Bio.Phylo.Newick module

Classes corresponding to Newick trees, also used for Nexus trees.

See classes in Bio.Nexus: Trees.Tree, Trees.NodeData, and Nodes.Chain.

class Bio.Phylo.Newick.Tree(root=None, rooted=False, id=None, name=None, weight=1.0)

Bases: Bio.Phylo.BaseTree.Tree

Newick Tree object.

__init__(self, root=None, rooted=False, id=None, name=None, weight=1.0)

Initialize parameters for a Newick tree object.

class Bio.Phylo.Newick.Clade(branch_length=None, name=None, clades=None, confidence=None, comment=None)

Bases: Bio.Phylo.BaseTree.Clade

Newick Clade (sub-tree) object.

__init__(self, branch_length=None, name=None, clades=None, confidence=None, comment=None)

Initialize parameters for a Newick Clade object.