- Update to 1.6.1

PR:		132122
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer

3 files changed, 216 insertions, 683 deletions

diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index 3d733736464a..679c9ca1af79 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -6,362 +6,133 @@
 #
 
 PORTNAME=	bioperl-run
-PORTVERSION=	1.4
-PORTREVISION=	1
+PORTVERSION=	1.6.1
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/ \
 		CPAN
 PKGNAMEPREFIX=	p5-
+DISTNAME=	BioPerl-run-${PORTVERSION}
 
 MAINTAINER=	mauricio@arareko.net
 COMMENT=	Wrapper modules for common bioinformatics tools
 
-BUILD_DEPENDS=	p5-bioperl=1.4_2:${PORTSDIR}/biology/p5-bioperl \
+BUILD_DEPENDS=	p5-bioperl=1.6.0:${PORTSDIR}/biology/p5-bioperl \
+		${SITE_PERL}/IPC/Run.pm:${PORTSDIR}/devel/p5-IPC-Run \
 		${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 CONFLICTS=	p5-bioperl-run-1.[13579]*
 
-PERL_CONFIGURE=	YES
+PERL_MODBUILD=	YES
+WRKSRC=		${WRKDIR}/BioPerl-run-1.6.0
 
-MAN3=		Bio::Factory::EMBOSS.3 \
-		Bio::Tools::Run::Alignment::Blat.3 \
-		Bio::Tools::Run::Alignment::Clustalw.3 \
-		Bio::Tools::Run::Alignment::DBA.3 \
-		Bio::Tools::Run::Alignment::Lagan.3 \
-		Bio::Tools::Run::Alignment::Sim4.3 \
-		Bio::Tools::Run::Alignment::StandAloneFasta.3 \
-		Bio::Tools::Run::Alignment::TCoffee.3 \
-		Bio::Tools::Run::Analysis.3 \
-		Bio::Tools::Run::Analysis::soap.3 \
-		Bio::Tools::Run::AnalysisFactory.3 \
-		Bio::Tools::Run::AnalysisFactory::Pise.3 \
-		Bio::Tools::Run::AnalysisFactory::soap.3 \
-		Bio::Tools::Run::Coil.3 \
-		Bio::Tools::Run::EMBOSSApplication.3 \
-		Bio::Tools::Run::EMBOSSacd.3 \
-		Bio::Tools::Run::Eponine.3 \
-		Bio::Tools::Run::FootPrinter.3 \
-		Bio::Tools::Run::Genewise.3 \
-		Bio::Tools::Run::Genscan.3 \
-		Bio::Tools::Run::Hmmer.3 \
-		Bio::Tools::Run::Hmmpfam.3 \
-		Bio::Tools::Run::Mdust.3 \
-		Bio::Tools::Run::Phylo::Molphy::ProtML.3 \
-		Bio::Tools::Run::Phylo::PAML::Codeml.3 \
-		Bio::Tools::Run::Phylo::PAML::Yn00.3 \
-		Bio::Tools::Run::Phylo::Phylip::Base.3 \
-		Bio::Tools::Run::Phylo::Phylip::Consense.3 \
-		Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
-		Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \
-		Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \
-		Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \
-		Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \
-		Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \
-		Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \
-		Bio::Tools::Run::PiseApplication.3 \
-		Bio::Tools::Run::PiseApplication::CSR.3 \
-		Bio::Tools::Run::PiseApplication::Puzzle.3 \
-		Bio::Tools::Run::PiseApplication::abiview.3 \
-		Bio::Tools::Run::PiseApplication::addquart.3 \
-		Bio::Tools::Run::PiseApplication::align2model.3 \
-		Bio::Tools::Run::PiseApplication::alistat.3 \
-		Bio::Tools::Run::PiseApplication::antigenic.3 \
-		Bio::Tools::Run::PiseApplication::assp.3 \
-		Bio::Tools::Run::PiseApplication::backtranseq.3 \
-		Bio::Tools::Run::PiseApplication::bambe.3 \
-		Bio::Tools::Run::PiseApplication::banana.3 \
-		Bio::Tools::Run::PiseApplication::bionj.3 \
-		Bio::Tools::Run::PiseApplication::biosed.3 \
-		Bio::Tools::Run::PiseApplication::bl2seq.3 \
-		Bio::Tools::Run::PiseApplication::blast2.3 \
-		Bio::Tools::Run::PiseApplication::blimps.3 \
-		Bio::Tools::Run::PiseApplication::blimps_block.3 \
-		Bio::Tools::Run::PiseApplication::blimps_matrix.3 \
-		Bio::Tools::Run::PiseApplication::boxshade.3 \
-		Bio::Tools::Run::PiseApplication::btwisted.3 \
-		Bio::Tools::Run::PiseApplication::cai.3 \
-		Bio::Tools::Run::PiseApplication::cap.3 \
-		Bio::Tools::Run::PiseApplication::cds.3 \
-		Bio::Tools::Run::PiseApplication::chaos.3 \
-		Bio::Tools::Run::PiseApplication::charge.3 \
-		Bio::Tools::Run::PiseApplication::checktrans.3 \
-		Bio::Tools::Run::PiseApplication::chips.3 \
-		Bio::Tools::Run::PiseApplication::cirdna.3 \
-		Bio::Tools::Run::PiseApplication::clique.3 \
-		Bio::Tools::Run::PiseApplication::clustalw.3 \
-		Bio::Tools::Run::PiseApplication::clustalw_convert.3 \
-		Bio::Tools::Run::PiseApplication::codcmp.3 \
-		Bio::Tools::Run::PiseApplication::coderet.3 \
-		Bio::Tools::Run::PiseApplication::codnocod.3 \
-		Bio::Tools::Run::PiseApplication::codontree.3 \
-		Bio::Tools::Run::PiseApplication::codonw.3 \
-		Bio::Tools::Run::PiseApplication::comalign.3 \
-		Bio::Tools::Run::PiseApplication::combat.3 \
-		Bio::Tools::Run::PiseApplication::compseq.3 \
-		Bio::Tools::Run::PiseApplication::con_filter.3 \
-		Bio::Tools::Run::PiseApplication::confmat.3 \
-		Bio::Tools::Run::PiseApplication::cons.3 \
-		Bio::Tools::Run::PiseApplication::consense.3 \
-		Bio::Tools::Run::PiseApplication::consensus.3 \
-		Bio::Tools::Run::PiseApplication::cpgplot.3 \
-		Bio::Tools::Run::PiseApplication::cpgreport.3 \
-		Bio::Tools::Run::PiseApplication::cusp.3 \
-		Bio::Tools::Run::PiseApplication::cutseq.3 \
-		Bio::Tools::Run::PiseApplication::dan.3 \
-		Bio::Tools::Run::PiseApplication::dca.3 \
-		Bio::Tools::Run::PiseApplication::decorate.3 \
-		Bio::Tools::Run::PiseApplication::degapseq.3 \
-		Bio::Tools::Run::PiseApplication::descseq.3 \
-		Bio::Tools::Run::PiseApplication::dialign2.3 \
-		Bio::Tools::Run::PiseApplication::diffseq.3 \
-		Bio::Tools::Run::PiseApplication::digest.3 \
-		Bio::Tools::Run::PiseApplication::distmat.3 \
-		Bio::Tools::Run::PiseApplication::distquart.3 \
-		Bio::Tools::Run::PiseApplication::dnadist.3 \
-		Bio::Tools::Run::PiseApplication::dnapars.3 \
-		Bio::Tools::Run::PiseApplication::dollop.3 \
