Documentation
High-level user guide
Command-line NeXML validation script
Modules
Phylogenetic analysis using perl
Single key/value annotation, used within dictionary
Container for annotations, attaches to other objects
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
List of things, super class for many objects
Container of matrix 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 tree nodes
Mediator for links between taxa and other objects
Single predicate/object annotation, attached to an xml-writable subject
Annotation value adaptor, no direct usage
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
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
Graphics format writer used by treedrawer, 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
Drop-in XML DOM support for Bio::Phylo
XML DOM document mappings to the XML::LibXML package
XML DOM document mappings to the XML::Twig package
Abstract interface class for flexible XML document object model implementation
XML DOM element mappings to the XML::LibXML package
XML DOM mappings to the XML::Twig package
Abstract interface class for flexible XML document object model implementation
Errors ($@) that are objects
Utility class for generating object IDs. No serviceable parts inside.
Logger of internal messages of several severity levels
Superclass for objects that serialize to NeXML
Provides
in lib/Bio/Phylo/Util/Exceptions.pm