Errors

no_pod_errors

bioperl-run-1.5.2_005-RC/Bio/Tools/Run/PiseApplication/dca.pm -- Around line 28: Non-ASCII character seen before =encoding in 'Füllen,'. Assuming UTF-8 bioperl-run-1.5.2_005-RC/Bio/Tools/Run/PiseApplication/mreps.pm -- Around line 30: Non-ASCII character seen before =encoding in 'Århus'. Assuming UTF-8

no_unauthorized_packages

• Bio::Installer::EMBOSS
• Bio::Installer::Generic
• Bio::Installer::Muscle
• Bio::Installer::Probcons
• Bio::Tools::Run::Alignment::Amap
• Bio::Tools::Run::Alignment::Exonerate
• Bio::Tools::Run::Alignment::Kalign
• Bio::Tools::Run::Alignment::MAFFT
• Bio::Tools::Run::Alignment::Muscle
• Bio::Tools::Run::Alignment::Probalign
• Bio::Tools::Run::Alignment::Probcons
• Bio::Tools::Run::Cap3
• Bio::Tools::Run::Phrap
• Bio::Tools::Run::Phylo::LVB

prereq_matches_use

• Bio::Assembly::IO
• Bio::Cluster::SequenceFamily
• Bio::Tools::Phylo::PAML
• HTTP::Request::Common
• IO::String
• LWP
• LWP::UserAgent
• SOAP::Lite
• XML::Parser::PerlSAX

proper_libs

Bio/Factory/EMBOSS.pm, Bio/Installer/Clustalw.pm, Bio/Installer/EMBOSS.pm, Bio/Installer/Generic.pm, Bio/Installer/Muscle.pm, Bio/Installer/PAML.pm, Bio/Installer/Probcons.pm, Bio/Installer/TCoffee.pm, Bio/Tools/Run/AbstractRunner.pm, Bio/Tools/Run/Alignment/Amap.pm, Bio/Tools/Run/Alignment/Blat.pm, Bio/Tools/Run/Alignment/Clustalw.pm, Bio/Tools/Run/Alignment/DBA.pm, Bio/Tools/Run/Alignment/Exonerate.pm, Bio/Tools/Run/Alignment/Kalign.pm, Bio/Tools/Run/Alignment/Lagan.pm, Bio/Tools/Run/Alignment/MAFFT.pm, Bio/Tools/Run/Alignment/Muscle.pm, Bio/Tools/Run/Alignment/Probalign.pm, Bio/Tools/Run/Alignment/Probcons.pm, Bio/Tools/Run/Alignment/Sim4.pm, Bio/Tools/Run/Alignment/StandAloneFasta.pm, Bio/Tools/Run/Alignment/TCoffee.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis/soap.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis/soap.pm, Bio/Tools/Run/AnalysisFactory.pm, Bio/Tools/Run/AnalysisFactory/Pise.pm, Bio/Tools/Run/AnalysisFactory/soap.pm, Bio/Tools/Run/Cap3.pm, Bio/Tools/Run/Coil.pm, Bio/Tools/Run/EMBOSSApplication.pm, Bio/Tools/Run/EMBOSSacd.pm, Bio/Tools/Run/Eponine.pm, Bio/Tools/Run/FootPrinter.pm, Bio/Tools/Run/Genewise.pm, Bio/Tools/Run/Genscan.pm, Bio/Tools/Run/Hmmer.pm, Bio/Tools/Run/JavaRunner.pm, Bio/Tools/Run/Mdust.pm, Bio/Tools/Run/Phrap.pm, Bio/Tools/Run/Phylo/Forester/SDI.pm, Bio/Tools/Run/Phylo/LVB.pm, Bio/Tools/Run/Phylo/Molphy/ProtML.pm, Bio/Tools/Run/Phylo/PAML/Baseml.pm, Bio/Tools/Run/Phylo/PAML/Codeml.pm, Bio/Tools/Run/Phylo/PAML/Evolver.pm, Bio/Tools/Run/Phylo/PAML/Yn00.pm, Bio/Tools/Run/Phylo/Phylip/Base.pm, Bio/Tools/Run/Phylo/Phylip/Consense.pm, Bio/Tools/Run/Phylo/Phylip/DrawGram.pm, Bio/Tools/Run/Phylo/Phylip/DrawTree.pm, Bio/Tools/Run/Phylo/Phylip/Neighbor.pm, Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm, Bio/Tools/Run/Phylo/Phylip/ProtDist.pm, Bio/Tools/Run/Phylo/Phylip/ProtPars.pm, Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm, Bio/Tools/Run/PiseApplication.pm, Bio/Tools/Run/PiseApplication/CSR.pm, Bio/Tools/Run/PiseApplication/Puzzle.pm, Bio/Tools/Run/PiseApplication/abiview.pm, Bio/Tools/Run/PiseApplication/addquart.pm, Bio/Tools/Run/PiseApplication/align2model.pm, Bio/Tools/Run/PiseApplication/alistat.pm, Bio/Tools/Run/PiseApplication/antigenic.pm, Bio/Tools/Run/PiseApplication/assp.pm, Bio/Tools/Run/PiseApplication/backtranseq.pm, Bio/Tools/Run/PiseApplication/bambe.pm, Bio/Tools/Run/PiseApplication/banana.pm, Bio/Tools/Run/PiseApplication/bionj.pm, Bio/Tools/Run/PiseApplication/biosed.pm, Bio/Tools/Run/PiseApplication/bl2seq.pm, Bio/Tools/Run/PiseApplication/blast2.pm, Bio/Tools/Run/PiseApplication/blimps.pm, Bio/Tools/Run/PiseApplication/blimps_block.pm, Bio/Tools/Run/PiseApplication/blimps_matrix.pm, Bio/Tools/Run/PiseApplication/boxshade.pm, Bio/Tools/Run/PiseApplication/btwisted.pm, Bio/Tools/Run/PiseApplication/cai.pm, Bio/Tools/Run/PiseApplication/cap.pm, Bio/Tools/Run/PiseApplication/cds.pm, Bio/Tools/Run/PiseApplication/chaos.pm, Bio/Tools/Run/PiseApplication/charge.pm, Bio/Tools/Run/PiseApplication/checktrans.pm, Bio/Tools/Run/PiseApplication/chips.pm, Bio/Tools/Run/PiseApplication/cirdna.pm, Bio/Tools/Run/PiseApplication/clique.pm, Bio/Tools/Run/PiseApplication/clustalw.pm, Bio/Tools/Run/PiseApplication/clustalw_convert.pm, Bio/Tools/Run/PiseApplication/codcmp.pm, Bio/Tools/Run/PiseApplication/coderet.pm, Bio/Tools/Run/PiseApplication/codnocod.pm, Bio/Tools/Run/PiseApplication/codontree.pm, Bio/Tools/Run/PiseApplication/codonw.pm, Bio/Tools/Run/PiseApplication/comalign.pm, Bio/Tools/Run/PiseApplication/combat.pm, Bio/Tools/Run/PiseApplication/compseq.pm, Bio/Tools/Run/PiseApplication/con_filter.pm, Bio/Tools/Run/PiseApplication/confmat.pm, Bio/Tools/Run/PiseApplication/cons.pm, Bio/Tools/Run/PiseApplication/consense.pm, Bio/Tools/Run/PiseApplication/consensus.pm, Bio/Tools/Run/PiseApplication/cpgplot.pm, Bio/Tools/Run/PiseApplication/cpgreport.pm, Bio/Tools/Run/PiseApplication/cusp.pm, Bio/Tools/Run/PiseApplication/cutseq.pm, Bio/Tools/Run/PiseApplication/dan.pm, Bio/Tools/Run/PiseApplication/dca.pm, Bio/Tools/Run/PiseApplication/decorate.pm, Bio/Tools/Run/PiseApplication/degapseq.pm, Bio/Tools/Run/PiseApplication/descseq.pm, Bio/Tools/Run/PiseApplication/dialign2.pm, Bio/Tools/Run/PiseApplication/diffseq.pm, Bio/Tools/Run/PiseApplication/digest.pm, Bio/Tools/Run/PiseApplication/distmat.pm, Bio/Tools/Run/PiseApplication/distquart.pm, Bio/Tools/Run/PiseApplication/dnadist.pm, Bio/Tools/Run/PiseApplication/dnapars.pm, Bio/Tools/Run/PiseApplication/dollop.pm, Bio/Tools/Run/PiseApplication/domainer.pm, Bio/Tools/Run/PiseApplication/dotmatcher.pm, Bio/Tools/Run/PiseApplication/dotpath.pm, Bio/Tools/Run/PiseApplication/dottup.pm, Bio/Tools/Run/PiseApplication/drawgram.pm, Bio/Tools/Run/PiseApplication/drawpyr.pm, Bio/Tools/Run/PiseApplication/drawtree.pm, Bio/Tools/Run/PiseApplication/dreg.pm, Bio/Tools/Run/PiseApplication/druid.pm, Bio/Tools/Run/PiseApplication/dsc.pm, Bio/Tools/Run/PiseApplication/dssp.pm, Bio/Tools/Run/PiseApplication/einverted.pm, Bio/Tools/Run/PiseApplication/emma.pm, Bio/Tools/Run/PiseApplication/emowse.pm, Bio/Tools/Run/PiseApplication/environ.pm, Bio/Tools/Run/PiseApplication/eprimer3.pm, Bio/Tools/Run/PiseApplication/equicktandem.pm, Bio/Tools/Run/PiseApplication/est2genome.pm, Bio/Tools/Run/PiseApplication/etandem.pm, Bio/Tools/Run/PiseApplication/extractfeat.pm, Bio/Tools/Run/PiseApplication/extractseq.pm, Bio/Tools/Run/PiseApplication/fasta.pm, Bio/Tools/Run/PiseApplication/fastdnaml.pm, Bio/Tools/Run/PiseApplication/fastrna.pm, Bio/Tools/Run/PiseApplication/filtersites.pm, Bio/Tools/Run/PiseApplication/findkm.pm, Bio/Tools/Run/PiseApplication/fitch.pm, Bio/Tools/Run/PiseApplication/fmtseq.pm, Bio/Tools/Run/PiseApplication/freak.pm, Bio/Tools/Run/PiseApplication/fuzznuc.pm, Bio/Tools/Run/PiseApplication/fuzzpro.pm, Bio/Tools/Run/PiseApplication/fuzztran.pm, Bio/Tools/Run/PiseApplication/gb2xml.pm, Bio/Tools/Run/PiseApplication/geecee.pm, Bio/Tools/Run/PiseApplication/genscan.pm, Bio/Tools/Run/PiseApplication/getblock.pm, Bio/Tools/Run/PiseApplication/getorf.pm, Bio/Tools/Run/PiseApplication/gff2ps.pm, Bio/Tools/Run/PiseApplication/gibbs.pm, Bio/Tools/Run/PiseApplication/gibbs_scan.pm, Bio/Tools/Run/PiseApplication/golden.pm, Bio/Tools/Run/PiseApplication/grailclnt.pm, Bio/Tools/Run/PiseApplication/gruppi.pm, Bio/Tools/Run/PiseApplication/helixturnhelix.pm, Bio/Tools/Run/PiseApplication/hmmalign