Attachment 143175 Details for Bug 190342 – p5-bioperl-1.6.923.patch

[patch] p5-bioperl-1.6.923.patch

p5-bioperl-1.6.923.patch (text/plain), 141.51 KB, created by Muhammad Moinur Rahman on 2014-05-28 14:30:00 UTC

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Creator: Muhammad Moinur Rahman

Created: 2014-05-28 14:30:00 UTC

Size: 141.51 KB

patch

obsolete

>diff -ruN /usr/ports//biology/p5-bioperl/Makefile ./Makefile
>--- /usr/ports//biology/p5-bioperl/Makefile	2014-04-09 15:49:02.000000000 +0600
>+++ ./Makefile	2014-05-28 18:39:33.004379957 +0600
>@@ -2,18 +2,19 @@
> # $FreeBSD: head/biology/p5-bioperl/Makefile 350675 2014-04-09 09:49:02Z bapt $
> 
> PORTNAME=	bioperl
>-PORTVERSION=	1.6.1
>-PORTREVISION=	4
>+PORTVERSION=	1.6.923
> CATEGORIES=	biology perl5
>-MASTER_SITES=	http://bioperl.org/DIST/ \
>-		CPAN
>+MASTER_SITES=	CPAN
>+MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
> PKGNAMEPREFIX=	p5-
> DISTNAME=	BioPerl-${PORTVERSION}
> 
> MAINTAINER=	wen@FreeBSD.org
> COMMENT=	A collection of Perl modules for bioinformatics
> 
>-BROKEN=		not staged
>+LICENSE=	ART10 GPLv1
>+LICENSE_COMB=	dual
>+
> BUILD_DEPENDS=	p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \
> 		p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
> 		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \
>@@ -38,7 +39,6 @@
> 		p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
> 		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
> 		p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \
>-		p5-AcePerl>=0:${PORTSDIR}/biology/p5-AcePerl \
> 		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
> 		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
> 		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
>@@ -53,954 +53,40 @@
> 		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
> 		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
> 		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
>-		p5-URI>=0:${PORTSDIR}/net/p5-URI
>+		p5-URI>=0:${PORTSDIR}/net/p5-URI \
>+		p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \
>+		p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \
>+		p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \
>+		p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \
>+		p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \
>+		p5-Error>=0:${PORTSDIR}/lang/p5-Error
> 
> RUN_DEPENDS:=	${BUILD_DEPENDS}
> 
>-#CONFLICTS=	p5-bioperl-1.[13579]*
>-
> USES=		perl5
> USE_PERL5=	modbuild
> 
>-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_einfo.pl.1 \
>-		bp_extract_feature_seq.pl.1 \
>-		bp_fast_load_gff.pl.1 \
>-		bp_fastam9_to_table.pl.1 \
>-		bp_fetch.pl.1 \
>-		bp_filter_search.pl.1 \
>-		bp_flanks.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_hivq.pl.1 \
>-		bp_hmmer_to_table.pl.1 \
>-		bp_index.pl.1 \
>-		bp_load_gff.pl.1 \
>-		bp_local_taxonomydb_query.pl.1 \
>-		bp_make_mrna_protein.pl.1 \
>-		bp_mask_by_search.pl.1 \
>-		bp_meta_gff.pl.1 \
>-		bp_mrtrans.pl.1 \
>-		bp_mutate.pl.1 \
>-		bp_nexus2nh.pl.1 \
>-		bp_nrdb.pl.1 \
>-		bp_oligo_count.pl.1 \
>-		bp_pairwise_kaks.pl.1 \
>-		bp_parse_hmmsearch.pl.1 \
>-		bp_process_gadfly.pl.1 \
>-		bp_process_sgd.pl.1 \
>-		bp_process_wormbase.pl.1 \
>-		bp_query_entrez_taxa.pl.1 \
>-		bp_remote_blast.pl.1 \
>-		bp_revtrans-motif.pl.1 \
>-		bp_search2BSML.pl.1 \
>-		bp_search2alnblocks.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_seqretsplit.pl.1 \
>-		bp_split_seq.pl.1 \
>-		bp_sreformat.pl.1 \
>-		bp_taxid4species.pl.1 \
>-		bp_taxonomy2tree.pl.1 \
>-		bp_translate_seq.pl.1 \
>-		bp_tree2pag.pl.1 \
>-		bp_unflatten_seq.pl.1
>-
>-MAN3=		Bio::Align::AlignI.3 \
>-		Bio::Align::DNAStatistics.3 \
>-		Bio::Align::PairwiseStatistics.3 \
>-		Bio::Align::ProteinStatistics.3 \
>-		Bio::Align::StatisticsI.3 \
>-		Bio::Align::Utilities.3 \
>-		Bio::AlignIO.3 \
>-		Bio::AlignIO::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 \
>-		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::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 \
>-		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::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 \
>-		Bio::Assembly::Contig.3 \
>-		Bio::Assembly::ContigAnalysis.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 \
>-		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::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 \
>-		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::BinarySearch.3 \
>-		Bio::DB::GFF.3 \
>-		Bio::DB::GFF::Adaptor::ace.3 \
>-		Bio::DB::GFF::Adaptor::berkeleydb.3 \
>-		Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 \
>-		Bio::DB::GFF::Adaptor::biofetch.3 \
>-		Bio::DB::GFF::Adaptor::biofetch_oracle.3 \
>-		Bio::DB::GFF::Adaptor::dbi.3 \
>-		Bio::DB::GFF::Adaptor::dbi::caching_handle.3 \
>-		Bio::DB::GFF::Adaptor::dbi::iterator.3 \
>-		Bio::DB::GFF::Adaptor::dbi::mysql.3 \
>-		Bio::DB::GFF::Adaptor::dbi::mysqlace.3 \
>-		Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3 \
>-		Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 \
>-		Bio::DB::GFF::Adaptor::dbi::oracle.3 \
>-		Bio::DB::GFF::Adaptor::dbi::oracleace.3 \
>-		Bio::DB::GFF::Adaptor::dbi::pg.3 \
>-		Bio::DB::GFF::Adaptor::dbi::pg_fts.3 \
>-		Bio::DB::GFF::Adaptor::memory.3 \
>-		Bio::DB::GFF::Adaptor::memory::feature_serializer.3 \
>-		Bio::DB::GFF::Adaptor::memory::iterator.3 \
>-		Bio::DB::GFF::Aggregator.3 \
>-		Bio::DB::GFF::Aggregator::alignment.3 \
>-		Bio::DB::GFF::Aggregator::clone.3 \
>-		Bio::DB::GFF::Aggregator::coding.3 \
>-		Bio::DB::GFF::Aggregator::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 \
>-		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::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::DBI::Pg.3 \
>-		Bio::DB::SeqFeature::Store::DBI::SQLite.3 \
>-		Bio::DB::SeqFeature::Store::berkeleydb3.3 \
>-		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::DBLinkContainerI.3 \
>-		Bio::Das::FeatureTypeI.3 \
>-		Bio::Das::SegmentI.3 \
>-		Bio::DasI.3 \
>-		Bio::DescribableI.3 \
>-		Bio::Event::EventGeneratorI.3 \
>-		Bio::Event::EventHandlerI.3 \
>-		Bio::Expression::Contact.3 \
>-		Bio::Expression::DataSet.3 \
>-		Bio::Expression::FeatureGroup.3 \
>-		Bio::Expression::FeatureGroup::FeatureGroupMas50.3 \
>-		Bio::Expression::FeatureI.3 \
>-		Bio::Expression::FeatureSet::FeatureSetMas50.3 \
>-		Bio::Expression::Platform.3 \
