Christopher Fields > BioPerl-Run-1.006900

BioPerl-Run-1.006900

This Release BioPerl-Run-1.006900  [Download] [Browse 21 Apr 2011
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
AUTHORS
Build.PL
Changes
INSTALL
LICENSE
MANIFEST
META.json
README

Modules

Bio::DB::ESoap Client for the NCBI Entrez EUtilities SOAP server      
Bio::DB::ESoap::WSDL WSDL parsing for Entrez SOAP EUtilities      
Bio::DB::SoapEUtilities Interface to the NCBI Entrez web service *BETA*      
Bio::DB::SoapEUtilities::DocSumAdaptor Handle for Entrez SOAP DocSums      
Bio::DB::SoapEUtilities::DocSumAdaptor::docsum      
Bio::DB::SoapEUtilities::FetchAdaptor Conversion of Entrez SOAP messages to BioPerl objects      
Bio::DB::SoapEUtilities::FetchAdaptor::seq Fetch adaptor for 'seq' efetch SOAP messages      
Bio::DB::SoapEUtilities::FetchAdaptor::species Fetch adaptor for 'taxonomy' efetch SOAP messages      
Bio::DB::SoapEUtilities::GQueryAdaptor Handle for Entrez SOAP GlobalQuery items      
Bio::DB::SoapEUtilities::GQueryAdaptor::gquery      
Bio::DB::SoapEUtilities::LinkAdaptor Handle for Entrez SOAP LinkSets      
Bio::DB::SoapEUtilities::LinkAdaptor::linkset      
Bio::DB::SoapEUtilities::Result Accessor object for SoapEUtilities results      
Bio::Factory::EMBOSS EMBOSS application factory class      
Bio::Installer::Clustalw DESCRIPTION of Object      
Bio::Installer::EMBOSS DESCRIPTION of Object      
Bio::Installer::Generic DESCRIPTION of Object      
Bio::Installer::Hyphy DESCRIPTION of Object      
Bio::Installer::Muscle DESCRIPTION of Object      
Bio::Installer::PAML DESCRIPTION of Object      
Bio::Installer::Probcons DESCRIPTION of Object      
Bio::Installer::SLR DESCRIPTION of Object      
Bio::Installer::TCoffee DESCRIPTION of Object      
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      
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      
Bio::Tools::Run::Alignment::Gmap Wrapper for running gmap.      
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      
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      
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      
Bio::Tools::Run::Alignment::Pal2Nal Wrapper for Pal2Nal      
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      
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      
Bio::Tools::Run::Alignment::Proda 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 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::Job      
Bio::Tools::Run::Analysis::Job::soap      
Bio::Tools::Run::Analysis::Utils      
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::soap A SOAP-based access to the list of analysis tools      
Bio::Tools::Run::AssemblerBase base class for wrapping external assemblers      
Bio::Tools::Run::BEDTools Run wrapper for the BEDTools suite of programs *BETA*      
Bio::Tools::Run::BEDTools::Config Configuration data for bowtie commands      
Bio::Tools::Run::BWA Run wrapper for the BWA short-read assembler *BETA*      
Bio::Tools::Run::BWA::Config Configuration data for BWA commands      
Bio::Tools::Run::BlastPlus A wrapper for NCBI's blast+ suite      
Bio::Tools::Run::BlastPlus::Config      
Bio::Tools::Run::Bowtie Run wrapper for the Bowtie short-read assembler *BETA*      
Bio::Tools::Run::Bowtie::Config Configuration data for bowtie commands      
Bio::Tools::Run::Cap3 wrapper for CAP3      
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::ERPIN Wrapper for local execution of the ERPIN suite of programs.      
Bio::Tools::Run::Ensembl 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 Object for execution of the Eponine which is a mammalian TSS predictor      
Bio::Tools::Run::FootPrinter wrapper for the FootPrinter program      
Bio::Tools::Run::Genemark Wrapper for local execution of the GeneMark family of programs.      