-		Bio::Tools::Run::PiseApplication::domainer.3 \
-		Bio::Tools::Run::PiseApplication::dotmatcher.3 \
-		Bio::Tools::Run::PiseApplication::dotpath.3 \
-		Bio::Tools::Run::PiseApplication::dottup.3 \
-		Bio::Tools::Run::PiseApplication::drawgram.3 \
-		Bio::Tools::Run::PiseApplication::drawpyr.3 \
-		Bio::Tools::Run::PiseApplication::drawtree.3 \
-		Bio::Tools::Run::PiseApplication::dreg.3 \
-		Bio::Tools::Run::PiseApplication::druid.3 \
-		Bio::Tools::Run::PiseApplication::dsc.3 \
-		Bio::Tools::Run::PiseApplication::dssp.3 \
-		Bio::Tools::Run::PiseApplication::einverted.3 \
-		Bio::Tools::Run::PiseApplication::emma.3 \
-		Bio::Tools::Run::PiseApplication::emowse.3 \
-		Bio::Tools::Run::PiseApplication::environ.3 \
-		Bio::Tools::Run::PiseApplication::eprimer3.3 \
-		Bio::Tools::Run::PiseApplication::equicktandem.3 \
-		Bio::Tools::Run::PiseApplication::est2genome.3 \
-		Bio::Tools::Run::PiseApplication::etandem.3 \
-		Bio::Tools::Run::PiseApplication::extractfeat.3 \
-		Bio::Tools::Run::PiseApplication::extractseq.3 \
-		Bio::Tools::Run::PiseApplication::fasta.3 \
-		Bio::Tools::Run::PiseApplication::fastdnaml.3 \
-		Bio::Tools::Run::PiseApplication::fastrna.3 \
-		Bio::Tools::Run::PiseApplication::filtersites.3 \
-		Bio::Tools::Run::PiseApplication::findkm.3 \
-		Bio::Tools::Run::PiseApplication::fitch.3 \
-		Bio::Tools::Run::PiseApplication::fmtseq.3 \
-		Bio::Tools::Run::PiseApplication::freak.3 \
-		Bio::Tools::Run::PiseApplication::fuzznuc.3 \
-		Bio::Tools::Run::PiseApplication::fuzzpro.3 \
-		Bio::Tools::Run::PiseApplication::fuzztran.3 \
-		Bio::Tools::Run::PiseApplication::gb2xml.3 \
-		Bio::Tools::Run::PiseApplication::geecee.3 \
-		Bio::Tools::Run::PiseApplication::genscan.3 \
-		Bio::Tools::Run::PiseApplication::getblock.3 \
-		Bio::Tools::Run::PiseApplication::getorf.3 \
-		Bio::Tools::Run::PiseApplication::gff2ps.3 \
-		Bio::Tools::Run::PiseApplication::gibbs.3 \
-		Bio::Tools::Run::PiseApplication::gibbs_scan.3 \
-		Bio::Tools::Run::PiseApplication::golden.3 \
-		Bio::Tools::Run::PiseApplication::grailclnt.3 \
-		Bio::Tools::Run::PiseApplication::gruppi.3 \
-		Bio::Tools::Run::PiseApplication::helixturnhelix.3 \
-		Bio::Tools::Run::PiseApplication::hmmalign.3 \
-		Bio::Tools::Run::PiseApplication::hmmbuild.3 \
-		Bio::Tools::Run::PiseApplication::hmmcalibrate.3 \
-		Bio::Tools::Run::PiseApplication::hmmconvert.3 \
-		Bio::Tools::Run::PiseApplication::hmmemit.3 \
-		Bio::Tools::Run::PiseApplication::hmmer2sam.3 \
-		Bio::Tools::Run::PiseApplication::hmmfetch.3 \
-		Bio::Tools::Run::PiseApplication::hmmpfam.3 \
-		Bio::Tools::Run::PiseApplication::hmmscore.3 \
-		Bio::Tools::Run::PiseApplication::hmmsearch.3 \
-		Bio::Tools::Run::PiseApplication::hmoment.3 \
-		Bio::Tools::Run::PiseApplication::homology.3 \
-		Bio::Tools::Run::PiseApplication::html4blast.3 \
-		Bio::Tools::Run::PiseApplication::iep.3 \
-		Bio::Tools::Run::PiseApplication::infoalign.3 \
-		Bio::Tools::Run::PiseApplication::infoseq.3 \
-		Bio::Tools::Run::PiseApplication::interface.3 \
-		Bio::Tools::Run::PiseApplication::isochore.3 \
-		Bio::Tools::Run::PiseApplication::kitsch.3 \
-		Bio::Tools::Run::PiseApplication::lassap.3 \
-		Bio::Tools::Run::PiseApplication::lgicsearch.3 \
-		Bio::Tools::Run::PiseApplication::lindna.3 \
-		Bio::Tools::Run::PiseApplication::listor.3 \
-		Bio::Tools::Run::PiseApplication::loadseq.3 \
-		Bio::Tools::Run::PiseApplication::lvb.3 \
-		Bio::Tools::Run::PiseApplication::makehist.3 \
-		Bio::Tools::Run::PiseApplication::map.3 \
-		Bio::Tools::Run::PiseApplication::marscan.3 \
-		Bio::Tools::Run::PiseApplication::maskfeat.3 \
-		Bio::Tools::Run::PiseApplication::maskseq.3 \
-		Bio::Tools::Run::PiseApplication::matcher.3 \
-		Bio::Tools::Run::PiseApplication::megamerger.3 \
-		Bio::Tools::Run::PiseApplication::melting.3 \
-		Bio::Tools::Run::PiseApplication::merger.3 \
-		Bio::Tools::Run::PiseApplication::mfold.3 \
-		Bio::Tools::Run::PiseApplication::mix.3 \
-		Bio::Tools::Run::PiseApplication::modelfromalign.3 \
-		Bio::Tools::Run::PiseApplication::most.3 \
-		Bio::Tools::Run::PiseApplication::mreps.3 \
-		Bio::Tools::Run::PiseApplication::msa.3 \
-		Bio::Tools::Run::PiseApplication::msbar.3 \
-		Bio::Tools::Run::PiseApplication::mspcrunch.3 \
-		Bio::Tools::Run::PiseApplication::mview_alig.3 \
-		Bio::Tools::Run::PiseApplication::mview_blast.3 \
-		Bio::Tools::Run::PiseApplication::mwfilter.3 \
-		Bio::Tools::Run::PiseApplication::needle.3 \
-		Bio::Tools::Run::PiseApplication::neighbor.3 \
-		Bio::Tools::Run::PiseApplication::newcpgreport.3 \
-		Bio::Tools::Run::PiseApplication::newcpgseek.3 \
-		Bio::Tools::Run::PiseApplication::newseq.3 \
-		Bio::Tools::Run::PiseApplication::njdist.3 \
-		Bio::Tools::Run::PiseApplication::nnssp.3 \
-		Bio::Tools::Run::PiseApplication::notseq.3 \
-		Bio::Tools::Run::PiseApplication::nrscope.3 \
-		Bio::Tools::Run::PiseApplication::nthseq.3 \
-		Bio::Tools::Run::PiseApplication::octanol.3 \
-		Bio::Tools::Run::PiseApplication::oddcomp.3 \
-		Bio::Tools::Run::PiseApplication::palindrome.3 \
-		Bio::Tools::Run::PiseApplication::pam.3 \
-		Bio::Tools::Run::PiseApplication::parciquart.3 \
-		Bio::Tools::Run::PiseApplication::pars.3 \
-		Bio::Tools::Run::PiseApplication::pasteseq.3 \
-		Bio::Tools::Run::PiseApplication::patmatdb.3 \
-		Bio::Tools::Run::PiseApplication::patmatmotifs.3 \
-		Bio::Tools::Run::PiseApplication::patser.3 \
-		Bio::Tools::Run::PiseApplication::pdbsearch.3 \
-		Bio::Tools::Run::PiseApplication::pepcoil.3 \
-		Bio::Tools::Run::PiseApplication::pepinfo.3 \
