- Re-add p5-bioperl-devel, development version of biology/p5-bioperl

  (A collection of Perl modules for bioinformatics)

PR:		ports/89497
Submitted by:	Mauricio Herrera Cuadra <arareko@yahoo.com>

6 files changed, 2586 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 1af48c9dff8e..f5958aff4c2e 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -45,6 +45,7 @@
     SUBDIR += p5-Bio-ASN1-EntrezGene
     SUBDIR += p5-Bio-Das
     SUBDIR += p5-bioperl
+    SUBDIR += p5-bioperl-devel
     SUBDIR += paml
     SUBDIR += phylip
     SUBDIR += platon
diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile
new file mode 100644
index 000000000000..1e2dd4078f9d
--- /dev/null
+++ b/biology/p5-bioperl-devel/Makefile
@@ -0,0 +1,944 @@
+# 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=	1.5.1
+CATEGORIES=	biology perl5
+MASTER_SITES=	http://bioperl.org/DIST/
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	mauricio@arareko.net
+COMMENT=	A collection of Perl modules for bioinformatics (developer release)
+
+BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/perl5.8 \
+		${LOCALBASE}/lib/perl5/${PERL_VER}/${PERL_ARCH}/DB_File.pm:${PORTSDIR}/lang/perl5.8 \
+		${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${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 \
+		${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
+		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
+		${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
+		${SITE_PERL}/Text/Shellwords.pm:${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}/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.[0-46-9]*
+
+PERL_CONFIGURE=	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_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_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::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::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::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::memory.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::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::RefSeq.3 \
+		Bio::DB::Registry.3 \
+		Bio::DB::SeqHound.3 \
+		Bio::DB::SeqI.3 \
+		Bio::DB::SwissProt.3 \
+		Bio::DB::Taxonomy.3 \
+		Bio::DB::Taxonomy::entrez.3 \
+		Bio::DB::Taxonomy::flatfile.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::FeatureGroup.3 \
+		Bio::Expression::FeatureI.3 \
+		Bio::Expression::ProbeI.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::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::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::generic.3 \
+		Bio::Graphics::Glyph::graded_segments.3 \
+		Bio::Graphics::Glyph::group.3 \
+		Bio::Graphics::Glyph::heterogeneous_segments.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::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::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::IO::SRS.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::FPCMarker.3 \
+		Bio::Map::LinkageMap.3 \
+		Bio::Map::LinkagePosition.3 \
+		Bio::Map::MapI.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::Physical.3 \
+		Bio::Map::Position.3 \
+		Bio::Map::PositionI.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::Ontology.3 \
+		Bio::Ontology::OntologyEngineI.3 \
+		Bio::Ontology::OntologyI.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::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::Err.3 \
+		Bio::Root::Exception.3 \
+		Bio::Root::Global.3 \