.pm, Bio/Tools/Run/PiseApplication/hmmbuild.pm, Bio/Tools/Run/PiseApplication/hmmcalibrate.pm, Bio/Tools/Run/PiseApplication/hmmconvert.pm, Bio/Tools/Run/PiseApplication/hmmemit.pm, Bio/Tools/Run/PiseApplication/hmmer2sam.pm, Bio/Tools/Run/PiseApplication/hmmfetch.pm, Bio/Tools/Run/PiseApplication/hmmpfam.pm, Bio/Tools/Run/PiseApplication/hmmscore.pm, Bio/Tools/Run/PiseApplication/hmmsearch.pm, Bio/Tools/Run/PiseApplication/hmoment.pm, Bio/Tools/Run/PiseApplication/homology.pm, Bio/Tools/Run/PiseApplication/html4blast.pm, Bio/Tools/Run/PiseApplication/iep.pm, Bio/Tools/Run/PiseApplication/infoalign.pm, Bio/Tools/Run/PiseApplication/infoseq.pm, Bio/Tools/Run/PiseApplication/interface.pm, Bio/Tools/Run/PiseApplication/isochore.pm, Bio/Tools/Run/PiseApplication/kitsch.pm, Bio/Tools/Run/PiseApplication/lassap.pm, Bio/Tools/Run/PiseApplication/lindna.pm, Bio/Tools/Run/PiseApplication/listor.pm, Bio/Tools/Run/PiseApplication/loadseq.pm, Bio/Tools/Run/PiseApplication/lvb.pm, Bio/Tools/Run/PiseApplication/makehist.pm, Bio/Tools/Run/PiseApplication/map.pm, Bio/Tools/Run/PiseApplication/marscan.pm, Bio/Tools/Run/PiseApplication/maskfeat.pm, Bio/Tools/Run/PiseApplication/maskseq.pm, Bio/Tools/Run/PiseApplication/matcher.pm, Bio/Tools/Run/PiseApplication/megamerger.pm, Bio/Tools/Run/PiseApplication/melting.pm, Bio/Tools/Run/PiseApplication/merger.pm, Bio/Tools/Run/PiseApplication/mfold.pm, Bio/Tools/Run/PiseApplication/mix.pm, Bio/Tools/Run/PiseApplication/modelfromalign.pm, Bio/Tools/Run/PiseApplication/most.pm, Bio/Tools/Run/PiseApplication/mreps.pm, Bio/Tools/Run/PiseApplication/msa.pm, Bio/Tools/Run/PiseApplication/msbar.pm, Bio/Tools/Run/PiseApplication/mspcrunch.pm, Bio/Tools/Run/PiseApplication/mview_alig.pm, Bio/Tools/Run/PiseApplication/mview_blast.pm, Bio/Tools/Run/PiseApplication/mwfilter.pm, Bio/Tools/Run/PiseApplication/needle.pm, Bio/Tools/Run/PiseApplication/neighbor.pm, Bio/Tools/Run/PiseApplication/newcpgreport.pm, Bio/Tools/Run/PiseApplication/newcpgseek.pm, Bio/Tools/Run/PiseApplication/newseq.pm, Bio/Tools/Run/PiseApplication/njdist.pm, Bio/Tools/Run/PiseApplication/nnssp.pm, Bio/Tools/Run/PiseApplication/notseq.pm, Bio/Tools/Run/PiseApplication/nrscope.pm, Bio/Tools/Run/PiseApplication/nthseq.pm, Bio/Tools/Run/PiseApplication/octanol.pm, Bio/Tools/Run/PiseApplication/oddcomp.pm, Bio/Tools/Run/PiseApplication/palindrome.pm, Bio/Tools/Run/PiseApplication/pam.pm, Bio/Tools/Run/PiseApplication/parciquart.pm, Bio/Tools/Run/PiseApplication/pars.pm, Bio/Tools/Run/PiseApplication/pasteseq.pm, Bio/Tools/Run/PiseApplication/patmatdb.pm, Bio/Tools/Run/PiseApplication/patmatmotifs.pm, Bio/Tools/Run/PiseApplication/patser.pm, Bio/Tools/Run/PiseApplication/pdbsearch.pm, Bio/Tools/Run/PiseApplication/pepcoil.pm, Bio/Tools/Run/PiseApplication/pepinfo.pm, Bio/Tools/Run/PiseApplication/pepnet.pm, Bio/Tools/Run/PiseApplication/pepstats.pm, Bio/Tools/Run/PiseApplication/pepwheel.pm, Bio/Tools/Run/PiseApplication/pepwindow.pm, Bio/Tools/Run/PiseApplication/pepwindowall.pm, Bio/Tools/Run/PiseApplication/pestfind.pm, Bio/Tools/Run/PiseApplication/pftools.pm, Bio/Tools/Run/PiseApplication/phiblast.pm, Bio/Tools/Run/PiseApplication/phyml.pm, Bio/Tools/Run/PiseApplication/pima.pm, Bio/Tools/Run/PiseApplication/plotcon.pm, Bio/Tools/Run/PiseApplication/plotorf.pm, Bio/Tools/Run/PiseApplication/plsearch.pm, Bio/Tools/Run/PiseApplication/polydot.pm, Bio/Tools/Run/PiseApplication/pratt.pm, Bio/Tools/Run/PiseApplication/predator.pm, Bio/Tools/Run/PiseApplication/preg.pm, Bio/Tools/Run/PiseApplication/prettyalign.pm, Bio/Tools/Run/PiseApplication/prettyplot.pm, Bio/Tools/Run/PiseApplication/prettyseq.pm, Bio/Tools/Run/PiseApplication/primersearch.pm, Bio/Tools/