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BioPerl-run-1.6.1
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Modules

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::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::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::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::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::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
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
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::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::TigrAssembler
Wrapper for local execution of TIGR Assembler v2.0
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::tRNAscanSE
Wrapper for local execution of tRNAscan-SE

Provides

Bio::Tools::Run::Analysis::Job
in Bio/Tools/Run/Analysis.pm
Bio::Tools::Run::Analysis::Job::soap
in Bio/Tools/Run/Analysis/soap.pm
Bio::Tools::Run::Analysis::Utils
in Bio/Tools/Run/Analysis.pm

Other files