Finally, we checked the impact of the exact distance method used inside DISTIQUE (Additional file 1: Figure S5), using a variety of methods implemented inside FastME  and PhyD*  on both mammalian and avian datasets. There were substantial variations of accuracy among distance methods, especially on the avian dataset. PhyD* tended to have more error, and among methods implemented in FastME, balanced minimum evolution (BME) with SPR moves had the highest accuracy. We chose this option of FastME in the default DISTIQUE.