- Update to 1.6.0

PR: ports/131989 Submitted by: maintainer
author: Renato Botelho <garga@FreeBSD.org> 2009-02-23 19:31:43 +0000
committer: Renato Botelho <garga@FreeBSD.org> 2009-02-23 19:31:43 +0000
commit: 58d4bedcf436d78626be690db5da02da3064a913 (patch)
tree: c2e5451b22b6a0bfd1d4f7e4f822421fa25a7333 /biology
parent: Update to 0.6.4 (diff)
6 files changed, 1559 insertions, 1082 deletions
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 10fea6cdf8d2..18f9dbdd3bc8 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -6,100 +6,140 @@
 #
 
 PORTNAME=	bioperl
-PORTVERSION=	1.4
-PORTREVISION=	2
+PORTVERSION=	1.6.0
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/ \
 		CPAN
 PKGNAMEPREFIX=	p5-
+DISTNAME=	BioPerl-${PORTVERSION}
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of Perl modules for bioinformatics
 
-# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
-# prevents a flood of build-time warnings.
-BUILD_DEPENDS=	${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
-		${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
+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 \
-		${SITE_PERL}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
+		${SITE_PERL}/SOAP/Lite.pm:${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 \
-		${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \
-		${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+		${SITE_PERL}/XML/SAX.pm:${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 \
-		${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
-		${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \
+		${SITE_PERL}/XML/Writer.pm:${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 \
-		${SITE_PERL}/Parse/RecDescent.pm:${PORTSDIR}/devel/p5-Parse-RecDescent \
-		${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \
-		${SITE_PERL}/Test/Simple.pm:${PORTSDIR}/devel/p5-Test-Simple \
-		${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords
+		${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
+		${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
+		${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \
+		${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \
+		${SITE_PERL}/Algorithm/Munkres.pm:${PORTSDIR}/math/p5-Algorithm-Munkres \
+		${SITE_PERL}/Array/Compare.pm:${PORTSDIR}/misc/p5-Array-Compare \
+		${SITE_PERL}/GraphViz.pm:${PORTSDIR}/graphics/p5-GraphViz \
+		${SITE_PERL}/${PERL_ARCH}/Math/Random.pm:${PORTSDIR}/math/p5-Math-Random \
+		${SITE_PERL}/PostScript/TextBlock.pm:${PORTSDIR}/print/p5-PostScript \
+		${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \
+		${SITE_PERL}/Text/ParseWords.pm:${PORTSDIR}/textproc/p5-Text-ParseWords \
+		${SITE_PERL}/URI/Escape.pm:${PORTSDIR}/net/p5-URI
+
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 CONFLICTS=	p5-bioperl-1.[13579]*
 
-PERL_CONFIGURE=	YES
+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_dbsplit.pl.1 \
+		bp_download_query_genbank.pl.1 \
 		bp_extract_feature_seq.pl.1 \
 		bp_fast_load_gff.pl.1 \
-		bp_feature_draw.pl.1 \
+		bp_fastam9_to_table.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_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_pg_bulk_load_gff.pl.1 \
+		bp_parse_hmmsearch.pl.1 \
 		bp_process_gadfly.pl.1 \
-		bp_process_ncbi_human.pl.1 \
 		bp_process_sgd.pl.1 \
 		bp_process_wormbase.pl.1 \
+		bp_query_entrez_taxa.pl.1 \
 		bp_remote_blast.pl.1 \
 		bp_search2BSML.pl.1 \
 		bp_search2alnblocks.pl.1 \
 		bp_search2gff.pl.1 \
+		bp_search2table.pl.1 \
 		bp_search2tribe.pl.1 \
-		bp_search_overview.pl.1 \
 		bp_seq_length.pl.1 \
 		bp_seqconvert.pl.1 \
+		bp_seqret.pl.1 \
+		bp_seqretsplit.pl.1 \
 		bp_split_seq.pl.1 \
 		bp_sreformat.pl.1 \
 		bp_taxid4species.pl.1 \
-		bp_translate_seq.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::Handler::GenericAlignHandler.3 \
+		Bio::AlignIO::arp.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 \
@@ -109,10 +149,13 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::AlignIO::nexus.3 \
 		Bio::AlignIO::pfam.3 \
 		Bio::AlignIO::phylip.3 \
+		Bio::AlignIO::po.3 \
+		Bio::AlignIO::proda.3 \
 		Bio::AlignIO::prodom.3 \
 		Bio::AlignIO::psi.3 \
 		Bio::AlignIO::selex.3 \
 		Bio::AlignIO::stockholm.3 \
+		Bio::AlignIO::xmfa.3 \
 		Bio::AnalysisI.3 \
 		Bio::AnalysisParserI.3 \
 		Bio::AnalysisResultI.3 \
@@ -123,8 +166,12 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Annotation::DBLink.3 \
 		Bio::Annotation::OntologyTerm.3 \
 		Bio::Annotation::Reference.3 \
+		Bio::Annotation::Relation.3 \
 		Bio::Annotation::SimpleValue.3 \
 		Bio::Annotation::StructuredValue.3 \
+		Bio::Annotation::TagTree.3 \
+		Bio::Annotation::Target.3 \
+		Bio::Annotation::Tree.3 \
 		Bio::Annotation::TypeManager.3 \
 		Bio::AnnotationCollectionI.3 \
 		Bio::AnnotationI.3 \
@@ -133,8 +180,11 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Assembly::IO.3 \
 		Bio::Assembly::IO::ace.3 \
 		Bio::Assembly::IO::phrap.3 \
+		Bio::Assembly::IO::tigr.3 \
 		Bio::Assembly::Scaffold.3 \
 		Bio::Assembly::ScaffoldI.3 \
+		Bio::Assembly::Singlet.3 \
+		Bio::Assembly::Tools::ContigSpectrum.3 \
 		Bio::Biblio.3 \
 		Bio::Biblio::Article.3 \
 		Bio::Biblio::BiblioBase.3 \
@@ -176,6 +226,7 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -190,12 +241,17 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Coordinate::Utils.3 \
 		Bio::DB::Ace.3 \
 		Bio::DB::Biblio::biofetch.3 \
+		Bio::DB::Biblio::eutils.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::EntrezGene.3 \
+		Bio::DB::Expression.3 \
+		Bio::DB::Expression::geo.3 \
 		Bio::DB::Failover.3 \
 		Bio::DB::Fasta.3 \
 		Bio::DB::FileCache.3 \
@@ -205,11 +261,11 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -217,19 +273,25 @@ MAN3=		Bio::Align::AlignI.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_iterator.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::gene.3 \
 		Bio::DB::GFF::Aggregator::match.3 \
 		Bio::DB::GFF::Aggregator::none.3 \
+		Bio::DB::GFF::Aggregator::orf.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 \
@@ -250,25 +312,53 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::DB::GFF::Util::Rearrange.3 \
 		Bio::DB::GenBank.3 \
 		Bio::DB::GenPept.3 \
