section 3pm · Library functions 📚

34259 pages · page 16 of 172

all 3 (100762)33ssl (6156)3B (42)3G (1100)3I (51)3LIBIIO (1)3NCARG (834)3OpenMPI (1)3PVM (71)3Sympa (164)3U (96)3WN (5)3alc (212)3alleg4 (923)3alleg5 (1063)3am (31)3ast (63)3attr (4)3avr (983)3bobcat (143)3brotli (4)3bsd (239)3caca (346)3cl (1)3clc (322)3cocci (1)3coin2 (588)3coin3 (753)3coin4 (918)3compat (22)3const (18)3ctype (1)3curses (18)3cvc (2)3cxx (1060)3debug (15)3edit (1)3em (198)3embree3 (113)3embree4 (127)3erl (623)3f (128)3form (106)3freebsd (1)3fun (1)3gl (467)3gle (14)3go (1)3guile (1)3gv (7)3hal (49)3head (3)3http (66)3itcl (17)3itk (6)3iv (354)3iwidget (52)3java (1)3libmawk (10)3libunwind (29)3lua (13)3m17n (257)3m_cli2 (8)3menu (88)3monocypher (73)3nas (130)3ncurses (703)3nx (5)3o (437)3ossl (6166)3ossp (2)3p (882)3pcap (75)3perl (820)3pg13 (68)3pg14 (72)3pg15 (72)3pg16 (72)3pg17 (72)3pg18 (72)3php (1)3plplot (175)3pm (34259)3pmc (296)3posix (882)3pub (150)3python (1)3qt (832)3r (1)3readline (2)3rheolef (13)3rtapi (66)3ruby (1)3scm (459)3sharp (1)3so (8)3ssl (6930)3stap (807)3str (19)3supp (19)3t (35)3tcl (1477)3tcllib (1)3tclx (25)3tiff (60)3tk (513)3tls (13)3trf (28)3ts (239)3type (466)3valkey (395)3visa (2)3x (1069)

B (continued)

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✨
Bio::Tradis::CommandLine::RemoveFastqTags(3pm)Remove given tags from the start of the sequence✨
Bio::Tradis::CommandLine::RunMapping(3pm)Perform mapping✨
Bio::Tradis::CommandLine::TradisAnalysis(3pm)Perform full tradis analysis✨
Bio::Tradis::CommandLine::TradisBam(3pm)Adds tags to sequences if tags are present✨
Bio::Tradis::DetectTags(3pm)Detect tr tags in BAM file✨
Bio::Tradis::Exception(3pm)Exceptions for input data✨
Bio::Tradis::FilterTags(3pm)Filter tags in a fastq file✨
Bio::Tradis::Map(3pm)Perform mapping✨
Bio::Tradis::Parser::Bam(3pm)Very basic BAM parser. Limited functionality.✨
Bio::Tradis::Parser::Cigar(3pm)Take in a cigar string and output start and end relative to the reference sequence✨
Bio::Tradis::Parser::Fastq(3pm)Basic FastQ parser.✨
Bio::Tradis::RemoveTags(3pm)Remove tags from seqs a fastq file✨
Bio::Tradis::RunTradis(3pm)Perform all steps required for a tradis analysis✨
Bio::Tradis::Samtools(3pm)Change samtools syntax depending on version found✨
Bio::Tradis::TradisPlot(3pm)Generate plots as part of a tradis analysis✨
Bio::Tree::AnnotatableNode(3pm)A Tree Node with support for annotation✨
Bio::Tree::Compatible(3pm)Testing compatibility of phylogenetic trees with nested taxa.✨
Bio::Tree::DistanceFactory(3pm)Construct a tree using distance based methods✨
Bio::Tree::Node(3pm)A Simple Tree Node✨
Bio::Tree::NodeI(3pm)Interface describing a Tree Node✨
Bio::Tree::NodeNHX(3pm)A Simple Tree Node with support for NHX tags✨
Bio::Tree::RandomFactory(3pm)TreeFactory for generating Random Trees✨
Bio::Tree::Statistics(3pm)Calculate certain statistics for a Tree✨
Bio::Tree::Tree(3pm)An implementation of the TreeI interface.✨
Bio::Tree::TreeFunctionsI(3pm)Decorated Interface implementing basic Tree exploration methods✨
Bio::Tree::TreeI(3pm)A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.✨
Bio::TreeIO(3pm)Parser for Tree files✨
Bio::TreeIO::cluster(3pm)A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output✨
Bio::TreeIO::lintree(3pm)Parser for lintree output trees✨
Bio::TreeIO::newick(3pm)parsing and writing of Newick/PHYLIP/New Hampshire format✨
Bio::TreeIO::NewickParser(3pm)newick string parser✨
Bio::TreeIO::nexus(3pm)A TreeIO driver module for parsing Nexus tree output from PAUP✨
Bio::TreeIO::nhx(3pm)TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.✨