The disagree method uses a novel algorithm that compares two trees and returns the taxa that make the disagreement between those trees. It uses an iterative algorithm that works at four levels of comparison. At level 1 it removes one taxon every time and calculates the gain (reduction in the split distance) between two trees. The taxon that produces most gain is removed for the following iterations. This procedure is repeated until the split distance is zero. The second, third and fourth levels remove 2, 3 and 4 taxa every time, respectively, and then calculate the gain.
How to run: the value of the parameter '-m' must be 'all' or 'disagree' to run the disagree method.
Click here to see a schematic algorithm of the method or click here to see a graphical example.
The disagree method has been tested in approximately a thousand of comparisons of trees obtained from known protein families. Click here to see the results.