BioPerl-Run documentation

• BioPerl-Run - README
• BioPerl-Run - Changes
• BioPerl-Run - INSTALL
• BioPerl-Run - META.yml
• BioPerl-Run Build.PL
• Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server  [view source]
• Bio::DB::ESoap::WSDL - WSDL parsing for Entrez SOAP EUtilities  [view source]
• Bio::DB::SoapEUtilities - Interface to the NCBI Entrez web service *BETA*  [view source]
• Bio::DB::SoapEUtilities::DocSumAdaptor - Handle for Entrez SOAP DocSums  [view source]
• Bio::DB::SoapEUtilities::FetchAdaptor - Conversion of Entrez SOAP messages to BioPerl objects  [view source]
• Bio::DB::SoapEUtilities::FetchAdaptor::seq - Fetch adaptor for 'seq'  [view source]
• Bio::DB::SoapEUtilities::FetchAdaptor::species - Fetch adaptor for  [view source]
• Bio::DB::SoapEUtilities::GQueryAdaptor - Handle for Entrez SOAP GlobalQuery items  [view source]
• Bio::DB::SoapEUtilities::LinkAdaptor - Handle for Entrez SOAP LinkSets  [view source]
• Bio::DB::SoapEUtilities::Result - Accessor object for SoapEUtilities results  [view source]
• Bio::Installer::Clustalw - DESCRIPTION of Object  [view source]
• Bio::Installer::EMBOSS - DESCRIPTION of Object  [view source]
• Bio::Installer::Generic - DESCRIPTION of Object  [view source]
• Bio::Installer::Hyphy - DESCRIPTION of Object  [view source]
• Bio::Installer::Muscle - DESCRIPTION of Object  [view source]
• Bio::Installer::PAML - DESCRIPTION of Object  [view source]
• Bio::Installer::Probcons - DESCRIPTION of Object  [view source]
• Bio::Installer::SLR - DESCRIPTION of Object  [view source]
• Bio::Installer::TCoffee - DESCRIPTION of Object  [view source]
• Bio::Tools::Run::Alignment::Amap - Object for the calculation of an  [view source]
• Bio::Tools::Run::Alignment::DBA - Object for the alignment of two  [view source]
• Bio::Tools::Run::Alignment::Gmap - Wrapper for running gmap.  [view source]
• Bio::Tools::Run::Alignment::Kalign - Object for the calculation of an  [view source]
• Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)  [view source]
• Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools  [view source]
• Bio::Tools::Run::Alignment::Pal2Nal - Wrapper for Pal2Nal  [view source]
• Bio::Tools::Run::Alignment::Probalign - Object for the calculation of  [view source]
• Bio::Tools::Run::Alignment::Proda - Object for the calculation of sets  [view source]
• Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows  [view source]
• Bio::Tools::Run::Alignment::StandAloneFasta - Object for the local  [view source]
• Bio::Tools::Run::Analysis - Module representing any (remote or local)  [view source]
• Bio::Tools::Run::AnalysisFactory - A directory of analysis tools  [view source]
• Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools  [view source]
• Bio::Tools::Run::AssemblerBase - base class for wrapping external assemblers  [view source]
• Bio::Tools::Run::BEDTools - Run wrapper for the BEDTools suite of programs *BETA*  [view source]
• Bio::Tools::Run::BEDTools::Config - Configuration data for bowtie commands  [view source]
• Bio::Tools::Run::BlastPlus - A wrapper for NCBI's blast+ suite  [view source]
• Bio::Tools::Run::BlastPlus::Config  [view source]
• Bio::Tools::Run::Bowtie - Run wrapper for the Bowtie short-read assembler *BETA*  [view source]
• Bio::Tools::Run::Bowtie::Config - Configuration data for bowtie commands  [view source]
• Bio::Tools::Run::BWA - Run wrapper for the BWA short-read assembler *BETA*  [view source]
• Bio::Tools::Run::BWA::Config - Configuration data for BWA commands  [view source]
• Bio::Tools::Run::Cap3 - wrapper for CAP3  [view source]
• Bio::Tools::Run::Coil - wrapper for ncoils program  [view source]
• Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers  [view source]
• Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications  [view source]
• Bio::Tools::Run::Ensembl - A simplified front-end for setting up the registry  [view source]
• Bio::Tools::Run::Eponine - Object for execution of the Eponine which  [view source]
• Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of  [view source]
• Bio::Tools::Run::FootPrinter - wrapper for the FootPrinter program  [view source]
• Bio::Tools::Run::Genemark - Wrapper for local execution of the GeneMark  [view source]