+		Bio::Root::HTTPget.3 \
+		Bio::Root::IO.3 \
+		Bio::Root::IOManager.3 \
+		Bio::Root::Object.3 \
+		Bio::Root::Root.3 \
+		Bio::Root::RootI.3 \
+		Bio::Root::Storable.3 \
+		Bio::Root::Utilities.3 \
+		Bio::Root::Vector.3 \
+		Bio::Root::Version.3 \
+		Bio::Root::Xref.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::HSPFactory.3 \
+		Bio::Search::HSP::HSPI.3 \
+		Bio::Search::HSP::PSLHSP.3 \
+		Bio::Search::HSP::PsiBlastHSP.3 \
+		Bio::Search::HSP::WABAHSP.3 \
+		Bio::Search::Hit::BlastHit.3 \
+		Bio::Search::Hit::Fasta.3 \
+		Bio::Search::Hit::GenericHit.3 \
+		Bio::Search::Hit::HMMERHit.3 \
+		Bio::Search::Hit::HitFactory.3 \
+		Bio::Search::Hit::HitI.3 \
+		Bio::Search::Hit::PsiBlastHit.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::HMMERResult.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::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::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::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::swiss.3 \
+		Bio::SeqIO::tab.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::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::Blast.3 \
+		Bio::Tools::Blast::HSP.3 \
+		Bio::Tools::Blast::HTML.3 \
+		Bio::Tools::Blast::Sbjct.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::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::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::SeqAnal.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::WWW.3 \
+		Bio::Tools::WebBlat.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 \
+		biodatabases.3 \
+		biodesign.3 \
+		bioperl.3 \
+		bioscripts.3 \
+		bptutorial.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}
+	${MKDIR} ${EXAMPLESDIR}
+	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${DOCSDIR}
+.for doc in AUTHORS BUGS Changes DEPRECATED FAQ 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
new file mode 100644
index 000000000000..670a4e402603
--- /dev/null
+++ b/biology/p5-bioperl-devel/distinfo
@@ -0,0 +1,3 @@
+MD5 (bioperl-1.5.1.tar.gz) = f510c871a1d17ac4ccc8ad3e6c9bad17
+SHA256 (bioperl-1.5.1.tar.gz) = 128ecbdbb22a75e165f844e38795915a909f3134c6558cd3a4d83e5ab597ea1a
+SIZE (bioperl-1.5.1.tar.gz) = 6810301
diff --git a/biology/p5-bioperl-devel/files/patch-Makefile.PL b/biology/p5-bioperl-devel/files/patch-Makefile.PL
new file mode 100644
index 000000000000..7790c998f8c2
--- /dev/null
+++ b/biology/p5-bioperl-devel/files/patch-Makefile.PL
@@ -0,0 +1,56 @@
+--- Makefile.PL.orig	Sun Oct  9 17:16:18 2005
++++ Makefile.PL	Wed Nov 30 13:58:20 2005
+@@ -41,7 +41,7 @@
+ 	     'XML::SAX'                 => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
+ 	     'XML::SAX::Base'                 => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
+ 	     'XML::SAX::Writer'         => '0.0/New style SAX parser/Writers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
+- 	     'Bio::ANS1::EntrezGene'    => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene'
++ 	     'Bio::ASN1::EntrezGene'    => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene'
+ # Bio::Microarray is not in core bioperl yet
+ #	     'enum'                     => '0.0/C style enumerated types and bitmask flags 
+ # in Perl/Bio::Microarray::Affymetrix::*',
+@@ -95,7 +95,7 @@
+ sub prompt_for_biodbgff {
+   if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
+     print "\n** Bio::DB::GFF Tests section** \n";
+-    my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n');