>-		Bio::Expression::ProbeI.3 \
>-		Bio::Expression::Sample.3 \
>-		Bio::Factory::AnalysisI.3 \
>-		Bio::Factory::ApplicationFactoryI.3 \
>-		Bio::Factory::DriverFactory.3 \
>-		Bio::Factory::FTLocationFactory.3 \
>-		Bio::Factory::LocationFactoryI.3 \
>-		Bio::Factory::MapFactoryI.3 \
>-		Bio::Factory::ObjectBuilderI.3 \
>-		Bio::Factory::ObjectFactory.3 \
>-		Bio::Factory::ObjectFactoryI.3 \
>-		Bio::Factory::SeqAnalysisParserFactory.3 \
>-		Bio::Factory::SeqAnalysisParserFactoryI.3 \
>-		Bio::Factory::SequenceFactoryI.3 \
>-		Bio::Factory::SequenceProcessorI.3 \
>-		Bio::Factory::SequenceStreamI.3 \
>-		Bio::Factory::TreeFactoryI.3 \
>-		Bio::FeatureHolderI.3 \
>-		Bio::FeatureIO.3 \
>-		Bio::FeatureIO::bed.3 \
>-		Bio::FeatureIO::gff.3 \
>-		Bio::FeatureIO::gtf.3 \
>-		Bio::FeatureIO::interpro.3 \
>-		Bio::FeatureIO::ptt.3 \
>-		Bio::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 \
>-		Bio::LiveSeq::Chain.3 \
>-		Bio::LiveSeq::ChainI.3 \
>-		Bio::LiveSeq::DNA.3 \
>-		Bio::LiveSeq::Exon.3 \
>-		Bio::LiveSeq::Gene.3 \
>-		Bio::LiveSeq::IO::BioPerl.3 \
>-		Bio::LiveSeq::IO::Loader.3 \
>-		Bio::LiveSeq::Intron.3 \
>-		Bio::LiveSeq::Mutation.3 \
>-		Bio::LiveSeq::Mutator.3 \
>-		Bio::LiveSeq::Prim_Transcript.3 \
>-		Bio::LiveSeq::Range.3 \
>-		Bio::LiveSeq::Repeat_Region.3 \
>-		Bio::LiveSeq::Repeat_Unit.3 \
>-		Bio::LiveSeq::SeqI.3 \
>-		Bio::LiveSeq::Transcript.3 \
>-		Bio::LiveSeq::Translation.3 \
>-		Bio::LocatableSeq.3 \
>-		Bio::Location::Atomic.3 \
>-		Bio::Location::AvWithinCoordPolicy.3 \
>-		Bio::Location::CoordinatePolicyI.3 \
>-		Bio::Location::Fuzzy.3 \
>-		Bio::Location::FuzzyLocationI.3 \
>-		Bio::Location::NarrowestCoordPolicy.3 \
>-		Bio::Location::Simple.3 \
>-		Bio::Location::Split.3 \
>-		Bio::Location::SplitLocationI.3 \
>-		Bio::Location::WidestCoordPolicy.3 \
>-		Bio::LocationI.3 \
>-		Bio::Map::Clone.3 \
>-		Bio::Map::Contig.3 \
>-		Bio::Map::CytoMap.3 \
>-		Bio::Map::CytoMarker.3 \
>-		Bio::Map::CytoPosition.3 \
>-		Bio::Map::EntityI.3 \
>-		Bio::Map::FPCMarker.3 \
>-		Bio::Map::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 \
>-		Bio::Matrix::PSM::PsmI.3 \
>-		Bio::Matrix::PSM::SiteMatrix.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 \
>-		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::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::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 \
>-		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::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 \
>-		Bio::PopGen::Marker.3 \
>-		Bio::PopGen::MarkerI.3 \
>-		Bio::PopGen::PopStats.3 \
>-		Bio::PopGen::Population.3 \
>-		Bio::PopGen::PopulationI.3 \
>-		Bio::PopGen::Simulation::Coalescent.3 \
>-		Bio::PopGen::Simulation::GeneticDrift.3 \
>-		Bio::PopGen::Statistics.3 \
>-		Bio::PopGen::TagHaplotype.3 \
>-		Bio::PopGen::Utilities.3 \
>-		Bio::PrimarySeq.3 \
>-		Bio::PrimarySeqI.3 \
>-		Bio::PullParserI.3 \
>-		Bio::Range.3 \
>-		Bio::RangeI.3 \
>-		Bio::Restriction::Analysis.3 \
>-		Bio::Restriction::Enzyme.3 \
>-		Bio::Restriction::Enzyme::MultiCut.3 \
>-		Bio::Restriction::Enzyme::MultiSite.3 \
>-		Bio::Restriction::EnzymeCollection.3 \
>-		Bio::Restriction::EnzymeI.3 \
>-		Bio::Restriction::IO.3 \
>-		Bio::Restriction::IO::bairoch.3 \
>-		Bio::Restriction::IO::base.3 \
>-		Bio::Restriction::IO::itype2.3 \
>-		Bio::Restriction::IO::prototype.3 \
>-		Bio::Restriction::IO::withrefm.3 \
>-		Bio::Root::Build.3 \
>-		Bio::Root::Exception.3 \
>-		Bio::Root::HTTPget.3 \
>-		Bio::Root::IO.3 \
>-		Bio::Root::Root.3 \
>-		Bio::Root::RootI.3 \
>-		Bio::Root::Storable.3 \
>-		Bio::Root::Test.3 \
>-		Bio::Root::Test::Warn.3 \
>-		Bio::Root::Utilities.3 \
>-		Bio::Root::Version.3 \
>-		Bio::Search::BlastStatistics.3 \
>-		Bio::Search::BlastUtils.3 \
>-		Bio::Search::DatabaseI.3 \
>-		Bio::Search::GenericDatabase.3 \
>-		Bio::Search::GenericStatistics.3 \
>-		Bio::Search::HSP::BlastHSP.3 \
>-		Bio::Search::HSP::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::Search::Tiling::MapTileUtils.3 \
>-		Bio::Search::Tiling::MapTiling.3 \
>-		Bio::Search::Tiling::TilingI.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::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::gmap_f9.3 \
>-		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 \
>-		Bio::Seq::SeqFactory.3 \
>-		Bio::Seq::SeqFastaSpeedFactory.3 \
>-		Bio::Seq::SeqWithQuality.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 \
>-		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::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 \
>-		Bio::SeqIO::pir.3 \
>-		Bio::SeqIO::pln.3 \
>-		Bio::SeqIO::qual.3 \
>-		Bio::SeqIO::raw.3 \
>-		Bio::SeqIO::scf.3 \
>-		Bio::SeqIO::strider.3 \
>-		Bio::SeqIO::swiss.3 \
>-		Bio::SeqIO::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 \
>-		Bio::SimpleAnalysisI.3 \
>-		Bio::Species.3 \
>-		Bio::Structure::Atom.3 \
>-		Bio::Structure::Chain.3 \
>-		Bio::Structure::Entry.3 \
>-		Bio::Structure::IO.3 \
>-		Bio::Structure::IO::pdb.3 \
>-		Bio::Structure::Model.3 \
>-		Bio::Structure::Residue.3 \
>-		Bio::Structure::SecStr::DSSP::Res.3 \
>-		Bio::Structure::SecStr::STRIDE::Res.3 \
>-		Bio::Structure::StructureI.3 \
>-		Bio::Symbol::Alphabet.3 \
>-		Bio::Symbol::AlphabetI.3 \
>-		Bio::Symbol::DNAAlphabet.3 \
>-		Bio::Symbol::ProteinAlphabet.3 \
>-		Bio::Symbol::Symbol.3 \
>-		Bio::Symbol::SymbolI.3 \
>-		Bio::Taxon.3 \
>-		Bio::Taxonomy.3 \
>-		Bio::Taxonomy::FactoryI.3 \
>-		Bio::Taxonomy::Node.3 \
>-		Bio::Taxonomy::Taxon.3 \
>-		Bio::Taxonomy::Tree.3 \
>-		Bio::Tools::AlignFactory.3 \
>-		Bio::Tools::Alignment::Consed.3 \
>-		Bio::Tools::Alignment::Trim.3 \
>-		Bio::Tools::Analysis::DNA::ESEfinder.3 \
>-		Bio::Tools::Analysis::Protein::Domcut.3 \
>-		Bio::Tools::Analysis::Protein::ELM.3 \
>-		Bio::Tools::Analysis::Protein::GOR4.3 \
>-		Bio::Tools::Analysis::Protein::HNN.3 \
>-		Bio::Tools::Analysis::Protein::Mitoprot.3 \
>-		Bio::Tools::Analysis::Protein::NetPhos.3 \
>-		Bio::Tools::Analysis::Protein::Scansite.3 \
>-		Bio::Tools::Analysis::Protein::Sopma.3 \
>-		Bio::Tools::Analysis::SimpleAnalysisBase.3 \
>-		Bio::Tools::AnalysisResult.3 \
>-		Bio::Tools::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::EUtilities::Summary::ItemContainerI.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::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 \