-		Bio::Tools::Run::PiseApplication::pepnet.3 \
-		Bio::Tools::Run::PiseApplication::pepstats.3 \
-		Bio::Tools::Run::PiseApplication::pepwheel.3 \
-		Bio::Tools::Run::PiseApplication::pepwindow.3 \
-		Bio::Tools::Run::PiseApplication::pepwindowall.3 \
-		Bio::Tools::Run::PiseApplication::pestfind.3 \
-		Bio::Tools::Run::PiseApplication::pftools.3 \
-		Bio::Tools::Run::PiseApplication::phiblast.3 \
-		Bio::Tools::Run::PiseApplication::pima.3 \
-		Bio::Tools::Run::PiseApplication::plotcon.3 \
-		Bio::Tools::Run::PiseApplication::plotorf.3 \
-		Bio::Tools::Run::PiseApplication::plsearch.3 \
-		Bio::Tools::Run::PiseApplication::polydot.3 \
-		Bio::Tools::Run::PiseApplication::pratt.3 \
-		Bio::Tools::Run::PiseApplication::predator.3 \
-		Bio::Tools::Run::PiseApplication::preg.3 \
-		Bio::Tools::Run::PiseApplication::prettyalign.3 \
-		Bio::Tools::Run::PiseApplication::prettyplot.3 \
-		Bio::Tools::Run::PiseApplication::prettyseq.3 \
-		Bio::Tools::Run::PiseApplication::primersearch.3 \
-		Bio::Tools::Run::PiseApplication::primo.3 \
-		Bio::Tools::Run::PiseApplication::prodom.3 \
-		Bio::Tools::Run::PiseApplication::profit.3 \
-		Bio::Tools::Run::PiseApplication::prophecy.3 \
-		Bio::Tools::Run::PiseApplication::prophet.3 \
-		Bio::Tools::Run::PiseApplication::prose.3 \
-		Bio::Tools::Run::PiseApplication::prot_nucml.3 \
-		Bio::Tools::Run::PiseApplication::protal2dna.3 \
-		Bio::Tools::Run::PiseApplication::protdist.3 \
-		Bio::Tools::Run::PiseApplication::protpars.3 \
-		Bio::Tools::Run::PiseApplication::pscan.3 \
-		Bio::Tools::Run::PiseApplication::psiblast.3 \
-		Bio::Tools::Run::PiseApplication::psort2.3 \
-		Bio::Tools::Run::PiseApplication::pyramids.3 \
-		Bio::Tools::Run::PiseApplication::pyreval.3 \
-		Bio::Tools::Run::PiseApplication::qstar.3 \
-		Bio::Tools::Run::PiseApplication::quicktree.3 \
-		Bio::Tools::Run::PiseApplication::readnexus.3 \
-		Bio::Tools::Run::PiseApplication::readseq.3 \
-		Bio::Tools::Run::PiseApplication::recoder.3 \
-		Bio::Tools::Run::PiseApplication::redata.3 \
-		Bio::Tools::Run::PiseApplication::remap.3 \
-		Bio::Tools::Run::PiseApplication::repeats.3 \
-		Bio::Tools::Run::PiseApplication::restover.3 \
-		Bio::Tools::Run::PiseApplication::restrict.3 \
-		Bio::Tools::Run::PiseApplication::revseq.3 \
-		Bio::Tools::Run::PiseApplication::rnadistance.3 \
-		Bio::Tools::Run::PiseApplication::rnaeval.3 \
-		Bio::Tools::Run::PiseApplication::rnafold.3 \
-		Bio::Tools::Run::PiseApplication::rnaga.3 \
-		Bio::Tools::Run::PiseApplication::rnaheat.3 \
-		Bio::Tools::Run::PiseApplication::rnainverse.3 \
-		Bio::Tools::Run::PiseApplication::rnapdist.3 \
-		Bio::Tools::Run::PiseApplication::rnasubopt.3 \
-		Bio::Tools::Run::PiseApplication::sam2hmmer.3 \
-		Bio::Tools::Run::PiseApplication::sampleseqs.3 \
-		Bio::Tools::Run::PiseApplication::saps.3 \
-		Bio::Tools::Run::PiseApplication::satellites.3 \
-		Bio::Tools::Run::PiseApplication::scan_for_matches.3 \
-		Bio::Tools::Run::PiseApplication::scope.3 \
-		Bio::Tools::Run::PiseApplication::scopparse.3 \
-		Bio::Tools::Run::PiseApplication::seqboot.3 \
-		Bio::Tools::Run::PiseApplication::seqgen.3 \
-		Bio::Tools::Run::PiseApplication::seqmatchall.3 \
-		Bio::Tools::Run::PiseApplication::seqsblast.3 \
-		Bio::Tools::Run::PiseApplication::seqstat.3 \
-		Bio::Tools::Run::PiseApplication::showalign.3 \
-		Bio::Tools::Run::PiseApplication::showfeat.3 \
-		Bio::Tools::Run::PiseApplication::showorf.3 \
-		Bio::Tools::Run::PiseApplication::showseq.3 \
-		Bio::Tools::Run::PiseApplication::shuffleseq.3 \
-		Bio::Tools::Run::PiseApplication::sigcleave.3 \
-		Bio::Tools::Run::PiseApplication::siggen.3 \
-		Bio::Tools::Run::PiseApplication::sigscan.3 \
-		Bio::Tools::Run::PiseApplication::silent.3 \
-		Bio::Tools::Run::PiseApplication::sirna.3 \
-		Bio::Tools::Run::PiseApplication::splitter.3 \
-		Bio::Tools::Run::PiseApplication::sreformat.3 \
-		Bio::Tools::Run::PiseApplication::stretcher.3 \
-		Bio::Tools::Run::PiseApplication::stride.3 \
-		Bio::Tools::Run::PiseApplication::stssearch.3 \
-		Bio::Tools::Run::PiseApplication::supermatcher.3 \
-		Bio::Tools::Run::PiseApplication::syco.3 \
-		Bio::Tools::Run::PiseApplication::tacg.3 \
-		Bio::Tools::Run::PiseApplication::tfscan.3 \
-		Bio::Tools::Run::PiseApplication::tipdate.3 \
-		Bio::Tools::Run::PiseApplication::tmap.3 \
-		Bio::Tools::Run::PiseApplication::toppred.3 \
-		Bio::Tools::Run::PiseApplication::tranalign.3 \
-		Bio::Tools::Run::PiseApplication::transeq.3 \
-		Bio::Tools::Run::PiseApplication::treealign.3 \
-		Bio::Tools::Run::PiseApplication::trimest.3 \
-		Bio::Tools::Run::PiseApplication::trimseq.3 \
-		Bio::Tools::Run::PiseApplication::trnascan.3 \
-		Bio::Tools::Run::PiseApplication::twofeat.3 \
-		Bio::Tools::Run::PiseApplication::unroot.3 \
-		Bio::Tools::Run::PiseApplication::vectorstrip.3 \
-		Bio::Tools::Run::PiseApplication::water.3 \
-		Bio::Tools::Run::PiseApplication::weighbor.3 \
-		Bio::Tools::Run::PiseApplication::whichdb.3 \
-		Bio::Tools::Run::PiseApplication::wise2.3 \
-		Bio::Tools::Run::PiseApplication::wobble.3 \
-		Bio::Tools::Run::PiseApplication::wordcount.3 \
-		Bio::Tools::Run::PiseApplication::wordmatch.3 \
-		Bio::Tools::Run::PiseApplication::wublast2.3 \
-		Bio::Tools::Run::PiseApplication::xblast.3 \
-		Bio::Tools::Run::PiseApplication::xpound.3 \
-		Bio::Tools::Run::PiseJob.3 \
-		Bio::Tools::Run::PiseJobParser.3 \
-		Bio::Tools::Run::PiseWorkflow.3 \
-		Bio::Tools::Run::Primate.3 \
-		Bio::Tools::Run::Primer3.3 \
-		Bio::Tools::Run::Prints.3 \