+		Bio::DB::GenericWebAgent.3 \
+		Bio::DB::HIV.3 \
+		Bio::DB::HIV::HIVAnnotProcessor.3 \
+		Bio::DB::HIV::HIVQueryHelper.3 \
 		Bio::DB::InMemoryCache.3 \
+		Bio::DB::LocationI.3 \
 		Bio::DB::MeSH.3 \
 		Bio::DB::NCBIHelper.3 \
+		Bio::DB::Qual.3 \
 		Bio::DB::Query::GenBank.3 \
+		Bio::DB::Query::HIVQuery.3 \
 		Bio::DB::Query::WebQuery.3 \
 		Bio::DB::QueryI.3 \
 		Bio::DB::RandomAccessI.3 \
 		Bio::DB::RefSeq.3 \
+		Bio::DB::ReferenceI.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::FeatureFileLoader.3 \
+		Bio::DB::SeqFeature::Store::GFF2Loader.3 \
+		Bio::DB::SeqFeature::Store::GFF3Loader.3 \
+		Bio::DB::SeqFeature::Store::LoadHelper.3 \
+		Bio::DB::SeqFeature::Store::Loader.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::TFBS.3 \
+		Bio::DB::TFBS::transfac_pro.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 \
@@ -276,19 +366,24 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -296,63 +391,27 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Factory::SequenceStreamI.3 \
 		Bio::Factory::TreeFactoryI.3 \
 		Bio::FeatureHolderI.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::cds.3 \
-		Bio::Graphics::Glyph::crossbox.3 \
-		Bio::Graphics::Glyph::diamond.3 \
-		Bio::Graphics::Glyph::dna.3 \
-		Bio::Graphics::Glyph::dot.3 \
-		Bio::Graphics::Glyph::ellipse.3 \
-		Bio::Graphics::Glyph::ex.3 \
-		Bio::Graphics::Glyph::extending_arrow.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::line.3 \
-		Bio::Graphics::Glyph::minmax.3 \
-		Bio::Graphics::Glyph::oval.3 \
-		Bio::Graphics::Glyph::pinsertion.3 \
-		Bio::Graphics::Glyph::primers.3 \
-		Bio::Graphics::Glyph::processed_transcript.3 \
-		Bio::Graphics::Glyph::redgreen_box.3 \
-		Bio::Graphics::Glyph::redgreen_segment.3 \
-		Bio::Graphics::Glyph::rndrect.3 \
-		Bio::Graphics::Glyph::ruler_arrow.3 \
-		Bio::Graphics::Glyph::segmented_keyglyph.3 \
-		Bio::Graphics::Glyph::segments.3 \
-		Bio::Graphics::Glyph::span.3 \
-		Bio::Graphics::Glyph::splice_site.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::xyplot.3 \
-		Bio::Graphics::Panel.3 \
-		Bio::Graphics::Pictogram.3 \
-		Bio::Graphics::RendererI.3 \
-		Bio::Graphics::Util.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::FeatureIO::vecscreen_simple.3 \
+		Bio::HandlerBaseI.3 \
 		Bio::IdCollectionI.3 \
 		Bio::IdentifiableI.3 \
 		Bio::Index::Abstract.3 \
 		Bio::Index::AbstractSeq.3 \
 		Bio::Index::Blast.3 \
+		Bio::Index::BlastTable.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::Stockholm.3 \
 		Bio::Index::SwissPfam.3 \
 		Bio::Index::Swissprot.3 \
 		Bio::LiveSeq::AARange.3 \
@@ -363,7 +422,6 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -386,34 +444,58 @@ MAN3=		Bio::Align::AlignI.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::Gene.3 \
+		Bio::Map::GeneMap.3 \
+		Bio::Map::GenePosition.3 \
+		Bio::Map::GeneRelative.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::Physical.3 \
 		Bio::Map::Position.3 \
+		Bio::Map::PositionHandler.3 \
+		Bio::Map::PositionHandlerI.3 \
 		Bio::Map::PositionI.3 \
+		Bio::Map::PositionWithSequence.3 \
+		Bio::Map::Prediction.3 \
+		Bio::Map::Relative.3 \
+		Bio::Map::RelativeI.3 \
 		Bio::Map::SimpleMap.3 \
+		Bio::Map::TranscriptionFactor.3 \
 		Bio::MapIO.3 \
+		Bio::MapIO::fpc.3 \
 		Bio::MapIO::mapmaker.3 \
 		Bio::Matrix::Generic.3 \
 		Bio::Matrix::IO.3 \
+		Bio::Matrix::IO::mlagan.3 \
 		Bio::Matrix::IO::phylip.3 \
 		Bio::Matrix::IO::scoring.3 \
 		Bio::Matrix::MatrixI.3 \
+		Bio::Matrix::Mlagan.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 \
@@ -422,8 +504,12 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Matrix::PSM::SiteMatrixI.3 \
 		Bio::Matrix::PhylipDist.3 \
 		Bio::Matrix::Scoring.3 \
+		Bio::MolEvol::CodonModel.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 \
@@ -434,7 +520,8 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -446,8 +533,10 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::OntologyIO::InterProParser.3 \
 		Bio::OntologyIO::dagflat.3 \
 		Bio::OntologyIO::goflat.3 \
+		Bio::OntologyIO::obo.3 \
 		Bio::OntologyIO::simplehierarchy.3 \
 		Bio::OntologyIO::soflat.3 \
+		Bio::ParameterBaseI.3 \
 		Bio::Perl.3 \
 		Bio::Phenotype::Correlate.3 \
 		Bio::Phenotype::MeSH::Term.3 \
@@ -459,10 +548,22 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Phenotype::OMIM::OMIMparser.3 \
 		Bio::Phenotype::Phenotype.3 \
 		Bio::Phenotype::PhenotypeI.3 \
+		Bio::PhyloNetwork.3 \
+		Bio::PhyloNetwork::Factory.3 \
+		Bio::PhyloNetwork::FactoryX.3 \
+		Bio::PhyloNetwork::GraphViz.3 \
+		Bio::PhyloNetwork::RandomFactory.3 \
+		Bio::PhyloNetwork::TreeFactory.3 \
+		Bio::PhyloNetwork::TreeFactoryMulti.3 \
+		Bio::PhyloNetwork::TreeFactoryX.3 \
+		Bio::PhyloNetwork::muVector.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 \
@@ -474,8 +575,11 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -488,50 +592,63 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Restriction::IO::bairoch.3 \
 		Bio::Restriction::IO::base.3 \
 		Bio::Restriction::IO::itype2.3 \
+		Bio::Restriction::IO::prototype.3 \
 		Bio::Restriction::IO::withrefm.3 \
-		Bio::Root::Err.3 \
+		Bio::Root::Build.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::Test.3 \
+		Bio::Root::Test::Warn.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::BlastPullHSP.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::HmmpfamHSP.3 \
+		Bio::Search::HSP::ModelHSP.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::BlastPullHit.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::HmmpfamHit.3 \
+		Bio::Search::Hit::ModelHit.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::BlastPullResult.3 \
 		Bio::Search::Result::BlastResult.3 \
+		Bio::Search::Result::CrossMatchResult.3 \
 		Bio::Search::Result::GenericResult.3 \
 		Bio::Search::Result::HMMERResult.3 \
+		Bio::Search::Result::HmmpfamResult.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 \
@@ -546,29 +663,40 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::SearchIO::Writer::HitTableWriter.3 \
 		Bio::SearchIO::Writer::ResultTableWriter.3 \
 		Bio::SearchIO::Writer::TextResultWriter.3 \
+		Bio::SearchIO::XML::BlastHandler.3 \
+		Bio::SearchIO::XML::PsiBlastHandler.3 \
 		Bio::SearchIO::axt.3 \
