- Released by
- CJFIELDS
- Version
- Release Date
- 2016-12-18
- Kwalitee
- 146.88
- Core Kwalitee
- 90.62
- LINKS
BioPerl-Run 1.007000
Files
- .travis.yml
- AUTHORS
- Build.PL
- Changes
- DEPENDENCIES
- INSTALL
- INSTALL.PROGRAMS
- INSTALL.SKIP
- LICENSE
- MANIFEST
- META.json
- META.yml
- README.md
- lib/Bio/DB/ESoap.pm
- lib/Bio/DB/ESoap/WSDL.pm
- lib/Bio/DB/SoapEUtilities.pm
- lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
- lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm
- lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm
- lib/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm
- lib/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
- lib/Bio/DB/SoapEUtilities/LinkAdaptor.pm
- lib/Bio/DB/SoapEUtilities/Result.pm
- lib/Bio/Factory/EMBOSS.pm
- lib/Bio/Installer/Clustalw.pm
- lib/Bio/Installer/EMBOSS.pm
- lib/Bio/Installer/Generic.pm
- lib/Bio/Installer/Hyphy.pm
- lib/Bio/Installer/Muscle.pm
- lib/Bio/Installer/PAML.pm
- lib/Bio/Installer/Probcons.pm
- lib/Bio/Installer/SLR.pm
- lib/Bio/Installer/TCoffee.pm
- lib/Bio/Tools/Run/Alignment/Amap.pm
- lib/Bio/Tools/Run/Alignment/Blat.pm
- lib/Bio/Tools/Run/Alignment/Clustalw.pm
- lib/Bio/Tools/Run/Alignment/DBA.pm
- lib/Bio/Tools/Run/Alignment/Exonerate.pm
- lib/Bio/Tools/Run/Alignment/Gmap.pm
- lib/Bio/Tools/Run/Alignment/Kalign.pm
- lib/Bio/Tools/Run/Alignment/Lagan.pm
- lib/Bio/Tools/Run/Alignment/MAFFT.pm
- lib/Bio/Tools/Run/Alignment/MSAProbs.pm
- lib/Bio/Tools/Run/Alignment/Muscle.pm
- lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
- lib/Bio/Tools/Run/Alignment/Probalign.pm
- lib/Bio/Tools/Run/Alignment/Probcons.pm
- lib/Bio/Tools/Run/Alignment/Proda.pm
- lib/Bio/Tools/Run/Alignment/Sim4.pm
- lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
- lib/Bio/Tools/Run/Alignment/TCoffee.pm
- lib/Bio/Tools/Run/Analysis.pm
- lib/Bio/Tools/Run/Analysis/soap.pm
- lib/Bio/Tools/Run/AnalysisFactory.pm
- lib/Bio/Tools/Run/AnalysisFactory/soap.pm
- lib/Bio/Tools/Run/AssemblerBase.pm
- lib/Bio/Tools/Run/BEDTools.pm
- lib/Bio/Tools/Run/BEDTools/Config.pm
- lib/Bio/Tools/Run/BWA.pm
- lib/Bio/Tools/Run/BWA/Config.pm
- lib/Bio/Tools/Run/BlastPlus.pm
- lib/Bio/Tools/Run/BlastPlus/Config.pm
- lib/Bio/Tools/Run/Bowtie.pm
- lib/Bio/Tools/Run/Bowtie/Config.pm
- lib/Bio/Tools/Run/Cap3.pm
- lib/Bio/Tools/Run/Coil.pm
- lib/Bio/Tools/Run/EMBOSSApplication.pm
- lib/Bio/Tools/Run/EMBOSSacd.pm
- lib/Bio/Tools/Run/ERPIN.pm
- lib/Bio/Tools/Run/Ensembl.pm
- lib/Bio/Tools/Run/Eponine.pm
- lib/Bio/Tools/Run/FootPrinter.pm
- lib/Bio/Tools/Run/Genemark.pm
- lib/Bio/Tools/Run/Genewise.pm
- lib/Bio/Tools/Run/Genscan.pm
- lib/Bio/Tools/Run/Glimmer.pm
- lib/Bio/Tools/Run/Hmmer.pm
- lib/Bio/Tools/Run/Infernal.pm