++    my $proceed = 'n'; # prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n');
+     if( $proceed =~ /^[yY]/) {
+       my $cfg = {dbd_driver => 'mysql'};
+       GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
+@@ -129,7 +129,7 @@
+ sub get_scripts_to_install {
+   print "\n*** Script Install Section ****\n";
+   print "\nBioperl comes with a number of useful scripts which you may wish to install.\n";
+-  my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a');
++  my $prompt_mode = 'a'; # prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a');
+   return if $prompt_mode =~ /^[nN]/;
+   my @scripts;
+   my $script_dir = './scripts';
+@@ -378,16 +378,16 @@
+ );
+ 
+ 
+-sub MY::manifypods {
+-  my $self = shift;
+-  #print STDERR "In manifypods moment\n";
+-  if( 1 ) {
+-    return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
+-  }
+-  else {
+-    return $self->SUPER::manifypods(@_);
+-  }
+-}
++#sub MY::manifypods {
++#  my $self = shift;
++#  #print STDERR "In manifypods moment\n";
++#  if( 1 ) {
++#    return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
++#  }
++#  else {
++#    return $self->SUPER::manifypods(@_);
++#  }
++#}
+ 
+ sub MY::clean {
+   package MY;
diff --git a/biology/p5-bioperl-devel/pkg-descr b/biology/p5-bioperl-devel/pkg-descr
new file mode 100644
index 000000000000..6ea2aedf8a8b
--- /dev/null
+++ b/biology/p5-bioperl-devel/pkg-descr
@@ -0,0 +1,11 @@
+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
new file mode 100644
index 000000000000..6643135c2a62
--- /dev/null
+++ b/biology/p5-bioperl-devel/pkg-plist
@@ -0,0 +1,1571 @@
+bin/bp_aacomp.pl
+bin/bp_biblio.pl
+bin/bp_biofetch_genbank_proxy.pl
+bin/bp_bioflat_index.pl
+bin/bp_biogetseq.pl
+bin/bp_blast2tree.pl
+bin/bp_bulk_load_gff.pl
+bin/bp_chaos_plot.pl
+bin/bp_classify_hits_kingdom.pl
+bin/bp_composite_LD.pl
+bin/bp_contig_draw.pl
+bin/bp_dbsplit.pl
+bin/bp_embl2picture.pl
+bin/bp_extract_feature_seq.pl
+bin/bp_fast_load_gff.pl
+bin/bp_fastam9_to_table.pl
+bin/bp_feature_draw.pl
+bin/bp_fetch.pl
+bin/bp_filter_search.pl
+bin/bp_flanks.pl
+bin/bp_frend.pl
+bin/bp_gccalc.pl
+bin/bp_genbank2gff.pl
+bin/bp_genbank2gff3.pl
+bin/bp_generate_histogram.pl
+bin/bp_glyphs1-demo.pl
+bin/bp_glyphs2-demo.pl
+bin/bp_heterogeneity_test.pl
+bin/bp_hmmer_to_table.pl
+bin/bp_index.pl
+bin/bp_load_gff.pl
+bin/bp_local_taxonomydb_query.pl
+bin/bp_make_mrna_protein.pl
+bin/bp_mask_by_search.pl
+bin/bp_meta_gff.pl
+bin/bp_mrtrans.pl
+bin/bp_mutate.pl
+bin/bp_nexus2nh.pl
+bin/bp_nrdb.pl
+bin/bp_oligo_count.pl
+bin/bp_pairwise_kaks.pl
+bin/bp_pg_bulk_load_gff.pl
+bin/bp_process_gadfly.pl
+bin/bp_process_sgd.pl
+bin/bp_process_wormbase.pl
+bin/bp_query_entrez_taxa.pl
+bin/bp_remote_blast.pl
+bin/bp_search2BSML.pl
+bin/bp_search2alnblocks.pl
+bin/bp_search2gff.pl
+bin/bp_search2table.pl
+bin/bp_search2tribe.pl
+bin/bp_search_overview.pl
+bin/bp_seq_length.pl
+bin/bp_seqconvert.pl
+bin/bp_seqret.pl
+bin/bp_split_seq.pl
+bin/bp_sreformat.pl
+bin/bp_taxid4species.pl
+bin/bp_translate_seq.pl
+bin/bp_tree2pag.pl
+bin/bp_unflatten_seq.pl
+%%SITE_PERL%%/Bio/Align/AlignI.pm
+%%SITE_PERL%%/Bio/Align/DNAStatistics.pm
+%%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm
+%%SITE_PERL%%/Bio/Align/ProteinStatistics.pm
+%%SITE_PERL%%/Bio/Align/StatisticsI.pm
+%%SITE_PERL%%/Bio/Align/Utilities.pm
+%%SITE_PERL%%/Bio/AlignIO.pm
+%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
+%%SITE_PERL%%/Bio/AlignIO/clustalw.pm