>-		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::Protparam.3 \
>-		Bio::Tools::Pseudowise.3 \
>-		Bio::Tools::QRNA.3 \
>-		Bio::Tools::RNAMotif.3 \
>-		Bio::Tools::RandomDistFunctions.3 \
>-		Bio::Tools::RepeatMasker.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::SeqPattern::Backtranslate.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::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 \
>-		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::phyloxml.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
>-
>-# now install all extra stuff (docs, examples, scripts, models)
>-NO_STAGE=	yes
>-
>-OPTIONS_DEFINE=	DOCS
>+OPTIONS_DEFINE=	DOCS PGTEST SQLITETEST
>+PGTEST_DESC=	Test PostGreSQL
>+SQLITETEST_DESC=	Test SQLite
>+PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
>+PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
>+SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
>+SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
> 
> .include <bsd.port.options.mk>
> 
> post-install:
>-	${MKDIR} ${DATADIR}
>-	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
>-	${MKDIR} ${EXAMPLESDIR}
>-	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
>+	${MKDIR} ${STAGEDIR}${DATADIR}
>+	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR}
>+	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
>+	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
> .if ${PORT_OPTIONS:MDOCS}
>-	${MKDIR} ${DOCSDIR}
>+	${MKDIR} ${STAGEDIR}${DOCSDIR}
> .for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
>-	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
>+	${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
> .endfor
>-	${CP} -R ${WRKSRC}/doc ${DOCSDIR}
>+	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}
> .endif
> 
> .include <bsd.port.mk>
>diff -ruN /usr/ports//biology/p5-bioperl/distinfo ./distinfo
>--- /usr/ports//biology/p5-bioperl/distinfo	2014-01-22 21:30:13.000000000 +0600
>+++ ./distinfo	2014-05-28 15:19:33.131207174 +0600
>@@ -1,2 +1,2 @@
>-SHA256 (BioPerl-1.6.1.tar.gz) = ac36dace2b4dd973567b02cce29158beac05fd672872ca8769e02bbddddc95a3
>-SIZE (BioPerl-1.6.1.tar.gz) = 10462526
>+SHA256 (BioPerl-1.6.923.tar.gz) = 6f6ada4ebd51ad223662e4b1ddcccc37a4fb8c47f3ecbbf060e6844d361730cd
>+SIZE (BioPerl-1.6.923.tar.gz) = 12562520
>diff -ruN /usr/ports//biology/p5-bioperl/files/patch-Bio-Root-Build.pm ./files/patch-Bio-Root-Build.pm
>--- /usr/ports//biology/p5-bioperl/files/patch-Bio-Root-Build.pm	2014-01-22 23:40:44.000000000 +0600
>+++ ./files/patch-Bio-Root-Build.pm	2014-05-28 15:51:47.688073934 +0600
>@@ -1,31 +1,33 @@
> --- Bio/Root/Build.pm.orig	2009-09-30 00:33:53.000000000 +0800
> +++ Bio/Root/Build.pm	2009-12-01 10:31:39.000000000 +0800
>-@@ -124,48 +124,8 @@
>+@@ -127,49 +127,9 @@
>          }
>      }
>      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 $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]/) {
>@@ -36,30 +38,34 @@
> -                $self->log_info("      - will not install group '$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'); 
>++    $self->log_info("  - willt install all scripts\n");
>++    $self->notes(chosen_scripts => 'all');
>+ 
>      print "\n";
>  }
>- 
>-@@ -1205,16 +1165,9 @@
>+@@ -1136,21 +1096,9 @@
>  sub prompt_for_network {
>      my ($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->notes('network' => 1);
> -        $self->log_info("  - will run internet-requiring tests\n");
>+-        my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n');
>+-        if ($use_email) {
>+-            my $address = $self->prompt("Enter email address:");
>+-            $self->notes(email => $address);
>+-        }
> -    }
> -    else {
> -        $self->notes(network => 0);
>@@ -70,4 +76,4 @@
> +    $self->log_info("  - will not run internet-requiring tests\n");
>  }
>  
>- 1;
>+ # override the build script warnings flag
>diff -ruN /usr/ports//biology/p5-bioperl/files/patch-Build.PL ./files/patch-Build.PL
>--- /usr/ports//biology/p5-bioperl/files/patch-Build.PL	2014-01-22 23:40:44.000000000 +0600
>+++ ./files/patch-Build.PL	2014-05-28 15:52:02.303073270 +0600
>@@ -1,22 +1,21 @@
> --- Build.PL.orig	2009-09-30 00:33:45.000000000 +0800
> +++ Build.PL	2009-12-01 10:25:51.000000000 +0800
>-@@ -37,7 +37,7 @@
>-                             'Test::More'                => 0,
>+@@ -187,7 +187,6 @@
>+                            },
>+ 
>+     build_requires      => {
>+-                            'CPAN'                      => 1.81,
>                              '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',
>-@@ -234,86 +234,9 @@
>+                             'Test::Most'                => 0,
>+@@ -376,86 +375,8 @@
>  
>  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 ('SQLite', 'mysql', 'Pg', 'Oracle') {
>@@ -26,7 +25,7 @@
> -                push(@driver_choices, $choice);
> -            }
> -        }
>--        
>+-
> -        my $driver;
> -        if (@driver_choices > 1) {
> -            my ($default) = $driver_choices[0] =~ /\[(.)/;
>@@ -47,19 +46,19 @@
> -        elsif ($driver =~ /^[sS]/) {
> -            $driver = 'SQLite';
> -        }
>--        
>+-
> -        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' || $driver eq 'SQLite') {
> -            $test_dsn = "dbi:$driver:dbname=$test_db";
>@@ -72,14 +71,14 @@
> -        if ($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",
>@@ -92,7 +91,7 @@
> -    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");
>diff -ruN /usr/ports//biology/p5-bioperl/pkg-plist ./pkg-plist
>--- /usr/ports//biology/p5-bioperl/pkg-plist	2014-01-22 21:16:56.000000000 +0600
>+++ ./pkg-plist	2014-05-28 16:43:39.173858543 +0600
>@@ -1,196 +1,891 @@
>-%%DATADIR%%/models/README
>-%%DATADIR%%/models/biblio.dia
>-%%DATADIR%%/models/bio_liveseq_variation.dia
>-%%DATADIR%%/models/bio_map.dia
>-%%DATADIR%%/models/bioperl.dia
>-%%DATADIR%%/models/bio_restriction.dia
>-%%DATADIR%%/models/coordinatemapper.dia
>-%%DATADIR%%/models/map_proposal.txt
>-%%DATADIR%%/models/maps_and_markers.dia
>-%%DATADIR%%/models/popgen.dia
>-%%DATADIR%%/models/population_proposal.txt
>-%%DATADIR%%/scripts/Bio-DB-EUtilities/einfo.PLS
>-%%DATADIR%%/scripts/Bio-DB-GFF/README
>-%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
>-%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS
>-%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS
>-%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff.PLS
>-%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.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_sgd.PLS
>-%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.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/DB-HIV/hivq.PLS
>-%%DATADIR%%/scripts/DB/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/README
>-%%DATADIR%%/scripts/biblio/TAG
>-%%DATADIR%%/scripts/biblio/biblio.PLS
>-%%DATADIR%%/scripts/das/README
>-%%DATADIR%%/scripts/das/TAG
>-%%DATADIR%%/scripts/index/TAG
>-%%DATADIR%%/scripts/index/bp_fetch.PLS
>-%%DATADIR%%/scripts/index/bp_index.PLS
>-%%DATADIR%%/scripts/index/bp_seqret.PLS
>-%%DATADIR%%/scripts/popgen/composite_LD.PLS
>-%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
>-%%DATADIR%%/scripts/searchio/README
>-%%DATADIR%%/scripts/searchio/TAG
>-%%DATADIR%%/scripts/searchio/fastam9_to_table.PLS
>-%%DATADIR%%/scripts/searchio/filter_search.PLS
>-%%DATADIR%%/scripts/searchio/hmmer_to_table.PLS
>-%%DATADIR%%/scripts/searchio/parse_hmmsearch.PLS
>-%%DATADIR%%/scripts/searchio/search2table.PLS
>-%%DATADIR%%/scripts/seq/TAG
>-%%DATADIR%%/scripts/seq/extract_feature_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/seqstats/TAG
>-%%DATADIR%%/scripts/seqstats/aacomp.PLS
>-%%DATADIR%%/scripts/seqstats/chaos_plot.PLS
>-%%DATADIR%%/scripts/seqstats/gccalc.PLS
>-%%DATADIR%%/scripts/seqstats/oligo_count.PLS
>-%%DATADIR%%/scripts/seq/translate_seq.PLS
>-%%DATADIR%%/scripts/seq/unflatten_seq.PLS
>-%%DATADIR%%/scripts/taxa/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/taxid4species.PLS
>-%%DATADIR%%/scripts/taxa/taxonomy2tree.PLS
>-%%DATADIR%%/scripts/tree/TAG
>-%%DATADIR%%/scripts/tree/blast2tree.PLS
>-%%DATADIR%%/scripts/tree/nexus2nh.PLS
>-%%DATADIR%%/scripts/tree/tree2pag.PLS
>-%%DATADIR%%/scripts/utilities/README
>-%%DATADIR%%/scripts/utilities/TAG
>-%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
>-%%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/remote_blast.PLS
>-%%DATADIR%%/scripts/utilities/revtrans-motif.PLS
>-%%DATADIR%%/scripts/utilities/search2BSML.PLS
>-%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
>-%%DATADIR%%/scripts/utilities/search2gff.PLS
>-%%DATADIR%%/scripts/utilities/search2tribe.PLS
>-%%DATADIR%%/scripts/utilities/seq_length.PLS
>-%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
>-%%EXAMPLESDIR%%/align/align_on_codons.pl
>-%%EXAMPLESDIR%%/align/aligntutorial.pl
>-%%EXAMPLESDIR%%/align/clustalw.pl
>-%%EXAMPLESDIR%%/align/simplealign.pl
>-%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl
>-%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl
>-%%EXAMPLESDIR%%/biblio/biblio_soap.pl
>-%%EXAMPLESDIR%%/bioperl.pl
>-%%EXAMPLESDIR%%/cluster/dbsnp.pl
>-%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
>-%%EXAMPLESDIR%%/contributed/prosite2perl.pl
>-%%EXAMPLESDIR%%/contributed/rebase2list.pl
>-%%EXAMPLESDIR%%/db/dbfetch
>-%%EXAMPLESDIR%%/db/est_tissue_query.pl
>-%%EXAMPLESDIR%%/db/gb2features.pl
>-%%EXAMPLESDIR%%/db/getGenBank.pl
>-%%EXAMPLESDIR%%/db/get_seqs.pl
>-%%EXAMPLESDIR%%/db/rfetch.pl
>-%%EXAMPLESDIR%%/db/use_registry.pl
>-%%EXAMPLESDIR%%/generate_random_seq.pl
>-%%EXAMPLESDIR%%/liveseq/change_gene.pl
>-%%EXAMPLESDIR%%/longorf.pl
>-%%EXAMPLESDIR%%/make_primers.pl
>-%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
>-%%EXAMPLESDIR%%/quality/svgtrace.pl
>-%%EXAMPLESDIR%%/rev_and_trans.pl
>-%%EXAMPLESDIR%%/revcom_dir.pl
>-%%EXAMPLESDIR%%/root/README
>-%%EXAMPLESDIR%%/root/exceptions1.pl
>-%%EXAMPLESDIR%%/root/exceptions2.pl
>-%%EXAMPLESDIR%%/root/exceptions3.pl
>-%%EXAMPLESDIR%%/root/exceptions4.pl
>-%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
>-%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
>-%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
>-%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
>-%%EXAMPLESDIR%%/root/lib/TestInterface.pm
>-%%EXAMPLESDIR%%/root/lib/TestObject.pm
>-%%EXAMPLESDIR%%/searchio/blast_example.pl
>-%%EXAMPLESDIR%%/searchio/custom_writer.pl
>-%%EXAMPLESDIR%%/searchio/hitwriter.pl
>-%%EXAMPLESDIR%%/searchio/hspwriter.pl
>-%%EXAMPLESDIR%%/searchio/htmlwriter.pl
>-%%EXAMPLESDIR%%/searchio/psiblast_features.pl
>-%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
>-%%EXAMPLESDIR%%/searchio/rawwriter.pl
>-%%EXAMPLESDIR%%/searchio/resultwriter.pl
>-%%EXAMPLESDIR%%/searchio/waba2gff3.pl
>-%%EXAMPLESDIR%%/searchio/waba2gff.pl
>-%%EXAMPLESDIR%%/sirna/TAG
>-%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
>-%%EXAMPLESDIR%%/structure/structure-io.pl
>-%%EXAMPLESDIR%%/subsequence.cgi
>-%%EXAMPLESDIR%%/tk/gsequence.pl
>-%%EXAMPLESDIR%%/tk/hitdisplay.pl
>-%%EXAMPLESDIR%%/tools/extract_genes.pl
>-%%EXAMPLESDIR%%/tools/gb_to_gff.pl
>-%%EXAMPLESDIR%%/tools/gff2ps.pl
>-%%EXAMPLESDIR%%/tools/parse_codeml.pl
>-%%EXAMPLESDIR%%/tools/psw.pl
>-%%EXAMPLESDIR%%/tools/reverse-translate.pl
>-%%EXAMPLESDIR%%/tools/run_genscan.pl
>-%%EXAMPLESDIR%%/tools/run_primer3.pl
>-%%EXAMPLESDIR%%/tools/seq_pattern.pl
>-%%EXAMPLESDIR%%/tools/standaloneblast.pl
>-%%EXAMPLESDIR%%/tree/paup2phylip.pl
>-%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
>-%%PORTDOCS%%%%DOCSDIR%%/BUGS
>-%%PORTDOCS%%%%DOCSDIR%%/Changes
>-%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
>-%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
>-%%PORTDOCS%%%%DOCSDIR%%/INSTALL
>-%%PORTDOCS%%%%DOCSDIR%%/LICENSE
>-%%PORTDOCS%%%%DOCSDIR%%/MANIFEST
>-%%PORTDOCS%%%%DOCSDIR%%/README
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Build.PL
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Changes
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/LICENSE
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/META.yml
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Makefile.PL
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/README
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/deob_index.pl
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_detail.cgi
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_flowchart.png
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_help.html
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_interface.cgi
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/excluded_modules.txt
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/lib/Deobfuscator.pm