Run/PiseApplication/primo.pm, Bio/Tools/Run/PiseApplication/prodom.pm, Bio/Tools/Run/PiseApplication/profit.pm, Bio/Tools/Run/PiseApplication/prophecy.pm, Bio/Tools/Run/PiseApplication/prophet.pm, Bio/Tools/Run/PiseApplication/prose.pm, Bio/Tools/Run/PiseApplication/prot_nucml.pm, Bio/Tools/Run/PiseApplication/protal2dna.pm, Bio/Tools/Run/PiseApplication/protdist.pm, Bio/Tools/Run/PiseApplication/protpars.pm, Bio/Tools/Run/PiseApplication/pscan.pm, Bio/Tools/Run/PiseApplication/psiblast.pm, Bio/Tools/Run/PiseApplication/psort2.pm, Bio/Tools/Run/PiseApplication/pyramids.pm, Bio/Tools/Run/PiseApplication/pyreval.pm, Bio/Tools/Run/PiseApplication/qstar.pm, Bio/Tools/Run/PiseApplication/quicktree.pm, Bio/Tools/Run/PiseApplication/readnexus.pm, Bio/Tools/Run/PiseApplication/readseq.pm, Bio/Tools/Run/PiseApplication/recoder.pm, Bio/Tools/Run/PiseApplication/redata.pm, Bio/Tools/Run/PiseApplication/remap.pm, Bio/Tools/Run/PiseApplication/repeats.pm, Bio/Tools/Run/PiseApplication/restover.pm, Bio/Tools/Run/PiseApplication/restrict.pm, Bio/Tools/Run/PiseApplication/revseq.pm, Bio/Tools/Run/PiseApplication/rnadistance.pm, Bio/Tools/Run/PiseApplication/rnaeval.pm, Bio/Tools/Run/PiseApplication/rnafold.pm, Bio/Tools/Run/PiseApplication/rnaga.pm, Bio/Tools/Run/PiseApplication/rnaheat.pm, Bio/Tools/Run/PiseApplication/rnainverse.pm, Bio/Tools/Run/PiseApplication/rnapdist.pm, Bio/Tools/Run/PiseApplication/rnasubopt.pm, Bio/Tools/Run/PiseApplication/sam2hmmer.pm, Bio/Tools/Run/PiseApplication/sampleseqs.pm, Bio/Tools/Run/PiseApplication/saps.pm, Bio/Tools/Run/PiseApplication/satellites.pm, Bio/Tools/Run/PiseApplication/scan_for_matches.pm, Bio/Tools/Run/PiseApplication/scope.pm, Bio/Tools/Run/PiseApplication/scopparse.pm, Bio/Tools/Run/PiseApplication/seqboot.pm, Bio/Tools/Run/PiseApplication/seqgen.pm, Bio/Tools/Run/PiseApplication/seqmatchall.pm, Bio/Tools/Run/PiseApplication/seqsblast.pm, Bio/Tools/Run/PiseApplication/seqstat.pm, Bio/Tools/Run/PiseApplication/showalign.pm, Bio/Tools/Run/PiseApplication/showfeat.pm, Bio/Tools/Run/PiseApplication/showorf.pm, Bio/Tools/Run/PiseApplication/showseq.pm, Bio/Tools/Run/PiseApplication/shuffleseq.pm, Bio/Tools/Run/PiseApplication/sigcleave.pm, Bio/Tools/Run/PiseApplication/siggen.pm, Bio/Tools/Run/PiseApplication/sigscan.pm, Bio/Tools/Run/PiseApplication/silent.pm, Bio/Tools/Run/PiseApplication/sirna.pm, Bio/Tools/Run/PiseApplication/splitter.pm, Bio/Tools/Run/PiseApplication/sreformat.pm, Bio/Tools/Run/PiseApplication/stretcher.pm, Bio/Tools/Run/PiseApplication/stride.pm, Bio/Tools/Run/PiseApplication/stssearch.pm, Bio/Tools/Run/PiseApplication/supermatcher.pm, Bio/Tools/Run/PiseApplication/syco.pm, Bio/Tools/Run/PiseApplication/tacg.pm, Bio/Tools/Run/PiseApplication/tfscan.pm, Bio/Tools/Run/PiseApplication/tipdate.pm, Bio/Tools/Run/PiseApplication/tmap.pm, Bio/Tools/Run/PiseApplication/toppred.pm, Bio/Tools/Run/PiseApplication/tranalign.pm, Bio/Tools/Run/PiseApplication/transeq.pm, Bio/Tools/Run/PiseApplication/treealign.pm, Bio/Tools/Run/PiseApplication/trimest.pm, Bio/Tools/Run/PiseApplication/trimseq.pm, Bio/Tools/Run/PiseApplication/trnascan.pm, Bio/Tools/Run/PiseApplication/twofeat.pm, Bio/Tools/Run/PiseApplication/unroot.pm, Bio/Tools/Run/PiseApplication/vectorstrip.pm, Bio/Tools/Run/PiseApplication/water.pm, Bio/Tools/Run/PiseApplication/weighbor.pm, Bio/Tools/Run/PiseApplication/whichdb.pm, Bio/Tools/Run/PiseApplication/wise2.pm, Bio/Tools/Run/PiseApplication/wobble.pm, Bio/Tools/Run/PiseApplication/wordcount.pm, Bio/Tools/Run/PiseApplication/wordmatch.pm, Bio/Tools/Run/PiseApplication/wublast2.pm, Bio/Tools/Run/PiseApplication/xblast.pm, Bio/Tools/Run/PiseApplication/xpound.pm, Bio/Tools/Run/PiseJob.pm, Bio/Tools/Run/PiseJobParser.pm, Bio/Tools/Run/PiseWorkflow.pm, Bio/Tools/Run/Primate.pm, Bio/Tools/Run/Primer3.pm, Bio/Tools/Run/Prints.pm, Bio/Tools/Run/Profile.pm, Bio/Tools/Run/Promoterwise.pm, Bio/Tools/Run/Pseudowise.pm, Bio/Tools/Run/RepeatMasker.pm, Bio/Tools/Run/Seg.pm, Bio/Tools/Run/Signalp.pm, Bio/Tools/Run/Tmhmm.pm, Bio/Tools/Run/TribeMCL.pm, Bio/Tools/Run/Vista.pm