-		Bio::Tools::Run::Profile.3 \
-		Bio::Tools::Run::Promoterwise.3 \
-		Bio::Tools::Run::Pseudowise.3 \
-		Bio::Tools::Run::RepeatMasker.3 \
-		Bio::Tools::Run::Seg.3 \
-		Bio::Tools::Run::Signalp.3 \
-		Bio::Tools::Run::Tmhmm.3 \
-		Bio::Tools::Run::TribeMCL.3 \
-		Bio::Tools::Run::Vista.3
+MAN1=	bp_bioperl_application_installer.pl.1 \
+	bp_multi_hmmsearch.pl.1 \
+	bp_panalysis.pl.1 \
+	bp_papplmaker.pl.1 \
+	bp_run_neighbor.pl.1 \
+	bp_run_protdist.pl.1
+
+MAN3=	Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
+	Bio::Tools::Run::Simprot.3 \
+	Bio::Tools::Run::Phylo::Phyml.3 \
+	Bio::Tools::Run::Phylo::LVB.3 \
+	Bio::Tools::Run::Alignment::Amap.3 \
+	Bio::Tools::Run::Tmhmm.3 \
+	Bio::Tools::Run::TigrAssembler.3 \
+	Bio::Tools::Run::Phylo::PAML::Baseml.3 \
+	Bio::Installer::Probcons.3 \
+	Bio::Tools::Run::Phylo::Phylip::Base.3 \
+	Bio::Tools::Run::Alignment::Exonerate.3 \
+	Bio::Tools::Run::Alignment::MAFFT.3 \
+	Bio::Tools::Run::Alignment::TCoffee.3 \
+	Bio::Tools::Run::Alignment::Sim4.3 \
+	Bio::Tools::Run::Analysis.3 \
+	Bio::Tools::Run::Phylo::PAML::Yn00.3 \
+	Bio::Tools::Run::Alignment::Clustalw.3 \
+	Bio::Tools::Run::Phylo::Molphy::ProtML.3 \
+	Bio::Tools::Run::Phylo::Hyphy::Base.3 \
+	Bio::Tools::Run::Meme.3 \
+	Bio::Tools::Run::MCS.3 \
+	Bio::Tools::Run::Eponine.3 \
+	Bio::Tools::Run::Alignment::Kalign.3 \
+	Bio::Tools::Run::TribeMCL.3 \
+	Bio::Tools::Run::Analysis::soap.3 \
+	Bio::Factory::EMBOSS.3 \
+	Bio::Installer::Clustalw.3 \
+	Bio::Tools::Run::Seg.3 \
+	Bio::Tools::Run::Alignment::Probcons.3 \
+	Bio::Tools::Run::RepeatMasker.3 \
+	Bio::Installer::TCoffee.3 \
+	Bio::Tools::Run::AnalysisFactory.3 \
+	Bio::Tools::Run::Cap3.3 \
+	Bio::Tools::Run::Alignment::Blat.3 \
+	Bio::Tools::Run::Phylo::PhyloBase.3 \
+	Bio::Tools::Run::Coil.3 \
+	Bio::Tools::Run::Promoterwise.3 \
+	Bio::Tools::Run::Alignment::Pal2Nal.3 \
+	Bio::Tools::Run::ERPIN.3 \
+	Bio::Tools::Run::Phylo::PAML::Evolver.3 \
+	Bio::Tools::Run::Phylo::Hyphy::REL.3 \
+	Bio::Tools::Run::Genscan.3 \
+	Bio::Tools::Run::EMBOSSApplication.3 \
+	Bio::Tools::Run::Phylo::Hyphy::Modeltest.3 \
+	Bio::Tools::Run::Match.3 \
+	Bio::Tools::Run::Phylo::Gumby.3 \
+	Bio::Tools::Run::Vista.3 \
+	Bio::Tools::Run::Phylo::Hyphy::SLAC.3 \
+	Bio::Tools::Run::Mdust.3 \
+	Bio::Tools::Run::Alignment::Proda.3 \
+	Bio::Installer::SLR.3 \
+	Bio::Tools::Run::Primate.3 \
+	Bio::Tools::Run::Infernal.3 \
+	Bio::Tools::Run::Genemark.3 \
+	Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \
+	Bio::Tools::Run::EMBOSSacd.3 \
+	Bio::Tools::Run::Hmmer.3 \
+	Bio::Tools::Run::AnalysisFactory::soap.3 \
+	Bio::Tools::Run::Alignment::Lagan.3 \
+	Bio::Installer::EMBOSS.3 \
+	Bio::Tools::Run::Phrap.3 \
+	Bio::Tools::Run::Alignment::Muscle.3 \
+	Bio::Tools::Run::tRNAscanSE.3 \
+	Bio::Tools::Run::Glimmer.3 \
+	Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \
+	Bio::Installer::PAML.3 \
+	Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \
+	Bio::Tools::Run::Phylo::Phast::PhyloFit.3 \
+	Bio::Installer::Hyphy.3 \
+	Bio::Tools::Run::Phylo::Phast::PhastCons.3 \
+	Bio::Tools::Run::Signalp.3 \
+	Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \
+	Bio::Installer::Generic.3 \
+	Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \
+	Bio::Tools::Run::Phylo::SLR.3 \
+	Bio::Tools::Run::FootPrinter.3 \
+	Bio::Tools::Run::Genewise.3 \
+	Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \
+	Bio::Tools::Run::RNAMotif.3 \
+	Bio::Tools::Run::Alignment::StandAloneFasta.3 \
+	Bio::Tools::Run::Alignment::Probalign.3 \
+	Bio::Tools::Run::Primer3.3 \
+	Bio::Tools::Run::Profile.3 \
+	Bio::Tools::Run::Phylo::Njtree::Best.3 \
+	Bio::Tools::Run::Phylo::QuickTree.3 \
+	Bio::Tools::Run::Pseudowise.3 \
+	Bio::Tools::Run::Alignment::DBA.3 \
+	Bio::Tools::Run::Phylo::Phylip::Consense.3 \
+	Bio::Tools::Run::Phylo::Semphy.3 \
+	Bio::Tools::Run::Ensembl.3 \
+	Bio::Tools::Run::Phylo::Gerp.3 \
+	Bio::Tools::Run::Phylo::PAML::Codeml.3 \
+	Bio::Installer::Muscle.3 \
+	Bio::Tools::Run::Prints.3 \
+	Bio::Tools::Run::Phylo::Hyphy::FEL.3
 
 # now install all extra stuff (docs, examples, scripts)
 post-install:
 	${MKDIR} ${DATADIR}
 	@${CP} -Rv ${WRKSRC}/scripts ${DATADIR}
-	${MKDIR} ${EXAMPLESDIR}
-	@${CP} -Rv ${WRKSRC}/examples/* ${EXAMPLESDIR}
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
 .for doc in AUTHORS Changes INSTALL.PROGRAMS README
diff --git a/biology/p5-bioperl-run/distinfo b/biology/p5-bioperl-run/distinfo
index 889ee4b564d2..b6ef133afd6e 100644
--- a/biology/p5-bioperl-run/distinfo
+++ b/biology/p5-bioperl-run/distinfo
@@ -1,3 +1,3 @@
-MD5 (bioperl-run-1.4.tar.gz) = 25914ab48d1ab0393ebb067a8f68a821
-SHA256 (bioperl-run-1.4.tar.gz) = 54eea327c8f80061d6c45e56b64d5c51daa20b723390eed1a3377f3a61645d86
-SIZE (bioperl-run-1.4.tar.gz) = 830774
+MD5 (BioPerl-run-1.6.1.tar.gz) = 15f53f5232b9ed58fa27662431935da8
+SHA256 (BioPerl-run-1.6.1.tar.gz) = 1ecf2f3a0dd606a1522642d6dd05f8641cd5c8788f3b53e19243f4121c4d4b80
+SIZE (BioPerl-run-1.6.1.tar.gz) = 4082463
diff --git a/biology/p5-bioperl-run/pkg-plist b/biology/p5-bioperl-run/pkg-plist
index ddc2754cc27a..eb1451a811cd 100644
--- a/biology/p5-bioperl-run/pkg-plist
+++ b/biology/p5-bioperl-run/pkg-plist
@@ -1,366 +1,128 @@
+bin/bp_papplmaker.pl
+bin/bp_panalysis.pl
+bin/bp_run_neighbor.pl
+bin/bp_multi_hmmsearch.pl
+bin/bp_bioperl_application_installer.pl
+bin/bp_run_protdist.pl
+%%DATADIR%%/scripts/bioperl_application_installer.PLS
+%%DATADIR%%/scripts/multi_hmmsearch.PLS
+%%DATADIR%%/scripts/panalysis.PLS
+%%DATADIR%%/scripts/papplmaker.PLS
