Program runtime for the approach described in this paper, in comparison to <i>Multi-SpaM</i>.

Column reference blocks contains the time to calculate the set of reference quartet blocks with the program Multi-SpaM. Column gaps contains the remaining runtime of our method, i.e. the time to find the respective second block for each reference block. As a comparison, column RAxML contains the runtime for running RAxML on the don’t-care positions of the reference blocks.