- lib/Bio/Tools/Run/MCS.pm
- lib/Bio/Tools/Run/Maq.pm
- lib/Bio/Tools/Run/Maq/Config.pm
- lib/Bio/Tools/Run/Match.pm
- lib/Bio/Tools/Run/Mdust.pm
- lib/Bio/Tools/Run/Meme.pm
- lib/Bio/Tools/Run/Minimo.pm
- lib/Bio/Tools/Run/Newbler.pm
- lib/Bio/Tools/Run/Phrap.pm
- lib/Bio/Tools/Run/Phylo/FastTree.pm
- lib/Bio/Tools/Run/Phylo/Gerp.pm
- lib/Bio/Tools/Run/Phylo/Gumby.pm
- lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
- lib/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
- lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
- lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
- lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
- lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
- lib/Bio/Tools/Run/Phylo/LVB.pm
- lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
- lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
- lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
- lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
- lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
- lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
- lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
- lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
- lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
- lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
- lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
- lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
- lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
- lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
- lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
- lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
- lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
- lib/Bio/Tools/Run/Phylo/PhyloBase.pm
- lib/Bio/Tools/Run/Phylo/Phyml.pm
- lib/Bio/Tools/Run/Phylo/QuickTree.pm
- lib/Bio/Tools/Run/Phylo/Raxml.pm
- lib/Bio/Tools/Run/Phylo/SLR.pm
- lib/Bio/Tools/Run/Phylo/Semphy.pm
- lib/Bio/Tools/Run/Primate.pm
- lib/Bio/Tools/Run/Primer3.pm
- lib/Bio/Tools/Run/Prints.pm
- lib/Bio/Tools/Run/Profile.pm
- lib/Bio/Tools/Run/Promoterwise.pm
- lib/Bio/Tools/Run/Pseudowise.pm
- lib/Bio/Tools/Run/RNAMotif.pm
- lib/Bio/Tools/Run/RepeatMasker.pm
- lib/Bio/Tools/Run/Samtools.pm
- lib/Bio/Tools/Run/Samtools/Config.pm
- lib/Bio/Tools/Run/Seg.pm
- lib/Bio/Tools/Run/Signalp.pm
- lib/Bio/Tools/Run/Simprot.pm
- lib/Bio/Tools/Run/StandAloneBlast.pm
- lib/Bio/Tools/Run/StandAloneBlastPlus.pm
- lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
- lib/Bio/Tools/Run/StandAloneNCBIBlast.pm
- lib/Bio/Tools/Run/StandAloneWUBlast.pm
- lib/Bio/Tools/Run/TigrAssembler.pm
- lib/Bio/Tools/Run/Tmhmm.pm
- lib/Bio/Tools/Run/TribeMCL.pm
- lib/Bio/Tools/Run/Vista.pm