 		Bio::SearchIO::blast.3 \
+		Bio::SearchIO::blast_pull.3 \
 		Bio::SearchIO::blasttable.3 \
 		Bio::SearchIO::blastxml.3 \
+		Bio::SearchIO::cross_match.3 \
+		Bio::SearchIO::erpin.3 \
 		Bio::SearchIO::exonerate.3 \
 		Bio::SearchIO::fasta.3 \
 		Bio::SearchIO::hmmer.3 \
+		Bio::SearchIO::hmmer_pull.3 \
+		Bio::SearchIO::infernal.3 \
 		Bio::SearchIO::megablast.3 \
 		Bio::SearchIO::psl.3 \
+		Bio::SearchIO::rnamotif.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 \
@@ -578,6 +706,10 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Seq::SequenceTrace.3 \
 		Bio::Seq::TraceI.3 \
 		Bio::SeqAnalysisParserI.3 \
+		Bio::SeqEvolution::DNAPoint.3 \
+		Bio::SeqEvolution::EvolutionI.3 \
+		Bio::SeqEvolution::Factory.3 \
+		Bio::SeqFeature::Annotated.3 \
 		Bio::SeqFeature::AnnotationAdaptor.3 \
 		Bio::SeqFeature::Collection.3 \
 		Bio::SeqFeature::CollectionI.3 \
@@ -595,40 +727,56 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::SeqFeature::Gene::TranscriptI.3 \
 		Bio::SeqFeature::Gene::UTR.3 \
 		Bio::SeqFeature::Generic.3 \
+		Bio::SeqFeature::Lite.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::Handler::GenericRichSeqHandler.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::embldriver.3 \
+		Bio::SeqIO::entrezgene.3 \
+		Bio::SeqIO::excel.3 \
 		Bio::SeqIO::exp.3 \
 		Bio::SeqIO::fasta.3 \
 		Bio::SeqIO::fastq.3 \
+		Bio::SeqIO::flybase_chadoxml.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::gbdriver.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 \
@@ -637,9 +785,15 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::SeqIO::qual.3 \
 		Bio::SeqIO::raw.3 \
 		Bio::SeqIO::scf.3 \
+		Bio::SeqIO::strider.3 \
 		Bio::SeqIO::swiss.3 \
+		Bio::SeqIO::swissdriver.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 \
@@ -661,6 +815,7 @@ MAN3=		Bio::Align::AlignI.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 \
@@ -680,25 +835,34 @@ MAN3=		Bio::Align::AlignI.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::ERPIN.3 \
 		Bio::Tools::ESTScan.3 \
+		Bio::Tools::EUtilities.3 \
+		Bio::Tools::EUtilities::Cookie.3 \
+		Bio::Tools::EUtilities::EUtilDataI.3 \
+		Bio::Tools::EUtilities::EUtilParameters.3 \
+		Bio::Tools::EUtilities::History.3 \
+		Bio::Tools::EUtilities::HistoryI.3 \
+		Bio::Tools::EUtilities::Info.3 \
+		Bio::Tools::EUtilities::Info::FieldInfo.3 \
+		Bio::Tools::EUtilities::Info::LinkInfo.3 \
+		Bio::Tools::EUtilities::Link.3 \
+		Bio::Tools::EUtilities::Link::LinkSet.3 \
+		Bio::Tools::EUtilities::Link::UrlLink.3 \
+		Bio::Tools::EUtilities::Query.3 \
+		Bio::Tools::EUtilities::Query::GlobalQuery.3 \
+		Bio::Tools::EUtilities::Summary.3 \
+		Bio::Tools::EUtilities::Summary::DocSum.3 \
+		Bio::Tools::EUtilities::Summary::Item.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 \
@@ -710,14 +874,19 @@ MAN3=		Bio::Align::AlignI.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::Infernal.3 \
 		Bio::Tools::Lucy.3 \
 		Bio::Tools::MZEF.3 \
+		Bio::Tools::Match.3 \
 		Bio::Tools::OddCodes.3 \
+		Bio::Tools::Phylo::Gerp.3 \
+		Bio::Tools::Phylo::Gumby.3 \
 		Bio::Tools::Phylo::Molphy.3 \
 		Bio::Tools::Phylo::Molphy::Result.3 \
 		Bio::Tools::Phylo::PAML.3 \
@@ -735,30 +904,47 @@ MAN3=		Bio::Align::AlignI.3 \
 		Bio::Tools::Profile.3 \
 		Bio::Tools::Promoterwise.3 \
 		Bio::Tools::PrositeScan.3 \
+		Bio::Tools::Protparam.3 \
 		Bio::Tools::Pseudowise.3 \
 		Bio::Tools::QRNA.3 \
+		Bio::Tools::RNAMotif.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::StandAloneNCBIBlast.3 \
+		Bio::Tools::Run::StandAloneWUBlast.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::Signalp::ExtendedSignalp.3 \
 		Bio::Tools::Sim4::Exon.3 \
 		Bio::Tools::Sim4::Results.3 \
+		Bio::Tools::Spidey::Exon.3 \
+		Bio::Tools::Spidey::Results.3 \
+		Bio::Tools::TandemRepeatsFinder.3 \
+		Bio::Tools::TargetP.3 \
 		Bio::Tools::Tmhmm.3 \
-		Bio::Tools::WWW.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::AnnotatableNode.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 \
@@ -769,10 +955,13 @@ MAN3=		Bio::Align::AlignI.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::phyloxml.3 \
 		Bio::TreeIO::svggraph.3 \
 		Bio::TreeIO::tabtree.3 \
 		Bio::UpdateableSeqI.3 \
@@ -787,17 +976,15 @@ MAN3=		Bio::Align::AlignI.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
+		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)
@@ -808,7 +995,7 @@ post-install:
 	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
-.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README
+.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST PLATFORMS README
 	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
 .endfor
 	${CP} -R ${WRKSRC}/doc ${DOCSDIR}
diff --git a/biology/p5-bioperl/distinfo b/biology/p5-bioperl/distinfo
index 76333518a015..2908ee9e9b23 100644
--- a/biology/p5-bioperl/distinfo
+++ b/biology/p5-bioperl/distinfo
@@ -1,3 +1,3 @@
-MD5 (bioperl-1.4.tar.gz) = 5ef3e6e824c3f444e788d7fc9bda1fcb
-SHA256 (bioperl-1.4.tar.gz) = 0e59ece6834c532d31f874e44b14f1c6cf103d465368c143bfac19cf49926b1a
-SIZE (bioperl-1.4.tar.gz) = 4902946
+MD5 (BioPerl-1.6.0.tar.gz) = ce38cba5f06aaf3c692c1a32218cde87
+SHA256 (BioPerl-1.6.0.tar.gz) = 46d7fce2a20128f8515a9690feb27d9fd65023a2f85c83dca781d0aa1ba1e889
+SIZE (BioPerl-1.6.0.tar.gz) = 6813396
diff --git a/biology/p5-bioperl/files/patch-Build.PL b/biology/p5-bioperl/files/patch-Build.PL
new file mode 100644
index 000000000000..b6f498ff7505
--- /dev/null
+++ b/biology/p5-bioperl/files/patch-Build.PL
@@ -0,0 +1,97 @@
+--- Build.PL.orig	2009-01-25 02:19:13.000000000 -0300
++++ Build.PL	2009-02-22 02:21:33.000000000 -0300
+@@ -36,7 +36,7 @@
+                             'Test::More'                => 0,
+                             'Module::Build'             => 0.2805,
+                             'Test::Harness'             => 2.62,
+-                            'CPAN'                      => 1.81
++                            #'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',
+@@ -214,83 +214,8 @@
+ 
+ sub prompt_for_biodb {
+     my $accept = shift;
+-    my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
+-                              "Bio::DB::SeqFeature::Store live database tests? ".
