section 3 · Library functions 📚

178720 pages · page 57 of 894

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B (continued)

Bio::Tools::EUtilities::Link::UrlLink(3pm)Class for EUtils UrlLinks.✨
Bio::Tools::EUtilities::Query(3pm)Parse and collect esearch, epost, espell, egquery information.✨
Bio::Tools::EUtilities::Query::GlobalQuery(3pm)Container class for egquery data.✨
Bio::Tools::EUtilities::Summary(3pm)Class for handling data output (XML) from esummary.✨
Bio::Tools::EUtilities::Summary::DocSum(3pm)Data object for document summary data from esummary.✨
Bio::Tools::EUtilities::Summary::Item(3pm)Simple layered object for DocSum item data.✨
Bio::Tools::EUtilities::Summary::ItemContainerI(3pm)Abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered).✨
Bio::Tools::Fgenesh(3pm)parse results of one Fgenesh run✨
Bio::Tools::FootPrinter(3pm)write sequence features in FootPrinter format✨
Bio::Tools::Geneid(3pm)Results of one geneid run✨
Bio::Tools::Genemark(3pm)Results of one Genemark run✨
Bio::Tools::Genewise(3pm)Results of one Genewise run✨
Bio::Tools::Genomewise(3pm)Results of one Genomewise run✨
Bio::Tools::Genscan(3pm)Results of one Genscan run✨
Bio::Tools::GFF(3pm)A Bio::SeqAnalysisParserI compliant GFF format parser✨
Bio::Tools::Glimmer(3pm)parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions✨
Bio::Tools::Grail(3pm)Results of one Grail run✨
Bio::Tools::GuessSeqFormat(3pm)Module for determining the sequence format of the contents of a file, a string, or through a filehandle.✨
Bio::Tools::HMMER::Domain(3pm)One particular domain hit from HMMER✨
Bio::Tools::HMMER::Results(3pm)Object representing HMMER output results✨
Bio::Tools::HMMER::Set(3pm)Set of identical domains from HMMER matches✨
Bio::Tools::Hmmpfam(3pm)Parser for Hmmpfam program✨
Bio::Tools::ipcress(3pm)Parse ipcress output and make features✨
Bio::Tools::isPcr(3pm)Parse isPcr output and make features✨
Bio::Tools::IUPAC(3pm)Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence✨
Bio::Tools::Lucy(3pm)Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR✨
Bio::Tools::Match(3pm)Parses output from Transfac's match(TM)✨
Bio::Tools::Motif(3pm)Perl implementation of the Motif protein subcellular localization method.✨
Bio::Tools::Motif::Match(3pm)Represents a match as reported by the Bio::Tools::Motif module.✨
Bio::Tools::Motif::Pattern(3pm)Represents a pattern used by the Bio::Tools::Motif module.✨
Bio::Tools::MZEF(3pm)Results of one MZEF run✨
Bio::Tools::OddCodes(3pm)Object holding alternative alphabet coding for one protein sequence✨
Bio::Tools::Phylo::Gerp(3pm)Parses output from GERP✨
Bio::Tools::Phylo::Molphy(3pm)parser for Molphy output✨
Bio::Tools::Phylo::Molphy::Result(3pm)container for data parsed from a ProtML run✨
Bio::Tools::Phylo::PAML(3pm)Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00✨
Bio::Tools::Phylo::PAML::Codeml(3pm)Parses output from the PAML program codeml✨
Bio::Tools::Phylo::PAML::ModelResult(3pm)A container for NSSite Model Result from PAML✨
Bio::Tools::Phylo::PAML::Result(3pm)A PAML result set object✨
Bio::Tools::Phylo::Phylip::ProtDist(3pm)parser for ProtDist output✨
Bio::Tools::pICalculator(3pm)calculate the isoelectric point of a protein✨
Bio::Tools::Prediction::Exon(3pm)A predicted exon feature✨
Bio::Tools::Prediction::Gene(3pm)a predicted gene structure feature✨
Bio::Tools::Primer3(3pm)Create input for and work with the output from the program primer3✨
Bio::Tools::Primer::Assessor::Base(3pm)base class for common assessor things✨
Bio::Tools::Primer::AssessorI(3pm)interface for assessing primer pairs✨
Bio::Tools::Primer::Feature(3pm)position of a single primer✨
Bio::Tools::Primer::Pair(3pm)two primers on left and right side✨
Bio::Tools::Prints(3pm)Parser for FingerPRINTScanII program✨
Bio::Tools::Profile(3pm)parse Profile output✨
Bio::Tools::Promoterwise(3pm)parser for Promoterwise tab format output✨
Bio::Tools::PrositeScan(3pm)Parser for ps_scan result✨
Bio::Tools::Pseudowise(3pm)Results of one Pseudowise run✨
Bio::Tools::PSort(3pm)Module implementing a method for predicting protein localization sites.✨
Bio::Tools::PSort::ModHMM(3pm)Wrapper for the Prodiv_TMHMM transmembrane helix predictor.✨
Bio::Tools::PSort::Module::AnalysisI(3pm)✨
Bio::Tools::PSort::Module::InputI(3pm)✨
Bio::Tools::PSort::Module::Motif(3pm)✨
Bio::Tools::PSort::Module::Null(3pm)✨
Bio::Tools::PSort::Module::OMPMotif(3pm)✨
Bio::Tools::PSort::Module::OutputI(3pm)✨
Bio::Tools::PSort::Module::Profile(3pm)✨
Bio::Tools::PSort::ModuleI(3pm)an interface class that all PSort modules should derive implement.✨
