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Bio::Phylo
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Phylogenetic analysis using perl
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0.17_RC9 |
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Bio::Phylo::Annotation
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Single key/value annotation, used within dictionary
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Bio::Phylo::Dictionary
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Container for annotations, attaches to other objects
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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::Tree
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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::Listable
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List of things, super class for many objects
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Bio::Phylo::Matrices
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Container of matrix 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::Matrix
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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::NodeMediator
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Mediator for links between tree nodes
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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::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::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 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::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::Svg
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Graphics format writer used by treedrawer, 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::Util::CONSTANT
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Global constants and utility functions
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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::XMLWritable
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Superclass for objects that serialize to NeXML
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