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Bio::DB::ESoap
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Client for the NCBI Entrez EUtilities SOAP server
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Bio::DB::ESoap::WSDL
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WSDL parsing for Entrez SOAP EUtilities
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Bio::DB::SoapEUtilities
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Interface to the NCBI Entrez web service *BETA*
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Bio::DB::SoapEUtilities::DocSumAdaptor
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Handle for Entrez SOAP DocSums
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Bio::DB::SoapEUtilities::DocSumAdaptor::docsum
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Bio::DB::SoapEUtilities::FetchAdaptor
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Conversion of Entrez SOAP messages to BioPerl objects
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Bio::DB::SoapEUtilities::FetchAdaptor::seq
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Fetch adaptor for 'seq' efetch SOAP messages
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Bio::DB::SoapEUtilities::FetchAdaptor::species
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Fetch adaptor for 'taxonomy' efetch SOAP messages
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Bio::DB::SoapEUtilities::GQueryAdaptor
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Handle for Entrez SOAP GlobalQuery items
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Bio::DB::SoapEUtilities::GQueryAdaptor::gquery
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Bio::DB::SoapEUtilities::LinkAdaptor
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Handle for Entrez SOAP LinkSets
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Bio::DB::SoapEUtilities::LinkAdaptor::linkset
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Bio::DB::SoapEUtilities::Result
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Accessor object for SoapEUtilities results
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Bio::Factory::EMBOSS
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EMBOSS application factory class
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Bio::Installer::Clustalw
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DESCRIPTION of Object
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Bio::Installer::EMBOSS
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DESCRIPTION of Object
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Bio::Installer::Generic
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DESCRIPTION of Object
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Bio::Installer::Hyphy
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DESCRIPTION of Object
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Bio::Installer::Muscle
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DESCRIPTION of Object
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Bio::Installer::PAML
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DESCRIPTION of Object
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Bio::Installer::Probcons
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DESCRIPTION of Object
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Bio::Installer::SLR
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DESCRIPTION of Object
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Bio::Installer::TCoffee
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DESCRIPTION of Object
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Bio::Tools::Run::Alignment::Amap
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Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program
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Bio::Tools::Run::Alignment::Blat
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Bio::Tools::Run::Alignment::Clustalw
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Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
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Bio::Tools::Run::Alignment::DBA
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Object for the alignment of two sequences using the DNA Block Aligner program.
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Bio::Tools::Run::Alignment::Exonerate
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Bio::Tools::Run::Alignment::Gmap
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Wrapper for running gmap.
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Bio::Tools::Run::Alignment::Kalign
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Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program
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Bio::Tools::Run::Alignment::Lagan
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Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
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Bio::Tools::Run::Alignment::MAFFT
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run the MAFFT alignment tools
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Bio::Tools::Run::Alignment::Muscle
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Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program
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Bio::Tools::Run::Alignment::Pal2Nal
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Wrapper for Pal2Nal
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Bio::Tools::Run::Alignment::Probalign
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Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program
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Bio::Tools::Run::Alignment::Probcons
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Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program
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Bio::Tools::Run::Alignment::Proda
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Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program.
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Bio::Tools::Run::Alignment::Sim4
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Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
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Bio::Tools::Run::Alignment::StandAloneFasta
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Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)
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Bio::Tools::Run::Alignment::TCoffee
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Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
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Bio::Tools::Run::Analysis
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Module representing any (remote or local) analysis tool
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Bio::Tools::Run::Analysis::Job
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Bio::Tools::Run::Analysis::Job::soap
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Bio::Tools::Run::Analysis::Utils
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Bio::Tools::Run::Analysis::soap
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A SOAP-based access to the analysis tools
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Bio::Tools::Run::AnalysisFactory
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A directory of analysis tools
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Bio::Tools::Run::AnalysisFactory::soap
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A SOAP-based access to the list of analysis tools
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Bio::Tools::Run::AssemblerBase
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base class for wrapping external assemblers
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Bio::Tools::Run::BEDTools
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Run wrapper for the BEDTools suite of programs *BETA*
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Bio::Tools::Run::BEDTools::Config
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Configuration data for bowtie commands
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Bio::Tools::Run::BWA
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Run wrapper for the BWA short-read assembler *BETA*
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Bio::Tools::Run::BWA::Config
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Configuration data for BWA commands
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Bio::Tools::Run::BlastPlus
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A wrapper for NCBI's blast+ suite
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Bio::Tools::Run::BlastPlus::Config
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Bio::Tools::Run::Bowtie
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Run wrapper for the Bowtie short-read assembler *BETA*
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Bio::Tools::Run::Bowtie::Config
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Configuration data for bowtie commands
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Bio::Tools::Run::Cap3
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wrapper for CAP3
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Bio::Tools::Run::Coil
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wrapper for ncoils program
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Bio::Tools::Run::EMBOSSApplication
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class for EMBOSS Applications
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Bio::Tools::Run::EMBOSSacd
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class for EMBOSS Application qualifiers
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Bio::Tools::Run::ERPIN
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Wrapper for local execution of the ERPIN suite of programs.
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Bio::Tools::Run::Ensembl
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A simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API.
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Bio::Tools::Run::Eponine
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Object for execution of the Eponine which is a mammalian TSS predictor
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Bio::Tools::Run::FootPrinter
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wrapper for the FootPrinter program
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Bio::Tools::Run::Genemark
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Wrapper for local execution of the GeneMark family of programs.
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Bio::Tools::Run::Genewise
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Object for predicting genes in a given sequence given a protein
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Bio::Tools::Run::Genscan
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Object for identifying genes in a given sequence given a matrix(for appropriate organisms).
