/ 
Bio-Phylo-0.16_RC1
River stage two • 9 direct dependents • 18 total dependents

Documentation

dndtag.pl
applies unique node labels to newick trees.
Bio::ObjectCompat
Bio::Phylo::Manual
Bio::Phylo v.0.16 user guide.

Modules

Bio::Phylo
Phylogenetic analysis using perl.
Bio::Phylo::Adaptor
Object adaptor for compatibility
Bio::Phylo::Adaptor::Bioperl::Node
Adaptor class for bioperl compatibility
Bio::Phylo::Adaptor::Bioperl::Tree
Adaptor class for bioperl compatibility
Bio::Phylo::Forest
The forest object, a set of phylogenetic trees.
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::Custom
Datatype subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Dna
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::Matrix
Character state matrix.
Bio::Phylo::Matrices::TypeSafeData
Superclass for objects that hold character data.
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::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::Taxa
An object-oriented module for managing taxa.
Bio::Phylo::Taxa::Taxon
The operational taxonomic unit.
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::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. No serviceable parts inside.
Bio::Phylo::Util::IDPool
Utility class for generating object IDs
Bio::Phylo::Util::XMLWritable
Superclass for objects that stringify to xml

Provides

Bio::Phylo::Adaptor::Bioperl::Datum
in lib/Bio/Phylo/Adaptor/Bioperl/Datum.pm
Bio::Phylo::Adaptor::Bioperl::Matrix
in lib/Bio/Phylo/Adaptor/Bioperl/Matrix.pm
Bio::Phylo::Matrices::Datatype::Continuous
in lib/Bio/Phylo/Matrices/Datatype/Continuous.pm
Bio::Phylo::Matrices::Datatype::Mixed
in lib/Bio/Phylo/Matrices/Datatype/Mixed.pm
Bio::Phylo::Matrices::Datum
in lib/Bio/Phylo/Matrices/Datum.pm
Bio::Phylo::Taxa::TaxaLinker
in lib/Bio/Phylo/Taxa/TaxaLinker.pm
Bio::Phylo::Taxa::TaxonLinker
in lib/Bio/Phylo/Taxa/TaxonLinker.pm

Other files