perl5/${PERL_VERSION}/${PERL_ARCH}/DB_File.pm:${PORTSDIR}/lang/${PERL_PORT} \
- ${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
- ${SITE_PERL}/Class/AutoClass.pm:${PORTSDIR}/devel/p5-Class-AutoClass \
- ${SITE_PERL}/Data/Stag/ITextWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \
- ${SITE_PERL}/Data/Stag/SxprWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \
- ${SITE_PERL}/Data/Stag/XMLWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \
- ${SITE_PERL}/GD/SVG.pm:${PORTSDIR}/graphics/p5-GD-SVG \
- ${SITE_PERL}/Graph/Directed.pm:${PORTSDIR}/math/p5-Graph \
- ${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
- ${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
- ${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
- ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
- ${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \
- ${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
- ${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
- ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
- ${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
- ${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \
- ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \
- ${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \
- ${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
- ${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
- ${SITE_PERL}/XML/SAX.pm:${PORTSDIR}/textproc/p5-XML-SAX \
- ${SITE_PERL}/XML/SAX/Base.pm:${PORTSDIR}/textproc/p5-XML-SAX \
- ${SITE_PERL}/XML/SAX/Writer.pm:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
- ${SITE_PERL}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \
- ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \
- ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
- ${SITE_PERL}/${PERL_ARCH}/Clone.pm:${PORTSDIR}/devel/p5-Clone \
- ${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \
- ${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \
- ${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \
- ${SITE_PERL}/${PERL_ARCH}/HTML/Entities.pm:${PORTSDIR}/www/p5-HTML-Parser \
- ${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \
- ${SITE_PERL}/${PERL_ARCH}/Storable.pm:${PORTSDIR}/devel/p5-Storable \
- ${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser
-RUN_DEPENDS= ${BUILD_DEPENDS}
-
-CONFLICTS= p5-bioperl-1.[02468]*
-
-LATEST_LINK= p5-bioperl-devel
-
-DEPRECATED= no longer under development
-EXPIRATION_DATE= 2009-05-31
-
-PERL_MODBUILD= YES
-
-MAN1= bp_aacomp.pl.1 \
- bp_biblio.pl.1 \
- bp_biofetch_genbank_proxy.pl.1 \
- bp_bioflat_index.pl.1 \
- bp_biogetseq.pl.1 \
- bp_blast2tree.pl.1 \
- bp_bulk_load_gff.pl.1 \
- bp_chaos_plot.pl.1 \
- bp_classify_hits_kingdom.pl.1 \
- bp_composite_LD.pl.1 \
- bp_contig_draw.pl.1 \
- bp_dbsplit.pl.1 \
- bp_embl2picture.pl.1 \
- bp_extract_feature_seq.pl.1 \
- bp_fast_load_gff.pl.1 \
- bp_fastam9_to_table.pl.1 \
- bp_feature_draw.pl.1 \
- bp_fetch.pl.1 \
- bp_filter_search.pl.1 \
- bp_flanks.pl.1 \
- bp_frend.pl.1 \
- bp_gccalc.pl.1 \
- bp_genbank2gff.pl.1 \
- bp_genbank2gff3.pl.1 \
- bp_generate_histogram.pl.1 \
- bp_glyphs1-demo.pl.1 \
- bp_glyphs2-demo.pl.1 \
- bp_heterogeneity_test.pl.1 \
- bp_hmmer_to_table.pl.1 \
- bp_index.pl.1 \
- bp_load_gff.pl.1 \
- bp_local_taxonomydb_query.pl.1 \
- bp_make_mrna_protein.pl.1 \
- bp_mask_by_search.pl.1 \
- bp_meta_gff.pl.1 \
- bp_mrtrans.pl.1 \
- bp_mutate.pl.1 \
- bp_nexus2nh.pl.1 \
- bp_nrdb.pl.1 \
- bp_oligo_count.pl.1 \
- bp_pairwise_kaks.pl.1 \
- bp_parse_hmmsearch.pl.1 \
- bp_process_gadfly.pl.1 \
- bp_process_sgd.pl.1 \
- bp_process_wormbase.pl.1 \
- bp_query_entrez_taxa.pl.1 \
- bp_remote_blast.pl.1 \
- bp_search_overview.pl.1 \
- bp_search2alnblocks.pl.1 \
- bp_search2BSML.pl.1 \
- bp_search2gff.pl.1 \
- bp_search2table.pl.1 \
- bp_search2tribe.pl.1 \
- bp_seq_length.pl.1 \
- bp_seqconvert.pl.1 \
- bp_seqret.pl.1 \
- bp_split_seq.pl.1 \
- bp_sreformat.pl.1 \
- bp_taxid4species.pl.1 \
- bp_taxonomy2tree.pl.1 \
- bp_translate_seq.pl.1 \
- bp_tree2pag.pl.1 \
- bp_unflatten_seq.pl.1
-
-MAN3= Bio::Align::AlignI.3 \
- Bio::Align::DNAStatistics.3 \
- Bio::Align::PairwiseStatistics.3 \
- Bio::Align::ProteinStatistics.3 \
- Bio::Align::StatisticsI.3 \
- Bio::Align::Utilities.3 \
- Bio::AlignIO.3 \
- Bio::AlignIO::bl2seq.3 \
- Bio::AlignIO::clustalw.3 \
- Bio::AlignIO::emboss.3 \
- Bio::AlignIO::fasta.3 \
- Bio::AlignIO::largemultifasta.3 \
- Bio::AlignIO::maf.3 \
- Bio::AlignIO::mase.3 \
- Bio::AlignIO::mega.3 \
- Bio::AlignIO::meme.3 \
- Bio::AlignIO::metafasta.3 \
- Bio::AlignIO::msf.3 \
- Bio::AlignIO::nexus.3 \
- Bio::AlignIO::pfam.3 \
- Bio::AlignIO::phylip.3 \
- Bio::AlignIO::po.3 \
- Bio::AlignIO::prodom.3 \
- Bio::AlignIO::psi.3 \
- Bio::AlignIO::selex.3 \
- Bio::AlignIO::stockholm.3 \
- Bio::AnalysisI.3 \
- Bio::AnalysisParserI.3 \
- Bio::AnalysisResultI.3 \
- Bio::AnnotatableI.3 \
- Bio::Annotation::AnnotationFactory.3 \
- Bio::Annotation::Collection.3 \
- Bio::Annotation::Comment.3 \
- Bio::Annotation::DBLink.3 \
- Bio::Annotation::OntologyTerm.3 \
- Bio::Annotation::Reference.3 \
- Bio::Annotation::SimpleValue.3 \
- Bio::Annotation::StructuredValue.3 \
- Bio::Annotation::Target.3 \
- Bio::Annotation::TypeManager.3 \
- Bio::AnnotationCollectionI.3 \
- Bio::AnnotationI.3 \
- Bio::Assembly::Contig.3 \
- Bio::Assembly::ContigAnalysis.3 \
- Bio::Assembly::IO.3 \
- Bio::Assembly::IO::ace.3 \
- Bio::Assembly::IO::phrap.3 \
- Bio::Assembly::Scaffold.3 \
- Bio::Assembly::ScaffoldI.3 \
- Bio::Assembly::Singlet.3 \
- Bio::Biblio.3 \
- Bio::Biblio::Article.3 \
- Bio::Biblio::BiblioBase.3 \
- Bio::Biblio::Book.3 \
- Bio::Biblio::BookArticle.3 \
- Bio::Biblio::IO.3 \
- Bio::Biblio::IO::medline2ref.3 \
- Bio::Biblio::IO::medlinexml.3 \
- Bio::Biblio::IO::pubmed2ref.3 \
- Bio::Biblio::IO::pubmedxml.3 \
- Bio::Biblio::Journal.3 \
- Bio::Biblio::JournalArticle.3 \
- Bio::Biblio::MedlineArticle.3 \
- Bio::Biblio::MedlineBook.3 \
- Bio::Biblio::MedlineBookArticle.3 \
- Bio::Biblio::MedlineJournal.3 \
- Bio::Biblio::MedlineJournalArticle.3 \
- Bio::Biblio::Organisation.3 \
- Bio::Biblio::Patent.3 \
- Bio::Biblio::Person.3 \
- Bio::Biblio::Proceeding.3 \
- Bio::Biblio::Provider.3 \
- Bio::Biblio::PubmedArticle.3 \
- Bio::Biblio::PubmedBookArticle.3 \
- Bio::Biblio::PubmedJournalArticle.3 \
- Bio::Biblio::Ref.3 \
- Bio::Biblio::Service.3 \
- Bio::Biblio::TechReport.3 \
- Bio::Biblio::Thesis.3 \
- Bio::Biblio::WebResource.3 \
- Bio::Cluster::ClusterFactory.3 \
- Bio::Cluster::FamilyI.3 \
- Bio::Cluster::SequenceFamily.3 \
- Bio::Cluster::UniGene.3 \
- Bio::Cluster::UniGeneI.3 \
- Bio::ClusterI.3 \
- Bio::ClusterIO.3 \
- Bio::ClusterIO::dbsnp.3 \
- Bio::ClusterIO::unigene.3 \
- Bio::CodonUsage::IO.3 \
- Bio::CodonUsage::Table.3 \
- Bio::ConfigData.3 \
- Bio::Coordinate::Chain.3 \
- Bio::Coordinate::Collection.3 \
- Bio::Coordinate::ExtrapolatingPair.3 \
- Bio::Coordinate::GeneMapper.3 \
