The TOPD program uses several methods to calculate the difference between two trees. All the methods work with single and multifamily trees using the FMTS program. A random analysis can be made in all of the methods as well.

         - Nodal: this method calculates the nodal distance between two trees.

         - Split: this method calculates the number of splits that disagree between two trees.

         - Quartets & Triplets: the software also calculates quartets, triplets and their indices.

         - Disagree: this method compare two trees and returns the taxa that disagree in both trees.

         - Ranking disagree: this perl script ranks the results of the disagree method

         - Boot-split Distance (BSD):The BSD method compares trees based on bootstrap values