Changes for version 0.17
- Fixed SVG tree drawing bug on multiple draws Added to_newick method for node objects Added set_root_below method for node objects Added NodeMediator class to manage node relations Added to_nexus method for taxa objects Added visit_pre_order, visit_level_order, visit_post_order methods for trees
Documentation
converts node ages to branch lengths.
creates paup commands to calculate bremer values using parsimony ratchet.
draws newick trees as svg drawings.
applies unique node labels to newick trees.
prunes a list of tips from input tree.
Object compatibility for phylogenetic software in OO perl
Bio::Phylo user guide.
Modules
Phylogenetic analysis using perl.
Object adaptor for compatibility
Adaptor class for bioperl compatibility
Adaptor class for bioperl compatibility
Adaptor class for bioperl compatibility
Adaptor class for bioperl compatibility
The forest object, a set of phylogenetic trees.
The tree node object.
The tree object.
Generates random trees.
Input and output of phylogenetic data.
Parent class for listable/iterator objects.
Holds a set of matrix objects.
Superclass for objects that validate character data.
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
Datatype subclass, no serviceable parts inside
The character state sequence object.
Character state matrix.
Superclass for objects that hold character data.
Mediator class to manage links between nodes.
Mediator class to manage links between objects.
Parses newick trees. No serviceable parts inside.
Parses nexus files. No serviceable parts inside.
Parses tab- (or otherwise) delimited matrices. No serviceable parts inside.
Parses lists of taxon names. No serviceable parts inside.
An object-oriented module for managing taxa.
Superclass for objects that link to taxa objects.
The operational taxonomic unit.
Superclass for objects that link to taxon objects.
An object-oriented facade for drawing trees.
Creates svg tree drawings. No serviceable parts inside.
Unparses a forest object into an MRP matrix. No serviceable parts inside.
Unparses newick trees. No serviceable parts inside.
Unparses nexus matrices. No serviceable parts inside.
Unparses pagel data files. No serviceable parts inside.
This package defines global constants and utility functions that operate on them.
Exception classes for Bio::Phylo.
Utility class for generating object IDs. No serviceable parts inside.
Logging for Bio::Phylo.
Superclass for objects that stringify to xml