+%%SITE_PERL%%/Bio/AlignIO/emboss.pm
+%%SITE_PERL%%/Bio/AlignIO/fasta.pm
+%%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm
+%%SITE_PERL%%/Bio/AlignIO/maf.pm
+%%SITE_PERL%%/Bio/AlignIO/mase.pm
+%%SITE_PERL%%/Bio/AlignIO/mega.pm
+%%SITE_PERL%%/Bio/AlignIO/meme.pm
+%%SITE_PERL%%/Bio/AlignIO/metafasta.pm
+%%SITE_PERL%%/Bio/AlignIO/msf.pm
+%%SITE_PERL%%/Bio/AlignIO/nexus.pm
+%%SITE_PERL%%/Bio/AlignIO/pfam.pm
+%%SITE_PERL%%/Bio/AlignIO/phylip.pm
+%%SITE_PERL%%/Bio/AlignIO/po.pm
+%%SITE_PERL%%/Bio/AlignIO/prodom.pm
+%%SITE_PERL%%/Bio/AlignIO/psi.pm
+%%SITE_PERL%%/Bio/AlignIO/selex.pm
+%%SITE_PERL%%/Bio/AlignIO/stockholm.pm
+%%SITE_PERL%%/Bio/AnalysisI.pm
+%%SITE_PERL%%/Bio/AnalysisParserI.pm
+%%SITE_PERL%%/Bio/AnalysisResultI.pm
+%%SITE_PERL%%/Bio/AnnotatableI.pm
+%%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm
+%%SITE_PERL%%/Bio/Annotation/Collection.pm
+%%SITE_PERL%%/Bio/Annotation/Comment.pm
+%%SITE_PERL%%/Bio/Annotation/DBLink.pm
+%%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm
+%%SITE_PERL%%/Bio/Annotation/Reference.pm
+%%SITE_PERL%%/Bio/Annotation/SimpleValue.pm
+%%SITE_PERL%%/Bio/Annotation/StructuredValue.pm
+%%SITE_PERL%%/Bio/Annotation/Target.pm
+%%SITE_PERL%%/Bio/Annotation/TypeManager.pm
+%%SITE_PERL%%/Bio/AnnotationCollectionI.pm
+%%SITE_PERL%%/Bio/AnnotationI.pm
+%%SITE_PERL%%/Bio/Assembly/Contig.pm
+%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm
+%%SITE_PERL%%/Bio/Assembly/IO.pm
+%%SITE_PERL%%/Bio/Assembly/IO/ace.pm
+%%SITE_PERL%%/Bio/Assembly/IO/phrap.pm
+%%SITE_PERL%%/Bio/Assembly/Scaffold.pm
+%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm
+%%SITE_PERL%%/Bio/Assembly/Singlet.pm
+%%SITE_PERL%%/Bio/Biblio.pm
+%%SITE_PERL%%/Bio/Biblio/Article.pm
+%%SITE_PERL%%/Bio/Biblio/BiblioBase.pm
+%%SITE_PERL%%/Bio/Biblio/Book.pm
+%%SITE_PERL%%/Bio/Biblio/BookArticle.pm
+%%SITE_PERL%%/Bio/Biblio/IO.pm
+%%SITE_PERL%%/Bio/Biblio/IO/medline2ref.pm
+%%SITE_PERL%%/Bio/Biblio/IO/medlinexml.pm
+%%SITE_PERL%%/Bio/Biblio/IO/pubmed2ref.pm
+%%SITE_PERL%%/Bio/Biblio/IO/pubmedxml.pm
+%%SITE_PERL%%/Bio/Biblio/Journal.pm
+%%SITE_PERL%%/Bio/Biblio/JournalArticle.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineArticle.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineBook.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineBookArticle.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineJournal.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineJournalArticle.pm
+%%SITE_PERL%%/Bio/Biblio/Organisation.pm
+%%SITE_PERL%%/Bio/Biblio/Patent.pm
+%%SITE_PERL%%/Bio/Biblio/Person.pm
+%%SITE_PERL%%/Bio/Biblio/Proceeding.pm
+%%SITE_PERL%%/Bio/Biblio/Provider.pm
+%%SITE_PERL%%/Bio/Biblio/PubmedArticle.pm
+%%SITE_PERL%%/Bio/Biblio/PubmedBookArticle.pm
+%%SITE_PERL%%/Bio/Biblio/PubmedJournalArticle.pm
+%%SITE_PERL%%/Bio/Biblio/Ref.pm
+%%SITE_PERL%%/Bio/Biblio/Service.pm
+%%SITE_PERL%%/Bio/Biblio/TechReport.pm
+%%SITE_PERL%%/Bio/Biblio/Thesis.pm
+%%SITE_PERL%%/Bio/Biblio/WebResource.pm
+%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm
+%%SITE_PERL%%/Bio/Cluster/FamilyI.pm
+%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm
+%%SITE_PERL%%/Bio/Cluster/UniGene.pm
+%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm
+%%SITE_PERL%%/Bio/ClusterI.pm
+%%SITE_PERL%%/Bio/ClusterIO.pm
+%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm
+%%SITE_PERL%%/Bio/ClusterIO/unigene.pm
+%%SITE_PERL%%/Bio/CodonUsage/IO.pm
+%%SITE_PERL%%/Bio/CodonUsage/Table.pm