+%%DATADIR%%/scripts/run_neighbor.PLS
+%%DATADIR%%/scripts/run_protdist.PLS
+@dirrm %%DATADIR%%/scripts
+@dirrm %%DATADIR%%
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/
 %%SITE_PERL%%/Bio/Factory/EMBOSS.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probalign.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Pal2Nal.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probcons.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Kalign.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm
-%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm
 %%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/Pise.pm
 %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/Coil.pm
-%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
-%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
-%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
-%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
-%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
-%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
-%%SITE_PERL%%/Bio/Tools/Run/Hmmpfam.pm
-%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/REL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree/Best.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Codeml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Baseml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Evolver.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Yn00.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/CSR.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/Puzzle.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/abiview.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/addquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/align2model.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/alistat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/antigenic.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/assp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/backtranseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bambe.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/banana.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bionj.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/biosed.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/bl2seq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blast2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps_block.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/blimps_matrix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/boxshade.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/btwisted.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cai.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cds.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/chaos.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/charge.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/checktrans.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/chips.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cirdna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clique.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clustalw.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/clustalw_convert.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codcmp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/coderet.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codnocod.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codontree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/codonw.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/comalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/combat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/compseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/con_filter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/confmat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cons.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/consense.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/consensus.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cpgplot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cpgreport.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cusp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/cutseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dca.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/decorate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/degapseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/descseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dialign2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/diffseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/digest.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/distmat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/distquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dnadist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dnapars.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dollop.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/domainer.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dotmatcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dotpath.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dottup.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawgram.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawpyr.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/drawtree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dreg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/druid.