- lib/Bio/Tools/Run/WrapperBase.pm
- lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
- lib/Bio/Tools/Run/tRNAscanSE.pm
- scripts/bioperl_application_installer.PLS
- scripts/multi_hmmsearch.PLS
- scripts/panalysis.PLS
- scripts/papplmaker.PLS
- scripts/run_neighbor.PLS
- scripts/run_protdist.PLS
- t/Amap.t
- t/AnalysisFactory_soap.t
- t/Analysis_soap.t
- t/BEDTools.t
- t/BWA.t
- t/Blat.t
- t/Bowtie.t
- t/Cap3.t
- t/Clustalw.t
- t/Coil.t
- t/Consense.t
- t/DBA.t
- t/DrawGram.t
- t/DrawTree.t
- t/EMBOSS.t
- t/Ensembl.t
- t/Eponine.t
- t/Exonerate.t
- t/FastTree.t
- t/FootPrinter.t
- t/Genemark.hmm.prokaryotic.t
- t/Genewise.t
- t/Genscan.t
- t/Gerp.t
- t/Glimmer2.t
- t/Glimmer3.t
- t/Gumby.t
- t/Hmmer.t
- t/Hyphy.t
- t/Infernal.t
- t/Kalign.t
- t/LVB.t
- t/Lagan.t
- t/MAFFT.t
- t/MCS.t
- t/MSAProbs.t
- t/Maq.t
- t/Match.t
- t/Mdust.t
- t/Meme.t
- t/Minimo.t
- t/Molphy.t
- t/Muscle.t
- t/Neighbor.t
- t/Newbler.t
- t/Njtree.t
- t/PAML.t
- t/Pal2Nal.t
- t/PhastCons.t
- t/Phrap.t
- t/Phyml.t
- t/Primate.t
- t/Primer3.t
- t/Prints.t
- t/Probalign.t
- t/Probcons.t
- t/Profile.t
- t/Promoterwise.t
- t/ProtDist.t
- t/ProtPars.t
- t/Pseudowise.t
- t/QuickTree.t
- t/Raxml.t
- t/RepeatMasker.t
- t/SABlastPlus.t
- t/SLR.t
- t/Samtools.t
- t/Seg.t
- t/Semphy.t
- t/SeqBoot.t
- t/Signalp.t
- t/Sim4.t
- t/Simprot.t
- t/SoapEU-function.t
- t/SoapEU-unit.t
- t/StandAloneFasta.t
- t/TCoffee.t
- t/TigrAssembler.t
- t/Tmhmm.t
- t/Tools/Run/Dummy.pm
- t/Tools/Run/Dummy/Config.pm
- t/Tools/Run/RemoteBlast.t
- t/Tools/Run/RemoteBlast_rpsblast.t
- t/Tools/Run/StandAloneBlast.t
- t/Tools/Run/WBCommandExts.t
- t/Tools/Run/WrapperBase.t
- t/TribeMCL.t
- t/Vista.t
- t/data/1.bg
- t/data/2.bg
- t/data/219877.cdna.fasta
- t/data/219877.tree
- t/data/277523.cdna.fasta
- t/data/277523.tree
- t/data/3.bg
- t/data/FootPrinter.seq.fa
- t/data/Ft.bam
- t/data/Ft.bed
- t/data/Ft.bed12
- t/data/Ft.frag.fas
- t/data/Genscan.FastA
- t/data/H_pylori_J99.fasta
- t/data/H_pylori_J99.glimmer2.icm
- t/data/H_pylori_J99.glimmer3.icm
- t/data/NM_002254.gb
- t/data/NM_002254.tfa
- t/data/Phrap.fa
- t/data/Primer3.fa
- t/data/Prints_prot.FastA
- t/data/TribeMCL.bls
- t/data/TribeMCL.desc
- t/data/amino.fa
- t/data/apes.multi_fasta
- t/data/apes.newick
- t/data/blat_dna.fa
- t/data/bowtie/indexes/e_coli.1.ebwt
- t/data/bowtie/indexes/e_coli.2.ebwt
- t/data/bowtie/indexes/e_coli.3.ebwt
- t/data/bowtie/indexes/e_coli.4.ebwt
- t/data/bowtie/indexes/e_coli.rev.1.ebwt
- t/data/bowtie/indexes/e_coli.rev.2.ebwt
- t/data/bowtie/reads/e_coli.cb
- t/data/bowtie/reads/e_coli_1000.fa
- t/data/bowtie/reads/e_coli_1000.fq
- t/data/bowtie/reads/e_coli_1000.raw
- t/data/bowtie/reads/e_coli_10000snp.fa