+-                              "y/n", 'n');
+-    
+-    if ($proceed) {
+-        my @driver_choices;
+-        foreach my $poss ('mysql', 'Pg', 'Oracle') {
+-            if (grep {/$poss/i} @drivers) {
+-                my $choice = $poss;
+-                $choice =~ s/^(.)/[$1]/;
+-                push(@driver_choices, $choice);
+-            }
+-        }
+-        
+-        my $driver;
+-        if (@driver_choices > 1) {
+-            my ($default) = $driver_choices[0] =~ /\[(.)/;
+-            $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
+-        }
+-        else {
+-            ($driver) = $driver_choices[0] =~ /\[(.)/;
+-        }
+-        if ($driver =~ /^[mM]/) {
+-            $driver = 'mysql';
+-        }
+-        elsif ($driver =~ /^[pP]/) {
+-            $driver = 'Pg';
+-        }
+-        elsif ($driver =~ /^[oO]/) {
+-            $driver = 'Oracle';
+-        }
+-        
+-        my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
+-                                     "This database should already be present but doesn't have to ".
+-                                     "be preloaded for any schema", 'test');
+-        my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
+-        my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
+-        my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
+-        
+-        my $use_host = 1;
+-        if ($test_host eq 'undef' || $test_host eq 'localhost') {
+-            $use_host = 0;
+-        }
+-        
+-        my $test_dsn;
+-        if ($driver eq 'Pg') {
+-            $test_dsn = "dbi:$driver:dbname=$test_db";
+-            $mysql_ok = 0;
+-        }
+-        else {
+-            $test_dsn = "dbi:$driver:database=$test_db";
+-            $mysql_ok = 0;
+-        }
+-        if ($use_host) {
+-            $test_dsn .= ";host=$test_host";
+-        }
+-        
+-        $build->notes(dbd_driver => $driver);
+-        $build->notes(test_db => $test_db);
+-        $build->notes(test_host => $test_host);
+-        $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
+-        $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
+-        $build->notes(test_dsn => $test_dsn);
+-        
+-        $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
+-                        "    Database $test_db\n",
+-                        "    Host     $test_host\n",
+-                        "    DSN      $test_dsn\n",
+-                        "    User     $test_user\n",
+-                        "    Password $test_pass\n");
+-        $build->log_info("  - will not run the BioDBSeqFeature live ".
+-                         "database tests (requires MySQL driver)\n") unless ($driver eq 'mysql');
+-    }
+-    else {
+-        $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
+-    }
+-    
++    my $proceed = 0;
++    $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
+     $build->log_info("\n");
+     return $proceed;
+ }
diff --git a/biology/p5-bioperl/files/patch-Build.pm b/biology/p5-bioperl/files/patch-Build.pm
new file mode 100644
index 000000000000..bdca7e89404b
--- /dev/null
+++ b/biology/p5-bioperl/files/patch-Build.pm
@@ -0,0 +1,73 @@
+--- Bio/Root/Build.pm.orig	2009-01-25 02:19:26.000000000 -0300
++++ Bio/Root/Build.pm	2009-02-22 02:24:05.000000000 -0300
+@@ -141,48 +141,8 @@
+         }
+     }
+     closedir($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 = $accept ? 'a' : $self->prompt($question, 'a');
+-    
+-    if ($prompt =~ /^[aA]/) {
+-        $self->log_info("  - will install all scripts\n");
+-        $self->notes(chosen_scripts => 'all');
+-    }
+-    elsif ($prompt =~ /^[iI]/) {
+-        $self->log_info("  - will install interactively:\n");
+-        
+-        my @chosen_scripts;
+-        foreach my $group_dir (@group_dirs) {
+-            my $group = File::Basename::basename($group_dir);
+-            print "    * group '$group' has:\n";
+-            
+-            my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)};
+-            foreach my $script_file (@script_files) {
+-                my $script = File::Basename::basename($script_file);
+-                print "      $script\n";
+-            }
+-            
+-            my $result = $self->prompt("    Install scripts for group '$group'? [y]es [n]o [q]uit", 'n');
+-            die if $result =~ /^[qQ]/;
+-            if ($result =~ /^[yY]/) {
+-                $self->log_info("      + will install group '$group'\n");
+-                push(@chosen_scripts, @script_files);
+-            }
+-            else {
+-                $self->log_info("      - will not install group '$group'\n");
+-            }
+-        }
+-        
+-        my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none';
+-        
+-        $self->notes(chosen_scripts => $chosen_scripts);
+-    }
+-    else {
+-        $self->log_info("  - won't install any scripts\n");
+-        $self->notes(chosen_scripts => 'none');
+-    }
+-    
++    $self->log_info("  - will install all scripts\n");
++    $self->notes(chosen_scripts => 'all');    
+     print "\n";
+ }
+ 
+@@ -1177,16 +1137,9 @@
+ sub prompt_for_network {
+     my ($self, $accept) = @_;
+ 
+-    my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
