The Nodal method first constructs the matrices from the two trees. These matrices are obtained by comparing the number of nodes that separate each taxon with the other taxa from the tree. Then it calculates the differences between the two matrices to obtain the distance between the two trees. The nodal distance score is calculated using the root-mean-squared distance (RMSD) of the two matrices. The RMSD is 0 for identical trees, and its value increases as the two trees become more different. The nodal distance score is the result of comparing two pruned trees, but we have added another score that considers the percentage of taxa that the two trees have in common.
How to run: the value of the parameter '-m' must be 'all' or 'nodal' to run the nodal method.
Click here to see a schematic description of the method or click here to see a graphical example.