We explore variants of DISTIQUE, changing the distance matrix (comparing all-pairs, all-pairs-max, tree-sum, and distance-sum; see Additional file 1: Algorithm S1), the number of anchoring rounds (2 to 8), and the use of consensus. To compare to other methods, we use the default distance-sum DISTIQUE (Additional file 1: Algorithm S2), with 2 or 8 rounds of anchoring. DISTIQUE is implemented in python and uses the Dendropy library  and uses the FastME  as its distance method (but we also tested PhyD* ).