+-    
+-    if ($proceed) {
+-        $self->notes(network => 1);
+-        $self->log_info("  - will run internet-requiring tests\n");
+-    }
+-    else {
+-        $self->notes(network => 0);
+-        $self->log_info("  - will not run internet-requiring tests\n");
+-    }
++    my $proceed = 0;
++    $self->notes(network => 0);
++    $self->log_info("  - will not run internet-requiring tests\n");
+ }
+ 
+ 1;
diff --git a/biology/p5-bioperl/files/patch-manify b/biology/p5-bioperl/files/patch-manify
deleted file mode 100644
index 9609fc951a0c..000000000000
--- a/biology/p5-bioperl/files/patch-manify
+++ /dev/null
@@ -1,29 +0,0 @@
---- Makefile.PL.orig	Sat Jan 10 00:11:42 2004
-+++ Makefile.PL	Sat Jan 10 00:12:15 2004
-@@ -358,16 +358,16 @@
- );
- 
- 
--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/pkg-plist b/biology/p5-bioperl/pkg-plist
index 5b1b57eec9bd..b9fb7f56c3fb 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1,843 +1,973 @@
-bin/bp_chaos_plot.pl
-bin/bp_composite_LD.pl
-bin/bp_pairwise_kaks.pl
+bin/bp_sreformat.pl
+bin/bp_seqconvert.pl
+bin/bp_parse_hmmsearch.pl
+bin/bp_seqret.pl
+bin/bp_tree2pag.pl
+bin/bp_meta_gff.pl
+bin/bp_nexus2nh.pl
+bin/bp_filter_search.pl
 bin/bp_flanks.pl
-bin/bp_translate_seq.pl
-bin/bp_feature_draw.pl
+bin/bp_seqfeature_gff3.pl
+bin/bp_generate_histogram.pl
+bin/bp_heterogeneity_test.pl
+bin/bp_split_seq.pl
 bin/bp_load_gff.pl
-bin/bp_biblio.pl
-bin/bp_fast_load_gff.pl
-bin/bp_search_overview.pl
-bin/bp_search2tribe.pl
+bin/bp_biogetseq.pl
 bin/bp_fetch.pl
-bin/bp_seq_length.pl
-bin/bp_search2gff.pl
-bin/bp_extract_feature_seq.pl
-bin/bp_pg_bulk_load_gff.pl
-bin/bp_sreformat.pl
+bin/bp_mutate.pl
+bin/bp_process_sgd.pl
 bin/bp_index.pl
 bin/bp_dbsplit.pl
+bin/bp_oligo_count.pl
+bin/bp_seq_length.pl
+bin/bp_seqfeature_load.pl
+bin/bp_process_gadfly.pl
+bin/bp_hmmer_to_table.pl
+bin/bp_fastam9_to_table.pl
+bin/bp_genbank2gff.pl
 bin/bp_biofetch_genbank_proxy.pl
+bin/bp_extract_feature_seq.pl
+bin/bp_search2gff.pl
+bin/bp_taxid4species.pl
+bin/bp_bulk_load_gff.pl
+bin/bp_blast2tree.pl
+bin/bp_make_mrna_protein.pl
+bin/bp_unflatten_seq.pl
+bin/bp_search2tribe.pl
 bin/bp_bioflat_index.pl
+bin/bp_seqfeature_delete.pl
+bin/bp_query_entrez_taxa.pl
+bin/bp_pairwise_kaks.pl
+bin/bp_fast_load_gff.pl
+bin/bp_chaos_plot.pl
+bin/bp_taxonomy2tree.pl
+bin/bp_mrtrans.pl
 bin/bp_search2alnblocks.pl
-bin/bp_local_taxonomydb_query.pl
-bin/bp_biogetseq.pl
-bin/bp_process_wormbase.pl
-bin/bp_search2BSML.pl
-bin/bp_taxid4species.pl
+bin/bp_download_query_genbank.pl
+bin/bp_nrdb.pl
 bin/bp_mask_by_search.pl
-bin/bp_mrtrans.pl
-bin/bp_process_gadfly.pl
 bin/bp_gccalc.pl
-bin/bp_seqconvert.pl
-bin/bp_oligo_count.pl
-bin/bp_process_ncbi_human.pl
-bin/bp_split_seq.pl
-bin/bp_remote_blast.pl
+bin/bp_composite_LD.pl
+bin/bp_classify_hits_kingdom.pl
 bin/bp_aacomp.pl
-bin/bp_heterogeneity_test.pl
-bin/bp_frend.pl
-bin/bp_generate_histogram.pl
-bin/bp_process_sgd.pl
-bin/bp_mutate.pl
-bin/bp_filter_search.pl
-bin/bp_genbank2gff.pl
-bin/bp_bulk_load_gff.pl
-bin/bp_nrdb.pl
-bin/bp_blast2tree.pl
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/.packlist
-%%SITE_PERL%%/biodatabases.pod
-%%SITE_PERL%%/biodesign.pod
-%%SITE_PERL%%/bptutorial.pl
-%%SITE_PERL%%/bioperl.pod
-%%SITE_PERL%%/bioscripts.pod
-%%SITE_PERL%%/Bio/MapIO.pm
-%%SITE_PERL%%/Bio/Seq.pm
-%%SITE_PERL%%/Bio/DasI.pm
-%%SITE_PERL%%/Bio/AnnotationCollectionI.pm
-%%SITE_PERL%%/Bio/SeqAnalysisParserI.pm
-%%SITE_PERL%%/Bio/SeqUtils.pm
-%%SITE_PERL%%/Bio/AnalysisResultI.pm
-%%SITE_PERL%%/Bio/SeqFeatureI.pm
-%%SITE_PERL%%/Bio/AnnotationI.pm
-%%SITE_PERL%%/Bio/SimpleAlign.pm
-%%SITE_PERL%%/Bio/SearchDist.pm
-%%SITE_PERL%%/Bio/Range.pm
-%%SITE_PERL%%/Bio/SeqI.pm
-%%SITE_PERL%%/Bio/IdCollectionI.pm
-%%SITE_PERL%%/Bio/Perl.pm
-%%SITE_PERL%%/Bio/ClusterI.pm
-%%SITE_PERL%%/Bio/Taxonomy.pm
-%%SITE_PERL%%/Bio/DescribableI.pm
-%%SITE_PERL%%/Bio/PrimarySeqI.pm
-%%SITE_PERL%%/Bio/AnnotatableI.pm
-%%SITE_PERL%%/Bio/TreeIO.pm
-%%SITE_PERL%%/Bio/Das/FeatureTypeI.pm
-%%SITE_PERL%%/Bio/Das/SegmentI.pm
-%%SITE_PERL%%/Bio/SeqIO.pm
-%%SITE_PERL%%/Bio/OntologyIO.pm
-%%SITE_PERL%%/Bio/DBLinkContainerI.pm
-%%SITE_PERL%%/Bio/AnalysisI.pm
-%%SITE_PERL%%/Bio/FeatureHolderI.pm
-%%SITE_PERL%%/Bio/AnalysisParserI.pm
-%%SITE_PERL%%/Bio/LocatableSeq.pm
-%%SITE_PERL%%/Bio/LocationI.pm
-%%SITE_PERL%%/Bio/Graphics.pm
-%%SITE_PERL%%/Bio/WebAgent.pm
-%%SITE_PERL%%/Bio/AlignIO.pm
-%%SITE_PERL%%/Bio/Biblio.pm
-%%SITE_PERL%%/Bio/RangeI.pm
-%%SITE_PERL%%/Bio/PrimarySeq.pm
-%%SITE_PERL%%/Bio/SearchIO.pm
-%%SITE_PERL%%/Bio/ClusterIO.pm
-%%SITE_PERL%%/Bio/SimpleAnalysisI.pm
-%%SITE_PERL%%/Bio/UpdateableSeqI.pm
-%%SITE_PERL%%/Bio/Species.pm
-%%SITE_PERL%%/Bio/IdentifiableI.pm
-%%SITE_PERL%%/Bio/MapIO/mapmaker.pm
-%%SITE_PERL%%/Bio/Expression/FeatureGroup.pm
-%%SITE_PERL%%/Bio/Expression/FeatureI.pm
-%%SITE_PERL%%/Bio/Expression/FeatureSet/FeatureSetMas50.pm
-%%SITE_PERL%%/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
-%%SITE_PERL%%/Bio/Align/StatisticsI.pm
+bin/bp_process_wormbase.pl
+bin/bp_local_taxonomydb_query.pl
+bin/bp_biblio.pl
+bin/bp_seqretsplit.pl
+bin/bp_remote_blast.pl
+bin/bp_genbank2gff3.pl
+bin/bp_search2table.pl
+bin/bp_search2BSML.pl
+bin/bp_translate_seq.pl
+bin/bp_pg_bulk_load_gff.pl
 %%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/Align/AlignI.pm