- Bio::Coordinate::Graph.3 \
- Bio::Coordinate::MapperI.3 \
- Bio::Coordinate::Pair.3 \
- Bio::Coordinate::Result.3 \
- Bio::Coordinate::Result::Gap.3 \
- Bio::Coordinate::Result::Match.3 \
- Bio::Coordinate::ResultI.3 \
- Bio::Coordinate::Utils.3 \
- Bio::DB::Ace.3 \
- Bio::DB::Biblio::biofetch.3 \
- Bio::DB::Biblio::eutils.3 \
- Bio::DB::Biblio::pdf.3 \
- Bio::DB::Biblio::soap.3 \
- Bio::DB::BiblioI.3 \
- Bio::DB::BioFetch.3 \
- Bio::DB::CUTG.3 \
- Bio::DB::DBFetch.3 \
- Bio::DB::EMBL.3 \
- Bio::DB::EUtilities.3 \
- Bio::DB::EUtilities::Cookie.3 \
- Bio::DB::EUtilities::ElinkData.3 \
- Bio::DB::EUtilities::efetch.3 \
- Bio::DB::EUtilities::egquery.3 \
- Bio::DB::EUtilities::einfo.3 \
- Bio::DB::EUtilities::elink.3 \
- Bio::DB::EUtilities::epost.3 \
- Bio::DB::EUtilities::esearch.3 \
- Bio::DB::EUtilities::esummary.3 \
- Bio::DB::EntrezGene.3 \
- Bio::DB::Expression.3 \
- Bio::DB::Expression::geo.3 \
- Bio::DB::Failover.3 \
- Bio::DB::Fasta.3 \
- Bio::DB::FileCache.3 \
- Bio::DB::Flat.3 \
- Bio::DB::Flat::BDB.3 \
- Bio::DB::Flat::BDB::embl.3 \
- Bio::DB::Flat::BDB::fasta.3 \
- Bio::DB::Flat::BDB::genbank.3 \
- Bio::DB::Flat::BDB::swiss.3 \
- Bio::DB::Flat::BDB::swissprot.3 \
- Bio::DB::Flat::BinarySearch.3 \
- Bio::DB::GDB.3 \
- Bio::DB::GenericWebDBI.3 \
- Bio::DB::GFF.3 \
- Bio::DB::GFF::Adaptor::ace.3 \
- Bio::DB::GFF::Adaptor::berkeleydb.3 \
- Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 \
- Bio::DB::GFF::Adaptor::biofetch.3 \
- Bio::DB::GFF::Adaptor::biofetch_oracle.3 \
- Bio::DB::GFF::Adaptor::dbi.3 \
- Bio::DB::GFF::Adaptor::dbi::caching_handle.3 \
- Bio::DB::GFF::Adaptor::dbi::iterator.3 \
- Bio::DB::GFF::Adaptor::dbi::mysql.3 \
- Bio::DB::GFF::Adaptor::dbi::mysqlace.3 \
- Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3 \
- Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 \
- Bio::DB::GFF::Adaptor::dbi::oracle.3 \
- Bio::DB::GFF::Adaptor::dbi::oracleace.3 \
- Bio::DB::GFF::Adaptor::dbi::pg.3 \
- Bio::DB::GFF::Adaptor::dbi::pg_fts.3 \
- Bio::DB::GFF::Adaptor::memory.3 \
- Bio::DB::GFF::Adaptor::memory::feature_serializer.3 \
- Bio::DB::GFF::Adaptor::memory::iterator.3 \
- Bio::DB::GFF::Aggregator.3 \
- Bio::DB::GFF::Aggregator::alignment.3 \
- Bio::DB::GFF::Aggregator::clone.3 \
- Bio::DB::GFF::Aggregator::coding.3 \
- Bio::DB::GFF::Aggregator::match.3 \
- Bio::DB::GFF::Aggregator::none.3 \
- Bio::DB::GFF::Aggregator::processed_transcript.3 \
- Bio::DB::GFF::Aggregator::so_transcript.3 \
- Bio::DB::GFF::Aggregator::transcript.3 \
- Bio::DB::GFF::Aggregator::ucsc_acembly.3 \
- Bio::DB::GFF::Aggregator::ucsc_ensgene.3 \
- Bio::DB::GFF::Aggregator::ucsc_genscan.3 \
- Bio::DB::GFF::Aggregator::ucsc_refgene.3 \
- Bio::DB::GFF::Aggregator::ucsc_sanger22.3 \
- Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3 \
- Bio::DB::GFF::Aggregator::ucsc_softberry.3 \
- Bio::DB::GFF::Aggregator::ucsc_twinscan.3 \
- Bio::DB::GFF::Aggregator::ucsc_unigene.3 \
- Bio::DB::GFF::Featname.3 \
- Bio::DB::GFF::Feature.3 \
- Bio::DB::GFF::Homol.3 \
- Bio::DB::GFF::RelSegment.3 \
- Bio::DB::GFF::Segment.3 \
- Bio::DB::GFF::Typename.3 \
- Bio::DB::GFF::Util::Binning.3 \
- Bio::DB::GFF::Util::Rearrange.3 \
- Bio::DB::GenBank.3 \
- Bio::DB::GenPept.3 \
- Bio::DB::InMemoryCache.3 \
- Bio::DB::LocationI.3 \
- Bio::DB::MeSH.3 \
- Bio::DB::NCBIHelper.3 \
- Bio::DB::Query::GenBank.3 \
- Bio::DB::Query::WebQuery.3 \
- Bio::DB::QueryI.3 \
- Bio::DB::RandomAccessI.3 \
- Bio::DB::ReferenceI.3 \
- Bio::DB::RefSeq.3 \
- Bio::DB::Registry.3 \
- Bio::DB::SeqFeature.3 \
- Bio::DB::SeqFeature::NormalizedFeature.3 \
- Bio::DB::SeqFeature::NormalizedFeatureI.3 \
- Bio::DB::SeqFeature::NormalizedTableFeatureI.3 \
- Bio::DB::SeqFeature::Segment.3 \
- Bio::DB::SeqFeature::Store.3 \
- Bio::DB::SeqFeature::Store::DBI::Iterator.3 \
- Bio::DB::SeqFeature::Store::DBI::mysql.3 \
- Bio::DB::SeqFeature::Store::GFF3Loader.3 \
- Bio::DB::SeqFeature::Store::bdb.3 \
- Bio::DB::SeqFeature::Store::berkeleydb.3 \
- Bio::DB::SeqFeature::Store::memory.3 \
- Bio::DB::SeqHound.3 \
- Bio::DB::SeqI.3 \
- Bio::DB::SeqVersion.3 \
- Bio::DB::SeqVersion::gi.3 \
- Bio::DB::SwissProt.3 \
- Bio::DB::Taxonomy.3 \
- Bio::DB::Taxonomy::entrez.3 \
- Bio::DB::Taxonomy::flatfile.3 \
- Bio::DB::Taxonomy::list.3 \
- Bio::DB::Universal.3 \
- Bio::DB::UpdateableSeqI.3 \
- Bio::DB::WebDBSeqI.3 \
- Bio::DB::XEMBL.3 \
- Bio::DB::XEMBLService.3 \
- Bio::DBLinkContainerI.3 \
- Bio::Das::FeatureTypeI.3 \
- Bio::Das::SegmentI.3 \
- Bio::DasI.3 \
- Bio::DescribableI.3 \
- Bio::Event::EventGeneratorI.3 \
- Bio::Event::EventHandlerI.3 \
- Bio::Expression::Contact.3 \
- Bio::Expression::DataSet.3 \
- Bio::Expression::FeatureGroup.3 \
- Bio::Expression::FeatureGroup::FeatureGroupMas50.3 \
- Bio::Expression::FeatureI.3 \
- Bio::Expression::FeatureSet::FeatureSetMas50.3 \
- Bio::Expression::Platform.3 \
- Bio::Expression::ProbeI.3 \
- Bio::Expression::Sample.3 \
- Bio::Factory::AnalysisI.3 \
- Bio::Factory::ApplicationFactoryI.3 \
- Bio::Factory::DriverFactory.3 \
- Bio::Factory::FTLocationFactory.3 \
- Bio::Factory::HitFactoryI.3 \
- Bio::Factory::LocationFactoryI.3 \
- Bio::Factory::MapFactoryI.3 \
- Bio::Factory::ObjectBuilderI.3 \
- Bio::Factory::ObjectFactory.3 \
- Bio::Factory::ObjectFactoryI.3 \
- Bio::Factory::ResultFactoryI.3 \
- Bio::Factory::SeqAnalysisParserFactory.3 \
- Bio::Factory::SeqAnalysisParserFactoryI.3 \
- Bio::Factory::SequenceFactoryI.3 \
- Bio::Factory::SequenceProcessorI.3 \
- Bio::Factory::SequenceStreamI.3 \
- Bio::Factory::TreeFactoryI.3 \
- Bio::FeatureHolderI.3 \
- Bio::FeatureIO.3 \
- Bio::FeatureIO::bed.3 \
- Bio::FeatureIO::gff.3 \
- Bio::FeatureIO::gtf.3 \
- Bio::FeatureIO::interpro.3 \
- Bio::FeatureIO::ptt.3 \
- Bio::Graph::Edge.3 \
- Bio::Graph::IO.3 \
- Bio::Graph::IO::dip.3 \
- Bio::Graph::IO::psi_xml.3 \
- Bio::Graph::ProteinGraph.3 \
- Bio::Graph::SimpleGraph.3 \
- Bio::Graph::SimpleGraph::Traversal.3 \
- Bio::Graphics.3 \
- Bio::Graphics::ConfiguratorI.3 \
- Bio::Graphics::Feature.3 \
- Bio::Graphics::FeatureBase.3 \
- Bio::Graphics::FeatureFile.3 \
- Bio::Graphics::FeatureFile::Iterator.3 \
- Bio::Graphics::Glyph.3 \
- Bio::Graphics::Glyph::Factory.3 \
- Bio::Graphics::Glyph::alignment.3 \
- Bio::Graphics::Glyph::anchored_arrow.3 \
- Bio::Graphics::Glyph::arrow.3 \
- Bio::Graphics::Glyph::box.3 \
- Bio::Graphics::Glyph::broken_line.3 \
- Bio::Graphics::Glyph::cds.3 \
- Bio::Graphics::Glyph::christmas_arrow.3 \
- Bio::Graphics::Glyph::crossbox.3 \
- Bio::Graphics::Glyph::dashed_line.3 \
- Bio::Graphics::Glyph::diamond.3 \
- Bio::Graphics::Glyph::dna.3 \
- Bio::Graphics::Glyph::dot.3 \
- Bio::Graphics::Glyph::dumbbell.3 \
- Bio::Graphics::Glyph::ellipse.3 \
- Bio::Graphics::Glyph::ex.3 \
- Bio::Graphics::Glyph::extending_arrow.3 \
- Bio::Graphics::Glyph::flag.3 \
- Bio::Graphics::Glyph::gene.3 \
- Bio::Graphics::Glyph::generic.3 \
- Bio::Graphics::Glyph::graded_segments.3 \
- Bio::Graphics::Glyph::group.3 \
