Nodal distance algorithm: calculating a phylogenetic tree comparison metric

Abstract

Maintaining a phylogenetic relationship repository requires the development of tools that are useful for mining the data stored in the repository. One way to query a database of phylogenetic information would be to compare phylogenetic trees. Because the only existing tree comparison methods are computationally intensive, this is not a reasonable task. Presented here is the nodal distance algorithm which has significantly less computation time than the most widely used comparison method, the partition metric. When the metric is calculated for trees where one species has been repositioned to a distant part of the tree no further computation is required as is needed for the partition metric. The nodal distance algorithm provides a method for comparing large sets of phylogenetic trees in a reasonable amount of time.