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Bio-Phylo-0.17_RC8
River stage two • 9 direct dependents • 18 total dependents
8 ++

Documentation

Bio::Phylo::Manual
Bio::Phylo user guide.

Modules

Bio::Phylo
Phylogenetic analysis using perl.
Bio::Phylo::Annotation
Segment in an object to annotate other objects with.
Bio::Phylo::Dictionary
An object to annotate other objects with.
Bio::Phylo::Factory
Object to instantiate other objects.
Bio::Phylo::Forest
The forest object, a set of phylogenetic trees.
Bio::Phylo::Forest::DrawNode
A tree node object with extra methods for tree drawing.
Bio::Phylo::Forest::DrawTree
A tree object with extra methods for tree drawing.
Bio::Phylo::Forest::Node
The tree node object.
Bio::Phylo::Forest::Tree
The tree object.
Bio::Phylo::Generator
Generates random trees.
Bio::Phylo::IO
Input and output of phylogenetic data.
Bio::Phylo::Listable
Parent class for listable/iterator objects.
Bio::Phylo::Matrices
Holds a set of matrix objects.
Bio::Phylo::Matrices::Datatype
Superclass for objects that validate character data.
Bio::Phylo::Matrices::Datatype::Continuous
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Custom
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Dna
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Mixed
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Protein
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Restriction
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Rna
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Standard
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datum
The character state sequence object.
Bio::Phylo::Matrices::Matrix
Character state matrix.
Bio::Phylo::Matrices::TypeSafeData
Superclass for objects that hold character data.
Bio::Phylo::Mediators::NodeMediator
Mediator class to manage links between nodes.
Bio::Phylo::Mediators::TaxaMediator
Mediator class to manage links between objects.
Bio::Phylo::Parsers::Newick
Parses newick trees. No serviceable parts inside.
Bio::Phylo::Parsers::Nexml
Parses nexml data. No serviceable parts inside.
Bio::Phylo::Parsers::Nexus
Parses nexus files. No serviceable parts inside.
Bio::Phylo::Parsers::Table
Parses tab- (or otherwise) delimited matrices. No serviceable parts inside.
Bio::Phylo::Parsers::Taxlist
Parses lists of taxon names. No serviceable parts inside.
Bio::Phylo::Parsers::Tolweb
Parses Tree of Life xml feed data. No serviceable parts inside.
Bio::Phylo::Project
Container object to collect related data
Bio::Phylo::Set
Object to manage subsets of the contents of listable containers
Bio::Phylo::Taxa
An object-oriented module for managing taxa.
Bio::Phylo::Taxa::TaxaLinker
Superclass for objects that link to taxa objects.
Bio::Phylo::Taxa::Taxon
The operational taxonomic unit.
Bio::Phylo::Taxa::TaxonLinker
Superclass for objects that link to taxon objects.
Bio::Phylo::Treedrawer
An object-oriented facade for drawing trees.
Bio::Phylo::Treedrawer::Svg
Creates svg tree drawings. No serviceable parts inside.
Bio::Phylo::Unparsers::Mrp
Unparses a forest object into an MRP matrix. No serviceable parts inside.
Bio::Phylo::Unparsers::Newick
Unparses newick trees. No serviceable parts inside.
Bio::Phylo::Unparsers::Nexml
Serializes Bio::Phylo objects to NeXML. No serviceable parts inside.
Bio::Phylo::Unparsers::Nexus
Unparses nexus matrices. No serviceable parts inside.
Bio::Phylo::Unparsers::Pagel
Unparses pagel data files. No serviceable parts inside.
Bio::Phylo::Util::CONSTANT
This package defines global constants and utility functions that operate on them.
Bio::Phylo::Util::Exceptions
Exception classes for Bio::Phylo.
Bio::Phylo::Util::IDPool
Utility class for generating object IDs. No serviceable parts inside.
Bio::Phylo::Util::Logger
Logging for Bio::Phylo.
Bio::Phylo::Util::XMLWritable
Superclass for objects that stringify to xml

Provides

Bio::Phylo::Util::StackTrace
in lib/Bio/Phylo/Util/Exceptions.pm

Other files