- Bio::Graphics::Glyph::heterogeneous_segments.3 \
- Bio::Graphics::Glyph::image.3 \
- Bio::Graphics::Glyph::lightning.3 \
- Bio::Graphics::Glyph::line.3 \
- Bio::Graphics::Glyph::merge_parts.3 \
- Bio::Graphics::Glyph::merged_alignment.3 \
- Bio::Graphics::Glyph::minmax.3 \
- Bio::Graphics::Glyph::oval.3 \
- Bio::Graphics::Glyph::pentagram.3 \
- Bio::Graphics::Glyph::pinsertion.3 \
- Bio::Graphics::Glyph::primers.3 \
- Bio::Graphics::Glyph::processed_transcript.3 \
- Bio::Graphics::Glyph::protein.3 \
- Bio::Graphics::Glyph::ragged_ends.3 \
- Bio::Graphics::Glyph::redgreen_box.3 \
- Bio::Graphics::Glyph::redgreen_segment.3 \
- Bio::Graphics::Glyph::repeating_shape.3 \
- Bio::Graphics::Glyph::rndrect.3 \
- Bio::Graphics::Glyph::ruler_arrow.3 \
- Bio::Graphics::Glyph::saw_teeth.3 \
- Bio::Graphics::Glyph::segmented_keyglyph.3 \
- Bio::Graphics::Glyph::segments.3 \
- Bio::Graphics::Glyph::so_transcript.3 \
- Bio::Graphics::Glyph::span.3 \
- Bio::Graphics::Glyph::splice_site.3 \
- Bio::Graphics::Glyph::text_in_box.3 \
- Bio::Graphics::Glyph::three_letters.3 \
- Bio::Graphics::Glyph::tic_tac_toe.3 \
- Bio::Graphics::Glyph::toomany.3 \
- Bio::Graphics::Glyph::track.3 \
- Bio::Graphics::Glyph::transcript.3 \
- Bio::Graphics::Glyph::transcript2.3 \
- Bio::Graphics::Glyph::translation.3 \
- Bio::Graphics::Glyph::triangle.3 \
- Bio::Graphics::Glyph::two_bolts.3 \
- Bio::Graphics::Glyph::wave.3 \
- Bio::Graphics::Glyph::weighted_arrow.3 \
- Bio::Graphics::Glyph::whiskerplot.3 \
- Bio::Graphics::Glyph::xyplot.3 \
- Bio::Graphics::Panel.3 \
- Bio::Graphics::Pictogram.3 \
- Bio::Graphics::RendererI.3 \
- Bio::Graphics::Util.3 \
- Bio::IdCollectionI.3 \
- Bio::IdentifiableI.3 \
- Bio::Index::Abstract.3 \
- Bio::Index::AbstractSeq.3 \
- Bio::Index::Blast.3 \
- Bio::Index::EMBL.3 \
- Bio::Index::Fasta.3 \
- Bio::Index::Fastq.3 \
- Bio::Index::GenBank.3 \
- Bio::Index::Hmmer.3 \
- Bio::Index::Qual.3 \
- Bio::Index::SwissPfam.3 \
- Bio::Index::Swissprot.3 \
- Bio::LiveSeq::AARange.3 \
- Bio::LiveSeq::Chain.3 \
- Bio::LiveSeq::ChainI.3 \
- Bio::LiveSeq::DNA.3 \
- Bio::LiveSeq::Exon.3 \
- Bio::LiveSeq::Gene.3 \
- Bio::LiveSeq::IO::BioPerl.3 \
- Bio::LiveSeq::IO::Loader.3 \
- Bio::LiveSeq::Intron.3 \
- Bio::LiveSeq::Mutation.3 \
- Bio::LiveSeq::Mutator.3 \
- Bio::LiveSeq::Prim_Transcript.3 \
- Bio::LiveSeq::Range.3 \
- Bio::LiveSeq::Repeat_Region.3 \
- Bio::LiveSeq::Repeat_Unit.3 \
- Bio::LiveSeq::SeqI.3 \
- Bio::LiveSeq::Transcript.3 \
- Bio::LiveSeq::Translation.3 \
- Bio::LocatableSeq.3 \
- Bio::Location::Atomic.3 \
- Bio::Location::AvWithinCoordPolicy.3 \
- Bio::Location::CoordinatePolicyI.3 \
- Bio::Location::Fuzzy.3 \
- Bio::Location::FuzzyLocationI.3 \
- Bio::Location::NarrowestCoordPolicy.3 \
- Bio::Location::Simple.3 \
- Bio::Location::Split.3 \
- Bio::Location::SplitLocationI.3 \
- Bio::Location::WidestCoordPolicy.3 \
- Bio::LocationI.3 \
- Bio::Map::Clone.3 \
- Bio::Map::Contig.3 \
- Bio::Map::CytoMap.3 \
- Bio::Map::CytoMarker.3 \
- Bio::Map::CytoPosition.3 \
- Bio::Map::EntityI.3 \
- Bio::Map::FPCMarker.3 \
- Bio::Map::LinkageMap.3 \
- Bio::Map::LinkagePosition.3 \
- Bio::Map::MapI.3 \
- Bio::Map::Mappable.3 \
- Bio::Map::MappableI.3 \
- Bio::Map::Marker.3 \
- Bio::Map::MarkerI.3 \
- Bio::Map::Microsatellite.3 \
- Bio::Map::OrderedPosition.3 \
- Bio::Map::OrderedPositionWithDistance.3 \
- Bio::Map::PositionHandler.3 \
- Bio::Map::PositionHandlerI.3 \
- Bio::Map::Physical.3 \
- Bio::Map::Position.3 \
- Bio::Map::PositionI.3 \
- Bio::Map::Relative.3 \
- Bio::Map::RelativeI.3 \
- Bio::Map::SimpleMap.3 \
- Bio::MapIO.3 \
- Bio::MapIO::fpc.3 \
- Bio::MapIO::mapmaker.3 \
- Bio::Matrix::Generic.3 \
- Bio::Matrix::IO.3 \
- Bio::Matrix::IO::phylip.3 \
- Bio::Matrix::IO::scoring.3 \
- Bio::Matrix::MatrixI.3 \
- Bio::Matrix::PSM::IO.3 \
- Bio::Matrix::PSM::IO::mast.3 \
- Bio::Matrix::PSM::IO::masta.3 \
- Bio::Matrix::PSM::IO::meme.3 \
- Bio::Matrix::PSM::IO::psiblast.3 \
- Bio::Matrix::PSM::IO::transfac.3 \
- Bio::Matrix::PSM::InstanceSite.3 \
- Bio::Matrix::PSM::InstanceSiteI.3 \
- Bio::Matrix::PSM::ProtMatrix.3 \
- Bio::Matrix::PSM::ProtPsm.3 \
- Bio::Matrix::PSM::Psm.3 \
- Bio::Matrix::PSM::PsmHeader.3 \
- Bio::Matrix::PSM::PsmHeaderI.3 \
- Bio::Matrix::PSM::PsmI.3 \
- Bio::Matrix::PSM::SiteMatrix.3 \
- Bio::Matrix::PSM::SiteMatrixI.3 \
- Bio::Matrix::PhylipDist.3 \
- Bio::Matrix::Scoring.3 \
- Bio::Ontology::DocumentRegistry.3 \
- Bio::Ontology::GOterm.3 \
- Bio::Ontology::InterProTerm.3 \
- Bio::Ontology::OBOEngine.3 \
- Bio::Ontology::OBOterm.3 \
- Bio::Ontology::Ontology.3 \
- Bio::Ontology::OntologyEngineI.3 \
- Bio::Ontology::OntologyI.3 \
- Bio::OntologyIO::obo.3 \
- Bio::Ontology::OntologyStore.3 \
- Bio::Ontology::Path.3 \
- Bio::Ontology::PathI.3 \
- Bio::Ontology::Relationship.3 \
- Bio::Ontology::RelationshipFactory.3 \
- Bio::Ontology::RelationshipI.3 \
- Bio::Ontology::RelationshipType.3 \
- Bio::Ontology::SimpleGOEngine.3 \
- Bio::Ontology::SimpleGOEngine::GraphAdaptor.3 \
- Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 \
- Bio::Ontology::SimpleOntologyEngine.3 \
- Bio::Ontology::Term.3 \
- Bio::Ontology::TermFactory.3 \
- Bio::Ontology::TermI.3 \
- Bio::OntologyIO.3 \
- Bio::OntologyIO::Handlers::BaseSAXHandler.3 \
- Bio::OntologyIO::Handlers::InterProHandler.3 \
- Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 \
- Bio::OntologyIO::InterProParser.3 \
- Bio::OntologyIO::dagflat.3 \
- Bio::OntologyIO::goflat.3 \
- Bio::OntologyIO::simplehierarchy.3 \
- Bio::OntologyIO::soflat.3 \
- Bio::Perl.3 \
- Bio::Phenotype::Correlate.3 \
- Bio::Phenotype::MeSH::Term.3 \
- Bio::Phenotype::MeSH::Twig.3 \
- Bio::Phenotype::Measure.3 \
- Bio::Phenotype::OMIM::MiniMIMentry.3 \
- Bio::Phenotype::OMIM::OMIMentry.3 \
- Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3 \
- Bio::Phenotype::OMIM::OMIMparser.3 \
- Bio::Phenotype::Phenotype.3 \
- Bio::Phenotype::PhenotypeI.3 \
- Bio::PopGen::Genotype.3 \
- Bio::PopGen::GenotypeI.3 \
- Bio::PopGen::HtSNP.3 \
- Bio::PopGen::IO.3 \
- Bio::PopGen::IO::csv.3 \
- Bio::PopGen::IO::hapmap.3 \
- Bio::PopGen::IO::phase.3 \
- Bio::PopGen::IO::prettybase.3 \
- Bio::PopGen::Individual.3 \
- Bio::PopGen::IndividualI.3 \
- Bio::PopGen::Marker.3 \
- Bio::PopGen::MarkerI.3 \
- Bio::PopGen::PopStats.3 \
- Bio::PopGen::Population.3 \
- Bio::PopGen::PopulationI.3 \
- Bio::PopGen::Simulation::Coalescent.3 \
- Bio::PopGen::Simulation::GeneticDrift.3 \
- Bio::PopGen::Statistics.3 \
- Bio::PopGen::TagHaplotype.3 \
- Bio::PopGen::Utilities.3 \
- Bio::PrimarySeq.3 \
- Bio::PrimarySeqI.3 \
- Bio::PullParserI.3 \
- Bio::Range.3 \
- Bio::RangeI.3 \
- Bio::Restriction::Analysis.3 \
- Bio::Restriction::Enzyme.3 \
- Bio::Restriction::Enzyme::MultiCut.3 \
- Bio::Restriction::Enzyme::MultiSite.3 \
- Bio::Restriction::EnzymeCollection.3 \
- Bio::Restriction::EnzymeI.3 \
- Bio::Restriction::IO.3 \
- Bio::Restriction::IO::bairoch.3 \
