Figure 2

Determination of a good value for base log b. We simulated 550 fissions on a data set of 7 tetrapod species (see Section Results) and evaluate the ability of ARt-DeCo to recover broken adjacencies by the simulated fissions for different values for the base log b. On the x axis is the multiplicative factor of $⌈{\left(\frac{1-p\left(S\right)}{p\left(S\right)}\right)}^{{}^{\frac{1}{Br}}}⌉,$ where Br = 1. As we can see on the graph, there is a phase change at 1.0, meaning that from this value a good number of adjacencies can be proposed. Increasing the multiplicative factor does not qualitatively change the results. This experiment was repeated for different numbers of simulated fissions (see Additional file 2) and different species trees, and in all cases results exhibited the same profile.