Documentation
High-level user guide
Modules
Phylogenetic analysis using perl
Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007
Creator of objects, reduces hardcoded class names in code
Container for tree objects
Tree node with extra methods for tree drawing
Tree with extra methods for tree drawing
Node in a phylogenetic tree
Phylogenetic tree
Generator of tree topologies
Front end for parsers and serializers
Objects with unique identifiers
List of things, super class for many objects
Container of matrix objects
A character (column) in a matrix
Container of character objects
Validator of character state data
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Validator subclass, no serviceable parts inside
Character state sequence
Character state matrix
Superclass for objects that contain character data
Mediator for links between taxa and other objects
XML DOM support for Bio::Phylo
XML DOM Abstract class for flexible document object model implementation
XML DOM document mappings to the XML::LibXML package
XML DOM document mappings to the XML::Twig package
XML DOM Abstract class for flexible document object model implementation
XML DOM element mappings to the XML::LibXML package
XML DOM mappings to the XML::Twig package
Functions for dealing with XML entities
Single predicate/object annotation, attached to an xml-writable subject
Annotation value adaptor, no direct usage
Superclass for objects that serialize to NeXML
Superclass for parsers used by Bio::Phylo::IO
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Parser used by Bio::Phylo::IO, no serviceable parts inside
Base class for phylogenetic web services
Base class for phylogenetic web service clients
Represents a PhyloWS web resource
Represents a PhyloWS resource description
Base class for phylogenetic web services
PhyloWS service wrapper for Timetree
PhyloWS service wrapper for Tree of Life
PhyloWS service wrapper for uBio ClassificationBank records
PhyloWS service wrapper for uBio NameBank records
Container for related data
Subset of the parts inside a container
Container of taxon objects
Superclass for objects that link to taxa objects
Operational taxonomic unit
Superclass for objects that link to taxon objects
Visualizer of tree shapes
Abstract graphics writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Graphics format writer used by treedrawer, no serviceable parts inside
Superclass for unparsers used by Bio::Phylo::IO
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Global constants and utility functions
Utility class for importing external dependencies. No serviceable parts inside.
Errors ($@) that are objects
Utility class for generating object IDs. No serviceable parts inside.
Logger of internal messages of several severity levels
Utility class for managing optional superclasses. No serviceable parts inside.
Stack traces for exceptions
Provides
in lib/Bio/Phylo/Models/Substitution/Dna.pm
in lib/Bio/Phylo/Models/Substitution/Dna/F81.pm
in lib/Bio/Phylo/Models/Substitution/Dna/GTR.pm
in lib/Bio/Phylo/Models/Substitution/Dna/HKY85.pm
in lib/Bio/Phylo/Models/Substitution/Dna/JC69.pm
in lib/Bio/Phylo/Models/Substitution/Dna/K80.pm