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/00.load.t
>-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/pod.t
>-%%PORTDOCS%%%%DOCSDIR%%/doc/README
>-%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%
>+bin/bp_aacomp.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_das_server.pl
>+bin/bp_dbsplit.pl
>+bin/bp_download_query_genbank.pl
>+bin/bp_extract_feature_seq.pl
>+bin/bp_fast_load_gff.pl
>+bin/bp_fastam9_to_table.pl
>+bin/bp_fetch.pl
>+bin/bp_filter_search.pl
>+bin/bp_flanks.pl
>+bin/bp_gccalc.pl
>+bin/bp_genbank2gff.pl
>+bin/bp_genbank2gff3.pl
>+bin/bp_generate_histogram.pl
>+bin/bp_heterogeneity_test.pl
>+bin/bp_hivq.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_netinstall.pl
>+bin/bp_nexus2nh.pl
>+bin/bp_nrdb.pl
>+bin/bp_oligo_count.pl
>+bin/bp_pairwise_kaks.pl
>+bin/bp_parse_hmmsearch.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_revtrans-motif.pl
>+bin/bp_search2BSML.pl
>+bin/bp_search2alnblocks.pl
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> %%SITE_PERL%%/Bio/AlignIO/arp.pm
> %%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
>@@ -204,10 +899,10 @@
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> %%SITE_PERL%%/Bio/AlignIO/metafasta.pm
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>@@ -215,20 +910,14 @@
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>+%%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
>@@ -350,7 +1011,6 @@
> %%SITE_PERL%%/Bio/DB/GFF/Aggregator/match.pm
> %%SITE_PERL%%/Bio/DB/GFF/Aggregator/none.pm
> %%SITE_PERL%%/Bio/DB/GFF/Aggregator/orf.pm
>-%%SITE_PERL%%/Bio/DB/GFF/Aggregator.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
>@@ -371,32 +1031,33 @@
> %%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/GFF.pm
> %%SITE_PERL%%/Bio/DB/GenBank.pm
> %%SITE_PERL%%/Bio/DB/GenPept.pm
> %%SITE_PERL%%/Bio/DB/GenericWebAgent.pm
>+%%SITE_PERL%%/Bio/DB/HIV.pm
> %%SITE_PERL%%/Bio/DB/HIV/HIVAnnotProcessor.pm
> %%SITE_PERL%%/Bio/DB/HIV/HIVQueryHelper.pm
> %%SITE_PERL%%/Bio/DB/HIV/lanl-schema.xml
>-%%SITE_PERL%%/Bio/DB/HIV.pm
> %%SITE_PERL%%/Bio/DB/InMemoryCache.pm
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>+%%SITE_PERL%%/Bio/DB/IndexedBase.pm
> %%SITE_PERL%%/Bio/DB/LocationI.pm
> %%SITE_PERL%%/Bio/DB/MeSH.pm
> %%SITE_PERL%%/Bio/DB/NCBIHelper.pm
> %%SITE_PERL%%/Bio/DB/Qual.pm
> %%SITE_PERL%%/Bio/DB/Query/GenBank.pm
> %%SITE_PERL%%/Bio/DB/Query/HIVQuery.pm
>-%%SITE_PERL%%/Bio/DB/QueryI.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/ReferenceI.pm
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>+%%SITE_PERL%%/Bio/DB/SeqFeature.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedFeature.pm
>+%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedFeatureI.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Segment.pm
>+%%SITE_PERL%%/Bio/DB/SeqFeature/Store.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/Iterator.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/Pg.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
>@@ -407,40 +1068,33 @@
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/LoadHelper.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/Loader.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/bdb.pm
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>+%%SITE_PERL%%/Bio/DB/SeqFeature/Store/berkeleydb3.pm
> %%SITE_PERL%%/Bio/DB/SeqFeature/Store/memory.pm
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> %%SITE_PERL%%/Bio/DB/SeqHound.pm
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> %%SITE_PERL%%/Bio/DB/SeqVersion.pm
>+%%SITE_PERL%%/Bio/DB/SeqVersion/gi.pm
> %%SITE_PERL%%/Bio/DB/SwissProt.pm
> %%SITE_PERL%%/Bio/DB/TFBS.pm
> %%SITE_PERL%%/Bio/DB/TFBS/transfac_pro.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/Taxonomy/greengenes.pm
> %%SITE_PERL%%/Bio/DB/Taxonomy/list.pm
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>+%%SITE_PERL%%/Bio/DB/Taxonomy/silva.pm
> %%SITE_PERL%%/Bio/DB/Universal.pm
> %%SITE_PERL%%/Bio/DB/UpdateableSeqI.pm
> %%SITE_PERL%%/Bio/DB/WebDBSeqI.pm
>+%%SITE_PERL%%/Bio/DBLinkContainerI.pm
> %%SITE_PERL%%/Bio/Das/FeatureTypeI.pm
>-%%SITE_PERL%%/Bio/DasI.pm
> %%SITE_PERL%%/Bio/Das/SegmentI.pm
>+%%SITE_PERL%%/Bio/DasI.pm
> %%SITE_PERL%%/Bio/DescribableI.pm
>+%%SITE_PERL%%/Bio/Draw/Pictogram.pm
> %%SITE_PERL%%/Bio/Event/EventGeneratorI.pm
> %%SITE_PERL%%/Bio/Event/EventHandlerI.pm
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> %%SITE_PERL%%/Bio/Factory/AnalysisI.pm
> %%SITE_PERL%%/Bio/Factory/ApplicationFactoryI.pm
> %%SITE_PERL%%/Bio/Factory/DriverFactory.pm
>@@ -448,29 +1102,22 @@
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> %%SITE_PERL%%/Bio/Factory/ObjectFactory.pm
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>+%%SITE_PERL%%/Bio/Factory/ObjectFactoryI.pm
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>+%%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
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>-%%SITE_PERL%%/Bio/FeatureIO.pm
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> %%SITE_PERL%%/Bio/HandlerBaseI.pm
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>+%%SITE_PERL%%/Bio/Index/AbstractSeq.pm
> %%SITE_PERL%%/Bio/Index/Blast.pm
>+%%SITE_PERL%%/Bio/Index/BlastTable.pm
> %%SITE_PERL%%/Bio/Index/EMBL.pm
> %%SITE_PERL%%/Bio/Index/Fasta.pm
> %%SITE_PERL%%/Bio/Index/Fastq.pm
>@@ -481,8 +1128,8 @@
> %%SITE_PERL%%/Bio/Index/SwissPfam.pm
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>+%%SITE_PERL%%/Bio/LiveSeq/ChainI.pm
> %%SITE_PERL%%/Bio/LiveSeq/DNA.pm
> %%SITE_PERL%%/Bio/LiveSeq/Exon.pm
> %%SITE_PERL%%/Bio/LiveSeq/Gene.pm
>@@ -502,14 +1149,14 @@
> %%SITE_PERL%%/Bio/Location/Atomic.pm
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> %%SITE_PERL%%/Bio/Location/Fuzzy.pm
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>+%%SITE_PERL%%/Bio/Location/FuzzyLocationI.pm
> %%SITE_PERL%%/Bio/Location/NarrowestCoordPolicy.pm
> %%SITE_PERL%%/Bio/Location/Simple.pm
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>+%%SITE_PERL%%/Bio/Location/SplitLocationI.pm
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>+%%SITE_PERL%%/Bio/LocationI.pm
> %%SITE_PERL%%/Bio/Map/Clone.pm
> %%SITE_PERL%%/Bio/Map/Contig.pm
> %%SITE_PERL%%/Bio/Map/CytoMap.pm
>@@ -517,91 +1164,92 @@
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>+%%SITE_PERL%%/Bio/Map/Gene.pm
