Bio-Phylo documentation

• Bio-Phylo - README
• Bio-Phylo - META.yml
• Bio-Phylo Makefile.PL
• Bio::Phylo - Phylogenetic analysis using perl  [view source]
• Bio::Phylo::EvolutionaryModels - Evolutionary models for phylogenetic trees and methods to sample these  [view source]
• Bio::Phylo::Factory - Creator of objects, reduces hardcoded class names in code  [view source]
• Bio::Phylo::Forest - Container for tree objects  [view source]
• Bio::Phylo::Forest::DrawNode - Tree node with extra methods for tree drawing  [view source]
• Bio::Phylo::Forest::DrawTree - Tree with extra methods for tree drawing  [view source]
• Bio::Phylo::Forest::Node - Node in a phylogenetic tree  [view source]
• Bio::Phylo::Forest::Tree - Phylogenetic tree  [view source]
• Bio::Phylo::Generator - Generator of tree topologies  [view source]
• Bio::Phylo::Identifiable - Objects with unique identifiers  [view source]
• Bio::Phylo::IO - Front end for parsers and serializers  [view source]
• Bio::Phylo::Listable - List of things, super class for many objects  [view source]
• Bio::Phylo::Manual - High-level user guide  [view source]
• Bio::Phylo::Matrices - Container of matrix objects  [view source]
• Bio::Phylo::Matrices::Character - A character (column) in a matrix  [view source]
• Bio::Phylo::Matrices::Characters - Container of character objects  [view source]
• Bio::Phylo::Matrices::Datatype - Validator of character state data  [view source]
• Bio::Phylo::Matrices::Datatype::Continuous - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Custom - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Dna - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Mixed - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Protein - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Restriction - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Rna - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datatype::Standard - Validator subclass,  [view source]
• Bio::Phylo::Matrices::Datum - Character state sequence  [view source]
• Bio::Phylo::Matrices::Matrix - Character state matrix  [view source]
• Bio::Phylo::Matrices::TypeSafeData - Superclass for objects that contain  [view source]
• Bio::Phylo::Mediators::TaxaMediator - Mediator for links between taxa and other objects  [view source]
• Bio::Phylo::NeXML::DOM - XML DOM support for Bio::Phylo  [view source]
• Bio::Phylo::NeXML::DOM::Document - XML DOM Abstract class for  [view source]
• Bio::Phylo::NeXML::DOM::Document::Libxml - XML DOM document mappings to the  [view source]
• Bio::Phylo::NeXML::DOM::Document::Twig - XML DOM document mappings to the  [view source]
• Bio::Phylo::NeXML::DOM::Element - XML DOM Abstract class for  [view source]
• Bio::Phylo::NeXML::DOM::Element::Libxml - XML DOM element mappings to the  [view source]
• Bio::Phylo::NeXML::DOM::Element::Twig - XML DOM mappings to the  [view source]
• Bio::Phylo::NeXML::Meta - Single predicate/object annotation, attached to an  [view source]
• Bio::Phylo::NeXML::Meta::XMLLiteral - Annotation value adaptor, no direct usage  [view source]
• Bio::Phylo::NeXML::Writable - Superclass for objects that serialize to NeXML  [view source]
• Bio::Phylo::Parsers::Abstract - Superclass for parsers used by Bio::Phylo::IO  [view source]
• Bio::Phylo::Parsers::Fasta - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Json - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Newick - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Nexml - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Nexus - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Phylip - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Phyloxml - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Table - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Taxlist - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Parsers::Tolweb - Parser used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Project - Container for related data  [view source]
• Bio::Phylo::Set - Subset of the parts inside a container  [view source]
• Bio::Phylo::Taxa - Container of taxon objects  [view source]
• Bio::Phylo::Taxa::TaxaLinker - Superclass for objects that link to taxa objects  [view source]
• Bio::Phylo::Taxa::Taxon - Operational taxonomic unit  [view source]
• Bio::Phylo::Taxa::TaxonLinker - Superclass for objects that link to taxon objects  [view source]
• Bio::Phylo::Treedrawer - Visualizer of tree shapes  [view source]
• Bio::Phylo::Treedrawer::Abstract - Abstract graphics writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Canvas - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Gif - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Jpeg - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Pdf - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Png - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Processing - Graphics format writer used by treedrawer,  [view source]
• Bio::Phylo::Treedrawer::Svg - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Treedrawer::Swf - Graphics format writer used by treedrawer, no  [view source]
• Bio::Phylo::Unparsers::Abstract - Superclass for unparsers used by Bio::Phylo::IO  [view source]
• Bio::Phylo::Unparsers::Fasta - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Json - Serializer used by Bio::Phylo::IO, no serviceable  [view source]
• Bio::Phylo::Unparsers::Mrp - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Newick - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Nexml - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Nexus - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Pagel - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Phylip - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Unparsers::Phyloxml - Serializer used by Bio::Phylo::IO, no serviceable parts inside  [view source]
• Bio::Phylo::Util::CONSTANT - Global constants and utility functions  [view source]
• Bio::Phylo::Util::Dependency - Utility class for importing external  [view source]
• Bio::Phylo::Util::Exceptions - Errors ($@) that are objects  [view source]
• Bio::Phylo::Util::IDPool - Utility class for generating object IDs. No serviceable parts inside.  [view source]
• Bio::Phylo::Util::Logger - Logger of internal messages of several severity  [view source]
• Bio::Phylo::Util::OptionalInterface - Utility class for managing optional  [view source]
• Bio::Phylo::Util::StackTrace - Stack traces for exceptions  [view source]