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dsc.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/dssp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/einverted.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/emma.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/emowse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/environ.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/eprimer3.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/equicktandem.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/est2genome.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/etandem.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/extractfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/extractseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fasta.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fastdnaml.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fastrna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/filtersites.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/findkm.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fitch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fmtseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/freak.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzznuc.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzzpro.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/fuzztran.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gb2xml.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/geecee.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/genscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/getblock.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/getorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gff2ps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gibbs.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gibbs_scan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/golden.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/grailclnt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/gruppi.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/helixturnhelix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmbuild.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmcalibrate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmconvert.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmemit.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmer2sam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmfetch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmpfam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmscore.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmmsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/hmoment.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/homology.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/html4blast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/iep.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/infoalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/infoseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/interface.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/isochore.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/kitsch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lassap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lgicsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lindna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/listor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/loadseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/lvb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/makehist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/map.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/marscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/maskfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/maskseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/matcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/megamerger.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/melting.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/merger.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mfold.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mix.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/modelfromalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/most.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mreps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/msa.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/msbar.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mspcrunch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mview_alig.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mview_blast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/mwfilter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/needle.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/neighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newcpgreport.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newcpgseek.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/newseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/njdist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nnssp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/notseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nrscope.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/nthseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/octanol.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/oddcomp.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/palindrome.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pam.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/parciquart.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pars.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pasteseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patmatdb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patmatmotifs.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/patser.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pdbsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepcoil.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepinfo.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepnet.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepstats.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwheel.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwindow.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pepwindowall.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pestfind.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pftools.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/phiblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pima.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plotcon.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plotorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/plsearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/polydot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pratt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/predator.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/preg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prettyalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prettyplot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prettyseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/primersearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/primo.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prodom.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/profit.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prophecy.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prophet.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prose.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/prot_nucml.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/protal2dna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/protdist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/protpars.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/psiblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/psort2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pyramids.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/pyreval.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/qstar.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/quicktree.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/readnexus.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/readseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/recoder.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/redata.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/remap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/repeats.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/restover.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/restrict.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/revseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnadistance.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnaeval.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnafold.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnaga.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnaheat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnainverse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnapdist.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/rnasubopt.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sam2hmmer.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sampleseqs.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/saps.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/satellites.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/scan_for_matches.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/scope.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/scopparse.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqboot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqgen.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqmatchall.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqsblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/seqstat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showfeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showorf.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/showseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/shuffleseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigcleave.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/siggen.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/silent.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sirna.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/splitter.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sreformat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stretcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stride.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stssearch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/supermatcher.