- Bio::Restriction::IO::base.3 \
- Bio::Restriction::IO::itype2.3 \
- Bio::Restriction::IO::withrefm.3 \
- Bio::Root::Exception.3 \
- Bio::Root::HTTPget.3 \
- Bio::Root::IO.3 \
- Bio::Root::Root.3 \
- Bio::Root::RootI.3 \
- Bio::Root::Storable.3 \
- Bio::Root::Version.3 \
- Bio::Search::BlastStatistics.3 \
- Bio::Search::BlastUtils.3 \
- Bio::Search::DatabaseI.3 \
- Bio::Search::GenericDatabase.3 \
- Bio::Search::GenericStatistics.3 \
- Bio::Search::HSP::BlastHSP.3 \
- Bio::Search::HSP::FastaHSP.3 \
- Bio::Search::HSP::GenericHSP.3 \
- Bio::Search::HSP::HMMERHSP.3 \
- Bio::Search::HSP::HmmpfamHSP.3 \
- Bio::Search::HSP::HSPFactory.3 \
- Bio::Search::HSP::HSPI.3 \
- Bio::Search::HSP::PSLHSP.3 \
- Bio::Search::HSP::PsiBlastHSP.3 \
- Bio::Search::HSP::PullHSPI.3 \
- Bio::Search::HSP::WABAHSP.3 \
- Bio::Search::Hit::BlastHit.3 \
- Bio::Search::Hit::Fasta.3 \
- Bio::Search::Hit::GenericHit.3 \
- Bio::Search::Hit::HmmpfamHit.3 \
- Bio::Search::Hit::HMMERHit.3 \
- Bio::Search::Hit::HitFactory.3 \
- Bio::Search::Hit::HitI.3 \
- Bio::Search::Hit::PsiBlastHit.3 \
- Bio::Search::Hit::PullHitI.3 \
- Bio::Search::Iteration::GenericIteration.3 \
- Bio::Search::Iteration::IterationI.3 \
- Bio::Search::Processor.3 \
- Bio::Search::Result::BlastResult.3 \
- Bio::Search::Result::GenericResult.3 \
- Bio::Search::Result::HmmpfamResult.3 \
- Bio::Search::Result::HMMERResult.3 \
- Bio::Search::Result::PullResultI.3 \
- Bio::Search::Result::ResultFactory.3 \
- Bio::Search::Result::ResultI.3 \
- Bio::Search::Result::WABAResult.3 \
- Bio::Search::SearchUtils.3 \
- Bio::Search::StatisticsI.3 \
- Bio::SearchDist.3 \
- Bio::SearchIO.3 \
- Bio::SearchIO::EventHandlerI.3 \
- Bio::SearchIO::FastHitEventBuilder.3 \
- Bio::SearchIO::IteratedSearchResultEventBuilder.3 \
- Bio::SearchIO::SearchResultEventBuilder.3 \
- Bio::SearchIO::SearchWriterI.3 \
- Bio::SearchIO::Writer::BSMLResultWriter.3 \
- Bio::SearchIO::Writer::GbrowseGFF.3 \
- Bio::SearchIO::Writer::HSPTableWriter.3 \
- Bio::SearchIO::Writer::HTMLResultWriter.3 \
- Bio::SearchIO::Writer::HitTableWriter.3 \
- Bio::SearchIO::Writer::ResultTableWriter.3 \
- Bio::SearchIO::Writer::TextResultWriter.3 \
- Bio::SearchIO::axt.3 \
- Bio::SearchIO::blast.3 \
- Bio::SearchIO::blasttable.3 \
- Bio::SearchIO::blastxml.3 \
- Bio::SearchIO::exonerate.3 \
- Bio::SearchIO::fasta.3 \
- Bio::SearchIO::hmmer.3 \
- Bio::SearchIO::hmmer_pull.3 \
- Bio::SearchIO::megablast.3 \
- Bio::SearchIO::psl.3 \
- Bio::SearchIO::sim4.3 \
- Bio::SearchIO::waba.3 \
- Bio::SearchIO::wise.3 \
- Bio::Seq.3 \
- Bio::Seq::BaseSeqProcessor.3 \
- Bio::Seq::EncodedSeq.3 \
- Bio::Seq::LargeLocatableSeq.3 \
- Bio::Seq::LargePrimarySeq.3 \
- Bio::Seq::LargeSeq.3 \
- Bio::Seq::LargeSeqI.3 \
- Bio::Seq::Meta.3 \
- Bio::Seq::Meta::Array.3 \
- Bio::Seq::MetaI.3 \
- Bio::Seq::PrimaryQual.3 \
- Bio::Seq::PrimedSeq.3 \
- Bio::Seq::QualI.3 \
- Bio::Seq::Quality.3 \
- Bio::Seq::RichSeq.3 \
- Bio::Seq::RichSeqI.3 \
- Bio::Seq::SeqBuilder.3 \
- Bio::Seq::SeqFactory.3 \
- Bio::Seq::SeqFastaSpeedFactory.3 \
- Bio::Seq::SeqWithQuality.3 \
- Bio::Seq::SequenceTrace.3 \
- Bio::Seq::TraceI.3 \
- Bio::SeqAnalysisParserI.3 \
- Bio::SeqFeature::Annotated.3 \
- Bio::SeqFeature::AnnotationAdaptor.3 \
- Bio::SeqFeature::Collection.3 \
- Bio::SeqFeature::CollectionI.3 \
- Bio::SeqFeature::Computation.3 \
- Bio::SeqFeature::FeaturePair.3 \
- Bio::SeqFeature::Gene::Exon.3 \
- Bio::SeqFeature::Gene::ExonI.3 \
- Bio::SeqFeature::Gene::GeneStructure.3 \
- Bio::SeqFeature::Gene::GeneStructureI.3 \
- Bio::SeqFeature::Gene::Intron.3 \
- Bio::SeqFeature::Gene::NC_Feature.3 \
- Bio::SeqFeature::Gene::Poly_A_site.3 \
- Bio::SeqFeature::Gene::Promoter.3 \
- Bio::SeqFeature::Gene::Transcript.3 \
- Bio::SeqFeature::Gene::TranscriptI.3 \
- Bio::SeqFeature::Gene::UTR.3 \
- Bio::SeqFeature::Generic.3 \
- Bio::SeqFeature::PositionProxy.3 \
- Bio::SeqFeature::Primer.3 \
- Bio::SeqFeature::SiRNA::Oligo.3 \
- Bio::SeqFeature::SiRNA::Pair.3 \
- Bio::SeqFeature::Similarity.3 \
- Bio::SeqFeature::SimilarityPair.3 \
- Bio::SeqFeature::Tools::FeatureNamer.3 \
- Bio::SeqFeature::Tools::IDHandler.3 \
- Bio::SeqFeature::Tools::TypeMapper.3 \
- Bio::SeqFeature::Tools::Unflattener.3 \
- Bio::SeqFeature::TypedSeqFeatureI.3 \
- Bio::SeqFeatureI.3 \
- Bio::SeqI.3 \
- Bio::SeqIO.3 \
- Bio::SeqIO::FTHelper.3 \
- Bio::SeqIO::MultiFile.3 \
- Bio::SeqIO::abi.3 \
- Bio::SeqIO::ace.3 \
- Bio::SeqIO::agave.3 \
- Bio::SeqIO::alf.3 \
- Bio::SeqIO::asciitree.3 \
- Bio::SeqIO::bsml.3 \
- Bio::SeqIO::bsml_sax.3 \
- Bio::SeqIO::chadoxml.3 \
- Bio::SeqIO::chaos.3 \
- Bio::SeqIO::chaosxml.3 \
- Bio::SeqIO::ctf.3 \
- Bio::SeqIO::embl.3 \
- Bio::SeqIO::entrezgene.3 \
- Bio::SeqIO::excel.3 \
- Bio::SeqIO::exp.3 \
- Bio::SeqIO::fasta.3 \
- Bio::SeqIO::fastq.3 \
- Bio::SeqIO::game.3 \
- Bio::SeqIO::game::featHandler.3 \
- Bio::SeqIO::game::gameHandler.3 \
- Bio::SeqIO::game::gameSubs.3 \
- Bio::SeqIO::game::gameWriter.3 \
- Bio::SeqIO::game::seqHandler.3 \
- Bio::SeqIO::gcg.3 \
- Bio::SeqIO::genbank.3 \
- Bio::SeqIO::interpro.3 \
- Bio::SeqIO::kegg.3 \
- Bio::SeqIO::largefasta.3 \
- Bio::SeqIO::lasergene.3 \
- Bio::SeqIO::locuslink.3 \
- Bio::SeqIO::metafasta.3 \
- Bio::SeqIO::phd.3 \
- Bio::SeqIO::pir.3 \
- Bio::SeqIO::pln.3 \
- Bio::SeqIO::qual.3 \
- Bio::SeqIO::raw.3 \
- Bio::SeqIO::scf.3 \
- Bio::SeqIO::strider.3 \
- Bio::SeqIO::swiss.3 \
- Bio::SeqIO::tab.3 \
- Bio::SeqIO::table.3 \
- Bio::SeqIO::tigr.3 \
- Bio::SeqIO::tigrxml.3 \
- Bio::SeqIO::tinyseq.3 \
- Bio::SeqIO::tinyseq::tinyseqHandler.3 \
- Bio::SeqIO::ztr.3 \
- Bio::SeqUtils.3 \
- Bio::SimpleAlign.3 \
- Bio::SimpleAnalysisI.3 \
- Bio::Species.3 \
- Bio::Structure::Atom.3 \
- Bio::Structure::Chain.3 \
- Bio::Structure::Entry.3 \
- Bio::Structure::IO.3 \
- Bio::Structure::IO::pdb.3 \
- Bio::Structure::Model.3 \
- Bio::Structure::Residue.3 \
- Bio::Structure::SecStr::DSSP::Res.3 \
- Bio::Structure::SecStr::STRIDE::Res.3 \
- Bio::Structure::StructureI.3 \
- Bio::Symbol::Alphabet.3 \
- Bio::Symbol::AlphabetI.3 \
- Bio::Symbol::DNAAlphabet.3 \
- Bio::Symbol::ProteinAlphabet.3 \
- Bio::Symbol::Symbol.3 \
- Bio::Symbol::SymbolI.3 \
- Bio::Taxon.3 \
- Bio::Taxonomy.3 \
- Bio::Taxonomy::FactoryI.3 \
- Bio::Taxonomy::Node.3 \
- Bio::Taxonomy::Taxon.3 \
- Bio::Taxonomy::Tree.3 \
- Bio::Tools::AlignFactory.3 \
- Bio::Tools::Alignment::Consed.3 \
- Bio::Tools::Alignment::Trim.3 \
- Bio::Tools::Analysis::DNA::ESEfinder.3 \
- Bio::Tools::Analysis::Protein::Domcut.3 \
- Bio::Tools::Analysis::Protein::ELM.3 \
- Bio::Tools::Analysis::Protein::GOR4.3 \
- Bio::Tools::Analysis::Protein::HNN.3 \
- Bio::Tools::Analysis::Protein::Mitoprot.3 \
- Bio::Tools::Analysis::Protein::NetPhos.3 \
- Bio::Tools::Analysis::Protein::Scansite.3 \
- Bio::Tools::Analysis::Protein::Sopma.3 \
- Bio::Tools::Analysis::SimpleAnalysisBase.3 \
- Bio::Tools::AnalysisResult.3 \
- Bio::Tools::BPbl2seq.3 \
- Bio::Tools::BPlite.3 \
- Bio::Tools::BPlite::HSP.3 \
