Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper provides a theoretical foundation for the use of TAGs in phylogenetics. We provide a formal definition of TAG that - unlike previous definition - does not depend on the order in which input trees are provided. In the consensus case, when all input trees have the same leaf labels, we describe algorithms for constructing majority-rule and strict consensus trees using the TAG. When the input trees do not have identical sets of leaf labels, we describe how to determine if the input trees are compatible and, if they are compatible, to construct a supertree that contains the input trees.