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>+%%SITE_PERL%%/Bio/MapIO/mapmaker.pm
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> %%SITE_PERL%%/Bio/Ontology/OBOEngine.pm
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>+%%SITE_PERL%%/Bio/Ontology/Ontology.pm
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> %%SITE_PERL%%/Bio/Ontology/SimpleOntologyEngine.pm
>+%%SITE_PERL%%/Bio/Ontology/Term.pm
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>+%%SITE_PERL%%/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
>+%%SITE_PERL%%/Bio/OntologyIO/InterProParser.pm
>+%%SITE_PERL%%/Bio/OntologyIO/dagflat.pm
>+%%SITE_PERL%%/Bio/OntologyIO/goflat.pm
>+%%SITE_PERL%%/Bio/OntologyIO/obo.pm
>+%%SITE_PERL%%/Bio/OntologyIO/simplehierarchy.pm
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> %%SITE_PERL%%/Bio/ParameterBaseI.pm
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>@@ -609,72 +1257,70 @@
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>+%%SITE_PERL%%/Bio/PhyloNetwork/FactoryX.pm
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> %%SITE_PERL%%/Bio/PhyloNetwork/RandomFactory.pm
>+%%SITE_PERL%%/Bio/PhyloNetwork/TreeFactory.pm
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> %%SITE_PERL%%/Bio/Restriction/IO/itype2.pm
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> %%SITE_PERL%%/Bio/Search/GenericStatistics.pm
> %%SITE_PERL%%/Bio/Search/HSP/BlastHSP.pm
>@@ -701,6 +1347,28 @@
> %%SITE_PERL%%/Bio/Search/Hit/ModelHit.pm
> %%SITE_PERL%%/Bio/Search/Hit/PsiBlastHit.pm
> %%SITE_PERL%%/Bio/Search/Hit/PullHitI.pm
>+%%SITE_PERL%%/Bio/Search/Hit/hmmer3Hit.pm
>+%%SITE_PERL%%/Bio/Search/Iteration/GenericIteration.pm
>+%%SITE_PERL%%/Bio/Search/Iteration/IterationI.pm
>+%%SITE_PERL%%/Bio/Search/Processor.pm
>+%%SITE_PERL%%/Bio/Search/Result/BlastPullResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/BlastResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/CrossMatchResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/GenericResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/HMMERResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/HmmpfamResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/PullResultI.pm
>+%%SITE_PERL%%/Bio/Search/Result/ResultFactory.pm
>+%%SITE_PERL%%/Bio/Search/Result/ResultI.pm
>+%%SITE_PERL%%/Bio/Search/Result/WABAResult.pm
>+%%SITE_PERL%%/Bio/Search/Result/hmmer3Result.pm
>+%%SITE_PERL%%/Bio/Search/SearchUtils.pm
>+%%SITE_PERL%%/Bio/Search/StatisticsI.pm
>+%%SITE_PERL%%/Bio/Search/Tiling/MapTileUtils.pm
>+%%SITE_PERL%%/Bio/Search/Tiling/MapTiling.pm
>+%%SITE_PERL%%/Bio/Search/Tiling/TilingI.pm
>+%%SITE_PERL%%/Bio/SearchDist.pm
>+%%SITE_PERL%%/Bio/SearchIO.pm
> %%SITE_PERL%%/Bio/SearchIO/EventHandlerI.pm
> %%SITE_PERL%%/Bio/SearchIO/FastHitEventBuilder.pm
> %%SITE_PERL%%/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
>@@ -726,70 +1394,77 @@
> %%SITE_PERL%%/Bio/SearchIO/fasta.pm
> %%SITE_PERL%%/Bio/SearchIO/gmap_f9.pm
> %%SITE_PERL%%/Bio/SearchIO/hmmer.pm
>+%%SITE_PERL%%/Bio/SearchIO/hmmer2.pm
>+%%SITE_PERL%%/Bio/SearchIO/hmmer3.pm
> %%SITE_PERL%%/Bio/SearchIO/hmmer_pull.pm
> %%SITE_PERL%%/Bio/SearchIO/infernal.pm
> %%SITE_PERL%%/Bio/SearchIO/megablast.pm
>-%%SITE_PERL%%/Bio/SearchIO.pm
> %%SITE_PERL%%/Bio/SearchIO/psl.pm
> %%SITE_PERL%%/Bio/SearchIO/rnamotif.pm
> %%SITE_PERL%%/Bio/SearchIO/sim4.pm
> %%SITE_PERL%%/Bio/SearchIO/waba.pm
> %%SITE_PERL%%/Bio/SearchIO/wise.pm
>-%%SITE_PERL%%/Bio/Search/Iteration/GenericIteration.pm
>-%%SITE_PERL%%/Bio/Search/Iteration/IterationI.pm
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>+%%SITE_PERL%%/Bio/SeqFeature/CollectionI.pm
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>+%%SITE_PERL%%/Bio/SeqFeature/Gene/ExonI.pm
> %%SITE_PERL%%/Bio/SeqFeature/Gene/GeneStructure.pm
>+%%SITE_PERL%%/Bio/SeqFeature/Gene/GeneStructureI.pm
> %%SITE_PERL%%/Bio/SeqFeature/Gene/Intron.pm
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>+%%SITE_PERL%%/Bio/SeqFeature/Gene/TranscriptI.pm
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> %%SITE_PERL%%/Bio/SeqFeature/SiRNA/Oligo.pm
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>-%%SITE_PERL%%/Bio/SeqFeature/SimilarityPair.pm
> %%SITE_PERL%%/Bio/SeqFeature/Similarity.pm
>+%%SITE_PERL%%/Bio/SeqFeature/SimilarityPair.pm
>+%%SITE_PERL%%/Bio/SeqFeature/SubSeq.pm
> %%SITE_PERL%%/Bio/SeqFeature/Tools/FeatureNamer.pm
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> %%SITE_PERL%%/Bio/SeqFeature/TypedSeqFeatureI.pm
>+%%SITE_PERL%%/Bio/SeqFeatureI.pm
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> %%SITE_PERL%%/Bio/SeqIO/MultiFile.pm
>@@ -804,21 +1479,22 @@
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>+%%SITE_PERL%%/Bio/SeqIO/embldriver.pm
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>+%%SITE_PERL%%/Bio/SeqIO/game.pm
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>+%%SITE_PERL%%/Bio/SeqIO/gbxml.pm
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>@@ -826,74 +1502,57 @@
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>@@ -903,8 +1562,8 @@
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>-bin/bp_process_wormbase.pl
>-bin/bp_query_entrez_taxa.pl
>-bin/bp_remote_blast.pl
>-bin/bp_revtrans-motif.pl
>-bin/bp_search2BSML.pl
>-bin/bp_search2alnblocks.pl
>-bin/bp_search2gff.pl
>-bin/bp_search2table.pl
>-bin/bp_search2tribe.pl
>-bin/bp_seqconvert.pl
>-bin/bp_seqfeature_delete.pl
>-bin/bp_seqfeature_gff3.pl
>-bin/bp_seqfeature_load.pl
>-bin/bp_seq_length.pl
>-bin/bp_seqret.pl
>-bin/bp_seqretsplit.pl
>-bin/bp_split_seq.pl
>-bin/bp_sreformat.pl
>-bin/bp_taxid4species.pl
>-bin/bp_taxonomy2tree.pl
>-bin/bp_translate_seq.pl
>-bin/bp_tree2pag.pl
>-bin/bp_unflatten_seq.pl
>-@dirrm %%DATADIR%%/scripts/Bio-DB-EUtilities
>-@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
>-@dirrm %%DATADIR%%/scripts/Bio-SeqFeature-Store
>-@dirrm %%DATADIR%%/scripts/DB
>-@dirrm %%DATADIR%%/scripts/DB-HIV
>-@dirrm %%DATADIR%%/scripts/biblio
>-@dirrm %%DATADIR%%/scripts/das
>-@dirrm %%DATADIR%%/scripts/index
>-@dirrm %%DATADIR%%/scripts/popgen
>-@dirrm %%DATADIR%%/scripts/searchio
>-@dirrm %%DATADIR%%/scripts/seq
>-@dirrm %%DATADIR%%/scripts/seqstats
>-@dirrm %%DATADIR%%/scripts/taxa
>-@dirrm %%DATADIR%%/scripts/tree
>-@dirrm %%DATADIR%%/scripts/utilities
>-@dirrm %%DATADIR%%/models
>-@dirrm %%DATADIR%%/scripts