use_warnings

Bio::Factory::EMBOSS, Bio::Installer::Clustalw, Bio::Installer::EMBOSS, Bio::Installer::Generic, Bio::Installer::Muscle, Bio::Installer::PAML, Bio::Installer::Probcons, Bio::Installer::TCoffee, Bio::Tools::Run::AbstractRunner, Bio::Tools::Run::Alignment::Amap, Bio::Tools::Run::Alignment::Blat, Bio::Tools::Run::Alignment::Clustalw, Bio::Tools::Run::Alignment::DBA, Bio::Tools::Run::Alignment::Exonerate, Bio::Tools::Run::Alignment::Kalign, Bio::Tools::Run::Alignment::Lagan, Bio::Tools::Run::Alignment::MAFFT, Bio::Tools::Run::Alignment::Muscle, Bio::Tools::Run::Alignment::Probalign, Bio::Tools::Run::Alignment::Probcons, Bio::Tools::Run::Alignment::Sim4, Bio::Tools::Run::Alignment::StandAloneFasta, Bio::Tools::Run::Alignment::TCoffee, Bio::Tools::Run::Analysis, Bio::Tools::Run::Analysis::soap, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::AnalysisFactory::Pise, Bio::Tools::Run::AnalysisFactory::soap, Bio::Tools::Run::Cap3, Bio::Tools::Run::Coil, Bio::Tools::Run::EMBOSSApplication, Bio::Tools::Run::EMBOSSacd, Bio::Tools::Run::Eponine, Bio::Tools::Run::FootPrinter, Bio::Tools::Run::Genewise, Bio::Tools::Run::Genscan, Bio::Tools::Run::Hmmer, Bio::Tools::Run::JavaRunner, Bio::Tools::Run::Mdust, Bio::Tools::Run::Phrap, Bio::Tools::Run::Phylo::Forester::SDI, Bio::Tools::Run::Phylo::LVB, Bio::Tools::Run::Phylo::Molphy::ProtML, Bio::Tools::Run::Phylo::PAML::Baseml, Bio::Tools::Run::Phylo::PAML::Codeml, Bio::Tools::Run::Phylo::PAML::Evolver, Bio::Tools::Run::Phylo::PAML::Yn00, Bio::Tools::Run::Phylo::Phylip::Base, Bio::Tools::Run::Phylo::Phylip::Consense, Bio::Tools::Run::Phylo::Phylip::DrawGram, Bio::Tools::Run::Phylo::Phylip::DrawTree, Bio::Tools::Run::Phylo::Phylip::Neighbor, Bio::Tools::Run::Phylo::Phylip::PhylipConf, Bio::Tools::Run::Phylo::Phylip::ProtDist, Bio::Tools::Run::Phylo::Phylip::ProtPars, Bio::Tools::Run::Phylo::Phylip::SeqBoot, Bio::Tools::Run::PiseApplication, Bio::Tools::Run::PiseApplication::CSR, Bio::Tools::Run::PiseApplication::Puzzle, Bio::Tools::Run::PiseApplication::abiview, Bio::Tools::Run::PiseApplication::addquart, Bio::Tools::Run::PiseApplication::align2model, Bio::Tools::Run::PiseApplication::alistat, Bio::Tools::Run::PiseApplication::antigenic, Bio::Tools::Run::PiseApplication::assp, Bio::Tools::Run::PiseApplication::backtranseq, Bio::Tools::Run::PiseApplication::bambe, Bio::Tools::Run::PiseApplication::banana, Bio::Tools::Run::PiseApplication::bionj, Bio::Tools::Run::PiseApplication::biosed, Bio::Tools::Run::PiseApplication::bl2seq, Bio::Tools::Run::PiseApplication::blast2, Bio::Tools::Run::PiseApplication::blimps, Bio::Tools::Run::PiseApplication::blimps_block, Bio::Tools::Run::PiseApplication::blimps_matrix, Bio::Tools::Run::PiseApplication::boxshade, Bio::Tools::Run::PiseApplication::btwisted, Bio::Tools::Run::PiseApplication::cai, Bio::Tools::Run::PiseApplication::cap, Bio::Tools::Run::PiseApplication::cds, Bio::Tools::Run::PiseApplication::chaos, Bio::Tools::Run::PiseApplication::charge, Bio::Tools::Run::PiseApplication::checktrans, Bio::Tools::Run::PiseApplication::chips, Bio::Tools::Run::PiseApplication::cirdna, Bio::Tools::Run::PiseApplication::clique, Bio::Tools::Run::PiseApplication::clustalw, Bio::Tools::Run::PiseApplication::clustalw_convert, Bio::Tools::Run::PiseApplication::codcmp, Bio::Tools::Run::PiseApplication