📦 libbio-perl-run-perl

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Bio::DB::ESoap(3pm)Client for the NCBI Entrez EUtilities SOAP server✨
Bio::DB::ESoap::WSDL(3pm)WSDL parsing for Entrez SOAP EUtilities✨
Bio::DB::SoapEUtilities(3pm)Interface to the NCBI Entrez web service *BETA*✨
Bio::DB::SoapEUtilities::DocSumAdaptor(3pm)Handle for Entrez SOAP DocSums✨
Bio::DB::SoapEUtilities::FetchAdaptor(3pm)Conversion of Entrez SOAP messages to BioPerl objects✨
Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)Fetch adaptor for 'seq' efetch SOAP messages✨
Bio::DB::SoapEUtilities::FetchAdaptor::species(3pm)Fetch adaptor for 'taxonomy' efetch SOAP messages✨
Bio::DB::SoapEUtilities::GQueryAdaptor(3pm)Handle for Entrez SOAP GlobalQuery items✨
Bio::DB::SoapEUtilities::LinkAdaptor(3pm)Handle for Entrez SOAP LinkSets✨
Bio::DB::SoapEUtilities::Result(3pm)Accessor object for SoapEUtilities results✨
Bio::Factory::EMBOSS(3pm)EMBOSS application factory class✨
Bio::Tools::Run::Alignment::Amap(3pm)Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program✨
Bio::Tools::Run::Alignment::Blat(3pm)wrapper modules for the Blat program✨
Bio::Tools::Run::Alignment::DBA(3pm)Object for the alignment of two sequences using the DNA Block Aligner program.✨
Bio::Tools::Run::Alignment::Exonerate(3pm)wrapper for the exonerate alignment program✨
Bio::Tools::Run::Alignment::Gmap(3pm)Wrapper for running gmap.✨
Bio::Tools::Run::Alignment::Kalign(3pm)Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program✨
Bio::Tools::Run::Alignment::Lagan(3pm)Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)✨
Bio::Tools::Run::Alignment::MAFFT(3pm)run the MAFFT alignment tools✨
Bio::Tools::Run::Alignment::MSAProbs(3pm)Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program✨
Bio::Tools::Run::Alignment::Muscle(3pm)Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program✨
Bio::Tools::Run::Alignment::Pal2Nal(3pm)Wrapper for Pal2Nal✨
Bio::Tools::Run::Alignment::Probalign(3pm)Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program✨
Bio::Tools::Run::Alignment::Probcons(3pm)Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program✨
Bio::Tools::Run::Alignment::Proda(3pm)Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program.✨
Bio::Tools::Run::Alignment::Sim4(3pm)Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences✨
Bio::Tools::Run::Alignment::StandAloneFasta(3pm)Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)✨
Bio::Tools::Run::Analysis::soap(3pm)A SOAP-based access to the analysis tools✨
Bio::Tools::Run::AnalysisFactory::soap(3pm)A SOAP-based access to the list of analysis tools✨
Bio::Tools::Run::BEDTools(3pm)Run wrapper for the BEDTools suite of programs *BETA*✨
Bio::Tools::Run::BEDTools::Config(3pm)Configuration data for bowtie commands✨
Bio::Tools::Run::BlastPlus(3pm)A wrapper for NCBI's blast+ suite✨
Bio::Tools::Run::Coil(3pm)wrapper for ncoils program✨
Bio::Tools::Run::EMBOSSacd(3pm)class for EMBOSS Application qualifiers✨
Bio::Tools::Run::EMBOSSApplication(3pm)class for EMBOSS Applications✨
Bio::Tools::Run::Ensembl(3pm)A simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API.✨
Bio::Tools::Run::Eponine(3pm)Object for execution of the Eponine which is a mammalian TSS predictor✨
Bio::Tools::Run::ERPIN(3pm)Wrapper for local execution of the ERPIN suite of programs.✨
Bio::Tools::Run::FootPrinter(3pm)wrapper for the FootPrinter program✨
Bio::Tools::Run::Genemark(3pm)Wrapper for local execution of the GeneMark family of programs.✨
Bio::Tools::Run::Genewise(3pm)Object for predicting genes in a given sequence given a protein✨
Bio::Tools::Run::Genscan(3pm)Object for identifying genes in a given sequence given a matrix(for appropriate organisms).✨
Bio::Tools::Run::Glimmer(3pm)Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.✨
Bio::Tools::Run::Hmmer(3pm)Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch✨
Bio::Tools::Run::Infernal(3pm)Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore✨
Bio::Tools::Run::Match(3pm)Wrapper for Transfac's match(TM)✨
Bio::Tools::Run::MCS(3pm)Wrapper for MCS✨
Bio::Tools::Run::Mdust(3pm)Perl extension for Mdust nucleotide filtering✨
Bio::Tools::Run::Phylo::FastTree(3pm)Bio::Tree getter from DNA alignment✨
