Object to hold one phylogeny element (and its subelements.) Extended version of Bio::Tree.
CladeRelation object. This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade.
Array of confidence object
String. Description of tree.
String. Name of tree (name subelement of phylogeny element).
Array of Property object. Allows for typed and referenced properties from external resources to be attached.
Boolean. Can be used to indicate that the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent data, such as gene duplications).
Boolean. Required element.
SequenceRelation object. This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology.
String. Indicate the type of phylogeny (i.e. 'gene tree').
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 154 def initialize super @sequence_relations =  @clade_relations =  @confidences =  @properties =  @other =  end