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Version: 1.2.2

Bio::Tools::Run::Analysis - Module representing any analysis tool

Bio::Tools::Run::AnalysisFactory - A directory of analysis tools

Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules

Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml

Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip program Consense

Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA Block Aligner program.

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::Factory::EMBOSS - EMBOSS appliaction factory class

Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers

Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

Bio::Tools::Run::Eponine - Object for execution of the Eponine which is a mammalian TSS predictor

CGI::FormBuilder::Template::Fast - FormBuilder interface to CGI::FastTemplate

CGI::FormBuilder::Field - Internally used to create a FormBuilder field

CGI::FormBuilder::Source::File - Initialize FormBuilder from external file

Bio::Tools::Run::FootPrinter - Wrapper for FootPrinter Program

CGI::FormBuilder - Easily generate and process stateful forms

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.

CGI::FormBuilder::Template::HTML - FormBuilder interface to HTML::Template

Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools

Mdust - Perl extension for Mdust nucleotide filtering

CGI::FormBuilder::Messages - Localized message support for FormBuilder

CGI::FormBuilder::Multi - Create multi-page FormBuilder forms

Bio::Tools::Run::AnalysisFactory::Pise - A class to create Pise application objects.

Bio::Tools::Run::PiseApplication - A class manage Pise programs information, configuring parameters and submit jobs.

Bio::Tools::Run::PiseJob - A class to manage Pise jobs.

Bio::Tools::Run::PiseJobParser - A class to parse a Pise server XHTML output.

Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using promoterwise

Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip program protdist

Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML

Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a L<Bio::Tree> object from a multiple alignment file or a SimpleAlign object

Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence

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::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot

Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences

Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools

CGI::FormBuilder::Source - Source adapters for FormBuilder

CGI::FormBuilder::Template - Template adapters for FormBuilder

CGI::FormBuilder::Template::Text - FormBuilder interface to Text::Template

Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes in a given protein seequence.

CGI::FormBuilder::Template::TT2 - FormBuilder interface to Template Toolkit

CGI::FormBuilder::Util - Utility functions for FormBuilder

Bio::Tools::Run::Phylo::PAML::CodeML - Wrapper aroud the PAML program codeml