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Christopher Fields > BioPerl-Run

BioPerl-Run

This Release BioPerl-Run-1.007002  [Download] [Browse 14 Sep 2017
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
AUTHORS
Build.PL
Changes
INSTALL
LICENSE
MANIFEST
META.json

Modules

Bio::DB::ESoap Client for the NCBI Entrez EUtilities SOAP server     1.007002
Bio::DB::ESoap::WSDL WSDL parsing for Entrez SOAP EUtilities     1.007002
Bio::DB::SoapEUtilities Interface to the NCBI Entrez web service *BETA*     1.007002
Bio::DB::SoapEUtilities::DocSumAdaptor Handle for Entrez SOAP DocSums     1.007002
Bio::DB::SoapEUtilities::DocSumAdaptor::docsum     1.007002
Bio::DB::SoapEUtilities::FetchAdaptor Conversion of Entrez SOAP messages to BioPerl objects     1.007002
Bio::DB::SoapEUtilities::FetchAdaptor::seq Fetch adaptor for 'seq' efetch SOAP messages     1.007002
Bio::DB::SoapEUtilities::FetchAdaptor::species Fetch adaptor for 'taxonomy' efetch SOAP messages     1.007002
Bio::DB::SoapEUtilities::GQueryAdaptor Handle for Entrez SOAP GlobalQuery items     1.007002
Bio::DB::SoapEUtilities::GQueryAdaptor::gquery     1.007002
Bio::DB::SoapEUtilities::LinkAdaptor Handle for Entrez SOAP LinkSets     1.007002
Bio::DB::SoapEUtilities::LinkAdaptor::linkset     1.007002
Bio::DB::SoapEUtilities::Result Accessor object for SoapEUtilities results     1.007002
Bio::Factory::EMBOSS EMBOSS application factory class     1.007002
Bio::Installer::EMBOSS DESCRIPTION of Object     1.007002
Bio::Installer::Generic DESCRIPTION of Object     1.007002
Bio::Installer::Hyphy DESCRIPTION of Object     1.007002
Bio::Installer::Muscle DESCRIPTION of Object     1.007002
Bio::Installer::Probcons DESCRIPTION of Object     1.007002
Bio::Installer::SLR DESCRIPTION of Object     1.007002
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     1.007002
Bio::Tools::Run::Alignment::Blat     1.007002
Bio::Tools::Run::Alignment::DBA Object for the alignment of two sequences using the DNA Block Aligner program.     1.007002
Bio::Tools::Run::Alignment::Exonerate     1.007002
Bio::Tools::Run::Alignment::Gmap Wrapper for running gmap.     1.007002
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     1.007002
Bio::Tools::Run::Alignment::Lagan Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)     1.007002
Bio::Tools::Run::Alignment::MAFFT run the MAFFT alignment tools     1.007002
Bio::Tools::Run::Alignment::MSAProbs Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program     1.007002
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     1.007002
Bio::Tools::Run::Alignment::Pal2Nal Wrapper for Pal2Nal     1.007002
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     1.007002
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     1.007002
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.     1.007002
Bio::Tools::Run::Alignment::Sim4 Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences     1.007002
Bio::Tools::Run::Alignment::StandAloneFasta Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)     1.007002
Bio::Tools::Run::Analysis Module representing any (remote or local) analysis tool     1.007002
Bio::Tools::Run::Analysis::Job     1.007002
Bio::Tools::Run::Analysis::Job::soap     1.007002
Bio::Tools::Run::Analysis::Utils     1.007002
Bio::Tools::Run::Analysis::soap A SOAP-based access to the analysis tools     1.007002
Bio::Tools::Run::AnalysisFactory A directory of analysis tools     1.007002
Bio::Tools::Run::AnalysisFactory::soap A SOAP-based access to the list of analysis tools     1.007002
