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BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
1 ++

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::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::LinkAdaptor
Handle for Entrez SOAP LinkSets
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::MSAProbs
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
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::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::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::FastTree
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::BatchFile
Wrapper for custom execution of Hyphy batch files
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
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::Raxml
Bio::Tools::Run::Phylo::SLR
Wrapper around the SLR program
Bio::Tools::Run::Phylo::Semphy
Wrapper for Semphy
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::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::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.
Bio::Tools::Run::StandAloneBlastPlus
Compute with NCBI's blast+ suite *ALPHA*
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods
Provides BLAST methods to StandAloneBlastPlus
Bio::Tools::Run::StandAloneNCBIBlast
Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
Bio::Tools::Run::StandAloneWUBlast
Object for the local execution of WU-Blast.
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
Wrapper for Vista
Bio::Tools::Run::WrapperBase
A Base object for wrappers around executables
Bio::Tools::Run::WrapperBase::CommandExts
Extensions to WrapperBase for handling programs with commands *ALPHA*
Bio::Tools::Run::tRNAscanSE
Wrapper for local execution of tRNAscan-SE

Provides

Bio::DB::SoapEUtilities::DocSumAdaptor::docsum
in lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
Bio::DB::SoapEUtilities::GQueryAdaptor::gquery
in lib/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
Bio::DB::SoapEUtilities::LinkAdaptor::linkset
in lib/Bio/DB/SoapEUtilities/LinkAdaptor.pm
Bio::Tools::Run::Analysis::Job
in lib/Bio/Tools/Run/Analysis.pm
Bio::Tools::Run::Analysis::Job::soap
in lib/Bio/Tools/Run/Analysis/soap.pm
Bio::Tools::Run::Analysis::Utils
in lib/Bio/Tools/Run/Analysis.pm
Bio::Tools::Run::BlastPlus::Config
in lib/Bio/Tools/Run/BlastPlus/Config.pm

Other files