Bio::Tools::Run::Phylo::Gerp(3pm)Wrapper for GERP✨
Bio::Tools::Run::Phylo::Hyphy::Base(3pm)Hyphy wrapping base methods✨
Bio::Tools::Run::Phylo::Hyphy::BatchFile(3pm)Wrapper for custom execution of Hyphy batch files✨
Bio::Tools::Run::Phylo::Hyphy::FEL(3pm)Wrapper around the Hyphy FEL analysis✨
Bio::Tools::Run::Phylo::Hyphy::Modeltest(3pm)Wrapper around the Hyphy Modeltest analysis✨
Bio::Tools::Run::Phylo::Hyphy::REL(3pm)Wrapper around the Hyphy REL analysis✨
Bio::Tools::Run::Phylo::Hyphy::SLAC(3pm)Wrapper around the Hyphy SLAC analysis✨
Bio::Tools::Run::Phylo::LVB(3pm)Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1.✨
Bio::Tools::Run::Phylo::Molphy::ProtML(3pm)A wrapper for the Molphy pkg app ProtML✨
Bio::Tools::Run::Phylo::Njtree::Best(3pm)Wrapper around the Njtree (Njtree/phyml) best program.✨
Bio::Tools::Run::Phylo::Phast::PhastCons(3pm)Wrapper for footprinting using phastCons✨
Bio::Tools::Run::Phylo::Phast::PhyloFit(3pm)Wrapper for phyloFit✨
Bio::Tools::Run::Phylo::Phylip::Base(3pm)Base object for Phylip modules✨
Bio::Tools::Run::Phylo::Phylip::Consense(3pm)Wrapper for the phylip program Consense✨
Bio::Tools::Run::Phylo::Phylip::DrawGram(3pm)use Phylip DrawTree program to draw phylograms or phenograms✨
Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)use Phylip DrawTree program to draw trees✨
Bio::Tools::Run::Phylo::Phylip::Neighbor(3pm)Wrapper for the phylip program neighbor by Joseph Felsenstein for creating a phylogenetic tree(either through Neighbor or UPGMA) based on protein distances based on amino substitution rate. 14 Nov…✨
Bio::Tools::Run::Phylo::Phylip::PhylipConf(3pm)manage Phylip menu configuration✨
Bio::Tools::Run::Phylo::Phylip::ProtDist(3pm)Wrapper for the phylip program protdist✨
Bio::Tools::Run::Phylo::Phylip::ProtPars(3pm)Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object 14 Nov 2002 Shawn Works with Phylip version 3.6✨
Bio::Tools::Run::Phylo::Phylip::SeqBoot(3pm)Wrapper for the phylip program SeqBoot✨
Bio::Tools::Run::Phylo::Phyml(3pm)Wrapper for rapid reconstruction of phylogenies using Phyml✨
Bio::Tools::Run::Phylo::QuickTree(3pm)Wrapper for rapid reconstruction of phylogenies using QuickTree✨
Bio::Tools::Run::Phylo::Raxml(3pm)Bio::Tree getter from DNA alignment through raxml✨
Bio::Tools::Run::Phylo::Semphy(3pm)Wrapper for Semphy✨
Bio::Tools::Run::Phylo::SLR(3pm)Wrapper around the SLR program✨
Bio::Tools::Run::Primate(3pm)wrapper for Primate, Guy Slater's near exact match finder for short sequence tags.✨
Bio::Tools::Run::Primer3(3pm)Create input for and work with the output from the program primer3✨
Bio::Tools::Run::Prints(3pm)PRINTS fingerprint identification algorithm✨
Bio::Tools::Run::Profile(3pm)wrapper for the pfscan program✨
Bio::Tools::Run::Promoterwise(3pm)Wrapper for aligning two sequences using promoterwise✨
Bio::Tools::Run::Pseudowise(3pm)Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence✨
Bio::Tools::Run::RepeatMasker(3pm)Wrapper for RepeatMasker Program✨
Bio::Tools::Run::RNAMotif(3pm)Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune✨
Bio::Tools::Run::Samtools(3pm)a run wrapper for the samtools suite *BETA*✨
Bio::Tools::Run::Samtools::Config(3pm)configurator for Bio::Tools::Run::Samtools✨
Bio::Tools::Run::Seg(3pm)Object for identifying low complexity regions in a given protein seequence.✨
Bio::Tools::Run::Signalp(3pm)wrapper for the Signalp program✨
Bio::Tools::Run::Simprot(3pm)Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree✨
Bio::Tools::Run::StandAloneBlast(3pm)Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.✨
Bio::Tools::Run::StandAloneBlastPlus(3pm)Compute with NCBI's blast+ suite *ALPHA*✨
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3pm)Provides BLAST methods to StandAloneBlastPlus✨
Bio::Tools::Run::StandAloneNCBIBlast(3pm)Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.✨
Bio::Tools::Run::StandAloneWUBlast(3pm)Object for the local execution of WU-Blast.✨
Bio::Tools::Run::Tmhmm(3pm)Object for identifying transmembrane helixes in a given protein seequence.✨
Bio::Tools::Run::TribeMCL(3pm)Markov method for CLustering proteins✨
Bio::Tools::Run::tRNAscanSE(3pm)Wrapper for local execution of tRNAscan-SE✨
Bio::Tools::Run::Vista(3pm)Wrapper for Vista✨