Bio::Tools::Run::AssemblerBase base class for wrapping external assemblers     1.007002
Bio::Tools::Run::BEDTools Run wrapper for the BEDTools suite of programs *BETA*     1.007002
Bio::Tools::Run::BEDTools::Config Configuration data for bowtie commands     1.007002
Bio::Tools::Run::BWA Run wrapper for the BWA short-read assembler *BETA*     1.007002
Bio::Tools::Run::BWA::Config Configuration data for BWA commands     1.007002
Bio::Tools::Run::BlastPlus A wrapper for NCBI's blast+ suite     1.007002
Bio::Tools::Run::BlastPlus::Config     1.007002
Bio::Tools::Run::Bowtie Run wrapper for the Bowtie short-read assembler *BETA*     1.007002
Bio::Tools::Run::Bowtie::Config Configuration data for bowtie commands     1.007002
Bio::Tools::Run::Cap3 wrapper for CAP3     1.007002
Bio::Tools::Run::Coil wrapper for ncoils program     1.007002
Bio::Tools::Run::EMBOSSApplication class for EMBOSS Applications     1.007002
Bio::Tools::Run::EMBOSSacd class for EMBOSS Application qualifiers     1.007002
Bio::Tools::Run::ERPIN Wrapper for local execution of the ERPIN suite of programs.     1.007002
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.     1.007002
Bio::Tools::Run::Eponine Object for execution of the Eponine which is a mammalian TSS predictor     1.007002
Bio::Tools::Run::FootPrinter wrapper for the FootPrinter program     1.007002
Bio::Tools::Run::Genemark Wrapper for local execution of the GeneMark family of programs.     1.007002
Bio::Tools::Run::Genewise Object for predicting genes in a given sequence given a protein     1.007002
Bio::Tools::Run::Genscan Object for identifying genes in a given sequence given a matrix(for appropriate organisms).     1.007002
Bio::Tools::Run::Glimmer Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.     1.007002
Bio::Tools::Run::Hmmer Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch     1.007002
Bio::Tools::Run::Infernal Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore     1.007002
Bio::Tools::Run::MCS Wrapper for MCS     1.007002
Bio::Tools::Run::Maq Run wrapper for the Maq short-read assembler *BETA*     1.007002
Bio::Tools::Run::Maq::Config Configuration data for maq commands     1.007002
Bio::Tools::Run::Match Wrapper for Transfac's match(TM)     1.007002
Bio::Tools::Run::Mdust Perl extension for Mdust nucleotide filtering     1.007002
Bio::Tools::Run::Meme Wrapper for Meme Program     1.007002
Bio::Tools::Run::Minimo Wrapper for local execution of the Minimo assembler     1.007002
Bio::Tools::Run::Newbler Wrapper for local execution of Newbler     1.007002
Bio::Tools::Run::Phrap a wrapper for running Phrap     1.007002
Bio::Tools::Run::Phylo::FastTree     1.007002
Bio::Tools::Run::Phylo::Gerp Wrapper for GERP     1.007002
Bio::Tools::Run::Phylo::Gumby Wrapper for gumby     1.007002
Bio::Tools::Run::Phylo::Hyphy::Base Hyphy wrapping base methods     1.007002
Bio::Tools::Run::Phylo::Hyphy::BatchFile Wrapper for custom execution of Hyphy batch files     1.007002
Bio::Tools::Run::Phylo::Hyphy::FEL Wrapper around the Hyphy FEL analysis     1.007002
Bio::Tools::Run::Phylo::Hyphy::Modeltest Wrapper around the Hyphy Modeltest analysis     1.007002
Bio::Tools::Run::Phylo::Hyphy::REL Wrapper around the Hyphy REL analysis     1.007002
Bio::Tools::Run::Phylo::Hyphy::SLAC Wrapper around the Hyphy SLAC analysis     1.007002
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.     1.007002
Bio::Tools::Run::Phylo::Molphy::ProtML A wrapper for the Molphy pkg app ProtML     1.007002
Bio::Tools::Run::Phylo::Njtree::Best Wrapper around the Njtree (Njtree/phyml) best program.     1.007002