- Bio::Tools::BPlite::Iteration.3 \
- Bio::Tools::BPlite::Sbjct.3 \
- Bio::Tools::BPpsilite.3 \
- Bio::Tools::Blat.3 \
- Bio::Tools::CodonTable.3 \
- Bio::Tools::Coil.3 \
- Bio::Tools::ECnumber.3 \
- Bio::Tools::EMBOSS::Palindrome.3 \
- Bio::Tools::EPCR.3 \
- Bio::Tools::ESTScan.3 \
- Bio::Tools::Eponine.3 \
- Bio::Tools::Est2Genome.3 \
- Bio::Tools::ERPIN.3 \
- Bio::Tools::Fgenesh.3 \
- Bio::Tools::FootPrinter.3 \
- Bio::Tools::GFF.3 \
- Bio::Tools::Gel.3 \
- Bio::Tools::Geneid.3 \
- Bio::Tools::Genemark.3 \
- Bio::Tools::Genewise.3 \
- Bio::Tools::Genomewise.3 \
- Bio::Tools::Genscan.3 \
- Bio::Tools::Glimmer.3 \
- Bio::Tools::Grail.3 \
- Bio::Tools::GuessSeqFormat.3 \
- Bio::Tools::HMM.3 \
- Bio::Tools::HMMER::Domain.3 \
- Bio::Tools::HMMER::Results.3 \
- Bio::Tools::HMMER::Set.3 \
- Bio::Tools::Hmmpfam.3 \
- Bio::Tools::IUPAC.3 \
- Bio::Tools::Lucy.3 \
- Bio::Tools::MZEF.3 \
- Bio::Tools::OddCodes.3 \
- Bio::Tools::Phylo::Molphy.3 \
- Bio::Tools::Phylo::Molphy::Result.3 \
- Bio::Tools::Phylo::PAML.3 \
- Bio::Tools::Phylo::PAML::ModelResult.3 \
- Bio::Tools::Phylo::PAML::Result.3 \
- Bio::Tools::Phylo::Phylip::ProtDist.3 \
- Bio::Tools::Prediction::Exon.3 \
- Bio::Tools::Prediction::Gene.3 \
- Bio::Tools::Primer3.3 \
- Bio::Tools::Primer::Assessor::Base.3 \
- Bio::Tools::Primer::AssessorI.3 \
- Bio::Tools::Primer::Feature.3 \
- Bio::Tools::Primer::Pair.3 \
- Bio::Tools::Prints.3 \
- Bio::Tools::Profile.3 \
- Bio::Tools::Promoterwise.3 \
- Bio::Tools::PrositeScan.3 \
- Bio::Tools::Pseudowise.3 \
- Bio::Tools::QRNA.3 \
- Bio::Tools::RandomDistFunctions.3 \
- Bio::Tools::RepeatMasker.3 \
- Bio::Tools::RestrictionEnzyme.3 \
- Bio::Tools::RNAMotif.3 \
- Bio::Tools::Run::GenericParameters.3 \
- Bio::Tools::Run::ParametersI.3 \
- Bio::Tools::Run::RemoteBlast.3 \
- Bio::Tools::Run::StandAloneBlast.3 \
- Bio::Tools::Run::WrapperBase.3 \
- Bio::Tools::Seg.3 \
- Bio::Tools::SeqPattern.3 \
- Bio::Tools::SeqStats.3 \
- Bio::Tools::SeqWords.3 \
- Bio::Tools::SiRNA.3 \
- Bio::Tools::SiRNA::Ruleset::saigo.3 \
- Bio::Tools::SiRNA::Ruleset::tuschl.3 \
- Bio::Tools::Sigcleave.3 \
- Bio::Tools::Signalp.3 \
- Bio::Tools::Sim4::Exon.3 \
- Bio::Tools::Sim4::Results.3 \
- Bio::Tools::Spidey::Exon.3 \
- Bio::Tools::Spidey::Results.3 \
- Bio::Tools::Tmhmm.3 \
- Bio::Tools::dpAlign.3 \
- Bio::Tools::ipcress.3 \
- Bio::Tools::isPcr.3 \
- Bio::Tools::pICalculator.3 \
- Bio::Tools::pSW.3 \
- Bio::Tools::tRNAscanSE.3 \
- Bio::Tree::AlleleNode.3 \
- Bio::Tree::Compatible.3 \
- Bio::Tree::DistanceFactory.3 \
- Bio::Tree::Draw::Cladogram.3 \
- Bio::Tree::Node.3 \
- Bio::Tree::NodeI.3 \
- Bio::Tree::NodeNHX.3 \
- Bio::Tree::RandomFactory.3 \
- Bio::Tree::Statistics.3 \
- Bio::Tree::Tree.3 \
- Bio::Tree::TreeFunctionsI.3 \
- Bio::Tree::TreeI.3 \
- Bio::TreeIO.3 \
- Bio::TreeIO::TreeEventBuilder.3 \
- Bio::TreeIO::cluster.3 \
- Bio::TreeIO::lintree.3 \
- Bio::TreeIO::newick.3 \
- Bio::TreeIO::nexus.3 \
- Bio::TreeIO::nhx.3 \
- Bio::TreeIO::pag.3 \
- Bio::TreeIO::svggraph.3 \
- Bio::TreeIO::tabtree.3 \
- Bio::UpdateableSeqI.3 \
- Bio::Variation::AAChange.3 \
- Bio::Variation::AAReverseMutate.3 \
- Bio::Variation::Allele.3 \
- Bio::Variation::DNAMutation.3 \
- Bio::Variation::IO.3 \
- Bio::Variation::IO::flat.3 \
- Bio::Variation::IO::xml.3 \
- Bio::Variation::RNAChange.3 \
- Bio::Variation::SNP.3 \
- Bio::Variation::SeqDiff.3 \
- Bio::Variation::VariantI.3 \
- Bio::WebAgent.3
-
-.include <bsd.port.pre.mk>
-
-.if ${PERL_LEVEL} < 500800
-BUILD_DEPENDS+= ${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp
-.if ${PERL_LEVEL} < 500600
-IGNORE= requires Perl 5.6 or better
-.endif
-.endif
-
-# now install all extra stuff (docs, examples, scripts, models)
-post-install:
- ${MKDIR} ${DATADIR}
- ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
-.if !defined(NOPORTEXAMPLES)
- ${MKDIR} ${EXAMPLESDIR}
- ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
-.endif
-.if !defined(NOPORTDOCS)
- ${MKDIR} ${DOCSDIR}
-.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README
- ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
-.endfor
- ${CP} -R ${WRKSRC}/doc ${DOCSDIR}
-.endif
-
-.include <bsd.port.post.mk>
diff --git a/biology/p5-bioperl-devel/distinfo b/biology/p5-bioperl-devel/distinfo
deleted file mode 100644
index 05e52069e19b..000000000000
--- a/biology/p5-bioperl-devel/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 (bioperl-1.5.2_102.tar.gz) = 4890481c5beb33e129b65b922fb0c126
-SHA256 (bioperl-1.5.2_102.tar.gz) = 277c74c785afc05ad1d9dbe938677639c33130487d15bdc4a7a10e033137bada
-SIZE (bioperl-1.5.2_102.tar.gz) = 5919092
diff --git a/biology/p5-bioperl-devel/files/patch-Build.PL b/biology/p5-bioperl-devel/files/patch-Build.PL
deleted file mode 100644
index 58442ee46006..000000000000
--- a/biology/p5-bioperl-devel/files/patch-Build.PL
+++ /dev/null
@@ -1,19 +0,0 @@
---- Build.PL.orig Wed Feb 14 05:37:47 2007
-+++ Build.PL Sun Jun 15 02:24:07 2008
-@@ -32,7 +32,6 @@
- 'Test::More' => 0,
- 'Module::Build' => 0.2805,
- 'Test::Harness' => 2.62,
-- 'CPAN' => 1.81
- },
- recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
- 'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
-@@ -174,7 +173,7 @@
- }
-
- sub prompt_for_biodbgff {
-- my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
-+ my $proceed = undef; # $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
-
- if ($proceed) {
- my @driver_choices;
diff --git a/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm b/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm
deleted file mode 100644
index 5f627035c3f3..000000000000
--- a/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm
+++ /dev/null
@@ -1,20 +0,0 @@
---- ModuleBuildBioperl.pm.orig 2007-02-14 05:37:47.000000000 -0600
-+++ ModuleBuildBioperl.pm 2008-10-17 23:16:52.000000000 -0500
-@@ -93,7 +93,7 @@
- closedir($scripts_dir);
- my $question = $int_ok ? "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll Bioperl scripts or [n]one?";
-
-- my $prompt = $self->prompt($question, 'a');
-+ my $prompt = 'a'; # $self->prompt($question, 'a');
-
- if ($prompt =~ /^[aA]/) {
- $self->log_info(" - will install all scripts\n");
-@@ -328,7 +328,7 @@
-
- $status->{message} .= "\n (wanted for $why, used by $by_what)";
-
-- my $installed = $self->install_optional($modname, $preferred_version, $status->{message});
-+ my $installed = 'skip'; # $self->install_optional($modname, $preferred_version, $status->{message});
- next if $installed eq 'ok';
- $status->{message} = $installed unless $installed eq 'skip';
- }
diff --git a/biology/p5-bioperl-devel/pkg-descr b/biology/p5-bioperl-devel/pkg-descr
deleted file mode 100644
index 6ea2aedf8a8b..000000000000
--- a/biology/p5-bioperl-devel/pkg-descr
+++ /dev/null
@@ -1,11 +0,0 @@
-The Bioperl Project is an international association of developers of open
-source Perl tools for bioinformatics, genomics and life science research.