>-@dirrm %%DATADIR%%
>-@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
>-@dirrm %%EXAMPLESDIR%%/align
>-@dirrm %%EXAMPLESDIR%%/biblio
>-@dirrm %%EXAMPLESDIR%%/cluster
>-@dirrm %%EXAMPLESDIR%%/contributed
>-@dirrm %%EXAMPLESDIR%%/db
>-@dirrm %%EXAMPLESDIR%%/liveseq
>-@dirrm %%EXAMPLESDIR%%/popgen
>-@dirrm %%EXAMPLESDIR%%/quality
>-@dirrm %%EXAMPLESDIR%%/root/lib/Bio
>-@dirrm %%EXAMPLESDIR%%/root/lib
>-@dirrm %%EXAMPLESDIR%%/root
>-@dirrm %%EXAMPLESDIR%%/searchio
>-@dirrm %%EXAMPLESDIR%%/sirna
>-@dirrm %%EXAMPLESDIR%%/structure
>-@dirrm %%EXAMPLESDIR%%/tk
>-@dirrm %%EXAMPLESDIR%%/tools
>-@dirrm %%EXAMPLESDIR%%/tree
>-@dirrm %%EXAMPLESDIR%%
>+man/man1/bp_aacomp.pl.1.gz
>+man/man1/bp_biofetch_genbank_proxy.pl.1.gz
>+man/man1/bp_bioflat_index.pl.1.gz
>+man/man1/bp_biogetseq.pl.1.gz
>+man/man1/bp_blast2tree.pl.1.gz
>+man/man1/bp_bulk_load_gff.pl.1.gz
>+man/man1/bp_chaos_plot.pl.1.gz
>+man/man1/bp_classify_hits_kingdom.pl.1.gz
>+man/man1/bp_composite_LD.pl.1.gz
>+man/man1/bp_dbsplit.pl.1.gz
>+man/man1/bp_download_query_genbank.pl.1.gz
>+man/man1/bp_extract_feature_seq.pl.1.gz
>+man/man1/bp_fast_load_gff.pl.1.gz
>+man/man1/bp_fastam9_to_table.pl.1.gz
>+man/man1/bp_fetch.pl.1.gz
>+man/man1/bp_filter_search.pl.1.gz
>+man/man1/bp_flanks.pl.1.gz
>+man/man1/bp_gccalc.pl.1.gz
>+man/man1/bp_genbank2gff.pl.1.gz
>+man/man1/bp_genbank2gff3.pl.1.gz
>+man/man1/bp_generate_histogram.pl.1.gz
>+man/man1/bp_heterogeneity_test.pl.1.gz
>+man/man1/bp_hivq.pl.1.gz
>+man/man1/bp_hmmer_to_table.pl.1.gz
>+man/man1/bp_index.pl.1.gz
>+man/man1/bp_load_gff.pl.1.gz
>+man/man1/bp_local_taxonomydb_query.pl.1.gz
>+man/man1/bp_make_mrna_protein.pl.1.gz
>+man/man1/bp_mask_by_search.pl.1.gz
>+man/man1/bp_meta_gff.pl.1.gz
>+man/man1/bp_mrtrans.pl.1.gz
>+man/man1/bp_mutate.pl.1.gz
>+man/man1/bp_netinstall.pl.1.gz
>+man/man1/bp_nexus2nh.pl.1.gz
>+man/man1/bp_nrdb.pl.1.gz
>+man/man1/bp_oligo_count.pl.1.gz
>+man/man1/bp_pairwise_kaks.pl.1.gz
>+man/man1/bp_parse_hmmsearch.pl.1.gz
>+man/man1/bp_process_gadfly.pl.1.gz
>+man/man1/bp_process_sgd.pl.1.gz
>+man/man1/bp_process_wormbase.pl.1.gz
>+man/man1/bp_query_entrez_taxa.pl.1.gz
>+man/man1/bp_remote_blast.pl.1.gz
>+man/man1/bp_revtrans-motif.pl.1.gz
>+man/man1/bp_search2BSML.pl.1.gz
>+man/man1/bp_search2alnblocks.pl.1.gz
>+man/man1/bp_search2gff.pl.1.gz
>+man/man1/bp_search2table.pl.1.gz
>+man/man1/bp_search2tribe.pl.1.gz
>+man/man1/bp_seq_length.pl.1.gz
>+man/man1/bp_seqconvert.pl.1.gz
>+man/man1/bp_seqcut.pl.1.gz
>+man/man1/bp_seqfeature_load.pl.1.gz
>+man/man1/bp_seqpart.pl.1.gz
>+man/man1/bp_seqret.pl.1.gz
>+man/man1/bp_seqretsplit.pl.1.gz
>+man/man1/bp_split_seq.pl.1.gz
>+man/man1/bp_sreformat.pl.1.gz
>+man/man1/bp_taxid4species.pl.1.gz
>+man/man1/bp_taxonomy2tree.pl.1.gz
>+man/man1/bp_translate_seq.pl.1.gz
>+man/man1/bp_tree2pag.pl.1.gz
>+man/man1/bp_unflatten_seq.pl.1.gz
>+%%DATADIR%%/models/README
>+%%DATADIR%%/models/biblio.dia
>+%%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/population_proposal.txt
>+%%DATADIR%%/scripts/Bio-DB-GFF/README
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_generate_histogram.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_load_gff.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_meta_gff.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_gadfly.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_sgd.pl
>+%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_wormbase.pl
>+%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
>+%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
>+%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
>+%%DATADIR%%/scripts/DB-HIV/bp_hivq.pl
>+%%DATADIR%%/scripts/DB/TAG
>+%%DATADIR%%/scripts/DB/bp_biofetch_genbank_proxy.pl
>+%%DATADIR%%/scripts/DB/bp_bioflat_index.pl
>+%%DATADIR%%/scripts/DB/bp_biogetseq.pl
>+%%DATADIR%%/scripts/DB/bp_flanks.pl
>+%%DATADIR%%/scripts/README
>+%%DATADIR%%/scripts/das/README
>+%%DATADIR%%/scripts/das/TAG
>+%%DATADIR%%/scripts/das/bp_das_server.pl
>+%%DATADIR%%/scripts/index/TAG
>+%%DATADIR%%/scripts/index/bp_fetch.pl
>+%%DATADIR%%/scripts/index/bp_index.pl
>+%%DATADIR%%/scripts/index/bp_seqret.pl
>+%%DATADIR%%/scripts/popgen/bp_composite_LD.pl
>+%%DATADIR%%/scripts/popgen/bp_heterogeneity_test.pl
>+%%DATADIR%%/scripts/searchio/README
>+%%DATADIR%%/scripts/searchio/TAG
>+%%DATADIR%%/scripts/searchio/bp_fastam9_to_table.pl
>+%%DATADIR%%/scripts/searchio/bp_filter_search.pl
>+%%DATADIR%%/scripts/searchio/bp_hmmer_to_table.pl
>+%%DATADIR%%/scripts/searchio/bp_parse_hmmsearch.pl
>+%%DATADIR%%/scripts/searchio/bp_search2table.pl
>+%%DATADIR%%/scripts/seq/TAG
>+%%DATADIR%%/scripts/seq/bp_extract_feature_seq.pl
>+%%DATADIR%%/scripts/seq/bp_make_mrna_protein.pl
>+%%DATADIR%%/scripts/seq/bp_seqconvert.pl
>+%%DATADIR%%/scripts/seq/bp_seqcut.pl
>+%%DATADIR%%/scripts/seq/bp_seqpart.pl
>+%%DATADIR%%/scripts/seq/bp_seqretsplit.pl
>+%%DATADIR%%/scripts/seq/bp_split_seq.pl
>+%%DATADIR%%/scripts/seq/bp_translate_seq.pl
>+%%DATADIR%%/scripts/seq/bp_unflatten_seq.pl
>+%%DATADIR%%/scripts/seqstats/TAG
>+%%DATADIR%%/scripts/seqstats/bp_aacomp.pl
>+%%DATADIR%%/scripts/seqstats/bp_chaos_plot.pl
>+%%DATADIR%%/scripts/seqstats/bp_gccalc.pl
>+%%DATADIR%%/scripts/seqstats/bp_oligo_count.pl
>+%%DATADIR%%/scripts/taxa/TAG
>+%%DATADIR%%/scripts/taxa/bp_classify_hits_kingdom.pl
>+%%DATADIR%%/scripts/taxa/bp_local_taxonomydb_query.pl
>+%%DATADIR%%/scripts/taxa/bp_query_entrez_taxa.pl
>+%%DATADIR%%/scripts/taxa/bp_taxid4species.pl
>+%%DATADIR%%/scripts/taxa/bp_taxonomy2tree.pl
>+%%DATADIR%%/scripts/tree/TAG
>+%%DATADIR%%/scripts/tree/bp_blast2tree.pl
>+%%DATADIR%%/scripts/tree/bp_nexus2nh.pl
>+%%DATADIR%%/scripts/tree/bp_tree2pag.pl
>+%%DATADIR%%/scripts/utilities/README
>+%%DATADIR%%/scripts/utilities/TAG
>+%%DATADIR%%/scripts/utilities/bp_dbsplit.pl
>+%%DATADIR%%/scripts/utilities/bp_download_query_genbank.pl
>+%%DATADIR%%/scripts/utilities/bp_mask_by_search.pl
>+%%DATADIR%%/scripts/utilities/bp_mrtrans.pl
>+%%DATADIR%%/scripts/utilities/bp_mutate.pl
>+%%DATADIR%%/scripts/utilities/bp_netinstall.pl
>+%%DATADIR%%/scripts/utilities/bp_nrdb.pl
>+%%DATADIR%%/scripts/utilities/bp_pairwise_kaks.pl
>+%%DATADIR%%/scripts/utilities/bp_remote_blast.pl
>+%%DATADIR%%/scripts/utilities/bp_revtrans-motif.pl
>+%%DATADIR%%/scripts/utilities/bp_search2BSML.pl
>+%%DATADIR%%/scripts/utilities/bp_search2alnblocks.pl
