Changes for version 0.05
- Added lots more tree methods Unified parsing and unparsing in a single IO module Newick parser now correctly parses multiline strings Implemented exceptions: Bio::Phylo::Exceptions There is a discussion forum: http://www.cpanforum.com/dist/Bio-Phylo Autovivification of blessed hashes now prevented by using 'fields' Implemented a single iterator interface for trees, tree objects, matrices, etc. Implemented a separate treedrawer object for SVG drawings Updated and expanded the documentation
Documentation
Bio::Phylo user guide.
Modules
Phylogenetic analysis using perl.
Global constants for Bio::Phylo. No serviceable parts inside.
Exception classes for Bio::Phylo. No serviceable parts inside.
The forest object, a set of phylogenetic trees.
The tree node object.
The tree object.
Generates random trees.
Input and output of phylogenetic data.
Abstract class for listable/iterator objects.
Holds a set of matrix objects.
The alignment object to aggregate sequences.
The single observations object.
The matrix object to aggregate datum objects.
The molecular sequence object.
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.
The operational taxonomic unit.
An object-oriented facade for drawing trees.
Creates svg tree drawings. No serviceable parts inside.
Unparses newick trees. No serviceable parts inside.
Unparses pagel data files. No serviceable parts inside.