-
-Bioperl is a collection of object-oriented Perl modules created by the
-Bioperl Project. It forms the basis of a large number of bioinformatics and
-genomics applications.
-
-(For an interesting aside on "How Perl saved the Human Genome Project", see
-http://bioperl.org/GetStarted/tpj_ls_bio.html)
-
-WWW: http://bioperl.org/
diff --git a/biology/p5-bioperl-devel/pkg-plist b/biology/p5-bioperl-devel/pkg-plist
deleted file mode 100644
index ef4214006d49..000000000000
--- a/biology/p5-bioperl-devel/pkg-plist
+++ /dev/null
@@ -1,1272 +0,0 @@
-bin/bp_sreformat.pl
-bin/bp_contig_draw.pl
-bin/bp_tree2pag.pl
-bin/bp_meta_gff.pl
-bin/bp_flanks.pl
-bin/bp_heterogeneity_test.pl
-bin/bp_feature_draw.pl
-bin/bp_biogetseq.pl
-bin/bp_genbank2gff.pl
-bin/bp_seqfeature_load.pl
-bin/bp_seq_length.pl
-bin/bp_frend.pl
-bin/bp_fastam9_to_table.pl
-bin/bp_taxid4species.pl
-bin/bp_glyphs1-demo.pl
-bin/bp_blast2tree.pl
-bin/bp_gccalc.pl
-bin/bp_seqret.pl
-bin/bp_query_entrez_taxa.pl
-bin/bp_glyphs2-demo.pl
-bin/bp_search2alnblocks.pl
-bin/bp_taxonomy2tree.pl
-bin/bp_mask_by_search.pl
-bin/bp_aacomp.pl
-bin/bp_composite_LD.pl
-bin/bp_biblio.pl
-bin/bp_process_wormbase.pl
-bin/bp_embl2picture.pl
-bin/bp_local_taxonomydb_query.pl
-bin/bp_genbank2gff3.pl
-bin/bp_search2BSML.pl
-bin/bp_seqconvert.pl
-bin/bp_parse_hmmsearch.pl
-bin/bp_nexus2nh.pl
-bin/bp_nrdb.pl
-bin/bp_split_seq.pl
-bin/bp_filter_search.pl
-bin/bp_generate_histogram.pl
-bin/bp_load_gff.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_process_gadfly.pl
-bin/bp_hmmer_to_table.pl
-bin/bp_bulk_load_gff.pl
-bin/bp_biofetch_genbank_proxy.pl
-bin/bp_extract_feature_seq.pl
-bin/bp_search2gff.pl
-bin/bp_unflatten_seq.pl
-bin/bp_make_mrna_protein.pl
-bin/bp_mrtrans.pl
-bin/bp_search2tribe.pl
-bin/bp_bioflat_index.pl
-bin/bp_pairwise_kaks.pl
-bin/bp_fast_load_gff.pl
-bin/bp_chaos_plot.pl
-bin/bp_classify_hits_kingdom.pl
-bin/bp_remote_blast.pl
-bin/bp_search2table.pl
-bin/bp_translate_seq.pl
-bin/bp_search_overview.pl
-bin/bp_pg_bulk_load_gff.pl
-%%SITE_PERL%%/Bio/Align/Utilities.pm
-%%SITE_PERL%%/Bio/Align/AlignI.pm
-%%SITE_PERL%%/Bio/Align/DNAStatistics.pm
-%%SITE_PERL%%/Bio/Align/ProteinStatistics.pm
-%%SITE_PERL%%/Bio/Align/StatisticsI.pm
-%%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm
-%%SITE_PERL%%/Bio/AlignIO/mega.pm
-%%SITE_PERL%%/Bio/AlignIO/prodom.pm
-%%SITE_PERL%%/Bio/AlignIO/emboss.pm
-%%SITE_PERL%%/Bio/AlignIO/mase.pm
-%%SITE_PERL%%/Bio/AlignIO/phylip.pm
-%%SITE_PERL%%/Bio/AlignIO/maf.pm
-%%SITE_PERL%%/Bio/AlignIO/pfam.pm
-%%SITE_PERL%%/Bio/AlignIO/nexus.pm
-%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
-%%SITE_PERL%%/Bio/AlignIO/msf.pm
-%%SITE_PERL%%/Bio/AlignIO/psi.pm
-%%SITE_PERL%%/Bio/AlignIO/po.pm
-%%SITE_PERL%%/Bio/AlignIO/clustalw.pm
-%%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm
-%%SITE_PERL%%/Bio/AlignIO/fasta.pm
-%%SITE_PERL%%/Bio/AlignIO/metafasta.pm
-%%SITE_PERL%%/Bio/AlignIO/stockholm.pm
-%%SITE_PERL%%/Bio/AlignIO/meme.pm
-%%SITE_PERL%%/Bio/AlignIO/selex.pm
-%%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm
-%%SITE_PERL%%/Bio/Annotation/Target.pm
-%%SITE_PERL%%/Bio/Annotation/SimpleValue.pm
-%%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm
-%%SITE_PERL%%/Bio/Annotation/Reference.pm
-%%SITE_PERL%%/Bio/Annotation/Collection.pm
-%%SITE_PERL%%/Bio/Annotation/DBLink.pm
-%%SITE_PERL%%/Bio/Annotation/StructuredValue.pm
-%%SITE_PERL%%/Bio/Annotation/Comment.pm
-%%SITE_PERL%%/Bio/Annotation/TypeManager.pm
-%%SITE_PERL%%/Bio/Assembly/IO/phrap.pm
-%%SITE_PERL%%/Bio/Assembly/IO/ace.pm
-%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm
-%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm
-%%SITE_PERL%%/Bio/Assembly/Singlet.pm
-%%SITE_PERL%%/Bio/Assembly/Contig.pm
-%%SITE_PERL%%/Bio/Assembly/Scaffold.pm
-%%SITE_PERL%%/Bio/Assembly/IO.pm
-%%SITE_PERL%%/Bio/Biblio/IO/medline2ref.pm
-%%SITE_PERL%%/Bio/Biblio/IO/pubmedxml.pm
-%%SITE_PERL%%/Bio/Biblio/IO/pubmed2ref.pm
-%%SITE_PERL%%/Bio/Biblio/IO/medlinexml.pm
-%%SITE_PERL%%/Bio/Biblio/PubmedBookArticle.pm
-%%SITE_PERL%%/Bio/Biblio/Provider.pm
-%%SITE_PERL%%/Bio/Biblio/IO.pm
-%%SITE_PERL%%/Bio/Biblio/BiblioBase.pm
-%%SITE_PERL%%/Bio/Biblio/Thesis.pm
-%%SITE_PERL%%/Bio/Biblio/Article.pm
-%%SITE_PERL%%/Bio/Biblio/Organisation.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineJournalArticle.pm
-%%SITE_PERL%%/Bio/Biblio/BookArticle.pm
-%%SITE_PERL%%/Bio/Biblio/Journal.pm
-%%SITE_PERL%%/Bio/Biblio/PubmedJournalArticle.pm
-%%SITE_PERL%%/Bio/Biblio/Ref.pm
-%%SITE_PERL%%/Bio/Biblio/TechReport.pm
-%%SITE_PERL%%/Bio/Biblio/Person.pm
-%%SITE_PERL%%/Bio/Biblio/WebResource.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineBook.pm
-%%SITE_PERL%%/Bio/Biblio/JournalArticle.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineBookArticle.pm
-%%SITE_PERL%%/Bio/Biblio/Patent.pm
-%%SITE_PERL%%/Bio/Biblio/Service.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineArticle.pm
-%%SITE_PERL%%/Bio/Biblio/PubmedArticle.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineJournal.pm
-%%SITE_PERL%%/Bio/Biblio/Proceeding.pm
-%%SITE_PERL%%/Bio/Biblio/Book.pm
-%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm
-%%SITE_PERL%%/Bio/Cluster/UniGene.pm
-%%SITE_PERL%%/Bio/Cluster/FamilyI.pm
-%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm
-%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm
-%%SITE_PERL%%/Bio/ClusterIO/unigene.pm
-%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm
-%%SITE_PERL%%/Bio/CodonUsage/Table.pm
-%%SITE_PERL%%/Bio/CodonUsage/IO.pm
-%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm
-%%SITE_PERL%%/Bio/Coordinate/Result/Match.pm
-%%SITE_PERL%%/Bio/Coordinate/Graph.pm
-%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm
-%%SITE_PERL%%/Bio/Coordinate/Result.pm
-%%SITE_PERL%%/Bio/Coordinate/MapperI.pm
-%%SITE_PERL%%/Bio/Coordinate/Utils.pm
-%%SITE_PERL%%/Bio/Coordinate/Chain.pm
-%%SITE_PERL%%/Bio/Coordinate/Collection.pm
-%%SITE_PERL%%/Bio/Coordinate/Pair.pm
-%%SITE_PERL%%/Bio/Coordinate/ResultI.pm
-%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
-%%SITE_PERL%%/Bio/DB/Biblio/pdf.pm
-%%SITE_PERL%%/Bio/DB/Biblio/biofetch.pm
-%%SITE_PERL%%/Bio/DB/Biblio/eutils.pm
-%%SITE_PERL%%/Bio/DB/Biblio/soap.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/Cookie.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/elink.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/esearch.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/einfo.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/efetch.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/epost.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/esummary.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/ElinkData.pm
-%%SITE_PERL%%/Bio/DB/EUtilities/egquery.pm
-%%SITE_PERL%%/Bio/DB/Expression/geo.pm
-%%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm
-%%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm
-%%SITE_PERL%%/Bio/DB/Flat/BDB/fasta.pm
-%%SITE_PERL%%/Bio/DB/Flat/BDB/swissprot.pm
-%%SITE_PERL%%/Bio/DB/Flat/BDB/embl.pm
-%%SITE_PERL%%/Bio/DB/Flat/BDB.pm
-%%SITE_PERL%%/Bio/DB/Flat/BinarySearch.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysql.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/iterator.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracle.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/iterator.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/ace.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/so_transcript.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/alignment.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/match.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/transcript.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/none.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/clone.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/coding.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/processed_transcript.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
-%%SITE_PERL%%/Bio/DB/GFF/Util/Rearrange.pm
-%%SITE_PERL%%/Bio/DB/GFF/Util/Binning.pm
-%%SITE_PERL%%/Bio/DB/GFF/Feature.pm
-%%SITE_PERL%%/Bio/DB/GFF/Typename.pm
-%%SITE_PERL%%/Bio/DB/GFF/Homol.pm
-%%SITE_PERL%%/Bio/DB/GFF/Segment.pm
-%%SITE_PERL%%/Bio/DB/GFF/Featname.pm
-%%SITE_PERL%%/Bio/DB/GFF/Aggregator.pm
-%%SITE_PERL%%/Bio/DB/GFF/RelSegment.pm
-%%SITE_PERL%%/Bio/DB/Query/WebQuery.pm
-%%SITE_PERL%%/Bio/DB/Query/GenBank.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/mysql.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/Iterator.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store/bdb.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store/GFF3Loader.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store/memory.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store/berkeleydb.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedFeatureI.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Store.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/Segment.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedFeature.pm
-%%SITE_PERL%%/Bio/DB/SeqVersion/gi.pm
-%%SITE_PERL%%/Bio/DB/Taxonomy/list.pm
-%%SITE_PERL%%/Bio/DB/Taxonomy/entrez.pm
-%%SITE_PERL%%/Bio/DB/Taxonomy/flatfile.pm
-%%SITE_PERL%%/Bio/DB/Flat.pm
-%%SITE_PERL%%/Bio/DB/SwissProt.pm
-%%SITE_PERL%%/Bio/DB/BiblioI.pm
-%%SITE_PERL%%/Bio/DB/Failover.pm
-%%SITE_PERL%%/Bio/DB/UpdateableSeqI.pm
-%%SITE_PERL%%/Bio/DB/RefSeq.pm
-%%SITE_PERL%%/Bio/DB/NCBIHelper.pm
-%%SITE_PERL%%/Bio/DB/Fasta.pm
-%%SITE_PERL%%/Bio/DB/ReferenceI.pm
-%%SITE_PERL%%/Bio/DB/RandomAccessI.pm
-%%SITE_PERL%%/Bio/DB/BioFetch.pm
-%%SITE_PERL%%/Bio/DB/WebDBSeqI.pm
-%%SITE_PERL%%/Bio/DB/SeqFeature.pm
-%%SITE_PERL%%/Bio/DB/SeqVersion.pm
-%%SITE_PERL%%/Bio/DB/SeqI.pm
-%%SITE_PERL%%/Bio/DB/GenBank.pm
-%%SITE_PERL%%/Bio/DB/MeSH.pm
-%%SITE_PERL%%/Bio/DB/EMBL.pm
-%%SITE_PERL%%/Bio/DB/Taxonomy.pm
-%%SITE_PERL%%/Bio/DB/DBFetch.pm
-%%SITE_PERL%%/Bio/DB/Ace.pm
-%%SITE_PERL%%/Bio/DB/Expression.pm
-%%SITE_PERL%%/Bio/DB/InMemoryCache.pm
-%%SITE_PERL%%/Bio/DB/EntrezGene.pm
-%%SITE_PERL%%/Bio/DB/FileCache.pm
-%%SITE_PERL%%/Bio/DB/SeqHound.pm
-%%SITE_PERL%%/Bio/DB/QueryI.pm
-%%SITE_PERL%%/Bio/DB/XEMBL.pm
-%%SITE_PERL%%/Bio/DB/EUtilities.pm
-%%SITE_PERL%%/Bio/DB/XEMBLService.pm
-%%SITE_PERL%%/Bio/DB/CUTG.pm
-%%SITE_PERL%%/Bio/DB/Universal.pm
-%%SITE_PERL%%/Bio/DB/GFF.pm
-%%SITE_PERL%%/Bio/DB/GDB.pm
-%%SITE_PERL%%/Bio/DB/Registry.pm
-%%SITE_PERL%%/Bio/DB/GenericWebDBI.pm
-%%SITE_PERL%%/Bio/DB/LocationI.pm
-%%SITE_PERL%%/Bio/DB/GenPept.pm
-%%SITE_PERL%%/Bio/Das/SegmentI.pm
-%%SITE_PERL%%/Bio/Das/FeatureTypeI.pm
-%%SITE_PERL%%/Bio/Event/EventHandlerI.pm
-%%SITE_PERL%%/Bio/Event/EventGeneratorI.pm
-%%SITE_PERL%%/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
-%%SITE_PERL%%/Bio/Expression/FeatureSet/FeatureSetMas50.pm
-%%SITE_PERL%%/Bio/Expression/ProbeI.pm
-%%SITE_PERL%%/Bio/Expression/DataSet.pm
-%%SITE_PERL%%/Bio/Expression/Platform.pm
-%%SITE_PERL%%/Bio/Expression/FeatureGroup.pm
-%%SITE_PERL%%/Bio/Expression/FeatureI.pm
-%%SITE_PERL%%/Bio/Expression/Contact.pm
-%%SITE_PERL%%/Bio/Expression/Sample.pm
-%%SITE_PERL%%/Bio/Factory/ObjectFactory.pm
-%%SITE_PERL%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/LocationFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/DriverFactory.pm
-%%SITE_PERL%%/Bio/Factory/ObjectFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/HitFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/ApplicationFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/FTLocationFactory.pm
-%%SITE_PERL%%/Bio/Factory/SequenceProcessorI.pm
-%%SITE_PERL%%/Bio/Factory/MapFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/AnalysisI.pm