::coderet, Bio::Tools::Run::PiseApplication::codnocod, Bio::Tools::Run::PiseApplication::codontree, Bio::Tools::Run::PiseApplication::codonw, Bio::Tools::Run::PiseApplication::comalign, Bio::Tools::Run::PiseApplication::combat, Bio::Tools::Run::PiseApplication::compseq, Bio::Tools::Run::PiseApplication::con_filter, Bio::Tools::Run::PiseApplication::confmat, Bio::Tools::Run::PiseApplication::cons, Bio::Tools::Run::PiseApplication::consense, Bio::Tools::Run::PiseApplication::consensus, Bio::Tools::Run::PiseApplication::cpgplot, Bio::Tools::Run::PiseApplication::cpgreport, Bio::Tools::Run::PiseApplication::cusp, Bio::Tools::Run::PiseApplication::cutseq, Bio::Tools::Run::PiseApplication::dan, Bio::Tools::Run::PiseApplication::dca, Bio::Tools::Run::PiseApplication::decorate, Bio::Tools::Run::PiseApplication::degapseq, Bio::Tools::Run::PiseApplication::descseq, Bio::Tools::Run::PiseApplication::dialign2, Bio::Tools::Run::PiseApplication::diffseq, Bio::Tools::Run::PiseApplication::digest, Bio::Tools::Run::PiseApplication::distmat, Bio::Tools::Run::PiseApplication::distquart, Bio::Tools::Run::PiseApplication::dnadist, Bio::Tools::Run::PiseApplication::dnapars, Bio::Tools::Run::PiseApplication::dollop, Bio::Tools::Run::PiseApplication::domainer, Bio::Tools::Run::PiseApplication::dotmatcher, Bio::Tools::Run::PiseApplication::dotpath, Bio::Tools::Run::PiseApplication::dottup, Bio::Tools::Run::PiseApplication::drawgram, Bio::Tools::Run::PiseApplication::drawpyr, Bio::Tools::Run::PiseApplication::drawtree, Bio::Tools::Run::PiseApplication::dreg, Bio::Tools::Run::PiseApplication::druid, Bio::Tools::Run::PiseApplication::dsc, Bio::Tools::Run::PiseApplication::dssp, Bio::Tools::Run::PiseApplication::einverted, Bio::Tools::Run::PiseApplication::emma, Bio::Tools::Run::PiseApplication::emowse, Bio::Tools::Run::PiseApplication::environ, Bio::Tools::Run::PiseApplication::eprimer3, Bio::Tools::Run::PiseApplication::equicktandem, Bio::Tools::Run::PiseApplication::est2genome, Bio::Tools::Run::PiseApplication::etandem, Bio::Tools::Run::PiseApplication::extractfeat, Bio::Tools::Run::PiseApplication::extractseq, Bio::Tools::Run::PiseApplication::fasta, Bio::Tools::Run::PiseApplication::fastdnaml, Bio::Tools::Run::PiseApplication::fastrna, Bio::Tools::Run::PiseApplication::filtersites, Bio::Tools::Run::PiseApplication::findkm, Bio::Tools::Run::PiseApplication::fitch, Bio::Tools::Run::PiseApplication::fmtseq, Bio::Tools::Run::PiseApplication::freak, Bio::Tools::Run::PiseApplication::fuzznuc, Bio::Tools::Run::PiseApplication::fuzzpro, Bio::Tools::Run::PiseApplication::fuzztran, Bio::Tools::Run::PiseApplication::gb2xml, Bio::Tools::Run::PiseApplication::geecee, Bio::Tools::Run::PiseApplication::genscan, Bio::Tools::Run::PiseApplication::getblock, Bio::Tools::Run::PiseApplication::getorf, Bio::Tools::Run::PiseApplication::gff2ps, Bio::Tools::Run::PiseApplication::gibbs, Bio::Tools::Run::PiseApplication::gibbs_scan, Bio::Tools::Run::PiseApplication::golden, Bio::Tools::Run::PiseApplication::grailclnt, Bio::Tools::Run::PiseApplication::gruppi, Bio::Tools::Run::PiseApplication::helixturnhelix, Bio::Tools::Run::PiseApplication::hmmalign, Bio::Tools::Run::PiseApplication::hmmbuild, Bio::Tools::Run::PiseApplication::hmmcalibrate, Bio::Tools::Run::PiseApplication::hmmconvert, Bio::Tools::Run::PiseApplication::hmmemit, Bio::Tools::Run::PiseApplication::hmmer2sam, Bio::Tools::Run::PiseApplication::hmmfetch, Bio::Tools::Run::PiseApplication::hmmpfam, Bio::Tools::Run::PiseApplication::hmmscore, Bio::Tools::Run::PiseApplication::hmmsearch, Bio::Tools::Run::PiseApplication::hmoment, Bio::Tools::Run::PiseApplication::homology, Bio::Tools::Run::PiseApplication::html4blast, Bio::Tools::