Comparisons between tree topologies provide important information for many evolutionary studies. TreeKo is a method that allows the comparison of any two tree topologies, even those with missing leaves and duplications. This is important in genome-wide analysis since many trees do not have exact leaf pairings and therefore most tree comparison methods are rendered useless.

In order to calculate the distance between two trees that contain duplications, treeKo first prunes the trees so that you obtain a list of trees that only contain one-to-one orthologs. Each collection of pruned trees is then compared to the other and two distances are calculated depending on whether the presence of duplication and loss events are considered a difference or not.