+%%SITE_PERL%%/Bio/Coordinate/Chain.pm
+%%SITE_PERL%%/Bio/Coordinate/Collection.pm
+%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm
+%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
+%%SITE_PERL%%/Bio/Coordinate/Graph.pm
+%%SITE_PERL%%/Bio/Coordinate/MapperI.pm
+%%SITE_PERL%%/Bio/Coordinate/Pair.pm
+%%SITE_PERL%%/Bio/Coordinate/Result.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Match.pm
+%%SITE_PERL%%/Bio/Coordinate/ResultI.pm
+%%SITE_PERL%%/Bio/Coordinate/Utils.pm
+%%SITE_PERL%%/Bio/DB/Ace.pm
+%%SITE_PERL%%/Bio/DB/Biblio/biofetch.pm
+%%SITE_PERL%%/Bio/DB/Biblio/eutils.pm
+%%SITE_PERL%%/Bio/DB/Biblio/pdf.pm
+%%SITE_PERL%%/Bio/DB/Biblio/soap.pm
+%%SITE_PERL%%/Bio/DB/BiblioI.pm
+%%SITE_PERL%%/Bio/DB/BioFetch.pm
+%%SITE_PERL%%/Bio/DB/CUTG.pm
+%%SITE_PERL%%/Bio/DB/DBFetch.pm
+%%SITE_PERL%%/Bio/DB/EMBL.pm
+%%SITE_PERL%%/Bio/DB/Failover.pm
+%%SITE_PERL%%/Bio/DB/Fasta.pm
+%%SITE_PERL%%/Bio/DB/FileCache.pm
+%%SITE_PERL%%/Bio/DB/Flat.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/embl.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/fasta.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/swissprot.pm
+%%SITE_PERL%%/Bio/DB/Flat/BinarySearch.pm
+%%SITE_PERL%%/Bio/DB/GDB.pm
+%%SITE_PERL%%/Bio/DB/GFF.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/ace.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/iterator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysql.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracle.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/iterator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/alignment.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/clone.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/coding.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/match.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/none.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/processed_transcript.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/so_transcript.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/transcript.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_refgene.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/ucsc_softberry.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
+%%SITE_PERL%%/Bio/DB/GFF/Featname.pm
+%%SITE_PERL%%/Bio/DB/GFF/Feature.pm
+%%SITE_PERL%%/Bio/DB/GFF/Homol.pm
+%%SITE_PERL%%/Bio/DB/GFF/RelSegment.pm
+%%SITE_PERL%%/Bio/DB/GFF/Segment.pm
+%%SITE_PERL%%/Bio/DB/GFF/Typename.pm
+%%SITE_PERL%%/Bio/DB/GFF/Util/Binning.pm
+%%SITE_PERL%%/Bio/DB/GFF/Util/Rearrange.pm
+%%SITE_PERL%%/Bio/DB/GenBank.pm
+%%SITE_PERL%%/Bio/DB/GenPept.pm
+%%SITE_PERL%%/Bio/DB/InMemoryCache.pm
+%%SITE_PERL%%/Bio/DB/MANIFEST
+%%SITE_PERL%%/Bio/DB/Makefile.PL
+%%SITE_PERL%%/Bio/DB/MeSH.pm
+%%SITE_PERL%%/Bio/DB/NCBIHelper.pm
+%%SITE_PERL%%/Bio/DB/Query/GenBank.pm
+%%SITE_PERL%%/Bio/DB/Query/WebQuery.pm
+%%SITE_PERL%%/Bio/DB/QueryI.pm
+%%SITE_PERL%%/Bio/DB/RandomAccessI.pm
+%%SITE_PERL%%/Bio/DB/RefSeq.pm
+%%SITE_PERL%%/Bio/DB/Registry.pm
+%%SITE_PERL%%/Bio/DB/SeqHound.pm
+%%SITE_PERL%%/Bio/DB/SeqI.pm
+%%SITE_PERL%%/Bio/DB/SwissProt.pm
+%%SITE_PERL%%/Bio/DB/Taxonomy.pm
+%%SITE_PERL%%/Bio/DB/Taxonomy/entrez.pm
+%%SITE_PERL%%/Bio/DB/Taxonomy/flatfile.pm
+%%SITE_PERL%%/Bio/DB/Universal.pm
+%%SITE_PERL%%/Bio/DB/UpdateableSeqI.pm
+%%SITE_PERL%%/Bio/DB/WebDBSeqI.pm
+%%SITE_PERL%%/Bio/DB/XEMBL.pm
+%%SITE_PERL%%/Bio/DB/XEMBLService.pm
+%%SITE_PERL%%/Bio/DBLinkContainerI.pm
+%%SITE_PERL%%/Bio/Das/FeatureTypeI.pm
