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::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::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::Analysis::soap - A SOAP-based access to the analysis tools
• Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools
• 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::BlastPlus - A wrapper for NCBI's blast+ suite
• 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::Phylo::FastTree
• Bio::Tools::Run::Phylo::Gerp - Wrapper for GERP
• 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::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::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::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