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Bio::Phylo
[source]
[v 0.37]
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Analysis and manipulation of phylogenies. |
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Bio::Phylo::EvolutionaryModels
[source]
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Evolutionary models for phylogenetic trees and methods to sample these |
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Bio::Phylo::Factory
[source]
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Creator of objects, reduces hardcoded class names in code |
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Bio::Phylo::Forest
[source]
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Container for tree objects |
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Bio::Phylo::Forest::DrawNode
[source]
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Tree node with extra methods for tree drawing |
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Bio::Phylo::Forest::DrawTree
[source]
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Tree with extra methods for tree drawing |
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Bio::Phylo::Forest::Node
[source]
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Node in a phylogenetic tree |
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Bio::Phylo::Forest::Tree
[source]
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Phylogenetic tree |
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Bio::Phylo::Generator
[source]
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Generator of tree topologies |
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Bio::Phylo::Identifiable
[source]
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Objects with unique identifiers |
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Bio::Phylo::IO
[source]
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Front end for parsers and serializers |
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Bio::Phylo::Listable
[source]
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List of things, super class for many objects |
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Bio::Phylo::Matrices
[source]
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Container of matrix objects |
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Bio::Phylo::Matrices::Character
[source]
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A character (column) in a matrix |
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Bio::Phylo::Matrices::Characters
[source]
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Container of character objects |
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Bio::Phylo::Matrices::Datatype
[source]
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Validator of character state data |
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Bio::Phylo::Matrices::Datatype::Continuous
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Custom
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Dna
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Mixed
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Protein
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Restriction
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Rna
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datatype::Standard
[source]
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Validator subclass, |
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Bio::Phylo::Matrices::Datum
[source]
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Character state sequence |
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Bio::Phylo::Matrices::Matrix
[source]
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Character state matrix |
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Bio::Phylo::Matrices::TypeSafeData
[source]
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Superclass for objects that contain |
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Bio::Phylo::Mediators::TaxaMediator
[source]
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Mediator for links between taxa and other objects |
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Bio::Phylo::NeXML::DOM
[source]
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XML DOM support for Bio::Phylo |
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Bio::Phylo::NeXML::DOM::Document
[source]
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XML DOM Abstract class for |
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Bio::Phylo::NeXML::DOM::Document::Libxml
[source]
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XML DOM document mappings to the |
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Bio::Phylo::NeXML::DOM::Document::Twig
[source]
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XML DOM document mappings to the |
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Bio::Phylo::NeXML::DOM::Element
[source]
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XML DOM Abstract class for |
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Bio::Phylo::NeXML::DOM::Element::Libxml
[source]
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XML DOM element mappings to the |
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Bio::Phylo::NeXML::DOM::Element::Twig
[source]
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XML DOM mappings to the |
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Bio::Phylo::NeXML::Meta
[source]
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Single predicate/object annotation, attached to an |
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Bio::Phylo::NeXML::Meta::XMLLiteral
[source]
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Annotation value adaptor, no direct usage |
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Bio::Phylo::NeXML::Writable
[source]
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Superclass for objects that serialize to NeXML |
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Bio::Phylo::Parsers::Abstract
[source]
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Superclass for parsers used by Bio::Phylo::IO |
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Bio::Phylo::Parsers::Fasta
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Json
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Newick
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Nexml
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Nexus
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Phylip
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Phyloxml
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Table
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Taxlist
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Parsers::Tolweb
[source]
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Parser used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Project
[source]
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Container for related data |
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Bio::Phylo::Set
[source]
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Subset of the parts inside a container |
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Bio::Phylo::Taxa
[source]
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Container of taxon objects |
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Bio::Phylo::Taxa::TaxaLinker
[source]
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Superclass for objects that link to taxa objects |
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Bio::Phylo::Taxa::Taxon
[source]
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Operational taxonomic unit |
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Bio::Phylo::Taxa::TaxonLinker
[source]
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Superclass for objects that link to taxon objects |
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Bio::Phylo::Treedrawer
[source]
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Visualizer of tree shapes |
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Bio::Phylo::Treedrawer::Abstract
[source]
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Abstract graphics writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Canvas
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Gif
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Jpeg
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Pdf
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Png
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Processing
[source]
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Graphics format writer used by treedrawer, |
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Bio::Phylo::Treedrawer::Svg
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Treedrawer::Swf
[source]
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Graphics format writer used by treedrawer, no |
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Bio::Phylo::Unparsers::Abstract
[source]
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Superclass for unparsers used by Bio::Phylo::IO |
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Bio::Phylo::Unparsers::Fasta
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Json
[source]
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Serializer used by Bio::Phylo::IO, no serviceable |
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Bio::Phylo::Unparsers::Mrp
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Newick
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Nexml
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Nexus
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Pagel
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Phylip
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Unparsers::Phyloxml
[source]
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Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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Bio::Phylo::Util::CONSTANT
[source]
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Global constants and utility functions |
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Bio::Phylo::Util::Dependency
[source]
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Utility class for importing external |
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Bio::Phylo::Util::Exceptions
[source]
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Errors ($@) that are objects |
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Bio::Phylo::Util::IDPool
[source]
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Utility class for generating object IDs. No serviceable parts inside. |
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Bio::Phylo::Util::Logger
[source]
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Logger of internal messages of several severity |
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Bio::Phylo::Util::OptionalInterface
[source]
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Utility class for managing optional |
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Bio::Phylo::Util::StackTrace
[source]
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Stack traces for exceptions |
