Phylogenetic analysis using perl.

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.

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 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. (For extra per-node formatting, attach a hash reference to the node, like so: $node->set_generic( 'svg' => { 'stroke' => 'red' } ), which outlines the node, and branch leading up to it, in red.)

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.

Global constants for Bio::Phylo. No serviceable parts inside.

Exception classes for Bio::Phylo. No serviceable parts inside.

Utility class for generating object IDs