- t/data/bowtie/reads/e_coli_10000snp.fq
- t/data/bowtie/reads/e_coli_1000_1.fa
- t/data/bowtie/reads/e_coli_1000_1.fq
- t/data/bowtie/reads/e_coli_1000_2.fa
- t/data/bowtie/reads/e_coli_1000_2.fq
- t/data/campycoli.fas
- t/data/cel-cbr-fam.aln
- t/data/codeml.mlc
- t/data/coil_protein_input
- t/data/consense.treefile
- t/data/consensus.cns
- t/data/cysprot.fa
- t/data/cysprot.msf
- t/data/cysprot.raxml.tre
- t/data/cysprot.stockholm
- t/data/cysprot1a.fa
- t/data/cysprot1a.msf
- t/data/cysprot1b.fa
- t/data/cysprot1b.msf
- t/data/dba1a.fa
- t/data/dba1b.fa
- t/data/dba2.fa
- t/data/dna1.fa
- t/data/dna2.fa
- t/data/dna_seqs1.phy
- t/data/e_coli.bed3
- t/data/e_coli_1.bedpe
- t/data/e_coli_2.bedpe
- t/data/ecolitst.fa
- t/data/efetch_seq.wsdl
- t/data/elink_result.xml
- t/data/eponine.fa
- t/data/esearch_result.xml
- t/data/esum_result.xml
- t/data/eutils.wsdl
- t/data/exonerate_cdna.fa
- t/data/exonerate_cdna_rev.fa
- t/data/exonerate_genomic.fa
- t/data/exonerate_genomic_rev.fa
- t/data/fasta.fa
- t/data/fastalib.fa
- t/data/fastaprot.fa
- t/data/fontfile
- t/data/gb_result.xml
- t/data/gerp/ENr111.gerp.tree
- t/data/gerp/ENr111.mfa.gz
- t/data/gf-s85.phylip
- t/data/gumby/hmrd.mfa
- t/data/gumby/hmrd.tree
- t/data/gumby/human.gff
- t/data/gumby/readme.txt
- t/data/her2-edited.fasta
- t/data/hmmpfam_protein_input
- t/data/human.genomic
- t/data/hyphy1.fasta
- t/data/hyphy1.tree
- t/data/lagan_dna.fa
- t/data/longnames.aln
- t/data/lvb.fa
- t/data/lvb_sequential.phy
- t/data/neighbor.dist
- t/data/new_dna.fa
- t/data/new_pep.fa
- t/data/njtree_aln2.nucl.mfa
- t/data/pal2nal.aln
- t/data/pal2nal.nuc
- t/data/pfam_sample_R11
- t/data/primate_query.fa
- t/data/primate_target.fa
- t/data/prints.dat
- t/data/profile_prot.FastA
- t/data/prosite.dat
- t/data/protpars.phy
- t/data/ps1.fa
- t/data/purine.1.sto
- t/data/purine.added.fa
- t/data/purine.all.fa
- t/data/purine.c.cm
- t/data/purine.cm
- t/data/r1.fq
- t/data/r1bwa.fq
- t/data/r2.fq
- t/data/r2bwa.fq
- t/data/repeatmasker.fa
- t/data/road.pep
- t/data/sample_dataset_1.fa
- t/data/sample_dataset_1.qual
- t/data/sample_dataset_1_aligned.fa
- t/data/segmask_data.asn
- t/data/semphy.seq
- t/data/semphy.tree
- t/data/signalp_input_protein
- t/data/sim4_cdna.fa
- t/data/sim4_database.fa
- t/data/sim4_genomic.fa
- t/data/simprot_tree.nh
- t/data/species_tree_njtree.nh
- t/data/taxdump/names.dmp
- t/data/taxdump/nodes.dmp
- t/data/test-aln.msf
- t/data/test-query.fas
- t/data/test-spa-p.fas
- t/data/test-spa.fas
- t/data/test.txt
- t/data/test_prot.FastA
- t/data/testaln.phylip
- t/data/transfac.dat
- t/data/tree_of_life
- t/data/treefile.example
- t/data/vista.cls
- t/data/vista.gff
- t/data/xprt.gb
- t/gmap-run.t
- t/tRNAscanSE.t