We compared the three algorithms, all-pairs, tree-sum, and distance-sum (the last two with eight rounds of anchor sampling), and observed that the distance-sum is competitive with all-pairs and outperforms tree-sum (Table 1). The difference between all-pairs and distance-sum was never more than 1 %. Distance-sum consistently outperformed tree-sum, by as much as 5 % in some cases, despite the fact that tree-sum is provably consistent and distance-sum has not been proved consistent. Thus, we chose to set the default DISTIQUE implementation to distance-sum. Table 1DISTIQUE variants on simulated datasetsDataset#genesAll-pairsTree-sumDistance-sumavian-0.5X1000 0.10 0.110.11avian-1X1000 0.08 0.09 0.08 avian-2X1000 0.05 0.080.06mammalian-0.2X200 0.11 0.13 0.11 mammalian-0.5X200 0.06 0.120.07mammalian-1X200 0.04 0.08 0.04 mammalian-2X200 0.02 0.04 0.02 simphySize-10500.030.030.03simphySize-102000.020.020.02simphySize-1010000.020.020.02simphySize-5050 0.07 0.10 0.07 simphySize-50200 0.04 0.07 0.04 simphySize-5010000.030.040.04simphySize-10050 0.08 0.11 0.08 simphySize-100200 0.05 0.06 0.05 simphySize-1001000 0.03 0.050.04Distance-sum and tree-sum are both based on 8 rounds. For simPhy-size, all-pairs could not finish given two days of running time for more than 100 species. Where there is at least 1 % difference between methods, the best method is shown in bold