Home · Authors · Recent · News · Mirrors · FAQ · Feedback

in  
Sendu Bala > bioperl-run-1.5.2_100

bioperl-run-1.5.2_100

This Release bioperl-run-1.5.2_100  [Download] [Browse]  06 Dec 2006 ** UNAUTHORIZED RELEASE **
Links [ Discussion Forum ] [ View/Report Bugs (1) ] [ Dependencies ] [ Other Tools ]
CPAN Testers PASS (1)   FAIL (10)   UNKNOWN (1)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating (0 Reviews) [ Rate this distribution ]
License Artistic
Special Files
AUTHORS
Build.PL
 Changes
INSTALL
 MANIFEST
META.yml
 Makefile.PL
README

Modules

Bio::Factory::EMBOSS EMBOSS application factory class      
Bio::Installer::Clustalw DESCRIPTION of Object   UNAUTHORIZED  
Bio::Installer::EMBOSS DESCRIPTION of Object   UNAUTHORIZED  
Bio::Installer::Generic DESCRIPTION of Object   UNAUTHORIZED  
Bio::Installer::Muscle DESCRIPTION of Object   UNAUTHORIZED  
Bio::Installer::PAML DESCRIPTION of Object   UNAUTHORIZED  
Bio::Installer::Probcons DESCRIPTION of Object   UNAUTHORIZED  
Bio::Installer::TCoffee DESCRIPTION of Object   UNAUTHORIZED  
Bio::Tools::Run::AbstractRunner      
Bio::Tools::Run::Alignment::Amap Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Blat      
Bio::Tools::Run::Alignment::Clustalw 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 Object for the alignment of two sequences using the DNA Block Aligner program.      
Bio::Tools::Run::Alignment::Exonerate   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Kalign Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Lagan Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)      
Bio::Tools::Run::Alignment::MAFFT run the MAFFT alignment tools   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Muscle Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Probalign Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Probcons Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program   UNAUTHORIZED  
Bio::Tools::Run::Alignment::Sim4 Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences      
Bio::Tools::Run::Alignment::StandAloneFasta Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)      
Bio::Tools::Run::Alignment::TCoffee 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 Module representing any (remote or local) analysis tool      
Bio::Tools::Run::Analysis::soap A SOAP-based access to the analysis tools      
Bio::Tools::Run::AnalysisFactory A directory of analysis tools      
Bio::Tools::Run::AnalysisFactory::Pise A class to create Pise application objects.      
Bio::Tools::Run::AnalysisFactory::soap A SOAP-based access to the list of analysis tools      
Bio::Tools::Run::Cap3 wrapper for Cap3   UNAUTHORIZED  
Bio::Tools::Run::Coil wrapper for ncoils program      
Bio::Tools::Run::EMBOSSApplication class for EMBOSS Applications      
Bio::Tools::Run::EMBOSSacd class for EMBOSS Application qualifiers      
Bio::Tools::Run::Eponine Object for execution of the Eponine which is a mammalian TSS predictor      
Bio::Tools::Run::FootPrinter Wrapper for FootPrinter Program      
Bio::Tools::Run::Genewise Object for predicting genes in a given sequence given a protein      
Bio::Tools::Run::Genscan Object for identifying genes in a given sequence given a matrix(for appropriate organisms).      
Bio::Tools::Run::Hmmer Wrapper for local execution of hmmsearch ,hmmbuild, hmmcalibrate, hmmalign, hmmpfam      
Bio::Tools::Run::JavaRunner run java programs      
Bio::Tools::Run::Mdust Perl extension for Mdust nucleotide filtering      
Bio::Tools::Run::Phrap a wrapper for running Phrap   UNAUTHORIZED  
Bio::Tools::Run::Phylo::Forester::SDI      
Bio::Tools::Run::Phylo::LVB 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.   UNAUTHORIZED  
Bio::Tools::Run::Phylo::Molphy::ProtML A wrapper for the Molphy pkg app ProtML      
Bio::Tools::Run::Phylo::PAML::Baseml Wrapper aroud the PAML program baseml   UNAUTHORIZED  
Bio::Tools::Run::Phylo::PAML::Codeml Wrapper aroud the PAML program codeml      
Bio::Tools::Run::Phylo::PAML::Evolver Wrapper aroud the PAML program evolver   UNAUTHORIZED  
Bio::Tools::Run::Phylo::PAML::Yn00 Wrapper aroud the PAML program yn00      
Bio::Tools::Run::Phylo::Phylip::Base Base object for Phylip modules      
Bio::Tools::Run::Phylo::Phylip::Consense Wrapper for the phylip program Consense      
Bio::Tools::Run::Phylo::Phylip::DrawGram use Phylip DrawTree program to draw phylograms or phenograms      
Bio::Tools::Run::Phylo::Phylip::DrawTree use Phylip DrawTree program to draw trees      
Bio::Tools::Run::Phylo::Phylip::Neighbor 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.      
Bio::Tools::Run::Phylo::Phylip::PhylipConf      
Bio::Tools::Run::Phylo::Phylip::ProtDist Wrapper for the phylip program protdist      
Bio::Tools::Run::Phylo::Phylip::ProtPars Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object      
Bio::Tools::Run::Phylo::Phylip::SeqBoot Wrapper for the phylip program SeqBoot      
Bio::Tools::Run::PiseApplication A class manage Pise programs information, configuring parameters and submit jobs.      
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 A class to manage Pise jobs.      
Bio::Tools::Run::PiseJobParser A class to parse a Pise server XHTML output.      
Bio::Tools::Run::PiseWorkflow      
Bio::Tools::Run::Primate      
Bio::Tools::Run::Primer3 Create input for and work with the output from the program primer3      
Bio::Tools::Run::Prints      
Bio::Tools::Run::Profile      
Bio::Tools::Run::Promoterwise Wrapper for aligning two sequences using promoterwise      
Bio::Tools::Run::Pseudowise Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence      
Bio::Tools::Run::RepeatMasker Wrapper for RepeatMasker Program      
Bio::Tools::Run::Seg Object for identifying low complexity regions in a given protein seequence.      
Bio::Tools::Run::Signalp      
Bio::Tools::Run::Tmhmm Object for identifying transmembrane helixes in a given protein seequence.      
Bio::Tools::Run::TribeMCL      
Bio::Tools::Run::Vista      
ModuleBuildBioperl     1.0050021

Documentation

Wrapper for Primate, Guy Slater's near exact match finder for short sequence tags.  
bioperl_application_installer downloads and installs runnables  
multi_hmmsearch perform a hmmsearch into multiple FASTA files using an INDEX file  
panalysis.PLS An example/tutorial script how to access analysis tools  
papplmaker.PLS Analysis tools module generator  
run_neighbor run Phylip's 'neighbor' program through Bioperl  
59829 Uploads, 19142 Distributions 76422 Modules, 7845 Uploaders
hosted by YellowBot
do. tag. write. share.