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/syco.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tacg.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tfscan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tipdate.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tmap.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/toppred.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tranalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/transeq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/treealign.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimest.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimseq.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trnascan.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/twofeat.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/unroot.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/vectorstrip.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/water.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/weighbor.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/whichdb.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wise2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wobble.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordcount.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordmatch.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wublast2.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xblast.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xpound.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseJob.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseJobParser.pm
-%%SITE_PERL%%/Bio/Tools/Run/PiseWorkflow.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PhyloBase.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/SLR.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Semphy.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
+%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
+%%SITE_PERL%%/Bio/Tools/Run/ERPIN.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
+%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
+%%SITE_PERL%%/Bio/Tools/Run/Match.pm
 %%SITE_PERL%%/Bio/Tools/Run/Primate.pm
-%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
+%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
+%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
+%%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
+%%SITE_PERL%%/Bio/Tools/Run/Simprot.pm
+%%SITE_PERL%%/Bio/Tools/Run/MCS.pm
+%%SITE_PERL%%/Bio/Tools/Run/Coil.pm
+%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
 %%SITE_PERL%%/Bio/Tools/Run/Prints.pm
-%%SITE_PERL%%/Bio/Tools/Run/Profile.pm
+%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
+%%SITE_PERL%%/Bio/Tools/Run/Vista.pm
+%%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm
+%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
+%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
 %%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm
-%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
-%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
-%%SITE_PERL%%/Bio/Tools/Run/Seg.pm
+%%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm
+%%SITE_PERL%%/Bio/Tools/Run/Cap3.pm
+%%SITE_PERL%%/Bio/Tools/Run/Glimmer.pm
+%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
 %%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
+%%SITE_PERL%%/Bio/Tools/Run/Meme.pm
+%%SITE_PERL%%/Bio/Tools/Run/RNAMotif.pm
+%%SITE_PERL%%/Bio/Tools/Run/Seg.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genemark.pm
+%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
+%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
+%%SITE_PERL%%/Bio/Tools/Run/Profile.pm
 %%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
-%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
-%%SITE_PERL%%/Bio/Tools/Run/Vista.pm
-%%DATADIR%%/scripts/panalysis.PLS
-%%DATADIR%%/scripts/papplmaker.PLS
-%%DATADIR%%/scripts/run_neighbor.PLS
-%%DATADIR%%/scripts/run_protdist.PLS
-%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
-%%PORTDOCS%%%%DOCSDIR%%/Changes
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%EXAMPLESDIR%%/pise/blast-kun.pl
-%%EXAMPLESDIR%%/pise/blast2.pl
-%%EXAMPLESDIR%%/pise/clustalw.pl
-%%EXAMPLESDIR%%/pise/dnadist.data
-%%EXAMPLESDIR%%/pise/dnadist.pl
-%%EXAMPLESDIR%%/pise/genscan.pl
-%%EXAMPLESDIR%%/pise/needle.pl
-%%EXAMPLESDIR%%/pise/phylo-kun.pl
-%%EXAMPLESDIR%%/pise/toppred.pl
-@dirrm %%EXAMPLESDIR%%/pise
-@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%DATADIR%%/scripts
-@dirrm %%DATADIR%%
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/PiseApplication
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
+%%SITE_PERL%%/Bio/Tools/Run/Ensembl.pm
+%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
+%%SITE_PERL%%/Bio/Installer/EMBOSS.pm
+%%SITE_PERL%%/Bio/Installer/Muscle.pm
+%%SITE_PERL%%/Bio/Installer/Clustalw.pm
+%%SITE_PERL%%/Bio/Installer/SLR.pm
+%%SITE_PERL%%/Bio/Installer/Probcons.pm
+%%SITE_PERL%%/Bio/Installer/TCoffee.pm
+%%SITE_PERL%%/Bio/Installer/Hyphy.pm
+%%SITE_PERL%%/Bio/Installer/Generic.pm
+%%SITE_PERL%%/Bio/Installer/PAML.pm
+@dirrm %%SITE_PERL%%/Bio/Installer
 @dirrm %%SITE_PERL%%/Bio/Tools/Run/Analysis
 @dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
+@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo
 @dirrmtry %%SITE_PERL%%/Bio/Tools/Run
 @dirrmtry %%SITE_PERL%%/Bio/Tools
-@dirrmtry %%SITE_PERL%%/Bio/Factory
 @dirrmtry %%SITE_PERL%%/Bio