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Bio::Tools::Run::Glimmer
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Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.
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Bio::Tools::Run::Hmmer
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Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
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Bio::Tools::Run::Infernal
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Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore
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Bio::Tools::Run::MCS
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Wrapper for MCS
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Bio::Tools::Run::Maq
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Run wrapper for the Maq short-read assembler *BETA*
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Bio::Tools::Run::Maq::Config
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Configuration data for maq commands
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Bio::Tools::Run::Match
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Wrapper for Transfac's match(TM)
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Bio::Tools::Run::Mdust
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Perl extension for Mdust nucleotide filtering
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Bio::Tools::Run::Meme
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Wrapper for Meme Program
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Bio::Tools::Run::Minimo
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Wrapper for local execution of the Minimo assembler
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Bio::Tools::Run::Newbler
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Wrapper for local execution of Newbler
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Bio::Tools::Run::Phrap
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a wrapper for running Phrap
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Bio::Tools::Run::Phylo::Gerp
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Wrapper for GERP
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Bio::Tools::Run::Phylo::Gumby
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Wrapper for gumby
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Bio::Tools::Run::Phylo::Hyphy::Base
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Hyphy wrapping base methods
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Bio::Tools::Run::Phylo::Hyphy::FEL
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Wrapper around the Hyphy FEL analysis
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Bio::Tools::Run::Phylo::Hyphy::Modeltest
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Wrapper around the Hyphy Modeltest analysis
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Bio::Tools::Run::Phylo::Hyphy::REL
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Wrapper around the Hyphy REL analysis
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Bio::Tools::Run::Phylo::Hyphy::SLAC
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Wrapper around the Hyphy SLAC analysis
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Bio::Tools::Run::Phylo::LVB
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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.
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Bio::Tools::Run::Phylo::Molphy::ProtML
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A wrapper for the Molphy pkg app ProtML
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Bio::Tools::Run::Phylo::Njtree::Best
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Wrapper around the Njtree (Njtree/phyml) best program.
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Bio::Tools::Run::Phylo::PAML::Baseml
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Wrapper aroud the PAML program baseml
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Bio::Tools::Run::Phylo::PAML::Codeml
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Wrapper aroud the PAML program codeml
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Bio::Tools::Run::Phylo::PAML::Evolver
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Wrapper aroud the PAML program evolver
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Bio::Tools::Run::Phylo::PAML::Yn00
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Wrapper aroud the PAML program yn00
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Bio::Tools::Run::Phylo::Phast::PhastCons
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Wrapper for footprinting using phastCons
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Bio::Tools::Run::Phylo::Phast::PhyloFit
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Wrapper for phyloFit
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Bio::Tools::Run::Phylo::Phylip::Base
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Base object for Phylip modules
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Bio::Tools::Run::Phylo::Phylip::Consense
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Wrapper for the phylip program Consense
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Bio::Tools::Run::Phylo::Phylip::DrawGram
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use Phylip DrawTree program to draw phylograms or phenograms
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Bio::Tools::Run::Phylo::Phylip::DrawTree
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use Phylip DrawTree program to draw trees
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Bio::Tools::Run::Phylo::Phylip::Neighbor
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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.
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Bio::Tools::Run::Phylo::Phylip::PhylipConf
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Bio::Tools::Run::Phylo::Phylip::ProtDist
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Wrapper for the phylip program protdist
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Bio::Tools::Run::Phylo::Phylip::ProtPars
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Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object
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Bio::Tools::Run::Phylo::Phylip::SeqBoot
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Wrapper for the phylip program SeqBoot
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Bio::Tools::Run::Phylo::PhyloBase
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base module for phylo wrappers
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Bio::Tools::Run::Phylo::Phyml
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Wrapper for rapid reconstruction of phylogenies using Phyml
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Bio::Tools::Run::Phylo::QuickTree
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Wrapper for rapid reconstruction of phylogenies using QuickTree
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Bio::Tools::Run::Phylo::SLR
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Wrapper around the SLR program
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Bio::Tools::Run::Phylo::Semphy
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Wrapper for Semphy
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Bio::Tools::Run::Primate
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for Primate, Guy Slater's near exact match finder for short sequence tags.
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Bio::Tools::Run::Primer3
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Create input for and work with the output from the program primer3
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Bio::Tools::Run::Prints
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Bio::Tools::Run::Profile
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Bio::Tools::Run::Promoterwise
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Wrapper for aligning two sequences using promoterwise
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Bio::Tools::Run::Pseudowise
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Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence
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Bio::Tools::Run::RNAMotif
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Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune
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Bio::Tools::Run::RepeatMasker
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Wrapper for RepeatMasker Program
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Bio::Tools::Run::Samtools
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a run wrapper for the samtools suite *BETA*
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Bio::Tools::Run::Samtools::Config
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configurator for Bio::Tools::Run::Samtools
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Bio::Tools::Run::Seg
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Object for identifying low complexity regions in a given protein seequence.
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Bio::Tools::Run::Signalp
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Bio::Tools::Run::Simprot
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Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
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Bio::Tools::Run::StandAloneBlastPlus
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Compute with NCBI's blast+ suite *ALPHA*
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Bio::Tools::Run::TigrAssembler
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Wrapper for local execution of TIGR Assembler v2
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Bio::Tools::Run::Tmhmm
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Object for identifying transmembrane helixes in a given protein seequence.
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Bio::Tools::Run::TribeMCL
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Bio::Tools::Run::Vista
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Bio::Tools::Run::tRNAscanSE
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Wrapper for local execution of tRNAscan-SE
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