Bio::Tools::PSort::Pathway(3pm)an object used to define the pathway that is traversed while doing a psort analysis.✨
Bio::Tools::PSort::Profile(3pm)Perl implementation of the Profile protein subcellular localization method.✨
Bio::Tools::PSort::Profile::Match(3pm)Represents a match as reported by the Bio::Tools::Motif module.✨
Bio::Tools::PSort::SVMLoc(3pm)Perl bindings for the libsvm Support Vector Machine library in Psortb.✨
Bio::Tools::PSort::SVMLoc::DataSet(3pm)A DataSet object for the Bio::Tools::PSort::SVMLoc Support Vector Machine.✨
Bio::Tools::QRNA(3pm)A Parser for qrna output✨
Bio::Tools::RandomDistFunctions(3pm)A set of routines useful for generating random data in different distributions✨
Bio::Tools::RepeatMasker(3pm)a parser for RepeatMasker output✨
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::Clustalw(3pm)Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw 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::Alignment::TCoffee(3pm)Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program✨
Bio::Tools::Run::Analysis(3pm)Module representing any (remote or local) analysis tool✨
Bio::Tools::Run::Analysis::soap(3pm)A SOAP-based access to the analysis tools✨
Bio::Tools::Run::AnalysisFactory(3pm)A directory of 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::GenericParameters(3pm)An object for the parameters used to run 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::HMMTOP(3pm)Wrapper for the HMMTOP transmembrane helix predictor.✨
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::ParametersI(3pm)A Base object for the parameters used to run programs✨
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::PAML::Baseml(3pm)Wrapper aroud the PAML program baseml✨
Bio::Tools::Run::Phylo::PAML::Codeml(3pm)Wrapper aroud the PAML program codeml✨
Bio::Tools::Run::Phylo::PAML::Evolver(3pm)Wrapper aroud the PAML program evolver✨
Bio::Tools::Run::Phylo::PAML::Yn00(3pm)Wrapper aroud the PAML program yn00✨
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::PhyloBase(3pm)✨
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::RemoteBlast(3pm)Object for remote execution of the NCBI Blast via HTTP✨
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✨
Bio::Tools::Run::WrapperBase(3pm)A Base object for wrappers around executables✨
Bio::Tools::Run::WrapperBase::CommandExts(3pm)Extensions to WrapperBase for handling programs with commands *ALPHA*✨
Bio::Tools::Seg(3pm)parse "seg" output✨
Bio::Tools::SeqPattern(3pm)represent a sequence pattern or motif✨
Bio::Tools::SeqPattern::Backtranslate(3pm)reverse translate protein patterns✨
Bio::Tools::SeqStats(3pm)Object holding statistics for one particular sequence✨
Bio::Tools::SeqWords(3pm)Object holding n-mer statistics for a sequence✨
Bio::Tools::Sigcleave(3pm)Bioperl object for sigcleave analysis✨
Bio::Tools::Signal(3pm)✨
Bio::Tools::Signalp(3pm)parser for Signalp output✨
Bio::Tools::Signalp::ExtendedSignalp(3pm)enhanced parser for Signalp output✨
Bio::Tools::Sim4::Exon(3pm)A single exon determined by an alignment✨
Bio::Tools::Sim4::Results(3pm)Results of one Sim4 run✨
Bio::Tools::Spidey::Exon(3pm)A single exon determined by an alignment✨
Bio::Tools::Spidey::Results(3pm)Results of a Spidey run✨
Bio::Tools::SVMLoc(3pm)Perl implementation of the SVM based protein subcellular localization method.✨
Bio::Tools::TandemRepeatsFinder(3pm)a parser for Tandem Repeats Finder output✨
Bio::Tools::TargetP(3pm)Results of one TargetP run✨
Bio::Tools::Tmhmm(3pm)parse TMHMM output (TransMembrane HMM)✨
Bio::Tools::tRNAscanSE(3pm)A parser for tRNAscan-SE output✨
Bio::Tradis(3pm)Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308✨
Bio::Tradis::AddTagsToSeq(3pm)Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.✨
Bio::Tradis::Analysis::Exceptions(3pm)Custom exceptions✨
Bio::Tradis::Analysis::InsertSite(3pm)Take in a bam file and plot the start position of each read✨
Bio::Tradis::CombinePlots(3pm)Combine multiple plotfiles and generate updated statistics for the combined files✨
Bio::Tradis::CommandLine::AddTags(3pm)Add given tags to the start of the sequence✨
Bio::Tradis::CommandLine::CheckTags(3pm)Check for presence of tr tag in BAM file✨
Bio::Tradis::CommandLine::FilterFastqTags(3pm)Remove given tags from the start of the sequence✨
Bio::Tradis::CommandLine::PlotCombine(3pm)Combine multiple plotfiles and generate updated statistics for the combined files✨
Bio::Tradis::CommandLine::PlotTradis(3pm)Generate plots as part of a tradis analysis✨