-%%SITE_PERL%%/Bio/TreeIO/nhx.pm
-%%SITE_PERL%%/Bio/TreeIO/tabtree.pm
-%%SITE_PERL%%/Bio/TreeIO/TreeEventBuilder.pm
-%%SITE_PERL%%/Bio/TreeIO/lintree.pm
-%%SITE_PERL%%/Bio/TreeIO/svggraph.pm
-%%SITE_PERL%%/Bio/TreeIO/nexus.pm
-%%SITE_PERL%%/Bio/TreeIO/newick.pm
-%%SITE_PERL%%/Bio/AlignIO/selex.pm
-%%SITE_PERL%%/Bio/AlignIO/meme.pm
-%%SITE_PERL%%/Bio/AlignIO/mase.pm
+%%SITE_PERL%%/Bio/AlignIO/Handler/GenericAlignHandler.pm
+%%SITE_PERL%%/Bio/AlignIO/mega.pm
+%%SITE_PERL%%/Bio/AlignIO/xmfa.pm
 %%SITE_PERL%%/Bio/AlignIO/prodom.pm
-%%SITE_PERL%%/Bio/AlignIO/psi.pm
-%%SITE_PERL%%/Bio/AlignIO/msf.pm
-%%SITE_PERL%%/Bio/AlignIO/metafasta.pm
-%%SITE_PERL%%/Bio/AlignIO/pfam.pm
-%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
 %%SITE_PERL%%/Bio/AlignIO/emboss.pm
-%%SITE_PERL%%/Bio/AlignIO/mega.pm
-%%SITE_PERL%%/Bio/AlignIO/nexus.pm
+%%SITE_PERL%%/Bio/AlignIO/mase.pm
 %%SITE_PERL%%/Bio/AlignIO/phylip.pm
+%%SITE_PERL%%/Bio/AlignIO/proda.pm
 %%SITE_PERL%%/Bio/AlignIO/maf.pm
-%%SITE_PERL%%/Bio/AlignIO/fasta.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/arp.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/Tree.pm
+%%SITE_PERL%%/Bio/Annotation/DBLink.pm
+%%SITE_PERL%%/Bio/Annotation/StructuredValue.pm
+%%SITE_PERL%%/Bio/Annotation/Relation.pm
+%%SITE_PERL%%/Bio/Annotation/TagTree.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/tigr.pm
+%%SITE_PERL%%/Bio/Assembly/IO/ace.pm
+%%SITE_PERL%%/Bio/Assembly/Tools/ContigSpectrum.pm
+%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm
+%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm
+%%SITE_PERL%%/Bio/Assembly/Singlet.pm
+%%SITE_PERL%%/Bio/Assembly/Scaffold.pm
+%%SITE_PERL%%/Bio/Assembly/Contig.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/BiblioBase.pm
+%%SITE_PERL%%/Bio/Biblio/IO.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/biofetch.pm
+%%SITE_PERL%%/Bio/DB/Biblio/eutils.pm
+%%SITE_PERL%%/Bio/DB/Biblio/soap.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/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
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+%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS
 %%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/load_ucsc.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/meta_gff.PLS
 %%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/process_ncbi_human.PLS
 %%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
+%%DATADIR%%/scripts/das/README
+%%DATADIR%%/scripts/das/TAG
+%%DATADIR%%/scripts/DB/biofetch_genbank_proxy.PLS
+%%DATADIR%%/scripts/DB/bioflat_index.PLS
+%%DATADIR%%/scripts/DB/biogetseq.PLS
+%%DATADIR%%/scripts/DB/flanks.PLS
+%%DATADIR%%/scripts/DB/TAG
+%%DATADIR%%/scripts/index/bp_fetch.PLS
+%%DATADIR%%/scripts/index/bp_index.PLS
+%%DATADIR%%/scripts/index/bp_seqret.PLS
+%%DATADIR%%/scripts/index/TAG
+%%DATADIR%%/scripts/tree/blast2tree.PLS
+%%DATADIR%%/scripts/tree/nexus2nh.PLS
+%%DATADIR%%/scripts/tree/TAG
+%%DATADIR%%/scripts/tree/tree2pag.PLS
+%%DATADIR%%/scripts/biblio/biblio.PLS
+%%DATADIR%%/scripts/biblio/TAG
+%%DATADIR%%/scripts/searchio/parse_hmmsearch.PLS
 %%DATADIR%%/scripts/searchio/filter_search.PLS
-%%DATADIR%%/scripts/seq/TAG
-%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
+%%DATADIR%%/scripts/searchio/hmmer_to_table.PLS
+%%DATADIR%%/scripts/searchio/fastam9_to_table.PLS
+%%DATADIR%%/scripts/searchio/README
+%%DATADIR%%/scripts/searchio/search2table.PLS
+%%DATADIR%%/scripts/searchio/TAG
+%%DATADIR%%/scripts/seq/unflatten_seq.PLS
+%%DATADIR%%/scripts/seq/make_mrna_protein.PLS
 %%DATADIR%%/scripts/seq/seqconvert.PLS
+%%DATADIR%%/scripts/seq/seqretsplit.PLS
 %%DATADIR%%/scripts/seq/split_seq.PLS
+%%DATADIR%%/scripts/seq/TAG
 %%DATADIR%%/scripts/seq/translate_seq.PLS
-%%DATADIR%%/scripts/seqstats/TAG
+%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
 %%DATADIR%%/scripts/seqstats/aacomp.PLS
 %%DATADIR%%/scripts/seqstats/chaos_plot.PLS
 %%DATADIR%%/scripts/seqstats/gccalc.PLS
 %%DATADIR%%/scripts/seqstats/oligo_count.PLS
-%%DATADIR%%/scripts/taxa/TAG
+%%DATADIR%%/scripts/seqstats/TAG
+%%DATADIR%%/scripts/taxa/classify_hits_kingdom.PLS
 %%DATADIR%%/scripts/taxa/local_taxonomydb_query.PLS
+%%DATADIR%%/scripts/taxa/query_entrez_taxa.PLS
+%%DATADIR%%/scripts/taxa/TAG
 %%DATADIR%%/scripts/taxa/taxid4species.PLS
-%%DATADIR%%/scripts/popgen/composite_LD.PLS
-%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
-%%DATADIR%%/scripts/install_bioperl_scripts.pl
-%%DATADIR%%/models/population_proposal.txt
-%%DATADIR%%/models/README
-%%DATADIR%%/models/bio_liveseq_variation.dia
-%%DATADIR%%/models/bio_map.dia
-%%DATADIR%%/models/bio_restriction.dia
-%%DATADIR%%/models/bioperl.dia
-%%DATADIR%%/models/coordinatemapper.dia
-%%DATADIR%%/models/map_proposal.txt
-%%DATADIR%%/models/maps_and_markers.dia
-%%DATADIR%%/models/popgen.dia
-%%DATADIR%%/models/biblio.dia
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrm %%SITE_PERL%%/Bio/Das
-@dirrm %%SITE_PERL%%/Bio/MapIO
-@dirrm %%SITE_PERL%%/Bio/Expression/FeatureSet
-@dirrm %%SITE_PERL%%/Bio/Expression/FeatureGroup
-@dirrm %%SITE_PERL%%/Bio/Expression
+%%DATADIR%%/scripts/taxa/taxonomy2tree.PLS
+%%DATADIR%%/scripts/utilities/TAG
+%%DATADIR%%/scripts/utilities/bp_nrdb.PLS
+%%DATADIR%%/scripts/utilities/bp_sreformat.PLS