• Bio::Tools::Run::Genewise - Object for predicting genes in a  [view source]
• Bio::Tools::Run::Genscan - Object for identifying genes in a  [view source]
• Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer,  [view source]
• Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild,  [view source]
• Bio::Tools::Run::Infernal - Wrapper for local execution of cmalign, cmbuild,  [view source]
• Bio::Tools::Run::Maq - Run wrapper for the Maq short-read assembler *BETA*  [view source]
• Bio::Tools::Run::Maq::Config - Configuration data for maq commands  [view source]
• Bio::Tools::Run::Match - Wrapper for Transfac's match(TM)  [view source]
• Bio::Tools::Run::MCS - Wrapper for MCS  [view source]
• Bio::Tools::Run::Meme - Wrapper for Meme Program  [view source]
• Bio::Tools::Run::Minimo - Wrapper for local execution of the Minimo assembler  [view source]
• Bio::Tools::Run::Newbler - Wrapper for local execution of Newbler  [view source]
• Bio::Tools::Run::Phrap - a wrapper for running Phrap  [view source]
• Bio::Tools::Run::Phylo::Gumby - Wrapper for gumby  [view source]
• Bio::Tools::Run::Phylo::Hyphy::FEL - Wrapper around the Hyphy FEL analysis  [view source]
• Bio::Tools::Run::Phylo::Hyphy::Modeltest - Wrapper around the Hyphy Modeltest analysis  [view source]
• Bio::Tools::Run::Phylo::Hyphy::REL - Wrapper around the Hyphy REL analysis  [view source]
• Bio::Tools::Run::Phylo::Hyphy::SLAC - Wrapper around the Hyphy SLAC analysis  [view source]
• Bio::Tools::Run::Phylo::LVB - Object for using the LVB program to create  [view source]
• Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML  [view source]
• Bio::Tools::Run::Phylo::Njtree::Best - Wrapper around the Njtree (Njtree/phyml) best program.  [view source]
• Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml  [view source]
• Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml  [view source]
• Bio::Tools::Run::Phylo::PAML::Evolver - Wrapper aroud the PAML program evolver  [view source]
• Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00  [view source]
• Bio::Tools::Run::Phylo::Phast::PhastCons - Wrapper for footprinting using  [view source]
• Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit  [view source]
• Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules  [view source]
• Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip  [view source]
• Bio::Tools::Run::Phylo::Phylip::DrawGram - use Phylip DrawTree program to draw phylograms or phenograms  [view source]
• Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree  [view source]
• Bio::Tools::Run::Phylo::Phylip::Neighbor - Wrapper for the phylip  [view source]
• Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip  [view source]
• Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a L object from a multiple alignment file or a SimpleAlign object  [view source]
• Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip  [view source]
• Bio::Tools::Run::Phylo::Phyml - Wrapper for rapid reconstruction of phylogenies using Phyml  [view source]
• Bio::Tools::Run::Phylo::QuickTree - Wrapper for rapid reconstruction of  [view source]
• Bio::Tools::Run::Phylo::Semphy - Wrapper for Semphy  [view source]
• Bio::Tools::Run::Primer3 - Create input for and work with the output  [view source]
• Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using  [view source]
• Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a  [view source]
• Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program  [view source]
• Bio::Tools::Run::RNAMotif - Wrapper for local execution of rnamotif, rm2ct,  [view source]
• Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*  [view source]
• Bio::Tools::Run::Samtools::Config - configurator for Bio::Tools::Run::Samtools  [view source]
• Bio::Tools::Run::Seg - Object for identifying low complexity  [view source]
• Bio::Tools::Run::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree  [view source]
• Bio::Tools::Run::StandAloneBlastPlus - Compute with NCBI's blast+ suite *ALPHA*  [view source]
• Bio::Tools::Run::TigrAssembler - Wrapper for local execution of TIGR Assembler  [view source]
• Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes  [view source]
• Bio::Tools::Run::tRNAscanSE - Wrapper for local execution of tRNAscan-SE  [view source]