+%%SITE_PERL%%/Bio/Das/SegmentI.pm
+%%SITE_PERL%%/Bio/DasI.pm
+%%SITE_PERL%%/Bio/DescribableI.pm
+%%SITE_PERL%%/Bio/Event/EventGeneratorI.pm
+%%SITE_PERL%%/Bio/Event/EventHandlerI.pm
+%%SITE_PERL%%/Bio/Expression/FeatureGroup.pm
+%%SITE_PERL%%/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
+%%SITE_PERL%%/Bio/Expression/FeatureI.pm
+%%SITE_PERL%%/Bio/Expression/FeatureSet/FeatureSetMas50.pm
+%%SITE_PERL%%/Bio/Expression/ProbeI.pm
+%%SITE_PERL%%/Bio/Factory/AnalysisI.pm
+%%SITE_PERL%%/Bio/Factory/ApplicationFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/DriverFactory.pm
+%%SITE_PERL%%/Bio/Factory/FTLocationFactory.pm
+%%SITE_PERL%%/Bio/Factory/HitFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/LocationFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/MapFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/ObjectBuilderI.pm
+%%SITE_PERL%%/Bio/Factory/ObjectFactory.pm
+%%SITE_PERL%%/Bio/Factory/ObjectFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/ResultFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/SeqAnalysisParserFactory.pm
+%%SITE_PERL%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/SequenceFactoryI.pm
+%%SITE_PERL%%/Bio/Factory/SequenceProcessorI.pm
+%%SITE_PERL%%/Bio/Factory/SequenceStreamI.pm
+%%SITE_PERL%%/Bio/Factory/TreeFactoryI.pm
+%%SITE_PERL%%/Bio/FeatureHolderI.pm
+%%SITE_PERL%%/Bio/FeatureIO.pm
+%%SITE_PERL%%/Bio/FeatureIO/bed.pm
+%%SITE_PERL%%/Bio/FeatureIO/gff.pm
+%%SITE_PERL%%/Bio/FeatureIO/gtf.pm
+%%SITE_PERL%%/Bio/FeatureIO/interpro.pm
+%%SITE_PERL%%/Bio/Graph/Edge.pm
+%%SITE_PERL%%/Bio/Graph/IO.pm
+%%SITE_PERL%%/Bio/Graph/IO/dip.pm
+%%SITE_PERL%%/Bio/Graph/IO/psi_xml.pm
+%%SITE_PERL%%/Bio/Graph/ProteinGraph.pm
+%%SITE_PERL%%/Bio/Graph/SimpleGraph.pm
+%%SITE_PERL%%/Bio/Graph/SimpleGraph/Traversal.pm
+%%SITE_PERL%%/Bio/Graphics.pm
+%%SITE_PERL%%/Bio/Graphics/ConfiguratorI.pm
+%%SITE_PERL%%/Bio/Graphics/Feature.pm
+%%SITE_PERL%%/Bio/Graphics/FeatureFile.pm
+%%SITE_PERL%%/Bio/Graphics/FeatureFile/Iterator.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/Factory.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/alignment.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/anchored_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/box.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/broken_line.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/cds.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/christmas_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/crossbox.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/dashed_line.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/diamond.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/dna.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/dot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/dumbbell.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ellipse.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ex.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/extending_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/flag.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/generic.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/graded_segments.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/group.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/heterogeneous_segments.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/lightning.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/line.