-%%SITE_PERL%%/Bio/Factory/ObjectBuilderI.pm
-%%SITE_PERL%%/Bio/Factory/ResultFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/SequenceFactoryI.pm
-%%SITE_PERL%%/Bio/Factory/SequenceStreamI.pm
-%%SITE_PERL%%/Bio/Factory/SeqAnalysisParserFactory.pm
-%%SITE_PERL%%/Bio/Factory/TreeFactoryI.pm
-%%SITE_PERL%%/Bio/FeatureIO/bed.pm
-%%SITE_PERL%%/Bio/FeatureIO/interpro.pm
-%%SITE_PERL%%/Bio/FeatureIO/gff.pm
-%%SITE_PERL%%/Bio/FeatureIO/gtf.pm
-%%SITE_PERL%%/Bio/FeatureIO/ptt.pm
-%%SITE_PERL%%/Bio/Graph/IO/dip.pm
-%%SITE_PERL%%/Bio/Graph/IO/psi_xml.pm
-%%SITE_PERL%%/Bio/Graph/SimpleGraph/Traversal.pm
-%%SITE_PERL%%/Bio/Graph/Edge.pm
-%%SITE_PERL%%/Bio/Graph/ProteinGraph.pm
-%%SITE_PERL%%/Bio/Graph/SimpleGraph.pm
-%%SITE_PERL%%/Bio/Graph/IO.pm
-%%SITE_PERL%%/Bio/Graphics/FeatureFile/Iterator.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wave.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/segmented_keyglyph.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/box.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/cds.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/extending_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/so_transcript.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/gene.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/group.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/whiskerplot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/processed_transcript.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/minmax.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/generic.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/merge_parts.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/rndrect.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/two_bolts.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/three_letters.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ex.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/protein.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/pentagram.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/diamond.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ellipse.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/saw_teeth.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/oval.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/anchored_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/pinsertion.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/toomany.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/graded_segments.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/dna.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/image.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/triangle.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/alignment.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ragged_ends.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/lightning.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/redgreen_box.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/christmas_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/Factory.pm
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diff --git a/biology/p5-bioperl-run-devel/Makefile b/biology/p5-bioperl-run-devel/Makefile
deleted file mode 100644
index a1d374b88660..000000000000
--- a/biology/p5-bioperl-run-devel/Makefile
+++ /dev/null
@@ -1,392 +0,0 @@
-# New ports collection makefile for: p5-bioperl-run-devel
-# Date created: 21 February 2006
-# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net>
-#
-# $FreeBSD$
-#
-
-PORTNAME= bioperl-run
-PORTVERSION= 1.5.1
-PORTREVISION= 1
-CATEGORIES= biology perl5
-MASTER_SITES= http://bioperl.org/DIST/
-PKGNAMEPREFIX= p5-
-
-MAINTAINER= mauricio@arareko.net
-COMMENT= Wrapper modules for common bioinformatics tools (developer release)
-
-BUILD_DEPENDS= p5-bioperl=1.5.1_1:${PORTSDIR}/biology/p5-bioperl-devel \
- ${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
-RUN_DEPENDS= ${BUILD_DEPENDS}
-
-BROKEN= this port needs dependency update to p5-bioperl=1.5.2 and Build.PL mechanism
-
-CONFLICTS= p5-bioperl-run-1.[02468]*
-
-LATEST_LINK= p5-bioperl-run-devel
-
-DEPRECATED= no longer under development
-EXPIRATION_DATE= 2009-05-31
-
-PERL_CONFIGURE= YES
-
-MAN3= Bio::Factory::EMBOSS.3 \
- Bio::Installer::Clustalw.3 \
- Bio::Installer::EMBOSS.3 \
- Bio::Installer::Generic.3 \
- Bio::Installer::PAML.3 \
- Bio::Installer::Probcons.3 \
- Bio::Installer::TCoffee.3 \
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- Bio::Tools::Run::Alignment::DBA.3 \
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- Bio::Tools::Run::Alignment::Lagan.3 \
- Bio::Tools::Run::Alignment::MAFFT.3 \
- Bio::Tools::Run::Alignment::Muscle.3 \
- Bio::Tools::Run::Alignment::Probcons.3 \
- Bio::Tools::Run::Alignment::Sim4.3 \
- Bio::Tools::Run::Alignment::StandAloneFasta.3 \
- Bio::Tools::Run::Alignment::TCoffee.3 \
- Bio::Tools::Run::Analysis.3 \
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- Bio::Tools::Run::PiseApplication::newcpgreport.3 \
- Bio::Tools::Run::PiseApplication::newcpgseek.3 \
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- Bio::Tools::Run::PiseApplication::nnssp.3 \
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- Bio::Tools::Run::PiseApplication::restover.3 \
- Bio::Tools::Run::PiseApplication::restrict.3 \
- Bio::Tools::Run::PiseApplication::revseq.3 \
- Bio::Tools::Run::PiseApplication::rnadistance.3 \
- Bio::Tools::Run::PiseApplication::rnaeval.3 \
- Bio::Tools::Run::PiseApplication::rnafold.3 \
- Bio::Tools::Run::PiseApplication::rnaga.3 \
- Bio::Tools::Run::PiseApplication::rnaheat.3 \
- Bio::Tools::Run::PiseApplication::rnainverse.3 \
- Bio::Tools::Run::PiseApplication::rnapdist.3 \
- Bio::Tools::Run::PiseApplication::rnasubopt.3 \
- Bio::Tools::Run::PiseApplication::sam2hmmer.3 \
- Bio::Tools::Run::PiseApplication::sampleseqs.3 \
- Bio::Tools::Run::PiseApplication::saps.3 \
- Bio::Tools::Run::PiseApplication::satellites.3 \
- Bio::Tools::Run::PiseApplication::scan_for_matches.3 \
- Bio::Tools::Run::PiseApplication::scope.3 \
- Bio::Tools::Run::PiseApplication::scopparse.3 \
- Bio::Tools::Run::PiseApplication::seqboot.3 \
- Bio::Tools::Run::PiseApplication::seqgen.3 \
- Bio::Tools::Run::PiseApplication::seqmatchall.3 \
- Bio::Tools::Run::PiseApplication::seqsblast.3 \
- Bio::Tools::Run::PiseApplication::seqstat.3 \
- Bio::Tools::Run::PiseApplication::showalign.3 \
- Bio::Tools::Run::PiseApplication::showfeat.3 \
- Bio::Tools::Run::PiseApplication::showorf.3 \
- Bio::Tools::Run::PiseApplication::showseq.3 \
- Bio::Tools::Run::PiseApplication::shuffleseq.3 \
- Bio::Tools::Run::PiseApplication::sigcleave.3 \
- Bio::Tools::Run::PiseApplication::siggen.3 \
- Bio::Tools::Run::PiseApplication::sigscan.3 \
- Bio::Tools::Run::PiseApplication::silent.3 \
- Bio::Tools::Run::PiseApplication::sirna.3 \
- Bio::Tools::Run::PiseApplication::splitter.3 \
- Bio::Tools::Run::PiseApplication::sreformat.3 \
- Bio::Tools::Run::PiseApplication::stretcher.3 \
- Bio::Tools::Run::PiseApplication::stride.3 \
- Bio::Tools::Run::PiseApplication::stssearch.3 \
- Bio::Tools::Run::PiseApplication::supermatcher.3 \
- Bio::Tools::Run::PiseApplication::syco.3 \
- Bio::Tools::Run::PiseApplication::tacg.3 \
- Bio::Tools::Run::PiseApplication::tfscan.3 \
- Bio::Tools::Run::PiseApplication::tipdate.3 \
- Bio::Tools::Run::PiseApplication::tmap.3 \
- Bio::Tools::Run::PiseApplication::toppred.3 \
- Bio::Tools::Run::PiseApplication::tranalign.3 \
- Bio::Tools::Run::PiseApplication::transeq.3 \
- Bio::Tools::Run::PiseApplication::treealign.3 \
- Bio::Tools::Run::PiseApplication::trimest.3 \
- Bio::Tools::Run::PiseApplication::trimseq.3 \
- Bio::Tools::Run::PiseApplication::trnascan.3 \
- Bio::Tools::Run::PiseApplication::twofeat.3 \
- Bio::Tools::Run::PiseApplication::unroot.3 \
- Bio::Tools::Run::PiseApplication::vectorstrip.3 \
- Bio::Tools::Run::PiseApplication::water.3 \
- Bio::Tools::Run::PiseApplication::weighbor.3 \
- Bio::Tools::Run::PiseApplication::whichdb.3 \
- Bio::Tools::Run::PiseApplication::wise2.3 \
- Bio::Tools::Run::PiseApplication::wobble.3 \
- Bio::Tools::Run::PiseApplication::wordcount.3 \
- Bio::Tools::Run::PiseApplication::wordmatch.3 \
- Bio::Tools::Run::PiseApplication::wublast2.3 \
- Bio::Tools::Run::PiseApplication::xblast.3 \
- Bio::Tools::Run::PiseApplication::xpound.3 \
- Bio::Tools::Run::PiseJob.3 \
- Bio::Tools::Run::PiseJobParser.3 \
- Bio::Tools::Run::PiseWorkflow.3 \
- Bio::Tools::Run::Primate.3 \
- Bio::Tools::Run::Primer3.3 \
- Bio::Tools::Run::Prints.3 \
- Bio::Tools::Run::Profile.3 \
- Bio::Tools::Run::Promoterwise.3 \
- Bio::Tools::Run::Pseudowise.3 \
- Bio::Tools::Run::RepeatMasker.3 \
- Bio::Tools::Run::Seg.3 \
- Bio::Tools::Run::Signalp.3 \
- Bio::Tools::Run::Tmhmm.3 \
- Bio::Tools::Run::TribeMCL.3 \
- Bio::Tools::Run::Vista.3
-
-# now install all extra stuff (docs, examples, scripts)
-post-install:
- ${MKDIR} ${DATADIR}
- @${CP} -Rv ${WRKSRC}/scripts ${DATADIR}
- ${MKDIR} ${EXAMPLESDIR}
- @${CP} -Rv ${WRKSRC}/examples/* ${EXAMPLESDIR}
-.if !defined(NOPORTDOCS)
- ${MKDIR} ${DOCSDIR}
-.for doc in AUTHORS Changes INSTALL.PROGRAMS README
- ${INSTALL_DATA} ${WRKSRC}/${doc} ${DOCSDIR}
-.endfor
-.endif
-
-.include <bsd.port.mk>
diff --git a/biology/p5-bioperl-run-devel/distinfo b/biology/p5-bioperl-run-devel/distinfo
deleted file mode 100644
index e20711cc19d2..000000000000
--- a/biology/p5-bioperl-run-devel/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 (bioperl-run-1.5.1.tar.gz) = dbfce41fa5d86dab5fd1d6af4196c646
-SHA256 (bioperl-run-1.5.1.tar.gz) = d9e1f5bdff5541376cab1c8b7e8db9bedbbb7b6f76b965d55dc20122a98f93e8
-SIZE (bioperl-run-1.5.1.tar.gz) = 864369
diff --git a/biology/p5-bioperl-run-devel/pkg-descr b/biology/p5-bioperl-run-devel/pkg-descr
deleted file mode 100644
index e6b90ec6ac9f..000000000000
--- a/biology/p5-bioperl-run-devel/pkg-descr
+++ /dev/null
@@ -1,5 +0,0 @@
-Bioperl-run contain modules that provides a PERL interface to various
-bioinformatics applications. This allows various applications to be used
-with common Bioperl objects.
-
-WWW: http://bioperl.org/
diff --git a/biology/p5-bioperl-run-devel/pkg-plist b/biology/p5-bioperl-run-devel/pkg-plist
deleted file mode 100644
index f3d3e2196c37..000000000000
--- a/biology/p5-bioperl-run-devel/pkg-plist
+++ /dev/null
@@ -1,383 +0,0 @@
-%%SITE_PERL%%/Bio/Factory/EMBOSS.pm
-%%SITE_PERL%%/Bio/Installer/Clustalw.pm
-%%SITE_PERL%%/Bio/Installer/EMBOSS.pm
-%%SITE_PERL%%/Bio/Installer/Generic.pm
-%%SITE_PERL%%/Bio/Installer/PAML.pm
-%%SITE_PERL%%/Bio/Installer/Probcons.pm
-%%SITE_PERL%%/Bio/Installer/TCoffee.pm
-%%SITE_PERL%%/Bio/Tools/Run/AbstractRunner.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probcons.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm
-%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
-%%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/Pise.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/Coil.pm
-%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
-%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
-%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
-%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
-%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
-%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
-%%SITE_PERL%%/Bio/Tools/Run/JavaRunner.pm