+%%DATADIR%%/scripts/utilities/dbsplit.PLS
+%%DATADIR%%/scripts/utilities/download_query_genbank.PLS
+%%DATADIR%%/scripts/utilities/mask_by_search.PLS
+%%DATADIR%%/scripts/utilities/mutate.PLS
+%%DATADIR%%/scripts/utilities/pairwise_kaks.PLS
+%%DATADIR%%/scripts/utilities/README
+%%DATADIR%%/scripts/utilities/remote_blast.PLS
+%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
+%%DATADIR%%/scripts/utilities/search2BSML.PLS
+%%DATADIR%%/scripts/utilities/search2gff.PLS
+%%DATADIR%%/scripts/utilities/search2tribe.PLS
+%%DATADIR%%/scripts/utilities/seq_length.PLS
+%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
+%%DATADIR%%/scripts/README
 @dirrm %%SITE_PERL%%/Bio/Align
-@dirrm %%SITE_PERL%%/Bio/TreeIO
+@dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
 @dirrm %%SITE_PERL%%/Bio/AlignIO
-@dirrm %%SITE_PERL%%/Bio/Index
-@dirrm %%SITE_PERL%%/Bio/Symbol
-@dirrm %%SITE_PERL%%/Bio/Ontology
-@dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
-@dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
-@dirrm %%SITE_PERL%%/Bio/Phenotype
-@dirrm %%SITE_PERL%%/Bio/ClusterIO
-@dirrm %%SITE_PERL%%/Bio/PopGen/Simulation
-@dirrm %%SITE_PERL%%/Bio/PopGen/IO
-@dirrm %%SITE_PERL%%/Bio/PopGen
-@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
-@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
-@dirrm %%SITE_PERL%%/Bio/SeqFeature/Tools
-@dirrm %%SITE_PERL%%/Bio/SeqFeature
+@dirrm %%SITE_PERL%%/Bio/Annotation
+@dirrm %%SITE_PERL%%/Bio/Assembly/IO
+@dirrm %%SITE_PERL%%/Bio/Assembly/Tools
+@dirrm %%SITE_PERL%%/Bio/Assembly
+@dirrm %%SITE_PERL%%/Bio/Biblio/IO
+@dirrm %%SITE_PERL%%/Bio/Biblio
 @dirrm %%SITE_PERL%%/Bio/Cluster
-@dirrm %%SITE_PERL%%/Bio/Seq/Meta
-@dirrm %%SITE_PERL%%/Bio/Seq
+@dirrm %%SITE_PERL%%/Bio/ClusterIO
 @dirrm %%SITE_PERL%%/Bio/CodonUsage
-@dirrm %%SITE_PERL%%/Bio/Annotation
 @dirrm %%SITE_PERL%%/Bio/Coordinate/Result
 @dirrm %%SITE_PERL%%/Bio/Coordinate
+@dirrm %%SITE_PERL%%/Bio/DB/Biblio
+@dirrm %%SITE_PERL%%/Bio/DB/Expression
+@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
+@dirrm %%SITE_PERL%%/Bio/DB/Flat
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
+@dirrm %%SITE_PERL%%/Bio/DB/GFF
+@dirrm %%SITE_PERL%%/Bio/DB/HIV
+@dirrm %%SITE_PERL%%/Bio/DB/Query
+@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI
+@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store
+@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature
+@dirrm %%SITE_PERL%%/Bio/DB/SeqVersion
+@dirrm %%SITE_PERL%%/Bio/DB/TFBS
+@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
+@dirrm %%SITE_PERL%%/Bio/DB
+@dirrm %%SITE_PERL%%/Bio/Das
+@dirrm %%SITE_PERL%%/Bio/Event
+@dirrm %%SITE_PERL%%/Bio/Expression/FeatureGroup
+@dirrm %%SITE_PERL%%/Bio/Expression/FeatureSet
+@dirrm %%SITE_PERL%%/Bio/Expression
+@dirrm %%SITE_PERL%%/Bio/Factory
+@dirrm %%SITE_PERL%%/Bio/FeatureIO
+@dirrm %%SITE_PERL%%/Bio/Index
+@dirrm %%SITE_PERL%%/Bio/LiveSeq/IO
+@dirrm %%SITE_PERL%%/Bio/LiveSeq
+@dirrm %%SITE_PERL%%/Bio/Location
+@dirrm %%SITE_PERL%%/Bio/Map
+@dirrm %%SITE_PERL%%/Bio/MapIO
 @dirrm %%SITE_PERL%%/Bio/Matrix/IO
 @dirrm %%SITE_PERL%%/Bio/Matrix/PSM/IO
 @dirrm %%SITE_PERL%%/Bio/Matrix/PSM
 @dirrm %%SITE_PERL%%/Bio/Matrix
-@dirrm %%SITE_PERL%%/Bio/Tree
-@dirrm %%SITE_PERL%%/Bio/Structure/IO
-@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
-@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
-@dirrm %%SITE_PERL%%/Bio/Structure/SecStr
-@dirrm %%SITE_PERL%%/Bio/Structure
-@dirrm %%SITE_PERL%%/Bio/Assembly/IO
-@dirrm %%SITE_PERL%%/Bio/Assembly
-@dirrm %%SITE_PERL%%/Bio/Map
+@dirrm %%SITE_PERL%%/Bio/MolEvol
+@dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
+@dirrm %%SITE_PERL%%/Bio/Ontology
+@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
+@dirrm %%SITE_PERL%%/Bio/OntologyIO
+@dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
+@dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
+@dirrm %%SITE_PERL%%/Bio/Phenotype
+@dirrm %%SITE_PERL%%/Bio/PhyloNetwork
+@dirrm %%SITE_PERL%%/Bio/PopGen/IO
+@dirrm %%SITE_PERL%%/Bio/PopGen/Simulation
+@dirrm %%SITE_PERL%%/Bio/PopGen
+@dirrm %%SITE_PERL%%/Bio/Root/Test
+@dirrm %%SITE_PERL%%/Bio/Root
 @dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
 @dirrm %%SITE_PERL%%/Bio/Restriction/IO
 @dirrm %%SITE_PERL%%/Bio/Restriction
-@dirrm %%SITE_PERL%%/Bio/LiveSeq/IO
-@dirrm %%SITE_PERL%%/Bio/LiveSeq
-@dirrm %%SITE_PERL%%/Bio/Root
-@dirrm %%SITE_PERL%%/Bio/Search/Result
-@dirrm %%SITE_PERL%%/Bio/Search/Iteration
 @dirrm %%SITE_PERL%%/Bio/Search/HSP
 @dirrm %%SITE_PERL%%/Bio/Search/Hit
+@dirrm %%SITE_PERL%%/Bio/Search/Iteration
+@dirrm %%SITE_PERL%%/Bio/Search/Result
 @dirrm %%SITE_PERL%%/Bio/Search
-@dirrm %%SITE_PERL%%/Bio/Event
 @dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
+@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
 @dirrm %%SITE_PERL%%/Bio/SearchIO
-@dirrm %%SITE_PERL%%/Bio/Factory
-@dirrm %%SITE_PERL%%/Bio/Variation/IO
-@dirrm %%SITE_PERL%%/Bio/Variation
-@dirrm %%SITE_PERL%%/Bio/Tools/Run
-@dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS
-@dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
-@dirrm %%SITE_PERL%%/Bio/Tools/Primer
+@dirrm %%SITE_PERL%%/Bio/Seq/Meta
+@dirrm %%SITE_PERL%%/Bio/Seq
+@dirrm %%SITE_PERL%%/Bio/SeqEvolution
+@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