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/merge_parts.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/merged_alignment.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/minmax.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/oval.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/pentagram.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/pinsertion.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/primers.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/processed_transcript.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ragged_ends.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/redgreen_box.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/redgreen_segment.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/repeating_shape.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/rndrect.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ruler_arrow.pm
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+@dirrm %%EXAMPLESDIR%%/root/lib/Bio
+@dirrm %%EXAMPLESDIR%%/root/lib
+@dirrm %%EXAMPLESDIR%%/root
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+@dirrm %%EXAMPLESDIR%%/liveseq
+@dirrm %%EXAMPLESDIR%%/db
+@dirrm %%EXAMPLESDIR%%/contributed
+@dirrm %%EXAMPLESDIR%%/cluster
+@dirrm %%EXAMPLESDIR%%/biographics
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+@dirrm %%EXAMPLESDIR%%/align
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+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/html
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/fo
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/common
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/stylesheet
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/ent
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/txt
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/pdf
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html/images
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs/graphics
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples/graphics
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/faq
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%DATADIR%%/scripts/utilities
+@dirrm %%DATADIR%%/scripts/tree
+@dirrm %%DATADIR%%/scripts/taxa
+@dirrm %%DATADIR%%/scripts/seqstats
+@dirrm %%DATADIR%%/scripts/seq
+@dirrm %%DATADIR%%/scripts/searchio
+@dirrm %%DATADIR%%/scripts/popgen
+@dirrm %%DATADIR%%/scripts/index
+@dirrm %%DATADIR%%/scripts/graphics
+@dirrm %%DATADIR%%/scripts/das
+@dirrm %%DATADIR%%/scripts/biographics
+@dirrm %%DATADIR%%/scripts/biblio
+@dirrm %%DATADIR%%/scripts/DB
+@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
+@dirrm %%DATADIR%%/scripts
+@dirrm %%DATADIR%%/models
+@dirrm %%DATADIR%%
+@unexec rmdir %D/%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio 2>/dev/null || true
+@dirrm %%SITE_PERL%%/Bio/Variation/IO
+@dirrm %%SITE_PERL%%/Bio/Variation
+@dirrm %%SITE_PERL%%/Bio/TreeIO
+@dirrm %%SITE_PERL%%/Bio/Tree/Draw
+@dirrm %%SITE_PERL%%/Bio/Tree
+@dirrm %%SITE_PERL%%/Bio/Tools/Spidey
+@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
+@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
+@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA
+@dirrm %%SITE_PERL%%/Bio/Tools/Run
+@dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
+@dirrm %%SITE_PERL%%/Bio/Tools/Primer
+@dirrm %%SITE_PERL%%/Bio/Tools/Prediction
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo
+@dirrm %%SITE_PERL%%/Bio/Tools/HMMER
