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Bio::Phylo
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Phylogenetic analysis using perl
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0.55 |
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Bio::Phylo::EvolutionaryModels
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Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007
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Bio::Phylo::Factory
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Creator of objects, reduces hardcoded class names in code
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Bio::Phylo::Forest
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Container for tree objects
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Bio::Phylo::Forest::DrawNode
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Tree node with extra methods for tree drawing
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Bio::Phylo::Forest::DrawTree
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Tree with extra methods for tree drawing
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Bio::Phylo::Forest::Node
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Node in a phylogenetic tree
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Bio::Phylo::Forest::NodeRole
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Extra behaviours for a node in a phylogenetic tree
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Bio::Phylo::Forest::Tree
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Phylogenetic tree
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Bio::Phylo::Forest::TreeRole
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Extra behaviours for a phylogenetic tree
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Bio::Phylo::Generator
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Generator of tree topologies
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Bio::Phylo::IO
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Front end for parsers and serializers
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Bio::Phylo::Identifiable
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Objects with unique identifiers
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Bio::Phylo::Listable
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List of things, super class for many objects
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Bio::Phylo::ListableRole
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Extra functionality for things that are lists
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Bio::Phylo::Matrices
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Container of matrix objects
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Bio::Phylo::Matrices::Character
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A character (column) in a matrix
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Bio::Phylo::Matrices::Characters
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Container of character objects
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Bio::Phylo::Matrices::Datatype
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Validator of character state data
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Bio::Phylo::Matrices::Datatype::Continuous
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Custom
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Dna
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Mixed
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Protein
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Restriction
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Rna
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datatype::Standard
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Validator subclass, no serviceable parts inside
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Bio::Phylo::Matrices::Datum
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Character state sequence
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Bio::Phylo::Matrices::DatumRole
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Extra behaviours for a character state sequence
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Bio::Phylo::Matrices::Matrix
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Character state matrix
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Bio::Phylo::Matrices::MatrixRole
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Extra behaviours for a character state matrix
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Bio::Phylo::Matrices::TypeSafeData
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Superclass for objects that contain character data
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Bio::Phylo::Mediators::TaxaMediator
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Mediator for links between taxa and other objects
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Bio::Phylo::Models::Substitution::Dna
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Bio::Phylo::Models::Substitution::Dna::F81
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Bio::Phylo::Models::Substitution::Dna::GTR
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Bio::Phylo::Models::Substitution::Dna::HKY85
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Bio::Phylo::Models::Substitution::Dna::JC69
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Bio::Phylo::Models::Substitution::Dna::K80
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Bio::Phylo::NeXML::DOM
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XML DOM support for Bio::Phylo
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Bio::Phylo::NeXML::DOM::Document
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XML DOM Abstract class for flexible document object model implementation
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Bio::Phylo::NeXML::DOM::Document::Libxml
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XML DOM document mappings to the XML::LibXML package
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Bio::Phylo::NeXML::DOM::Document::Twig
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XML DOM document mappings to the XML::Twig package
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Bio::Phylo::NeXML::DOM::Element
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XML DOM Abstract class for flexible document object model implementation
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Bio::Phylo::NeXML::DOM::Element::Libxml
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XML DOM element mappings to the XML::LibXML package
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Bio::Phylo::NeXML::DOM::Element::Twig
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XML DOM mappings to the XML::Twig package
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Bio::Phylo::NeXML::Entities
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Functions for dealing with XML entities
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Bio::Phylo::NeXML::Meta
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Single predicate/object annotation, attached to an xml-writable subject
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Bio::Phylo::NeXML::Meta::XMLLiteral
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Annotation value adaptor, no direct usage
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Bio::Phylo::NeXML::Writable
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Superclass for objects that serialize to NeXML
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Bio::Phylo::Parsers::Abstract
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Superclass for parsers used by Bio::Phylo::IO
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Bio::Phylo::Parsers::Adjacency
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Fasta
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Figtree
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Json
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Newick
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Nexml
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Nexus
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Phylip
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Phyloxml
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Table
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Taxlist
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Tnrs
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Tolweb
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Ubiocbmeta
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Ubiometa
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Parsers::Ubiosearch
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Parser used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::PhyloWS
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Base class for phylogenetic web services
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Bio::Phylo::PhyloWS::Client
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Base class for phylogenetic web service clients
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Bio::Phylo::PhyloWS::Resource
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Represents a PhyloWS web resource
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Bio::Phylo::PhyloWS::Resource::Description
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Represents a PhyloWS resource description
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Bio::Phylo::PhyloWS::Service
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Base class for phylogenetic web services
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Bio::Phylo::PhyloWS::Service::Timetree
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PhyloWS service wrapper for Timetree
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Bio::Phylo::PhyloWS::Service::Tolweb
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PhyloWS service wrapper for Tree of Life
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Bio::Phylo::PhyloWS::Service::UbioClassificationBank
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PhyloWS service wrapper for uBio ClassificationBank records
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Bio::Phylo::PhyloWS::Service::UbioNameBank
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PhyloWS service wrapper for uBio NameBank records
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Bio::Phylo::Project
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Container for related data
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Bio::Phylo::Set
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Subset of the parts inside a container
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Bio::Phylo::Taxa
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Container of taxon objects
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Bio::Phylo::Taxa::TaxaLinker
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Superclass for objects that link to taxa objects
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Bio::Phylo::Taxa::Taxon
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Operational taxonomic unit
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Bio::Phylo::Taxa::TaxonLinker
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Superclass for objects that link to taxon objects
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Bio::Phylo::Treedrawer
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Visualizer of tree shapes
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Bio::Phylo::Treedrawer::Abstract
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Abstract graphics writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Canvas
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Gif
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Jpeg
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Pdf
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Png
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Processing
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Svg
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Treedrawer::Swf
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Graphics format writer used by treedrawer, no serviceable parts inside
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Bio::Phylo::Unparsers::Abstract
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Superclass for unparsers used by Bio::Phylo::IO
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Bio::Phylo::Unparsers::Adjacency
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Cdao
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Fasta
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Hennig86
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Html
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Json
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Mrp
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Newick
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Nexml
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Nexus
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Pagel
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Phylip
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Phyloxml
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Rss1
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Unparsers::Taxlist
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Serializer used by Bio::Phylo::IO, no serviceable parts inside
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Bio::Phylo::Util::CONSTANT
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Global constants and utility functions
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Bio::Phylo::Util::CONSTANT::Int
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Integer constants, no serviceable parts inside
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Bio::Phylo::Util::Dependency
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Utility class for importing external dependencies. No serviceable parts inside.
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Bio::Phylo::Util::Exceptions
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Errors ($@) that are objects
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Bio::Phylo::Util::IDPool
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Utility class for generating object IDs. No serviceable parts inside.
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Bio::Phylo::Util::Logger
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Logger of internal messages of several severity levels
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Bio::Phylo::Util::MOP
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Meta-object programming, no serviceable parts inside
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Bio::Phylo::Util::OptionalInterface
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Utility class for managing optional superclasses. No serviceable parts inside.
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Bio::Phylo::Util::StackTrace
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Stack traces for exceptions
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Bio::PhyloRole
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Extra behaviours for the base class
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0.50 |
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