-%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Forester/SDI.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Baseml.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Codeml.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Yn00.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/CSR.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/Puzzle.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/abiview.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/addquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/align2model.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/alistat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/antigenic.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/assp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/backtranseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bambe.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/banana.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bionj.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/biosed.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bl2seq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blast2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps_block.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps_matrix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/boxshade.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/btwisted.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cai.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cds.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/chaos.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/charge.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/checktrans.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/chips.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cirdna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clique.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clustalw.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clustalw_convert.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codcmp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/coderet.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codnocod.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codontree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codonw.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/comalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/combat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/compseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/con_filter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/confmat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cons.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/consense.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/consensus.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cpgplot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cpgreport.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cusp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cutseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dca.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/decorate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/degapseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/descseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dialign2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/diffseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/digest.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/distmat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/distquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dnadist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dnapars.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dollop.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/domainer.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dotmatcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dotpath.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dottup.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawgram.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawpyr.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawtree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dreg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/druid.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dsc.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dssp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/einverted.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/emma.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/emowse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/environ.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/eprimer3.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/equicktandem.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/est2genome.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/etandem.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/extractfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/extractseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fasta.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fastdnaml.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fastrna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/filtersites.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/findkm.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fitch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fmtseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/freak.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzznuc.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzzpro.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzztran.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gb2xml.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/geecee.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/genscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/getblock.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/getorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gff2ps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gibbs.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gibbs_scan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/golden.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/grailclnt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gruppi.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/helixturnhelix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmbuild.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmcalibrate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmconvert.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmemit.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmer2sam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmfetch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmpfam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmscore.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmoment.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/homology.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/html4blast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/iep.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/infoalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/infoseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/interface.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/isochore.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/kitsch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lassap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lindna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/listor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/loadseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lvb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/makehist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/map.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/marscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/maskfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/maskseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/matcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/megamerger.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/melting.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/merger.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mfold.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/modelfromalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/most.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mreps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/msa.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/msbar.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mspcrunch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mview_alig.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mview_blast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mwfilter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/needle.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/neighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newcpgreport.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newcpgseek.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/njdist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nnssp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/notseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nrscope.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nthseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/octanol.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/oddcomp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/palindrome.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/parciquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pars.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pasteseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patmatdb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patmatmotifs.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patser.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pdbsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepcoil.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepinfo.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepnet.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepstats.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwheel.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwindow.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwindowall.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pestfind.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pftools.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/phiblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pima.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plotcon.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plotorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/polydot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pratt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/predator.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/preg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prettyalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prettyplot.pm
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-%%EXAMPLESDIR%%/pise/phylo-kun.pl
-%%EXAMPLESDIR%%/pise/toppred.pl
-@dirrm %%EXAMPLESDIR%%/pise
-@dirrm %%EXAMPLESDIR%%
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-@dirrm %%DATADIR%%/scripts
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-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Forester
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
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-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run
-@dirrmtry %%SITE_PERL%%/Bio/Tools
-@dirrm %%SITE_PERL%%/Bio/Installer
-@dirrmtry %%SITE_PERL%%/Bio/Factory
-@dirrmtry %%SITE_PERL%%/Bio
generated by cgit (git 2.34.1) at 2025-02-24 14:56:19 +0800