Bio::Tools::Run::Phylo::Phast::PhastCons Wrapper for footprinting using phastCons     1.007002
Bio::Tools::Run::Phylo::Phast::PhyloFit Wrapper for phyloFit     1.007002
Bio::Tools::Run::Phylo::Phylip::Base Base object for Phylip modules     1.007002
Bio::Tools::Run::Phylo::Phylip::Consense Wrapper for the phylip program Consense     1.007002
Bio::Tools::Run::Phylo::Phylip::DrawGram use Phylip DrawTree program to draw phylograms or phenograms     1.007002
Bio::Tools::Run::Phylo::Phylip::DrawTree use Phylip DrawTree program to draw trees     1.007002
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.     1.007002
Bio::Tools::Run::Phylo::Phylip::PhylipConf     1.007002
Bio::Tools::Run::Phylo::Phylip::ProtDist Wrapper for the phylip program protdist     1.007002
Bio::Tools::Run::Phylo::Phylip::ProtPars Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object     1.007002
Bio::Tools::Run::Phylo::Phylip::SeqBoot Wrapper for the phylip program SeqBoot     1.007002
Bio::Tools::Run::Phylo::PhyloBase base module for phylo wrappers     1.007002
Bio::Tools::Run::Phylo::Phyml Wrapper for rapid reconstruction of phylogenies using Phyml     1.007002
Bio::Tools::Run::Phylo::QuickTree Wrapper for rapid reconstruction of phylogenies using QuickTree     1.007002
Bio::Tools::Run::Phylo::Raxml     1.007002
Bio::Tools::Run::Phylo::SLR Wrapper around the SLR program     1.007002
Bio::Tools::Run::Phylo::Semphy Wrapper for Semphy     1.007002
Bio::Tools::Run::Primate for Primate, Guy Slater's near exact match finder for short sequence tags.     1.007002
Bio::Tools::Run::Primer3 Create input for and work with the output from the program primer3     1.007002
Bio::Tools::Run::Prints     1.007002
Bio::Tools::Run::Profile     1.007002
Bio::Tools::Run::Promoterwise Wrapper for aligning two sequences using promoterwise     1.007002
Bio::Tools::Run::Pseudowise Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence     1.007002
Bio::Tools::Run::RNAMotif Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune     1.007002
Bio::Tools::Run::RepeatMasker Wrapper for RepeatMasker Program     1.007002
Bio::Tools::Run::Samtools a run wrapper for the samtools suite *BETA*     1.007002
Bio::Tools::Run::Samtools::Config configurator for Bio::Tools::Run::Samtools     1.007002
Bio::Tools::Run::Seg Object for identifying low complexity regions in a given protein seequence.     1.007002
Bio::Tools::Run::Signalp     1.007002
Bio::Tools::Run::Simprot Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree     1.007002
Bio::Tools::Run::StandAloneBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.     1.007002
Bio::Tools::Run::StandAloneBlastPlus Compute with NCBI's blast+ suite *ALPHA*     1.007002
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.     1.007002
Bio::Tools::Run::StandAloneWUBlast Object for the local execution of WU-Blast.     1.007002
Bio::Tools::Run::TigrAssembler Wrapper for local execution of TIGR Assembler v2     1.007002
Bio::Tools::Run::Tmhmm Object for identifying transmembrane helixes in a given protein seequence.     1.007002
Bio::Tools::Run::TribeMCL     1.007002
Bio::Tools::Run::Vista     1.007002
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables     1.007002
Bio::Tools::Run::tRNAscanSE Wrapper for local execution of tRNAscan-SE     1.007002

Documentation

Bio::Tools::Run::StandAloneBlastPlus::BlastMethods Provides BLAST methods to StandAloneBlastPlus  
Bio::Tools::Run::WrapperBase::CommandExts Extensions to WrapperBase for handling programs with commands *ALPHA*  
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  

Other Files

README.md