Package Bio :: Package Nexus :: Module Trees
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Module Trees

source code

Tree class to handle phylogenetic trees.

Provides a set of methods to read and write newick-format tree descriptions,
get information about trees (monphyly of taxon sets, congruence between trees,
common ancestors,...) and to manipulate trees (reroot trees, split terminal
nodes).

Classes [hide private]
  TreeError
  NodeData
Stores tree-relevant data associated with nodes (e.g.
  Tree
Represents a tree using a chain of nodes with on predecessor (=ancestor) and multiple successors (=subclades).
Functions [hide private]
 
consensus(trees, threshold=0.5, outgroup=None)
Compute a majority rule consensus tree of all clades with relative frequency>=threshold from a list of trees.
source code
Variables [hide private]
  PRECISION_BRANCHLENGTH = 6
  PRECISION_SUPPORT = 6
  NODECOMMENT_START = '[&'
  NODECOMMENT_END = ']'
  __package__ = 'Bio.Nexus'