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::Glimmer Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.      
Bio::Tools::Run::Hmmer Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch      
Bio::Tools::Run::Infernal Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore      
Bio::Tools::Run::MCS Wrapper for MCS      
Bio::Tools::Run::Maq Run wrapper for the Maq short-read assembler *BETA*      
Bio::Tools::Run::Maq::Config Configuration data for maq commands      
Bio::Tools::Run::Match Wrapper for Transfac's match(TM)      
Bio::Tools::Run::Mdust Perl extension for Mdust nucleotide filtering      
Bio::Tools::Run::Meme Wrapper for Meme Program      
Bio::Tools::Run::Minimo Wrapper for local execution of the Minimo assembler      
Bio::Tools::Run::Newbler Wrapper for local execution of Newbler      
Bio::Tools::Run::Phrap a wrapper for running Phrap      
Bio::Tools::Run::Phylo::Gerp Wrapper for GERP      
Bio::Tools::Run::Phylo::Gumby Wrapper for gumby      
Bio::Tools::Run::Phylo::Hyphy::Base Hyphy wrapping base methods      
Bio::Tools::Run::Phylo::Hyphy::FEL Wrapper around the Hyphy FEL analysis      
Bio::Tools::Run::Phylo::Hyphy::Modeltest Wrapper around the Hyphy Modeltest analysis      
Bio::Tools::Run::Phylo::Hyphy::REL Wrapper around the Hyphy REL analysis      
Bio::Tools::Run::Phylo::Hyphy::SLAC Wrapper around the Hyphy SLAC analysis      
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.      
Bio::Tools::Run::Phylo::Molphy::ProtML A wrapper for the Molphy pkg app ProtML      
Bio::Tools::Run::Phylo::Njtree::Best Wrapper around the Njtree (Njtree/phyml) best program.      
Bio::Tools::Run::Phylo::PAML::Baseml Wrapper aroud the PAML program baseml      
Bio::Tools::Run::Phylo::PAML::Codeml Wrapper aroud the PAML program codeml      
Bio::Tools::Run::Phylo::PAML::Evolver Wrapper aroud the PAML program evolver      
Bio::Tools::Run::Phylo::PAML::Yn00 Wrapper aroud the PAML program yn00      
Bio::Tools::Run::Phylo::Phast::PhastCons Wrapper for footprinting using phastCons      
Bio::Tools::Run::Phylo::Phast::PhyloFit Wrapper for phyloFit      
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::Phylo::PhyloBase base module for phylo wrappers      
Bio::Tools::Run::Phylo::Phyml Wrapper for rapid reconstruction of phylogenies using Phyml      
Bio::Tools::Run::Phylo::QuickTree Wrapper for rapid reconstruction of phylogenies using QuickTree      
Bio::Tools::Run::Phylo::SLR Wrapper around the SLR program      
Bio::Tools::Run::Phylo::Semphy Wrapper for Semphy      
Bio::Tools::Run::Primate for Primate, Guy Slater's near exact match finder for short sequence tags.      
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::RNAMotif Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune      
Bio::Tools::Run::RepeatMasker Wrapper for RepeatMasker Program      
Bio::Tools::Run::Samtools a run wrapper for the samtools suite *BETA*      
Bio::Tools::Run::Samtools::Config configurator for Bio::Tools::Run::Samtools      
Bio::Tools::Run::Seg Object for identifying low complexity regions in a given protein seequence.      
Bio::Tools::Run::Signalp      
Bio::Tools::Run::Simprot Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree      
Bio::Tools::Run::StandAloneBlastPlus Compute with NCBI's blast+ suite *ALPHA*      
Bio::Tools::Run::TigrAssembler Wrapper for local execution of TIGR Assembler v2      
Bio::Tools::Run::Tmhmm Object for identifying transmembrane helixes in a given protein seequence.      
Bio::Tools::Run::TribeMCL      
Bio::Tools::Run::Vista      
Bio::Tools::Run::tRNAscanSE Wrapper for local execution of tRNAscan-SE      

Documentation

Bio::Tools::Run::StandAloneBlastPlus::BlastMethods Provides BLAST methods to StandAloneBlastPlus  
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 'protdist' program through Bioperl