>+%%DATADIR%%/scripts/utilities/bp_search2gff.pl
>+%%DATADIR%%/scripts/utilities/bp_search2tribe.pl
>+%%DATADIR%%/scripts/utilities/bp_seq_length.pl
>+%%DATADIR%%/scripts/utilities/bp_sreformat.pl
>+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
>+%%PORTDOCS%%%%DOCSDIR%%/BUGS
>+%%PORTDOCS%%%%DOCSDIR%%/Changes
>+%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
>+%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
>+%%PORTDOCS%%%%DOCSDIR%%/INSTALL
>+%%PORTDOCS%%%%DOCSDIR%%/LICENSE
>+%%PORTDOCS%%%%DOCSDIR%%/MANIFEST
>+%%PORTDOCS%%%%DOCSDIR%%/README
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Build.PL
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Changes
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/LICENSE
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/META.yml
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Makefile.PL
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/README
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/deob_index.pl
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/run-deobfuscator-update.pl
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_detail.cgi
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_flowchart.png
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_help.html
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_interface.cgi
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/excluded_modules.txt
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/lib/Deobfuscator.pm
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/00.load.t
>+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/pod.t
>+%%PORTDOCS%%%%DOCSDIR%%/doc/README
>+%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/FastAlign.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/align_on_codons.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/aligntutorial.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/clustalw.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/simplealign.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bioperl.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cluster/dbsnp.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/prosite2perl.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/rebase2list.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/dbfetch
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/est_tissue_query.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/gb2features.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/getGenBank.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/get_seqs.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/rfetch.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/use_registry.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/generate_random_seq.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/quality/svgtrace.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/reverse-translate.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl
> @dirrm %%SITE_PERL%%/Bio/Align
> @dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
> @dirrm %%SITE_PERL%%/Bio/AlignIO
>@@ -1157,14 +1944,11 @@
> @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/ClusterIO
> @dirrm %%SITE_PERL%%/Bio/CodonUsage
> @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
>@@ -1185,12 +1969,9 @@
> @dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
> @dirrm %%SITE_PERL%%/Bio/DB
> @dirrm %%SITE_PERL%%/Bio/Das
>+@dirrm %%SITE_PERL%%/Bio/Draw
> @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
>@@ -1202,10 +1983,11 @@
> @dirrm %%SITE_PERL%%/Bio/Matrix/PSM
> @dirrm %%SITE_PERL%%/Bio/Matrix
> @dirrm %%SITE_PERL%%/Bio/MolEvol
>-@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
>-@dirrm %%SITE_PERL%%/Bio/OntologyIO
>+@dirrm %%SITE_PERL%%/Bio/Nexml
> @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
>@@ -1216,17 +1998,18 @@
> @dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
> @dirrm %%SITE_PERL%%/Bio/Restriction/IO
> @dirrm %%SITE_PERL%%/Bio/Restriction
>-@dirrm %%SITE_PERL%%/Bio/Root/Test
> @dirrm %%SITE_PERL%%/Bio/Root
> @dirrm %%SITE_PERL%%/Bio/Search/HSP
> @dirrm %%SITE_PERL%%/Bio/Search/Hit
>-@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
>-@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
>-@dirrm %%SITE_PERL%%/Bio/SearchIO
> @dirrm %%SITE_PERL%%/Bio/Search/Iteration
> @dirrm %%SITE_PERL%%/Bio/Search/Result
> @dirrm %%SITE_PERL%%/Bio/Search/Tiling
> @dirrm %%SITE_PERL%%/Bio/Search
>+@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
>+@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
>+@dirrm %%SITE_PERL%%/Bio/SearchIO
>+@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
>@@ -1236,8 +2019,6 @@
> @dirrm %%SITE_PERL%%/Bio/SeqIO/game
> @dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
> @dirrm %%SITE_PERL%%/Bio/SeqIO
>-@dirrm %%SITE_PERL%%/Bio/Seq/Meta
>-@dirrm %%SITE_PERL%%/Bio/Seq
> @dirrm %%SITE_PERL%%/Bio/Structure/IO
> @dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
> @dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
>@@ -1250,11 +2031,6 @@
> @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
>@@ -1263,6 +2039,7 @@
> @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/WrapperBase
> @dirrm %%SITE_PERL%%/Bio/Tools/Run
> @dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern
> @dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
>@@ -1276,3 +2053,43 @@
> @dirrm %%SITE_PERL%%/Bio/TreeIO
> @dirrm %%SITE_PERL%%/Bio/Variation/IO
> @dirrm %%SITE_PERL%%/Bio/Variation
>+@dirrm %%DATADIR%%/models
>+@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
>+@dirrm %%DATADIR%%/scripts/Bio-DB-SeqFeature-Store
>+@dirrm %%DATADIR%%/scripts/DB
>+@dirrm %%DATADIR%%/scripts/DB-HIV
>+@dirrm %%DATADIR%%/scripts/das
>+@dirrm %%DATADIR%%/scripts/index
>+@dirrm %%DATADIR%%/scripts/popgen
>+@dirrm %%DATADIR%%/scripts/searchio
>+@dirrm %%DATADIR%%/scripts/seq
>+@dirrm %%DATADIR%%/scripts/seqstats
>+@dirrm %%DATADIR%%/scripts/taxa
>+@dirrm %%DATADIR%%/scripts/tree
>+@dirrm %%DATADIR%%/scripts/utilities
>+@dirrm %%DATADIR%%/scripts
>+@dirrm %%DATADIR%%
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/quality
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree
>+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

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Attachments on bug 190342: 143175