+@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
+@dirrm %%SITE_PERL%%/Bio/SeqFeature/Tools
+@dirrm %%SITE_PERL%%/Bio/SeqFeature
+@dirrm %%SITE_PERL%%/Bio/SeqIO/Handler
+@dirrm %%SITE_PERL%%/Bio/SeqIO/game
+@dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
+@dirrm %%SITE_PERL%%/Bio/SeqIO
+@dirrm %%SITE_PERL%%/Bio/Structure/IO
+@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
+@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
+@dirrm %%SITE_PERL%%/Bio/Structure/SecStr
+@dirrm %%SITE_PERL%%/Bio/Structure
+@dirrm %%SITE_PERL%%/Bio/Symbol
+@dirrm %%SITE_PERL%%/Bio/Taxonomy
 @dirrm %%SITE_PERL%%/Bio/Tools/Alignment
-@dirrm %%SITE_PERL%%/Bio/Tools/Blast
-@dirrm %%SITE_PERL%%/Bio/Tools/Prediction
-@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo
-@dirrm %%SITE_PERL%%/Bio/Tools/BPlite
 @dirrm %%SITE_PERL%%/Bio/Tools/Analysis/DNA
 @dirrm %%SITE_PERL%%/Bio/Tools/Analysis/Protein
 @dirrm %%SITE_PERL%%/Bio/Tools/Analysis
+@dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS
+@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Info
+@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Link
+@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Query
+@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Summary
+@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities
 @dirrm %%SITE_PERL%%/Bio/Tools/HMMER
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
+@dirrm %%SITE_PERL%%/Bio/Tools/Phylo
+@dirrm %%SITE_PERL%%/Bio/Tools/Prediction
+@dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
+@dirrm %%SITE_PERL%%/Bio/Tools/Primer
+@dirrm %%SITE_PERL%%/Bio/Tools/Run
+@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
+@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA
+@dirrm %%SITE_PERL%%/Bio/Tools/Signalp
+@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
+@dirrm %%SITE_PERL%%/Bio/Tools/Spidey
 @dirrm %%SITE_PERL%%/Bio/Tools
-@dirrm %%SITE_PERL%%/Bio/Graphics/FeatureFile
-@dirrm %%SITE_PERL%%/Bio/Graphics/Glyph
-@dirrm %%SITE_PERL%%/Bio/Graphics
-@dirrm %%SITE_PERL%%/Bio/Taxonomy
-@dirrm %%SITE_PERL%%/Bio/DB/Biblio
-@dirrm %%SITE_PERL%%/Bio/DB/Query
-@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
-@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
-@dirrm %%SITE_PERL%%/Bio/DB/Flat
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
-@dirrm %%SITE_PERL%%/Bio/DB/GFF
-@dirrm %%SITE_PERL%%/Bio/DB
-@dirrm %%SITE_PERL%%/Bio/Biblio/IO
-@dirrm %%SITE_PERL%%/Bio/Biblio
-@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
-@dirrm %%SITE_PERL%%/Bio/OntologyIO
-@dirrm %%SITE_PERL%%/Bio/Location
-@dirrm %%SITE_PERL%%/Bio/SeqIO/game
-@dirrm %%SITE_PERL%%/Bio/SeqIO
+@dirrm %%SITE_PERL%%/Bio/Tree/Draw
+@dirrm %%SITE_PERL%%/Bio/Tree
+@dirrm %%SITE_PERL%%/Bio/TreeIO
+@dirrm %%SITE_PERL%%/Bio/Variation/IO
+@dirrm %%SITE_PERL%%/Bio/Variation
 @dirrm %%SITE_PERL%%/Bio
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/faq
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples/graphics
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs/graphics
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html/images
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/pdf
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/sgml
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%EXAMPLESDIR%%/align
+@dirrm %%EXAMPLESDIR%%/root/lib/Bio
+@dirrm %%EXAMPLESDIR%%/root/lib
+@dirrm %%EXAMPLESDIR%%/root
 @dirrm %%EXAMPLESDIR%%/tools
 @dirrm %%EXAMPLESDIR%%/tk
-@dirrm %%EXAMPLESDIR%%/tree
+@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
+@dirrm %%EXAMPLESDIR%%/structure
 @dirrm %%EXAMPLESDIR%%/sirna
 @dirrm %%EXAMPLESDIR%%/searchio
-@dirrm %%EXAMPLESDIR%%/root/lib/Bio
-@dirrm %%EXAMPLESDIR%%/root/lib
-@dirrm %%EXAMPLESDIR%%/root
 @dirrm %%EXAMPLESDIR%%/db
+@dirrm %%EXAMPLESDIR%%/align
 @dirrm %%EXAMPLESDIR%%/biblio
-@dirrm %%EXAMPLESDIR%%/popgen
-@dirrm %%EXAMPLESDIR%%/biographics
+@dirrm %%EXAMPLESDIR%%/quality
+@dirrm %%EXAMPLESDIR%%/tree
 @dirrm %%EXAMPLESDIR%%/cluster
 @dirrm %%EXAMPLESDIR%%/contributed
 @dirrm %%EXAMPLESDIR%%/liveseq
-@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
+@dirrm %%EXAMPLESDIR%%/popgen
 @dirrm %%EXAMPLESDIR%%
-@dirrm %%DATADIR%%/scripts/index
-@dirrm %%DATADIR%%/scripts/utilities
-@dirrm %%DATADIR%%/scripts/DB
-@dirrm %%DATADIR%%/scripts/biblio
+@dirrm %%DATADIR%%/models
+@dirrm %%DATADIR%%/scripts/popgen
+@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
+@dirrm %%DATADIR%%/scripts/Bio-SeqFeature-Store
 @dirrm %%DATADIR%%/scripts/das
-@dirrm %%DATADIR%%/scripts/graphics
+@dirrm %%DATADIR%%/scripts/DB
+@dirrm %%DATADIR%%/scripts/index
 @dirrm %%DATADIR%%/scripts/tree
-@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
+@dirrm %%DATADIR%%/scripts/biblio
 @dirrm %%DATADIR%%/scripts/searchio
 @dirrm %%DATADIR%%/scripts/seq
 @dirrm %%DATADIR%%/scripts/seqstats
 @dirrm %%DATADIR%%/scripts/taxa
-@dirrm %%DATADIR%%/scripts/popgen
+@dirrm %%DATADIR%%/scripts/utilities
 @dirrm %%DATADIR%%/scripts
-@dirrm %%DATADIR%%/models
 @dirrm %%DATADIR%%
author	Renato Botelho <garga@FreeBSD.org>	2009-02-23 19:31:43 +0000
committer	Renato Botelho <garga@FreeBSD.org>	2009-02-23 19:31:43 +0000
commit	58d4bedcf436d78626be690db5da02da3064a913 (patch)
tree	c2e5451b22b6a0bfd1d4f7e4f822421fa25a7333 /biology
parent	Update to 0.6.4 (diff)