Run::PiseApplication::iep, Bio::Tools::Run::PiseApplication::infoalign, Bio::Tools::Run::PiseApplication::infoseq, Bio::Tools::Run::PiseApplication::interface, Bio::Tools::Run::PiseApplication::isochore, Bio::Tools::Run::PiseApplication::kitsch, Bio::Tools::Run::PiseApplication::lassap, Bio::Tools::Run::PiseApplication::lindna, Bio::Tools::Run::PiseApplication::listor, Bio::Tools::Run::PiseApplication::loadseq, Bio::Tools::Run::PiseApplication::lvb, Bio::Tools::Run::PiseApplication::makehist, Bio::Tools::Run::PiseApplication::map, Bio::Tools::Run::PiseApplication::marscan, Bio::Tools::Run::PiseApplication::maskfeat, Bio::Tools::Run::PiseApplication::maskseq, Bio::Tools::Run::PiseApplication::matcher, Bio::Tools::Run::PiseApplication::megamerger, Bio::Tools::Run::PiseApplication::melting, Bio::Tools::Run::PiseApplication::merger, Bio::Tools::Run::PiseApplication::mfold, Bio::Tools::Run::PiseApplication::mix, Bio::Tools::Run::PiseApplication::modelfromalign, Bio::Tools::Run::PiseApplication::most, Bio::Tools::Run::PiseApplication::mreps, Bio::Tools::Run::PiseApplication::msa, Bio::Tools::Run::PiseApplication::msbar, Bio::Tools::Run::PiseApplication::mspcrunch, Bio::Tools::Run::PiseApplication::mview_alig, Bio::Tools::Run::PiseApplication::mview_blast, Bio::Tools::Run::PiseApplication::mwfilter, Bio::Tools::Run::PiseApplication::needle, Bio::Tools::Run::PiseApplication::neighbor, Bio::Tools::Run::PiseApplication::newcpgreport, Bio::Tools::Run::PiseApplication::newcpgseek, Bio::Tools::Run::PiseApplication::newseq, Bio::Tools::Run::PiseApplication::njdist, Bio::Tools::Run::PiseApplication::nnssp, Bio::Tools::Run::PiseApplication::notseq, Bio::Tools::Run::PiseApplication::nrscope, Bio::Tools::Run::PiseApplication::nthseq, Bio::Tools::Run::PiseApplication::octanol, Bio::Tools::Run::PiseApplication::oddcomp, Bio::Tools::Run::PiseApplication::palindrome, Bio::Tools::Run::PiseApplication::pam, Bio::Tools::Run::PiseApplication::parciquart, Bio::Tools::Run::PiseApplication::pars, Bio::Tools::Run::PiseApplication::pasteseq, Bio::Tools::Run::PiseApplication::patmatdb, Bio::Tools::Run::PiseApplication::patmatmotifs, Bio::Tools::Run::PiseApplication::patser, Bio::Tools::Run::PiseApplication::pdbsearch, Bio::Tools::Run::PiseApplication::pepcoil, Bio::Tools::Run::PiseApplication::pepinfo, Bio::Tools::Run::PiseApplication::pepnet, Bio::Tools::Run::PiseApplication::pepstats, Bio::Tools::Run::PiseApplication::pepwheel, Bio::Tools::Run::PiseApplication::pepwindow, Bio::Tools::Run::PiseApplication::pepwindowall, Bio::Tools::Run::PiseApplication::pestfind, Bio::Tools::Run::PiseApplication::pftools, Bio::Tools::Run::PiseApplication::phiblast, Bio::Tools::Run::PiseApplication::phyml, Bio::Tools::Run::PiseApplication::pima, Bio::Tools::Run::PiseApplication::plotcon, Bio::Tools::Run::PiseApplication::plotorf, Bio::Tools::Run::PiseApplication::plsearch, Bio::Tools::Run::PiseApplication::polydot, Bio::Tools::Run::PiseApplication::pratt, Bio::Tools::Run::PiseApplication::predator, Bio::Tools::Run::PiseApplication::preg, Bio::Tools::Run::PiseApplication::prettyalign, Bio::Tools::Run::PiseApplication::prettyplot, Bio::Tools::Run::PiseApplication::prettyseq, Bio::Tools::Run::PiseApplication::primersearch, Bio::Tools::Run::PiseApplication::primo, Bio::Tools::Run::PiseApplication::prodom, Bio::Tools::Run::PiseApplication::profit, Bio::Tools::Run::PiseApplication::prophecy, Bio::Tools::Run::PiseApplication::prophet, Bio::Tools::Run::PiseApplication::prose, Bio::Tools::Run::PiseApplication::prot_nucml, Bio::Tools::Run::PiseApplication::protal2dna, Bio::Tools::Run::PiseApplication::protdist, Bio::Tools::Run::PiseApplication::protpars, Bio::Tools::Run::PiseApplication::pscan, Bio::