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Bio-Phylo-0.16_RC4
River stage two • 9 direct dependents • 18 total dependents
8 ++

Documentation

age2bl.pl
converts node ages to branch lengths.
bremer.pl
creates paup commands to calculate bremer values using parsimony ratchet.
dnd2svg.pl
draws newick trees as svg drawings.
dndtag.pl
applies unique node labels to newick trees.
droptip.pl
prunes a list of tips from input tree.
Bio::ObjectCompat
Object compatibility for phylogenetic software in OO perl
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::Datum
Adaptor class for bioperl compatibility
Bio::Phylo::Adaptor::Bioperl::Matrix
Adaptor class for bioperl 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::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::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::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 taxa 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::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::XMLWritable
Superclass for objects that stringify to xml

Other files