+@dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS
+@dirrm %%SITE_PERL%%/Bio/Tools/Blast
+@dirrm %%SITE_PERL%%/Bio/Tools/BPlite
+@dirrm %%SITE_PERL%%/Bio/Tools/Analysis/Protein
+@dirrm %%SITE_PERL%%/Bio/Tools/Analysis/DNA
+@dirrm %%SITE_PERL%%/Bio/Tools/Analysis
+@dirrm %%SITE_PERL%%/Bio/Tools/Alignment
+@dirrm %%SITE_PERL%%/Bio/Tools
+@dirrm %%SITE_PERL%%/Bio/Taxonomy
+@dirrm %%SITE_PERL%%/Bio/Symbol
+@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
+@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
+@dirrm %%SITE_PERL%%/Bio/Structure/SecStr
+@dirrm %%SITE_PERL%%/Bio/Structure/IO
+@dirrm %%SITE_PERL%%/Bio/Structure
+@dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
+@dirrm %%SITE_PERL%%/Bio/SeqIO/game
+@dirrm %%SITE_PERL%%/Bio/SeqIO
+@dirrm %%SITE_PERL%%/Bio/SeqFeature/Tools
+@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
+@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
+@dirrm %%SITE_PERL%%/Bio/SeqFeature
+@dirrm %%SITE_PERL%%/Bio/Seq/Meta
+@dirrm %%SITE_PERL%%/Bio/Seq
+@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
+@dirrm %%SITE_PERL%%/Bio/SearchIO
+@dirrm %%SITE_PERL%%/Bio/Search/Result
+@dirrm %%SITE_PERL%%/Bio/Search/Iteration
+@dirrm %%SITE_PERL%%/Bio/Search/Hit
+@dirrm %%SITE_PERL%%/Bio/Search/HSP
+@dirrm %%SITE_PERL%%/Bio/Search
+@dirrm %%SITE_PERL%%/Bio/Root
+@dirrm %%SITE_PERL%%/Bio/Restriction/IO
+@dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
+@dirrm %%SITE_PERL%%/Bio/Restriction
+@dirrm %%SITE_PERL%%/Bio/PopGen/Simulation
+@dirrm %%SITE_PERL%%/Bio/PopGen/IO
+@dirrm %%SITE_PERL%%/Bio/PopGen
+@dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
+@dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
+@dirrm %%SITE_PERL%%/Bio/Phenotype
+@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
+@dirrm %%SITE_PERL%%/Bio/OntologyIO
+@dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
+@dirrm %%SITE_PERL%%/Bio/Ontology
+@dirrm %%SITE_PERL%%/Bio/Matrix/PSM/IO
+@dirrm %%SITE_PERL%%/Bio/Matrix/PSM
+@dirrm %%SITE_PERL%%/Bio/Matrix/IO
+@dirrm %%SITE_PERL%%/Bio/Matrix
+@dirrm %%SITE_PERL%%/Bio/MapIO
+@dirrm %%SITE_PERL%%/Bio/Map
+@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/Graphics/Glyph
+@dirrm %%SITE_PERL%%/Bio/Graphics/FeatureFile
+@dirrm %%SITE_PERL%%/Bio/Graphics
+@dirrm %%SITE_PERL%%/Bio/Graph/SimpleGraph
+@dirrm %%SITE_PERL%%/Bio/Graph/IO
+@dirrm %%SITE_PERL%%/Bio/Graph
+@dirrm %%SITE_PERL%%/Bio/FeatureIO
+@dirrm %%SITE_PERL%%/Bio/Factory
+@dirrm %%SITE_PERL%%/Bio/Expression/FeatureSet
+@dirrm %%SITE_PERL%%/Bio/Expression/FeatureGroup
+@dirrm %%SITE_PERL%%/Bio/Expression
+@dirrm %%SITE_PERL%%/Bio/Event
+@dirrm %%SITE_PERL%%/Bio/Das
+@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
+@dirrm %%SITE_PERL%%/Bio/DB/Query
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
+@dirrm %%SITE_PERL%%/Bio/DB/GFF
+@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
+@dirrm %%SITE_PERL%%/Bio/DB/Flat
+@dirrm %%SITE_PERL%%/Bio/DB/Biblio
+@dirrm %%SITE_PERL%%/Bio/DB
+@dirrm %%SITE_PERL%%/Bio/Coordinate/Result
+@dirrm %%SITE_PERL%%/Bio/Coordinate
+@dirrm %%SITE_PERL%%/Bio/CodonUsage
+@dirrm %%SITE_PERL%%/Bio/ClusterIO
+@dirrm %%SITE_PERL%%/Bio/Cluster
+@dirrm %%SITE_PERL%%/Bio/Biblio/IO
+@dirrm %%SITE_PERL%%/Bio/Biblio
+@dirrm %%SITE_PERL%%/Bio/Assembly/IO
+@dirrm %%SITE_PERL%%/Bio/Assembly
+@dirrm %%SITE_PERL%%/Bio/Annotation
+@dirrm %%SITE_PERL%%/Bio/AlignIO
+@dirrm %%SITE_PERL%%/Bio/Align
+@unexec rmdir %D/%%SITE_PERL%%/Bio 2>/dev/null || true