Tools::Run::PiseApplication::psiblast, Bio::Tools::Run::PiseApplication::psort2, Bio::Tools::Run::PiseApplication::pyramids, Bio::Tools::Run::PiseApplication::pyreval, Bio::Tools::Run::PiseApplication::qstar, Bio::Tools::Run::PiseApplication::quicktree, Bio::Tools::Run::PiseApplication::readnexus, Bio::Tools::Run::PiseApplication::readseq, Bio::Tools::Run::PiseApplication::recoder, Bio::Tools::Run::PiseApplication::redata, Bio::Tools::Run::PiseApplication::remap, Bio::Tools::Run::PiseApplication::repeats, Bio::Tools::Run::PiseApplication::restover, Bio::Tools::Run::PiseApplication::restrict, Bio::Tools::Run::PiseApplication::revseq, Bio::Tools::Run::PiseApplication::rnadistance, Bio::Tools::Run::PiseApplication::rnaeval, Bio::Tools::Run::PiseApplication::rnafold, Bio::Tools::Run::PiseApplication::rnaga, Bio::Tools::Run::PiseApplication::rnaheat, Bio::Tools::Run::PiseApplication::rnainverse, Bio::Tools::Run::PiseApplication::rnapdist, Bio::Tools::Run::PiseApplication::rnasubopt, Bio::Tools::Run::PiseApplication::sam2hmmer, Bio::Tools::Run::PiseApplication::sampleseqs, Bio::Tools::Run::PiseApplication::saps, Bio::Tools::Run::PiseApplication::satellites, Bio::Tools::Run::PiseApplication::scan_for_matches, Bio::Tools::Run::PiseApplication::scope, Bio::Tools::Run::PiseApplication::scopparse, Bio::Tools::Run::PiseApplication::seqboot, Bio::Tools::Run::PiseApplication::seqgen, Bio::Tools::Run::PiseApplication::seqmatchall, Bio::Tools::Run::PiseApplication::seqsblast, Bio::Tools::Run::PiseApplication::seqstat, Bio::Tools::Run::PiseApplication::showalign, Bio::Tools::Run::PiseApplication::showfeat, Bio::Tools::Run::PiseApplication::showorf, Bio::Tools::Run::PiseApplication::showseq, Bio::Tools::Run::PiseApplication::shuffleseq, Bio::Tools::Run::PiseApplication::sigcleave, Bio::Tools::Run::PiseApplication::siggen, Bio::Tools::Run::PiseApplication::sigscan, Bio::Tools::Run::PiseApplication::silent, Bio::Tools::Run::PiseApplication::sirna, Bio::Tools::Run::PiseApplication::splitter, Bio::Tools::Run::PiseApplication::sreformat, Bio::Tools::Run::PiseApplication::stretcher, Bio::Tools::Run::PiseApplication::stride, Bio::Tools::Run::PiseApplication::stssearch, Bio::Tools::Run::PiseApplication::supermatcher, Bio::Tools::Run::PiseApplication::syco, Bio::Tools::Run::PiseApplication::tacg, Bio::Tools::Run::PiseApplication::tfscan, Bio::Tools::Run::PiseApplication::tipdate, Bio::Tools::Run::PiseApplication::tmap, Bio::Tools::Run::PiseApplication::toppred, Bio::Tools::Run::PiseApplication::tranalign, Bio::Tools::Run::PiseApplication::transeq, Bio::Tools::Run::PiseApplication::treealign, Bio::Tools::Run::PiseApplication::trimest, Bio::Tools::Run::PiseApplication::trimseq, Bio::Tools::Run::PiseApplication::trnascan, Bio::Tools::Run::PiseApplication::twofeat, Bio::Tools::Run::PiseApplication::unroot, Bio::Tools::Run::PiseApplication::vectorstrip, Bio::Tools::Run::PiseApplication::water, Bio::Tools::Run::PiseApplication::weighbor, Bio::Tools::Run::PiseApplication::whichdb, Bio::Tools::Run::PiseApplication::wise2, Bio::Tools::Run::PiseApplication::wobble, Bio::Tools::Run::PiseApplication::wordcount, Bio::Tools::Run::PiseApplication::wordmatch, Bio::Tools::Run::PiseApplication::wublast2, Bio::Tools::Run::PiseApplication::xblast, Bio::Tools::Run::PiseApplication::xpound, Bio::Tools::Run::PiseJob, Bio::Tools::Run::PiseJobParser, Bio::Tools::Run::PiseWorkflow, Bio::Tools::Run::Primate, Bio::Tools::Run::Primer3, Bio::Tools::Run::Prints, Bio::Tools::Run::Profile, Bio::Tools::Run::Promoterwise, Bio::Tools::Run::Pseudowise, Bio::Tools::Run::RepeatMasker, Bio::Tools::Run::Seg, Bio::Tools::Run::Signalp, Bio::Tools::Run::Tmhmm, Bio::Tools::Run::TribeMCL, Bio::Tools::Run::Vista