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Phylogenetic analysis using perl.

Version: 0.16

Bio::Phylo::Adaptor - Object adaptor for compatibility - converts node ages to branch lengths. - creates paup commands to calculate bremer values using parsimony ratchet.

Bio::Phylo::Util::CONSTANT - This package defines global constants and utility functions that operate on them.

Bio::Phylo::Matrices::Datatype::Continuous - Datatype subclass, no serviceable parts inside

Bio::Phylo::Matrices::Datatype::Custom - Datatype subclass, no serviceable parts inside

Bio::Phylo::Matrices::Datatype - Superclass for objects that validate character data.

Bio::Phylo::Matrices::Datum - The character state sequence object.

Bio::Phylo::Matrices::Datatype::Dna - Datatype subclass, no serviceable parts inside - draws newick trees as svg drawings. - applies unique node labels to newick trees. - prunes a list of tips from input tree.

Bio::Phylo::Util::Exceptions - Exception classes for Bio::Phylo.

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::Phylo::Forest - The forest object, a set of phylogenetic trees.

CGI::FormBuilder - Easily generate and process stateful forms

Bio::Phylo::Generator - Generates random trees.

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

Bio::Phylo::Util::IDPool - Utility class for generating object IDs. No serviceable parts inside.

Bio::Phylo::IO - Input and output of phylogenetic data.

Bio::Phylo::Listable - Parent class for listable/iterator objects.

Bio::Phylo::Manual - Bio::Phylo v.0.16 user guide.

Bio::Phylo::Matrices - Holds a set of matrix objects.

Bio::Phylo::Matrices::Matrix - Character state matrix.

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

Bio::Phylo::Matrices::Datatype::Mixed - Datatype subclass, no serviceable parts inside

Bio::Phylo::Unparsers::Mrp - Unparses a forest object into an MRP matrix. No serviceable parts inside.

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

Bio::Phylo::Unparsers::Newick - Unparses newick trees. No serviceable parts inside.

Bio::Phylo::Unparsers::Nexus - Unparses nexus matrices. No serviceable parts inside.

Bio::Phylo::Forest::Node - The tree node object.

Bio::ObjectCompat - Object compatibility for phylogenetic software in OO perl

Bio::Phylo::Unparsers::Pagel - Unparses pagel data files. No serviceable parts inside.

Bio::Phylo - Phylogenetic analysis using perl.

Bio::Phylo::Matrices::Datatype::Protein - Datatype subclass, no serviceable parts inside

Bio::Phylo::Matrices::Datatype::Restriction - Datatype subclass, no serviceable parts inside

Bio::Phylo::Matrices::Datatype::Rna - Datatype subclass, no serviceable parts inside

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

Bio::Phylo::Matrices::Datatype::Standard - Datatype subclass, no serviceable parts inside

Bio::Phylo::Treedrawer::Svg - Creates svg tree drawings. No serviceable parts inside.

Bio::Phylo::Parsers::Table - Parses tab- delimited matrices. No serviceable parts inside.

Bio::Phylo::Taxa - An object-oriented module for managing taxa.

Bio::Phylo::Taxa::TaxaLinker - Superclass for objects that link to taxa objects.

Bio::Phylo::Mediators::TaxaMediator - Mediator class to manage links between objects.

Bio::Phylo::Parsers::Taxlist - Parses lists of taxon names. No serviceable parts inside.

Bio::Phylo::Taxa::Taxon - The operational taxonomic unit.

Bio::Phylo::Taxa::TaxonLinker - Superclass for objects that link to taxa objects.

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

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

Bio::Phylo::Forest::Tree - The tree object.

Bio::Phylo::Treedrawer - An object-oriented facade for drawing trees.

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

Bio::Phylo::Matrices::TypeSafeData - Superclass for objects that hold character data.

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

Bio::Phylo::Util::XMLWritable - Superclass for objects that stringify to xml